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Science and Freethinking

Everyone has a religion, a raison d’être, and mine was once Dawkins’. I had the same disdain for people of faith that he does, only I could have put him to shame with the power and passion of my argumentation.

But something happened. As a result of my equally passionate love of science, logic, and reason, I realized that I had been conned. The creation story of my atheistic, materialistic religion suddenly made no sense.

This sent a shock wave through both my mind and my soul. Could it be that I’m not just the result of random errors filtered by natural selection? Am I just the product of the mindless, materialistic processes that “only legitimate scientists” all agree produced me? Does my life have any ultimate purpose or meaning? Am I just a meat-machine with no other purpose than to propagate my “selfish genes”?

Ever since I was a child I thought about such things, but I put my blind faith in the “scientists” who taught me that all my concerns were irrelevant, that science had explained, or would eventually explain, everything in purely materialistic terms.

But I’m a freethinker, a legitimate scientist. I follow the evidence wherever it leads. And the evidence suggests that the universe and living systems are the product of an astronomically powerful creative intelligence.

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686 Responses to Science and Freethinking

  1. You’ve been quite prolific lately with these testimonials. What gives?

  2. Hang it, Gil! I think you should write a book with your testimony, exactly how and why you changed your course. There’s a lot of technical books out there, but a dearth of convincing testimonies backed up by facts and evidences.

  3. Looks to me like you’ve kept the same high-certainty, low-level-of-relevant-scholarship attitude, you just switched sides while doing so. Actually coming to grips with the scientific literature on some specific biological topic would be worth a thousand defiant testimonials.

  4. In the following videos, Fazale (Fuz) Rana PhD. Biochemisty, relates his journey from being a practicing ‘scientific atheist’ to being a practicing ‘scientific Christian’. Much like Gil’s testimony, far from science being a hinderance to his faith in God, Fuz relates how science has dramatically enhanced and solidified his faith that God personally cares for each of us. In the last two videos, it is pleasant to watch Fuz’s joy explaining recent discoveries in science, as well as science in general, as he relates some of the new stunning molecular complexities of life to a novice;

    Dr. Fuz Rana discusses the beauty and elegance of biochemistry
    http://www.youtube.com/user/Re.....zxYPO62Ygc

    Fazale (Fuz) Rana – The Cell’s Design – part 1 of 2
    http://www.mynewday.tv/tv-show.....rt-1-of-2/

    Fazale (Fuz) Rana – The Cell’s Design – Part 2 of 2
    http://www.mynewday.tv/tv-show.....rt-2-of-2/

  5. Isn’t it about time you said something new in there posts of yours, Gil? I’m partial to intelligent design, but it does you no favours repeating the same old “I used to be an atheist, you know!”, time after time. One would almost be lead to think you are proud of your atheist history.

  6. Hi Nick,

    Would you be so kind as to select a single piece of “scientific literature on some specific biological topic” that provides important evidence for your belief that human beings evolved from a single-celled eukaryotic ancestor mainly through a process of natural selection acting upon random mutations, and describe in your own terms how it manages to do that?

    Many Thanks.

  7. “The creation story of my atheistic, materialistic religion suddenly made no sense.”

    So do now you believe the six day creation story in Genesis?

  8. Chris Doyle,

    You asked for “a single piece” of literature on the genealogy of humans. It’s a long story, going back billions of years, but a good place to start is the divergence of chimpanzees and humans about 10 million years ago.

    Here is an overview of the comparative genetics of the two species:

    http://genome.cshlp.org/conten.....6.full.pdf

    When you’ve digested that, you can explore the literature further for earlier genealogical relationships. Warning: that literature is vast and it will take some time and patience.

  9. Here are a few notes that don’t take so much time or patience to digest, nor do the notes make misleading arguments based on ‘non-established assumptions’ about the ability of neo-Darwinian processes to traverse universe wide chasms between functional sequences in sequence space:

    Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny – Casey Luskin – June 2011
    Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)
    http://www.evolutionnews.org/2.....47041.html

    Could Chance Arrange the Code for (Just) One Gene?
    “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
    http://www.creationsafaris.com/epoi_c10.htm

    “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: – Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.”
    http://www.mendeley.com/resear.....yme-folds/

    Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:
    The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species.
    http://www.ncbi.nlm.nih.gov/pubmed/15716009

    New level of genetic diversity in human RNA sequences uncovered
    Excerpt: A detailed comparison of DNA and RNA in human cells has uncovered a surprising number of cases where the corresponding sequences are not, as has long been assumed, identical. The RNA-DNA differences generate proteins that do not precisely match the genes that encode them.,,, Nearly half of the RDDs uncovered in the new study cannot be explained by the activity of deaminase enzymes, however, indicating that unknown processes must be modifying the RNA sequence, either during or after transcription. ,,, Although all of the individuals analyzed in the study had a large number of RDDs, there was a great deal of variability in the specific RDDs found in each person’s genetic material.”
    http://www.physorg.com/news/20.....ences.html

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

  10. Hi Daniel,

    Please re-read my original request to Nick in full. Your reference is almost irrelevant and certainly not “important”.

    Similarity is as much an indication of common design as it is common ancestry. Then, of course, if you look at the large differences in the ‘y’ chromosome and all the extra DNA that chimps have generally then the conclusion you would draw from that reference is based on cherry picked evidence. IOW, bad science.

    But the main problem you have is that, even if I (like you) also just assumed the truth of common ancestry between humans and chimps, this sheds no light whatsoever on the mechanism behind the divergence. If it turned out to be an Intelligently Designed mechanism (not natural selection acting upon random mutations) then the likes of you and Nick will look like proper chumps!

    Please try again. And try harder.

  11. Programming of Life: Warning; this video contains graphic images of extreme complexity in cells that should not be viewed by atheists of any age or gender.
    http://www.vimeo.com/27798192

  12. Hi, Chris,

    You are the best judge of whether a reference in the way of a response is irrelevant or important to you.

    And you are entitled to pick whichever cherries from the data that you like. Have you read this particular basket of cherries:

    http://twu.ca/academics/scienc.....venema.pdf

    It’s not peer-reviewed scholarly literature, but it covers the ground well, I think.

    If it turned out to be an Intelligently Designed mechanism (not natural selection acting upon random mutations) then the likes of you and Nick will look like proper chumps!

    Actually, I’d be thrilled to see a better explanation! But it has to be an explanation. Are there any ID mechanisms in the running that a molecular biologist could evaluate? I ask because I think that molecules have to be in there somewhere. Don’t you agree?

  13. Daniel,

    See these peer-reviewed papers which detail how an intelligent designer might have created first life. They are still largely hypothetical, but as you examine them you’ll see that they are far ahead of any support for undirected chemical abiogenesis.

    But this has nothing to do with ID. Why is it so difficult to understand that intelligence or the lack thereof has nothing to do with mechanisms? I don’t know whether you’re typing on a keyboard, dictating, or paralyzed from the neck down and blinking morse code, or whether you’re using a computer, phone, or Wii remote. Should I question whether these posts come from a person because I don’t know the mechanisms? Do you need to know how a computer chip was manufactured to believe that it was? This is simple.

  14. Thanks for the further response, Daniel.

    There’s a very important distinction to be made between people like you and me: there are those, like you and Nick, who believe that human beings evolved from a single-celled eukaryotic ancestor mainly through a process of natural selection acting upon random mutations. Everyone else, like me and most of the participants here at UD, reject that claim.

    Now, I perfectly understand that there are all sorts of reasons that people find to choose which side of the divide they want to position themselves in. I would even go so far as to suggest that in most cases, those reasons are very subjective and emotional regardless of which side of the divide you find yourself in. Uncommon Descent is not a forum to explore such reasons (such topics of discussions bear more fruit when held one-to-one, preferably face-to-face).

    Uncommon Descent is a forum to present objective reasoning, observational evidence and experimental results to support or reject Intelligent Design (or, conversely, atheistic evolution). I’ve asked Nick to “put up” some evidence for his evolutionist beliefs. He has not yet answered (maybe timezone differences, maybe indifference to me, possibly inability to respond to my request). You answered on his behalf with an appeal to evidence for common ancestry. I explained why an appeal to common ancestry is barely relevant and certainly unimportant.

    Now, I have no idea what mechanisms were involved in creating Stonehenge, or indeed many of the other amazing artifacts bequeathed to us by antiquity. I also find things like “Out of place artifacts” (OOPARTS) absolutely fascinating and mysterious. I wouldn’t even assert that any of these things have definite human origins. What I do know, without a shadow of a doubt, is that they were Intelligently Designed. Furthermore, I now know that a mere cell is perhaps the most stunningly sophisticated and complicated thing in existence. I don’t know what mechanism was involved in creating the first cell, but I do know, without a shadow of a doubt, that it was Intelligently Designed.

    That said, I remain open to the (albeit, vastly diminished) possibility that the cell made itself and, even, that a eukaryotic cell evolved into a human being. But, without evidence, that door closes. The fact that humans and chimpanzees share similarities does not remotely constitute that evidence. My Samsung Galaxy S shares similarities with an iPhone. Big deal.

    The onus is on people like you, Daniel, and Nick, to support your position with evidence. Because, if your position is indeed true, then you should be able to identify an important piece of evidence that it rests upon. If human-chimp similarity is the best that you can do, then that says it all really.

  15. Good reference, once again, thanks bornagain77!

  16. Daniel King, I noticed you cited a Dennis Venema paper. Perhaps you could help us locate Dennis Venema for he seems to be missing in action, for he is currently wanted for questioning, by Casey Luskin, for making completely unsubstantiated claims of the power of purely neo-Darwinian processes to produce ‘meaningful information’ sufficient to give rise to the origination of novel genes and proteins!!

    Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information
    http://www.evolutionnews.org/2.....51051.html

    As well, in the paper you cited I noticed that Venema had used the ‘junk DNA argument’, yet Jonathan Wells recently wrote a book, The Myth Of Junk DNA, that blew gaping holes in that argument!!! Did you miss that book?

    notes:

    The Myth of Junk DNA by Jonathan Wells
    http://www.mythofjunkdna.com/

    The Myth of Junk DNA Grows With the Telling – July 2011
    Since the publication of Jonathan Wells’ The Myth of Junk DNA, many articles have come out documenting more functions for non-protein-coding DNA. It looks like Dr. Wells sampled the water just as the tide was starting to come in, and it’s still rising. Richard Dawkins, Larry Moran, and other proponents of junk DNA should move to higher ground.
    http://www.evolutionnews.org/2.....48311.html

    Jonathan Wells: On Francis Collins and Junk DNA – video
    http://www.youtube.com/watch?v=hksGZcqJ5h4

    Francis Collins, Darwin of the Gaps, and the Fallacy Of Junk DNA – video
    http://www.evolutionnews.org/2.....40361.html

    “Pseudogenes Shrink Gaps for Theistic Darwinian Evolutionists Collins & Giberson”- audio podcast
    http://intelligentdesign.podom.....0_25-07_00

    Vitamin C pseudogene refutation By Jonathan Wells – from appendix of ‘The Myth Of Junk DNA’ pages 109-114 by Jonathan Wells
    https://docs.google.com/document/pub?id=18LV9Xp1RJv4k2KRQDOpN3_cjSCwBC_XXb8WGVNP4L8M

    Reference Notes For Jonathan Wells’ Book – The Myth Of Junk DNA – Hundreds of Studies Outlining Function for ‘Junk’ DNA
    http://docs.google.com/viewer?.....xHdM_e731g

    etc.. etc.. etc..

  17. No Problem Chris, that is a cool video!

  18. The onus is on people like you, Daniel, and Nick, to support your position with evidence. Because, if your position is indeed true, then you should be able to identify an important piece of evidence that it rests upon. If human-chimp similarity is the best that you can do, then that says it all really.

    Thanks, Chris. As I originally proposed, human-chimp genetic similarity is a recent piece of evidence in a long and complicated story. I think it is of signal importance. But you don’t think it is important and you reject its relevance (or the relevance of any other genetic comparisons among organisms) to the history of life on earth. Fair enough. I’m satisfied that I’ve made the effort, however feeble.

    If you haven’t read the Venema article I linked to, you might enjoy it anyway.

  19. ScottAndrews:

    Why is it so difficult to understand that intelligence or the lack thereof has nothing to do with mechanisms?

    I was just wondering how a postulated “intelligence” might be a scientific explanation for the diversity and history of life on Earth. Without a mechanism, where’s the science?

  20. Daniel King, it seems to me that you are riding a bunch of your confidence on the human-ape genetic similarity horse,,, Venema comments on the supposed genetic similarity here:

    Genesis and the Genome: Genomics Evidence for Human-Ape Common Ancestry and Ancestral Hominid Population Sizes – Dennis R. Venema
    Excerpt: The human genome has approximately 3.0 x 10^9 nucleotides; of this number, 2.7 x 10^9 nucleotides match the chimpanzee genome with only a 1.23% difference between the species.(6) In short, the vast majority of the human genome matches the chimpanzee genome with only rare differences. The inclusion of sequence alignment gaps between the two genomes that are thought to have arisen through either insertions or deletions (so-called “indel” mutations) drives the identity of the two genomes down to about 95%.(7) Restricting the comparison to the sequences responsible for coding for proteins raises the value to 99.4%.(8) By any measure, humans and chimpanzees have genomes that are highly homologous and readily interpreted as modified copies of an original ancestral genome.
    http://twu.ca/academics/scienc.....venema.pdf

    Yet Daniel, the genetic similarity, between man and apes, contrary to what you may have been told, repeatedly, by Venema and others, turns out to be not nearly as strong as neo-Darwinists have led the general public to believe. In fact, as hard as it may be for you to believe, there is a severe bias in genetic similarity studies to strip genetic dissimilarities because of neo-Darwinian philosophical bias, and not because of any warrant from the evidence! If you don’t believe that scientists could be so prejudiced as to let a philosophical bias interfere with their results, This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 ‘ORFan’ genes, that are completely unique to humans and not found in any other species, were stripped from the 20,500 gene count of humans simply because the (neo-Darwinian) scientists could not find corresponding genes in primates. In other words the evolution of humans from primates was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!

    Human Gene Count Tumbles Again – 2008
    Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes. Although this was strong evidence that the sequences were not true protein-coding genes, it was not quite convincing enough to justify their removal from the human gene catalogs. Two other scenarios could, in fact, explain their absence from other mammalian genomes. For instance, the genes could be unique among primates, new inventions that appeared after the divergence of mouse and dog ancestors from primate ancestors. Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes.
    http://www.sciencedaily.com/re.....161406.htm

    The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true.

    If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because of their preconceived neo-Darwinian bias, they would have found that there is ample reason to believe that the ‘ORFans’ may very well encode for biologically important proteins:

    A survey of orphan enzyme activities
    Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles.
    http://www.biomedcentral.com/1471-2105/8/244

    Dr. Howard Ochman – Dept. of Biochemistry at the University of Arizona
    Excerpt of Proposal: The aims of this proposal are to investigate this enigmatic class of genes by elucidating the source and functions of “ORFans”, i.e., sequences within a genome that encode proteins having no homology (and often no structural similarity) to proteins in any other genome. Moreover, the uniqueness of ORFan genes prohibits use of any of homology-based methods that have traditionally been employed to establish gene function.,,, Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins.
    http://www.uncommondescent.com.....ent-358868

    In fact it turns out that the authors of the ‘kick the ORFans out in the street’ paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded for important proteins but chose to ignore it in favor of their preconceived evolutionary bias:
    http://www.uncommondescent.com.....ent-358547

    Moreover the ‘anomaly’ of unique ORFan genes is found in every new genome sequenced:

    Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references
    http://www.vimeo.com/17135166

    As well, completely contrary to evolutionary thought, these ‘new’ ORFan genes are found to be just as essential as ‘old’ genes for maintaining life:

    Age doesn’t matter: New genes are as essential as ancient ones – December 2010
    Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
    http://www.sciencedaily.com/re.....142523.htm

    New genes in Drosophila quickly become essential. – December 2010
    Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
    http://www.sciencemag.org/cont.....2.abstract

    Daniel, hopefully you can clearly see, from just this one study, how severely biased neo-Darwinists can be with genetic similarity studies. You can ride your confidence on such studies if you want, but this clearly is not solid science and thus that exactly why it is more than fair for IDists to demand actual evidence from neo-Darwinists for their claims that these changes can happen instead of just biased genetic similarity studies, as Casey Luskin is currently asking Dennis Venema for on ENV, as I referenced earlier.

    Also of note, if you are really impressed with genetic similarities, exactly what do you make of this following study Daniel??

    Kangaroo genes close to humans
    Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
    http://www.reuters.com/article.....P020081118

    As for myself Daniel, I’m just left wondering exactly where evolutionists should place the kangaroos on their cartoon drawings that show man evolving from apes. :)

  21. Daniel,

    That’s a very good question, but it has nothing to do with ID. Read the FAQ and understand what ID is. Pick it apart if you wish to. But in order to do so you must correctly understand it.
    Sort of like if someone said, “Evolution is stupid – fish don’t turn into frogs!” Even if one disagrees with something they must understand it in order to coherently argue against it.

  22. I think people understand what the “official” definition is, but I think they get confused by how that translates into typical posts on ID supporting forums. Posts which are frequently religious, and which frequently denounce atheism.

    If ID is agnostic about the designer and the mechanism of design, and the times and places where design intervention took place, it is also a-theistic — without a theistic position.

    The other thing that confuses some of us is the question of why ID is relevant in the world of science if it has no entailments — no propositions that suggest research into mechanisms, times, places, etc.

    It would seem that ID proponents want to walk mainstream science into a box in which it lacks answers to many questions and in which it is not allowed to seek answers. the rather long OOL thread is an example of an argument that mainstream research is having rather limited success, and as a result of the difficulty, should be abandoned.

    this line of argument is incomprehensible to most scientists, because really difficult problems are the most interesting.

  23. Morning Petrushka,

    Intelligent Design is to theism, what evolution is to atheism: not an absolutely necessary connection but often a supportive one. But don’t you think it is sufficient to identify design in nature? I mean, if that fact became widely accepted it would certainly shake things up, particularly in the Western world. I don’t know who made Stonehenge, or how they made it, but that doesn’t prevent us from studying Stonehenge and marvelling at it.

    The only thing evolution has brought to science is a somewhat dismissive explanatory commentary:

    “The eagle’s hunting abilities are thanks to evolution”
    “Termites have evolved the ability to create an air-conditioned termite’s nest”
    “Men are unfaithful because they have evolved the instinct to sleep around”

    When neo-darwinism falls, we will be able to revisit this commentary and in most cases simply replace expressions such as “over time, x somehow evolved the ability to y” with an expression like “x was designed to have the ability to y”.

    We do not need to know anything about the designer(s) if we simply want to do what science does now: study nature and learn from it through observations and experiments.

    As for OOL research, once we’ve established that abiogenesis is an atheistic fairy-tale, would you not agree that many will be appalled by the waste of time, money and, indeed, careers that an erroneous belief in abiogenesis resulted in? Or do you think that the alchemists who wasted their lives trying to convert lead into gold were actually making the best use of their time?

    Really challenging ideas are the most interesting and some problems have no solution (usually because you’re asking the wrong questions or relying on false assumptions).

  24. But don’t you think it is sufficient to identify design in nature?

    Absolutely not. As Elizabeth has taken some pains to point out, evolution has a candidate for the designer. ID does not. Evolution cannot cite every mutation in “pathetic detail.” but it can cite instances of every mechanism required to explain current life in terms of common descent. OOL is still in the rough, but it is very young.

    We do not have the history of the solar system in pathetic detail, but we no know — as was suspected all along — that solar system formation is common, possibly universal. The mechanism that result in more or less stable orbits for multiple planets do not require intervention, as Newton proposed.

    It took astronomy 400 years from the first assertion there was a solar system to reach its current state of knowledge, and it still lacks many historical details and explanatory details.

    Hard problems are hard. That is why they take a long time. Of course we are not asking the right questions. That is always the case when you can’t find an answer in science.

    But when was the last time in astronomy or chemistry that the right question involved intentional design by a volitional agent?

    I suppose my chief objection to ID is not that it is wrong — something that cannot be demonstrated — but that it doesn’t ask any interesting questions that can be answered through research. At least not so far.

  25. Petrushka, perhaps you would care to show the ‘pathetic detail’ of just one novel, functional, protein/gene, that actually does something other than ‘stick’ to ATP every 1 in 10^12 tries, originating by purely neo-Darwinian processes???

    As well, perhaps you would care to learn of Kepler’s view of a ‘tinkering’ God, and the sheer poverty of the ‘chaos’ that underlies the basis of the materialistic/atheistic philosophy to explain such mathematical perfection which has been found to govern this universe????

    Kepler saw the world as the material embodiment of mathematical forms present within God before the act of creation. ‘Why waste words?’ he wrote, ‘Geometry existed before the Creation, is co-eternal with the mind of God, is God himself … geometry provided God with a model for the Creation.’ Thus, ‘where matter is, there is geometry.’
    Because he believed that the world was a reflection of God, who was a perfect being, according to Kepler it must necessarily be a perfect world, and therefore the manifestation of sublime geometric principles. ‘It is absolutely necessary that the work of such a perfect creator should be of the greatest beauty.’ (Kepler) (Wertheim, Pythagoras’ Trousers, 1997)
    http://www.spaceandmotion.com/.....Kepler.htm

    here is another interesting quote from the site on ‘consensus science’:

    I wish, my dear Kepler, that we could have a good laugh together at the extraordinary stupidity of the mob. What do you think of the foremost philosophers of this University? In spite of my oft-repeated efforts and invitations, they have refused, with the obstinacy of a glutted adder, to look at the planets or Moon or my telescope. (Galileo Galilei)

  26. ID’s candidate for design is an actual Designer or Designers. All of the greatest scientists who ever lived believed in the same, solitary Designer: God. But science only gives us the tools to Study the Book of Nature so we can learn about Creation, and confirm that everything has indeed been designed for a purpose. But the Book of Nature doesn’t tell us much about what that purpose is.

    Evolution, on the other hand, specifically atheistic evolution, does not offer any such knowledge. It merely says everything made itself by accident. Atheistic evolutionists take all of the overwhelming evidence for design and try to re-invent it as an illusion brought about by natural selection acting upon random mutations. That’s not science, that’s just wishful thinking. That indisputable fact has been confirmed here, and elsewhere, over and over again by the continued failure of evolutionists to provide any detailed evidence to support their belief that humans evolved from a single-celled eukaryotic organism through purely naturalistic processes.

    Ultimately, your big problem lies in the fact that you have put your faith in science, and science alone. Consequently, you are searching for answers to the wrong questions and, like the chemist trying to turn lead into gold, finding comfort and validity, in the process of searching; no matter how elusive the answers are proving to be and how much of the devil is in the “pathetic detail”.

    The Book of Nature was not written to provide all the answers we need. There are other Books, other fields of knowledge beyond science that serve that purpose. A good starting point would be to ask the right questions in the first place and not allow yourself to be restricted by institutionalised thinking and a priori commitments to materialism.

  27. As Elizabeth and countless others — including Micheal Denton — have pointed out, God can use evolution to effect design.

    One could argue whether the specific current state of life is destiny, or whether evolution is free to explore alternate scenarios, but evolution designs, and it is not automatically atheistic to say so.

    As others on this site have also pointed out, science seeks to find the background regularities in nature, against which miracles and interventions might be discerned. Even the Catholic church does this when attempting to verify miracles.

    What other procedure makes sense? If you don’t look for regularities, you are blinded by voluntary ignorance.

    As you point out, science can only seek regularities. that is the point of Lewontin’s statement, when you quote the whole statement rather than a snippet.

  28. Petrushka, if there was evidence for evolution, I would merely become a theistic evolutionist: my worldview would barely be altered. It would be wrong to say that theistic evolutionists believe that evolution, by itself, designs. No, evolution would just be a mechanism that the Intelligent Designer used. There is no problem for me accepting that possibility if that is where the evidence leads. A number of ID proponents accept common ancestry (I’m not one of them), but, you must agree, there is a crucial and unbridgeable gap between mere evidence for common ancestry and the evidence that you must provide to demonstrate that human beings evolved from a single-celled eukaryote through a process of natural selection acting upon random mutations.

    This is why I placed the emphasis on atheistic evolutionists: people who believe that the universe and everything in it all made itself, by accident, without purpose or design, people who believe that all life evolved purely naturalistically, from non-living chemicals, and that death brings only oblivion.

    As all of the greatest scientists who ever lived believed, the regularities that we observe in the universe only make sense in light of the Supreme Being who wrote the Laws of Nature and created an ordered universe for us to dwell in.

    Or are you saying we can only study things like Stonehenge if we assume it made itself by naturalistic means? Because, you know, design and engineering is ultimately a regular and ordered process: and nature provides us with the highest levels of design and engineering and as such, this can only be explained in terms of Intelligent Design.

    Truth is not reducible to everything that can be learned from the scientific method. Imposing methodological naturalism on science merely makes it even more difficult for science to determine truth.

  29. as to ‘science can only seek regularities’

    Meyer and Nelson on a Failed Explanation for the Origin of the Genetic Code – Jonathan M. – August 2011
    Excerpt: ‘codes and digital information are categories of effects uniformly associated with intelligent causes. Indeed, to the extent that Yarus and others have succeeded in establishing affinities between codons and amino acids, they did so only as a direct consequence of their own intelligent manipulation and intervention.’
    http://www.evolutionnews.org/2.....50121.html

    “A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107.”
    (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

    The DNA Code – Solid Scientific Proof Of Intelligent Design – Perry Marshall – video
    http://www.metacafe.com/watch/4060532

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    http://www-qa.scitopics.com/Th.....iency.html

    The Capabilities of Chaos and Complexity – David L. Abel – 2009
    Excerpt: “A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Stephen C. Meyer – Signature In The Cell:
    “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”
    http://www.evolutionnews.org/2.....ligen.html

    Three subsets of sequence complexity and their relevance to biopolymeric information – David L Abel and Jack T Trevors:
    Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction…No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization…It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute.
    http://www.biomedcentral.com/c.....2-2-29.pdf

    Biological Information: The Puzzle of Life that Darwinism Hasn’t Solved – Stephen C. Meyer
    Thus, as my book Signature in the Cell shows, Joyce’s experiments not only demonstrate that self-replication itself depends upon information-rich molecules, but they also confirm that intelligent design is the only known means by which information arises.
    http://www.evolutionnews.org//.....e_puz.html

    The Origin of Life: An RNA World? – Jonathan M. – August 22, 2011 (Refutation of Nick Matzke)
    Excerpt Summary & Conclusion
    We have explored just a small handful of the confounding difficulties confronting the chemical origin of life. This is not a god-of-the-gaps argument, as Matzke claims, but rather a positive argument, based on our uniform and repeated experience of cause-and-effect. It is not based on what we don’t know, but on what we do know: that intelligence is a necessary and sufficient condition for the production of novel complex and functionally specified information. The design inference is based on sound and conventional scientific methodology. It utilizes the historical or abductive method and infers to the best explanation from multiple competing hypotheses.
    http://www.evolutionnews.org/2.....49871.html

    There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs — intelligent design. We know this from our uniform experience and from the design filter — a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).)

    Stephen Meyer describes the intelligent design argument as follows:

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.

    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

    Stephen C. Meyer – The Scientific Basis For the Intelligent Design Inference – video
    http://www.metacafe.com/watch/4104651

    Certainly seems like a solid ‘scientific regularity’ to me Petrushka!!!

  30. Petrushka, perhaps you would care to show the ‘pathetic detail’ of just one novel, functional, protein/gene, that actually does something other than ‘stick’ to ATP every 1 in 10^12 tries, originating by purely neo-Darwinian processes???

    Here’s some functional proteins derived by selection. You will invoke the buzzword “designed,” but be aware that no one can design protein coding sequences. You can only select them.

    No one knows how to predict how a coding sequence will fold, and Douglas Axe has asserted there are no shortcuts.

  31. Petrushka, you are simply completely out of touch with reality if you think your cited experiment proves ‘purely’ neo-Darwinian processes can produce novel functional proteins and or genes. Wishful thinking, denialism, fantasy world, and pseudo-scientific posturing are few other, of the ‘nicer’, adjectives that come to mind!!!

    De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth
    Excerpt: A central challenge of synthetic biology is to enable the growth of living systems using parts that are not derived from nature, but designed and synthesized in the laboratory. As an initial step toward achieving this goal, we probed the ability of a collection of >10^6 de novo designed proteins to provide biological functions necessary to sustain cell growth. Our collection of proteins was drawn from a combinatorial library of 102-residue sequences, designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles.,,,
    http://www.plosone.org/article.....ne.0015364

    And Petrushka, other than your seemingly pathological need to deny the overwhelmingly obvious evidence for a ‘design’ in life, why in blue blazes would you be forced to use such a ‘Designed’ experiment to try to prove purely ‘natural’ neo-Darwinian processes can generate functional genes/proteins??? Surely it is because you are forced to do so against your will, for if you had any evidence whatsoever, of purely neo-Darwinian processes generating novel functional proteins/genes, then you would do certainly cite that evidence rather than be embarrassed by such a pathetic citation that was supposedly supporting your atheistic neo-Darwinian position!!!

  32. How do you suppose the libraries are “designed”?

    Check it out.

    Do you think it is possible to know what an arbitrary coding sequence will produce, or do you suppose sequences are selected?

    Think about the process, not just the words.

  33. Petrushka, I don’t have to think about it,,, Intelligent agents were directly involved!!! The burning question is not whether neo-Darwinian processes, ‘aided by a guiding intelligence’, can produce functional proteins, the burning question is whether neo-Darwinian processes, and only neo-Darwinian processes, can generate functional genes and/or proteins.

  34. How do you suppose the libraries are “designed”?

    Check it out.

    Do you think it is possible to know what an arbitrary coding sequence will produce, or do you suppose sequences are selected?

    Think about the process, not just the words.

  35. Petrushka,

    I think people understand what the “official” definition is, but I think they get confused by how that translates into typical posts on ID supporting forums. Posts which are frequently religious, and which frequently denounce atheism.

    I agree. I think that sends a confusing, mixed signal.

    It would seem that ID proponents want to walk mainstream science into a box in which it lacks answers to many questions and in which it is not allowed to seek answers.

    ID offers no reason not to consider mechanisms or seek answers. It’s just that it, in itself, is not that science. But it might point us in the right direction to find those answers. If we’re seeking an undirected explanation for something that was directed, or vice versa, then we’re looking in the wrong place.

    The only case I’ve seen of not being allowed to seek answers is when investigating the mere possibility of intelligent design is discouraged.

  36. I butchered my blockquote tag. That’s me quoting you, replying, quoting you, and replying again (as I’m sure you guessed.)

  37. Petrushka, with such a ‘handicapped’ ability to discern what is actually happening in this experiment, and see that intelligence played a foundational role, it is no wonder that you believe in neo-Darwinism no matter what evidence is presented to you!

  38. Nick – I am really curious. Have you ever applied actual mathematical/ statistical algorithms to your confidence in the adequacy of darwinism/materialism. All I ever hear from atheist/materialist/physicalist/darwinist types are hand-waving arguments about look at this phenotype similarity ( which does not impress me because it has no bearing on the design/non-design question at all) , or consider how many years and then extend micro arguments to macro…

    I never see anything which tries to pin down real numbers. The only brave attempts I have seen to actually use real numbers come from design people ( Richard Sternberg, Douglas Axe ) and those who are not for design but publish articles which critique evolution and OOL theories ( Paul Davies, Bob Shapiro ).

    What I would really like to see from the evolutionary community is an honest statement like “We have no real quantitive arguments – but our gut feeling given this evidence is that it confirms evolution.” Without quantitative statistical numbers please get off the high horse of “scientific surety” and admit you are making a choice based on guesswork.

    Maybe then you will show a little more respect to your ideological opponents.

  39. Experiments are always designed. Do you think chemistry knows whither it is taking place in a lab or in a living thing?

    You are avoiding a key question. Is it possible to design proteins without using Darwinian selection?

    Take a look at how sequence libraries are generated. Find an example where sequences are designed from first principles rather than using selection.

  40. Chris: “But don’t you think it is sufficient to identify design in nature?”

    Petrushka: “Absolutely not. As Elizabeth has taken some pains to point out, evolution has a candidate for the designer. ID does not.”

    Sorry, but Elizabeth has missed the boat on this issue. Elizabeth’s recent interactions on these threads leave much to be desired from a standpoint of logic and scientific reasoning. There is absolutely no logical reason ID needs to identify the designer, however much you would like, from your own philosophical preferences, for ID to do so.

    Evolution can’t have a candidate for the designer because it claims there isn’t one. If you mean that evolution claims things came about through purely mechanistic processes, then sure, evolution has put forth a candidate for its designer substitute: purely mechanistic processes (albeit a wholly vague, highly-disputable, and wildly speculative one). That’s what a mechanistic theory needs to show, that a purely mechanistic process did it (or at least is plausible, to be taken seriously in the first place). ID is not a mechanistic theory. ID is not a theory of everything. ID is a very limited ascertainment of certain artifacts of design left behind. It does not pretend to explain the exact mechanistic process *because it is not a mechanistic theory*. You can dislike that all you want. You and Elizabeth can kick and scream and complain and berate design proponents for not going beyond their theory. But that is a problem with your bias, not a problem with ID.

  41. Petrushka you state:

    Experiments are always designed.

    OK let’s look at experiments ‘designed’ to detect what ONLY neo-Darwinian processes can do since that is the specific question we want to answer and not at experiments ‘designed’ to detect what intelligence AND neo-Darwinian processes can do since that is not the question we want to answer. i.e. What can PURELY neo-Darwinian processes do???

    Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species…
    (Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).)
    http://www.evolutionnews.org/2.....42191.html

    Four decades worth of lab work is surveyed here:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

    How about the oft cited example of antibiotic resistance?

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    Excerpt: Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” ,,, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding.
    http://www.trueorigin.org/bacteria01.asp

    That don’t seem to be helping Petrushka! How about we look really, really, close at very sensitive growth rates and see if we can catch almighty evolution in action???

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    Shoot that don’t seem to be helping Petrushka. Perhaps we just got to give the almighty power of neo-Darwinism ‘room to breathe’? How about we ‘open the floodgates’ to the almighty power of Darwinian Evolution and look at Lenski’s Long Term Evolution Experiment and see what we can find after 50,000 generations, which is equivalent to somewhere around 1,000,000 years of human evolution???

    Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information – September 2011
    Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT.
    (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)
    http://www.evolutionnews.org/2.....51051.html

    Now that just can’t be right Petrushka!! Man we should really start to be seeing some neo-Darwinian fireworks by 50,000 generations!!! Hey I know what we can do! How about we see what happened when the ‘top five’ mutations from Lenski’s experiment were combined??? Surely now the Darwinian magic will start flowing, baby!!!

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    Now Petrushka, something is going terribly wrong here!!! Tell you what Petrushka, let’s just forget trying to observe evolution in the lab, I mean it really is kind of cramp in the lab you know, and now let’s REALLY open the floodgates and let’s see what the almighty power of neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal??? Surely now almighty neo-Darwinian evolution will flex its awesomely powerful muscles and forever make those IDiots cower in terror!!!

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2....._edge.html

    Now Petrushka, there is something terribly wrong here!!! After looking high and low and everywhere in between, we can’t seem to find the almighty power of neo-Darwinism anywhere!! Shoot we can’t even find ANY power of neo-Darwinism whatsoever!!! Perhaps you know all this, and this is why you are trying your absolute darnedest to sell the ‘Designed’ experiment as confirmation of Darwinian evolution??? :)

  42. Why don’t you just stay on topic and answer my question?

    How do you design protein coding sequences without using selection? Is there some shortcut not known to Douglas Axe?

  43. LOL,

    Why don’t you just stay on topic and answer my question?

    LOL, Petrushka, sorry I thought purely neo-Darwinian evolution was the question. Oh well, since I’m not interested in your ‘Design plus Darwinism’ question, I guess I will go watch some videos.

  44. Your failure to answer the question is very obvious to the onlookers.

  45. Petrushka,

    Experiments are always designed. Do you think chemistry knows whither it is taking place in a lab or in a living thing?

    It doesn’t. But a better question is, how can it ever be known whether such chemistry would take place outside of the lab experiment? A designed experiment demonstrates what can happen in a designed experiment but always leaves uncertainty that the same results would occur elsewhere.

    One illustration (I forget the source) put it this way: Someone can play eighteen holes of golf. Does that demonstrate that the ball can move from the first tee through all eighteen holes without the player?

  46. Petrushka,

    The paper specifically refers to the de novo proteins as synthetic and designed.

    The selection process used to create the library bears no resemblance to Darwinian selection. It tested individual proteins to see whether they would fold. Only after a set of proteins was selected was any experimentation done on living organisms.

    Thomas Edison tested thousands of filaments for light bulbs and selected what worked best, but we would hardly cite that as evidence that selection trumps design.

  47. Now this question is actually interesting, though not for the reason that petrushka would prefer:

    Experiments are always designed. Do you think chemistry knows whither it is taking place in a lab or in a living thing?

    Personally I don’t think atomic particles are aware of anything, and yet:

    Genesis, Quantum Physics and Reality
    Excerpt: Simply put, an experiment on Earth can be made in such a way that it determines if one photon comes along either on the right or the left side or if it comes (as a wave) along both sides of the gravitational lens (of the galaxy) at the same time. However, how could the photons have known billions of years ago that someday there would be an earth with inhabitants on it, making just this experiment? ,,, This is big trouble for the multi-universe theory and for the “hidden-variables” approach.
    http://www.asa3.org/ASA/PSCF/2.....r.html.ori

    Hmmm, and if that wasn’t, to use Einstein’s word, ‘spooky’ enough:

    Here is the key experiment that led Wigner to his Nobel Prize winning work on quantum symmetries:

    Eugene Wigner
    Excerpt: To express this basic experience in a more direct way: the world does not have a privileged center, there is no absolute rest, preferred direction, unique origin of calendar time, even left and right seem to be rather symmetric. The interference of electrons, photons, neutrons has indicated that the state of a particle can be described by a vector possessing a certain number of components. As the observer is replaced by another observer (working elsewhere, looking at a different direction, using another clock, perhaps being left-handed), the state of the very same particle is described by another vector, obtained from the previous vector by multiplying it with a matrix. This matrix transfers from one observer to another.
    http://www.reak.bme.hu/Wigner_.....io/wb1.htm

    i.e. In the experiment the ‘world’ (i.e. the universe) does not have a ‘privileged center’. Yet strangely, the conscious observer does exhibit a ‘privileged center’. This is since the ‘matrix’, which determines which vector will be used to describe the ‘symmetry of the atomic particles being ‘observed’ in the experiment, is ‘observer-centric’ in its origination! Thus explaining Wigner’s dramatic statement, “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.”

    Now exactly how in blue blazes do photons know billions of years in advance if a experiment will be preformed to see which side of a galaxy they will pass on, and exactly how in blue blazes do atomic particles in a experiment know if a different observer is performing a experiment??? Materialism simply offers no coherent explanation but Theism certainly does!!!,,, As to the chemistry in living systems, there is an interesting anomaly that merits note:

    “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79
    http://www.uncommondescent.com.....ent-369806

    Spooky huh? Gets spookier to, because that same type of quantum action that caused the photon to ‘know’ billions of years in advance if a experiment would be preformed on earth to detect the photon,,,

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182

    ,,,is the same type of quantum action that has recently been discovered in molecular biology!!!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Now I don’t know about atheists, but as for myself, and for several of my close friends, finding something that blatantly defies time and space on a massive scale within our bodies is very comforting to our overall Theistic beliefs!!

  48. Nick,

    I examined the evidence and logic, and determined that you and those of your persuasion are promoting a thesis that cannot be defended on scientific, rational, mathematical or evidential grounds, and have therefore resorted to intimidation and vilification as the only recourse in an attempt to defend an indefensible, dying philosophy, disguised and promoted as “science.”

    The fact that I am a legitimate scientist who followed the evidence where it led, and a former militant, obnoxious atheist like you, is what really pisses you off.

  49. The selection process used to create the library bears no resemblance to Darwinian selection. It tested individual proteins to see whether they would fold.

    LOL. In a living thing that kind of selection would never happen?

    I’m curious. How is selection not Darwinian?

    You might think I’m being frivolous, but I’m not. ID proponents are continually using analogies to engineering. Software, airplanes and such. When a human engineer designs a product, he can look up the properties of materials and find their strength, weight, cost and such.

    There is no such database for protein coding sequences. And ID proponents have gone to great pains to point out that such a database would take more resources than are available in the universe. And Douglas Axe has asserted that there are no shortcuts. No rules of thumb that tell you what the effect will be of modifying a base pair.

    Sow how does a designer of proteins proceed without using Darwinian selection? How do you build a sequence library that codes for folding, and how do you build a subset that might contain useful folds without selection?

    Are you really trying to say that that chemistry behaves differently in the lab than it does in the wild?

    Or are you attacking a fundamental methodology that seeks to isolate the variables being studied?

  50. LOL!

    How about: “Warning! Materialists are cautioned not to view this material. May cause extreme cognitive dissonance.”

  51. Hi,

    I think the fallacy of evolutionary thinking is that it puts the cart before the horse. There is no evidence of genuinely complex systems appearing spontaneously.

    On the other hand, theory of semantic information maintains that for successful transmission of information not only does one have to have an agreement about the language, but also about the alphabet and, most importantly, about information semantics, i.e. what is to be considered “true” or “false”.

    Say, e.g. you have a string “dhfgdhg???????????f”, most our colleagues here won’t have a clue what it is but to me as a Russian speaker part of it makes sense because the Cyrillic letters in fact read “spanner”. However, it is not it. More importantly, the originator of the message must know beforehand that I, as a receiver, have an idea about what a spanner is like. Otherwise, the string no matter how informative it is will remain jibberish for the receiver.

    So, before information is relayed over a channel successfully, a number of a priori set conditions must be satisfied. To assume that these conditions were being worked out on the way is utterly implausible to me, as we have absolutely no evidence supporting such an assumption.

  52. Sorry, the Cyrillics did not work :)

  53. Petrushka,

    You are right. Selection is possible. No objections. And TOE is possible. No objections. The problem with TOE is that it is highly unlikely in our universe. It is so unlikely that it does not make sense to talk about this as a working scientific theory.

  54. ScottAndrews As to:

    Only after a set of proteins was selected was any experimentation done on living organisms.

    Moreover 4 genes were ‘knocked-out’ before the designed/selected proteins were even inserted, and when the designed/selected proteins were inserted they merely ‘rescued the cells, and did not increase the functional information over and above what was already present before the genes were knocked out! In fact I would hold the position that even after several rounds of ‘compensatory mutations’, by the highly sophisticated programming that is inside the cell, that the cells still did not return to its original level of ‘robustness/fitness’ when compared to the parent strains robustness/fitness! It is also interesting to note that in skimming over Behe’s ‘First Rule’ paper,

    EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS,
    AND “THE FIRST RULE OF ADAPTIVE EVOLUTION”
    http://www.lehigh.edu/~inbios/....._paper.pdf

    ,,,that I noticed, in TABLE 4, that both of the supposed ‘gain of function’ mutations listed by Dr. Behe, that Nick Matzke seems to be so enamored with, are such ‘forced’ deletions preceding ‘compensatory mutations’ events,,,

    Investigator action-
    Viruses manipulated to be defective
    Deletion of 19 intercistronic nucleotides from RNA virus MS2
    containing Shine-Dalgarno sequence and two hairpins

    Underlying mutation –
    One revertant deleted 6 nucleotides; another duplicated an adjoining 14- nucleotide sequence; missing functional coded elements substantially restored (Compensatory mutations!)

    Investigator action-
    4 nucleotide deletion in lysis gene of MS2

    Underlying mutation -
    Reading frame restored by deletions, insertions (Compensatory mutations!)

    Thus as with Petrushka’s forced example, it seems that our atheistic neo-Darwinian commentators, have been reduced to beggars of any evidence whatsoever, pathetically searching for proof of neo-Darwinian evolution by first removing information from a cell, and then either letting the programming of the cell calculate compensatory mutations, and/or introducing some epigenetic information in the form of designed/selected proteins that is then compensated for by the sophisticated programming in the cell.

    note:

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

  55. first removing information from a cell, and then either letting the programming of the cell calculate compensatory mutations, and/or introducing some epigenetic information in the form of designed/selected proteins that is then compensated for by the sophisticated programming in the cell.

    The question you posed asked for an example of a novel protein originating via Darwinian processes. I cited an example of a novel, functional protein, and asked a simple question:

    How could it have been designed without using Darwinian selection? How could anyone design a protein coding sequence without using selection? How were the sequence libraries used in the experiment produced? How could they have been designed while not using selection?

    So far you haven’t addressed my question.

  56. The problem with TOE is that it is highly unlikely in our universe. It is so unlikely that it does not make sense to talk about this as a working scientific theory.

    How did you work that out? Can you explain how you calculated the probability of evolution happening in our universe?

  57. Petrushka,

    How could it have been designed without using Darwinian selection?

    It is interesting the cherry picking you will go to to try to deny design, for from the abstract we read:

    De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth
    Excerpt: designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles.,,,
    http://www.plosone.org/article.....ne.0015364

    Thus the investigators, from their knowledge of stable protein structures, clearly imparted information about where a likely functional protein would be found in a search space. But what is interesting in this is that we don’t even know for sure if the supposedly functional proteins were truly functional in doing any useful molecular functions in the cell or if the protein, which you have presupposed to be molecularly functional, has done anything at all other than introducing epigenetic information BACK INTO the genome sufficient to ‘rescue the cells’ from the genetic deletion events that were imposed on them by the investigators. Perhaps the extremely sophisticated programming in the cell used the epigenetic information, from the supposedly functional protein, in a completely unexpected way to introduce a compensatory mutation calculation on the genetic deletion events. Thus, until you can satisfy that question, it is simply unwarranted for you to say for sure that a truly functional protein was found by the design/selection process that you have chosen to focus on. Thus you are not even sure if in this extremely biased example that selection (from a library of ‘quasi-designed’ proteins) has done what you think it has done!!!

    Welcome to CoSBi – (Computational and Systems Biology)
    Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas.

    Cells Are Like Robust Computational Systems, – June 2009
    Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,”We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail.”
    http://www.sciencedaily.com/re.....103205.htm

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

    Now Petrushka, a more appropriate, and far more honest, example that you should have used, to illustrate the extraordinary effort it takes for humans (who are considered intelligent agents by the way!!!) to find a specific protein, in conjunction with the ‘selection process’, that will perform a specific function is found here:

    Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator – Fazale Rana
    Excerpt of Review: ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?”
    http://www.amazon.com/gp/product/0801072093

    Now Petrushka, I highly doubt you will start using this example to honestly show the limits for what even human intelligence added to ‘selecting the best candidate’ can accomplish, but none-the-less, a honest person would readily admit that this is severely damaging to claims that neo-Darwinian processes accomplished alone what it could not with the best of human assistance!!!

  58. Petrushka:

    How could it have been designed without using Darwinian selection? How could anyone design a protein coding sequence without using selection? How were the sequence libraries used in the experiment produced? How could they have been designed while not using selection?

    1- Darwinian selection isn’t selection at all- it is a result of three processes

    2- A targeted search will do just fine as a design mechanism to design proteins.

  59. Re 10.1.1.1.2 by DrBot

    DrBot,

    “How did you work that out? Can you explain how you calculated the probability of evolution happening in our universe?”

    It was not me who showed that. I think it has been discussed a number of times here on this site.

    Once again.

    The probabilistic resources of the universe (taking into account the size of the search space of available configurations, the rarity and isolation of solutions in that space and finally, the timeframe of 10^17 seconds) are not enough to spointaneously generate such huge an amount of information without intelligent agency.

    Please refer to the FAQ page of this website, Question 25 where it discusses the issue. I find this credible enough. It agrees well with common sense to me.

    Also, please see here and here for a number of articles on this subject, notably on the capability of chaos to cause genuine self-organisation of matter.

    I find the arguments against the plausibility of spontaneous generation of information convincing enough as they agree with practice and common sense.

  60. You keep going off on tangents and avoiding the question.

    How were the sequence libraries designed? Looking at the literature, they were created using random variation and selection.

    As for your epigenetic claims, you are accusing the authors of fraud and the journal editors of incompetence. Pretty strong stuff. Perhaps you should write to them.

  61. The proteins were not derived via natural selection.

    The sequences the proteins were derived from were artificial- scientists made them.

  62. Petrushka et al. :

    While O have not followed all the discussion here, I would like to make a couple of comments about the paper linked by Petrushka. Very simply:

    1) The starting library of 1.5 x 10^6 sequences is definitely designed. While it is not designed for a specific activity, it is designed to more likely give sequences that fold in a specific way. That is a very strong design choice, which makes the selected library equivalent to a much bigger random library (very difficult to say how bigger).

    From the paper:

    Because folding into a stable 3-dimensional structure is a prerequisite for most biological functions, we did not construct this collection of proteins from random sequences. Instead, we used the binary code strategy for protein design, shown previously to facilitate the production of large combinatorial libraries of folded proteins.

    and:

    In brief, the binary code strategy posits that stably folded proteins can be encoded by specifying the sequence pattern of polar and nonpolar residues (the binary pattern) to coincide with the exposed and buried parts of a structure, respectively.

    and:

    For the current studies, we used the binary code strategy to design and construct a library of sequences designed to fold into 102-residue 4-helix bundles.

    No doubts about the design here, I suppose. I am aware of no “non designed” scenario that would allow auch a library to be spontaneously generated in a random system.

    This point, alone, changes completely the meaning of the paper. But there is more.

    2) It is a rescue study. Now, that is a big limit. They have correctly shown that a few sequences in their library can rescue a hew knockout strains, although with minimal efficay, but failed to demonstrate what the mechanism of rescue is. In particular, although they tried a lot of indirect strategies, there is no evidence from their work of what the new sequences do, or that they have, even at low level, the same activity that is lacking in the knockout strain. From the paper:

    We also purified several of the de novo proteins. (To avoid contamination by the natural enzyme, purifications were from strains deleted for the natural gene.) We tested these purified proteins for the enzymatic activities deleted in the respective auxotrophs, but were unable to detect activity that was reproducibly above the controls.

    IOWs, as far as we can say, the new proteins do not exhibit the same function as the knockout protein they rescue, not even at very low levels. The fact remains that they provide a minimal rescue, but we don’t know what they really do.

    That means that we can in no way know, at present, how complex is the “rescue function” found in the designed library.

    That’s all. And, I would say, that’s enough.

  63. The probabilistic resources of the universe (taking into account the size of the search space of available configurations, the rarity and isolation of solutions in that space and finally, the timeframe of 10^17 seconds) are not enough to spointaneously generate such huge an amount of information without intelligent agency.

    You said this:

    The problem with TOE is that it is highly unlikely in our universe.

    then responded with a claim that isn’t about TOE – the Theory of Evolution. Please can you explain why evolution is unlikely in our universe, not why abiogenesis is unlikely – remember, evolution will occur whenever you have differential reproduction with variance, the replicators could have been designed, or not, it makes no difference to the theory of evolution because it is not a theory of biogenesis.

    If you want me to address biogenesis then you need to provide a better argument that that – the universe is not a soup of chaos, it has structure and rules so most of the arguments (the infinite monkey ones) don’t apply because they don’t allow for the nested contingencies we routinely see in physical (non-living) processes. Infinite monkeys are unlikely to produce lots of patterns we routinely see in the universe that are a result of purely natural processes because the ONLY produce randomness.

  64. Petrushka,

    The study demonstrates what happens when first, proteins are selected using an intelligently designed test, and second, are tested with living organisms.

    What bearing does that have on the supposed ability of the organisms themselves to create and test new proteins on themselves? The two concepts are fundamentally different.

    If Edison could have automated the process of testing filaments rather than testing each one, would that make his process darwinian? Would we say, “Who invented the light bulb? No one. Selection did it.” The entire process, from beginning to end, is intentional, intelligent, and designed.

    You confuse intentionally designing, enabling, and executing a search with that same search executing with no intention, design, or enabling.

  65. One sometimes hears the expression: “I don’t have enough faith to be an atheist”.

    The discussion above covers some of the major unfounded assumptions – beliefs – of materialistic darwinism. My guess is there are hundreds of others.

    But has anyone condensed the list down to, say, a set of top 20 major unproven assumptions embodied in the accidental-mud-to-mozart believers?

    A list, link or reference would be much appreciated!

  66. Petrushka, you, emotionally, state;

    As for your epigenetic claims, you are accusing the authors of fraud and the journal editors of incompetence. Pretty strong stuff. Perhaps you should write to them.

    But alas, I am merely looking at the results:

    De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth
    Abstract: A central challenge of synthetic biology is to enable the growth of living systems using parts that are not derived from nature, but designed and synthesized in the laboratory. As an initial step toward achieving this goal, we probed the ability of a collection of >106 de novo designed proteins to provide biological functions necessary to sustain cell growth. Our collection of proteins was drawn from a combinatorial library of 102-residue sequences, designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles. We probed the capacity of proteins from this library to function in vivo by testing their abilities to rescue 27 different knockout strains of Escherichia coli, each deleted for a conditionally essential gene. Four different strains – ?serB, ?gltA, ?ilvA, and ?fes – were rescued by specific sequences from our library. Further experiments demonstrated that a strain simultaneously deleted for all four genes was rescued by co-expression of four novel sequences. Thus, cells deleted for ~0.1% of the E. coli genome (and ~1% of the genes required for growth under nutrient-poor conditions) can be sustained by sequences designed de novo.
    http://www.plosone.org/article.....ne.0015364

    Thus Petrushka, the experiment itself does not establish any specific molecular functionality, novel or otherwise, for the proteins, but the experiment merely notes that the presence of ‘specific sequences from our library’ ‘rescued’ four genes by co-expression of ‘four novel sequences’;!!! Do they note ANY molecular functionality of the proteins whatsoever??? NO they don’t!!! Thus, whatever you may think this experiment says for the generation of functional proteins, the plain fact of the matter is that you have not established your case that any novel functional protein was actually generated but have only established that ‘the presence of ‘specific sequences from our library’ ‘rescued’ four genes by co-expression of ‘four novel sequences’

    Perhaps this apparent propensity of yours to read far more into experimental results than are actually there is what makes you such a dogmatic neo-Darwinist??? One who refuses to dine on the ‘overwhelming’ evidence for design, but instead chooses to rummage through the bottom of trash cans looking for whatever morsel, however putrid, to satisfy your never ending hunger to deny design!

  67. Bot said: “evolution will occur whenever you have differential reproduction with variance.” That, of course, is simply not true. And Bot doesn’t even attempt to substantiate his claim. I suspect he’ll go on about Intelligently Designed hardware being programmed by Intelligently Designers to achieve a planned goal providing all the evidence he needs. But let’s look at the real world instead.

    Bacteria, perhaps the creatures with the most evolutionary advantages on this planet, has not evolved into anything at all: no body parts, no organs, no body plans, nothing except bacteria. Bacteria have not evolved into things like fish, birds, roses or humans. They are the same today as they were 3 billion years ago. The variance in “Differential reproduction with variance” is limited to trivial variety within the pre-existing and pre-defined strain or species it occurs in.

  68. DrBot

    remember, evolution will occur whenever you have differential reproduction with variance

    No, variance will occur whenever you have differential reproduction with variance. If by “evolution” you only mean that reproductions are not all exact clones, then your statement is correct. If by “evolution” you mean apparently open-ended improvement, that’s not warranted.

  69. DrBot:

    I don’t see how anyone can really separate the problem of abiogenesis from the problem of evolution. After all, about half of basic protein domains were already present in LUCA, so I suppose they were generated in the course of abiogenesis or not a lot of time after that. Maybe we should remember that many of the basic proteins, complex proteins, that we observe on life are absolutely necessary for replication itself. So, if those proteins were generated to allow replication, why shouldn’t the same mechanism be responsible for the generation of the other half of basic protein domains, the half which gradually appeared after LUCA and after abiogenesis?

    You may say that the proteins in LUCA, the proteins necessary for any known biological replication, were generated by evolution of different replicators, such as in the RNA world or similar. My answer is simple: there is no evidence of that. As far as we can say, it’s only a fairy tale. Like every non design OOL theory at present.

    But I can concede that evolution after OOL can be approched independently. And the ID theory can well show that it cannot be explained by a non design theory.

    You are wrong, however, at least IMO, when you say:

    the universe is not a soup of chaos, it has structure and rules so most of the arguments (the infinite monkey ones) don’t apply because they don’t allow for the nested contingencies we routinely see in physical (non-living) processes. Infinite monkeys are unlikely to produce lots of patterns we routinely see in the universe that are a result of purely natural processes because the ONLY produce randomness.

    I think you miss the point. The biological context is well known and specific. The “probabilistic resources of the universe” have been used by Dembski (as the UPB of 10^150, 500 bits) as an upper limit to what a random system can generate in the physioal universe. A very generous limit, I would say. But it can certainly be applied to a limited biological system. A protein of 150 aminoacids is beyond that limit, if the target space is small enough and if no selectable intermediaries can be shown.

    But for me, for a realistic biological system, like our earth and its life span, a much lower limit is enough. I have proposed many times 130 or 150 bits, that is about 30 – 35 AAs. No random biological system can reasonably explore that search space in realistic earth times.

    And I must remind you that the mechanism proposed by the darwinian theory for variation are absolutely random. There are no “nested contingencies” that can make the generation of a new AAs sequence anything but random in respect to the functional sequences of proteins. No known biochemical law favours sequences that can fold and have biological activity. Random variation is, indeed, random.

    You may say: but natural selection is not. I know. NS is a principle of necessity. It has its powers and its limitations. Both have been discussed here. But it can act only on what has been randomly generated. And it must not be considered a divinity, or a fairy tale. Wherever you assume that NS has acted, you have to ahow that it could act. IOWs, in any tentative explanation of the emergence of a complex protein function, you have to show that the complexity of any step which is supposed to emerge randomly is in the range of what random variation can realistically do. IOWs, you must deconstruct the sequence into simpler, naturally selectable steps, which has never been done. instead of appealing to “nested contingencies” that don’t exist.

  70. Bacteria, perhaps the creatures with the most evolutionary advantages on this planet, has not evolved into anything at all: no body parts, no organs, no body plans, nothing except bacteria. Bacteria have not evolved into things like fish, birds, roses or humans. They are the same today as they were 3 billion years ago.

    You are simply demonstrating that you don’t understand evolution – As you implied, bacteria are very successful, why change if you don’t need to. Also, how did you determine that bacteria today are the same as they were 3 billion years ago?

    It looks like you may be stuck on a teleological issue. There is no end goal in evolution, no rules that say everything must get more complex, it is just a process – it is what you get when you have differential reproduction with variance.

  71. If by “evolution” you mean apparently open-ended improvement, that’s not warranted.

    No I don’t mean open ended improvement and in biology evolution does not imply open ended improvement. Evolution is highly constrained.

    No, variance will occur whenever you have differential reproduction with variance.

    No, variance will occur whenever you have reproduction with variance. When you add in differential reproduction – where some ‘varieties’ will produce more offspring than others – then you get evolution.

  72. DrBot,

    When you add in differential reproduction – where some ‘varieties’ will produce more offspring than others – then you get evolution.

    The first part of your sentence is correct. Differential variation means, expressly, that there will be more of some variations than of others. Why does that mean you get evolution? One does not necessarily follow the other.

  73. Dr Bot,

    Of course I understand the distinction between the problem of OOL and that of evolution. But I still think that the basic reasoning to show abiogenesis and evolution are implausible is the same. Whenever there is enough novelty between taxa, the same reasoning applies as per the implausibility of abiogenetic OOL. The ID claim is the same: spontaneous generation of information is implausible.

    One cannot throw the same solution method at every problem. It so happens that at a microlevel what you describe occurs given an adaptible biological system. However the information leaps between taxa preclude continuous evolution.

  74. On the contrary, Bot, I think it is you who misunderstands evolution. An absolutely essential component of evolutionist belief is ‘ambition’. If you want to claim that there is scientific support for your belief that human beings evolved from a single-celled eukaryotic ancestor then you need to show a whole lot more ambition than mere “differential reproduction with variance”. You need to provide some serious evidence too.

    And you can’t have your cake and eat it either. You can’t pretend that bacteria have apparently evolved at the same time as implying that they didn’t need to. Especially when you almost admit that they haven’t changed in 3 billion years (albeit through a misleading rhetorical question like “why change if you don’t need to?”). So, which one is it, Bot? Have bacteria evolved or haven’t they? If the former what have they evolved into apart from bacteria? Nothing else at all? Where’s the ambition?

    If bacteria cannot and did not evolve into human beings (let alone anything else), then why should we believe that human beings (or indeed anything else) have evolved from a single-celled eukaryotic ancestor (and other creatures with dramatically less evolutionary advantages than bacteria)?

    It is simply not good enough to try and ignore the need for evolution to be far-reaching and ambitious with comments like “There is no end goal in evolution, no rules that say everything must get more complex”. The fact is, you and I are here having this discussion and if this event was an unintended accident the onus is on you to explain (with detailed evidence) how lifeforms as astounding as human beings could have evolved from a single-celled eukaryote. Please note, dismissive assumptions that explain nothing (like “evolution will occur whenever you have differential reproduction with variance”) are no substitute for reason and evidence.

  75. Petrushka, And from gpuccio’s Doctoral eye for detail, in such research papers, we find:

    We also purified several of the de novo proteins. (To avoid contamination by the natural enzyme, purifications were from strains deleted for the natural gene.) We tested these purified proteins for the enzymatic activities deleted in the respective auxotrophs, but were unable to detect activity that was reproducibly above the controls.

    IOWs, as far as we can say, the new proteins do not exhibit the same function as the knockout protein they rescue, not even at very low levels. The fact remains that they provide a minimal rescue, but we don’t know what they really do.
    http://www.uncommondescent.com.....ethinking/

    not exactly what you were hoping for was it Petrushka?

  76. I don’t see how anyone can really separate the problem of abiogenesis from the problem of evolution.

    How would you separate the theory of plate tectonics from the theory of planetary formation?

    I take your point in part though, for evolution to occur you need replicating entities so their origin needs to be explained, but the theory of evolution relates to what happens when you have those entities, not how they were created. There is a line between the two but until we know exactly how the first replicators came to exist and by what process then we can’t draw the line clearly – If they were intelligently designed with half of the basic protein domains present then that is the point at which evolution starts.

    The “probabilistic resources of the universe” have been used by Dembski (as the UPB of 10^150, 500 bits) as an upper limit to what a random system can generate in the physioal universe.

    Yes, but we are not talking about totally random systems so I think you are missing the point. Nested contingencies in this context have nothing directly to do with biology, it is about chemistry and physics. Random systems do not generate regular or complex patterns like crystals or sedimentary layers. Some ‘configurations of matter’ may be effectively impossible to find by a random search because they are the result of a series of contingent interactions (nested contingencies) but actually occur easily in the universe because of the way matter behaves – Reaction A enables B which enables C and D etc ..

    I keep seeing the ‘randomness cannot generate this’ argument put forth here and I think it is a bad argument because it doesn’t take into account how physics and chemistry work.

    I’m not using this to argue that abiogenesis could have happened, I’m trying to make the point that IF it happened it wouldn’t have been the result of all the bits coming together all at once from a soup of atoms, it would have been a result of many of the required bits forming through chemical processes, then coming together. You don’t need to generate 130 bits in one go, what you have are segmented bit ‘chunks’ which, if put together in the right order, for a replicator.

    Think about it this way, how many bits are required for a proto cell membrane? If a suitable membrane can result from natural processes (as I think people have already shown) then those bits are already present in the environment, they don’t need to form spontaneously with everything else.

    This reminds me of an issue I have with the whole idea of measuring things in functional bits – if you have a minimal replicator of 130 bits and you remove one bit, it stops being a replicator and therefore has zero functional bits – put the bit back and you have 130 functional bits – zero to 130 bits in one move! Or course I’m not arguing that this happened, I’m trying to make the point that the difference between a replicator with 130 bits of functional information, and a chemical soup with zero functional bits could only be a dozen bits.

  77. On the contrary, Bot, I think it is you who misunderstands evolution. An absolutely essential component of evolutionist belief is ‘ambition’.

    I think you must be talking about a different sort of evolution than the one biologists are referring to.

    evolution will occur whenever you have differential reproduction with variance

    Erosion will occur when you have fluid flow over a surface, falling will occur when you have an unsupported mass in a gravity well – more unjustified assumptions!

  78. Differential variation means, expressly, that there will be more of some variations than of others so the varieties that produce more will start to dominate the population.

    Of course if the environment is uniform and static then you will get stasis, but if it is variable and changing then the criteria for reproductive success will change and so will subsequent populations, and populations in different parts of the environment will change in different ways.

    So yes, I stand corrected – you need a non uniform environment as well as differential reproduction with variance.

  79. DrBot,

    How do the variations “know” whether the criteria for reproductive success has changed? They have no awareness of the criteria or purpose to meet it.

    Aside from that, variance is still just variance regardless of the environment. Why should variance in a non-uniform environment lead to evolution? I can understand why someone might think it might, but the dots from variance to evolution are still not connected. Those are very important dots.

  80. Bot, I can understand why increasing numbers of evolutionists don’t want to face up to the massively increased problems that evolution must solve. So they take refuge in vague phrases like “evolution will occur whenever you have differential reproduction with variance” rather than try to explain, with evidence, how it is that such “evolution” can turn a single-celled eukaryote (though not a prokaryote) into a human being.

    At least Charles Darwin, wrong as he was about almost everything, was brave enough to confront the problem head-on!

    So, you believe the evidence to support statements like “Erosion will occur when you have fluid flow over a surface” and “falling will occur when you have an unsupported mass in a gravity well” is equivalent to the evidence that human beings (and all other plants and animals) evolved from a single-celled eukaryote? If not, if in fact you have no evidence to support this belief, then who are you trying to kid? On the other hand, if you do have evidence, why not talk about that instead of erosion and gravity?

  81. How do the variations “know” whether the criteria for reproductive success has changed? They have no awareness of the criteria or purpose to meet it.

    Why do they need to know? If the criteria has changed then so does the reproductive success of each entity, ones that were most successful may now be less successful than some other varieties.

    This isn’t exactly difficult or controversial, even grossly over simplified computer models can illustrate how this very simple mechanism works – and the entities in the model don’t need to know that the criteria for success has changed.

  82. Chris, there is evidence in abundance – but none of it relates to the theory of evolution that you seem to believe exists, it all relates to the one that biologists have developed.

  83. While it is not designed for a specific activity, it is designed to more likely give sequences that fold in a specific way. That is a very strong design choice, which makes the selected library equivalent to a much bigger random library (very difficult to say how bigger).

    My point is the library is selected. Can you think of a way to design protein coding sequences without using selection?

    Another point is that while the library used in the experiment is a selected subset of a purely random set, the original set was produces by a stochastic process.

    It did not require resources larger than the universe to produce and refine via selection. It was done with very limited resources compared with the number of microbes that might be found in a shovel full of earth.

    So I have two points.

    1. Protein coding sequences cannot be designed without using the Darwinian process of selection. That is how the “designed” library was produced. The functional set was the result of further selection. Anyone here is free to suggest a method that does not require Darwinian selection.

    2. If this can be done in the limited time available to the experiment, it suggests the landscape of functional sequences is not as rugged as some have asserted.

    I might note that no one thinks coding sequences pop up in fully optimized form. Optimization would be microevolution.

  84. So, Bot, apart from your lack of responsiveness and substantiation, you now deny that evolution needs to explain the evolution of man from microbe. And this is my problem not yours? You are a time-waster, sir.

  85. DrBot,

    My point is that whether the criteria for success changes or doesn’t has no affect on what type of variations can arise and what they can accomplish.

    The second question I raised is how changes in the success criteria enable variations to accomplish evolution. That part is very controversial, at least among those who ask the question.

    Whether the environment is uniform or static determines how the differential variation differentiates. Got that. But in neither case does that variation result in evolution. That’s the leap of faith.

  86. Correction – uniform or static non-uniform

  87. DrBot, as to:

    I keep seeing the ‘randomness cannot generate this’ argument put forth here and I think it is a bad argument because it doesn’t take into account how physics and chemistry work.

    Actually physics and chemistry has been rigidly looked at, and a null hypothesis has been put forth as a result of that thorough examination;

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    “The Origin-of-Life Prize” ® (hereafter called “the Prize”) will be awarded for proposing a highly plausible natural-process mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. The explanation must be consistent with empirical biochemical, kinetic, and thermodynamic concepts as further delineated herein, and be published in a well-respected, peer-reviewed science journal(s).
    http://lifeorigin.info/

    Of particular interest to you, on the preceding site, is this paper: ‘The capabilities of chaos and complexity’

    Programming of Life – Information – Shannon, Functional & Prescriptive – video
    http://www.youtube.com/user/Pr.....3s1BXfZ-3w

  88. Also, how did you determine that bacteria today are the same as they were 3 billion years ago?

    Genomics is allowing us to trace evolution at the gene level, even in microbes. One can find varieties of the same gene, and eventually we will be able to find lineages of individual genes.

    It’s a bit like finding fossils.

  89. My point is that whether the criteria for success changes or doesn’t has no affect on what type of variations can arise and what they can accomplish.

    Everything but the last bit is correct. Variations are random with respect to fitness. What they accomplish is actually defined by the criteria for success, so the last bit is completely wrong.

    If some members of a population have a trait that makes it easier for them to digest a particular food type, but that food type is rare, then it doesn’t give any real advantage. If the environment changes, or the population moves, so that this food source becomes abundant then those with the digestive trait will have a greater chance of surviving and reproducing than those without.

    The second question I raised is how changes in the success criteria enable variations to accomplish evolution. That part is very controversial, at least among those who ask the question.

    But not amongst those who have answered it.

  90. You are a time-waster, sir.

    Yes, I often feel like I am wasting my time here ;)

    I haven’t yet been blessed with a knighthood so you need only refer to me as Dr, not Sir.

  91. DrBot,

    This statement is fundamentally illogical and highlights the fallacious thinking I’m trying to, well, highlight.

    Everything but the last bit is correct. Variations are random with respect to fitness. What they accomplish is actually defined by the criteria for success, so the last bit is completely wrong.

    How is what anything accomplishes ever defined by the criteria for success? What something accomplishes is defined by what it can accomplish and by what it does. If it meets criteria then it does, or else it does not. That statement makes no sense whatsoever.

    You say

    If some members of a population have a trait …those with the digestive trait will have a greater chance of surviving and reproducing

    Do you see why the claim that this happened because it was the criteria for success is not an explanation? What of species that are extinct? Did they have no criteria for success?

    Those are two good reasons why it makes no sense to say that “what they accomplish is actually defined by the criteria for success.”

    But not amongst those who have answered it.

    Perhaps you could invite one of them to join the discussion. :)

  92. You certainly are if you think you’re saying anything that will trouble those of us who don’t share your blind faith in neo-darwinism. I mean, you’re not even giving us pause for thought. Just unsupported claims that are easily refuted. Evolutionists like you, Bot, only seek to reassure ID proponents like me, that the truth is on our side.

    If you were half as qualified as you think you are this would simply not be the case. You’d present us with debate-ending evidence and cogent arguments, rather than bluffing and blustering your way through.

    If this is the best that our critics have to offer, then we can be very confident indeed. :-)

  93. Could it be that I’m not just the result of random errors filtered by natural selection? Am I just the product of the mindless, materialistic processes that “only legitimate scientists” all agree produced me?

    Since randomness exists as best as we can determine (as defined by mathematics/science) this presents many Christians with the following dilemma:
    1) God does not exist,
    2) God does exist but is not omnipotent, or
    3) God does exist and is omnipotent and so too randomness, for they are not mutually exclusive

    Many neo-Darwinian scientists, as well as some of their critics, have concluded that, if evolution is a radically contingent materialistic process driven by natural selection and random genetic variation, then there can be no place in it for divine providential causality. A growing body of scientific critics of neo-Darwinism point to evidence of design (e.g., biological structures that exhibit specified complexity) that, in their view, cannot be explained in terms of a purely contingent process and that neo-Darwinians have ignored or misinterpreted. The nub of this currently lively disagreement involves scientific observation and generalization concerning whether the available data support inferences of design or chance, and cannot be settled by theology. But it is important to note that, according to the Catholic understanding of divine causality, true contingency in the created order is not incompatible with a purposeful divine providence. Divine causality and created causality radically differ in kind and not only in degree. Thus, even the outcome of a truly contingent natural process can nonetheless fall within God’s providential plan for creation.

  94. The answer to that dilemma is found at Ecclesiastes 9:11.

    The race is not to the swift
    or the battle to the strong,
    nor does food come to the wise
    or wealth to the brilliant
    or favor to the learned;
    but time and chance happen to them all.

    Omnipotence and randomness are not mutually exclusive. Having the ability to foresee the outcome of random events does not necessitate the use of such foresight and does not make those events any less random.

  95. I agree

  96. Petrushka,

    A protein domain of 150 amino acids gives us N=20^150 states max. Proton transfer in hydrogen-bonded water is the fastest chemical reaction known to occur within around femtosecond (10^-15). Let’s say we want to check all permutations by blind brute force search at the fastest rate. Simple maths shows it takes much longer than 10^17 seconds, the accepted bound on the age of the universe. That is just for 1 protein domain…

    Now it depends of course, how many states are meaningful of those N. This varies from protein to protein but overall, meaningful states are known to be very rare AND isolated in the solution spaces.

    There is simply not enough time to go through all that by blind search. The only other alternative (apart from design) is to say our blind search is lucky to encounter a solution state very early on. But the chance of this happening is ridiculously slim. You may choose to believe in that chance. I don’t because it is not physically meaningful. I am not sure if there is any physically meaningful number of that order of magnitude to compare against. Maybe only the number of monkeys…

  97. This statement is fundamentally illogical and highlights the fallacious thinking I’m trying to, well, highlight.

    Well I would agree that I expressed it poorly, but as for illogical …

    How is what anything accomplishes ever defined by the criteria for success? What something accomplishes is defined by what it can accomplish and by what it does. If it meets criteria then it does, or else it does not. That statement makes no sense whatsoever.

    If the ultimate criteria for success is reproduction then you accomplish nothing if you don’t reproduce – How could you accomplish anything if there is no criteria by which you judge accomplishment?

    Perhaps this is just a muddle over word meanings – when I said “What they accomplish” I was talking about how much a particular trait contributes to reproductive success, not just that organisms with different traits are different.

    If some members of a population have a trait …those with the digestive trait will have a greater chance of surviving and reproducing

    Do you see why the claim that this happened because it was the criteria for success is not an explanation? What of species that are extinct? Did they have no criteria for success?

    No, it isn’t an explanation and it is not what I said. I did not claim that the variation happened because of anything, just that variation has consequences in terms of reproductive success.

    1-> Organisms are born, each is a little different than others in the population.
    2-> Those properties, in the context of the environment, determine reproductive success.

    Those are two good reasons why it makes no sense to say that “what they accomplish is actually defined by the criteria for success.”

    How do you know if you have actually accomplished anything (as opposed to just doing stuff) if you have no criteria to measure your performance?

    How could someone claim to have accomplished the task of climbing mount Everest if they do not have ‘climbing mount Everest’ as the criteria for success?

  98. DrBot,

    Understood, that’s not what you meant to express. But what did you mean to express?

    Your statement which led to this was to the effect that variation in a uniform environment produces little change while variation in a changing environment produces evolution.

    My response is that variation is just variation, regardless of the environment. You seem to imply that the changing environment raises a challenge, and that life is compelled to rise to it. That a changing environment results in evolution assumes that variation can result in evolution. (We’re far enough in the discussion that I’ll assume we mean the same thing by “evolution.”)

    There’s a holy grail out there that no one seems to want to bring home and show off. On what do you base the conclusion that any variation, regardless of the environment, results in extensive evolution rather than just small variations?

    I can stand one domino on its end and stack ten more on top of it without it falling over. If I told you that by extrapolation I could balance a thousand more on top, would you believe me? Wouldn’t you at least question how I came to that conclusion? I’ve been following this forum for some time and this same question gets raised several times each day. Everyone seems to maintain that is has been answered, but in thousands of posts no one seems to get around to addressing it head on. The one who does will be more famous than Darwin.

  99. DrBot:

    I see that BA has anticipated me, and quoted the paper by Abel which explains very well a few fundamental concepts:

    “Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors”

    The link is:

    http://www.ncbi.nlm.nih.gov/pm.....2-2-29.pdf

    Another very good paper by Abel is the follwing:

    “Constraints vs. Controls”

    http://www.bentham.org/open/to.....4TOCSJ.pdf

    So, I will try to answer briefly your points:

    If they were intelligently designed with half of the basic protein domains present then that is the point at which evolution starts.

    But my point is very simple: if half of the basic protein domains were designed in the beginning of life, the best expalnation for the remaining half that emerged after is that they were designed too. There is no reason at all to invoke a different mechanism, and especially one that obviously does not work.
    That’s why the problem of OOL is so strictly connected to the problem of evolution (except in the minds of darwinists): because the same mechanism that generated the tremendous amount of information necessary for the first biological replicators to exist can certainly well explain their successive evolution.

    Yes, but we are not talking about totally random systems so I think you are missing the point.

    You are missing the point. The point is that RV, in the darwinian model, is a totally random system. Do you want to deny that?

    Nested contingencies in this context have nothing directly to do with biology, it is about chemistry and physics.

    The laws of chemistry and physics have absolutely no role in determining the specific sequence of nucleotides in a protein gene that codes for the specific sequence of AAs that gives a functional protein. That sequence is a set of specific configuration of what Abel cals “configurable switches”, that is switches that, in themselves, could take different values according to the laws of chemistry and physics, but take specific functional values because a designer inputs that information. THat has nothing to do with necessity laws. No necessity law of chemistry or physics can make nucleotides assume the sequence in a DNA gene which corresponds, trhough the symbolic key of the genetic code, to the sequence of AAs in myoglobn, just to make an example. That should be very clear to anyone who has a fundamental understanding of biochemistry and biology.

    Random systems do not generate regular or complex patterns like crystals or sedimentary layers.

    Proteins are not crystals or sedimentary layers. You are falling here in the common error of conflating what Abel calls “ordered sequences” with what Abel calls “functional sequences” (see the first of the two papers. A crystal is ordered. A protein is not ordered, but is functional. There is a big difference. You cannot apply the concept of self-ordering, a la Prygogine, to proteins or protein coding genes. It does not work. It is simply wrong.

    The sequence of nucleotides in a protein coding gene does not depend on laws of chenistry, or on self-ordering principles of physics, any more than the sequence of words in Shakespeare’s Hamlet depends on the chemistry of ink and paper. Both are examples of functional information obtained by the superimposing of a functional order to configurable switches. Both are the product of conscious design.

    I keep seeing the ‘randomness cannot generate this’ argument put forth here and I think it is a bad argument because it doesn’t take into account how physics and chemistry work.

    Again, this is simple nonsense. See before.

    You don’t need to generate 130 bits in one go, what you have are segmented bit ‘chunks’ which, if put together in the right order, for a replicator.

    The simplest known biological replicator needs hundreds of complex proteins, and a lot of other information. It is beyonf the dreams of any possible random system. And evolution cannot happen unless you already have a biological replicator. It’s as simple as that.
    Well, indeed evolution, as conceived by darwinists, cannot happen even if you already have biological replicators :)

    Think about it this way, how many bits are required for a proto cell membrane? If a suitable membrane can result from natural processes (as I think people have already shown) then those bits are already present in the environment, they don’t need to form spontaneously with everything else.

    Are you saying that proto cell membranes are biologcial replicators? That they can evolve? Where are these strange beings? Where are they gathered in great numbers and concentrations, ready to do their part in the ritual of OOL? Hey, do you really believe these myths? All OOL theories are only that, myths, and bad myths indeed.

    This reminds me of an issue I have with the whole idea of measuring things in functional bits – if you have a minimal replicator of 130 bits and you remove one bit, it stops being a replicator and therefore has zero functional bits – put the bit back and you have 130 functional bits – zero to 130 bits in one move! Or course I’m not arguing that this happened, I’m trying to make the point that the difference between a replicator with 130 bits of functional information, and a chemical soup with zero functional bits could only be a dozen bits.

    This is a common error of thought, too. In your example, the functional information in the 130 bits of the replicator is already there, and working, and you must explain how it was generated.

    Obviously, you can suppress the function by changing only one bit, at least in some cases. And so? You keep the other 129 functional bits, and so it is perfectly true that one bit mutation (which is in the range of RV) can indeed restore the function.
    And so? The problem is, still: how did you get the other 129 bits right? By a random search?
    Can you see the difference?

    In desgin, you can well adjust 130 configurable switches one after another, because you, the designer, know what you want to obtain. And the function can well appear only at the end of the design. What’s the problem?

    It’s in a random walk that you cannot do that. Each single configuration of each bit cannot be implemented or kept, unless it confers a “reproductive advantage”. That’s the hard law of natural selection, the law that makes natural selection as almost useless tool for true evolution.

    Design can do that. Natural selection can’t. It’s as simple as that.

  100. Petrushka:

    Another point is that while the library used in the experiment is a selected subset of a purely random set, the original set was produces by a stochastic process.

    I don’t think you are right. Here is the procedure followed to build the library:

    “A general strategy is described for the de novo design of proteins. In this strategy the sequence locations of hydrophobic and hydrophilic residues were specified explicitly, but the precise identities of the side chains were not constrained and varied extensively. This strategy was tested by constructing a large collection of synthetic genes whose protein products were designed to fold into four-helix bundle proteins. Each gene encoded a different amino acid sequence, but all sequences shared the same pattern of polar and nonpolar residues. Characterization of the expressed proteins indicated that most of the designed sequences folded into compact alpha-helical structures. Thus, a simple binary code of polar and nonpolar residues arranged in the appropriate order can drive polypeptide chains to collapse into globular alpha-helical folds.”

    Am I missing something?

    Protein coding sequences cannot be designed without using the Darwinian process of selection. That is how the “designed” library was produced. The functional set was the result of further selection. Anyone here is free to suggest a method that does not require Darwinian selection.

    All wrong. First of all, it does not seem that the library was designed using darwinian selection, or any selection at all. It was designed by a specific algorithm.

    But even if a sequence were designed by coupling RV and selection (which is perfectly possible), still it would be RV + intelligent selection.

    As I have told you many times, intelligent selection is not darwinain selection. It is design.

    I hate to remind you, but “darwinan selection” is only, exclusively, “natural selection”, that is expansion of the replicators that replicate better.

    But, again, you will pretend not to understand that simple concept.

  101. Nice post gpuccio! Petrushka, I’m listing another paper that may help you see just how badly neo-Darwinists have faired in this area of trying to mimic proteins found in nature:

    Here is a critique of the failed attempt to evolve a ‘fit’ protein to replace a protein in a virus which had a gene knocked out:

    New Genes: Putting the Theory Before the Evidence – January 2011
    Excerpt: In this study evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

    What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host. Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

    The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory.
    But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

    And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology.

    Did the evolutionists conclude that proteins did not evolve? Did they suggest their findings are a problem for evolution? Did they even do so little as discuss the possibility that this one particular protein they studied may not have evolved?

    No. There is not even a hint from the evolutionists there is a problem. In fact, the results are, in typical fashion, interpreted according to evolution. As usual, the evolutionists simply explained that evolution must have, somehow, solved the problem:
    http://darwins-god.blogspot.co.....efore.html

    Petrushka, I already showed you what this but it bears worth repeating:

    Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator – Fazale Rana
    Excerpt of Review: ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?”
    http://www.amazon.com/gp/product/0801072093

    Petrushka, moreover, the proteins we find in life are found to be optimal which is completely contrary to these results we find, and indeed for what we should expect from some neo-Darwinian process that just so happened to stumble on to appropriate solutions accidentally:

    William Bialek – Professor Of Physics – Princeton University:
    Excerpt: “A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,,”
    http://www.princeton.edu/~wbialek/wbialek.html

  102. It’s in a random walk that you cannot do that. Each single configuration of each bit cannot be implemented or kept, unless it confers a “reproductive advantage”.

    That’s simply untrue. Both in theory and in the data. Most fixed mutations are neutral or nearly neutral. This has been known since before 1950 and has been mainstream for well over 50 years.

    It depends on population size. In large populations, favorable mutations tend to get fixed. In small populations, neutral mutations predominate.

    This fits both observation and simulations of population genetics.

    In living things, selection can monitor unlimited dimensions.

  103. Petrushka, you state (without reference);

    It depends on population size. In large populations, favorable mutations tend to get fixed. In small populations, neutral mutations predominate.

    This fits both observation and simulations of population genetics.

    Yet, despite what you believe, most mutations are shown to have a ‘unexpectedly’ small negative effect;:

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt:,,,Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    and even granting favorable ‘neutral’ mutation status to most mutations still does nothing to undermine the CORRECT genetic entropy model of compensating the slightly negative mutations:

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net

    As for ‘observation’ of fixation of mutations

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    Moreover, with existing population genetics models, evolution is shown to be impossible:

    Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology – video
    http://www.metacafe.com/watch/4165203

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.
    http://www.discovery.org/a/9461

    Dr. Sanford calculates it would take 12 million years to “fix” a single base pair mutation into a population. He further calculates that to create a gene with 1000 base pairs, it would take 12 million x 1000 or 12 billion years. This is obviously too slow to support the creation of the human genome containing 3 billion base pairs.
    http://www.detectingtruth.com/?p=66

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

    Perhaps you would like to apply for the job Petrushka since you seem to be so CONNEDvinced that neo-Darwinism is true?!? But I give you a clue Petrushka, population genetics will never, ever, be ‘fixed’ because neo-Darwinism ain’t the way we got here!

    All Things Bright And Beautiful – Canon In D – Pachebel
    http://www.metacafe.com/watch/4082996/

  104. I’m working on it.

  105. As I have told you many times, intelligent selection is not darwinain selection. It is design.

    OK, selection is design regardless of how it happens.

    “Intelligent” selection monitors on or two dimensions. Natural selection is open to all possible advantages simultaneously, even ones that are invisible to humans.

    If you want a dog with a longer tail, or a pigeon with some distinctive visual feature, intelligent selection will get you to a goal faster.

    But natural evolution has no goal. It is simply the result of differential reproduction. It doesn’t care which of nearly limitless possibilities confers the advantage. It fixes mutations that confer no advantage, but which occasionally lead to an advantage. It wanders down blind alleys, and most of them lead to extinction.

    If things are designed, why are 99 percent of designs extinct?

  106. Petrushka:

    For once, I quote myself:

    But, again, you will pretend not to understand that simple concept.

    Ditto.

  107. Petrushka:

    That’s simply untrue. Both in theory and in the data. Most fixed mutations are neutral or nearly neutral. This has been known since before 1950 and has been mainstream for well over 50 years.

    As it should have been known since the beginning of rational thought that neutral mutations, even if they occasionally and randomly expand, change nothing in the computation of probabilities in a random walk, and therefore are essentially useless and don’t explan anything. Occasional random expansion has the same probabilities of hitting a functional target as occasional lucky mutation. That is, practically none.

    You darwinists shoud make up your minds. If we kindly point out that a random system can generate practically nothing useful, immediately you start adoring the powers of non random natural selection. But if we gently remind you that those powers are minimal, you are ready to seek refuge under the protecting wings of some random component, like genetic drift.

    Well, I will state it very simply: RV in all its forms, plus natural selection in its only form (expansion of the best replicators) can do practically nothing. Certainly, it cannot generate complex functional information.

    But don’t worry, you can keep your faith and be happy.

  108. “If things are designed, why are 99 percent of designs extinct?”

    I think because we live in an imperfect world. It opens up a vent for philosophical discussions but that the world is imperfect can still be supported scientifically. If you wish to ask further questions such as why is it imperfect, the discourse is bound to be philosophical.

  109. Your statement which led to this was to the effect that variation in a uniform environment produces little change while variation in a changing environment produces evolution.

    If the environment is static then at most you will get neutral drift. What will typically happen is that the population will start to converge at a local maxima. In other words if the population is good enough and there is no pressure to change then there will be little or no change – they will only start to change again of the selection criteria changes.

    My response is that variation is just variation, regardless of the environment. You seem to imply that the changing environment raises a challenge, and that life is compelled to rise to it.

    No, that is not what I implied.

    That a changing environment results in evolution assumes that variation can result in evolution.

    The ability to reproduce successfully is determined primarily by two things – the properties of the organism and the environment they exist in.

    Organisms with certain traits, in a particular environment, will reproduce more than others.

    If the environment changes then a trait that was beneficial in the old environment may be less beneficial in the new one and a trait that was of no benefit, or even detrimental in the old environment could be an advantage in the new one.

    And pay attention to my use of the words ‘could’ and ‘may’ not ‘will’.

    There’s a holy grail out there that no one seems to want to bring home and show off. On what do you base the conclusion that any variation, regardless of the environment, results in extensive evolution rather than just small variations?

    You can’t disregard the environment – It ultimately determines which traits are beneficial. Beneficial traits will tend to dominate a population – this isn’t controversial, it is obvious – If a new disease wipes out all but a minority who have some form of resistance then the emerging population will be dominated by organisms with the resistive trait.

    Can you explain how your domino metaphor relates to the discussion?

  110. But my point is very simple: if half of the basic protein domains were designed in the beginning of life, the best expalnation for the remaining half that emerged after is that they were designed too. There is no reason at all to invoke a different mechanism, and especially one that obviously does not work.

    Why – given all the evidence for common descent?

    Yes, but we are not talking about totally random systems so I think you are missing the point.

    You are missing the point. The point is that RV, in the darwinian model, is a totally random system. Do you want to deny that?

    Perhaps you didn’t read my comment. We were discussing abiogenesis, not evolution. Random variation is random, otherwise it wouldn’t be called random variation ;) but we were talking about the ability of the universe to create arrangements of matter that function as a self replicator and I made the perfectly valid point that probability calculations based purely on a random search are not good mo0dels for how the universe works – there are no nested contingencies in a random search, just randomness, but in a complex chemical environment some things naturally follow from others, and consequently lead to more, creating a string of events that are contingent on earlier events – this is what nested contingencies are.

    The probability of finding matter arranged in orderly layers is different if you are talking about a random search as opposed to a set of physical processes involving tidal forces, liquids and eroding solids.

    The laws of chemistry and physics have absolutely no role in determining the specific sequence of nucleotides in a protein gene that codes for the specific sequence of AAs that gives a functional protein. …

    So there is absolutely no physical relationship between the format of a protein gene and the and the protein it produces?

    Random systems do not generate regular or complex patterns like crystals or sedimentary layers.

    Proteins are not crystals or sedimentary layers.

    No. You are not actually addressing the point I am making.

    The simplest known biological replicator needs hundreds of complex proteins, and a lot of other information.

    Yes, so what is the simplest possible replicator?

    Are you saying that proto cell membranes are biologcial replicators?

    Nope, I am saying that Lipid bilayers can form naturally.

    if you have a minimal replicator of 130 bits and you remove one bit, it stops being a replicator and therefore has zero functional bits – put the bit back and you have 130 functional bits – zero to 130 bits in one move!

    This is a common error of thought, too. In your example, the functional information in the 130 bits of the replicator is already there, and working, and you must explain how it was generated.

    Obviously, you can suppress the function by changing only one bit, at least in some cases. And so? You keep the other 129 functional bits, and so it is perfectly true that one bit mutation (which is in the range of RV) can indeed restore the function.
    And so? The problem is, still: how did you get the other 129 bits right? By a random search?
    Can you see the difference?

    I think you have misunderstood the concept of functional information. We are talking about a minimal self replicator (one that cannot be any simpler) Function is defined as the ability to self replicate, if it does not self replicate then it does not function. If you remove one bit it will not function (because it cannot be any simpler) so removing one bit leaves you with something that is not a self replicator and by definition has zero functional bits.

    Here are a couple of examples of cellular components that can form naturally:

    Lipid bilayers
    amino acids

    Now IF these components form part of a functioning replicator then how many bits of functional information does each of these components contribute to the replicator?

    If these ‘building blocks’ occur naturally then calculating the probability of the functional bits that they would contribute to a replicator as part of a random search makes no sense – they already exist! – you need to base the probability calculation on the likelihood of these bits coming together, not all being created at once.

    I’ll try the monkey typewriter metaphor – When the monkeys bash away at the keyboard they produce random strings of characters and you can work out some probability of them tying recognisable words, and then phrases. But if the keyboard has keys that produce whole words then the probability of them producing recognisable sentences changes.

    This is why probability calculations that assumes every bit of functional information has to form all at once is wrong, the calculation should be based on the likelihood of extant building blocks forming the right structure, not on all the building blocks forming all at once in the correct structure at the same time.

    Do you understand the difference?

    It’s in a random walk that you cannot do that. Each single configuration of each bit cannot be implemented or kept, unless it confers a “reproductive advantage”. That’s the hard law of natural selection, the law that makes natural selection as almost useless tool for true evolution.

    Again, chemistry is not a random walk. Some ‘configuration bits’ can be extant, the bits required to describe Lipid bilayers already exist if it has occurred naturally, they do not require selection pressures to exist or to persist, just the right chemical conditions.

  111. Petrushka, you, again with no reference, state:

    If things are designed, why are 99 percent of designs extinct?

    Yet, contrary to what you may believe, or even ‘want’ to believe, this is a lie; One persistent misrepresentation, that evolutionists continually portray of the fossil record, is that 99.9%+ of all species that have ever existed on earth are now extinct because of the many ‘evolutionary transitions’ that must have happened if neo-Darwinism were true. Yet the fact of the matter is that 40 to 80% of all current living species found on the earth are represented fairly deeply in the fossil record.

    The Fossil Record – The Myth Of +99.9% Extinct Species – Dr. Arthur Jones – video
    http://www.metacafe.com/watch/4028115

    “Stasis in the Fossil Record: 40-80% of living forms today are represented in the fossil record, despite being told in many text books that only about 0.1% are in this category. The rocks testify that no macro-evolutionary change has ever occurred. With the Cambrian Explosion complex fish, trilobites and other creatures appear suddenly without any precursors. Evidence of any transitional forms in the fossil record is highly contentious.”
    Paul James-Griffiths via Dr. Arthur Jones

    In fact, according to this recent census, there are around 230,000 marine species living today,

    Marine Species Census – Nov. 2009
    Excerpt: The researchers have found about 5,600 new species on top of the 230,000 known. They hope to add several thousand more by October 2010, when the census will be done.
    http://news.yahoo.com/s/ap/200.....ine_census

    Whereas, we only have about a quarter of a million different species collected in our museums.

    “Now, after over 120 years of the most extensive and painstaking geological exploration of every continent and ocean bottom, the picture is infinitely more vivid and complete than it was in 1859. Formations have been discovered containing hundreds of billions of fossils and our museums now are filled with over 100 million fossils of 250,000 different species. The availability of this profusion of hard scientific data should permit objective investigators to determine if Darwin was on the right track. What is the picture which the fossils have given us? … The gaps between major groups of organisms have been growing even wider and more undeniable. They can no longer be ignored or rationalized away with appeals to imperfection of the fossil record.” Luther D. Sunderland, Darwin’s Enigma 1988, Fossils and Other Problems, 4th edition, Master Books, p. 9

    “The evidence we find in the geological record is not nearly as compatible with Darwinian natural selection as we would like it to be …. We now have a quarter of a million fossil species but the situation hasn’t changed much. The record of evolution is surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than in Darwin’s time … so Darwin’s problem has not been alleviated”.
    David Raup, Curator of Geology at Chicago’s Field Museum of Natural History

    “There is no need to apologize any longer for the poverty of the fossil record. In some ways, it has become almost unmanageably rich and discovery is outpacing integration. The fossil record nevertheless continues to be composed mainly of gaps.”
    Professor of paleontology – Glasgow University, T. Neville George

    “Evolution requires intermediate forms between species and paleontology does not provide them.”
    David Kitts – Paleontologist

    “The long-term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists” –
    Stephen Jay Gould – Harvard

    “Given the fact of evolution, one would expect the fossils to document a gradual steady change from ancestral forms to the descendants. But this is not what the paleontologist finds. Instead, he or she finds gaps in just about every phyletic series.” -
    Ernst Mayr-Professor Emeritus, Museum of Comparative Zoology at Harvard University

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.” Robert L Carroll – Paleontologist

    ,,,Darwinism predicts we should have literally millions and millions of transitional fossil forms yet there are only a few dozen or so highly contested fossils claimed as transitional forms, none of which are uncontested. Moreover, the fossil record is overwhelmingly characterized by sudden appearance and overall stasis of form, with only bounded variation of that form to be found after a species/kind ‘sudden’ appearance in the fossil record:

    Ancient Fossils That Have Not Changed For Millions Of Years – video
    http://www.metacafe.com/watch/4113820

    THE FOSSILS IN THE CREATION MUSEUM – 1000′s of pictures of ancient ‘living’ fossils that have not changed for millions of years:
    http://www.fossil-museum.com/f.....8;limit=30

    Fossils Without Evolution – June 2010
    Excerpt: New fossils continue to turn up around the world. Many of them have an amazing characteristic in common: they look almost exactly like their living counterparts, despite being millions of years old,,,
    http://www.creationsafaris.com.....#20100618a

    The Unknown Origin of Pterosaurs – video
    http://www.youtube.com/watch?v=XP6htc371fM

    Bat Evolution? – No Transitional Fossils! – video
    http://www.metacafe.com/watch/6003501/

    Australonycteris clarkae is the oldest bat ever found in the fossil record at 54.6 million years old. The ear bones of Australonycteris show that it could navigate using echolocation just like modern bats.
    http://www.uncommondescent.com.....ent-340412

    ==============

    C. S. Lewis has his own distinctive view on ‘evolution’;

    C.S. Lewis – Evolution and The Christian Experience – video
    http://www.metacafe.com/watch/7060815/

  112. The laws of chemistry and physics have absolutely no role in determining the specific sequence of nucleotides in a protein gene that codes for the specific sequence of AAs that gives a functional protein. That sequence is a set of specific configuration of what Abel cals “configurable switches”, that is switches that, in themselves, could take different values according to the laws of chemistry and physics, but take specific functional values because a designer inputs that information. THat has nothing to do with necessity laws. No necessity law of chemistry or physics can make nucleotides assume the sequence in a DNA gene which corresponds, trhough the symbolic key of the genetic code, to the sequence of AAs in myoglobn, just to make an example. That should be very clear to anyone who has a fundamental understanding of biochemistry and biology.

    This is a point I’ve heard before but never so clearly articulated. Kudos to gpuccio.

  113. Brooke Fraser – C.S. Lewis Song – Music Video
    http://www.youtube.com/watch?v=wo-e2BjICCY

  114. Corrected link:
    Brooke Fraser – C.S. Lewis Song – Music Video
    http://www.youtube.com/watch?v=kMRFbc5KVaM

  115. DrBot,

    Spontaneous organisation of matter into systems with complex formal relationships between components has not been observed to date. What has been observed is merely self-ordering that has a minimum amount of associated information. This strongly suggests that self-organisation is an impossibility.

    Common sense suggests that instruction/plan goes before construction of complex systems. At least, the collective experience of humanity teaches us so. Why should biology be an exception?

    Formally, for information to be transmitted, a number of a priori satisfied conditions must be met, notably as regards the agreement on information semantics between the sender and the receiver.

    “This is why probability calculations that assumes every bit of functional information has to form all at once is wrong”

    Is it about climbing Mt Improbable from the back? I think that by the time a trait can be used exaptationally by anything, this anything must already be a very complex system. Exaptation does happen but its capabilities are very limited. The complexity gaps are in fact chasms.

  116. The extinction figures will necessarily include families and orders that no longer exist. Extinction figures, by definition, would not include transitionals.

    Just in the human lineage, we have numerous species that have no living descendants.

  117. You darwinists shoud make up your minds. If we kindly point out that a random system can generate practically nothing useful, immediately you start adoring the powers of non random natural selection.

    Neutral theory is well established. It is fairly easy to demonstrate in software. It is fairly easy to demonstrate in living things by tracing the lineage of neutral or neutral alleles.

    I find it interesting that when “intelligent” selection is demonstrated in the laboratory, you say it can accomplish anything, but “natural” selection can accomplish nothing.

    I suppose if you cannot get past the concept of targets and goals, you would have a point. Natural selection does not reach targets or goals.

  118. Isn’t this a theological objection (and a poor one, at that), rather than a scientific one, Petrushka? If not, then please explain which particular observations or experiments lead you to conclude that extinction is incompatible with Intelligent Design theory?

  119. “Natural selection does not reach targets or goals” but it does turn microbes into humans. What’s the difference?

  120. Chris,

    Good point.

    Taken to its extreme, the TOE maintains that humans have appeared here by fluke and that religion is a mental virus.

    Sometimes I think that perhaps it is just the TOE that is a mental virus.

    Personally, I prefer something that does have a purpose to something that does not.

  121. DrBot,

    You’re falling back to rather neutral statements that nearly everyone agrees on. I suppose that’s a good thing.

    A single variation may or may not convey a benefit, and if the environment changes, the criteria that determine whether a variation is beneficial also changes.

    The question (unless I’ve completely lost track of it between the threads) is how that relates to what we commonly call evolution. Variation may explain difference in color, digestion, or resistance to a disease. It does not explain spiderwebs, wings, or carnivorous plants.

    That is the relevance of the domino illustration. It appears that you extrapolate the causes of such notable variations between species from the small variations within species. It’s unfounded, like extrapolating that I can balance 1,000 dominoes because I can balance ten. It sounds reasonable until you try it.

    You haven’t explicitly stated that extrapolation, but you have said that differential variation leads to evolution. It sounds like the same thing. Am I misunderstanding? How does differential variation lead to evolution?

  122. Petrushka:

    Natural selection does not reach targets or goals.

    Indeed. Nor does it reach any complex functional result.

  123. Petrushka,

    Your point about targets and goals is taken. The typical illustration is monkeys typing Shakespeare, but that is too specific a target. A more fitting illustration would be monkeys creating pages of coherent writing in any language using any means available, not limited to English or typewriters or Shakespeare. They could make their own language and/or alphabet. It doesn’t even have to be witty or insightful.

    Do you see how removing the goals or targets does not make the scenario more plausible? A specific target, be it a type of life or a species, it not the problem. The problem is that any type of function whatsoever is a tiny target compared to non-function. Probabilistic resources would take an eternity to produce what intelligence can do in seconds.

  124. Petrushka:

    Neutral theory is well established. It is fairly easy to demonstrate in software. It is fairly easy to demonstrate in living things by tracing the lineage of neutral or neutral alleles.

    I am in no way denying that neutral mutations occur. They do occur. And they are very useful to trace the connections between species and their history. My simple point, stated many times as clearly as possible I suppose, is that neutral mutations do not add anything to the analysis of the random system, whether they randomly expand by genetic drift or not. They are simply irrelevant to the subject of functional information. They are only one form of RV, and nothing more.

  125. Petrushka;

    Extinction figures, by definition, would not include transitionals.

    But are not all species merely transitional in the overall neo-Darwinian framework??? Just who made neo-Darwinists the judges of what is to be considered transitional and what is not to be when the theory itself dictates that all life is as such??? Oh that’s right, I almost forgot, neo-Darwinism is molded to fit whatever the evidence says instead of actually predicting what the discovered evidence will say!!!

    As well I seem to recall a bit of a HUGE problem for neo-Darwinists even proving that major morphological transitions are even possible, by their genetic reductionism model, since mutations to DNA never produce morphological novelty!!!

    Hopeful monsters,’ transposons, and the Metazoan radiation:
    Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable “hopeful monsters” render these explanations untenable.
    Paleobiologists Douglas Erwin and James Valentine

    “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan).”
    Michael John Denton page 172 of Uncommon Dissent

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

    The Sheer Lack Of Evidence For Macro Evolution – William Lane Craig – video
    http://www.metacafe.com/watch/4023134

    As Stephen Meyer states at the end of this following video, ‘You can mutate DNA till the cows come home and it will not effect Body Plan morphogenesis!” (paraphrase)

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer
    “Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    Modern Synthesis of Neo-Darwinism (Genetic Reductionism) Is Dead – Paul Nelson – video
    http://www.metacafe.com/watch/5548184/

    Evidence for speciation???

    neo-Darwinian reductive aterialists do not seem to notice that their theory of evolution expects and even demands there should be undeniably clear evidence for a genetically, and morphologically, unique species on earth somewhere since man first suddenly appeared on earth. Indeed there should be numerous unambiguous examples they could produce to silence their many critics.

    “Perhaps the most obvious challenge is to demonstrate evolution empirically. There are, arguably, some 2 to 10 million species on earth. The fossil record shows that most species survive somewhere between 3 and 5 million years. In that case, we ought to be seeing small but significant numbers of originations (new species) .. every decade.”
    Keith Stewart Thomson, Professor of Biology and Dean of the Graduate School, Yale University (Nov. -Dec. American Scientist, 1997 pg. 516)

    In fact, instead of any origination of any new species on the earth, what we see now is massive extinction of species:

    The current rate of extinction is from 100 to 10,000 species a year. This is between 100 and 1000 times faster than our best estimate of historical rates. (of note: it is thought that the “impact of man” is accelerating the extinction rate).
    http://www.sciencedaily.com/re.....073106.htm

    Moreover, a neo-Darwinian reductive materialist will try to assert evolution of species is happening all the time, all over the place. Yet, once again the hard evidence betrays the materialist in his attempts to validate his atheistic evolutionary scenario.

    The Mirage of “Evolution Before Our Eyes” – August 2011
    Excerpt:,,,the important implication of the massive study by Oregon State University zoologist Josef C. Uyeda and his colleagues. They write in PNAS: “Even though rapid, short-term evolution often occurs in intervals shorter than 1 [million years], the changes are constrained and do not accumulate over time.”
    http://www.evolutionnews.org/2.....49911.html

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.”
    R. Milner, Encyclopedia of Evolution (1990)

    “Despite a close watch, we have witnessed no new species emerge in the wild in recorded history. Also, most remarkably, we have seen no new animal species emerge in domestic breeding. That includes no new species of fruitflies in hundreds of millions of generations in fruitfly studies, where both soft and harsh pressures have been deliberately applied to the fly populations to induce speciation. And in computer life, where the term “species” does not yet have meaning, we see no cascading emergence of entirely new kinds of variety beyond an initial burst. In the wild, in breeding, and in artificial life, we see the emergence of variation. But by the absence of greater change, we also clearly see that the limits of variation appear to be narrowly bounded, and often bounded within species.”
    Kevin Kelly from his book, “Out of Control”
    http://www.uncommondescent.com.....ent-392638

    New Research on Epistatic Interactions Shows “Overwhelmingly Negative” Fitness Costs and Limits to Evolution – Casey Luskin June 8, 2011
    Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn’t run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
    http://www.evolutionnews.org/2.....47151.html

  126. DrBot:

    Why – given all the evidence for common descent?

    What do you mean? I do believe in common descent. Design is perfectly compatible with common descent. I know that many IDists don’t accept common descent. I do.

    in a complex chemical environment some things naturally follow from others, and consequently lead to more, creating a string of events that are contingent on earlier events – this is what nested contingencies are. The probability of finding matter arranged in orderly layers is different if you are talking about a random search as opposed to a set of physical processes involving tidal forces, liquids and eroding solids.

    Please show, with some evidence, how your contingencies lead to biological replicators, to proteins, to DNA, and so on. Then I will listen to your “argument”. We must talk science, not phylosophy or myth or religion.

    So there is absolutely no physical relationship between the format of a protein gene and the and the protein it produces?

    No. The connection is purely symbolic and informational.

    No. You are not actually addressing the point I am making.

    Yes, I am. I am saying that the symbolic, digital, comp’lex and functional information we find in protein genes has nothing to do with the order we find in crystals.

    Yes, so what is the simplest possible replicator?

    The simplest biological replicators we know are the simplest autonomous bacteria. Being an empirical person, I consider that my model of biological replicator. Show me something different, and we can discuss. Again, this is a place for science, not for imaginary hypothetical possibilities without any trace of evidence.

    Nope, I am saying that Lipid bilayers can form naturally.

    OK. That’s good news for lipid bilayers, not for biological replicators.

    I think you have misunderstood the concept of functional information. We are talking about a minimal self replicator (one that cannot be any simpler) Function is defined as the ability to self replicate, if it does not self replicate then it does not function. If you remove one bit it will not function (because it cannot be any simpler) so removing one bit leaves you with something that is not a self replicator and by definition has zero functional bits.

    No. If I am writing a complex computer program of one gygabyte, and when it is ready and functional I take away one bit and make it crash, I still have the almost complete program, which has been designed with labor and patience and intelligence. It will be enough to correct one bit to have the whole thing.

    I think I understand very well the concept of functional complexity. I have been discussing it in dpth here for years. If you want to compute the functional complexity of a functional sequence, you have to compute the probability of finding it by a random walk starting from a random, unrelated state. Not certainly starting from the almost complete thing. I believe that you should make some deeper reflection on the concept of functional complexity.

    Here are a couple of examples of cellular components that can form naturally: Lipid bilayers, amino acids

    OK, and so? And please, bear in mind that one thing is that they can perhaps form naturally, another thing is that they really form naturally in natural comditions, and in quantities and concentrations useful to some purpose.

    Now IF these components form part of a functioning replicator then how many bits of functional information does each of these components contribute to the replicator?</cite

    When I compute the functional information of a protein gene or a protein sequence, I concede as granted that aminoac ids are already present in the system. The only functional information that I am computing is that necessary to get the right functional sequence of the aminoacids. And that calculation is only for one single protein. So, in this context, the already existing aminoacids are not adding any bit of functional information to the computation if the functional information in the functional sequence. Is that clear?

    If these ‘building blocks’ occur naturally then calculating the probability of the functional bits that they would contribute to a replicator as part of a random search makes no sense – they already exist! – you need to base the probability calculation on the likelihood of these bits coming together, not all being created at once.

    Exactly my point. That’s what I do.

    I’ll try the monkey typewriter metaphor – When the monkeys bash away at the keyboard they produce random strings of characters and you can work out some probability of them tying recognisable words, and then phrases. But if the keyboard has keys that produce whole words then the probability of them producing recognisable sentences changes.

    Nucleotides are letters, not words. The biological system has not words, only letters, as building blocks. Please, check your understanding of DNA and the DNA code.

    And by the way, even if monkeys taped words, and not letters, the probabilities of outputting Hamlet would still be ridiculous. Do you want to try to compute them?

    This is why probability calculations that assumes every bit of functional information has to form all at once is wrong, the calculation should be based on the likelihood of extant building blocks forming the right structure, not on all the building blocks forming all at once in the correct structure at the same time. Do you understand the difference?

    NO. What are your “building blocks”? I am speaking of the probabilities of nucleotides, which are all present in the medium and have the same probability to be part of a DNA molecule, to arrange in a functional sequence. Or just to change an existing sequemce into a completely new one through random variation. Each nucleotide is a building block. There are four of them. To have a new functional protein of 100 AAs, you have to arrange 300 nucleotides in the right sequence. That’s all.

    Again, chemistry is not a random walk. Some ‘configuration bits’ can be extant, the bits required to describe Lipid bilayers already exist if it has occurred naturally, they do not require selection pressures to exist or to persist, just the right chemical conditions.

    Chemistry has nothing to do with gene sequences, as I have said many times. Do you admit that, for a biological replicator to exist, gene sequences had to appear at some time? Well, chemistry cannot do that. I can’t see why you cannot accept that simple concept.

  127. Please show, with some evidence, how your contingencies lead to biological replicators, to proteins, to DNA, and so on.

    Why? I’m an abiogenesis skeptic!

    Then I will listen to your “argument”. We must talk science, not phylosophy or myth or religion.

    So you will only listen to my argument that the way these probabilities are calculated is wrong unless I demonstrate how complete abiogenesis works.

    Ok, but first please show in complete detail how the designer created life, what methods they used etc (apart from just !POOF! ) I won’t listen to your arguments unless you tell me how goddidit!

    No. The connection is purely symbolic and informational.

    Sounds like magic to me ;) Got any science to back that up?

    The simplest biological replicators we know are the simplest autonomous bacteria. Being an empirical person, I consider that my model of biological replicator. Show me something different, and we can discuss. Again, this is a place for science, not for imaginary hypothetical possibilities without any trace of evidence.

    So your probability calculations could be deeply flawed – imagine doing this for something that can fly, I ask what is the minimum required for something to fly or glide, you point me to a 1920′s aircraft, OK, well here is my paper aeroplane.

    If you REALLY want to calculate the probability of a self replicator forming via chemistry then you need to try and understand what the minimum requirements are for self replication – They could be drastically less than the simplest life we can see today, but they may not, and even if we can determine that minimum it is still not directly related to biology because we need to show that this replicator could have formed and then led to biology. This is, in part, what some in the OOL community are actually doing (you know, real research)

    THE POINT is that the probability calculations you make are meaningless without this knowledge. Discovering a drastically simpler replicator, that is a viable FUCA, than the ones you make the calculation on would completely change the result of that calculation.

    bear in mind that one thing is that they can perhaps form naturally, another thing is that they really form naturally in natural comditions, and in quantities and concentrations useful to some purpose.

    Yes, I understand the ID position that chemistry in the lab never happens in reality. It’s not that I am arguing that it DID happen, just pointing out that it CAN, and if it can then that affects how you calculate probabilities.

    If you want to compute the functional complexity of a functional sequence, you have to compute the probability of finding it by a random walk starting from a random, unrelated state. Not certainly starting from the almost complete thing. I believe that you should make some deeper reflection on the concept of functional complexity.

    If you know that it is possible for many of the required sub components to form naturally, just not all connected together in the right way, they your search should NOT assume that you start WITHOUT some of the components already present.

    To use the computer code methphor, if I know that some functions can occur naturally then the random search does not have to find them. This affects the probability calculation of finding a working program.

    Exactly my point. That’s what I do.

    So Lipid bilayers and amino acids form essential parts of a functioning replicator but contribute no functional information?

    Or are you saying that you know which components can form naturally, and have discounted them from the calculation – in which case show me the evidence to back up your assumptions!

    Nucleotides are letters, not words. The biological system has not words, only letters, as building blocks. Please, check your understanding of DNA and the DNA code.

    What has DNA got to do with it? I was, as you can see in what I wrote, referring to the chemical components that would be required for a minimal self replicator. If many of these components (Lipid bilayers and amino acids) are extant then they, in terms of the monkey methaphor, are words, not letters.

    And by the way, even if monkeys taped words, and not letters, the probabilities of outputting Hamlet would still be ridiculous. Do you want to try to compute them?

    Why don’t you have a go – then you may understand the point that the probabilities in that scenario are different than the random letter one – THAT IS MY POINT – if you want to make a good argument about probabilities then you need to start by understanding what probabilities you are actually calculating! That producing shakespeare is still unlikely even when whole words are available is actually irrelevant to my point. It is about how you calculate the probabilities, and from an ID perspective it is about doing the math and the science correctly. Probability calculations are meaningless unless your starting assumptions are actually realistic and reflect reality.

    Chemistry has nothing to do with gene sequences, as I have said many times. Do you admit that

    So gene sequences exist independently of chemistry! Glad you made that clear, now can you show me an example of a functioning gene sequence that is not based on chemistry?

  128. DrBot,

    So Lipid bilayers and amino acids form essential parts of a functioning replicator but contribute no functional information?

    Suppose you take the parts for a home gym (I use this only because I know they are a pain to put together,) add random components from ten other home gyms and dump them all on the floor.

    True, some information is present in the form of completed parts which may fit together. But in what sense does it contribute to anything functional? It’s not functional without the instructions that distinguish relevant parts from irrelevant parts, describe how to assemble them, and how the finished product will work. And you need someone to process and follow those instructions.

    How much information is that? It renders the presence of potentially functional parts irrelevant. That’s why I find such speculation so curious. It leaps from the potential formation of components with potential functionality and imagines them all assembled and working together.

  129. How much information is that? It renders the presence of potentially functional parts irrelevant.

    Thats the whole point – how much information is it?

    Just saying – well its lots – isn’t very scientific.

  130. You don’t think it is a lot? You’re going to ignore it unless someone else counts it for you? How scientific is that?

  131. You don’t think it is a lot? You’re going to ignore it unless someone else counts it for you? How scientific is that?

    So it is my responsibility to provide the calculations that show that your example has the ‘lots of info’ that you claim it has? well at least ID is consistent in what it demands ;)

    When it comes to the probabilities involved with OOL, the only people actually doing any real work that can narrow down exactly what the probabilities are, are the OOL researchers. ID is not actually doing any research in this area as far as I can see, they are just making claims about the probabilities of events that we know very little about. The actual scientists meanwhile are trying to increase our knowledge of these events.

  132. DrBot,

    So it is my responsibility to provide the calculations that show that your example has the ‘lots of info’ that you claim it has?

    No, I’m not asking you to calculate the information required in my example. (I didn’t give you nearly enough information.) But if you claim that the possible formation of what may or may not have been early cell components make the assembly of self-replicators plausible, you should already have considered those factors rather than optimistically ignoring them.

    When it comes to the probabilities involved with OOL, the only people actually doing any real work that can narrow down exactly what the probabilities are, are the OOL researchers.

    I don’t see how an OOL researcher could narrow that down. How do you assess the information content of assembly instructions without knowing them? But I’d be curious to know what that estimate is.

    On the other hand, do you need to be an OOL researcher to guestimate that the assembly instructions for a self-replicator are upwards of 1,000 bits? Dead-on accuracy is not the issue here.

    I think most people will recognize how backwards it is that I am the one asked to estimate the amount of information required to assemble the components of a self-replicator. Isn’t the answer at least as important as determining whether those components can be synthesized?

    Here’s my generous estimate: More than 1000 bits. My basis? You can’t assemble a home gym with 1000 bits of information. And that doesn’t even include the tools which aren’t a part of the finished product.
    Is that more or less than what OOL researchers have estimated?

  133. The point you are commenting on as made by Chris is actually a really bad point. How does the evolution of humans indicate a purpose?

    I think your last sentence says it all.

  134. DrBot:

    Why? I’m an abiogenesis skeptic!

    You don’t believe it happened?

    So you will only listen to my argument that the way these probabilities are calculated is wrong unless I demonstrate how complete abiogenesis works.

    No, but at least some tentative explanation of how your “contingencies” should generate complex functional information would be appreciated.

    Sounds like magic to me Got any science to back that up?

    Sure. It is common knowledge, but as it seems that you are not specially acquainted with biology (nothing bad in that), I will try to sunnarize it for you. You can check all that I say anywhere.

    The protein gene is a sequence of nucleotides. They can be interpreted as the sequence of a protein through a symbolic code, known as the genetic code. That is a code in base four (four nucleotides) and made of codons of three nucleotides. It is a redundant code (64 values for 20 aminoacids plus stop codons).

    DNA works as a mass memory. Ir is a rather inert molecule, very appropriate for storing information. The DNA molecule has absolutely no chemical connection to the proteins whose information it contains.

    The synthesis of the protein from the DNA gene is made possible by two fundamental mechanisms: transcription and translation.

    Let’s skip transcriprion for the moment, and le’t focus on translation.

    Translation is the final process that transforms the information in the nucleotide sequence in the DNA gene into the real protein with its sequence of aminoacids.

    Now, translation is made possible by a very complex apparatus, made essentially of three components: the transfer RNAs, the aminoacyl-tRNA synthetases, and the ribosome.

    Let’s focus our attention on the synthetases. These are the pert of that complex machine which has the key to the translation. Indeed, they are 20 different proteins, very complex proteins, one for each aminoacid, divided in two classes. Each protein is made of hundreds of aminoacids, up to more than one thousand.

    It’s those proteins that match the right aminoacid to the correct tRNA, bearing the corresponding anticodon, ensuring that the code is correctly translated. There is no physical connection between the amionoacid and the anticodon, indeed they are at the two extremes of the tRNA molecule. It is the specific protein that is designed so that it may connect the rught aminoacid to the right tRNA.

    And guess waht allows each specific protein to recognize the correct amioacid and to bind it to the correct tRNA? Obviously, its specific sequence of AAs, humdreds of them for each of the 20 proteins. And what codes for that sequences? The corresponding DNA genes, regularly translated by the same mechanism.

    It sounds like magic? Yes, it does. But it is true.

  135. DrBot:

    THE POINT is that the probability calculations you make are meaningless without this knowledge. Discovering a drastically simpler replicator, that is a viable FUCA, than the ones you make the calculation on would completely change the result of that calculation.

    Well, then discover it. Good luck.
    In the meantime, my calculations are for things that exist (genes, proteins), and that darwinists try to explain with stupid theories. Again, I am interested in science, not imagination. Imagination is good to defend blind religions like darwinism. Science is about facts and their explanation.

    If you know that it is possible for many of the required sub components to form naturally, just not all connected together in the right way, they your search should NOT assume that you start WITHOUT some of the components already present.

    You evade, again. My calculations are about basic protein domains, that are functional units. You speak of subcomponents that do not exist. Imagination, again. Blind faith, again. What about facts?

    So Lipid bilayers and amino acids form essential parts of a functioning replicator but contribute no functional information?

    They contribute no functional information to protein sequences. That’s very obvious. I have never discussed lipid bilayers or the formation of aminoacids. I have given you all your lipid bilayers and all your amonacids for free, as a gift.

    What I want to know is how do you explain protein sequences, starting from your lipid bilayers and aminoacids, or whatever.

    Or are you saying that you know which components can form naturally, and have discounted them from the calculation – in which case show me the evidence to back up your assumptions!

    What assumptions? Again, I am just asking, how do you explain complex functional sequences, even if you already have the single aminaocids? How do you explain complex functional protein genes, even if you already have individual nucleotides? Is it so difficult to understand a simple question? How aminoacids or individual nuxcleotides were formed is irrelevant to that question. Let’s say they are there. The question is about the functional information in the digital sequence, not about the generation of the raw components of the sequence.

    What has DNA got to do with it? I was, as you can see in what I wrote, referring to the chemical components that would be required for a minimal self replicator. If many of these components (Lipid bilayers and amino acids) are extant then they, in terms of the monkey methaphor, are words, not letters.

    Again, what replicator? How can we discuss something that dioes not exist? I am discussing genes and proteins. They exist. They must be explained.

    if you want to make a good argument about probabilities then you need to start by understanding what probabilities you are actually calculating!

    But I have always been very clear about the probabilityies I am discussing. I am discussing the probability of generating the complex functional information present in basci protein domains by darwinain evolution. That is clear, simple and explicit.
    What you are talkinf of is not: hypothetical replicators, lipid bilayers that have nothing to do with protien information, words or building blocks that you never define, a whole lot of imaginary concepts, without a single fact or argument.

    So gene sequences exist independently of chemistry! Glad you made that clear, now can you show me an example of a functioning gene sequence that is not based on chemistry?

    It’s perfectly true. Gene sequences are not determined in any way by chemistry. They are read and transcripted and translated by complex biological machines that work using also the laws of chemistry, but their capacity to do what they do depends on their structure and informational content, not on the laws of chemistry.

    The genetic code is not a law of chemistry. It is a symbolic coresponcence between codons of nucleotides and aminoacids. No laws of chemistry connect the two things.

    It’s strange that you choose to refute such elementary concepts.

  136. gpuccio, I have been reading UD for over two years now. I have to say your last two posts IMO are the best (straightforward,clear and concise)take down of a design denier’s argument I have seen yet.

    Great stuff and I greatly appreciate the time you take to reply to and rebut darwinian arguments.

  137. Chris Doyle at 3.2.1.2.: “Similarity is as much an indication of common design as it is common ancestry.”

    Yeah, Daniel. Prove that all your fancy evidence showing familial similarities and common descent isn’t just an Intelligent Designer making things LOOK like evolution did it!

    Did it ever occur to you that maybe The Designer WANTS the species to be descended from each other in a nested heirarchy, just like evolution would have done it if The Designer hadn’t done it first?

    Thought not.

    Tattoo this on your chest, Darwin Boy: The Designer can design any way He wants. If He wants to make it look like mindless evolution did it, He can do so and there’s no way you will ever be able to prove He didn’t!

    So there!

  138. What I would really like to see from the ID community is an honest statement like, “We don’t really understand how evolution works, so we keep quoting these preposterously huge numbers that only apply to the weird misunderstanding of evolution that we believe in.”

    Some examples: Search spaces. A typical ID claim is that evolution has to search through the entire range of possible DNA patterns (for instance, 4^100 = 1.6^60 for a 100 base pair patch of DNA) to find the minute percentage of those patterns that are biologically usefull. I’d like to see a statement like, “We’re sorry for stating that evolution has to search through 1.6^60 combinations to find one that works. To do that would require changing all 100 base pairs at once and evolution obviously doesn’t do that. It actually changes one or two bases at once meaning it searches four or sixteen places that are very very near the known good position the parental organism occupies.”

    Or how about this one: “We’re very sorry that we said that information can’t be created without intelligent intervention. It turns out that every mutation creates new information and natural selection then weeds out the bad information and saves the biologically useful information.”

    Statements like these would go a long way towards – not exactly bringing credibility to ID, but at least reducing the jaw-droppingly dumb statements that automatically discredit it to anybody with some knowledge of evolution, informatics or biology.

  139. Steve,

    thank you. You are really very kind. Your feedback is sincerely appreciated.

  140. as to ‘differential reproduction’, that was mentioned previously in this thread, here is a interesting article that just came out on ENV that is somewhat directly related:

    Inconsistent Nature: The Enigma of Life’s Stupendous Prodigality – James Le Fanu
    Excerpt: Many species that might seem exceptionally well adapted for “the survival of the fittest” are surprisingly uncommon. The scarce African hunting dog has the highest kill rate of any predator on the savannah, while cheetahs may have no difficulty in feeding themselves thanks to their astonishing speediness — but are a hundred times less common than lions.
    http://www.evolutionnews.org/2.....51281.html

  141. It sounds like magic? Yes, it does. But it is true.

    LOL, no gpuccio it sounds like a MECHANISM based on physics and chemistry!

    Go back to school!

  142. DrBot,

    Not convincing enough.

    Darwinism fails to account for so complex a machinery of life. I guess that’s what GPuccio meant. This mechanism clearly could not have emerged spontaneously via natural selection over random change. That is simply operationally impossible! There is absolutely no evidence of anything remotely so complex emerging spontaneously.

  143. 24.1.1.1.3

    Timbo,

    Philosophy:

    It is your right to choose suitable explanations about what you see. You may even wish to accept solipsism. The point I am making is that I am free to choose whatever explanation seems to make more sense to me. As simple as that. The “no purpose/no goal” argumenation makes no sense to me because I see things contrary to that every day of my life.

    Why should anyone want to choose anything making sense for an explanation if ultimately nothing makes sense?

    Design argumentation on the whole was not born yesterday and it has deep roots in scientific/philosophical thought. It appeals to me more than nihilistic Darwinism.

    Now, as far as science is concerned, a common heuristic is to choose the simplest possible explanation. Darwinism offers much more complicated explanations compared to ID.

  144. Now, as far as science is concerned, a common heuristic is to choose the simplest possible explanation. Darwinism offers much more complicated explanations compared to ID.

    Which is simpler, e=mc2 or goddidit?
    In simplistic terms, goddidit is always a simpler explanation than any scientific theory because it explains everything by invoking an unknowable, all powerful entity. It also explains nothing for the same reasons.

  145. It’s perfectly true. Gene sequences are not determined in any way by chemistry. They are read and transcripted and translated by complex biological machines that work using also the laws of chemistry, but their capacity to do what they do depends on their structure and informational content, not on the laws of chemistry.

    The genetic code is not a law of chemistry. It is a symbolic coresponcence between codons of nucleotides and aminoacids. No laws of chemistry connect the two things.

    So, by implication, you can change what a gene does without making any physical changes to the organism in any way If this isn’t true then there HAS to be a connection between the two things that is based in MATTER!

    If it IS true then can you explain how I change the way genes work without changing any part of the organism?

  146. DrBot:

    I am afraid your “arguments” have fallen below any acceptable level. A pity, I thought you were quite reasonable, in the beginning.

    Well, I will leave you to explain, if you want, how the laws of electromagnetism completely explain the existence of Windows 7. Good luck, and have a good time.

  147. The complexity argument cannot be so easily dismissed as mere misunderstanding.

    One of few sensible critics of ID is Stuart Kauffman. He advocates for antichaos and holistic coevolution of everything. Correct me if I am wrong, but he has not been able to convincingly demonstrate so far how on earth spontaneous self-organisation is possible. True, he modelled evolution using Boolean networks and showed that structure could emerge from chaos. But what kind of structure? What kind of information is associated with this structure? Functional/Prescriptive information? I don’t think so. He already starts off at a point where his Boolean cell models are able to communicate.

    There are probabilistic measures of how much information you can reliably get as a spontaneous bonus. This is marginal and is not enough to explain the complexity levels of existing life.

    On a particular point, in order for mutations to kick off, you already have to have an horrendously complex system.

  148. dmullenix,

    “We’re sorry for stating that evolution has to search through 1.6^60 combinations to find one that works. To do that would require changing all 100 base pairs at once and evolution obviously doesn’t do that. It actually changes one or two bases at once meaning it searches four or sixteen places that are very very near the known good position the parental organism occupies.”

    The search does become simpler if you start from an existing functional DNA pattern and a parent organism ‘occupying a good position.’

    It’s like looking for a hidden treasure buried somewhere in the solar system. Step 1 – stand next to the buried treasure. Step 2 – search in the surrounding area. Step 2 sounds a whole lot simpler if it you don’t account for step 1.

  149. DrBot,

    Now the wheels have come off. You’re comparing an untested hypothesis to E=MC2, and ID to goddidit. So far your arguments have been logical, if faulty. Why are you now reverting to rhetoric?

  150. DrBot,

    We are talking about scientific explanations. You cannot legitimately compare e=mc^2 to GodDitIt. Wishful thinking is no science. If you like, God Did It so that e=mc^2 and it is beautisfully done! But the evolution argument lacks this beauty which once it was thought to have. Its facade has succumbed to the ravages of time.

  151. 152

    Just echoing a word of support. It’s clear to anyone reading these exchanges that you’ve actually bothered to learn chemistry and biology, and know the science rather thoroughly (if I recall you’re an MD!). This is why statements from Dr. Bot like “go back to school” are so deliciously ironic. Not only are the people making them usually completely clueless when it comes to science (i.e. devoid of scientific training), but they are usually positivists or empiricists philosophically and thus confuse their metaphysics for some kind of real scientific knowledge. They attach themselves as parasites to Darwinism (not being actual biologists) and use it as a pretense to belittle those who believe differently (see Dr. Bot here).

    This is kind of a rant, because I see it so often in modern people. If you’re religious for example, you must be irrational and hate ‘Science!’. I’m learning electrochemistry in conjunction with the operation of fuel cell engines. I’m also studying nuclear energetics/physics with respect to reactor theory. Clearly what I’m thinking about Dr. Bot, it how “goddidit,” and not E=Mc^2. It’d be funny if it weren’t so sad.

    Thanks for your posts gpuccio.

  152. Everything that a computer does depends on physical hardware – chemistry, and physics. All information that the observed designers (humans) encode into the memory is in the form of electrical signals within physical hardware. You cannot change the way information in memory maps to pixels on the screen without making some material change to the system – the laws of physics connect the memory state to the display state.

    The genetic code is not a law of chemistry. It is a symbolic coresponcence between codons of nucleotides and aminoacids. No laws of chemistry connect the two things.

    Show me some evidence that there is nothing physical that relates codons of nucleotides and aminoacids!

  153. You’re comparing an untested hypothesis to E=MC2, and ID to goddidit. So far your arguments have been logical, if faulty. Why are you now reverting to rhetoric?

    ID – a designer of unknown powers did things that made it happen. This argument can be inserted anywhere.

  154. DrBot,

    It’s not about what argument you can insert or where. It’s about why you insert it.

  155. DrBot,

    There is obviously a physical connection, otherwise one could not be translated to the other by physical processes.

    But the connection is arbitrary, not dependent on any law. The word “broccoli” explicitly refers to a certain vegetable, but there’s no law that says so. People speaking other languages may use other words. We could collectively decide to switch the meanings of “broccoli” and “sofa,” and then we would sit on broccoli and eat sofas. Laws cannot explain symbolic meaning.

  156. So gene sequences exist independently of chemistry!

    Dr Bot, if gene sequences were not independent of the physical properties of the carrier, then there would be no way they could function as representations leading to an effect, in other word, no symbols = no information. Additionally, if gene sequences were determined by the chemistry of their carrier, then there would be no way to input that information into the output sequence of the system (amino acids), in other words, no transfer of information = no constraint = no output.

    Instead of telling a practicing medical doctor they need to “go back to school” just because you fail to fully understand and appreciate a topic, perhaps you should bone up on the issues for yourself.
    Just saying…

  157. DrBot:

    Show me some evidence that there is nothing physical that relates codons of nucleotides and aminoacids!

    I have already done that. I have explained you how translation works. Please review the subject.

    As you seem to think that there is a connection, please explain what it is.

  158. Pardon gpuccio if I respond to this comment by DrBot:

    Show me some evidence that there is nothing physical that relates codons of nucleotides and aminoacids!

    I suppose DrBot says he wants to see evidence for something ‘non-material’ in the cell?

    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of materialism, to explain reality since quantum entanglement/information is now conclusively shown to be ‘non-local’ (i.e. instantaneous, as well as completely transcendent of any space-time (material) constraints):

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    This falsification for local realism (materialism), discussed by Aspect in the preceding video, was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    Quantum entanglement is shown to be related to ‘functional information’ by the following evidence;

    Quantum Entanglement and Information
    Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems.
    http://plato.stanford.edu/entries/qt-entangle/

    And yet Quantum Entanglement/Information, which falsified ‘local realism (reductive materialism), is found to be intertwined in the molecular basis life on a massive scale:

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    And indeed the ‘quantum computation’ accomplished by the non-local quantum entanglement/information within DNA is very impressive:

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;

    Quantum Entanglement and Teleportation – Anton Zeilinger – video
    http://www.metacafe.com/watch/5705317/

    And quantum teleporation has shown that atoms, which are suppose to be the basis from which functional information ‘emerges’, in the neo-Darwinian framework, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms are suppose to be the basis of!

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    How can quantum information/entanglement ‘emerge’ from any material basis of atoms when atoms are now shown to reduce to a transcendent basis of quantum information in the first place? i.e. It is IMPOSSIBLE for the ’cause’ of transcendent functional quantum information to reside within material particles!!!

  159. HouseStreetRoom:

    Thanks for the support. And yes, I am an MD.

    It’s specially difficult to discuss constructively with those who have not an understanding of the basics of biology, and yet believe that they know how things are. I try to stick to biological and scientific arguments, because that’s where the ID points are best understood and proved. But to discuss biology, it is necessary to understand the basics.

    I have met other dariwnist supoorters who refuses to admit the obvious, that the genetic code is a code, a simple truth that has been well known to biologists since when the genetic code was discovered (that’s why it was called a code!). But, usually, they based their positions on vague phylosophical and semantic reasons.

    DrBot seems to base his arguments only on his personal non understanding of biology. I am afraid that there is nothing to do in those cases.

    However, thank you again for your note.

  160. Moreover, the dispute between IDists and neo-Darwinists has, thus far, not focused on transcendent quantum information so much, if at all, but has instead focused on ‘classical information’ which is information that is encoded onto a material substrate;,

    “LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information” – Dembski, Marks
    http://evoinfo.org/publication.....ation-law/

    Yet, though the dispute between neo-Darwinists and IDist has been over ‘classical information, classical information is shown to be a subset of transcendent quantum information by the following method:

    This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (“Information is physical!” – Rolf Landauer) (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy.
    Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    And transcendent quantum information is shown, empirically, to be ‘conserved’ here:

    Quantum no-hiding theorem experimentally confirmed for first time – March 2011
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.
    http://www.physorg.com/news/20.....tally.html

    I would like to reiterate just how ‘spooky’, to use Einstein’s word, it is to find something that blatantly defies our concepts of time and space, on a massive scale, within our bodies;

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182

    Further note:

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    verse and music:

    John 1:1-3

    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made.

    Brooke Fraser – Lord of Lords(Legendado Português) -
    http://www.youtube.com/watch?v=rkF3iVjOZ1I

    Perhaps DrBot would like to tell us where the materialistic basis of information resides that is orchestrating the development of this human in a womb??

    Fearfully and Wonderfully Made – Glimpses At Human Development In The Womb – video
    http://www.metacafe.com/watch/4249713

    Jeremiah 1:5
    Before I formed you in the womb I knew you, before you were born I set you apart;,,

    =============

    Award-Winning Documentary – “Shocking!” – “180″ Movie
    http://www.youtube.com/watch?v=7y2KsU_dhwI

  161. I’ll rephrase this to be more accurate. The physical process of translation is the connection. Take away the translation, and there is no connection whatsoever. And it’s because there is no connection that the symbols are arbitrary. Just like “3″ means xxx and “4″ means xxxx – it’s only because we say they do. We could use “III” and “IV” or “6″ and “7″ instead. There is no law that can assign a symbolic code to a physical entity or process.

  162. If the process isn’t physical, what is it?
    Why can it be recapitulated in a test tube, using physical components alone?

    All the processes you describe (mRNA synthesis, translation, tRNA charging) rely on complimenting shapes and chemistries.

  163. The genetic code is not a law of chemistry. It is a symbolic coresponcence between codons of nucleotides and aminoacids. No laws of chemistry connect the two things.

    And as noted as recently as the Koonin book, no one knows how the cod originated.

    But in the last 400 years of science, which has been the more fruitful assumption: that regularities exist in nature that can be discovered, or that things that are not known are best explained by the intervention of unseen entities?

  164. Dr Bot, the components of the (information) system must have physical substrates in order to have a physical effect – that is (after all) what is actually observed; a system of physical representations, coordinated to physical protocols, leading to physical effects – with each of them remaining discrete. (It’s the same physical dynamic as in any other example of recorded information).

    But the physical makeup of the substrate does not determine the information contained within the system, nor the system itself.

  165. Just a general note: For several days I’ve been unable to load long pages here. They just died without completing. I’m sure many a tear has been shed over my absence.

    Just now I notice that long threads are broken up into pages. that seems to be a new feature, and it makes long thread load much faster.

    Unfortunately there’s still the problem that new posts don’t necessarily go at the end of the discussion, so you have to read through everything.

  166. The physical makeup of a protein determines how it functions. The physical makeup is translated by physical/chemical recognition and pairing of an tRNA and a mRNA template, which in turn is made by nucleotide/DNA pairing.

    It is humans who have assigned the symbols A,C,G,T,U and the amino acids. We could arbitrarily change what we call them (and do-W and Trp and (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid meaning the same thing).

    But tryptophan is a physical entity, one object. The moon is the moon, no matter what you name it.

  167. Petrushka,

    It is a different kettle of fish. The question is whether or not spontaneous self-organisation is operationally possible. Over the last 400 years there has been no evidence that would provide any grounds for the hypothesis of genuine self-organisation of matter without intelligent interference.

    Which is a more honest answer: that we can use/extrapolate “chance/necessity” without any grounds to explain life’s complexity, or that even though we can’t establish the particular mechanisms of intelligent agency we still can reliably detect it?

  168. So you suggest that if (anywhere in the cosmos) cytosine is found attached to thymine and then to adenine, then that means leucine should be added to a nearby protein?

    You see this as an inherent physical property of those three chemicals.

  169. Petrushka,

    But in the last 400 years of science, which has been the more fruitful assumption: that regularities exist in nature that can be discovered, or that things that are not known are best explained by the intervention of unseen entities?

    Take out the irrelevant word “unseen” and the answer is that neither is a good assumption. Regularities do exist in nature that can be discovered, and some things are best explained by the intervention of entities. If we assume either one then we’re likely to be wrong.

  170. Why does that prove it is a non-physical process?

    Non-inherent physical property does not equate with meta- or non-physical.

  171. Crystals self organize. Membranes, colloids and other surfaces, too.

    Self organization is observed. Design is inferred by analogy to human activities.

  172. And lets play a game with this–is this object designed? How could you tell?

    http://www.godunov.com/bucky/buckyball-3.gif

  173. I’m merely pointing out the obvious, that if you don’t look for regularities you don’t find them. The approach to investigation taken several hundred years ago has been fruitful.

    What would you substitute for “unseen” to characterize an entity that has no attributes?

    ID supported have no agreement on whether intervention is continuous, sporadic, or just once time at creation. And more importantly, no interest in reaching agreement.

    This is not a fruitful approach. With a few exceptions, ID research consists of reading the results of mainstream science and finding unanswered questions.

    To the extent that these questions will ever be answered, they will be answered by mainstream scientists looking for regularities. It has been that way for centuries, even when the overwhelming percentage of scientists were theists.

  174. DrRec:

    It is humans who have assigned the symbols A,C,G,T,U and the amino acids.

    What do you mean? The genetic code has been decoded by humans, not created by them. It took difficult research to understant which codond corresponded to which aminoacid. You seem to think that the code consists in assigning names. That is completely wrong.

    The code consists in the symbolic correspondence of codons to aminoacids, of objects to other objects that have nothing in common. That has not been created by humans, as I hope even you will understand.

    For instance, the following codons:

    CGU, CGC, CGA, CGG

    correspond symbolically to Arginine in the code. They are recognized by the translation system as a command to mount Arginine. But they have no special biochemical relationship with Arginine.

    It is of no relevance if we call the codon CGU or Andrew, and the aminoacid Arginin or Mary. Names are of no importance. The symbolic code is in the corrispondence of the codon made of those three nucleotides (CGU) to a specific aminoacid (Arginine) in the stored information and in the translation system, although there is no law of chemistry that connects those three nucleotides to that aminoacid.

    I cannot really be more clear that that. If you want to understand, understand. Otherwise, it’s your choice.

  175. Dr Rec,

    Either it is an inherent physical property, or it is a given/acquired property unrelated to its physical make-up.

    Now that we understand it is NOT an inherent physical property, we can argue what is causally adequate to explain the observed association.

    You may now wish to explain, just as GP asked you to do.

  176. I apologize for mis-posting.

    Post 32.2.1.1.i was in response to 32.2.1.2.1

  177. I’m glad we agree on that.

    “But they have no special biochemical relationship with Arginine.”

    Is false. Their biochemical relationship is mediated by the aminoacyl tRNA synthetase, which recognizes the anti-codon, and loads the tRNA with the appropriate amino acid.

    Physical recognition. Physical process.

    That you can imagine alternatives (and indeed, humans have expanded the genetic code–mostly by directed evolution) doesn’t make it a non-physical process.

  178. “Either it is an inherent physical property, or it is a given/acquired property unrelated to its physical make-up.”

    Or it is an acquired property directly related to its physical make-up.

  179. Petsrushka,

    I’m merely pointing out the obvious, that if you don’t look for regularities you don’t find them.

    I’ll point out the equally obvious, that if you don’t look for design you don’t find it. What does either have to do with anything?

    And what is this “fruitful” thing you keep mentioning, and how is it relevant? What is true of one thing may not be true of another. If I see a thing and wish to determine whether it was designed, should I examine, analyze, and reason, or should I just decide which conclusion is more fruitful? What is the “fruit” in “fruitful?” A correct conclusion, or just any conclusion at all? Please help me to understand.

  180. Petrushka,

    ID supported have no agreement on whether intervention is continuous, sporadic, or just once time at creation. And more importantly, no interest in reaching agreement.

    BTW, I wasn’t aware that the abiogenesis or darwinist camps (pretending they are separate) had come to any consensus on anything except that life formed and then something called “evolution” occurred, and that no intelligence was involved.

    When you claim to explain everything at least a little more consensus is reasonable to expect. You’re still stuck on your strawman concept of ID as an alternative explanation to all of biology, and that’s why you’re puzzled by the lack of consensus on matters ID does not address.

    Let me connect the dots from ID to specific explanations for what we observe in biology, as they are not the same thing: The first step in reverse-engineering is to determine that something was engineered. You cannot or will not even begin to reverse-engineer something if you do not know whether it was engineered or incorrectly assume that it was not.

    Actually it’s only one dot.

  181. DrRec,

    One should distinguish self-ordering (e.g. crystallisation) from genuine spontaneous self-organisation. There is a huge difference between the two. The latter has never been observed. Self-organisation involves formal relationships between components of a complex system.
    Crystallisation is far from this. More details on this, see David Abel on Capabilities of Chaos.

    Complex systems are routinely organised by intelligent agents.

  182. OK, let me rephrase. In the latest Shapiro book he describes evolution as a design process.

    He describes evolution as possibly conscious, and asserts that cells have trigger mechanisms that spur the creation of variation. He says cells obtain information from the environment and incorporate it into the genome.

    He likens biological evolution to the process by which the immune system generates antibodies. He invokes no miracles, no intervention, nothing but known physical processes.

    Now if you think he supports ID — as many people do — you can read between the lines and conclude he thinks this system is designed (possibly incorporated at creation?).

    But the simple fact is he asserts that purely physical processes are capable of driving evolution. Just as computers can process information by purely physical processes.

    Whatever his mainstream colleagues think of his book (apparently not much), he is well within the mainstream because he does not call upon unnamed entities, and he presents suggestions for research to validate his conjectures.

    That is what a search for a designer would look like. A description of the design process and a process by which it can be verified.

    All investigations of design begin with hypotheses about the nature of the designer, whether it be birds and nests, bees and hives, or humans and stone tools.

    You mention Stonehenge. You might mention the pyramids. There have been many books written asserting that humans are not capable of creating such large scale works without modern technology.

    Now one could approach this claim by calculating how much a human can lift without modern machinery, or one could go a bit farther and investigate how cathedrals were build and project these techniques backwards.

    If you did so you might come to the conclusion that the pyramids could not be built by humans unaided by some sort of alien technology.

    There in no logical or mathematical way to counter this. If you want to counter it you must demonstrate that it can be done. You must reinvent methods that could have been available, and you must show that they work. Of course this has been done in the case of Stonehenge.

    The interesting thing is that even if you do this you don’t really know how it was done. You only know it was physically possible.

    In the same way, we do not know that stone tools and ancient pottery were made by humans. We only know that it is highly plausible.

    Plausibility and consistency with all known facts are the criterion for detecting and validating design inferences.

  183. For instance, the following codons:

    CGU, CGC, CGA, CGG

    correspond symbolically to Arginine in the code. They are recognized by the translation system as a command to mount Arginine. But they have no special biochemical relationship with Arginine.

    If there is no physical correspondence then explain how I can make CGU, CGC, CGA, CGG mount Tyrosine?

  184. DrREC,

    Their biochemical relationship is mediated by the aminoacyl tRNA synthetase, which recognizes the anti-codon, and loads the tRNA with the appropriate amino acid.

    The ASCII code 65 is mediated by software in my computer, both of which are physical entities, and interpreted as the letter “A.” Does that indicate a necessary physical relationship between the stored bits and the number 65, or between the number 65 and the letter “A?”

    That the meaning of the codons is determined by the mediator, not by their own physical properties, indicates that with a different mediator they could have different meanings. I could assign values to combinations of them and use them to write sentences in English.

    The functions of coded information and interpreters may themselves depend on physical laws, but cannot be explained by them. There is a difference.

  185. That the meaning of the codons is determined by the mediator, not by their own physical properties, indicates that with a different mediator they could have different meanings.

    For a given mediator and codon the output will change when you change the codon, if you change the mediator you can also change the output – both are physical components of the system so their output is always determined by their physical properties.

  186. Petrushka,

    You say this,

    He describes evolution as possibly conscious, and asserts that cells have trigger mechanisms that spur the creation of variation.

    and this

    But the simple fact is he asserts that purely physical processes are capable of driving evolution.

    but then mysteriously with regard to ID you say this:

    If you want to counter it you must demonstrate that it can be done. You must reinvent methods that could have been available, and you must show that they work.

    You conspicuously excuse any non-intelligent explanation from this strict requirement. And, apparently without hope, you miss the point of Intelligent Design, which is demonstrated billions of times per day. I don’t think you want to understand it.

    That is what a search for a designer would look like. A description of the design process and a process by which it can be verified.

    I’m not aware of anyone scientifically searching for such a designer. Are you? If I heard of anyone I would pass your suggestion along, except that it’s wrong. Reverse engineering does not necessarily identify the engineers.

  187. DrBot:

    There is a specific enzyme, that is called Arginyl-tRNA synthetase. It is one of the 20 fundamental enzymes that decipher the genetic code. In E coli, it is made of 577 AAs, just to give an idea of its complexity.

    It recognizes the correct tRNA, with the anticodon corresponding to Arginine. It then binds Arginine to that tRNA, in a position that is completely separated from the anticodon. So, the tRNA with the anticodon for Arginin is charged with Arginin, and will mount Arginine at the correct site on the ribosome, guided by ots anticodon which interacts with the mRNA.

    All this is possible not because any chemical law connects CGU to Argninine, but because the 20 enzimes that read the genetic code have in their sequence the correct information to associate the correct aminoacid with the correct tRNA, bearing the correct anticodon. That’s how the information in the DNA, and then in the mRNA, is translated into its purposeful output, the protein.

    Chemical laws are obviously respected in all these chemical interactions, but it is only the information ib the DNA and in the enzymes that ensures the correct decoding of the symbolic information in the gene. And, as I have already pointed out, the information in the enzymes is derived, too, form information in other DNA genes (the genes that code for those 20 enzymes).

    I hope I don’t have to repeat all that again.

  188. DrRec:

    They have no biochemical relationship. The relationship is created by the information in the synthetase.

    To have a biochemical relationship means that the codon has some biochemical reason to react with Arginine, or to make it mounted in the protein. That is not true. The codon never interacts with Arginine.

    I agree that all the process is physical, exactly as the working of a software is physical. But that does not mean that the sequence of bits in a password has some specific electromagnetic connection with the output that the password commands in the software. The connection is created by the information by which the software works, not by the laws of physics, athough obviously the laws of physics are used by the designer to structure that information in a machine.

    I will not enter into the debate physyiocal not physical about information. I am not intersted in that. The simple point is that, without the information in the software, not physical laws would make the sequence of bits in a password have any power. or give any output.

    You confound the laws of necessity that govern chemistry and physoics with the laws of information that govern machines, including biological machines.

    Or maybe you just want to confound them, for your own purposes.

  189. DrBot,

    Of course we are describing a system made of physical components. But how do you explain the presence of a mediator that produces a functionally useful output rather than a useless one? How do you explain the presence of a code with the potential to be translated into a functional output? I can scribble letters and numbers all day long, and nothing is going to convert them into a functional anything. The process functions by natural laws, but what laws put it in place?

  190. This is plainly an equivocation. Either the association is caused by the chemical properties, or it is not.

    a) If it is caused by the physical properties, then it is not informational.

    b) If it it not caused by the physical properties, yet an association is nonetheless observed, then its inclusion within the system comes by some other means.

    In instance (b), the observed association would not have been caused by the physical properties of the component, but acquired or given to it because of those physical properties. It is a distinction you need to keep in mind.

    Now, you may wish to argue (and make your case) that the other means mentioned above is a completely unguided natural process. But what you cannot do is first claim the association is caused by the physical properties of the component, then failing any demonstration of that, come back to claim that its acquired because of those physical properties, and yet still fail at any demonstration.

  191. “I agree that all the process is physical”

    Excellent start.

    “The relationship is created by the information in the synthetase.”

    The the relationship is mediated by the physical properties of the synthetase, which physically matches the anticodon with the cognate amino acid. A number of biologists have suggested proto-tRNAs were self-charging, and I think some have been created by directed evolution, but I’d have to check for references.

    At any rate, these are acquired properties directly related to its physical make up of the system.

    “You confound the laws of necessity that govern chemistry and physoics with the laws of information that govern machines, including biological machines.”

    1) The laws of necessity? Please list them?

    2) Why would you predict something like translation must be governed by a law (I’ll define it Law universal and invariable)? Translation is governed by physical properties. It is also plastic, with different systems using different codons and amino acids. You seem puzzled that by this, and seem to equate it with unnatural, or designed. Why would such conformity, such that the ‘law of translation’ could be writ be an evolutionary prediction?

    3) “laws of information that govern machines, including biological machines” And what do you propose those are?

  192. “acquired or given to it because of those physical properties.”

    “Or it is an acquired property directly related to its physical make-up.”

    Distinction?

  193. Do you plan to address the actual content of my post?

  194. Not until it makes some point other than what I just said, and is corrected to remove things I didn’t.

    I’ve been arguing the process is physical. Everyone should be able to agree with that.

    I haven’t said the “association is caused by the physical properties” or “acquired because of those physical properties.”

    I would say it is a physical system that functions with certain physical properties. These functions were acquired.

  195. All this is possible not because any chemical law connects CGU to Argninine, but because the 20 enzimes that read the genetic code have in their sequence the correct information to associate the correct aminoacid with the correct tRNA, bearing the correct anticodon. That’s how the information in the DNA, and then in the mRNA, is translated into its purposeful output, the protein.

    Yes – it is a physical mechanism. The information you refer to is a property of the arrangement of matter and the rules that govern their interactions. This is what you just described.

    Change the configuration of the chemicals involved and you change the behavior of the system.

    it is only the information ib the DNA and in the enzymes that ensures the correct decoding of the symbolic information in the gene.

    That information you refer to is the physical configuration of the system – nothing more.

    I asked you to explain how these elements can work together to produce an output, yet have no biochemical relationship. You responded by describing the biochemical relationship.

  196. You conspicuously excuse any non-intelligent explanation from this strict requirement. And, apparently without hope, you miss the point of Intelligent Design, which is demonstrated billions of times per day. I don’t think you want to understand it.

    I haven’t excused evolution from this requirement. Thousands of biologist labor every day to demonstrate that evolution has the physical capability of doing what is necessary to explain common descent.

    Read the Koonin or Shapiro books and tell me what physical capability is lacking in order for the evolutionary explanation to be valid.

    I do miss the point of asserting that some unspecified thing was done by an unspecified agent having unspecified capabilities at unspecified times and places. That certainly isn’t what archaeologists do. It isn’t what forensic investigators do.

  197. The electromagnetic force (chemical bonding) is what makes “recognition” possible, not any kind of sentience or informational awareness.

    Aminoacyl-Transfer RNA Synthetases Read the Genetic Code
    Each aminoacyl-tRNA synthetase is highly specific for a given amino acid. Indeed, a synthetase will incorporate the incorrect amino acid only once in 10^4 or 10^5 catalytic reactions. How is this level of specificity achieved? Each aminoacyl-tRNA synthetase takes advantage of the properties of its amino acid substrate. Let us consider the challenge faced by threonyl-tRNA synthetase. Threonine is particularly similar to two other amino acids—namely, valine and serine. Valine has almost exactly the same shape as threonine, except that it has a methyl group in place of a hydroxyl group. Like threonine, serine has a hydroxyl group but lacks the methyl group. How can the threonyl-tRNA synthetase avoid coupling these incorrect amino acids to threonyl-tRNA?

    The structure of the amino acid-binding site of threonyl-tRNA synthetase reveals how valine is avoided. The enzyme contains a zinc ion, bound to the enzyme by two histidine residues and one cysteine residue. Like carbonic anhydrase, the remaining coordination sites are available for substrate binding. Threonine coordinates to the zinc ion through its amino group and its side-chain hydroxyl group. The side-chain hydroxyl group is further recognized by an aspartate residue that hydrogen bonds to it. The methyl group present in valine in place of this hydroxyl group cannot participate in these interactions; it is excluded from this active site and, hence, does not become adenylated and transferred to threonyl-tRNA (abbreviated tRNAThr). Note that the carboxylate group of the amino acid is available to attack the ?-phosphate group of ATP to form the aminoacyl adenylate. Other aminoacyl-tRNA synthetases have different strategies for recognizing their cognate amino acids; the use of a zinc ion appears to be unique to threonyl-tRNA synthetase.

    The zinc site is less well suited to discrimination against serine because this amino acid does have a hydroxyl group that can bind to the zinc. Indeed, with only this mechanism available, threonyl-tRNA synthetase does mistakenly couple serine to threonyl-tRNA at a rate 10^-2 to 10^-3 times that for threonine. As noted in Section 29.1.1, this error rate is likely to lead to many translation errors. How is a higher level of specificity achieved?

    Threonyl-tRNA synthetase can be incubated with tRNAThr that has been covalently linked with serine (Ser-tRNAThr); the tRNA has been “mischarged.” The reaction is immediate: a rapid hydrolysis of the aminoacyl-tRNA forms serine and free tRNA. In contrast, incubation with correctly charged Thr-tRNAThr results in no reaction. Thus, threonyl-tRNA synthetase contains an additional functional site that hydrolyzes Ser-tRNAThr but not Thr-tRNAThr. This editing site provides an opportunity for the synthetase to correct its mistakes and improve its fidelity to less than one mistake in 10^4…

  198. I agree, and I don’t understand what is so controversial. ID theory does not claim that the chemical processes that allow DNA to be copied are not natural and mechanical. If it did, then every instance of cell division would be directly attributed to (an) active intelligent design(ers).

  199. And a human being after all is just a composition of 65% of oxigen, carbon 18%, hydrogen 10%, nitrogen 3% Calcium 1.5%, traces of some other elements and enough iron to make one tiny nail.

  200. Besides, I consider evolution to be intelligent, at least sufficiently intelligent to do what is attributed to it. Evolution is a learning algorithm.

    Shapiro, who is supposedly ID friendly, agrees.

  201. DrBot,

    I’m repeating myself and perhaps beating a dead horse because I can’t imagine that you are saying what it sounds like you are saying.

    When an message encoded in abstract symbols is interpreted to follow instructions or produce an object, there is no necessary relationship between either the appearance or the form of the message and the actions or object, even though the process of interpretation follows natural laws.

    This is evident because a different interpreter can produce different instructions from the same message, just as a word can have two meanings in two languages or number 12 can have multiple meanings within a computer program.

    I can assign my own meaning to DNA. I can assign various values to different foods and use it to decide what to have for lunch each day. I can have a computer process it for me so that the process is transparently natural. Am I violating laws by associating the code with new outputs? Am I creating new laws? How can there be an intrinsic relationship between a given sequence and chicken noodle soup when there wasn’t one yesterday?

    Some would argue that the existence of any complex functional object requires forward thinking. I’ll put that aside. But what about a complex functional object which was produced and assembled from instructions translated from an abstract code expressed in a medium? Seriously, that doesn’t require forward thinking?

  202. If you do not respond to the actual content of my posts because you think I misrepresent you, then there is hardly any reason to continue, is there?

    I have no desire, nor need, to misrepresent you.

    So for that I apologize.

  203. Petrushka,

    I do miss the point of asserting that some unspecified thing was done by an unspecified agent having unspecified capabilities at unspecified times and places. That certainly isn’t what archaeologists do. It isn’t what forensic investigators do.

    If it were an unspecified thing, what would be even be talking about? Your amplification of “unspecified” is clearly rhetorical.

    Otherwise that’s exactly what forensic investigators do. This person was murdered with a gun. How do you know? From the holes in his chest and back. Who did it? I don’t know. Where’s the gun? Where’s the bullet? I don’t know.

    They draw their conclusions based on historical observations that bullets are the most common cause of such fatal holes, and that they are usually fired by people with guns. They do not draw their conclusions by acquiring every possible piece of information. Rather, their conclusions are the basis for investigating. Knowing the general cause of death tells others where to look for more specific details. That’s how it works in real life.

    We don’t prosecute until we know who fired the gun and perhaps prove it by finding the bullet. But imagine if we tied our hands by deciding that the apparent bullet holes were not grounds for an investigation? Imagine telling the guy who found the holes that they weren’t even grounds for a murder investigation because he hadn’t identified the gun, bullet, or shooter? How absurd.

    What irks me is that these standards you propose are so selective in their application. In what other context would you discourage the use of limited information to narrow the search for more specific information?

  204. DrBot:

    That information you refer to is the physical configuration of the system – nothing more. I asked you to explain how these elements can work together to produce an output, yet have no biochemical relationship. You responded by describing the biochemical relationship.

    You are really something. So, hamlet is the physical configuration of the ink, and nothing more. And information is a useless concept, certanly!

    Just to be clear, a functional configuration is not a biochemical relationship, it is an informational relationship realized by imposing a specific form to configurable switches that would never take that form only for spontaneous working of scientific laws.

    Yes, the functional configuration of a protein is certainly a physical state, but it is not certainly explainable by biochemical laws.

    To say that biochemical laws explain the sequence of myoglobin means that in some way you can put the necessary aminoacids in some system (where there is no specific information about the myoglobin sequence) and biochemical laws will cause the formation of the myoglobin sequence because of necessity interactions between the molecules.

    Tha

  205. Perhaps the confusion is because no one would suggest that the processes of cell replication are any less natural and mechanical than an IBM reading a punch card and printing an output. That’s common ground.
    So I presumed that we were considering whether natural laws can explain the existence of such a system and the information upon which it operates, not whether that operation follows natural laws. My bad.

  206. DrBot:

    That information you refer to is the physical configuration of the system – nothing more. I asked you to explain how these elements can work together to produce an output, yet have no biochemical relationship. You responded by describing the biochemical relationship.

    You are really something. So, Hamlet is the physical configuration of the ink, and nothing more. And information is a useless concept, certainly! This is materialism brought to its most obtuse consequences!

    Just to be clear, a functional configuration is not a biochemical relationship, it is an informational relationship realized by imposing a specific form to configurable switches that would never take that form only for spontaneous working of scientific laws.

    Yes, the functional configuration of a protein is certainly a physical state, but it is not certainly explainable by biochemical laws.

    To say that biochemical laws explain the sequence of myoglobin means that in some way you can put the necessary aminoacids in some system (where there is no specific information about the myoglobin sequence) and biochemical laws will cause the formation of the myoglobin sequence because of necessity interactions between the molecules.

    That is not true. That is a ridiculous way to consider things.

    You can certainly synthetise myoglobin in a cell free system, but you need the DNA or RNA or any equivalent input with the pertinent information. IOWs, you already have to know the sequence in advance. It’s useless to debate if that information is physical or non physical. That is phylosophy, and not relevant here. The only important point is that the information is necessary.

    Take away the information, and the chemical laws will never give the myoglobin molecule. It’s as simple as that.

  207. I apologize for erroneously posting an incomplete post…

  208. We don’t prosecute until we know who fired the gun and perhaps prove it by finding the bullet. But imagine if we tied our hands by deciding that the apparent bullet holes were not grounds for an investigation?

    ID has no concept of bullets, since it refuses to talk about the attributes of the designer.

    ID has no bullet holes since it refuses to discuss the details of when and where specific interventions happened.

    Point mutations happen.
    Duplications happen.
    Whole genome duplications happen.
    Recombinations happen.
    Transposons happen.
    Insertions happen.
    Frame shift happen.

    These are kinds of bullets. They are not mythical. They do not require outside intervention.

    They leave visible holes. Everything in your genome that is different from another person’s is the result of some kind of mutational bullet. This is true whether you are an atheist or a Biblical literalist.

    We know from countless experiments that genetic differences affect the phenotype. We know that some variants in any population have greater reproductive success. We also know from genomic studies that most alleles are neutral or nearly neutral. Genes for blue eyes and genes for brown eyes can both fix in a population.

    You may continue to argue about how good a shot nature is and whether nature had enough time, but evolution has all the bullets.

  209. Petrushka,

    I should have learned by now that some people will have fun with an illustration rather than take the point of it. But I’ll attempt to follow through.

    The inference that the hole was caused by a gun is validated by the past observations that guns cause most round holes in and out of dead people. I’m observing that a likely cause can be inferred from past observations. That is how much of historical science works.

    You proudly state the following, which I do not dispute:

    Point mutations happen.
    Duplications happen.
    Whole genome duplications happen.
    Recombinations happen.
    Transposons happen.
    Insertions happen.
    Frame shift happen.

    and you compare them to bullets. Both bullets and their effects are real. The events above are real, but their long-term effects are hypothetical. Why make such a hollow-pointless comparison?

    I understand that you might not agree with inferring biological design from observed design. But it is based on an observation, which is far more than anyone can say when using the above events to explain all of biological diversity. I’d say a mountain of observation, but that obscures the fact that any is more than none.

    As for your continued attempts to cite observed genetic differences and variations and extrapolate from them the origin of countless varied life forms, you’re firing blanks. :)

  210. I’m puzzled by your insistance we explain evolution by natural law.

    Thermodynamics determines protein fold, and so it and chemistry will delineate what sequences are useful.

    Within those limits, evolution is a process of mostly random inputs being filtered by potentially changing needs. Hardly the universal and absolute stuff of physical laws. Indeed, myoglobin has many functional sequences, and there are even more proteins unrelated to it that perform identical functions. Gould famously stated that if we could rewind the tape of evolution and play it again, the results would not be the same. Hardly the stuff of law.

    But does this make it untrue?

    There are natural stochastic processes not reducible to law. You can measure the half life of radioactive decay, but you can’t predict exactly when a atom will decay. Bismuth-212 decays to either thallium-208 or polonium-212 in a 60:40 ratio, but given a single atom, you can’t predict which. You can tell me the probabilities of a unbiased dice roll, but you can’t write a low predicting my next one.

    Your request that “chemical laws” give the myoglobin molecule (which one?) is just an abuse of the notion of physical laws.

  211. I understand that you might not agree with inferring biological design from observed design.

    Really? You’ve observed the designer of life at work?

  212. 213

    “There is no law that can assign a symbolic code to a physical entity or process.”

    Yup. Setting variables is always a choice. When we get here:

    var [?] = 10

    We have an infinite amount of character combinations to assign to that variable to represent the value of 10. Same with the dna, we have:

    var [?] = protein 1

    We have any possible combination/length of a,t,g,c to choose as our variable. None of the molecules a, t, g, or c chemically favor each other over another. How then does an unguided natural process choose a combination and length from the digits a,t,g,c and set that as the variable for
    protein 1, and the operating system in the cell supposed to know that that randomly selected variable means build protein 1?

    Once this clicks in the head the worldview snaps.

  213. Petrushka,

    Last I checked no one had observed any origin of life in progress by anyone, anyhow. But you must realize that by requiring such a direct observation you negate the very concept of historical science. Please, there’s enough unemployment.

  214. And what? Read my sentence that you cited again in which I contrast biological design with observed design rather than equating them.

  215. DrREC,

    The only thing you’re adding to natural law is “random inputs.” That doesn’t change much.

    You also mention filters and changing needs. But where did filters and things with needs come from? Natural laws and random inputs? Is need a natural law?

  216. “The only thing you’re adding to natural law is “random inputs.” That doesn’t change much.”

    It changes everything. Try writing a universal and absolute law predicting each radioactive decay in a gram of Bismuth-212. Impossible. Likewise with an evolutionary pathway.

  217. As I go to sleep I will ponder why you would compare radioactive decay with what would be the most astounding self-organizational, self-improving, self-pondering system ever to ponder itself. Perhaps we should listen to the radiation and see if it’s talking to us. “Stop using us for fuel,” it might say, “and it’s a generally bad idea to get too close.”

    Perhaps counting the bizarre things I’ve read today like they were sheep will cure my insomnia.

  218. “As I go to sleep I will ponder why you would compare radioactive decay with what would be the most astounding self-organizational, self-improving, self-pondering system ever to ponder itself. Perhaps we should listen to the radiation and see if it’s talking to us. “Stop using us for fuel,” it might say, “and it’s a generally bad idea to get too close.”

    Perhaps counting the bizarre things I’ve read today like they were sheep will cure my insomnia.”

    The analogy ends at the impact of random processes on deriving a physical law. I didn’t extend it past there, you did.

    I guess I’ll go to sleep wondering why so many on this site get so snarky; instead of taking the debate head-on.

  219. Last I checked no one had observed any origin of life in progress by anyone, anyhow.

    I could have sworn that the processes I listed dealt with evolution, not OOL.

    So I will stipulate that in any discussion I am in, that I don’t know how life got started, and I don’t think it’s stupid or ignorant to think it might have been a miracle or whatever.

    I think it’s the job of science to look for a naturalistic explanation, but we don’t have one.

    So anything I discuss on this forum is about evolution, not OOL. That means the cellular machinery is in place, the genetic code is in place.

    Having said that, I have to bring Shapiro into the discussion. He points out that the difference between mice an men is very small. He asserts that there are very few differences genes or proteins, and most of the differences are in developmental networks. In other words, microevolution. Nothing over the Edge.

  220. so many on this site get so snarky; instead of taking the debate head-on.

    To the extent of my time and knowledge (both of which are limited) I don’t mind taking the issues head on. Do you think there is information in DNA?

    If so, I would be interested to know how you define it, and if there are any physical entailments resulting from its existence. In other words, why do you consider it information, or not? Are there observable things that we can generalize to other forms of information, for instance?

  221. Thermodynamics only says, that we go to a minimum energy fold, it says NOTHING about how we get tot he highly specific sequence of AA’s [or behind it, bases in DNA] that give us a precisely functional protein as a result of such folding. And, you either know or should know that.

  222. ScottAndrews, leaving aside the OOL and how the present DNA system was developed, all modern life DOES start at the buried treasure and search only the immediate vicinity.

    Half the reality-based world has been trying to explain that to the various ID theorists for at least the last decade, but all we hear back in reply is how searching these enormous search spaces makes evolution impossible.

    Honest guys, we don’t search the entire solar system EVER. The only way we could possibly do that would be to change every single DNA base at once and that never happens.

  223. You are really something. So, Hamlet is the physical configuration of the ink, and nothing more. And information is a useless concept, certainly! This is materialism brought to its most obtuse consequences!

    Please try responding to the things I am actually saying instead of making up a position you want me to hold, then trying to knock that down.

    I get the fact that you want an explanation for HOW the arrangement of matter came about but you are failing to understand the issues being delineated. When you refer to Hamlet you have to remember it only makes sense (contains information) in the direct context of the whole of medieval England, and less directly (but contingent on) the development of language and human history)

    The information you refer to in a cell makes sense in the context of the cell, and is in the form of a physical arrangement of matter.

    When you say this:

    Take away the information, and the chemical laws will never give the myoglobin molecule. It’s as simple as that.

    you actually mean: Change the configuration – that is how you ‘take away the information’ but you keep talking about information in the context of the cell as if it is some immaterial property independent of the physical properties of the cell. It is entirely a property of the physical cell and if you think it is other, then provide empirical proof because there would be a Nobel Prize waiting if you did.

    To say that biochemical laws explain the sequence of myoglobin means that in some way you can put the necessary aminoacids in some system (where there is no specific information about the myoglobin sequence) and biochemical laws will cause the formation of the myoglobin sequence because of necessity interactions between the molecules.

    That is not true. That is a ridiculous way to consider things.

    Can you please provide an example of this – HOW do I put this information in WITHOUT arranging or re-arranging chemical elements and relying on their behavior?

    You have NEVER provided any example of HOW you change the information in something without changing something physical in any part of the system.

  224. I’ve never seen anything interesting about evolution from Stewart Kauffman so I’ve never read him closely. The whole search for a self-organizing principle seems futile to me unless you’re talking about something along the lines of atoms and very small molecules forming slightly larger molecules in a pond or underwater vent or under the earth.

    But all you need is to form one polymer that self-reproduces that way and you’re off. You don’t need DNA – nobody in OOL research things DNA had anything to do with OOL. It comes much later. A self-reproducing polymer is perfectly capabable of mutation. In fact, the trick is to keep it from varying too much.

    ID and creationism are both fixed on the idea that the first living thing was a cell of modern complexity. Such a cell is almost infintely unlikely as the first living thing. Think small molecules and you’ll be thinking about the same things as modern OOL researchers.

  225. DrRec – Bot:

    I must confess that I am a little puzzled by our couple of Doctors, not only because I get easily confused with similar names, worst of all nicknames, but because, while probably saying completely different things, they are strangely similar in the bizarre apporach they have to both cognitive issues and this discussion.

    For the sake of clarity, I will try to understand how tfhis discussion has “evolved”, filtered probably by random nonsense and obtuse selection.

    One of the doctors started the current trend by affirming more or less that everything was due to biochemical laws, that the arrangement of codons and aminoacids was explained by those laws. I (and others) have in good faith done our best to explain that such a view is wrong, because no biochemical, or other, laws of nature can explain the information in DNA genes that explains the information in functional proteins. Apparently, we got no results with the solert doctor, who stuck to his view, while denying even the concept of information and inviting me to go back to school (a rather terrifying perspective at my age, but after all, all life is a school!).

    In some mysterious way, the discussion partly shifted to the singular problem of whether information is physical or non physical, an issue that personally I consider devoid of any meaning, and especially of any utility. Consistently, I have tried, here like elsewhere, not to spend a word about it.

    In the meantime, I suppose the other doctor joined the conversation. From the last developments, it seems that his problem is that we are, for strange reasons, trying to explain biology by natural laws, “forgetting” that there is the random component (RV) and the filter of natural selection.

    Now, that’s really bizarre. Again for the sake of clarity, I want to summarize here that:

    1) The only reason why we were debating the absurd notion that the laws of necessity can explain, of themselves, biological information is that one of our two antagonists has repeatedly affirmed that, and not receded even in front of the strongest evidence.

    2) That those “laws of necessity” that are being debated in this context are obviously the laws of nature, such as gravity, electromagnetism, chemistry, and so on, as anyone who has really read our posts here should understand. In a word, the laws that operate and are described as a sequence of explicit cause and effect steps, where the probability of the final output is 1. That’s why they are called “laws of necessity”. It is usually understood that those laws explain well the working of machines, both mechanical and biological. In no way that means that they can explain the existence of those machines. Machines are designed, and work according to the laws of nature. It seems strange that I have to repeat such trivialities, but really this discussion has gone well beyond the range of common sense.

    3) That the whole of this blog, and of the ID theory, is dedicated exactly to discussing the other points, that is the role of random systems and of natural selection in explaining (I should say, in not explaining) biological information. The second doctor is maybe here here for the first time, if he does not understand that we have been discussing that in detail hundreds of times, and if he is commenting that we are “forgetting” that, only because at this moment we are discussing the opposite, and bizarre, view that necessity can explain it.

    I apologize if I have involuntarily confused the roles of our two interlocutors. The only reason is that I am confused by them, at all semantic levels.

  226. DrRec,

    “The moon is the moon, no matter what you name it.”

    Indeed. But what you are missing out is that in order for you and me to understand each other when either of us says “Moon” we need to have the same mapping between this sequence of letters and their agreed meaning. Overwhelming evidence suggests that in order for information systems to function, (i) the alphabet, (ii) the language and (iii) the semantics should be defined a priori between participants of future communications.

    To defend Darwinism, you need to reliably demonstrate that these three were spontaneously generated and (possibly) exapted simultaneously with the systems being built. It is a daunting task because what you need to demonstrate that goes contrary to everyday experience.

  227. DrBot:

    You have NEVER provided any example of HOW you change the information in something without changing something physical in any part of the system.

    Because I have never said that I can change the information without changing something physical. You must have imagined it.

    I have said explicitly, more than once, that I am not interetsed in debatin if information is physical or not.

    Wahat is it that you don’t understand in these simple statement taken for my post, exactly the one you are answerin?

    “Just to be clear, a functional configuration is not a biochemical relationship, it is an informational relationship realized by imposing a specific form to configurable switches that would never take that form only for spontaneous working of scientific laws.”

    Configurable switches are certanly physical entities. What is wrong with your understanding of words?

    And:

    “Yes, the functional configuration of a protein is certainly a physical state, but it is not certainly explainable by biochemical laws.”

    I have never said a word about information being “non physical”. I have simply explicitly avoided the issue.

    so, who is “making up a position you want me to hold, then trying to knock that down.”?

  228. Ah, GP:

    I see you too have had an exchange with our two objecting Drs, who have both been around for quite some time.

    (I do note, you have been obviously busy elsewhere for a considerable period — I missed your ever so refreshing remarks. I hope both your patients and your family are doing very well!)

    I have now come to a general conclusion about design theory and its evidence. The problem is NOT that the evidence is not there, or is vague, or is inconclusive.

    On the contrary, the evidence is all around us — this very thread is full of it, just in the form of the glyphs arranged to make symbolic strings that are meaningful and respond to a particular context. One, that as it is, is in the context of thoughts since Plato and Cicero, and which embeds a stream of developments since the 1830s in Mathematics, engineering, science, and more, also especially the world of the information technology revolution since the 1940′s. (So the case of Shakespeare is hardly isolated on such issues of context!)

    Nor is the evidence particularly hard for the unbiased observer to understand or accept.

    Indeed, the very fact that we all implicitly accept — solely on the evidence of posts embedding FSCI in this thread! — that they are not the product of monkeys battering away at keyboards or the equivalent, but instead are evidence of intelligent, designing, purposeful authors, is itself a strong demonstration that we all know intuitively that FSCI is a reliable sign of design.

    What is happening is that lo and behold, the same sign of FSCI is to be found in the heart of the living cell; which obviously is prior to our own existence and that of our first human ancestors.

    The person working by common good sense would easily see that forces of chance and necessity on the gamut of our observable cosmos — the only cosmos we actually have observational evidence for — cannot account for that, or for the codes required, or the algorithms and data structures expressed. And, remember, the reasonable threshold of complexity is 500 – 1,000 bits, where we are looking at 100,00 to 1 mn [on evidence of simplest observed life, and that points to the upper end of that scale], in a context where the scope of a config space DOUBLES for every additional bit. Just for 100,000 bits, we are talking 99,000 doublings beyond a threshold that is already hopelessly beyond the capacity of the observed cosmos. (And, if you want to propose a simpler architecture, kindly empirically demonstrate its plausibility and relevance.)

    It is incredible that this has to be pointed out yet again.

    There is but one known entity that can explain such: the deeply knowledgeable and skilled, purposeful intelligence.

    So, right there in the cells of our bodies, we have evidence that strongly points to powerful, knowledgeable intelligence that on the evidence and timelines usually accepted, would have had to be active since about 3.5 or more BYA. Intelligence of the same order of capability would also have had to be called upon to explain the 10 – 100 mn+ bits of additional information required to code for zygotes elaborating themselves into the dozens of basic body plans usually dated to about 500 – 600 MYA. So, we are talking of intelligence capable of truly long term, vast scope planing and foresight, regardless of how it was achieved.

    That is where the real problem gets injected, as we can ever so easily see from prof Richard Lewontin’s ever so revealing remarks about the dominant views of the elites of the scientific guild:

    . . . To Sagan, as to all but a few other scientists, it is self-evident [[actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . ] that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [[i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . .

    It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes</b [[another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [[i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door. [And for those taken in by the "quote mining" accusatory talking point that the immediately following words JUSTIFY the above behaviour, kindly read onward in the just linked.]

    In brutally frank short, we are up against question-begging, mind-closing deeply indoctrinated censorship, in the form of a new elite materialistic magisterium dressed in the holy lab coat. Censorship that is so deeply entrenched that not even patent absurdity — notice that utterly revealing “no matter how counter-intuitive, no matter how mystifying to the uninitiated . . . “ –can easily break its stranglehold.

    And, BTW, that also explains why any use of this citation is so stoutly resisted, as it lets the cat out of the bag so blatantly for all to see.

    So, you can see why I have now concluded that the problem is entrenched ideology, not evidence.

    We are dealing with the terror of and rage against even the foot of God.

    THAT is why, no matter how we highlight — and as has been highlighted since the days of Thaxton et al in 1984 in the very first technical ID book [as in, the leading objectors know or should know better] — that it is an inescapable limitation of the inference to design here that we cannot on the strength of there being a designer for life infer that it “must” be a designer beyond the cosmos, we see that ever so willfully loaded talking point. The “Creationists in a cheap tuxedo” talking point. And, of course, the “right wing Christo-fascist” talking point.

    (Such BTW reveal their ignorance of the roots and idea links of fascism: a statist, political messianistic ideology that is closely tied to socialism, though it operates in terms of alliances with cartels and imposition of the regulatory state, instead of outright expropriation. The trick in that, of course, is that at a certain level, control becomes de facto ownership. They need to read a bit more on Mussolini, and they need to explain why the even more dangerous form was called National SOCIALISM.)

    Ironically, there is a form of design inference that does point beyond our cosmos, cosmological design.

    We live in a credibly finely tuned cosmos set up at an operating point that is locally deeply isolated as an island of function that supports C-chemistry, cell based life. Set up so finely that it seems the equivalent of one grain of coarse sand to the mass of the visible matter of the observed cosmos, plus or minus, would be enough to destabilise it. That’s why, from Hoyle on, a significant number of astrophysicists and cosmologists have agreed that the common sense interpretation of physics is that someone has monkeyed with the physics of the cosmos and there are no blind forces in the cosmos worth the name.

    The joke that astrophysiscists have been rushing out of their observatories for the lunch our mediation by Hoyle and then lining up to be baptised into the First Church of God, Big Bang, has a bit of bite to it!

    Why then is there such a battle on design of life?

    History, not logic and epistemology.

    Across the back end of C19 and running up to mid C20, dismissing the ideas of Wallace et al, the positivistic atheists who usurped power in science, used dinosaurs etc as the icons of their claim that science had put God out of a job. And their heirs in the past generation, have locked and barred the door against him.

    But now, there is a suspicious knock on the door, and they are scared, scared, scared to open it . . .

    GEM of TKI

  229. GP: A strawman was set up and knocked over . . .

  230. Because I have never said that I can change the information without changing something physical. You must have imagined it.

    At last! you see, when you said this:

    The genetic code is not a law of chemistry. It is a symbolic coresponcence between codons of nucleotides and aminoacids. No laws of chemistry connect the two things.

    You are, as far as I can see, stating that there is no physical law that determines how codons of nucleotides correspond to amino acids. All I have been trying to point out is that the whole reason specific codons and nucleotides correspond to specific amino acids is because of biochemistry.

    Configurable switches are certanly physical entities. What is wrong with your understanding of words?

    well it is down to statements like this:

    No laws of chemistry connect the two things.

    Now there is a whole different issue:

    Just to be clear, a functional configuration is not a biochemical relationship, it is an informational relationship realized by imposing a specific form to configurable switches that would never take that form only for spontaneous working of scientific laws.

    There is a big claim there, care to back it up?

  231. Not by me.

  232. Hi,

    I hope you chaps will excuse my interference. But the issue seems pretty clear to me, even though I am not a biologist.

    1. We all agree that circular objects can be rolled. Right?

    2. But for some reason there is no agreement in admitting the simple fact that to use that physical property of rolling in a sophisticated device performing a function (say, a cart for carrying goods) it is necessary to have something else apart from that physical property, i.e. intelligence. Examples of this are ubiquitous. It is your hard part, evolutionists, to clearly demonstrate it can be done without intelligence.

  233. dmullenix,

    ScottAndrews, leaving aside the OOL and how the present DNA system was developed, all modern life DOES start at the buried treasure and search only the immediate vicinity.

    I understand your statement. But leaving aside OOL, present DNA, and all modern life is the problem. Explaining them is easy as long as you don’t explain them.

  234. The moon is the moon, no matter what you name it.

    And whenever it hits your eye like a big pizza pie, that’s amore.

    Dean’s Law.

  235. DrBot:

    Ahhh!!!

    You are, as far as I can see, stating that there is no physical law that determines how codons of nucleotides correspond to amino acids. All I have been trying to point out is that the whole reason specific codons and nucleotides correspond to specific amino acids is because of biochemistry.

    But do you at least understand what a law is? I repeat: tehre is no physical law that determines how codons of nucleotides correspond to nucleotides. A law is a law. If you know a law connecting codopns to aminoacids, please spell it!

    Codons are connected to aminoacid through a protopcopl, the translation apparatus. As the apparatus is made of molecules, those molecules certainly respect the laws of biochemistry. But the apparatus is not created by the laws of biochemistry. It’s the information stored in it that allow it to work.

    That seems to be clear to all, except you. I will not discuss that any furthur. If you have problems in understanding the obvious, I cannot solve them.

    There is a big claim there, care to back it up?

    No, let’s change the game. You do explain how and why a protein should take its form according to the laws of biopchemistry. Good luck.

  236. KF:

    thank you for remembering many true things. Sometimes it is good to hear what is true, just for a change…

  237. Petrushka,

    I was referring to this – “Really? You’ve observed the designer of life at work?” which I took as a reference to OOL.

    He points out that the difference between mice an men is very small.

    I’m sure he does. Let him come up with a functional selectable pathway between them and then we’ll see how small he thinks the difference is.

    If we redefine “microevolution” to mean evolution from mice to men then we need a new word for what used to be called microevolution. If that’s “micro” then what’s “macro?” (Just a few years ago there was denial that scientists even used that word, or macroevolution. Now they appear in research papers.)

  238. BTW, unlike some in this thread, Stuart Kauffman, a staunch evolutionist as he is, has a clear understanding of the problem we are discussing and a decade ago or even more, if I remember rightly, he promised to show experimentally that information can be generated spontaneously. If I am not mistaken, his antichaos paper was published in 1991.

  239. DrREC,

    The analogy ends at the impact of random processes on deriving a physical law. I didn’t extend it past there, you did.

    If one physical law is real and disperses particles and the other is imaginary and creates or modifies life then what was the point of the analogy?

    Randomness on a large scale can appear to mimic a pattern. Radioactive decay is predictable even though the individual events are random. Coin tosses tend to balance around 50/50 even though the individual events are random and one-sided.

    Unless you can somehow relate that to the formation of DNA information it is irrelevant.

    Natural laws themselves were evidently not an explanation because next you added randomness to supplement them. Randomness does not improve the picture.

    Information is neither random, which would result from randomness. Nor is it predictable, which would result from natural laws or random events that form a pattern.

    Natural laws explain the behavior of molecules which enable the transcription of the information in DNA. They do not explain the arrangement of that information, its content. They also fail to explain why such information would exist in a form that is meaningless by itself unless interpreted.

    Sorry for being snarky. Too much caffeine, not enough sleep.

  240. But do you at least understand what a law is?

    Yes.

    tehre is no physical law that determines how codons of nucleotides correspond to nucleotides.

    No, no single law, but I never claimed there was.

    If you know a law connecting codopns to aminoacids, please spell it!

    Go and read some introductory books on chemistry, they spell out the laws that determine how chemical systems behave. This might clear up your confusion!

    No, let’s change the game. You do explain how and why a protein should take its form according to the laws of biopchemistry. Good luck.

    Codons are connected to aminoacid through a protopcopl, the translation apparatus. This operates according to the laws of physics, it is a series of biochemical reactions. There are plenty of good textbooks that explain it in detail.

    But the apparatus is not created by the laws of biochemistry.

    I never said it was. Do you understand how this is a very different issue than how codons map to amino acids. When you say:

    tehre is no physical law that determines how codons of nucleotides correspond to nucleotides.

    you are making a claim about the function of the mechanism not its origin. It is your confusing conflation of the two that seems to lie at the root of this whole debate!

    When it does come to the actual origins, rather than declaring “the apparatus is not created by the laws of biochemistry” I maintain that I do not know, but I am very interested in hypotheses that attempt to understand the following scientific question:

    CAN the apparatus be created by the laws of biochemistry?

    And of course anyone who makes a genuine attempt to understand what the actual probabilities might be.

  241. Information is neither random, which would result from randomness. Nor is it predictable, which would result from natural laws or random events that form a pattern.

    Just to point out the obvious – A random string contains a lot more Shannon information than a non random string.

  242. But a random string lacks specificity.

  243. DrBot,

    A random string contains a lot more Shannon information than a non random string.

    Understood, but I’d hate to read that book or have someone stick that information in my DNA.

  244. Not necessarily. For example, I have a password program that generates random sequences that I can then specify to unlock a given account. While it doesn’t matter what I choose for the password, but random sequences are much harder to crack and so are more secure.

  245. Again, the analogy stops at the inability to describe the behavior of a system with randomness as natural law.

    You can garner statistics on radioactive decay, but you can’t predict the series.
    You can gather statistics on evolution, but because it is a product of random inputs filtered by changing environments, it will not be derived as a law.

    But again, what is your point? That processes with a random component should be reducible to natural law? Or that which cannot be reduced to natural law is false?

  246. “Do you think there is information in DNA?”

    I think there are physical bases, which template RNA and proteins, which perform enzymatic and other functions.

    “Are there observable things that we can generalize to other forms of information, for instance?”

    Yes. For example, we can take the sequence of the bases, and derive phylogenetic and evolutionary relationships.

  247. “One of the doctors started the current trend by affirming more or less that everything was due to biochemical laws,”

    I didn’t see this post. I saw DrBot explaining the function of the translation machinery is physical, and conforms to our understanding of thermodynamics, chemistry, physics etc.

    I did not see him saying the ORIGIN of that system did.

    Evolution has stochastic components, so is inherently non-deterministic, so won’t be reduced to law.

    I believe the request to describe the origin and evolution of the system by physical law is coming from ScottAndrews. Maybe you should adress your criticism to him.

    That being said, I defend that diverse input, acted on by selection, produce more fit outputs. If you call this information, it increases in natural processes. I can’t reduce that to a formal law. There is a substantial equivocation between nature and physical law. The series of radioactive decays of gram of a element that stochastically decay into one of several other elements can’t be reduced to law. It is natural. It happens. You can statistically describe it. Likewise evolution.

    But right now, can I write the physical law of the formation of myoglobin?

    No. Which myoglobin? And why myoglobin, when other animals use other proteins to do the same function.

    Evolution has a stochastic component. Ok?

  248. DrREC,

    Honestly, I’ve lost track of whom I’m discussing OOL or evolution with. So I’ll try not to attribute anything someone else said to you.

    There are two different phenomena. One is the existence of complex functional systems. The second consists of an abstract code containing the instructions for manufacturing pieces of such a system combined with components for supplying the materials, interpreting the code, manufacturing the pieces, and assembling them.

    Purely for the sake of argument, let’s say that the first requires no forward thinking or intent.

    The second requires both intent and planning. Neither natural laws, random inputs, nor any combination of them can account for it.

    To be random means that any number of possibilities might occur unpredictably. But randomness is limited. An event might have many possibilities, but they are typically not limitless.

    Flipping a coin is random. There are numerous possible outcomes – heads, tails, the edge, and other less likely outcomes. But you do not flip a coin and get an owl or a stapler.

    Likewise, molecules don’t mix to create life forms with an inexplicable drive to reproduce and overcome obstacles to their own existence until they eventually become owls or make staplers.

    You seem to confuse unpredictability with limitless possibility. You cannot declare anything plausible simply by declaring that there is a random component at work.

  249. “You cannot declare anything plausible simply by declaring that there is a random component at work.”

    Not what I said. I said it isn’t reducible to a formal physical law, which seemed to be what you, or someone was getting at.

    One point: the random inputs are filtered into outputs that are anything but.

    “Neither natural laws, random inputs, nor any combination of them can account for it.” is a strong conclusion, given that we observe complexity and functionality increasing in such processes, even from random sequences.

  250. DrREC,

    This is not a new point, it is a reassertion:

    the random inputs are filtered into outputs that are anything but.

    Agreed, you can filter random inputs into non-random outputs. Raindrops fall at random but then natural forces pool them into predictable puddles.

    But if they are filtered into an ice sculpture of a dolphin then the filter itself requires further explanation. Natural forces explain the puddle but not the ice sculpture.

    “Neither natural laws, random inputs, nor any combination of them can account for it.” is a strong conclusion, given that we observe complexity and functionality increasing in such processes, even from random sequences.

    If that were the case then it would be an incorrect conclusion. It’s provisional (which sounds nice but means very little in this case) but I stand by it.

  251. Your answer seems somewhat ambiguous, so may I press for clarity:

    Does this phenomena fit within any recognizable definiton of information, or not?

    Does its existence result in any physical entailments which may be generalized?

    For instance, I might suggest that information is an abstraction of a some-thing, symbolically represented in an arrangement of matter (such as the arrangement of nucleotides for instance). In such a case, the arranegment of matter (to serve as a representation to be decoded) would be a physical entailment that the information exists.

  252. “I might suggest that information is an abstraction of a some-thing, symbolically represented”

    Symbolic and abstract tend to get me here. Maybe an analogy would clarify things for me– If we took the physical cylindrical disk of a music box, is that information? It instructs the system how to make music, when translated by the keys. But is it abstract or symbolic? Does it possess “physical entailments which may be generalized” Can any music box anywhere play the song? Can a musician read the song off it, independent of the system that plays it (tone and speed would be indicated)?

  253. Good point.

  254. Rhampton7,

    The random sequence becomes specified as soon as you select it as your password. It is not interchangeable with any other random sequence. They characters were selected randomly but then you assigned meaning to them.

  255. The interesting thing about music boxes, some of them used punch cards as did some looms. Hypothetically, the punch cards are interchangable even though the output (respectively, music and fabric) would be very different.

  256. DrREC,

    But is it abstract or symbolic?

    Do you get music from the cylinder without the music box? Does the music require a cylinder and a music box, or could it be recorded on paper or even exist only in someone’s memory? If you destroy the cylinder does the information cease to exist?

    Yes, I’m just throwing out a ton of questions. One more: If someone who had never heard music found the cylinder, would they be able to derive music from it? They should be able to if the cylinder and the information are one and the same.

    The very nature of information is abstract, because has no intrinsic relationship with any medium or form. Words can be ink on paper, sounds in the air, or electrical currents interrupted at regular intervals. They can be stored in the chemicals in our brain. The words themselves can be replaced with words in another language or hand gestures that encompass the thought but not the words.

    Not all information reflects a thought, but all information of observed origin did originate with thoughts. Can anyone think of another way? How did the rest come about?

  257. but all information of observed origin did originate with thoughts

    Well that’s not true, and Intelligent Design theory claims only that FSCI greater than 500 bits must originate with intelligent thought. The sky is filled with information, emitted as energy, from a billion galaxies comprised of a billion stars. By capturing these photons with the right receiver, we can use them to re-construct the emitting body and the intervening space – that is, decipher the information contained within a simple message originating from an “unintelligent” source.

  258. Dr Rec. at 42.1.1.1
    Sorry for the delay. I think I understand your questions, which are valid. Allow me address them one at a time.

    Is the cylindrical disk of a music box information? I would say that it is not information itself, but like a book, it is a container of information. It is matter (a material medium) which has been arranged in order to contain information, in this case, the information required to reproduce a specific song.

    But is it abstract or symbolic? Yes, the information it contains is both, by necessity. The cylinder is an example of matter arranged to contain an abstract representation of a song. The individual and collective pins on the cylinder are iterative symbolic representations mapped to specific effects, in this case, the musical notes and melody of the original song as played in time. In a system with the appropriate protocols (tines which are spatially and tonally coordinated) for actualizing those representations, the song can indeed be reproduced. The input of information will constrain the output effect.

    Can any music box anywhere play the song? The representation contained in the cylinder is tied to specific protocols. A music box utilizing different protocols would not result in the same notes being played, as well as a possible change in tempo. On the other hand, if it were played in a music box of the same register but perhaps in a different octave, then the song would still be reproduced (albeit in a different octave).

    Can a musician read the song off it, independent of the system that plays it? I would think a craftsman familiar with such systems would likely do just that. Upon proper study, likely anyone could.

    Does it possess “physical entailments which may be generalized” Yes, I am certain it does, and that they can be demonstrated. I believe there is a list of four physical entailments of any such recorded information, and I believe that those entailments can be listed (as is scientifically appropriate) without reference to the source of the information. In other words, they can be listed without assuming any conclusions.

    Entailment #1: The first of these physical entailments is the most obvious; that is the symbolic representations themselves. Information is recorded by the arrangement of matter or energy in order to convey these representations (such as the ink on paper, or the magnetic lines left on a recording tape, or the pins arranged on a music box cylinder). These are examples of matter arranged to contain these representations, but by themselves, they cannot convey information. Another physical object is required.

    Entailment #2: The second physical entailment is what can easily be described as a protocol, and its inclusion on the list is easily understood. In order for one thing to represent another thing, it must be separate from it. As an example, an apple is an apple, but the word “apple” is a separate thing altogether. And if it is truly a separate thing, then there must be something to establish the relationship between the two, and that is what a protocol does. A protocol is a thing which establishes the relationship between a symbolic representation and the effect it represents. In the case of the word “apple”, we as humans have learned the protocols of our individual languages, and those protocols exist as neural patterns within our brains. These neural patterns are physical things, and they establish the relationship between the word “apple” and the fruit it represents. A bee dancing in a particular way during flight is a separate thing than having the other bees fly off in a particular direction, but the relationship between the two is established by a protocol which exists in the sensory systems of the bee. The function of the protocol is, therefore, to establish a rule that “this maps to that”, which is an immaterial relationship that otherwise wouldn’t exist.

    Entailment #3: The third physical thing on the list is the effect of the information. Bear in mind this central observation of all recorded information; all forms of such information are explicitly tied to having an effect (even if they never have that effect). For instance, there is information about which side of the road to drive on, the obvious effect of that information is having far fewer collisions. The effect of the bee’s dance is that the other bees fly off in the right direction. In all cases, recorded information is tied to having an effect, and the variations of those effects are extraordinary.

    Entailment #4: This fourth physical item is not an object; it is the dynamic relationship which is observed to exist between the other three physical objects (the representations, the protocols, and the effects). This is one of the key physical observations which allow information to exist at all. The representations, the protocols, and their resulting effects are three entirely discrete (separate) things, and they remain discrete at all times, no matter what form the information is in (written in words, demonstrated in a bee’s dance, or the extracted from the pins on a music box cylinder). For instance, the most obvious example is human language. The word “apple” is entirely separate from the fruit apple, and the protocol in our brain is entirely separate from both of those. They are three completely independent physical realities which share an observable relationship, with the protocol establishing the relationship between the word and the fruit (while the word and the fruit remain separate). This exact same dynamic can be observed in the bee’s dance, with the dance itself being a separate thing from the response of the other bees, and the protocol in the bee’s sensory system (causing the bees response) being separate from both of those. At no time does the representation (or the protocol) ever become the effect.

    So this list of four physical requirements (for recorded information) contains two physical objects (two discrete but coordinated arrangements of matter), a physical effect, and the dynamic relationship that exists between the other three. Each must be individually accounted for, and I think you’ll find their relationship in all forms of recorded information (in every example from human language, to computer and machine code, to a bee’s dance).

    This same dynamic relationship exists in the genome as well. During protein synthesis a selected sequence of nucleotides from the DNA chain are copied, and the iterative representations contained within that copy are then fed into the ribosome, forming the input of information into the ribosome complex. The output of that ribosome is a chain of amino acids, which will then become the protein being prescribed by the input sequence. The input of information is therefore driving the output production, but as in all other forms of information, the input and the output never physically interact. The exchange of information (from the input sequence to the output constraint) is made possible by a set of very special physical objects – the protocols – tRNA and it’s entourage of synthetase. Acting together they facilitate the transfer of information from the input to the output, and they do so by allowing each to remain physically discrete.

  259. DrRec:

    Not what I said. I said it isn’t reducible to a formal physical law, which seemed to be what you, or someone was getting at.

    Just to understand better the reciprocal positions, I would say that nobody in ID has ever believed that biological information is or should be reducible to a formal physical law or laws. As far as I can understand, that was only the bizarre position of DrBot.

    I think we can all agree that biological information cannot be explained by law alone. Even darwinists understand that (except maybe DrBot, if he is a darwinist).

    We are perfectly aware that the darwinian theory is an explicit explanation for biological informayion based on two components: Random variation and Natural Selection. The whole ID theory is about demonstrating that that explanation is completely wrong, and that a design inference is the best (indeed, the only) explanation that makes sense.

    We are perfectly aware that the NS part of the algorithm is a necessity mechanism, and that it cannot be treated probabilistically. But we are also very aware that the RV part of the algorithm must be treated probabilistically. And that’s what ID does.

    You say:

    “Neither natural laws, random inputs, nor any combination of them can account for it.” is a strong conclusion, given that we observe complexity and functionality increasing in such processes, even from random sequences.

    It is a strong conclusion, and it is a true conclusion, if it is expressed more completely.

    That would be a better way to put it:

    “Neither natural laws nor random inputs can account for the emergence of digital functionally specified complex information. A combination of them, like the darwinian theory, can be accepted only if the role of the random component is limited to produce outputs which are not dFSCI, and all the rest can be expalined by law.”

    In the specific case of the darwinian theory, that can be summed up in the following statement, that I have often made here, and that I maintain as true:

    The darwinian theory can work only if all the examples of dFSCI we can observe in protein genes (or in any other form of biological information) can be deconstructed in a series of explicit simpler steps satisfying the following properties:

    a) Each step can be expanded by NS, because it confers a reproductive advantage.

    b) The random transition from one step to the other is not complex, under any definition of complexity theshold appropriate for the physical random system we are dealing with.

    For any realistic model of a biological system, I have suggested many times that an upper threshold of 150 bits (about 35 aminoacids) is absolutely appropriate. IMO, it s still too generous, with all the experimental evidence fixing the limit at 2-5 aminoacids, but we in ID are notoriusly generous with our interlocutors.

    As far as I know, there is no example of complex biological information (such as that in basci protein domains) that has been explained in that way. IOWs, the darwinian theory has never explained any form of macroevolution.

    And it never will, because a point is very obvious to anyone who can observe reality without the ideological bias of reductionism: functional complex information is not desconstructable into simple additive steps. That is obvious in all designed things: language, software. It is equally obvious in biological information. The reason is very simple: it is impossible to build a complex functional structure, expressing a new complex function, as the sum of simple steps, each of them increasing the existing function or bearing a new function.

    It is impossible for any serious complex function. Even more if the only valid function in the system is reproductive advantage.

    IOWs, the darwinian theory does not work, and cannot explain biological information.

  260. As far as I know, there is no example of complex biological information (such as that in basci protein domains) that has been explained in that way. IOWs, the darwinian theory has never explained any form of macroevolution.

    There’s a problem is defining macro vs micro then. Shapiro seems to be saying the whole mammalian order is an example of microevolution.

    Comparing mice and men, the “genes” stay largely the same, but their deployment differs. The bones, ligaments, muscles, skin, and other tissues are similar, but their morphogeneses and growth follow distinct patterns. In other words, humans and mice share most of their proteins, and the most obvious differences in morphology and metabolism can be attributed to distinct regulatory patterns in late embryonic and postnatal development.

    Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2224-2227). FT Press. Kindle Edition.

  261. This is a reply to 3.3.1.2.2 ScottAndrews

    Your reply is a little unclear. Are you agreeing that all modern day life starts out in one of the sweet spots in the search space and “finds” new sweet spots for its offspring by searching only very near areas in the search space? If so, then we can dispose of about 2/3rd of all ID argumentation and concentrate on more useful topics.

    Regarding how the OOL occurred and how the DNA system was developed, I congratulate you on your wise debate strategy. Since both occurred billions of years ago and left no fossils that we know of, you don’t have to worry about someone plunking physical evidence on the table and saying, “Like this!”

    I actually like that strategy so much that I’m going to use it myself. As an ID advocate, please tell me how the first living thing was produced, what it looked like, how it worked and how it went on to develop the DNA system we see today.

    “The Intelligent Designer did it.” won’t do as an answer. That’s like me saying that chance combinations of atoms produced the first replicator and Darwinian evolution produced the DNA system.

    I’m asking you to provide me with the same answers you’re asking science for: What did the first self replicator look like? Was it a polymer? Then what was its structure. Was it a chain of chemical reactions that ended up with a new copy of the starting chemical? Then what was the chemical structure of the chemicals? When and where was it made? How did it work? And how did it develop the DNA system?

    Now you may well protest that ID doesn’t have those answers and I will certainly believe you since ID does no research in the OOL that I am aware of. Nevertheless, I expect you to answer those questions anyway, just like you expect science to answer yours. If you can’t or won’t – well, I really don’t expect you to. “The Designer did it.” is the most “detailed” answer ID has ever given to questions like these and I don’t expect any better answers ever due to ID doing no noticeable research in this field.

    As Dembski said, “ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories.” As far as I can tell, ID’s sole self-appoint task is to make futile attacks on on their straw-man misunderstandings of evolutionary theory and, on this blog at least, on science generally.

  262. Dmullenix, why is it that you accept that similarity is an identifying feature of all other established design series (or, maybe you don’t, maybe you think that the reason why mobile phones look similar is because they share a common ancestor) but yet fly off the handle when it is suggested that this also applies to a living design series?

    Let’s not pretend that your reaction is anything to do with reason or evidence here. Come on, be honest, why does the mere prospect of Intelligent Design provoke such a strong, negative emotional response in you (and others like you)?

  263. 3.3.1.2.3 by Dmullenix

    Hello,

    You quoted Dembski as saying: “ID is not a mechanistic theory.”

    Indeed not. To me it is a just litmus test for design. I don’t expect it to do anything apart from detecting a high probability of design based on information content.

  264. Then one is logically forced to turn for an explanation of the design, to the only process known to modify population genomes over time, and that would be evolution.

    No one disputes it happens. It’s just a matter of filling in the pathetic details.

    Just noting the complexity and saying, “Oh wow,” is stamp collecting.

    We have a science devoted to filling in the details.

  265. Rhampton7,

    Yes, when I say “information” I mean amounts greater than 500 bits. I do not mean a coin laying on the ground which could be a deliberate message but more than likely isn’t.

    A star emitting light is not information. If information is the physical state or activity of any object then the word has been rendered meaningless. Information = existence = everything.

    Information is abstract. It is not the light coming from the star. It states or describes it. It can also describe the absence of a star, a hypothetical star, or an imaginary one.

    Right now the language to describe information seems a bit convoluted. But surely from the above example you can see the difference between information and light coming from a star. The mediums containing information are real, but the content of the information need not reflect reality. For example, “I have two heads and six arms” is information. Do you see it?

  266. Petrushka, which process is more important: the one that is “known to modify population genomes over time” or the one that:

    a. designs the genome and puts it inside a nucleus complete with sophisticated nuclear pores inside a cell that
    b. contains a multitude of amazing membranes and structures such as ribosomes, centrioles, lysosomes, etc all of which then
    c. work in mind-bogglingly complicated and intricate ways with trillions of other cells to form all the biochemical systems, organs and body parts that comprise, say, a human being?

    “Filling in the pathetic details” (particularly within a neo-darwinian framework) for the former, sheds no light whatsoever on the latter.

  267. Dmullenix,

    Are you agreeing that all modern day life starts out in one of the sweet spots in the search space and “finds” new sweet spots for its offspring by searching only very near areas in the search space?

    If you remove the assumption of a “search space” from the origin, then yes I agree, because it’s a tautology. It reduces to “All modern day life is where it is.” It is the limitations of future searches and how they relate historically that are relevant.

    It is unreasonable for you to acknowledge that ID is determination of intelligent cause, not a mechanical explanation, and then demand one anyway. Why ask? Why bother?

    But I’ll answer you anyway. As I reply I’ll offer the sum of all modern OOL research, because to the extent that supports undirected chemical abiogenesis it supports ID slightly better. Each experiment demonstrates what chemists can synthesize and manipulate in a laboratory. That the stated results can be accomplished by intelligent design is demonstrated and documented. That they might occur otherwise remains uncertain.

    It’s still a work in progress. Not every detail has been worked out. But it is peer-reviewed research supporting numerous hypotheses that could eventually lead to a more detailed understanding of how life might have been intelligently designed. It’s not perfect, but that’s more than is available for any other theory.

  268. Petrushka,

    “No one disputes it (evolution – ES) happens.”

    This is a controversial statement similar to saying that since we can physically walk, we can walk to the Moon. The macroevolutionary model disregards multiple impasses on its way.

    As regards you definition of science, Darwinism is no science either because it cannot reliably fill in those details.

    I think to say: “we don’t know” or even “we can’t know” is more honest than to lie with smoke in mirrors instead of evidence.

  269. 47.1.1.1.2 ScottAndrews

    Scott,

    Yes, I understood the comment by RHapmton7 about specificity of random strings in this light. Their specificity is determined contextually. It is something akin to stating that absense of information can also be information.

  270. The random sequence itself doesn’t contain specificity, and that was my point RE 47.1.1 (Eugene S). It is the authentication function of a particular site that gives it a specific meaning. So the same random sequence that allows me to log-in to UD won’t allow me to log-in to gmail, though it may, by coincidence, allow a different user to log-in to some other account. Finally, there is nothing about the random sequence that determines it must be a password – given a different context, it could have another use altogether.

  271. It is unreasonable for you to acknowledge that ID is determination of intelligent cause, not a mechanical explanation, and then demand one anyway. Why ask? Why bother?

    To be fair, Evolutionary theory is a mechanical explanation, not a determination of cause (in regards to OOL) nor a determinant of intelligent interference (e.g. dog breeders can replace natural selection in many ways and still it’s an evolutionary process), yet there are some ID proponents who would argue so. So I understand the impulse to turn the argument against those who make it.

  272. Yes, exactly. The same random string can have meaning, no meaning, or multiple meanings. Meaning can be given to it or taken away without altering any representation of that string, whether it’s in bytes or carved on a tree.

    This demonstrates that the concept of meaningfulness is abstract. It is not a physical property of an object.

    Forgive me if I’m losing track of threads at this point. By the very definition of “abstract” it cannot be conceived by physical laws any more than justice or politeness can be. They do not exist until someone decides that they do. And randomness isn’t even the ballpark. So what else creates an abstraction?

  273. Hmm, I’m not sure I agree with your direction on this.

    Let’s say I have a device that captures photons and I detect a signal of a given wavelength. What is the message? That depends on the source. If I can determine it came from a star, then I can decipher it’s size, temperature, chemical composition, etc. However, I need to be careful not to mistake a star for sunlight reflected from a man-made satellite in geosynchronous orbit, because the photon sequence could be identical. While humans determine what the photons mean, the encoded message (abstraction) originated from an unintelligent source.

  274. Rhampton7,

    That depends on the source. If I can determine it came from a star, then I can decipher it’s size, temperature, chemical composition, etc.

    You’re confusing interpretation with observation. You are observing the wavelengths, not deciphering them. They are properties. Nothing has been encoded.

    You may record the wavelengths on paper or in a computer or even memorize them. That abstract representation of the properties of those photons is information.

    You may use that information to make further determinations about the source of the photons, which is also information.

    It’s easy to split hairs over the word “information,” which is why I would prefer a more precise term. Perhaps “abstraction” is it. The photons simply exist and move. When we assign numbers and meanings to them we create abstractions.

    That leads back to DNA. It is an abstract representation of proteins (and who knows what else.) We create and use our own abstractions countless times each day and yet no one has proposed how any natural laws could ever do so. Even the most seemingly useless abstraction has a purpose, and nature has no purposes.

  275. rhampton7:

    Let’s say I detect a signal that can be read as the sequence of 1000 decimal digits of pi. How would you interpret that?

    Or let’s say that the signal can be read, once found the simple correct code, as the sequence of nucletodes in the DNA gene of 100 known human proteins. How would you interpret that?

  276. You’re confusing interpretation with observation. You are observing the wavelengths, not deciphering them. They are properties. Nothing has been encoded.

    That’s what abstraction is – interpretation. What is encoded in the random sequence I use for a password? That depends on what is interpreting it. For the authentication function at the UD site, the random sequence encodes a single message, “TRUE”. Then again, a compiler for a home-made robot might recognize same sequence an instruction to “turn right”. That I can assign arbitrary meanings to a given sequence does not exclude the possibility that specific, predetermined meanings might also exist. Thus the photons emitted from a star encode multiple properties about the stellar body in the form of a wavelength.

  277. Petrushka, which process is more important:

    The most important hypothesis is always the one that has entailments and suggests lines of research. The most useful one will always be the one that includes agents that have been observed, or which have attributes that can be extended or confirmed or disconfirmed.

    Evolution does not explain the cell machinery or the genetic code, but it does explain how the genomes of populations change over time.

    Whether it’s a complete explanation remains to be seen, but it does lead to research into the details.

  278. I would recognize it as Pi, but what it might mean is something else.

    A spy ring might use a code book of messages that correspond to Pi of differing lengths:
    - Pi to the 999th digit means “I’m in trouble, pull me out”
    - Pi to the 1000th digit means “I’m in trouble, but don’t do anything because it would make the situation worse”
    - Pi to the 1001th digit means “My cover is blown”, etc…

    Then again, it might be someone who simply wants to share their of love Pi.

  279. Rhampton7,

    You went off track right at the end. You correctly describe attributing meaning to messages. In a separate post you described how arbitrary meanings could be assigned to the number of decimal digits of pi transmitted.

    But then we get to this:

    Thus the photons emitted from a star encode multiple properties about the stellar body in the form of a wavelength.

    The photons do not encode anything. The star emits them and off they go. We’re talking about abstractions. Emissions of photons are not abstractions of emissions of photons. They are emissions of photons. They have no meaning until you give it to them. You could draw conclusions from observing them, but those conclusions could be wrong and you could find new ones. Meanwhile the photons remain unchanged.

    Abstractions describe real things, imaginary things, potential things, even other abstractions. The word “abstraction” is one of many abstractions for all other abstractions. But things by themselves are not abstractions. Where do abstractions come from?

  280. We don’t know for a fact that Pluto orbits the sun. No one has seen it complete an orbit. We have a lot of experience with gravity, but we don’t know the details of Pluto’s orbit. Perhaps it will stray off the expected course and require a redefinition of gravity.

    We also have about 50 independent lines of evidence for evolution. (Not OOL, evolution.)

    We execute people on less evidence. What you require is tougher than what is available to any jury considering the guilt of a criminal.

    We determine paternity in courts of law with less evidence than there is for common descent. (Using exactly the same reasoning.)

  281. Emissions of photons are not abstractions of emissions of photons

    I agree that photons are not abstractions of themselves, but they are abstractions of the star.

    You could draw conclusions from observing them, but those conclusions could be wrong and you could find new ones.

    That’s a problem endemic to signal processing.

    abstractions describe real things, imaginary things, potential things, even other abstractions.

    A crater can be an abstraction of an impact body and simultaneously be a thing (geographical feature) unto itself, similarly a fossilized footprint can be an abstraction of the animal who lived long ago and and simultaneously be a depression in the surface of a rock.

  282. Photons are not abstractions of stars. Photons are effects of stars. Craters are not abstractions on impact bodies. They are holes caused by impact bodies.

    The very essence of abstraction is that it has no necessary subject. Genes are abstractions of proteins, but which proteins? The ones that were just produced? The ones before that? Maybe the proteins exist only in potentiality.

    Causes and effects can be inferred from the examples you provide, but they are necessarily related to specific physical subjects. They are not abstractions. The word “abstraction” exists specifically to make that distinction.

  283. The very essence of abstraction is that it has no necessary subject

    And by that definition a photon can be an abstraction because a photon can come from any number of sources, not necessarily a star, but this isn’t helping us to resolve our differences.

    I think the point of contention is whether abstraction is (can be) a “physical” association held by the determinant interpreter (in regards to biological information). That is, do chemical bonds dictate the meaning of a gene’s encoding instructions (to produce a protein)? To which I answer yes, but you seem to suggest no.

    Artificial proteins can be created without DNA/RNA by assembling chains of amino acids and knowing how nature will fold them. While we humans can design any kind of shape, we can not rewrite the rules that govern folding.

  284. Dr, it seems you’ve come and gone without leaving a response.

  285. Why wonder? Look it up.

    http://tolweb.org/Mammalia/15040

  286. rhampton:

    OK, but anyway we can infer that the message is designed, and that it intentionally and intelligently codes for the digits of pi. That’s the point: the design inference.

    The motive for the design, its higher level purpose, can be investigated by further hypotheses. But the first level motive (coding the digits of pi in a signal), IOWs theimmediate function, is easily inferred. And it is symbolic, and abstract.

  287. OK, but anyway we can infer that the message is designed

    What would you say if you saw the Fibonacci sequence encoded in a living thing?

    There are lots of things about your pi question that bother me. First of all I would like to know how you would know what base the message is code in. There is no obvious reason to expect base 10.

  288. 290

    Dr Rec, it appears that you’ve come and left several comments elsewhere, but again no response here.

  289. not exactly what you were hoping for was it Petrushka?

    I’m not sure why it should comfort an ID supporter that a novel protein can substitute for a “wild” protein. It blows Douglas Axe’s argument out of the water, because it vastly flattens the function landscape. Even more so if it has an alternate function that still supports life.

    How much more evidence could you ask for that change is not necessarily fatal?

  290. Petrushka, you are clearly living in fantasy land, first off, since you have ZERO instances of Darwinian evolution producing proteins, (of which you should have thousands upon thousands of instances of functional protein generation by purely neo-Darwinian processes, that you could point to if neo-Darwinism were actually true), you present a paper in which the authors readily admit they are using a design strategy to manufacture a protein, i laughed!!, yet when push came to shove, with you stamping your feet acting as if this paper has any scientific merit whatsoever for the question at hand, gpuccio comes along and points out that they have no idea whether a functional protein was actually generated or not for they detected ZERO enzymatic activity from the ‘designed’ protein they inserted. In fact, The most probable explanation, for what happened in the cell, is that the ‘minimal rescue’ of the cell, from the four ‘deleted’ essential genes, was accomplished by epigenetic information transfer from the designed protein sequence.,,, Thus, basically, to illustrate the ridiculous nature of your claim, the guys cut off the leg of a victim in a experiment and hand him a stick so that he can still get around, at a much diminished capability, moreover they humbly admit such trivial results,,, and yet, far from you grasping the limited result, you adamantly claim this is proof of the almighty power of neo-Darwinism for you! Sheer fantasy is what I call it for that what it truly is on your part!!!

  291. of which you should have thousands upon thousands of instances of functional protein generation by purely neo-Darwinian processes, that you could point to if neo-Darwinism were actually true)

    Why should I have thousands and thousands when in the 80+ million year history of mammals there are only a few proteins separating one mammal from another? Exactly what makes you think that the differences between mammals are due to new proteins?

    According to both Koonin and Shapiro, the evolution of most proteins took place billions of years ago, before there were multi-celled organisms. These are your guys, aren’t they? They have been endorsed by the powers at UD>

    The fact is that a sequence having no lineage with wild sequences can support life. If the particular strain of modified bacteria continues, the novel protein will be optimized.

  292. Petrushka;

    Why should I have thousands and thousands when in the 80+ million year history of mammals there are only a few proteins separating one mammal from another?

    Only a few proteins difference??? Really??? Now you wouldn’t lie to me would you Petrushka???

    Chimps are not like humans – May 2004
    Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that “83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect,” Sakaki said.
    http://cmbi.bjmu.edu.cn/news/0405/119.htm

    Chimp chromosome creates puzzles – 2004
    Excerpt: However, the researchers were in for a surprise. Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case. The researchers report in ‘Nature’ that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded. And 20% showed “significant structural changes”. In addition, there were nearly 68,000 regions that were either extra or missing between the two sequences, accounting for around 5% of the chromosome.,,, “we have seen a much higher percentage of change than people speculated.” The researchers also carried out some experiments to look at when and how strongly the genes are switched on. 20% of the genes showed significant differences in their pattern of activity.
    http://www.nature.com/news/199.....524-8.html

    Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny – Casey Luskin – June 2011
    Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)
    http://www.evolutionnews.org/2.....47041.html

    Critically Analyzing the Argument from Human/Chimpanzee Genetic Similarity – Casey Luskin – Part 8 of 8 in a series of articles refuting Dennis Venema’s claims for information generation by neo-Darwinian processes – September 2011
    Excerpt: we’re not talking about “small changes” but rather, as the journal Science explained, at the very least these differences entail “35 million base-pair changes, 5 million indels in each species, and 689 extra genes in humans.”[1]
    http://www.evolutionnews.org/2.....51321.html

    A False Trichotomy
    Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.”
    http://www.uncommondescent.com.....richotomy/

    Human Gene Count Tumbles Again – 2008
    Excerpt: Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences.
    http://www.sciencedaily.com/re.....161406.htm

    Human genes are multitaskers:
    Abstract: Genome-wide surveys of gene expression in 15 different tissues and cell lines have revealed that up to 94% of human genes generate more than one (protein) product.
    http://www.nature.com/news/200......1199.html

    New level of genetic diversity in human RNA sequences uncovered
    Excerpt: A detailed comparison of DNA and RNA in human cells has uncovered a surprising number of cases where the corresponding sequences are not, as has long been assumed, identical. The RNA-DNA differences generate proteins that do not precisely match the genes that encode them.,,, Nearly half of the RDDs uncovered in the new study cannot be explained by the activity of deaminase enzymes, however, indicating that unknown processes must be modifying the RNA sequence, either during or after transcription. ,,, Although all of the individuals analyzed in the study had a large number of RDDs, there was a great deal of variability in the specific RDDs found in each person’s genetic material.”
    http://www.physorg.com/news/20.....ences.html

    As for the gene/protein similarity we do share, well I’m not too impressed with that either!

    Kangaroo genes close to humans
    Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
    http://www.reuters.com/article.....P020081118

  293. I’m sure that both you and Luskin know lots more than Shapiro about genomics and molecular biology and are much more qualified to characterize the difference between chimps and humans.

    Now 22 is what percentage of the total complement of human proteins? would you characterize it as “most”?

    My sources say 20,000 to 25,000 human proteins, so 22 would be a tenth of one percent.

    The next question would be to look at the 22 genes that code for the different proteins and see how many base pairs have changed. How many coding sequences appear to be completely unrelated, even in part.

  294. I’m not sure why you are obsessed with kangaroos. Kangaroos are mammals, and I have been posting ever since the Koonin book came out that there are few protein differences separating mammals.

    Comparative genomics is not much more than a decade old, so there are bound to be surprises. The first big surprise was how few coding genes the were. The second big surprise, — one that keeps on coming — is how closely related everything is at the sequence level.

    When biologists speak of de novo genes, the underlying coding sequences are still ancient. It doesn’t take much to flip a sequence to code for a different protein. then you have to consider that genes can have insertions and deletions and other kinds of mutations in addition to point mutations.

    Long stretches of sequence remain identifiable as related to ancestral genes.

  295. Petrushka:

    I have not hypothesized that we receive something which incorporates pi. A single circle would be enough for that.

    That the Fibonacci sequence is found so often expressed in living things is certainly reason for reflection, but it is wrong to say that it is “encoded” in them.

    That’s why I asked for a message that can be read “as the sequence of 1000 decimal digits of pi”. Of course, it could be the sequence of the first 1000 digits of pi in another base, that would be the same. The important thing is that we receive a message that “codes”, thorugh a process of mathemathical abstraction, for the first n digits of pi.

  296. Hollywood aside, SETI folks are looking for an unmodulated carrier frequency. It is assumed that any encoded information would be lost to noise.

    But that doesn’t affect your hypothetical. Except in the sense that any signal encoded in DNA would be lost to noise over billions of years. Genetic entropy, you know.

    The fact that life in general hasn’t experienced genetic meltdown, even though countless species have gone extinct, indicates that the fitness landscape is not as rugged as ID proponents would allege.

  297. Petrushka:

    Was that an answer to my hypothetical? I must have missed something.

    Or was it the usual “change the subject” tactic?

  298. 300

    Rhampton7,

    I think the point of contention is whether abstraction is (can be) a “physical” association held by the determinant interpreter (in regards to biological information). That is, do chemical bonds dictate the meaning of a gene’s encoding instructions (to produce a protein)? To which I answer yes, but you seem to suggest no.

    If the abstraction (as in the case of DNA) is a physical association held by the determinant interpreter, then how is it that the meaning can be interpreted without that interpreter?

    The meaning in DNA is present whether or not it is being interpreted. Therefore the chemical bonds employed by the interpreter cannot give it its meaning. Moreover, would anyone argue that the interpreter is what arranged the DNA in the first place?

    Going back to your comparison of the photon: A photon is emitted from a star because of specific natural laws. What natural laws arranged the molecules in DNA to represent the proteins that form the simplest living thing?

    Photons reflect off a house and enable you to observe that there is a house. The photons are behaving according to natural laws. That is not the same as schematics for a house which describe the potential for a house, many houses, the house someone hopes to build but hasn’t, or a flawed house that wouldn’t stand.

    Do you see why the schematics are an abstraction and the photons are not?

  299. OK, back to the subject. Seeing the first 100 digits of pi would be equivalent to finding a watch on the beach.

    Now how is pi not changing the subject from evolution, which involves the differential success of individuals within a population? I see no relationship between the digits of pi and the genome. One is a relationship between idealized objects, and one is the real product of evolution.
    One is Platonic and occurs by definition of terms, and one is real and messy and constantly changing.

    As Shapiro points out:

    The one issue that has effectively been settled in a convincing way is the evidence for a process of evolutionary change over the past three billion years. The reason the answer to this question is so solid is that every new technological development in biological investigation—from the earliest days of paleontology through light microscopy and cytogenetics up to our current molecular sequence methodologies—has told the same story: living organisms, past and present, are related to each other, share evolutionary inventions, and have changed dramatically over the history of the Earth.

    Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2358-2362). FT Press. Kindle Edition.

    Evolution is life’s way of dealing with the unpredictable. We have seen that principle most clearly at work in the adaptive immune system, where antibodies have to be synthesized that can recognize unknown invaders. The fact that future adaptive needs are unknowable does not mean that filling those needs has to be a blind process. In immune system natural genetic engineering, and in evolutionary change in general, we have been able to discern regular features of genome restructuring that facilitate the production of novel molecular tools with an enhanced likelihood of real-world utility. A measure of success for the more informational perspective sketched out in this book will be the extent of future research into the cognitive cellular operations that have led to successful evolutionary inventions. We have a great deal to learn in this respect.

    Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2679-2684). FT Press. Kindle Edition.

  300. Colleagues,

    What an interesting discussion indeed.

    Petrushka,

    “One is a relationship between idealized objects, and one is the real product of evolution.”

    The latter is an open question. You assume something that must be rigorously proved. Such a rigorous proof is still missing in what is claimed to be a solid edifice of evolution. You say this over and over again as if the number of repetitions could reinforce the assertion. All we need is evidence that minor (i.e. microevolutionary) adaptational effects can really cause such huge complexity gaps as are observed between different forms of life.

    As regards observation vs interpretation I agree with Scott Andrews. Meaning/Interpretation is bestowed through intelligence agency. Complexity in the form of formal relationships/interfaces within systems composed of various interacting components can only be a result of intelligence at work. No evidence has been available to date to counter this observation. Indeed, machines using the laws of nature do not come about by themselves. Such a scenario is operationally impossible.

  301. Petrushka?

    Back to the subject?

    I had only made an example of a signal whose reception would allow a design inference.

    Do you agree on the design inference? That was the subject.

  302. Petrushka:

    You quote Shapiro:

    The fact that future adaptive needs are unknowable does not mean that filling those needs has to be a blind process. In immune system natural genetic engineering, and in evolutionary change in general, we have been able to discern regular features of genome restructuring that facilitate the production of novel molecular tools with an enhanced likelihood of real-world utility. A measure of success for the more informational perspective sketched out in this book will be the extent of future research into the cognitive cellular operations that have led to successful evolutionary inventions. We have a great deal to learn in this respect.

    Shapiro is saying that we’re not dealing with “random variation”; built-in “natural genetic engineering” programs produce, instead “enhanced” molecular tools. Do you see this theme here?

  303. Why yes, I see the theme. The immune system cranks out truly random variation until one of them works or the organism dies.

    Same wit populations. they manage to hit upon a change that solves an adaptive problem, or the species goes extinct.

    Did you note the part about future needs being unknowable?

  304. Petrushka:

    Why yes, I see the theme. The immune system cranks out truly random variation until one of them works or the organism dies.

    This is NOT what Shapiro is saying.

    When he writes: “production of novel molecular tools with an enhanced likelihood of real-world utility”, this is non-random behavior. You’re still thinking in typical neo-Darwinian terms. He’s moved well beyond that.

    You need to dig deeper.

  305. I have dug deeper. I have the book and I’ve read most of it.

    The response to the environment — producing a higher rate of mutations — is a non-random response.

    Producing genomic mutations rather than base pair mutations enhances the likelihood of finding something adaptive.

    But did you notice the part about not having foresight? the changes are still “random” with respect of adaptive value, just as are the trial balloons cranked out by the immune system.

  306. 308

    Petrushka,

    Producing genomic mutations rather than base pair mutations enhances the likelihood of finding something adaptive.

    Doing anything because it will or might have a beneficial effect requires foresight. The scenario you describe is something taking action to produce a desired effect. Desired, intended, whichever.

  307. 309

    My comment above (#49) was instigated by a materialist visitor who suggested that the ID proponents on this site won’t deal with the evidence “head-on”. Yet I am getting the distinct impression that the materialist visitors here don’t want to talk about the observable physical entailments of recorded information.

    Perhaps one of them will step up and refute the observations with equally observable evidence supporting a materialistic origin … ?

  308. ScottAndrews: “If you remove the assumption of a “search space” from the origin, then yes I agree, because it’s a tautology. It reduces to “All modern day life is where it is.” It is the limitations of future searches and how they relate historically that are relevant.
    I’m sorry, but that doesn’t begin to make sense. All modern life has DNA that’s in the sweet spot. How do we know this? Because all modern life is alive and it’s using its DNA to stay alive. No tautology there. That says nothing about how it got there or where it’s going. It “finds” sweet spots for its offspring by only changing one or two DNA base pairs at a time which means, for an organism with 1,000,000 base pairs, that its offspring’s DNA, which is identical to its parents except for one different base pair is 99.999 % the same as the parents. Thus the new DNA is very very close in the search space and likely to be in another sweet spot.

    I do NOT call ID a “determination of intelligent causes.” ID is a movement that BELIEVES there is an intelligent cause and WISHES it could find some evidence for this, but it has failed in every attempt.

    1: Dembski claimed that all CSI was evidence for design. But evolution produces CSI.

    2: Dembski came up with the Explanatory Filter. But that just “proves” that purely random process and purely lawful process won’t do anything. It isn’t even possible to put a two-step process, like evolution with its random variation and lawful natural selection into the EF.

    3: Dembski claimed that the “No Free Lunch” theorem somehow proves that evolution is impossible. It only proves that some search spaces, such as a random string of letters, can’t be searched efficiently by any known method and we have to use random searches or the equivalent.

    4: Behe claimed that some features of cellular life couldn’t be built by evolution. He forgot scaffolding and co-option.

    NOTICE THAT ALL FOUR OF THOSE DREAMS REQUIRE EVOLUTION TO BE FALSE and then they present themselves as the only possible alternative. I’m hardly the only person to notice this. Stephen Barr of “First Things” wrote about the same thing in “The End of Intelligent Design” on “First Things” – http://www.firstthings.com/ont.....ent-design

    ID is the BELIEF that there is a designer and the WISH that they could find some evidence of His existence. The cream of the ID theorists have been trying for well over a decade now and they haven’t come up with a single bit of evidence for a Designer that stands up to even the simplest scrutiny.

    As far as OOL is concerned, I’ll give you the sum of all ID OOL research: Nil.

  309. DMullenix,

    “ID is the BELIEF that there is a designer and the WISH that they could find some evidence of His existence.”

    Says who?

    ID is a litmus test that reliably identifies intelligent interference in cases where a priori knowledge of such interference is available independently.

    Evolutionism untenably holds on to the hypothesis that microeffects can be extrapolated to the grand scale of life. Today, after 150 years after macroevolution was proposed it still remains a hypothesis. The real trouble is that over those years it has become an ideology.

    Why can’t we see hypothetical abiogenesis type first self-replicators today? Because they have been invented by imaginations of wishful thinking biologists/chemists. If abiogenesis were a plasibility, it would be possible to observe it in nature now on mass.

    To put it plainly, self-assembling nanometre precision machinery without a designer is a nonsense. So the TOE is a complete bankrupt.

  310. dmullenix is sooooo confused:

    I do NOT call ID a “determination of intelligent causes.” ID is a movement that BELIEVES there is an intelligent cause and WISHES it could find some evidence for this, but it has failed in every attempt.

    Positive evidence has not only been found but has been presented. And all you can do is choke on it.

    1: Dembski claimed that all CSI was evidence for design. But evolution produces CSI.

    1- ID is not anti-evolution

    2- No one has ever observed blind and undirected processes producing CSI

    2: Dembski came up with the Explanatory Filter. But that just “proves” that purely random process and purely lawful process won’t do anything. It isn’t even possible to put a two-step process, like evolution with its random variation and lawful natural selection into the EF.

    Your ignorance is not a refutation as the EF considers both chance and necessity operating together. Also natural selection has been shown to be total BS in the grand scheme of evolution.

    3: Dembski claimed that the “No Free Lunch” theorem somehow proves that evolution is impossible. It only proves that some search spaces, such as a random string of letters, can’t be searched efficiently by any known method and we have to use random searches or the equivalent.

    Again ID is not anti-evolution and your position still doesn’t have any positive evidence.

    4: Behe claimed that some features of cellular life couldn’t be built by evolution. He forgot scaffolding and co-option.

    Except that is NOT what Behe said and you STILL don’t have any evidence that scaffolding nor co-option can do what you think.

  311. DM:

    Re: ID is the BELIEF that there is a designer and the WISH that they could find some evidence of His existence. The cream of the ID theorists have been trying for well over a decade now and they haven’t come up with a single bit of evidence for a Designer that stands up to even the simplest scrutiny.

    As far as OOL is concerned, I’ll give you the sum of all ID OOL research: Nil.

    Why do you — and your ilk — insist on willful strawmannish misrepresentations in the teeth of easily accessible corrective evidence to the contrary?

    1 –> First, ID is about inference to design as causal process, on empirically tested, reliable signs of design.

    2 –> You can even see that in the definition accessible through the resources tab at the top of this and every UD page.

    3 –> So, pardon directness, bu that is plainly needed: your misrepresentation is WILLFUL and IRRESPONSIBLE. And, it is thus deceptive, harmful and wrongful. Kindly, cease and desist from propagating agenda-serving deceit, starting with ceasing from willfully distorting the definition of Design Theory.

    4 –> As to OOL, the very first technical ID work, TMLO — 1984 [so there is no excuse for ignorance at this late stage . . . ], constituted not only a critical review but includes reporting of original research and key analysis and proposals on OOL studies.

    5 –> Subsequent to that, a great deal of life- related ID research [and a growing peer-review published corpus, despite all the efforts of the thought police censors in NCSE etc] is directly on or directly relevant to OOL issues and topics.

    6 –> You may wish to look at the DI list here (pay close attention to the work of Abel, Trevors, and co), and the work at the evolutionary informatics lab, here.

    7 –> You also simply assert that evolutionary processes produce CSI without intelligent direction, and appeal to the notion of the combination of chance and necessity being sufficient to — in the case of DNA in the living cell, create a von Neumann, self replicating molecular nanotechnology entity with codes [i.e. language], algorithms and data structures with co-ordinated executing machinery.

    8 –> Kindly identify where this astounding claim was demonstrated empirically, i.e. per observations; peer-reviewed article preferred. Actually, it is known that your side cannot do that, so kindly, withdraw this unwarranted assertion and apologise.

    [ . . . ]

  312. 9 –> The more modest claim would be that 500 – 1,000+ bits worth of functionally specific DNA, in a living population, has been observed to come about de novo from chance variations and differential reproductive success leading to descent with modifications. This, too, your side has not demonstrated and so the implication or claim should be likewise withdrawn.

    10 –> the yet more modest claim, would be that by selection for performance, on chance variations, you have been able to demonstrate the origin of FSCI. For this, Genetic Algorithms and the like have often been trotted out, sometimes rather triumphalistically.

    11 –> And, yet, closer inspection invariably reveals that the key input is intelligent design. As in Dr Schneider et al, this means YOU. The algoreit6hms are intelligently designed to produce a constricted outcome, and often that outcome is well within the relevant limit. This too has not been shown to any reasonable level of warrant.

    12 –> Instead, you and your ilk would be well advised to examine the issue that when we have high contingency plus complexity, with a requirement of fairly specific organisation to function in a system, the overwhelmingly vast majority of physically possible configs will predictably be non-functional.

    13 –> So, we naturally find an empirically easily seen pattern of islands of functional configs in a vast space of physically possible but non-functional configs. For, random disturbances will easily make text indecipherable, will make programs corrupt, will reduce pictures to snow, and will reduce machinery to junk. All of that is commonplace.

    14 –> Try the Humpty Dumpty exercise sometime: prick a living cell and decant its contents and wall into a small drop of fluid medium, where Brownian motion will move its components about at random.

    15 –> Ask yourself: is it reasonable to ever expect the cell to reassemble itself by forces of chance and necessity? Why or why not? What is this telling you about the significance of the islands of function and search challenge issues? [You can then explore the thought exercise here in my always linked, App 1]

    16 –> Then, to cap off, consider the discussion here on the significance of the log-reduced form of the Chi metric for CSI, and what it says about the validity of the explanatory filter considered on a per aspect basis (which can deal with the issue of combinations of chance and necessity, especially as we can see that the signature of necessity is low contingency, i.e high contingency traces to design and/or chance):

    Chi_500 = I*S – 500, bits beyond the solar system threshold.

    GEM of TKI

  313. ID is a litmus test that reliably identifies intelligent interference in cases where a priori knowledge of such interference is available independently.

    That’s a confusing statement. The term a priori implies a statement that is true by definition. If that is what you intend, it means your are defining the interference to be true by definition, and that is circular.

    That is inconsistent with independent evidence.

    Where we use the design inference in criminal forensics or in archaeology, we do have independent observations of human activity, human capabilities, human motives.

  314. 316

    Dmullenix,

    To say that everything searches the nearest space does depend upon a condition which is tautological – that everything is where it is. I’m pointing that out to you and you are in turn pointing it out back to me. I said it first.

    You state,

    It “finds” sweet spots for its offspring by only changing one or two DNA base pairs at a time which means, for an organism with 1,000,000 base pairs, that its offspring’s DNA, which is identical to its parents except for one different base pair is 99.999 % the same as the parents.

    apparently oblivious to the fact that it does not explain how it came to be in the “sweet spot” from which it is searching and where the heck 1,000,000 base pairs came from. I can climb Mount Everest if you place me six inches from the peak. “How did you reach the peak,” they will ask. “It’s easy, I stuck my arm out.” (And no, I am not using Mount Everest to imply that there is a single, specific target.)

    Although ID examines the finished product and not the process, I have provided you with an abundance of peer-reviewed research considering the specifics of how an intelligent designer might have assembled living things. You said there was no such evidence, and I have given it to you. Why are you ignoring it? You already know where to find it, but here’s a link to some of the research papers.

  315. Although ID examines the finished product and not the process, I have provided you with an abundance of peer-reviewed research considering the specifics of how an intelligent designer might have assembled living things.

    Odd, your link goes to publications by a person searching for paths to self-assembly.

  316. 318

    Petrushka,

    They are searching for paths to self-assembly by trying to assemble stuff. When they succeed they demonstrate that a given component can be designed. Whether it could self-assemble is always less certain.

    How is it possible to demonstrate in a controlled experiment what might assemble by chance without even better demonstrating what can be accomplished by design?

    All your bases are belong to us.

  317. but overall, meaningful states are known to be very rare AND isolated in the solution spaces.

    That seems to be something not agreed upon. the concept of landscape is about 70 years old and was invented by mainstream biologists.

    I would just point out two rather important things:

    1. No two individuals are genetically identical, other than identical twins. And yet countless individuals exist with countless variations in their genomes that are not fatal.

    2.The kinds of genetic changes that separate individuals from each other — and indeed species from each other — are mostly non-coding regulatory sequences. Far more variation is allowable in non-coding genes.

    For example, on another thread it was pointed out by an ID advocate that there are 22 proteins different in humans and chimpanzees. That’s a one tenth of one percent difference in coding genes. That’s about one new protein every quarter million years.

    The other differences will be found in regulatory networks. It’s much easier to survive differences in bone length or muscle mass than survive a defective protein coding gene.

    The really heavy lifting of inventing proteins was mostly done billions of years ago by bacteria. Now that we can sequence whole genomes, it has been noted that even newer proteins have sequence similarities that can be traced through lineages.

  318. How is it possible to demonstrate in a controlled experiment what might assemble by chance without even better demonstrating what can be accomplished by design?

    Science studies complex phenomena by trying to isolate and quantify the elements.

    A prototype might be Galileo trying to quantify the acceleration of gravity by rolling balls down an inclined plane. Or Newton extrapolating the behavior of cannonballs to the behavior of planets.

    I find it not surprising that n ID supporter would be unfamiliar with the most elementary concepts in scientific investigation. Ideas that are supposed to be learned while doing high school science projects.

    That seems to be why nearly every thread on this forum interprets mainstream science findings as supportive of ID. After all, experiments are designed.

  319. 321

    Petrushka,

    You’re missing the point by a mile and a half. I’m not arguing against the extrapolation or the interpretation. I’m supporting it. I’m taking the side of this abiogenesis research. I’m also using it to my advantage.

    Or Newton extrapolating the behavior of cannonballs to the behavior of planets.

    This is good, but it requires that Newton first quantifies the behavior of cannonballs. You can’t accept the behavior of the planets while denying the behavior of the cannonballs, can you?

    Likewise, how you can extrapolate what might happen “in the wild” from a controlled OOL experiment while simultaneously denying the literal results of that controlled experiment?

    If an experiment that produces fatty vesicles suggests that such events might occur by chance, then it conclusively demonstrates that they can be produced deliberately by repeating the experiment. If I am wrong then please tell me why I am wrong.

    I find it not surprising that n ID supporter would be unfamiliar with the most elementary concepts in scientific investigation. Ideas that are supposed to be learned while doing high school science projects.

    Actually I think it’s your reading comprehension that has failed us :) That’s why I’ve explained in more detail so that you can respond to my actual statement without making an irrelevant ad hominem accusation.

  320. If an experiment that produces fatty vesicles suggests that such events might occur by chance, then it conclusively demonstrates that they can be produced deliberately by repeating the experiment. If I am wrong then please tell me why I am wrong.

    OK, you are saying that anything (within reasonable bounds of time and energy expenditure) that can be produced without intervention can also be produced by humans or by an agent that has equivalent resources and capabilities.

    I see nothing wrong with that. But that is engineering. Copying.

    Douglas Axe has pointed out that it will be difficult to impossible to invent (rather than copy) protein sequences, because there is no short cut to knowing what kind of fold a sequence will produce.

    In engineering terms, this is equivalent to making a product out of materials having unknowable properties.

    When making sequence libraries, sequences are mass produces and selected for those that result in folds having certain characteristics. In at least one experiment, a small subset of these proved functional in a bacterium.

    But you have to realize that this required two levels of selection. There is no way to know in advance, from first principles, what kind of fold will be produced by an arbitrary sequence, or whether a fold of a certain class will in fact be functional.

    In other words, there is no foresight.

  321. If we’re seeking an undirected explanation for something that was directed, or vice versa, then we’re looking in the wrong place.

    Science can only look for regularities in nature. As others here have pointed out, one can only see intervention against a background of consistency.

    We know that mutations and genomic changes occur and we know that selection occurs. We don’t have any other candidates for the cause of change in the genomes of populations.

    Simply asserting that the known explanations are inadequate is not science. Science already knows that existing explanations are incomplete. That’s why there are still scientists, and why they are still doing research.

    If you know of another way, perhaps a direct way of observing intervention, perhaps you should share it. Otherwise it is the business of science to continue building on regularity.

  322. 324

    Petrushka,

    That’s very interesting.

    Science can only look for regularities in nature. As others here have pointed out, one can only see intervention against a background of consistency.

    What you see as objective I see as arbitrary. How do you perceive living cells (and people, and space shuttles, etc., etc.) as part of a background of consistency? With what are they consistent, and why?

  323. 325

    Petrushka,

    How on earth does this relate to what I said?

    OK, you are saying that anything (within reasonable bounds of time and energy expenditure) that can be produced without intervention can also be produced by humans or by an agent that has equivalent resources and capabilities.

    I see nothing wrong with that. But that is engineering. Copying.

    I’m saying that if the results of a controlled experiment can be extrapolated to suggest what might happen naturally, how much more do they demonstrate what can be done deliberately? It’s simple. Focus on that, and find the flaw in that logic.

    Instead, you’re making a pretzel out of it by saying that the controlled experiment is a copy of what has been extrapolated from the controlled experiment.

    Forget that. Explain to me how a controlled, repeatable experiment that results in the formation of fatty vesicles does not demonstrate that one can deliberately create fatty vesicles. Please do not evade my argument. Address it head on or not at all.

  324. 326

    Elizabeth Liddle first posted the link to this research. Perhaps she would like to weigh in.

    Consider this quote from the introduction of this paper.

    A simple synthetic cell, or protocell, must be able to grow, divide, and maintain heritable information. We are attempting to construct such a system through the integration of two complementary components: (1) a spatially localized replicating compartment or vesicle and (2) a spontaneously replicating genetic polymer.

    I understand that their aim is to support their hypothesis that this might relate to some form of undirected abiogenesis. Let me emphasize that I am not challenging this in any way.

    But does their research not also demonstrate how to produce the same result deliberately? In fact, which does it support better – that similar results could be obtained by repeating the experiment, or that similar results may have occurred outside such an experiment? I repeat that I am not challenging their conclusion, only adding my own.

    The unreasonable claim has been made repeatedly that ID does not offer any detailed explanation of how one might construct a living thing. It is unreasonable because that is not the subject of ID.

    That claim is nonetheless answered and that answer is tied to to validity of OOL research. Such research demonstrates what intelligent agents can deliberately accomplish. Those results cannot be invalidated without also invalidating their implications for abiogenesis. So take your pick. Heads we win, tails you lose.

  325. But does their research not also demonstrate how to produce the same result deliberately? In fact, which does it support better – that similar results could be obtained by repeating the experiment, or that similar results may have occurred outside such an experiment?

    The goal of science is to figure out how things work.

    Large problems have to be broken up into manageable chunks.

    For example, to study geology, someone has to study the properties of various rocks and minerals.

    There’s really no shortcut to understanding large, complex systems. You have to understand the pieces first, then study the interactions. Sometimes these can be done concurrently.

    The science of geology can enable the construction of safe skyscrapers, but that doesn’t mean that geological formations were designed by an intervening agent.

  326. 328

    Petrushka,

    You’re evading the point, whether intentionally I can’t say.
    You’re saying that they are dividing up the problem of abiogenesis into manageable chunks, because ” there’s really no shortcut to understanding large, complex systems.”

    Do you understand that I am not disputing this in any way whatsoever? Really, do you? Please read this carefully: I am agreeing with you. Yes, I know that this is how it works.

    However, at the same time, they are also dividing up the problem of how intelligent designers might produce life into the very same manageable chunks.

    I am not claiming that their data does not support their hypothesis. I am claiming that because their results are deliberately produced, their data even better supports the claim that such results can be deliberately produced.

    I can do something over and over, while carefully documenting the steps, to demonstrate that it could happen accidentally. And it’s not even my point to dispute that. But in doing so I’ve demonstrated even more conclusively that I can do it on purpose by following specific steps.

    Please address my logic directly rather than making irrelevant, condescending statements like “that’s how science works.”

  327. Petrushka,

    “The science of geology can enable the construction of safe skyscrapers, but that doesn’t mean that geological formations were designed by an intervening agent.”

    You are confusing the issue. Who says the opposite? ID does not say that. ID specifies when you can reliably infer design. Geological strata would fail the test because they lack specificity.

  328. 330

    But evolution produces CSI.

    “Evolution” does not have a mechanism to create information in the first place.

    You can’t simply assume what must be demonstrated.

  329. Once you have replication with heritable variation in reproductive success then you have a mechanism in place to create information.

    And that mechanism is what we call “evolution”.

  330. Kindly go look up the ISO’s OSI layercake comm system model — the same that is foundational to modern digital comms and the Internet.

    Observe that the physical layer is only the first of seven.

    Think about the implications of that.

  331. 333

    So if we start immediately killing every right-handed child (or perhaps just stop them from reproducing,) left-handedness will become more prevalent. Where does the new information come from, and when does the evolution kick in?

  332. Don’t forget that the AA coupler on the tRNA is standard.

  333. In that case such an entity is a 1-point island of function. If it is sufficiently complex, just try to replicate it by chance driven trial and error . . .

  334. Are you aware of how hard it is to create and sustain a carrier for long enough to count?

  335. 337

    Dr Liddle, I do believe the rise of recorded information has yet to be demonstrated. I think we are clear about that, are we not?

  336. Onlookers:

    I have skimmed throughthe above. It is astonishingly plain that the Darwinist objectors above are playing slectively hyperskeptical games.

    The functional units of a microprocessor are physical entities, and interact through electrical signals and states, but that in no way contradicts that the MPU is a programmed, digital coded information processing system.

    The physical layer is the substrate on which the info system sits. An adequate and mapped hardware subsystem is a necessary condition for the info system, but it is not a sufficient one. Indeed, things like Linux, etc can be implemented on vastly different physical systems.

    And, to manipulate that physical system, we use abstract symbols and modules at various levels, a famous example being the ISO OSI layercake comms system model used for digital telecommunications.

    Through this model, we have the ability for vastly diverse physical machines to interact on common protocols and processes for interaction.

    And, the likes of both Dr BOT and Dr REC know this, full well know this.

    When I therefore see a stunt like they have tried to pull above, it tells me they are simply playing the selectively hyperskeptical troll.

    Similarly, when we turn to the molecular biology of the cell, we find that we again deal with physical layers that make use of he materials, properties and forces of nature, but build up astonishingly sophisticated information systems on that substrate. It is we who have assigned the textual glyphs A, G, C, T, U to certain monomers used in the biochemical string data structures, but that does not mean that he four state digital system is reducible to the physical properties of the molecular species that happen to start with those letters. Nope, these molecules are strung to encode information, and that is used to regulate and carry out he creation of proteins for the cell’s use.

    So, as at now, the two Drs have reduced their credibility to zero.

    If they mean to hold out what they have said above as objections, these are objections they MUST know better than.

    So, if they are serious, they are being selectively hyperskeptical and thus self referentially absurd. They would never object to the information coded in a DVD, that it is based on physical properties of shiny films embedded in plastic. Yup, the materials, properties and forces of nature are being used to implement an intelligently designed information system.

    If they know these things and are instead trying to show up ID participants as ignorant, stupid, insane or wicked, they are guilty of a worse intellectual dereliction of duty. The duty of reasonableness and respect in discussion.

    In either case, they only succeeded in trying to derail a discussion that points to something that they patently would not wish to take seriously: that we are dealing with sophisticated information systems that are credibly beyond the reach of chance and necessity on the gamut of our cosmos, and for which we have only one known and indeed routine cause — intelligence.

    Which is precisely the design inference on digitally coded, functionally specific complex information.

    GEM of TKI

  337. 339

    Yes KF…and I am still waiting for a response to 49.

  338. Yes indeed, Upright BiPed. There is, as yet, no complete and supported theory of OOL.

    But what is also clear is that once you have a self-replicating system that replicates with heritable variance in reproductive success in a given environment, further information is constantly generated, and that information consist of information as to how best to thrive in that environment.

  339. The new information comes from the environment, and the population now has encoded within it the information that left-handedness is advantageous.

    This information is encoded in the form of increased prevalence in the population of genetic sequences that tend to promote left-handedness.

    Evolution “kicks in” as soon as you start systematically reducing the chances of reproduction of humans that demonstrate a particular heritable trait, in this case, right-handedness.

    Just as it would if you did the same with, say, parrots.

  340. 342

    But what is also clear is that once you have a self-replicating system that replicates with heritable variance in reproductive success…

    Dr Liddle, I am concerned with the evidence as we actually find it.

    Life as we know it does not ‘self-replicate with inheritable variance’ without utilizing a system of symbolic representations, as well as the machinery to process those representations. That machinery includes a coordinated system of protocols, leading to specific effects.

    You benignly admiting there is no theory for the rise of information (OOL), while simultaneously holding that you KNOW it wasn’t designed, is an abrogation of empirical responsibilities. That tactic is no more now than it has ever been in the past – it is a way to ignore the only cause actually demonstrated to be able to produce the effect in question.

    It is a compromise of empiricism for no reason other than the worldview of the the investigator. In other words, its bad science.

  341. Well, I wouldn’t call them “symbolic”, UBP. There are a set of molecules produce by living things that have a one-to-one-or-more mapping between RNA and amino acids.

    It is very easy to see how such a one-to-more-than-one mapping would be selected, because it is perfectly possible to have heritable variance in reproductive success without such a mapping, and the beginnings of such a mapping would tend to be advantageous.

    And I didn’t say there was no theory – I said there was no complete, supported theory. There are number of theories, some looking promising, and some giving rise to hypotheses that are supported by data.

  342. I’m not sure I understand your question. Engineering, whether of space shuttles or pest resistant crops, requires that things work in consistent ways, that petunias do not capriciously morph into teapots, and such.

    Discerning the regularities and consistencies is what science does.

    I would like to say laws of nature, but that term is frequently misunderstood. Laws of nature are in almost all cases, formulas that describe observed regularities.

  343. I agree that ID doesn’t need to “identify the designer”. But to have anything more than an argument from gaps, it needs to have some mechanisms.

    You need more than a designer to produce an artefact – you also need a craftman or artisan.

    Where is the evidence of of the artisan? Where are the tool marks? Where are the tools? What are the mechanisms by which the designs are implemented? What moves the molecules into the designed position, if not physics and chemistry? Where is the “gene gun”?

  344. How the heck does “I see nothing wrong with that” not answer your question.

    I merely think it’s a pointless question. The fact that something can be engineered does not mean it does not occur naturally.

    Diamond and other precious stones can be engineered.

    If living things can be engineered, that has no relevance to the issue of whether existing living things were engineered.

    It so happens, that I don’t think novel living things that are not copies can be engineered from scratch, except by using evolution. I gave my reasons.

  345. It is not a law of chemistry – other mappings are chemically possible.

    But a one-to-one-or-mapping is clearly going to transmit heritable information more faithfully than a more-than-one to more-than-one mapping, so a set of tRNA molecules that render the mapping more unambiguous is going to be selectable.

  346. ambiguous=ambiguously, oops.

  347. 349

    Of course you don’t like calling it a symbolic representation, Dr Liddle, but we’ve been though all of that before. The key is what explanations the physical evidence actually demonstrates.

    I am wondering here though – are you suggesting that cytosine-thymine-adenine inherently means ‘bind leucine to a nearby polypeptide?

    And if it is not an inherent physical property (which it is most certainly not) then exactly what material process are you suggesting is capable of establishing an immaterial relationship between two discrete objects?

  348. I don’t like calling it a “symbolic” system, UBP, because it isn’t one.

    And I’ve just explained (not for the first time) what the “material process” is that would result in organisms producine one of the many possible subsets of all possible tRNA molecules that provide a one-to-one-or-more mapping between codons and amino, namely natural selection.

    Organisms (or proto-organisms, if you like) that produced ambiguous mappings, i.e. had RNA sequences that coded for more than one tRNA molecule for each codon would produce less consistent phenotypes than those where those that coded for only one per codon.

    And once you have a phenotype that includes a useful protein, genotypes that produce that protein consistently are going to be more successful than those that sometimes produce a different protein.

  349. 351

    Elizabeth,

    It is very easy to see how such a one-to-more-than-one mapping would be selected, because it is perfectly possible to have heritable variance in reproductive success without such a mapping, and the beginnings of such a mapping would tend to be advantageous.

    What on earth are the beginnings of a mapping? What begins to map something, or does something just begin to map something? Hey, look! There’s some proteins! They must be having a hard time making more of themselves exactly the same without some sort of mapping to copy from, so I’ll help out. And while I’m at it, I’ll map a transcription process too. Gee, thanks, that’s advantageous! I’m making more of myself than ever!

    Sorry, but even without my little drama the idea is divorced from science and reality. And that’s the mean kind where you take your friends with you and the ice cube tray while you’re at it.

  350. 352

    I don’t like calling it a “symbolic” system, UBP, because it isn’t one

    That is very much an end conclusion Dr Liddle. I find it very interesting that in one breath you say there is no supported theory of OOL as of yet, then just one breath away you begin asserting conclusions on that very topic.

    In post #49 I described the physical entailments of recorded information. These are logically cohrerent and demonstrable. Yet you say that those entailments are wrong – you assert that despite the logic and observations, the the system “isn’t” symbolic.

    Can you please demonstrate this conclusion with observable evidence?

  351. 353

    Elizabeth,

    The new information comes from the environment, and the population now has encoded within it the information that left-handedness is advantageous.

    Maybe I need to stop reading this stuff, because I’m up to my waist in crazy. There were always left-handed people before we killed all the right-handed new people. Where’s the new information? How is being left-handed suddenly evolution?

  352. 354

    Petrushka,

    When you say, “one can only see intervention against a background of consistency,” I point out that you have an odd, arbitrary notion of consistency. Rocks, water, gases, crystals, some chemicals, self-replicating creatures made of self-replicating molecular machines carrying abstract blueprints of themselves, more rocks, more water.

    Hmmm, nothing stands out against that background of consistency.

  353. 355

    Petrushka,

    Let me repeat, how does that relate to what I said? I said

    I’m not arguing against the extrapolation or the interpretation. I’m supporting it. I’m taking the side of this abiogenesis research.

    Who is saying that something cannot occur naturally? Is there a way to make my font larger? I. Am. Not. Disputing. The. Abiogenesis. Research. I am embracing it with both arms, like in a Journey song.

    Then I am pointing out, for the umpteenth time, that to the extent it demonstrates what might happen outside of the experiment, it demonstrates what can be done deliberately with far greater certainty.

    Allow me to repeat what I said right after ‘forget everything else’ and right before ‘please address this head on.’

    Explain to me how a controlled, repeatable experiment that results in the formation of fatty vesicles does not demonstrate that one can deliberately create fatty vesicles.

    Nowhere in that sentence am I claiming that such fatty vesicles could not form naturally as proposed within the paper.

    And then perhaps we can retire the claim that there is no peer-reviewed research investigating how one might intentionally construct life, even though it has nothing to do with ID anyway.

  354. And then perhaps we can retire the claim that there is no peer-reviewed research investigating how one might intentionally construct life, even though it has nothing to do with ID anyway.

    I’m afraid a reasonable person, reading your reference to an intelligent designer, might have concluded that your citations were meant to be in support of intelligent design.

    But having gone round the Maypole several times, I accept your assurance that Szostak’s research has nothing to do with intelligent design.

    May I ask why your question is relevant to anything?

  355. 357

    Petrushka,

    Szostak suggests that the formation of fatty vesicles is a possible step toward the formation of life. He then details the steps taken to create such vesicles in the laboratory.

    Will you tell me that the paper only suggests how they might occur naturally but does not explain how one might create them deliberately? Again, that they might form outside the experiment is unknown, although I am explicitly not stating that is is impossible. I am not doubting the research. But it demonstrates even more conclusively that this possible component of early life can be deliberately engineered.

    Are you saying that Szostak did not in fact perform the experiments he said he did, or did not produce the results he published? I believe him.

  356. Rocks, water, gases, crystals, some chemicals, self-replicating creatures made of self-replicating molecular machines carrying abstract blueprints of themselves, more rocks, more water.

    Hmmm, nothing stands out against that background of consistency.

    Things are concrete. Descriptions are abstract. Things are neither consistent nor inconsistent. Processes can be consistent or inconsistent.

    So point out the violation of physics or chemistry required by Shapiro’s description of the processes in evolution.

    Processing information does not violate any known physical or chemical regularity. The immune system violates no laws of nature. Why would any adaptive system violate laws of nature?

  357. Why do you keep asking me if I disagree with something I’ve agreed with half a dozen times. I’m asking for the other shoe to drop. Why is this important?

  358. Petrushka,

    I am not a specialist in bioinformatics but I can say from an engineer’s point of view that even though a motorbike and a bike look almost the same, there is a huge difference at to how they work.

    IOW, I think that the differences in genomes must be measured objectively instead of just showing %-age differences. If I am not mistaken, I have read about certain genome metrics showing that mice and humans are more closely related to each other than two specific species of fruit flies.

    On another point, the number of various proteins in a bacteria and that in a human being are only one order of magnitude different. But what a difference it brings about!

    To be objective you have to have different metrics. This is a basic engineering (and common sense) consideration of relative importance of various constituents of a complex system.

    Bacteria remain bacteria in long lasting experiments in a test tube, which does not give a lot of confidence to common descent.

  359. Onlookers:

    On p 1 at 3+ above, DM said:

    But evolution produces CSI

    T%his is a typical example of 6the rhetoric of confident assertion driven by a priori evolutionary materialism. Translated: we “know” it all happened by evo, so macro-evo mechanisms [presumably Darwinist ones] MUST be capable of producing CSI. Therefore, we see the triumphalistic conclusion and declaration: “But evolution produces CSI.”

    Only problem: the only empirically and analytically well warranted causal source for CSI is design. And, that is driven by the challenge of getting TO islands of function in beyond astronomical config spaces, as has been explained in details over and over and over again, but willfully ignored.

    But, we don’t know that life forms exist in islands of funciton!

    Oh, yes we do, starting with the reality of deeply isolated protein fold domains. Multiply by the other reality that is so often denied: the genetic code for making proteins is exactly that, a CODE, working in the context of an algorithm. One further constrained by the need to create functionally folding proteins that do just what the cell needs, where it needs it, when it needs it. All, using machinery that comes form an earlier application of the same irreducibly complex system.

    Constraints such as above, eliminate the vast majority of the relevant config spaces of possible components and configurations of said components. Whether in pre life warm ponds etc, or in living forms that somehow must generate dozens of novel body plans.

    But, you see the realities of the information and organisation challenges and the resulting combinatorial explosion of possibilities, are given scant attention. For, we “know” that evolution has the magical capacity to surmount any and all barriers, as that is the only explanation allowed on the table by the a priori materialist magisterium in the holy lab coat.

    It happens that way because it “MUST” have happened that way. So, we “know” it happened that way.

    And if you object or question, that’s because you want to smuggle in — shudder — God into the hallowed halls of science.

    In short, question-begging on the grand scale.

    Oops.

    Time to de-program, and then actually think seriously about the information and organisation challenges we now know. And nope, these are not primarily biological challenges, they are challenges in embedded digital controller based system design.

    And any competent engineer will tell you trial and error just will not work for a complex, functionally specific, deeply integrated system.

    Which is Gil Dodgen’s main point that keeps on getting drowned out by the waves of distractive tangential rhetoric.

    GEM of TKI

  360. Eugene S. “ID is a litmus test that reliably identifies intelligent interference in cases where a priori knowledge of such interference is available independently.
    Let me rephrase that for you: “In every case where we know men have designed something, our empirically tested and reliable signs reliably indicate intelligent design.” No surprise there. The problem is that your tests and signs can’t distinguish between something “designed” by evolution and something designed by man. (Are you listening KF?)

    Where would you look for a self-replicator today and what would it look like? We’re talking about molecules here, something way too small to show up on any optical microscope. And maybe not even individual molecules. Some theories think the first self replicators were chains of chemical reactions that wound up producing the original molecule. You also have Darwin’s problem – if anything did get produced today, it would be eaten by some already existing advanced form of life.

    You believe that a “self-assembling nanometre precision machinery without a designer is a nonsense”. I believe those are called molecules.

    KF: ID has no “empirically tested, reliable signs of design”. I’ve gone through the main ID arguments and their fatal flaws in 3.3.1.2.6 above. If you have objections to anything I say there, please tell us all. But merely restating that ID is empirically tested and reliable cuts no ice. I will stick with I said in 3.3.1.2.6

    Where are the experiments in Thaxton? There are none. That’s a great DI list. Where is the OOL research of Abel and Trevors? They did none. Do you realize that list includes outright cranks like John A. Davison? He’s so loopy he’s been kicked off of every blog in the world including this one!

    “You also simply assert that evolutionary processes produce CSI without intelligent direction…”

    As I showed on another thread a month or two ago, Dembski himself shows the math that shows how changing any bit in a string produces new information that was not in the original string. “ABCDEFF” is different from “ABCDEFG” If the password is “ABCDEFF”, “ABCDEFG” will not be accepted because the two strings are different and contain different information. If you change one to the other, you have created new information.

    Meanwhile, you are still hung up on DNA and von Neumann replicators, neither of which has anything to do with the OOL.

    In 11 you are hung up on intelligently designed algorithms that are indeed designed – to mimic naturally occurring phenomena.

    ScottAndrews: The very first self replicator found a very simple sweet spot through sheer chance. The other information was added one or two bits at a time (or by duplicating already existing base pairs), which is how evolution works.

  361. ES:

    It is plain that P and ilk refuse to look at the significance of the simplified expression, the log reduced form of the Dembski metric, e.g. here:

    Chi_500 = I*S – 500, bits beyond the solar system threshold.

    A solar system scale blind search tracing to chance and necessity — it is a strawman that we ignore combinations — is looking at the equivalent of blindly pulling a one straw sized sample from a cubical haystack a light month across. Even if a solar system lurks therein, sampling theory tells us that overwhelmingly, such a sample will pull a typical result: straw.

    The only credible search for functionally specific configs in complex contexts, is intelligence. And, such designs can build in adaptability so that hill-climbing to niches within islands of function is not a credible counter argument.

    You need to give us a basis for seeing blind arrival at islands of function as less than a statistical miracle.

    GEM of TKI

  362. If I am not mistaken, I have read about certain genome metrics showing that mice and humans are more closely related to each other than two specific species of fruit flies.

    Mice an humans are mammals, and mammals are separated from each other mostly by changes in regulatory networks. Check out the Shapiro book on this.

    I don’t know the specifics on the fly case, but genetic differences are a function of time since divergence. Flies are fast breeding and have had more time to accumulate differences. Mammals are relatively recent.

  363. 3.3.1.2.23 dmullenix

    Dmullenix,

    Wonderful! The whole issue at the heart of ID is being able to abductively assert that the *best explanation available* is intelligent interference, not chance/necessity alone or any combination thereof. So ID *is* capable of distinguishing between natural cause and intelligent inferference. That is the whole point you disregard. So I cannot accept your point about molecules as a plausible cause of nanometre precision machinery in the cell. Maths shows it is operationally impossible.

    Could you present such a chemical reaction or a chain of reactions that effectively haphazardly can lead *now* to a self-assembling complex system? The answer is, no. The reason for this is strikingly simple: life is way too complex for that. You wish not to notice that. Well, it is your choice.

    I have long been fascinated by evolutionists’ ability to talk about non-existing evidence. If something is missing then, quite simply, it must have been experminated by predators. I won’t comment on this because it is below scientific standard.

    My argument was that for something to come about by chance (as is assumed about the first replicators), similar processes *must have been going on in huge numbers*. And it is not unreasonalble to assume that something like that must be going on massively now. Otherwise one is compelled to explain in pathetic detail why the conditions were so special then and not now. The question remains: why can we not observe something like that today? No clear answer.

  364. OOPSIE, did a recheck, missed a power of 10 in earlier calc. 3+ light days, makes no practical difference:

    Say, a typical straw weighs about a gram. 10^48 grams, is 10^42 metric tonnes. And, if a straw bale is roughly as dense as water, a 10^42 tonne cube would be as many cubic metres, or 10^14 m across. A light year is 9.46*10^15 m. The ratio is about 100:1, i.e. the cube is about 3 1/2 light days across. [BTW, this corrects an earlier estimate, pardon.] Even if a solar system were hiding in the stack — Pluto’s maximum orbital distance is 7.4 *10^12 m, ~ 1/10 the distance across and the sun — largest object in the solar system — is 1.39*10^9 m across, a one straw sized blind sample, by overwhelming likelihood, would pick up straw, not anything else. Small but significant blind samples of a population strongly tend to capture what is typical, not what is atypical. Narrow, unrepresentative zones of interest will tend to be missed by such a sample.

  365. 367

    Dmullenix,

    The very first self replicator found a very simple sweet spot through sheer chance.

    Need I point out the absurdity of this statement? A very simple self-replicator that found itself through chance? The sweet chariot of science must swing pretty low to touch that one.

    The other information was added one or two bits at a time (or by duplicating already existing base pairs), which is how evolution works.

    As has been stated ad nauseum, there is no evidence of selectable pathways consisting of one or two bits at a time or duplication that lead to anything significant. On top of that, if there were such selectable pathways, there is no evidence that they would be or were selected.

    We’re talking about new species and functions, not about how evolution works.

  366. 368

    Attributing differences to regulatory systems doesn’t change the picture much.
    Bats have longer forelimbs than rodents because their growths are regulated differently. But that doesn’t explain bats. There are countless other changes to their physiology required for those regulatory differences to be beneficial. Imagine a mouse with unusually long forelimbs. It wouldn’t live long.
    Beyond the physical changes there are the behavioral changes. Everyone likes to talk about the physical changes, but no one even wants to touch what sort of mutation, duplication, or regulation makes a rat with long forelimbs attempt flight rather than flopping around on the ground. To get an idea what that looks like, try gently tossing a rat.

    Shifting the explanation to regulatory networks changes nothing. The explanation still needs an explanation and the rest of the pieces have to fit together.

  367. 369

    Petrushka,

    If you agree that Szostak did indeed perform the experiments he said he did, then which does it demonstrate better:
    1) That his experiment could be repeated under the same conditions
    2) That something similar could happen “in the wild” apart from such an experiment.

    I’m not asking you to choose between one and the other. I’m asking you to decide which is demonstrated more conclusively by his experiment.

  368. That is very much an end conclusion Dr Liddle. I find it very interesting that in one breath you say there is no supported theory of OOL as of yet, then just one breath away you begin asserting conclusions on that very topic.

    I said there was no complete and supported theory of OOL. There are a number of theories, and parts of them are supported by data.

    And what I am saying above is that code for sets of tRNA molecules that provided a one-to-more than one mapping of codons to amino acids would tend to have selective advantage over sets that provided more-than-one to more-than-one mappings, so that is a perfectly viable Darwinian account of how such a mapping could have arisen.

    In post #49 I described the physical entailments of recorded information. These are logically cohrerent and demonstrable. Yet you say that those entailments are wrong – you assert that despite the logic and observations, the the system “isn’t” symbolic.

    Well, it isn’t. It’s simply a physical system. A set of RNA molecules (tRNA) are coded DNA then RNA (probably originally just RNA). That set includes just one molecule for each triplet, although more than one for each amino acid (there being more possible triplets than amino acids). So we have a set of tRNA molecules, with different codon binding site at one end of each one, and an amino acid binding site at the other, right?

    So we have an arbitrary mapping (arbitrary because presumably some other set of tRNA molecules could have done as well) between codons and amino acids. I don’t call this “symbolic” because the actual physical instantiation of the alleged “symbol” is crucial. The word DOG can be rendered in any material and still symbolise the animal we call a dog, which can then be expressed aloud or silently, in sign language However, a codon can only be rendered in nucleotides, and can only be translated into an amino acid by a specific physical molecule.

    But I do agree that the mapping is probably “arbitrary”. Not mysterious, however. Natural selection will favour non-ambigious mappings, and variants that code for sets of tRNA molecules that give ambiguous mappings will tend to reproduce less reliably.

    Can you please demonstrate this conclusion with observable evidence?

    Well, I could do a simulation I guess. I’ll set up a sim where I start with no mapping and let one emerge via natural selection of mappings that tend to be less ambiguous, and thus more likely to produce a useful “protein”. Would that do?

  369. What on earth are the beginnings of a mapping? What begins to map something, or does something just begin to map something? Hey, look! There’s some proteins! They must be having a hard time making more of themselves exactly the same without some sort of mapping to copy from, so I’ll help out. And while I’m at it, I’ll map a transcription process too. Gee, thanks, that’s advantageous! I’m making more of myself than ever!

    Well, obviously not :)

    “Mapping” here is metaphorical – what we are talking about is a set of tRNA molecules that have codon binding sites at one end (one for each of the set) and an amino acid binding site at the other. That means that if a string of RNA (mRNA) has a sequence of codons, each codon will tend to become occupied by the tRNA molecule that uniquely fits it, forming an array of tRNA molecules each of which then binds to its own amino acid, resulting in an amino acid sequence.

    That’s what we call the “mapping”. But set of tRNA molecules would work, as long as there is only one molecule for each possible codon, and sets that work (unambiguous sets, or, at least, less ambiguous sets) will tend to be selected over ambiguous sets.

    Sorry, but even without my little drama the idea is divorced from science and reality. And that’s the mean kind where you take your friends with you and the ice cube tray while you’re at it.

    Well, your cariacature certainly is :) Also divorced from anything anyone is suggesting! Not even divorced – not even a first date :)

  370. 372

    Dr Liddle I see your response. I am off for a short while, but will return and be happy to respond.

  371. 373

    Elizabeth,

    Back to the question. You said, “the beginnings of such a mapping would tend to be advantageous.”

    What do you mean by the ‘beginnings of such a mapping?’ How does it begin?

  372. I’m not asking you to choose between one and the other. I’m asking you to decide which is demonstrated more conclusively by his experiment.

    Well, a properly conducted experiment will give the same results if replicated independently. That is kind of the definition of a publishable experiment.

    But that is not the purpose of experiments, except when done as product research. Product research and development is a legitimate subset of science, but it isn’t what Szostak is doing.

    ID seeks to determine whether an existing object is the work of unaided nature or of “art.” Demonstrating that something could be a work of art does not contribute to answering that question. Demonstrating that it could be a work of nature does.

    so I ask again, where are you going with this?

  373. 375

    Petrushka,

    Here’s where I’m going, and I honestly didn’t expect to be spelling it out.

    Szostak performs a repeatable experiment. You say that it is not his intention merely to demonstrate a repeatable experiment, and you are correct. He has more in mind than performing a repeatable experiment.

    But he is still performing a repeatable experiment.

    Yes, his purpose is to demonstrate what unaided nature might do. He is not attempting to demonstrate “art.” But he is demonstrating it anyway.

    His experiments are intelligently designed and executed. This does not mean that they cannot indicate what might happen unaided, but they certainly do demonstrate what can be accomplished deliberately. They demonstrate the latter even more than they demonstrate the former.

    The experiments are the work of an intelligent designer. If they relate to how life may have arisen without design, then they also relate to how it may have been designed. This last paragraph sums it up, so if nothing else ignore the rest. This is the point. This where I am going and have gone with it. (I might keep going, but you have to catch up. :))

  374. Maybe I need to stop reading this stuff, because I’m up to my waist in crazy. There were always left-handed people before we killed all the right-handed new people. Where’s the new information? How is being left-handed suddenly evolution?

    Being left-handed isn’t evolution, but the change in frequency of left-handers in the population is, by at least one definition of evolution and the information is contained in that prevalence. If righthandedness was caused by a single allele, and that allele disappeared completely from the population, later evolutionary biologists might note the shift, and infer, correctly, that at some point in our descendents’ ancestry, there had been a selection bias in favour of left-handedness, i.e. would re-extract that information.

    But obviously in that case the bias would be due to “artificial selection”, not natural selection.

    To take a different example: now that women are able to postpone motherhood voluntarily, there will be selective pressure in favour of a later fertility window. Women who first try to conceive in their thirties, and who carry a cocktail of alleles that render them fertile into their thirties, are more likely to pass those alleles on to offspring than those whose alleles render them less fertile in their thirties (most of us).

    Now, new alleles are being generated all the time, and some of those will be alleles of the current set of genes that govern women’s fertility window; those new ones that tend to make it later will, with the existing ones, tend to become more prevalent, and those that tend to make it earlier will tend to become less so. Give women a few hundred more generations (or even a few tens – there is evidence that it is already happening) and it is likely that the fertile window for women will move later still, and fertility in our sixties or seventies may become quite common. Those women will bear alleles that do not now even exist. They may also live longer, as the same alleles are likely to be related to longevity.

    All this is speculation, of course, although well-founded speculation as already there are data that suggest this is happening. But speculation or not, I’ve just outlined how the environment (a culture in which fertility control is available to women) can imprint information (how to ensure that women who want to postpone childbirth can do so) on the human genome.

    This is not crazy, it’s straightforward reasoning.

  375. Well, we don’t know exactly how the mapping molecules that link RNA codons to specific amino acids began, Scott, not least because not surprisingly, the very earliest life forms and proto-life-forms haven’t left any fossils. However, we can still derive testable hypotheses from well-founded theories. More to the point, given that we know what the molecules are that accomplish the mapping process, we can test hypotheses about how such a mapping might have evolved. We can certainly try demonstrate that it is in principle evolvable, and I have some ideas about how to do such a demonstration using a simplified computer model. If the challenge is: could an arbitrary codon-amino acid mapping evolve by Darwinian processes? then I can see how it could (i.e. I can see how it could evolve by incremental steps, each conferring a reproductive advantage).

    I’m busy for the next few days, but if I have time, I’ll try to write a simulation at the weekend, or the weekend following.

  376. 378

    Dr Liddle,

    And what I am saying above is that code for sets of tRNA molecules that provided a one-to-more than one mapping of codons to amino acids would tend to have selective advantage over sets that provided more-than-one to more-than-one mappings, so that is a perfectly viable Darwinian account of how such a mapping could have arisen.

    I would like to be generous here. To say that a code (which produces products which were good at decoding it) would be favored over another code (which produces products which were less-good at decoding it) is not an answer to the origin or establishment of a code. If you’ll notice, in both of these two scenarios you’ve proposed, both the system and the code already exists, and the only question you’ve asked is if either of them works better than the other. There is nothing in your answer that even suggests a source of the code, as if codes are ubiquitous entities which are readily lying around. If the answers to science’s questions can be exemplified by the simplistic observation that living systems that function will exist longer than ones that don’t – then science has become a pointless enterprise. Please do not characterize your observation as a “perfectly viable Darwinian account” of how a code “could have arisen”. And if you insist on labeling it as such, then we can simply throw whatever remains of empiricism out the window.

    Dr Liddle, may I ask you to please spare me the Darwinian sales pitch? Having me react to it does neither of us any good whatsoever, and it’s time-consuming, and it’s boring. Can’t we just stick to evidence and reason? Those are the observations that I am interested in, and presumably, you would be too. Trust me; when you tell me systems that work better will survive longer than those that don’t, it does not cause me to gaze off into the distance and ponder the lavish explanatory power of the Darwinian project. It does something else altogether.

    - – - – - – - –

    In my prior post (#49), I had provided four physical entailments of recorded information. I described the observation of them as “logically coherent and demonstrable”. That description is explicitly tied to the codons being symbolic representations. You flatly stated that the system is not symbolic. I then asked you to provide (by observable evidence/reason) the support necessary for making that conclusion (in the face of contrary evidence).

    Let’s see what you’ve provided.

    Well, it isn’t. It’s simply a physical system. A set of RNA molecules (tRNA) are coded DNA then RNA (probably originally just RNA). That set includes just one molecule for each triplet, although more than one for each amino acid (there being more possible triplets than amino acids). So we have a set of tRNA molecules, with different codon binding site at one end of each one, and an amino acid binding site at the other, right?

    To say a code isn’t symbolic simply because it’s a physical system is no answer at all. Without exception, all codes are physically instantiated; after all, we live in a material universe. A red plastic ball is a physical thing Dr Liddle, but it cannot be explained without reference to something else. In any case, it appears here that you do not intend to provide any observable evidence to support your assertion that the mapping of nucleotides-to-amino acids is not accomplished by symbolic representation. You simply plan to assert it once again as a conclusion, and apparently intend to address none of the contrary evidence provided.

    So we have an arbitrary mapping (arbitrary because presumably some other set of tRNA molecules could have done as well) between codons and amino acids. I don’t call this “symbolic” because the actual physical instantiation of the alleged “symbol” is crucial.

    I agree that the mapping is arbitrary. You then go on to say that the alleged symbol can be disregarded as a symbol because its “physical instantiation … is crucial”. I am having a hard time parsing what exactly that means, but you’ve gone on to offer an example regarding the word “dog”.

    The word DOG can be rendered in any material and still symbolise the animal we call a dog, which can then be expressed aloud or silently, in sign language However, a codon can only be rendered in nucleotides, and can only be translated into an amino acid by a specific physical molecule.

    Oh boy. You are actually making a qualitative comparison between what can be accomplished by a human being (a conscious, prolific, symbol-maker) and what can be accomplished by a system dedicated to a specific effect. Shall we discontinue thinking of the machine code in an automated fabric loom as “symbolic” simply because (in that system) it can do no more than arrange the thread patterns in a fabric? For crying out loud, Dr Liddle!

    Dr Liddle, if it makes any difference to your way of thinking; under the right conditions, nucleotides could be used to operate a fabric loom, and the machine code from a fabric loom could be used to produce polypeptides. And the word “dog” can be spelled out in either system. I will leave it for you to figure out what the common denominator is.

    But I do agree that the mapping is probably “arbitrary”. Not mysterious, however. Natural selection will favour non-ambigious mappings, and variants that code for sets of tRNA molecules that give ambiguous mappings will tend to reproduce less reliably.

    So, having not made a single comment that stands supported by observation, you simply return to the Darwinian sales pitch.

    This is pointless.

    I think I will regret the tone of this post. I readily admit I personally cannot treat you as just any layperson – one with an open mind just wondering about the bigger issues of existence. Instead, you are a highly trained researcher with a specific position on these matters which you refuse to submit to scrutiny. Perhaps the unfortunate tone is simply a result of our positions. I must always lead with observable evidence because IDists are forever portrayed by your side as idiots and buffoons (if not threatening to civilization and evil among men). On the other hand, you can lead with fairy tales and broken logic for the simple reason that you are never called into question. Why don’t you do us both a favor? Take the physical entailments of recorded information as I provided them, and attack them directly. You say the system is not representational, then fine, provide some rationale that matches the observations that suggest it is. Allow me to respond to something besides the hogwash you typed out here.

    Substance – Dr Liddle – provide some!

  377. So? If this is true, it only means that people are too hasty where they should not be.

    This is beating about the bush. Show us that bacteria or fruit flies can produce other distinct species.

  378. Eugene S: “The whole issue at the heart of ID is being able to abductively assert that the *best explanation available* is intelligent interference, not chance/necessity alone or any combination thereof. So ID *is* capable of distinguishing between natural cause and intelligent interference.”

    Those two sentences encapsulate everything annoying about ID. Look at the first sentence:

    “The whole issue at the heart of ID is being able to abductively assert that the *best explanation available* is intelligent interference, not chance/necessity alone or any combination thereof.”

    Here’s the first line of Wikipedia’s entry on Abductive reasoning: “Abduction is a kind of logical inference described by Charles Sanders Peirce as ‘guessing’.”

    So ID guesses that intelligence is the best explanation, not evolution. Then look at the second sentence:

    “So ID *is* capable of distinguishing between natural cause and intelligent inferference.”

    You go directly from guessing to just plain asserting that ID can tell intelligence from evolution. Then, building on that non-sequitar you say you “…cannot accept your point about molecules as a plausible cause of nanometre precision machinery in the cell. Maths shows it is operationally impossible.

    Then you wind up by asking for all the details on first life and, apparently, a complete roadmap to present day life. Well, can I ask ID the same? What was the first living thing? When and where did it appear? How did it lead to modern life? And, in keeping with ID demands, I’d like a complete accounting of the transition, with every “poof” or whatever accounted for.

    And you close by demanding to see something reproduce right now. Never mind that the original replicator probably took millions of years to appear in a “laboratory” the size of the earth. Either produce another one right now, or ID wins.

    ScottAndrews “A very simple self-replicator that found itself through chance?”

    Science’s best guess is that a molecule simple enough to assemble through chance was self reproducing. ID’s best guess is that an Intelligent Designer, which necessarily has to be billions of times more complex that that molecule, either assembled itself through chance or somehow always existed. (The odds are the same in either case.) I’ll go with science.

    “As has been stated ad nauseum, there is no evidence of selectable pathways consisting of one or two bits at a time or duplication that lead to anything significant. On top of that, if there were such selectable pathways, there is no evidence that they would be or were selected.

    So what is the ID scenario? Start with describing the Intelligent Designer, in detail. Please don’t forget to tell us how He came to exist. Then describe the first living thing He made, then tell us the pathways that incrementally lead to modern life and while you’re at it, explain why exactly those pathways were selected and not some others.

  379. 3.3.1.2.29 dmullenix

    DMullenix,

    Your resorting to “science’s guess” is the best give-away I have ever seen! If you label evolutionism as “science”, I’d not choose “science” which tells nonsense. Fortunately, it is not proper science.

    I am afraid, it is down to you, evolutionists, to tackle the problem of infinite regression, not to ID.

  380. Pardon, distractively tangential. Please refocus. (Cf discussion here if you need further help on seeing the force of the points GD makes just above.)

  381. Pardon, burning strawman distraction led away to by a red herring. Design thought is not properly to be equated to “Creationism in a cheap tuxedo.” Cf the corrective under UD’s resources, here.

  382. Joseph at 55: “Positive evidence [for an Intelligent Designer] has not only been found but has been presented. And all you can do is choke on it.”

    So choke me. I’d love to hear this evidence. Tell me the one about the ontological argument. That’s my favorite.

    “1- ID is not anti-evolution”

    All of Dembski’s and Behe’s “proofs” depend on evolution not working. They then say, “Therefore ID”. That’s pretty much ID in a nutshell right there.

    “2- No one has ever observed blind and undirected processes producing CSI”

    Apolipoprotein AI. Wish I had some. Of course, you’re right that nobody actually witnessed the DNA as it mutated to produce the new specification. Of course, nobody’s ever seen the Intelligent Designer at work either. Could you show us some examples of the Intelligent Designer designing?

    “the EF considers both chance and necessity operating together.”

    The only time I ever saw Dembski attempt that, he failed miserably. If I remember correctly, he described something like randomly putting a needle down on a record and then playing the selection. The fact is that the EF can only measure random OR lawful. You can’t even put a combination into it.

    The EF goes like this:

    Input item to be tested.
    . Is it random? Then it’s not ID so Exit
    . Is it lawful? Then it’s not ID so Exit
    If you get this far, it’s ID

    Please show us how to fit random AND lawful into that. Maybe something like

    . Is it random AND lawful combined? Then it’s Darwin.

    “Again ID is not anti-evolution and your position still doesn’t have any positive evidence”

    You keep saying that, but if evolution is true, every ID “proof” falls flat on its face. The whole ID argument can be stated, “Evolution can’t do it, so ID.”

    “Except that is NOT what Behe said”

    I read his book. He walked it back later. If I remember, he now holds to a variation of “Evolution can’t produce CSI, therefore ID.”

    What do you think of his admission that if ID is true, then The Designer must have Designed the malaria parasite? I thought that telling that amount of truth took a lot of guts.

  383. BA:

    You strike gold again!

    Added as the very first video on the Intro-Summ page IOSE.

    GEM of TKI

  384. Apparently, it does not faze you that a split-off that on the conventional timeline is 150 MYA, and involves a major change/difference in manner of reproduction, is involved with such a genetic similarity that the scientists who discovered it were plainly shocked. Sadly telling.

  385. Positive evidence [for an Intelligent Designer] has not only been found but has been presented. And all you can do is choke on it.”

    So choke me.

    You are choked out.

    You want the evidence? Read a biology textbook. It is all in there.

    “1- ID is not anti-evolution”

    All of Dembski’s and Behe’s “proofs” depend on evolution not working.

    That is false. Your ignoarnce, while amusing, is not a refutation. ID argues against blind and undirected processes only- and that is only in certain circumstances as ID does not say design explains everything.


    “2- No one has ever observed blind and undirected processes producing CSI”

    Apolipoprotein AI.

    No evidence taht it arose via blind and undirected processes. Try again.

    “the EF considers both chance and necessity operating together.”

    The only time I ever saw Dembski attempt that, he failed miserably.

    The EF is how science operates- that is according to Newton himself. And I doubt you witnessed Dembski failing.

    The fact is that the EF can only measure random OR lawful. You can’t even put a combination into it.

    According to Dembski, you can. ya see even a rolling of the dice you have the law of gravity acting on those dice.

    The EF goes like this:

    Input item to be tested.
    . Is it random? Then it’s not ID so Exit
    . Is it lawful? Then it’s not ID so Exit
    If you get this far, it’s ID

    So you do think your ignorance means something. Strange.

    The EF goes like this:

    Start with an object/ event/ structure

    1- Is it do to law/ regularity/ necessity?

    2- Is it due to chance? (which also includes laws/ regularities/ necessities)

    3- Does it have a specification?

    If there isn’t any specification then we do not infer design even though the first two have been eliminated.

    “Again ID is not anti-evolution and your position still doesn’t have any positive evidence”

    You keep saying that, but if evolution is true, every ID “proof” falls flat on its face. The whole ID argument can be stated, “Evolution can’t do it, so ID.”

    Behe testified, under oath, that ID is not anti-evolution. ID is antidarwinian evolution.

    Here are more references for you to choke on:

    blockquote>
    Intelligent Design is NOT Creationism
    (MAY 2000)

    Scott refers to me as an intelligent design “creationist,” even though I clearly write in my book Darwin’s Black Box (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think “evolution occurred, but was guided by God.”- Dr Michael Behe

    Dr Behe has repeatedly confirmed he is OK with common ancestry. And he has repeatedly made it clear that ID is an argument against materialistic evolution (see below), ie necessity and chance.

    Then we have:

    What is Intelligent Design and What is it Challenging?- a short video featuring Stephen C. Meyer on Intelligent Design. He also makes it clear that ID is not anti-evolution.

    Next Dembski and Wells weigh in:

    The theory of intelligent design (ID) neither requires nor excludes speciation- even speciation by Darwinian mechanisms. ID is sometimes confused with a static view of species, as though species were designed to be immutable. This is a conceptual possibility within ID, but it is not the only possibility. ID precludes neither significant variation within species nor the evolution of new species from earlier forms. Rather, it maintains that there are strict limits to the amount and quality of variations that material mechanisms such as natural selection and random genetic change can alone produce. At the same time, it holds that intelligence is fully capable of supplementing such mechanisms, interacting and influencing the material world, and thereby guiding it into certain physical states to the exclusion of others. To effect such guidance, intelligence must bring novel information to expression inside living forms. Exactly how this happens remains for now an open question, to be answered on the basis of scientific evidence. The point to note, however, is that intelligence can itself be a source of biological novelties that lead to macroevolutionary changes. In this way intelligent design is compatible with speciation. page 109 of “The Design of Life”

    and

    And that brings us to a true either-or. If the choice between common design and common ancestry is a false either-or, the choice between intelligent design and materialistic evolution is a true either-or. Materialistic evolution does not only embrace common ancestry; it also rejects any real design in the evolutionary process. Intelligent design, by contrast, contends that biological design is real and empirically detectable regardless of whether it occurs within an evolutionary process or in discrete independent stages. The verdict is not yet in, and proponents of intelligent design themselves hold differing views on the extent of the evolutionary interconnectedness of organisms, with some even accepting universal common ancestry (ie Darwin’s great tree of life).
    Common ancestry in combination with common design can explain the similar features that arise in biology. The real question is whether common ancestry apart from common design- in other words, materialistic evolution- can do so. The evidence of biology increasingly demonstrates that it cannot.- Ibid page 142

    “Except that is NOT what Behe said”

    I read his book.

    Obviously you didn’t understand it. He explains ID is not anti-evolution just anti darwinism.

  386. Yet another rhetorical red herring led away to a handy strawman soaked in ad hominems and waiting to be burned, poisoning and polarising the atmosphere.

    Kindly, read the weak argument correctives page in the resources tab top this and every UD page, as the context of understanding and applying the definition of ID.

    If you are having worldview level issues [phil not sci], this page in the IOSE deals with that, and this one with the onward sociocultural significance.

    Those resources are only a few clicks and some hours of reading and viewing away.

  387. ES (& P): This update may help.

  388. Functionally specific sequences are indeed rare in config spaces, and may be clustered in isolated islands of function. The constraints required for function in a complex context guarantee that.

    It is evo mat refusal to acknowledge patent, easily observed facts like this [cf my post earlier this morning, zoom in on the text generation examples], that tells me we are not dealing with a reasonable view but ideology and indoctrination based on question-begging a prioris.

  389. 392

    Dmullenix,

    This is self-contradictory.

    Science’s best guess is that a molecule simple enough to assemble through chance was self reproducing.

    A ‘best guess’ with no specifics and based on no observation is not science. It is a guess made by people who are scientists. Do you see the difference?

    So what is the ID scenario? Start with describing the Intelligent Designer, in detail. Please don’t forget to tell us how He came to exist. Then describe the first living thing He made, then tell us the pathways that incrementally lead to modern life and while you’re at it, explain why exactly those pathways were selected and not some others.

    Somehow it persists. Perhaps we need a single link that we can post into comments whenever it comes up. In order to criticize ID you must understand the very concept. It’s a bit like discussing Citizen Kane with someone who thinks it’s a video game. How can they offer relevant criticism?

    Even still, there is plenty of peer-reviewed research in progress examining how designers might create the simplest components of life. It’s quite detailed and should put this irrelevant question to rest. I’ve been discussing it on the Science and Freethinking thread. I’m not starting over.

  390. Functionally specific sequences are indeed rare in config spaces, and may be clustered in isolated islands of function. The constraints required for function in a complex context guarantee that.

    Care to provide any evidence that all observed biology is not occupying a single continent of function?

    Forget other examples because we are not talking about non-biology, provide evidence that relates specifically to the functional entities being discusses.

  391. Petrushka sez (9.1.1.1.2):

    Mice an humans are mammals, and mammals are separated from each other mostly by changes in regulatory networks.

    That is the propaganda, however there isn’t any evidence to support that claim.

  392. Dr Bot:

    Plainly, you need to look at the current post here [to remind yourself of what the fossil record ACTUALLY shows -- as opposed to headlines and museum exhibits or textbook oversimplifications . . . ], and you should compare this here, on the underlying problem in protein space.

    Both reflecting the commonly observed implications of imposing specific functional constraints on a complex collection of components.

    Notice, Gould’s classic remark on the trade secret of paleontology, and its roots in Darwin, and his 2002 update.

    Sorry, you know this, or should know it, long since.

    And, plainly, the cited examples are biological.

    In fact, what is happening here is the usual brazen Darwinista switcheroo; assuming the default in the teeth of evidence, and demanding absoluter proof to the contrary or they will assert that their preferred idea is so.

    Nope, it is those who want to claim the equivalent of a perpetual motion machine of the second kind, who need to show their substantiation. EMPIRICALLY.

    GEM of TKI

  393. 3.3.1.1.1

    DMullenix,

    “ID and creationism are both fixed on the idea that the first living thing was a cell of modern complexity.”

    I don’t think that’s true. All ID says is that life is characterised by irreducible complexity, whereby for a given function you need collective and increadibly fine-tuned corredinated input from a set of components. Whenever any component is not present or malfunctional, no “composite” function exists. Now, climbing from the side of Mt Improbable by means of preadaptation does not help for the same reasons of info complexity. Preadaptation can do only so much.

    “But all you need is to form one polymer that self-reproduces that way and you’re off.”

    Well, give an example of such a polymer then. The chance for a smallest thing able to self-replicate to have emerged by itself is below what is operationally possible in our universe. If you choose to believe in such a possibility, it is up to you, but you don’t have the right to call it credible science.

    The information processing layer acting over the physical layer in complex systems is reliably the result of intelligent agency.

    Until such times as OOL’ers demonstrate spontaneous emergence of “simple” self-replicating polymers, this remains an unsubstantiated claim.

  394. 3.3.1.2.10
    Petrushka

    Sorry, I may have been unclear. What I meant was to say that we can establish if something has been a result of purposeful design and check our calculations by means of independently available data. Say we know for certain that Mr Petrushka wrote this post 3.3.1.2.10 (e.g. we observed that happenning), we then go and estimate the specified complexity of that post and correctly come to the conclusion that the post has been written by an intelligent agent.

  395. KF, Cheers!

  396. What I meant was to say that we can establish if something has been a result of purposeful design and check our calculations by means of independently available data.

    I’m not sure what you mean by that.

    If I were saying something along those lines I would mean that we can check the validity of natural selection by observing artificial selection and quantifying the likelihood of non-detrimental genetic changes. Things like selective breeding, or like the Lenski experiment, or the Russian experiment with tame foxes.

    We can, for example, count the genetic differences between two related species, not the time elapsed between divergence, and compare the inferred rate of change with observed rates of change.

    That is precisely what evolutionary biologists have been trying to do since Darwin. But now we are accumulating sequence data and will increasingly be able to apply actual numbers.

  397. 400

    Petrushka,

    “So point out the violation of physics or chemistry required by Shapiro’s description of the processes in evolution.”

    Where does a violation of physics or chemistry come into the picture? Do design and implementation violate physics or chemistry? Does anyone know of anything that does? It’s irrelevant.

    To ask whether something violates physics or chemistry is a meaningless litmus test, since nothing we know of or can describe does.

    To use it to screen out deliberate interference while allowing for some other process is arbitrary. It reflects only your personal preference. I’m all for preferences, but we need to be honest about them. There’s nothing wrong if your objection to ID boils down to “I don’t like it.” But we can’t start from our preferences and work backward trying to justify them.

  398. DM:

    ID and creationism are both fixed on the idea that the first living thing was a cell of modern complexity

    1 –> My old English teacher used to love to quot” “and joins equals.” In short, there you go again, inisisting on the Creationism in a cheap tuxedo smear that has long passed sell-by date.

    2 –> Next, if the living cell is comparable to a Jumbo jet, the typical component may be comparable to say an instrument on the flight deck.

    3 –> And while Hoyle chose the whole jumbo for his comparison, in fact a tornado in a junkyard is just as maximally unlikely to assemble say a D’
    Arsonval galvanometer based flight instrument as the whole Jumbo Jet. The same complexity-specificity threshold problem meets the one as the other, cf here.

    4 –> next, the criterion of living systems to be able to even conceivably evolve body plans is self replication based on stored info. That brings up the von Neumann Self Replicator. Which per observation, starts at about 100,000 bits of info worth of complexity.

    5 –> You may suggest a hypothetical self replicating autocatalytic molecule as an escape, but as ES said, you need to empirically, observationally demonstrate its existence, operations and its origin in a plausible prelife medium.

    6 –> Until you do so, you are doing the Darwinista switcheroo again, insisting on an agenda-serving speculation in the teeth of contrary empirical evidence, through imposing implicit materialism by a priori. As Lewontin let the cat out of the bag on.

    (And, FYI, denizens of the fever swamp objector sites, that is demonstrably NOT quote mining. [For your side to insist on that sort of patently false accusation in the teeth of evident facts and the use of the right of fair comment, is to be willfully misleading.] Of course, doubtless you find the terms I have used to describe, stinging. Even though they are accurate, and justified by facts. So, consider what it is like to be subjected to insistent willful false accusation, just plain vile mud slinging without any foundation — onlookers, this includes false accusations of perversion and child abuse, etc. — on any excuse and the holding of one’s family hostage under implicit mafioso style threats. And then, do better; show the broughtupcy your mothers tried to put into you, at the very least.)

    7 –> That evidence, as close as the organisation and info in posts in this thread, with billions of cases in point with no credible counter-cases, is that FSCO/I is produced by design.

    8 –> And as for the “of modern complexity part,” cf. here (scroll down to Fig I.9 and caption) — detour due to lost info, Blogger has an annoying post end clip-off bug — on what happened when investigators recently tried to find simpler cells of low genome size.

    GEM of TKI

  399. Elizabeth:

    The mapping is not accomplished by tRNAs, but by 20 very complex proteins, the aminoacyl tRNA synthetases.

    Would you agree that it is more “symbolic” that way, and above all much more difficult to explain?

  400. The mapping is determined by the set of tRNA molecules. A different set would give a different mapping.

    The protein assembly process is certainly accomplished by means of other enzymes.

    But we were talking about the “arbitrary” mapping of codons to specific amino acids, the “code”, that UBP is “information” that cannot be generated by Darwinian processes.

    No, I don’t think that the assembly process makes the thing more “symbolic”. Molecules aren’t symbols, they are what they are, not symbols for something else.

  401. 404

    This sounds just like the previous discussion. All things “are what they are,” even physical representations of symbolic codes.
    Holes punched in a Hollerith card
    aren’t anything magical, they are just holes. The processes for reading them and executing their instructions are performed by physical constructs.
    Does that mean that the holes in the card are not symbols for something?
    You can reduce the representation of any symbolic code to molecules or particles. You don’t deny the involvement of intelligent intervention in any other such case. What is different about this one?

  402. Information processing is a physical process. If it required intervention, computers would not be able to do it.

    No one knows (yet) how the code originated. You don’t. biologists don’t.

    But mainstream biologists are at least looking.

  403. 406

    Petrushka,

    I agree, if no one determined a system of coding for data and instructions and then designed and manufactured computers to process it, then computers would not be able to do it. No intervention there. That you can envision the very existence of computers processing information and posit a lack of intervention in the same sentence speaks volumes to the filters through which you view reality.

    And if by ‘looking’ you mean that ‘mainstream biologists’ have started from a priori, non-scientific assumptions while throwing the occasional rock at those who ask why, then yes, they are at least looking.

  404. 407

    I will let GP speak for himself, but I’d like to make a quick point or two.

    The mapping is determined by the set of tRNA molecules. A different set would give a different mapping.

    The mapping is accomplished by charged tRNA, and to become charged they require their entourage of synthetases (complex proteins which can identify individual tRNA and bind the proper amino acid to it, preparing them to physically interact in the exchange of information from input to output). This was mentioned briefly in my post at 49.

    GP is quite aware of the complexity of both these objects, and perhaps he will comment on them.

  405. Let’s set the goalposts somewhere and leave them fixed.

    The order of certainty in biology might look something like this:

    1. The earth is billions of years old.
    2. Life is billions of years old.
    3. Microbial life preceded multi-celled life.
    4. Multi-celled life changed over time, a fact evidenced by the fossil record.
    5. We have a theory describing the process of change. The details have been expanded on in the last 150 years.
    6. Many lines of evidence support the claim that multi-celled things are descended from a common ancestor.
    7. Microbes exchange genetic material, Descent is not as clear cut.

    I would call these seven items non-negotiable. They are true even if a mysterious entity has occasionally intervened.

    If you disagree, please indicate which statement(s) you think are wrong, and why.

  406. Dr Liddle,

    And what I am saying above is that code for sets of tRNA molecules that provided a one-to-more than one mapping of codons to amino acids would tend to have selective advantage over sets that provided more-than-one to more-than-one mappings, so that is a perfectly viable Darwinian account of how such a mapping could have arisen.

    I would like to be generous here. To say that a code (which produces products which were good at decoding it) would be favored over another code (which produces products which were less-good at decoding it) is not an answer to the origin or establishment of a code. If you’ll notice, in both of these two scenarios you’ve proposed, both the system and the code already exists, and the only question you’ve asked is if either of them works better than the other. There is nothing in your answer that even suggests a source of the code, as if codes are ubiquitous entities which are readily lying around. If the answers to science’s questions can be exemplified by the simplistic observation that living systems that function will exist longer than ones that don’t – then science has become a pointless enterprise. Please do not characterize your observation as a “perfectly viable Darwinian account” of how a code “could have arisen”. And if you insist on labeling it as such, then we can simply throw whatever remains of empiricism out the window.

    Yes, my answer does indeed “suggest the source the code”. And if you think that “the simplistic observation that living systems that function will exist longer than ones that don’t” is pointless, then you are missing a very important point!

    It is indeed “simplistic” – so simple that it was overlooked for a very long time. But for both Darwin and Wallace, the penny dropped.

    Yes, my explanation is speculative and it’s about “how a code could have arisen” because it addresses the claim that it could not have arisen, except by external intelligent input. We do not know, and may never know, how it did arise, but if we can figure out how it could have arisen by Darwinian processes, than the argument that it could not have so arisen, fails.

    Dr Liddle, may I ask you to please spare me the Darwinian sales pitch? Having me react to it does neither of us any good whatsoever, and it’s time-consuming, and it’s boring. Can’t we just stick to evidence and reason? Those are the observations that I am interested in, and presumably, you would be too. Trust me; when you tell me systems that work better will survive longer than those that don’t, it does not cause me to gaze off into the distance and ponder the lavish explanatory power of the Darwinian project. It does something else altogether.

    Well, that’s a shame, because it isn’t a “sales pitch”, it’s the basis of the theory. If you want to argue against the theory, then you need to understand what it actually is.

    In my prior post (#49), I had provided four physical entailments of recorded information. I described the observation of them as “logically coherent and demonstrable”. That description is explicitly tied to the codons being symbolic representations. You flatly stated that the system is not symbolic.

    Well, it isn’t, and I just explained why. A molecule is a physical object, not a symbol. A symbol can be rendered in any medium, and still be the same symbol. A molecule cannot.

    I then asked you to provide (by observable evidence/reason) the support necessary for making that conclusion (in the face of contrary evidence).

    I just did.

    Let’s see what you’ve provided.

    Well, it isn’t. It’s simply a physical system. A set of RNA molecules (tRNA) are coded DNA then RNA (probably originally just RNA). That set includes just one molecule for each triplet, although more than one for each amino acid (there being more possible triplets than amino acids). So we have a set of tRNA molecules, with different codon binding site at one end of each one, and an amino acid binding site at the other, right?

    To say a code isn’t symbolic simply because it’s a physical system is no answer at all.

    Of course it is. It’s fundamental. If something lacks the essential attributes of a symbol, it isn’t a symbol. And what we have in cells are a series of biochemical reactions.

    What makes DNA (or RNA) a “code” is the arbitrary mapping of codon to amino acid, but the arbitrariness neither renders it symbolic, nor evolvable by Darwinian mechanisms.

    Without exception, all codes are physically instantiated; after all, we live in a material universe. A red plastic ball is a physical thing Dr Liddle, but it cannot be explained without reference to something else. In any case, it appears here that you do not intend to provide any observable evidence to support your assertion that the mapping of nucleotides-to-amino acids is not accomplished by symbolic representation. You simply plan to assert it once again as a conclusion, and apparently intend to address none of the contrary evidence provided.

    I can “prove” it is not symbolic simply by drawing your attention to the fact that it is not. I can use your written name as a symbol for you. It will symbolise you whether it is written in pixels, ink, charcoal, carved in granite, or left by con trails, as long as there is someone who understands the convention by which those letter forms represent you, symbolically.

    But the chemicals that “understand” what a stretch of RNA “represents” are quite different. They only “understand” the code if it is “written” in nucleotides. And the reason they do so is that they are simply molecules, like the code itself, and they “read” the codon by virtue of their chemical configuration.

    Or do you dispute this?

    So we have an arbitrary mapping (arbitrary because presumably some other set of tRNA molecules could have done as well) between codons and amino acids. I don’t call this “symbolic” because the actual physical instantiation of the alleged “symbol” is crucial.

    I agree that the mapping is arbitrary. You then go on to say that the alleged symbol can be disregarded as a symbol because its “physical instantiation … is crucial”. I am having a hard time parsing what exactly that means, but you’ve gone on to offer an example regarding the word “dog”.

    The word DOG can be rendered in any material and still symbolise the animal we call a dog, which can then be expressed aloud or silently, in sign language However, a codon can only be rendered in nucleotides, and can only be translated into an amino acid by a specific physical molecule.

    Oh boy. You are actually making a qualitative comparison between what can be accomplished by a human being (a conscious, prolific, symbol-maker) and what can be accomplished by a system dedicated to a specific effect. Shall we discontinue thinking of the machine code in an automated fabric loom as “symbolic” simply because (in that system) it can do no more than arrange the thread patterns in a fabric? For crying out loud, Dr Liddle!

    Yes, you should certainly discontinue that thought. Or else, let us redefine the word symbol so that it can include templates.

    But that would undermine what I understand is your own position.

    Dr Liddle, if it makes any difference to your way of thinking; under the right conditions, nucleotides could be used to operate a fabric loom, and the machine code from a fabric loom could be used to produce polypeptides. And the word “dog” can be spelled out in either system. I will leave it for you to figure out what the common denominator is.

    Well, not the word “symbol” as it is normally used, certainly.

    But I do agree that the mapping is probably “arbitrary”. Not mysterious, however. Natural selection will favour non-ambigious mappings, and variants that code for sets of tRNA molecules that give ambiguous mappings will tend to reproduce less reliably.

    So, having not made a single comment that stands supported by observation, you simply return to the Darwinian sales pitch.

    This is pointless.

    It’s supported by reason. I spelled out my reasoning. If you choose to dismiss it as “sales pitch” then, yes, it probably is “pointless”.

    If you reject as inadmissable all Darwinian arguments, then there aren’t any arguments I can make for Darwinism!

    I think I will regret the tone of this post. I readily admit I personally cannot treat you as just any layperson – one with an open mind just wondering about the bigger issues of existence. Instead, you are a highly trained researcher with a specific position on these matters which you refuse to submit to scrutiny. Perhaps the unfortunate tone is simply a result of our positions. I must always lead with observable evidence because IDists are forever portrayed by your side as idiots and buffoons (if not threatening to civilization and evil among men). On the other hand, you can lead with fairy tales and broken logic for the simple reason that you are never called into question. Why don’t you do us both a favor? Take the physical entailments of recorded information as I provided them, and attack them directly. You say the system is not representational, then fine, provide some rationale that matches the observations that suggest it is. Allow me to respond to something besides the hogwash you typed out here.

    Substance – Dr Liddle – provide some!

  407. Yes, I agree that the mapping process is accomplished by the means you give.

    But the mapping itself – the “genetic code” is what it is because a specific subset of the possible total set of tRNA molecules are the only ones produced by the cell.

    A different subset would give a different code,

  408. Well try this on for size:

    Following the big numbers arguments of Douglas Axe and others, I deny that life can be designed except by evolution. I maintain, using the logic of Douglas Axe, that it is impossible to design a protein coding sequence except by “random” variation and selection.

    Not just in practice, but in principle.

    My reason is simple. Following the argument of Douglas Axe, there is no shortcut to knowing how a protein will fold, and not enough time or resources in the universe to compute functional sequences without trying lots and selecting them.

    Prove me wrong.

  409. Geological strata would fail the test because they lack specificity.

    That seems to depend on who you ask. For most of recorded history inanimate objects were considered to be designed for man’s comfort and amusement.

    It paints a bull’s eye around what is and assumes that whatever is, was the goal.

  410. 413

    Petrushka,

    Number 5 is debatable, not negotiable, and is by far the most important. There has never been a detailed process of change on which to expand. Some changes are observed, others are speculated, but the actual explanation of the process is somewhat like a cloud. Within that cloud are a bunch of vaguely proposed mechanisms, none of which have been connected to the changes in any detail. The only thing everyone seems sure of is that it couldn’t have been intelligent, which couldn’t be less scientific.

    #5 does not belong on a list of even provisional certainties. There is no theory describing the process of change.

    It’s a bit like a coroner who tells you that his subject was murdered by either a knife or a bullet or strangulation or poison or decapitation, or a combination of any or all of the above. When you ask how he knows, he explains that he heard the man must have been murdered, and that’s how it usually happens.

    So pass on #5, but you get extra points for mentioning 150 years which gives the appearance of added weight.

    #6 – Well phrased, because you mention evidence supporting the claim while stopping short of making the claim itself. There is evidence to that effect, which may also be evidence supporting other conclusions.

    But I’m talking ID, not theology, I won’t outright reject #6, but it’s fuzzy and questionable.

    Three questions are everything: How did it get here? How does it change? Why does it change?

    You use the word “mysterious” with the connotation that Scooby Doo and his friends should go hunting around the abandoned carnival for it. Mystery is good, and both OOL and evolutionary theory are over their heads in it.

  411. 414

    Petrushka,

    If you needed a protein that folded into a specific shape, which would you do? Test countless random proteins until one works, or start from the desired shape and work backwards?

    You have provided an excellent example demonstrating why intelligence surpasses random searches. It imagines results and plans to accomplish them.

    What’s funny is that you would decrease the capability of intelligence by assuming that it had to function using random searches. You’re intelligent. When you want to write something, do you begin with the idea and then select words, or do you randomly select and test words until they form an idea you might agree with?

  412. 415

    It’s not exactly the same thing, but consider Origami. Without even having a target, how many random folds would you have to attempt to come up with anything that would look like anything?
    It takes a lot of experience, but an Origami expert can imagine the shape and work backwards.

    Everyone tries to maximize probabilistic resources by stating that an evolutionary search has no goal. But as this example demonstrates, having a goal is everything.

  413. Elizabeth:

    UB is right. The “genetic code” is nothing else than the abstract correspondence (symbolic) between nucleotide triplets and aminoacids, a redundnat base four code for 20 “wprds” plus the stop codons.

    The information in DNA would be completely useless if the translation machine had not, implemented in its information, the key to the interpretation of the code, that is the key to the symbolic mapping.

    That key in no way is implemented in tRNAs, nor in mRNA, nor in the complex ribosome machine.

    The decoding information is in the 20 AARS, 20 proteins whose global compèlexity ranges in about 10000 aminoacids, and which are universally necessary to translation in all known living beings. Those proteins are extremely old, extremely complex, and we can still observe striking sequence similarities between the variants in archaea, bacteria and homo sapiens (and, I suppose, practically all living beings). They are a treasure of functional information without which no translation is possible.

    You say:

    “But the mapping itself – the “genetic code” is what it is because a specific subset of the possible total set of tRNA molecules are the only ones produced by the cell. A different subset would give a different code,”

    What do you mean? The tRNAs are passive carriers. Each AARS recognizes the right tRNA with the correct anticodon (by the information implemented in the complex structure of the protein), and couples it to the correct aminoacid. That’s the only reason why the correct aminoacid is mounted in the final protein (by the ribosome) in correspondence of the correct anticodon.

    Both tRNAs and the ribosome, in themselves, cannot couple the correct aminoacid to the correct codon. IOWs, they have no information about the correct code. It’s the AARS that accomplish that extraordinary informational task. They do that efficiently, with great control of the final result. They have been there for billions of years, doing exactly that.

    If we want to understand the functional information inherent in the protein synthesis process, we have to be clear about where it is. While a lot information is necessary to maintain the information in DNA, transcribe it correctly, and to build the protein, the information about the code is written in the 20 aminoacyl tRNA transferases.

    That is the information we have to explain, to explain the working of the genetic code.

  414. 417

    Hello again Dr Liddle,

    Yes, my answer does indeed “suggest the source the code”. And if you think that “the simplistic observation that living systems that function will exist longer than ones that don’t” is pointless, then you are missing a very important point!

    You are saying that the differential survival of a replicating system is the source of the code which causes the system to exist. But the differential survival of a physical system wouldn’t have happened until the code-driven system itself existed. (Alternatively, you can provide plausible evidence of a non-code-driven system providing inheritance, then point to the cause of a code arising within that system). In any case, differential survival is the result of an adaptive system in a variable environment, and it very obviously requires the system. This was already pointed out to you in my previous post. If something requires something else to exist before it can come into being, then it cannot logically be the cause of the thing it requires – because it doesn’t exist yet. .

    The point you think I am missing in this is one that schoolchildren get in grade-school biology class. I was one of them. Meanwhile, you’ll need to reformulate your proposal in a way that doesn’t contain this obvious flaw. Perhaps you can describe the properties of the process whereby something that doesn’t exist can cause something to happen.

    It is indeed “simplistic” – so simple that it was overlooked for a very long time. But for both Darwin and Wallace, the penny dropped.

    Well actually, the thoughts of Wallace have been buried in the cause of selling materialism for the past 150 years. And as for Darwin, you are abusing his theory by wearing it as a skull cap and applying it to scenarios before it even exists as Darwin proposed it. Darwin did not say that he explained the origin of Life, did he? And if you want to separate the origin of Life from the origin of the code, then you’ll need to do more than point at Darwin in 1859. His theory assumes (and subsumes) the code, it doesn’t explain it.

    Yes, my explanation is speculative and it’s about “how a code could have arisen” because it addresses the claim that it could not have arisen, except by external intelligent input. We do not know, and may never know, how it did arise, but if we can figure out how it could have arisen by Darwinian processes, than the argument that it could not have so arisen, fails.

    Your explanation points to no concrete observations, and it illogically applies Darwin’s theory to origins – prior to the onset of differential survival. It does so under the unquestioned presumption that an adaptive metabolizing replicator can come into existence in the real world without the organization provided by encoded information.

    Because of this unsupported assumption (supporting the misplaced use of Darwin’s theory) your proposal does not address the claim as you say it does. And it does not directly address the contrary evidence at all (beyond the assertion that it’s wrong) even though you’ve been invited to do so.

    I was interested in this statement: “but if we can figure out how it could have arisen by Darwinian processes, than the argument that it could not have so arisen, fails”. You are saying that what you call a speculative explanation can overturn substantive observable evidence to the contrary, and I am saying we can toss whatever remains of empiricism out the window. It’s lost its ranking in science – and you haven’t even figured out how “it could have arisen by Darwinian processes”. In a legal scenario, this would be considered the suppression of evidence ;) because that is exactly what it is.

    In my prior post (#49), I had provided four physical entailments of recorded information. I described the observation of them as “logically coherent and demonstrable”. That description is explicitly tied to the codons being symbolic representations. You flatly stated that the system is not symbolic.

    Well, it isn’t, and I just explained why. A molecule is a physical object, not a symbol. A symbol can be rendered in any medium, and still be the same symbol. A molecule cannot.

    This is horribly confused. You say that a molecule (hopefully meaning the sequence of nucleotides in DNA) is a physical object, not a symbol (or contain symbols). But any symbol that we could possibly observe (and share with each other) would have to be a physical object by necessity. How could it be any other way? Therefore being a physical object is hardly an impediment to also being a symbol – we haven’t observed any that aren’t.

    The remainder of this comment fails as well. You say that a symbol can be “rendered in any medium”, but a molecule can’t. It’s not the molecule that is being rendered Dr Liddle, it’s the symbol. In other words, if we make a symbol out of a block of wood, it can do nothing but remain a block of wood. The fact that it is a symbol extends beyond its physical existence. It’s a symbol because it has a relationship to something else, and is separate from it. Under the correct physical protocol, that relationship can be actualized to its physical effect.

    As to your remaining comments about the use of the word ‘symbol’, I may have to address them when I have time. I would like to ask you to consider something though. I am using the word “symbol” following Merriam-Webster’s definition of the word:

    SYMBOL : something that stands for or suggests something else by reason of relationship

    This is exactly the way I used the term in my post at #49, which I had asked you to address specifically. If your response is confusion over what is being “rendered” when something becomes a symbol, or you make the mistake that something being a physical object can’t also be a symbol, then you have failed to support your objection. If it’s any consolation to you, we can call it whatever you wish. It’s the physical entailments of it that matter.

  415. Yes, gpuccio, I know he is right, and so were you. There is no dispute about this.

    But that means that his argument has shifted from “information cannot be created by Chance and Necessity” to “the DNA coding system is irreducibly complex”.

    My point is that there is nothing in the intrinsic to an arbitrary code that is renders it incapable of evolving by Darwinian mechanisms.

  416. oops garbled edit:

    “My point is that there is nothing intrinsic to an arbitrary code that renders it incapable of evolving by Darwinian mechanisms.”

  417. Elizabeth:

    I respect your opinion, but obviously my motivated conviction is that practically nothing can really evolve by darwinian mechanisms, least of all an arbitrary code.

    And the real point is: the code, however it “evolved”, needs 20 very complex proteins to work, in all known instances in the world. Are you ready to explain how those 20 proteins, each of them hundreds of aminoacids long, “evolved” to make translation of the code possible? And, if you like, how those proteins evolved when the code and translation apparatus to decode it did not even exist?

    I know, I know: you will say what all darwinists say at that point, that “the code certainly evolved in simpler beings”, that “at that time it must certainly work without the 20 proteins”, and that “the proteins evolved later”, and similar fairy tales without any piece of evidence, or logic, to support them, except for the blind reductionist faith of darwinist and their fanatic need to rule out in principle any design explanation.

    In the meantime, the facts are facts:

    1) The 20 AARS are old proteins, certainly already present in LUCA, almost at the beginning of life on our planet.

    2) No translation can be observed without them.

    3) They are extremely complex, and obviously tailored to allow a symbolic connection between a nucleotide code and a protein output, according to a specific symbolic code knwon as the genetic code.

    4) Science has no credible model about how the code originated.

    5) Science has no credible model about how the 20 proteins that make the code work originated.

    6) Science has no credible model about how all the rest of the complex structures that make translation and synthesis of any single protein possible (ribosome RNA and proteins, transcription apparatus, and so on).

    Facts. But who cares about facts anymore?

  418. Upright BiPed: I must apologise for not getting to the end of your post earlier – I must have hit submit before I intended to.

    I think we need to get away from argument-by-definition (as we seem to use words in such different ways) and down to basics.

    My position is simply that the simplest self-replicator capable of replicating with heritable variance in reproductive success was probably simple enough that it can be explained by physics and chemistry. I don’t know that this is the case – there is, as we speak, no complete and compelling OOL model, although there are some promising bits of one.

    Your position appears to be (and I may be wrong) that there is something intrinsic to the nature of “information” that is unevolvable, is unlikely to occur by “Chance or Necessity” and is a prerequisite for subsequent evolution.

    Is this a fair statement of our differences?

    I’ll be back later to respond to your post in more detail.

    Cheers

    Lizzie

  419. Petrushka,

    “Information processing is a physical process. If it required intervention, computers would not be able to do it.”

    I am really sorry to write this. This is really below standard. Before this post of yours I thought you had a better idea of what information processing meant. Ok, let’s start from the beginning. How did computers come about? Spontaneously or did they involve intelligent intervention?

  420. Hi gpuccio!

    Thank you for your response. You are of course right that we do not, as yet, have a compelling complete model of the transition from non-replicating chemicals to the earliest DNA-using life forms.

    If the ID argument was simply that science does not know how this was achieved, and so we cannot rule out Intelligent agency, I would have no problem with it. But the argument would be trivial, because even if we did have a good model, it wouldn’t rule out Intelligent agency as well.

    But as I understand it, the ID argument is that we can positively infer from the complexity of what is purported to be the simplest possible Darwinian-capable life form that it must have been designed. This inference rests the unsupported assumption that the simplest Darwinian capable life-form was, indeed, complex.

    But we do not know this, either, yet repeatedly I see it argued here that the Darwinian model fails because the simplest-Darwinian-capable life-form was too complex to have arisen by chance.

    This begs the central question. The central question is not: “how could the first complex cells with ribozomes etc have come about by chance?” (answer: they couldn’t), but: “what simpler Darwinian-capable proto-organisms might be ancestral to those complex early cells, and could have come about by, if not chance, physico-chemical interactions in the conditions prevailing on early earth?”

    And the answer is simply that we do not yet know, and may never know, although there are, as I’ve said, a number of promising-looking hypotheses that make testable (and tested) predictions.

  421. 60.1.2.1.5
    Elizabeth Liddle

    I hope you and GPuccio will excuse my intervention. You are saying:

    “This inference rests the unsupported assumption that the simplest Darwinian capable life-form was, indeed, complex.”

    First of all, what do you mean by “complex”? Do you have any metrics in mind when you say “complex”?

    On another point, I am afraid what you think ID claims is wrong. ID claims that all known life forms are complex and specific. Complexity alone will go through the ID explanatory filter and is therefore insufficient for design inference. Failure to include specificity leads to misinterpretations about ID claims.

    Further, I can conjecture that even if we assume that protolife was simpler than what we have now (we have no evidence it was, to my limited knowledge), this protolife will still have to be complex and specific enough to enable replication and metabolism. You are right in saying that until such times as we have solid evidence we can only conjecture about possible retrodictions. But that does not invalidate ID reasoning.

  422. Elizabeth:

    But as I understand it, the ID argument is that we can positively infer from the complexity of what is purported to be the simplest possible Darwinian-capable life form that it must have been designed. This inference rests the unsupported assumption that the simplest Darwinian capable life-form was, indeed, complex.

    The ID argument is that anything with enough complex functional information is empirically found to be designed, and therefore design is the best explanation for complex functional information.

    Obviously, alternative explanations can always be considered. The ID inference is an inference, not a logical deduction. The point is neither to “rule out” design nor to “rule out” darwinism. Science is not about ruling out, but about giving credible explanations. Design is a credible explanation of complex functional information. Darwinism is not. Nor is any alternative explanation available. Therefore, design is the best scientific explanation available. It’s as simple as that.

    ID is not making any assumption about “the simplest Darwinian capable life-form”. ID, being empirical, reasons with what we know: the simples observed life forms. It’s darwinism that is constantly making vast assumptions about “simple darwinian life forms” which have never been observed, neither in nature nor in the lab (and, I am sure, never will, for the simple reason that they don’t exist). That’s why I say that all OOL theories are fairy tales: myths, living only in the remote hope that the unicorn will some day be observed.

    Well, I would rather bet on the unicorn, than on “simple darwinian life forms”!

    The simplest living beings we know of are bacteria and archea. That is the fact. You say there may be simpler biological replicating beings? No problem. Show them. In nature, or in the lab.

    Show them. This is science, after all. And after having shown them, please show also how they became the bacteria and archea that we know, that exist, that have to be explained. Step by step, by naturally selectable, reasonably simple random variation.

    But nobody can do that, obviously, because nobody can show what does not exists and cannot exist. Those impossible things are found in imagination, in myths, and in darwinian theory, not in real life. Simple darwinian capable life forms do not exist, not any more than conscious computers, the pet toy of the other big lie, strong AI.

    But there is more. ID does not need the OOL problem to falsify darwinism. Darwinism is falsified by any single complex protein that we observe in the biological world.

    Take isoleucyl-tRNA synthetase, for instance. Just to speak of something that exists. One of the famous 20 proteins.

    In E. coli. it is made of 938 aminoacids. 938! Now, I am not asking, for now, if it “evolved” in “simple darwinian capable life forms”, whatever they may be, or in normal bacteria which. for some strange reason, lacked it and went along with only 19 aminoacids in their proteins. Let’s skip that part, for now.

    I just ask: how were those 938 aminoacids found and arrnaged in a complex, functional protein which has more or less remained the same for the remaining 4 billion years? Withe the same structure and function, and a primary sequence that, today, still shows a striking similarity with the human form? (220 identities, 27%, and 373 positives, 47%, in a very simple alignment of 818 AAs, that anyone can make on pubmed protein blast page).

    So, how did that single protein emerge? Has darwinism any credible model for that? No.

    That is not necessarily OOL stuff. We have thousands of independent basic protein domains, each of them emerged at different times in natural history, each of them completely non explained by any darwinian model.

    No, ID does not need OOL to falsify darwinism. OOL is certainly the biggest problem, but any single complex protein is a problem big enough.

  423. 426

    Hi Dr Liddle,

    My position is that the information contained within the genome exemplifies the same physical entailments as any other form of recorded information known to exist. These are entirely observable entailments, which include two separate but coordinated arrangements of matter, a physical effect, and the dynamic relationship that exists between these three. The observations surrounding these entailments are logically coherent, and they require a mechanism in order to come into being.

    That mechanism will need the capacity to cause an arrangement of matter to arise which can serve as a physical representation; it will also need to cause a second arrangement of matter to arise and serve as a physical protocol. These two objects acting together will need to cause a physical effect, and the entire system will need to operate under the well-defined dynamics which are observed to exist.

    Our disagreement is/should be about what mechanism has these capacities.

  424. The ID argument is that anything with enough complex functional information is empirically found to be designed, and therefore design is the best explanation for complex functional information.

    Therefore your Intelligent Designer must be designed. Would you like to tell us about that?

    The simplest living beings we know of are bacteria and archea. That is the fact. You say there may be simpler biological replicating beings? No problem. Show them. In nature, or in the lab.

    Show them. This is science, after all. And after having shown them, please show also how they became the bacteria and archea that we know, that exist, that have to be explained. Step by step, by naturally selectable, reasonably simple random variation.

    Any possible Intelligent Designer would be almost infinitely more complex and thus that much less likely to exist than a First Self Replicator. We can’t show you the First Self Replicator, but we don’t see any trace of your Intelligent Designer either. Please show Him, in nature or in the lab. Please show also how He came to be. We won’t require the steps to be natural, but we want to know what they were and what evidence you have for them.

    If you can’t show Him, but insist that He exists anyway then excuse us if we also insist that the nearly infinitely more likely First Self Replicator existed.

  425. KF: On p 1 at 3+ above, DM said:

    But evolution produces CSI

    T%his is a typical example of 6the rhetoric of confident assertion driven by a priori evolutionary materialism. Translated: we “know” it all happened by evo, so macro-evo mechanisms [presumably Darwinist ones] MUST be capable of producing CSI. Therefore, we see the triumphalistic conclusion and declaration: “But evolution produces CSI.”

    No, evolution producing CSI is well-settled observation. An excellent example is the evolution of teosinte, which is a weedy grass, into modern maize (corn). Google teosinte maize evolution for plenty of pictures. Here’s one of both the start and end products: http://www.maizegenetics.net/d.....n-genetics

    This all happened within the last ten thousand years. Because teosinte is still alive and archeologists have uncovered actual samples of the intermediate products, we have a very good record of teosinte’s evolution into maize, complete with DNA samples of the start, end, and all intermediate steps.

    In fact, a group is using genetic engineering to re-manufacture those intermediate steps and we will soon have actual living examples of teosinte, corn and every single step between them.

    Some of the CSI that was developed while teosinte evolved into maize includes going from the 6 to 12 kernels in two rows of teosinte to the hundreds of kernels in 20 or more rows of maize, going from a tooth shatteringly hard seed coat of teosinte to the soft seed coat of maize and developing the corn cob. Look at the pictures in my cite for details.

    Let’s see – Complex Specified Information. New Information? No doubt about it and we hve the DNA to prove it. Specification? Not even you can deny that the specification for maize is radically different from that of teosinte, but if you try, I’m going to invite you to chew on some teosinte while I eat some corn and we’ll see who goes to the dentist. Complex? You might quibble that only about fifteen mutations (IIRC) were necessary to turn teosinte into maize, but if you do everybody is going to laugh at you. Fifteen very useful mutations in less than ten thousand years is better than one very useful mutation every thousand years. Say it’s only one. Then in a million years, you’ve got 1000 new, useful, mutations at two bits of information each. What was that limit you were talking about? Around 500 bits, wasn’t it?

    “Oh, but people were involved!” Yes, but they didn’t chanage any DNA. They just spotted new plants that were softer / bigger / tastier or otherwise improved because of their new mutations and planted them instead of the old varieties. This speeded things up ten thousand fold, but all of the Information was produced by mutations.

    It’s CSI and it’s produced by Darwinian Evolution.

  426. DMullenix,

    Look at an icon of Christ and you will see Him. Cf. the Gospel of John 14:8-9.

    Look everywhere in nature and you will see His works. But in oder to be able to see one has to renounce his old self and the insane “wisdom of the wise”, to become pure in heart.

  427. dmullenix:

    Therefore your Intelligent Designer must be designed. Would you like to tell us about that?

    Wrong. The only requirement for an intelligent designer is that he is a conscious intelligent being. That in no way implies that he must be complex, least of all designed. You are making gratuitous assumptions, based on your personal phylosophy of reality.

    Any possible Intelligent Designer would be almost infinitely more complex and thus that much less likely to exist than a First Self Replicator.

    Again, wrong and unsupported. Mere reductionist faith.

    We can’t show you the First Self Replicator

    That’s for sure!

    but we don’t see any trace of your Intelligent Designer either

    Wrong. dFSCI in biological information is a very strong “trace” of the intelligent designer, an empirical and scientific trace.

    Please show Him, in nature or in the lab.

    The presence of dFSCI in biological information is evidence for a designer, exactly as the proteome is evidence for LUCA. Both are scientific inferences.

    Please show also how He came to be. that is not requested to infer that a designer designed biological information. Anyway, if and when I find scientific evidence about that specific point, I will inform you. I am not a darwinist, and therefore I do not discuss here issues about which I have no scientific evidence.

    We won’t require the steps to be natural, but we want to know what they were and what evidence you have for them.

    I don’t have any scientific evidence of how the designer came to be, and therefore, consistently, I do nmot discuss that point. I have scientific evidence of how biological information came to be (through a design process), and therefore, consistently, I do discuss that point.

    If you can’t show Him, but insist that He exists anyway then excuse us if we also insist that the nearly infinitely more likely First Self Replicator existed.

    Your First Self Replicator is a supposed physical entity, and therefore it can certainly be produced in the lab, if it really can exist. Moreover, you all insist that it should be simple, therefore why is it so difficult to produce one in the lab?

    My designer is a conscious intelligent being, of whom I do not know anything, except that:

    a) he must be a conscious intelligent being, otherwise he could not generate dFSCI

    b) he must have at least some propertie, derived from observation of the things designed (biological information). That is a field completely open to scientific inquiry.

    But the existence of my designer is a scientific inference based on facts. You have no fact upon which to base your First Self Replicator.

  428. That’s nice, Eugene, but it isn’t really a response to dmullenix’s post.

    On the one hand, you say that you don’t believe that there could have been a simpler ancestor to the oldest known organisms because you haven’t seen evidence of one. On hand you say that you do believe in the Intelligent Designer because you look everywhere in nature and see His works.

    Why is that different from someone who says they look everywhere in nature, sees that living things are descended from earlier things with modification, and extrapolates that the earliest known things must have been descended from still earlier things with modification?

    In fact it is different, because we have actual testable hypotheses about those still earlier things, whereas I know of no testable hypothesis arising from the theory that the earliest known living things were created ex nihilo by Christ.

  429. dmullenix:

    I don’t want to invade KF’s discussion with you, but what you affirm ir really ridiculous.

    It’s CSI and it’s produced by Darwinian Evolution.

    You must be kidding! I quote from the site you refer to:

    “So how was this dramatic transformation accomplished?

    Domesticated maize was the result of repeated interaction with humans within the last 10,000 years. Early farmers selected and planted seed from those plants with beneficial traits, while eliminating seed from those plants with more undesirable features. As a result, alleles at those genes controlling favored traits increased in frequency within the population, while more “deleterious” alleles decreased. Such selection was made possible due to the tremendous natural variation present in Z. mays ssp. parviglumis (nucleotide diversity at silent sites has been measured as high as 2 to 3%).”

    Where is darwinian evolution here? Where is RV plus NS?

    What we have here is intelligent selection (made by humans) of already existing information.

    Intelligent selection is design.

    You say: “Yes, but they didn’t chanage any DNA.”

    And so? One of the best ways an intelligent designer can act is by intelligent selection repeatedly applied to random new variation, or better still to already existing variation. That’s design all the way. Darwinian evolution has nothing to do with that.

  430. gpuccio:

    The only requirement for an intelligent designer is that he is a conscious intelligent being. That in no way implies that he must be complex, least of all designed. You are making gratuitous assumptions, based on your personal phylosophy of reality.

    Can you explain how a conscious intelligent being could be also simple?

    Are you arguing that intelligence requires no complex physical substrate?

    If so, what is your basis for this assertion?

  431. In fact, to re-use (with variance!) an argument I frequently see here:

    All examples of intelligent designers we know of are complex biological organisms.

    Therefore the intelligent designer of living things must have been a complex biological organism.

    What is wrong with this argument?

  432. Yes, of course there is “intelligent selection”, gpuccio, dmullenix already said that.

    But the “creative” variance occurred by chance, the very thing ID people claim cannot happen.

    The features that were selected were not designed by anyone.

    Unless you are claiming that the hazards that befall evolving populations are intelligently designed? That the Intelligent Design input into evolution is at the level of deciding who breeds and who doesn’t? That seems rather Jovian to me!

  433. Elizabeth,

    DMullenix wanted to see Him. If s/he does not want to take my word for it, there is a way to check. And though it is extremely hard, it is possible.

    In this particular case, it is not science, it is faith. But science can never contradict faith, if both are correct. What is sometimes meant by science is, unfortunately, far from it.

    For faith you need credible revelation, for science, in a sense, too, with the only difference that scientific revelation is irrespective of the state of your heart, as it were. Anyone with the same tools and enough skill can reproduce your experiments and prove/disprove the correctness of your theory. But it does require some level of edication and skill.

    In spiritual life, it is the same. Millenia of mankind testify to the simple truth that in order to prove/disprove the validity of someone else’s spiritual experience, your “wireless” (your heart, i.e. the centre of your being) also has to function correctly. Unfortunately, human nature is deeply marred by sin and that makes it a lot harder for us.

    In Orthodox Christianity spiritual life is health-checked against the experience of the previous generations via Ecclesiastical Tradition.

    I hope you can see similarities. I think it was Blaise Pascal who said that the final word of science is the first word of the Bible. With all my respect to your opinions, I would definitely agree with Pascal on this point.

    When I say I don’t believe in the power of evolution to account for the diversity of life, I am speaking not only from my religious standpoint. From a scientific perspective, this disbelief is also well warranted.

  434. 437

    Dmullenix,

    It’s reasonable to expect that you should be able to accurately express what ID is, even if you disagree with it.

    Therefore your Intelligent Designer must be designed. Would you like to tell us about that?

    Why does this nonsense persist? If someone examines the site of a fire to determine whether arson was committed, must that same person identify the arsonist, and his parents, all the way back to a designer or some cell?

    What’s telling is that you choose to ask such questions in this case but not in that case. You clearly understand that every cause need not be explained by a deep regression of causes, and yet you ignore it when it suits you.

    Please explain why determining design requires identifying a designer while determining arson does not require identifying an arsonist.

  435. 438

    Dmullenix,

    Strike this. It’s reasonable to expect that you should be able to accurately express what ID is, even if you disagree with it. It doesn’t apply and I meant to delete it.

  436. Elizabet:

    One at a time:

    1) Yes, of course there is “intelligent selection”, gpuccio, dmullenix already said that. But the “creative” variance occurred by chance, the very thing ID people claim cannot happen.

    Completely wrong, I am afraid. ID says that a random system alone cannot generate dFSCI. ID says also that a random syste + NS cannot generate the kind of dFSCI we observe, for instance, in basci protein domains, unless that information can be shown to be deconstructable in simple, naturally selectable steps. Which is not.

    It is obvious that RV + intelligent selection can generate dFSCI. I will make the most trivial example: Dawkin’s “Weasel”. It is very easy to generate random variation, select the correct variation when it happens by comparing it to the known final result, fix it, and go on with further variation. The simple point is, the designer has to know the final output in advance, and input it in the system. It’s not exactly as powerful as writing directly the output, but it is very powerful just the same.

    Another, more indirect way to add information to a system is to measure for the specific function one wants to develop. In that way, the function is neasured and recognized, even at very low levels that would never be useful in a biological context, even if in itslef it could never give a reproductive advantage. It is intelligently selected and “rewarded” by the intervention of the designer, That’s how bottom up protein engineering is done. It is a powerful method of design, too.

    None of that is darwinian evolution. None of that is RV + NS. All of that is design.

    That the Intelligent Design input into evolution is at the level of deciding who breeds and who doesn’t?

    I have argued many times here that one of the possible ways design is implemented in ntural history if through intelligent selection of RV. There are many ways that could happen.

  437. From a scientific perspective, this disbelief is also well warranted.

    Well, for a start, in science we postulate, we do not “believe”. Our postulates may be supported, or infirmed by data.

    As of now, we postulate that the earliest known organisms were descended from still earlier ones. The alternative is to postulate that they were created ex nihilo, fully formed.

    The second is untestable, and the only grounds for “believing” it, must be religious, or, at best, of arguing from lack of an alternative model.

    But there is, in fact, an alternative model, which is the first. It lacks detail, right now, and is only partially supported by data, but there are some promising leads.

    This means that scientists do not “believe” that the earliest known organisms were descended from earlier simpler ones, but see no reason to postulate ex nihilo creation (for which there is no evidence at all) when some promising models, based on known mechanisms, are to hand.

    Instead, they simply say: “we do not know how the earliest known organisms came to be, but we have some promising leads that suggest that they evolved from simpler organisms and proto-organisms, possibly by a pathway something like this (insert OOL theory of your choice)”.

    In other words, neither belief nor disbelief is scientifically warranted, but nor is belief in ex nihilo creations. Disbelief in ex nihilo creation is somewhat warranted, or, at least, skepticism is well-grounded, because absolutely no mechanism is ever postulated for such an act by any agent, intelligent or otherwise.

  438. GP cannot fathom that natural selection is far more powerful than artificial selection, at least in terms of adapting populations to environmental change.

    Artificial selection monitors one, or a few, phenotypic features, while natural selection monitors all possible changes and all possible ways in which fitness might change.

    Using the Adam Smith metaphor, a command economy optimizes the production of buggy whips while the market economy is transitioning to automobiles. Directed evolution can only optimize what it can foresee. Natural selection moves in unforeseen directions.

  439. 442

    Elizabeth,

    Therefore the intelligent designer of living things must have been a complex biological organism.

    We also observe that intelligent designers are not restricted to designing after their own likeness. A person can design a car. It doesn’t take an intelligent car to do it.

    The property of intelligence is relevant, not the physical makeup of the agents. How often do physicists look for some particle or mass because certain properties seem to indicate it, while ruling out any known particle or mass?

  440. Natural selection is an oxymoron as nature doesn’t select and as a matter of fact NS is just a result of three processes- differential reproduction due to heritable random variation.

    Not only that ALL observations and experiences demonstrate that natural selection leads to a wobbling stability:

    Chapter IV of prominent geneticist Giuseppe Sermonti’s book Why is a Fly Not a Horse? is titled “Wobbling Stability”. In that chapter he discusses what I have been talking about in other threads- that populations oscillate. The following is what he has to say which is based on thorough scientific investigation:

    Sexuality has brought joy to the world, to the world of the wild beasts, and to the world of flowers, but it has brought an end to evolution. In the lineages of living beings, whenever absent-minded Venus has taken the upper hand, forms have forgotten to make progress. It is only the husbandman that has improved strains, and he has done so by bullying, enslaving, and segregating. All these methods, of course, have made for sad, alienated animals, but they have not resulted in new species. Left to themselves, domesticated breeds would either die out or revert to the wild state—scarcely a commendable model for nature’s progress.

    (snip a few paragraphs on peppered moths)

    Natural Selection, which indeed occurs in nature (as Bishop Wilberforce, too, was perfectly aware), mainly has the effect of maintaining equilibrium and stability. It eliminates all those that dare depart from the type—the eccentrics and the adventurers and the marginal sort. It is ever adjusting populations, but it does so in each case by bringing them back to the norm. We read in the textbooks that, when environmental conditions change, the selection process may produce a shift in a population’s mean values, by a process known as adaptation. If the climate turns very cold, the cold-adapted beings are favored relative to others.; if it becomes windy, the wind blows away those that are most exposed; if an illness breaks out, those in questionable health will be lost. But all these artful guiles serve their purpose only until the clouds blow away. The species, in fact, is an organic entity, a typical form, which may deviate only to return to the furrow of its destiny; it may wander from the band only to find its proper place by returning to the gang.

    Everything that disassembles, upsets proportions or becomes distorted in any way is sooner or later brought back to the type. There has been a tendency to confuse fleeting adjustments with grand destinies, minor shrewdness with signs of the times.

    It is true that species may lose something on the way—the mole its eyes, say, and the succulent plant its leaves, never to recover them again. But here we are dealing with unhappy, mutilated species, at the margins of their area of distribution—the extreme and the specialized. These are species with no future; they are not pioneers, but prisoners in nature’s penitentiary.

    The point being, that IF it were left to direct scientific observations, evolutionism fails miserably and all that is left is wishful thinking supported by speculation.

  441. Elizabeth:

    2) Can you explain how a conscious intelligent being could be also simple? Are you arguing that intelligence requires no complex physical substrate? If so, what is your basis for this assertion?

    In my model, which has also been the model of many thinkers, and philosophers, in the history of human thought, consciousness is in essence transcendental and simple. Its interface, that allow it to interact with the outer world, is often complex, at least in humans.
    Yes, I am arguing that consciusness and intelligence, in pure form, do not necessarily require any complex physical substrate. Maybe no physical substrate at all.
    The basis for that assertion is that cosnciousness exists, and is in no way explained by its physical interface. IOWs strong AI is a gross falsity.

    In fact, to re-use (with variance!) an argument I frequently see here: All examples of intelligent designers we know of are complex biological organisms. Therefore the intelligent designer of living things must have been a complex biological organism. What is wrong with this argument?

    It is an argument that can be made, but that is based on a series of assumptions which are, IMO, evidently false.
    The worst assumptions are those about human cosnciousness. One thing is to say that in humans design is certainly accomplished using a physical interface. Another thing is to say that conscious intelligent representations, the basis for design, are explained by the physical interface. If consciousness is not explained by the physical interface, either complex or not, then it must be accepted as an independent principle in our map of reality.

    If that is the case, we have no reason to beleive in advance that consciousness always requires a physical interface.

    Human have believed for millennia, basing their belief on both reason and experience, that consciousness exists independently of the physical interface. I certainly do believe that. There is nothing in all our knowledge that can falsify the “transcendental subject – physical interface” model. Indeed, it is the best explanation we have for our empirical experience of conscious events.

    It is rather obvious that ID infers the existence of a designer for biological information, but it is not likely that the designer is a human being. While the designer has to have conscious, intelligent, purposeful representation to design things, there is no reason that those representations must necessarily be implemented through a complex physical interface, like in humans.

  442. It isn’t nonsense. What is (IMO) nonsense, is this:

    If someone examines the site of a fire to determine whether arson was committed, must that same person identify the arsonist, and his parents, all the way back to a designer or some cell?

    That same person need not identify the arsonist, but must, beyond all reasonable doubt, demonstrate that the fire was deliberately started by a human being. In order to do so, a clear sequence of causal mechanisms must be established – what was the accelerant? Where was it poured? What ignited the fire? Could these patterns be explained by other causes? Did any human being have access to the materials, have any motive, have any opportunity? If so, was that human being able bodied, and able to carry out the alleged process?

    And that is crucial. You cannot (indeed you must not) conclude that a fire is due to arson without identifying the actual mechanisms by which the fire was started.

    In the case of ID, no such mechanism is ever advanced (apart from “front-loading” which is perfectly testable, but no-one seems to want to test it, and even then, no mechanism is ever, to my knowledge, advanced about how that first front-loaded genome was instantiated in molecular form within a viable cell). We are left to accept that some agent, using unknown physical means, created living things, continually directly adjusted (unless we go for front-loading) genomes so that useful variants would be created, perhaps adjusted the environment so that certain complex traits would be selected, made sure that what appears to us as random drift favoured certain variants without impacting on the statistics, and was itself (the intelligent agent) either complex but not designed, or not complex, yet able to do these things with neither tools nor brain at its disposal.

    Simply sitting back and saying: hmm, it looks designed so there must have been a designer, no we don’t know who the designer was, and how s/he did it is irrelevant to determining whether any designer did so, certainly wouldn’t (or shouldn’t) stand up in a court of law.

    If you want to know whether, you need to know how, and if you want to know how, you are going to need to speculate about who.

    If the fire was accelerated with the contents of a large drum of gasoline, then you can probably rule out people too puny to move such a thing.

    How were those first biological molecules moved into position, and what physical characteristics must the agent who did so have possessed? What evidence do we have that might shed light on these questions?

    And if we have none, how can ID claim to be “science”?

  443. “If you want to know whether, you need to know how.”

    Not necessarily. E.g. if you have locked a room with a 10 digit lock and find it unlocked, to deduce that it was unlocked by someone intelligent you do not have to know how they did it. Evolution rests upon the hypothesis that the door unlocked itself.

  444. gpuccio: thank you for your detailed response. Here is mine:

    In my model, which has also been the model of many thinkers, and philosophers, in the history of human thought, consciousness is in essence transcendental and simple. Its interface, that allow it to interact with the outer world, is often complex, at least in humans.
    Yes, I am arguing that consciusness and intelligence, in pure form, do not necessarily require any complex physical substrate. Maybe no physical substrate at all.
    The basis for that assertion is that cosnciousness exists, and is in no way explained by its physical interface. IOWs strong AI is a gross falsity.

    I disagree, in fact, but let me grant, for the sake of this discussion, that consciousness is a transcendental and simple property (whatever that means) that is separable from any physical substrate (that p-zombies, in other terms, are possible). Right now I am not concerned with consciousness but with intelligence. We know a lot about how intelligence works, even in models were “consciousness” is not assumed. Robotic devices can be “smart”, increasingly so.

    But your claim is that a being with no physical substrate, no logic circuits, no neurons, can be “smart”. To me, that seems to be a quite unjustified claim!

    The worst assumptions are those about human cosnciousness. One thing is to say that in humans design is certainly accomplished using a physical interface. Another thing is to say that conscious intelligent representations, the basis for design, are explained by the physical interface. If consciousness is not explained by the physical interface, either complex or not, then it must be accepted as an independent principle in our map of reality.

    Again, assuming that consciousness is not explained by the physical interface (I do not agree, but again will grant for the purpose of this discussion), the effects of consciousness must surely involve a physical interface? If, as pure disembodied consciousness, and even, let me grant for now, intelligence, I may be able to conceive the purpose of creating a great building, or work of literature how do I achieve this without interfacing with the physical world of bricks and paper? How do I lift those bricks into position? How do I move the pen across the paper?

    Your disembodied mind must, at the minimum, be an entity that exerts physical force, or else no matter how wonderful the conceived design, no execution of that design can occur. Are you arguing that your disembodied mind is nonetheless a physical force? A mass-less, energy-less physical force?

    Does your postulated Intelligent Designer in fact violate the 2nd Law of Thermodynamics? This seems a much a far “worse assumption” than any of mine!

    It is rather obvious that ID infers the existence of a designer for biological information, but it is not likely that the designer is a human being. While the designer has to have conscious, intelligent, purposeful representation to design things, there is no reason that those representations must necessarily be implemented through a complex physical interface, like in humans.

    In that case, how is the interface with physical reality achieved?

  445. ScottAndrews, say there’s been a fire in the woods. Exhaustive investigation reveals no trace whatsoever of any human being anywhere near the scene at any time near when the fire started.

    However, there are scores of rats running loose and they are gnawing on scores of boxes of “strike anywhere” matches. It is well documented that rats start fires gnawing on “strike anywhere” matches.

    Yet you insist that a human started the fire.

    Welcome to the world of ID.

  446. Scott, anything that designs a car must be more intelligent than the car.

    You will never get any kind of intelligence above that of an amoeba with less than a giga bit of information. And that’s a lowball estimate.

  447. No, evolution does not “rest upon the hypothesis that the door unlocked itself”.

    ID rests on the hypothesis that the door was unlocked by mysterious agent that left no fingerprints, nor any evidence that s/he exerts any physical force upon the world. Or even exists.

    In contrast, evolutionary theory posits a vast set of physical mechanisms, including physics and chemistry, to account for the creation of variance, and even reproduction, and the simple logic that if self-replicators replicate with heritable variance in reproductive success in the current environment, populations will adapt to their environment by evolving functions that maximise their ability to survive and reproduce.

  448. 451

    Dmullenix,

    What was the point of that little story? Why would anyone determine arson in that case? You’re avoiding the question. If the signs point to arson (accelerant, etc.) then do you call it arson or do you reason that it can’t be arson until you identify the arsonist and his ancestry? The question is simple.

    You apply rational standards in once case and then do a U-turn when it suits you to apply different standards. Apparently the greatest difference between the examples is you and your preference.

  449. 452

    Dmullenix,

    I’m blown away. Not because your point is irrelevant, but because you use the amount of information in an amoeba to support your argument when it suits you.

  450. “In contrast, evolutionary theory posits”

    With the only exception that it does not really work on the grand scale. The only reliable evidence that it works is on microlevel.

    In order to infer design of an object one does not have to replicate it. It is sufficient to analyse information the object carries. So the fingertips are there available for analysis.

  451. DMullenix,

    That is awesome! The only remaining bit to explain is how the strike anywhere matches came into being… So you assume your matches just spontaneously self-organised :)

  452. 455

    Elizabeth,

    evolutionary theory posits a vast set of physical mechanisms, including physics and chemistry, to account for the creation of variance, and even reproduction

    It posits everything and applies nothing. Which mechanisms account for reproduction? Apply these mechanisms to some specific variance, like mammalian lungs. You’ll quickly see that it becomes very high-level, and the physics and chemistry are nowhere to be found, like not-so-close friends on moving day.

  453. “Scott, anything that designs a car must be more intelligent than the car.”

    Excellent! I agree. But what’s more, the designer must be capable of running the project to successful completion.

    The Designer of our cosmos is indeed omniscient and omnipotent :) The only thing you are still missing out is that He does not have to have the same nature as the cosmos He created ex nihilo.

  454. Your citation of Sermonti explains a lot about your views in general. It would take a whole web site to unravel his books.

    I will only say that online reviews are available.

  455. I mean to be able to do it.

  456. I have argued many times here that one of the possible ways design is implemented in ntural history if through intelligent selection of RV. There are many ways that could happen.

    Correct me if I’m wrong, but it appears you are invoking foresight. Selecting variants for future need in some yet uncompleted structure.

    Is that a fair characterization?

  457. One at a time:

    1) Yes, of course there is “intelligent selection”, gpuccio, dmullenix already said that. But the “creative” variance occurred by chance, the very thing ID people claim cannot happen.

    Completely wrong, I am afraid. ID says that a random system alone cannot generate dFSCI. ID says also that a random syste + NS cannot generate the kind of dFSCI we observe, for instance, in basci protein domains, unless that information can be shown to be deconstructable in simple, naturally selectable steps. Which is not.

    Well, depending on what you mean by “a random system alone”, of course, a system in which variance is randomly generated, but without heritable variance in reproductive success, cannot generate anything much, certainly not an adaptive population, and therefore not FSCI (what does the d stand for?). So there is no disgreement there.

    However, the claim that a system in which variance is randomly generated and subject to natural selection i.e. where that genotypic variance results in heritable variance in reproductive success cannot result in dFSCI (or, at least in an adaptive population) certainly is in dispute, and we can see, for example, in evolutionary computer algorithms, that it does indeed. Not only that, but what evolves can be “irreducibly complex” in the sense that necessary precursor steps need not be advantageous, and can even be deleterious. So there is no principled reason for thinking that random heritable variance in reproductive success can’t result in evolving functions that optimise a population for its environment.

    Or, at any rate, you have not stated one!

    It is obvious that RV + intelligent selection can generate dFSCI. I will make the most trivial example: Dawkin’s “Weasel”.

    Yes, indeed it is, but, interestingly, “intelligent” selection is less, not more, likely to produce complex functions. If a dog breeder, for example, wants to breed a particular feature, and only selects for breeding, pups that seem to show mild traits of that feature, s/he may well fail, because a really effective version of the desired feature may require superficially “backward” steps. In Dawkins’ weasel program, there are no necessary backward steps on any path to the unique solution. In AVIDA, there are, and if an “intelligent agent” were to do the selecting, they could well fail to “breed from” individuals who were less fit than their peers, but who contain genomic sequences that are necessary for the most advanced function.

    Intelligent selection is a quick way of getting to a specific function, but it’s not the best way of evolving a fit population (which is evidenced, of course, by the poor health of many highly bred domestic species), and certainly not the best way of evolving complex functions (I don’t call floppy ears or a cute nose, “complex”!) such as EQU in AVIDA or wings, or eyes.

    It is very easy to generate random variation, select the correct variation when it happens by comparing it to the known final result, fix it, and go on with further variation.

    You have taken a wrong turn here, in fact two. First of all, in nature there is no “correct” variation. There is simply differential reproductive success. Organisms with genotypes that tend to produce thriving phenotypes will, by definition, be more likely to pass those genotypes on to descendents. So they are also, by definition, the “correct” genotypes for their environment – ones that work. And your second wrong turn is that no artificial selection system that I am aware of “fixes” “incorrect” variations before continuing. Variants that are undesired are simply not bred from, or given fewer opportunities to breed. This is true of Weasel, and of animal breeding. Nothing is “fixed” (at least not yet – genetic medicine may be on the horizon).

    The simple point is, the designer has to know the final output in advance, and input it in the system. It’s not exactly as powerful as writing directly the output, but it is very powerful just the same.

    Again you have taken a wrong turn. In evolutionary algorithms (not weasel, but almost every other one), the output of the evolving organisms is assessed against a criterion (just as it is, naturally, in wild species) but the organisms themselves as output is NOT specified.

    Let me give a real example. I can write an evolutionary algorithm that works as a classifier. I give it two sets of brain images, one from a patient group, and one from a healthy volunteer group. Starting with a population that has no better than 50:50 chance of correctly classifying each brain, I end up with a population that can correctly classify every brain. I then give it a set to classify, and hope that it also correctly classifies them.

    In other words, I start by specifying what output I want from the classifiers (correct classification of the brains), but I do not specify the parameters of the best classifiers. They have to evolve. Starting with randomly generated parameters, I selectively “breed” from those that, through chance, happen to do better than 50:50, and, from their offspring, again, selectively “breed” from the best, and so on.

    However, the output I am interested in is not the output from the classifier (correct classification) but the set of parameters evolved by the best classifier. And this output is not specified in advance. Indeed I have no idea what they are – what they give me is new information And I can plot those parameters on a brain image and note where the largest parameters are – and that tells me what brain areas differ between the patients and the healthy volunteers.

    That, surely, by any calculation, is FCSI – it’s functional, it’s complex, it’s specific, and it’s information, and it did not exist before it evolved within my algorithm. It was certainly not specified in any form by me.

    Another, more indirect way to add information to a system is to measure for the specific function one wants to develop. In that way, the function is neasured and recognized, even at very low levels that would never be useful in a biological context, even if in itslef it could never give a reproductive advantage. It is intelligently selected and “rewarded” by the intervention of the designer, That’s how bottom up protein engineering is done. It is a powerful method of design, too.

    Yes, that’s possible. But there are other ways in which neutral (i.e. non-advantageous) variants can get into the gene pool, and that is by drift. Indeed even slightly deleterious variants can do this, which is why EQU is able to evolve in AVIDA.

    None of that is darwinian evolution. None of that is RV + NS. All of that is design.

    Clearly artificial selection of non-advantageous traits because you anticipate that they may be a precursor of advantageous traits is design.

    None of the other things are, for the reasons I have given unless you stretch your use of the term so that it includes Darwinian processes themselves. Certainly intelligence is not required at the selection part (in better words: intelligence is not required to specify which variants should breed – that can be a direct result of phenotypic properties), and as I think you agree, it is not required at the production-of-variance part.

    So both components necessary for Darwinian evolution to occur are naturally occurring. No designer is required (except possibly to get the whole thing started, but that’s not an argument about Darwinian evolution, it’s an argument about organic chemistry).

    That the Intelligent Design input into evolution is at the level of deciding who breeds and who doesn’t?

    I have argued many times here that one of the possible ways design is implemented in ntural history if through intelligent selection of RV. There are many ways that could happen.

    Well, apart from the fact that none is required (things that breed better will breed more), how does your postulated bodiless ID affect who breeds and who doesn’t? What are these “many ways”?

  458. Why does that blow you away?

  459. You just moved the goal posts :)

    Arguing from analogy is fraught with problems.

    What I mean when I say that you need to know something about the designer is that you need a mechanism. This is as true of detecting arson as it is of detecting deliberately designed life.

    We know, when we infer arson, that we are, from the evidence, inferring that a physical person with physical arms, physical matches, and physical gasoline formed part of the causal chain that started the fire.

    Where, in ID theory, no matter what you think about a designer, are the physical mechanisms? How were the molecules moved, if not by a physical being, exerting physical force?

    In an arson investigation, if there is no evidence for the gasoline being placed at the scene of the fire, and ignited, then you can’t conclude arson. You’d have to conclude that the gasoline got spilled somehow (earthquake? tornado?), then was ignited by some spontaneous spark.

    The source of which you would then look for.

  460. You are not, presumably, suggesting that we do not know how reproduction occurs? If not, what are you asking?

    And I’m not sure what you mean by “physics and chemistry are nowhere to be found” with regard to specific variants. The entire field of genetics draws on both physics and chemistry.

    And in many cases we can identify the precise gene variants responsible for different features.

    I’m really not sure what the basis for your claim is!

  461. 464

    I blown away that someone could simultaneously argue that no intelligence is required and that too much intelligence is required. But you’re right, I shouldn’t even be phased.

  462. Round and round in circles we go!

    What I mean when I say that you need to know something about the designer is that you need a mechanism.

    Speaking of circles, how about that famous functionally specified complex organised set of rocks known as Stonehenge? By what mechanism was that assembled? And if we don’t know the mechanism, then does that mean it wasn’t designed and that we can’t even infer design? Because that is the conclusion you must draw from your line of reasoning, Lizzie. And, any serious thinker must agree that that’s obviously false.

    We do not need to know anything at all about the motivations, origins, powers or mechanisms of the Designer(s) to conclude that something has been Intelligently Designed for a purpose (nor do we need to know what that purpose is).

  463. 466

    Elizabeth,

    The trouble with analogies is that they are analogies.

    Where, in ID theory, no matter what you think about a designer, are the physical mechanisms? How were the molecules moved, if not by a physical being, exerting physical force?

    Just because the identifying marks of the case in the analogy are specific physical mechanisms, that doesn’t mean that the same must be so in any possible case.

    You could do analysis on a piece of writing and perhaps attribute it to a specific author without knowing whether it was originally typed, handwritten, dictated, or tapped in Morse code.

    As far as how those molecules are manipulated, you’ve readily admitted that abiogenesis research has no detailed explanations, only hypotheses supported by data. And that’s fine.
    And, as I’ve replied previously, any of that research could also be applied to determining how an intelligent agent might have created life. So to the extent that any other explanation is supported by physical evidence, so is this one.

  464. OK, I get what you are saying, thanks.

    Let me respond directly to your post:

    We also observe that intelligent designers are not restricted to designing after their own likeness. A person can design a car. It doesn’t take an intelligent car to do it.

    No indeed. But I don’t really get your point. Are you saying that an unintelligent agent can design an intelligent person? If so, I’d agree, and I’d call that “unintelligent agent” heritable variance in reproductive success :)

    The property of intelligence is relevant, not the physical makeup of the agents. How often do physicists look for some particle or mass because certain properties seem to indicate it, while ruling out any known particle or mass?

    And they do so by looking for traces of that missing particle. What are ID researchers doing to try to find traces of the missing Intelligent Designer?

    This is what I keep asking, and people keep telling me: you don’t need to know what it is, just that it exists.

    This isn’t how physics works. People inferred the existence of the luminiferous ether, and went looking for it. They couldn’t find it. Did they just shrug and say: well, we know it must be there, maybe it has no physical properties (which would be silly, because they inferred it from its apparent physical effects). No, instead, they revamped the whole of physics so that it hung together without requiring the missing ether.

    I don’t think your analogy does you a lot of good :)

  465. Elizabeth:

    Thank you for the interesting comments. I will try to answer briefly, even if, obviously, we are opening the discussion to deep aspects which necessarily touch many philosophical, and not merely scientific, points. Anyway, I will try to stay as empirical as possible.

    First of all, I would like to clarify that I do believe that consciousness in its essence is transcendental, independent of physical interface, and that it has a fundamental property that can be described as both cognition and feeling. In pure form, those aspects of consciousness are not tied to specific representations. In our experience of human consciousness, however, we usually represent what arrives to us through the interfece (for instance, the brain), but the cognitive and sentimental value of those representations are essentially a product of consciousness itself.

    So yes, intelligence can be completely separated from specific representations and form the interface. In us humans, intelligence works mainly through the brain interface, and uses its computing structures, but every meaning, purpose, sense of good and evil, pleasure and pain, are properties of consciousness, not of the physical computing apparatus.

    You say:

    But your claim is that a being with no physical substrate, no logic circuits, no neurons, can be “smart”. To me, that seems to be a quite unjustified claim!

    Why? There is nothing strange in that. Pure consciousness can be much more than “smart”: it can be wise.

    You say:

    Again, assuming that consciousness is not explained by the physical interface (I do not agree, but again will grant for the purpose of this discussion), the effects of consciousness must surely involve a physical interface?

    Sure. You are perfectly correct here. I absolutely agree.

    If, as pure disembodied consciousness, and even, let me grant for now, intelligence, I may be able to conceive the purpose of creating a great building, or work of literature how do I achieve this without interfacing with the physical world of bricks and paper? How do I lift those bricks into position? How do I move the pen across the paper?

    You certainly have to do all that.

    Your disembodied mind must, at the minimum, be an entity that exerts physical force, or else no matter how wonderful the conceived design, no execution of that design can occur. Are you arguing that your disembodied mind is nonetheless a physical force? A mass-less, energy-less physical force?

    Not exactly. I believe that my “disembodied mind” (the designer’s) does exactly what my own “disembodied mind connected to a physical brain” (my personal mind) does all the time: it interacts continuously in both directions with a physical structure (the brain, and in particular the neurons). In the case of the designer, the physical structure would not be a personal brain, but possibly the cells of biological beings to be designed for further evolution.

    As you are certainly a good knower of the field, you must be aware of some kinds of approach to the problem thaty resemble in some way my position, for instance Eccle’s. Many others have well argued here for models where the brain cells are influenced at subatomic level, in quantum modalities, by consciousness. You may have read, for instance, “The spiritual brain”, a well done review of some of these issues. Interesting insight about such problems can also be found in Penrose’s books, although his approach is slightly different.

    My approach is simple enough. Consciousness receives input from the brain, “reading” or “perceiving” its neuronal states. And it can also output to the brain, at quantum level probably, contrlling key aspects of the neuronal work without violating any known physical laws. The special nature of quantum reality allows that.

    That’s what happens every moment in our brains. Biological design could well be implemented by similar mechanisms. A “disembodied consciousness” can well “read” the existing information in biological cells, including the inputs from interactions of those cells with the environment, and output to those cells, controling crucial aspects of their informational history.

    I have suggested some key possible ways in which consciousness could “design” biological informatio directly:

    a) Controlling mutations, that would be at least in some cases not random, but guided. Let’s call this modality “guided variation”.

    b) Selecting random variations. Let’s call this modality “intelligent selection”.

    Guided variation and intelligent selection can well explain how the designer’s information and his purposes are implemented in biological information. No physical laws need to be violated in the process.

    Obviously, there is also the possibility that consciousness can act as a “force”, as you say. I am not excluding that. In that case, some kind of new force could in the future be observed, probably at subatomic level, in living beings, whose processes, being typically “far from equilibrium”, can at present scarcely be exhaustively described in terms of our known laws of matter.

    What I am saying is that such a “force” modality is really not necessary to convey information at the quantum level.

    Does your postulated Intelligent Designer in fact violate the 2nd Law of Thermodynamics? This seems a much a far “worse assumption” than any of mine!

    I have tried to explain that such an assumption is not necessary. The second law of thermodinamics can well rest in peace. It is essentially a probabilistic law, and strictly tied to the concept of information. Shakespeare did not violate it, I presume, while writing Hamlet, and yet Hamlet is one of the most wonderful examples of information being created by a consciousness (not by a brain, not by a brain…).

    For the biological designer, what we need is only a different model of interface between consciousness and matter, different from the one that daily works in us, and yet at the same time based on the same principles.

    In that case, how is the interface with physical reality achieved?

    Something like the following.

    The designer’s consciousness is aware of existing biological beings. It understands cognitively that existence, and it loves that existence, and yet it has a purpose, it wants to express more through that existence. So, the designer’s consciousness interacts with the information already there, graduallly or more likely rather abruptly, and shapes it in new forms, expressing new functions, through guided variation or intelligent selection or both, or through other modalities we still have to understand. Probably, no physical laws are violated. Or just laws that we still don’t understand well are used. The result is that new, crucial information is inputted, and new biological beings are engineered.

    That model can also apply to OOL, if the designer’s consciousness can perceive and arrange inanimate matter in the same way it perceives and arranges biological matter.

    The final result can be simple. Suppose a new protein is needed for a new project. Everything could happen in a way similar to what darwinist think: a gene is duplicated and inactivated; then the desinger acts in the sequence, changes nucleotides, through guided variation that is in perfect accord with all biochemical laws: only it is not random, but shaped by intelligence. Or he can fix random variation that is in accord with the project, like in the Weasel model. When the new gene has the desired form, it is ready to be activated, and to be inserted in the new project, and coordinated with all the other designed information that has been added in the meantime.

    As you certainly understand, I am not saying that things went that way. It’s just a very tentative scenario, to answer your questions about “how it could be possible”.

  466. We do not need to know anything at all about the motivations, origins, powers or mechanisms of the Designer(s) to conclude that something has been Intelligently Designed for a purpose (nor do we need to know what that purpose is).

    Yes, we do, Chris, if we are going to make a substantiated inference.

    Unless you are simply going to assert that some disembodied, massless, energy-less force managed to interact with the physical world, and thus violate the 2nd Law of Thermodynamics.

    Without leaving a trace.

  467. Elizabeth,

    You see, if you decide to stay within materialistic naturalism you are bound to face infinite regression of cause and effect, hence my sneer at the strike-anywhere matches. DMullinex’s matches are not a mere deficiency of analogy. They are bound to exist in this or that form in any such reductionistic scheme even though their names might be different. In your reasoning these matches are called the first abiotic self-replicator.

    The only sensible way out of this is to suppose there is the Originating Super-Cause that is outside of this world and is therefore not bound by any cause-effect necessity.

    A bonus one gets as a result of doing away with reductionism is gaining a purpose. In materialistic schemes purposes may only be myopic and local but never the final Aristotelian cause.

  468. Congratulations gpuccio! That is very lucid, and very brave.

    I think it is completely wrong, but much rather that than “not even wrong” :)

    Will be back later :)

    Cheers

    Lizzie

  469. Petrushka:

    Although there are many possible implementations, the logical principles of design are simple, and we can derive them form our experience as designers:

    a) The designer already has the information he wants to implement. Then he can do two differen things:

    a1) Directly write the information in the appropriate support.

    a2) Intelligently select and fix the correct information as it comes from random variation: that’s the case of the Weasel modle.

    b) The designer does nto have the final information, but has some form of specific understanding of how to find it. For instance, he knows the form of the search space and can shape the search algorithm so that finding the target is hugely more likely. Or he is just aware of the function to be expressed, and can measure it, even at very low levels, and shape intelligent selection based on measure and reward of that function after cycles of random variation.

    In all cases, the designer has some intelligent understanding of the problem to be solved. And a definite purpose in solving it.

    I don’t know if that’s what you mean by “invoking foresight”. If it is, well then I am doing exactly that.

  470. Cheers :)

    Giuseppe

  471. So, do you rule out a “substantiated inference” to the design of Stonehenge, Lizzie? Do you think we should be searching for an accidental, naturalistic explanation for its creation instead?

    Functional Complex Specified Organisation leaves all the trace we need (if you’re not allowing theological objections to distort your reasoning).

  472. 475

    Elizabeth,

    The point is simple. Why would you acknowledge that a carbon-based life form with DNA can build a car made of steel and other components, and then reason that only a carbon-based life form with DNA can build a carbon-based life form with DNA? What logic requires that?

    And they do so by looking for traces of that missing particle. What are ID researchers doing to try to find traces of the missing Intelligent Designer?

    Try indoctrinating every physicist with the idea that a particle or mass they don’t observe can’t possibly exist, and then see how far the search for it gets.

    If someone else wrote what you just did I would tell them to go read the FAQ and gain a fundamental understanding of what ID is so they could make informed comments. What is your excuse?

    Going back to the arson example, since when does a forensics investigator determine arson and then go hunting for the arsonist? He doesn’t. He writes up a report saying that it was arson and then leaves to go look at the next fire. Someone else looks for the arsonist.
    You see, science doesn’t stop because someone draws a conclusion. But that doesn’t mean that one series of tests answers everything. One conclusion leads to a new investigation.

    By your reasoning, the arsonist would examine the evidence and determine arson. The police would ask him who set the fire. He’d say, “I don’t know,” and then the police would tell him that it couldn’t be arson. No one would ever investigate or find arsonists because of their illogical basis for ruling out arson. That would be quite ignorant.

    This is simple. It gets repeated over and over, and then people like you who should know better by now go back to it again.

  473. 476

    Chris,

    Give it up. I should. Some people will rule out believing one thing unless they see it with their own two eyes and then apply a radically different standard when it suits their fancy. When you dig past all the lip service paid to reason and science there’s nothing but a personal preference waiting at the bottom.

  474. 61.1.1.1.1

    Elizabeth,

    Well, for a start, in science we postulate, we do not “believe”.

    A big-big no. Science rests on belief. The word “belief” is carved in the foundation of it.

    Scientific method rests on believing that

    (a) objective reality exists, and
    (b) we can establish a coherent understanding of the world.

    This is a belief. It is not possible to prove or refuiute this. Solipsism, e.g. does not believe that such a world picture reflects objective reality.

    Your postulates come a distant second. These postulates when formulated are also believed to be true. You see, in science that even E = m*c^2 is sometimes doubted :) But what is doubt if not the other side of belief?

  475. “Disbelief in creation is warranted.”

    Dear Elizabeth,

    The wisest people admitted that the only thing they knew was that they knew nothing. What warrant are you talking about? Skepticism, yes, at most.

    To answer the question about the existence of God in the negative, one has to know everything. As ethical scientists, we have no moral right of making such a negative claim until such times as we know that we know everything, we have looked for God everywhere and we haven’t met Him.

  476. The designer already has the information he wants to implement. Then he can do two differen things:

    Explain to me where the designer stores his database of functional sequences, since everyone seems to agree that the number of possible sequences exceeds the number of particles in the universe. And everyone, including Douglas Axe, agrees that there are no shortcuts to knowing how a coded sequence will fold when interpreted as a protein.

    Of course the folding problem is just the beginning. The problem is multiplied by the problem of determining fitness in the current environment. Not to mention the problem of foreseeing the future environment.

    How does the designer know what problem needs to be solved? In real life, complex design has to balance many factors.

    Natural selection finds a current optimum the same way the marketplace sets prices. The analogy remains as apt as it was 150 years ago. There is no single price. There are clouds of prices centered around a mean. The mean shifts, but there are always variants.

    If a designer is in control, why are variants necessary? Why does evolution appear to be analogous to a marketplace?

  477. So, do you rule out a “substantiated inference” to the design of Stonehenge, Lizzie? Do you think we should be searching for an accidental, naturalistic explanation for its creation instead?

    Functional Complex Specified Organisation leaves all the trace we need (if you’re not allowing theological objections to distort your reasoning).

    No Chris. In the case of Stonehenge we have a) means, motive and opportunity and b) we have no alternative explanation (Stonehenge doesn’t reproduce with heritable variance in reproductive success).

    In the case of living things we have no means, perhaps a motive, and know nothing about the opportunity. In contrast living things reproduce with heritable variance in reproductive success.

    Therefore I infer intelligent design and human artisanship in the first case, and Darwinian evolution in the second.

    Scott: Your charge is unsupported and unwarranted.

  478. Elizabeth,

    The point is simple. Why would you acknowledge that a carbon-based life form with DNA can build a car made of steel and other components, and then reason that only a carbon-based life form with DNA can build a carbon-based life form with DNA? What logic requires that?

    I didn’t reason any such thing.

    And they do so by looking for traces of that missing particle. What are ID researchers doing to try to find traces of the missing Intelligent Designer?

    Try indoctrinating every physicist with the idea that a particle or mass they don’t observe can’t possibly exist, and then see how far the search for it gets.

    Ignoring your pejorative word “indoctrinating” simply observe what happened when it occurred to Einstein that the luminiferous ether simply didn’t exist. His search got him quite far.

    If someone else wrote what you just did I would tell them to go read the FAQ and gain a fundamental understanding of what ID is so they could make informed comments. What is your excuse?

    It wasn’t a comment, it was a question, based on your own analogy, and my counter-anology. I require no “excuse” for asking it.

    Going back to the arson example, since when does a forensics investigator determine arson and then go hunting for the arsonist? He doesn’t. He writes up a report saying that it was arson and then leaves to go look at the next fire. Someone else looks for the arsonist.

    And a man is executed on spurious grounds. I’m not making this up.

    You see, science doesn’t stop because someone draws a conclusion.

    Unless it’s ID science apparently, when you are told to look at the FAQ if you ask a further question.

    But that doesn’t mean that one series of tests answers everything. One conclusion leads to a new investigation.

    Exactly.

    By your reasoning, the arsonist would examine the evidence and determine arson. The police would ask him who set the fire. He’d say, “I don’t know,” and then the police would tell him that it couldn’t be arson.

    Not at all. If the forensic scientist determined arson, by definition, he concluded that a human being had done it. And unfortunately, sometimes they are wrong.

    No one would ever investigate or find arsonists because of their illogical basis for ruling out arson. That would be quite ignorant.

    You seem confused.

    This is simple. It gets repeated over and over, and then people like you who should know better by now go back to it again.

    Also rude, which isn’t like you. harrumph. Will go and cool off.

  479. Elizabeth,

    Well, for a start, in science we postulate, we do not “believe”.

    A big-big no. Science rests on belief. The word “belief” is carved in the foundation of it.

    Scientific method rests on believing that

    (a) objective reality exists, and
    (b) we can establish a coherent understanding of the world.

    This is a belief. It is not possible to prove or refuiute this. Solipsism, e.g. does not believe that such a world picture reflects objective reality.

    I accept that science is predicated on these assumptions. I still would not call them “beliefs”. As you say, they can be neither refuted nor proven, so the only thing to do is to assume they are true and proceed on that basis. It seems to work very well.

    Your postulates come a distant second. These postulates when formulated are also believed to be true. You see, in science that even E = m*c^2 is sometimes doubted :) But what is doubt if not the other side of belief?

    Of course postulates are sometimes doubted. In fact they should all be doubted. That is actually my point. Belief has no place in science, merely provisional conclusions.

  480. 483

    Chris,

    Notice Elizabeth’s statement:

    Disbelief in ex nihilo creation is somewhat warranted, or, at least, skepticism is well-grounded, because absolutely no mechanism is ever postulated for such an act by any agent, intelligent or otherwise.

    You see, all we have to do is postulate a mechanism. And the standards aren’t very high at all. They believe anything that someone else can imagine.

    The answer is to simply postulate everything ever postulated in behalf of chemical abiogensis, except done intentionally rather than accidentally. It’s not a stretch because they are deliberately executed experiments, so it’s impossible to argue that they can support only accidental outcomes and not intentional ones.

    I’m not particularly impressed with anything they’ve found, but what matters is that it impresses them, and we can both match and exceed it.

  481. I’m really not sure what point you are making here, Scott.

    Clearly, if you postulate something, you need to couch it as a testable hypothesis, then test it against data.

    That’s how science works.

    You needn’t be impressed, but I am.

    cheers.

    Lizzie

  482. 485

    Elizabeth,

    Thanks for hitting your daily “That’s how science works.”

    We’ve been over this. Yes, they have hypotheses, and they have supported it with data. That’s fine. (Is that how science works? Remind me again.)

    The sum total of all of those experiments do not even make abiogenesis plausible. That’s why I’m not impressed, but don’t be distracted but that is not the point.

    You cannot hypothesize that A + B will synthesize Z, confirm it using testable data, and then declare that the outcome can only be reached unintentionally. You could reasonable claim that the same result could be achieved naturally, but the claim that it can be achieved intentionally is more surpassingly demonstrated.

    I am not disparaging the research. I am claiming it to support my position. It is research to determine how one might deliberately create a living organism. You and many others have insisted that no such research exists, but you are clearly mistaken.

  483. Elizabeth:

    d is for “digital”.

    However, the claim that a system in which variance is randomly generated and subject to natural selection i.e. where that genotypic variance results in heritable variance in reproductive success cannot result in dFSCI (or, at least in an adaptive population) certainly is in dispute

    I certainly dispute it can (I mean, generate dFSCI).

    and we can see, for example, in evolutionary computer algorithms, that it does indeed.

    I will not take again here the subject of genetic algorithms. I have done that too many times, and I frankly consider that a very boring subject. I will just sum up my absolute conviction: all genetic algorithms, as afr as I know and can understand, are at best implementations of intelligent design, never of RV + NS.

    So there is no principled reason for thinking that random heritable variance in reproductive success can’t result in evolving functions that optimise a population for its environment.

    Random heritable variance in reproductive success can’t result in dFSCI.

    Or, at any rate, you have not stated one!

    I have been stating reasons for yeras on this blog, probably also with you. I cannot each time start again from scratch!

    Yes, indeed it is, but, interestingly, “intelligent” selection is less, not more, likely to produce complex functions.

    Less than what? I can agree that intelligent selection + RV probably has some limits. I don’t think that very complex functions can be generated that way. For that, we probably need guided variation.
    But one thing is for sure: RV + NS has all the limits (whatever Petrushka can believe).

    Intelligent selection is a quick way of getting to a specific function, but it’s not the best way of evolving a fit population

    Well, intelligent selection can well be coupled to direct design and direct planning. You may have a general plan for a complex setting, a program, a software, and then need some specific function that you can develop by intelligent selection.

    You have taken a wrong turn here, in fact two. First of all, in nature there is no “correct” variation. There is simply differential reproductive success. Organisms with genotypes that tend to produce thriving phenotypes will, by definition, be more likely to pass those genotypes on to descendents. So they are also, by definition, the “correct” genotypes for their environment – ones that work. And your second wrong turn is that no artificial selection system that I am aware of “fixes” “incorrect” variations before continuing. Variants that are undesired are simply not bred from, or given fewer opportunities to breed. This is true of Weasel, and of animal breeding. Nothing is “fixed” (at least not yet – genetic medicine may be on the horizon).

    I don’t understand what you mean. I was not speaking of “nature”, but of intelligent selection. In Weasel, you know the phrase you want to obtain. While it would be certainly easier to write it directly, for some reason you choose to obtain it by RV and intelligetn selection. What has “nature” to do with that? Each time a letter changes, it is compared with the right solution, and that conditions what happens after. So, “correct” variation is when a letter corresponds to the solution. If the first letter happens to be “W”, that is correct variation.

    I am not interested in the details of how the algorithm “fixes” the result. Only Dawkins knows (or maybe only God!). But even fixation by negative selction is fixation just the same. And the fact remains that what is fixed is what has been considered “correct” because the algorithm already knew the solution.

    It is easy to fix a result by negative selection, once we have attained it. The only thing to do is to eliminate any new variation that “throws away” the result. That is intelligent selection just the same, because if you had no way to know that the result is “correct”, you could not fix it.

    The problem with NS is that it can only fix results that give reproductive advantage. Almost all functional results that are in the range of RV will not give any reproductive advantage. And those results that are not in the range of RV will never arise, and cannjot be obtained as the sum of simpler results. It’s as simple as that.

  484. Elizabeth:

    Again you have taken a wrong turn. In evolutionary algorithms (not weasel, but almost every other one), the output of the evolving organisms is assessed against a criterion (just as it is, naturally, in wild species) but the organisms themselves as output is NOT specified.

    No wrong turn at all. I was speaking of the Weasel. I know that in other algorithms the solution is not known in advance. In other algorithms, information is added to the system in other, indirect ways. But it is intelligent design just the same.

    Please, read again what I wrote and you will see that I have considered the various possibilities to add information.

    That, surely, by any calculation, is FCSI – it’s functional, it’s complex, it’s specific, and it’s information, and it did not exist before it evolved within my algorithm. It was certainly not specified in any form by me.

    Not so. You added a lot of information to the system. You defined who were the patients and who were the volunteers. You designed the algorithm to sdearch for the parameters. You defined the method, and the purpose of the search. If (and I am not sure of that) new dFSCI was created, it was created as a result of your intelligent intervention. Again, we have intelligent purpose, conscious representation, structured algorithms, intepretation of meanings. All that can be done only by an intelligent designer.

    Yes, that’s possible. But there are other ways in which neutral (i.e. non-advantageous) variants can get into the gene pool, and that is by drift.

    As discussed many times, drift and neutral variation do not modify the probabilities of random walks.

    So both components necessary for Darwinian evolution to occur are naturally occurring. No designer is required (except possibly to get the whole thing started, but that’s not an argument about Darwinian evolution, it’s an argument about organic chemistry).

    No. What is lacking in genetic algorithms is an implementation of NS. NS is absent there. All selection is intelligent selection, because the designer structures the system and decides the rules.

    In nature, the “evolved” being is supposed to expand because it really has reproductive advantage, in an environment that is completely unaware of it, and of the rules of its reproduction. IOWs, the environment is blind to the replicator.

    I have suggested to implement genetic algorithms that way, and everybody starts to evade that immediately.

    Let me see a replicator “evolve” by RV alone in a system not built for that purpose, just by developing reproductive advantage through RV. Let me see a computer virus become a much more complex computer virus, all alone, in normal computers, not in a system which simulates anything.

    NS cannot be “simulated”. It must be “implemented”. If you implement true NS, it will bring you nowhere, because a true complex reproductive advantage cannot be achieved in a blind environment by a replicator, not even by a simple computer virus.

    Well, In didn’t want to take again this subject, but you have brought me to it :)

    Well, apart from the fact that none is required (things that breed better will breed more), how does your postulated bodiless ID affect who breeds and who doesn’t? What are these “many ways”?

    Not if the breeding is guided by a breeder. One thing is to breed better in a blind environment, another thing to breed better because a breeder helps me.

    I think i have discussed a little the ways of implementation in the other post to you somewhere else here.

  485. Petrushka:

    Explain to me where the designer stores his database of functional sequences,

    Maybe memory?

    since everyone seems to agree that the number of possible sequences exceeds the number of particles in the universe.

    Well, not the number of functional sequences. Those are much less, whatever darwinists like to believe.

    And everyone, including Douglas Axe, agrees that there are no shortcuts to knowing how a coded sequence will fold when interpreted as a protein.

    There are certainly intelligent methods to discover it. Both top down and bottom up. They are certainly big shortcuts when compared to a random walk. Or to a random walk + NS.

    How does the designer know what problem needs to be solved? In real life, complex design has to balance many factors.

    That’s why we call him “intelligent”.

    If a designer is in control, why are variants necessary? Why does evolution appear to be analogous to a marketplace?

    Because the designer is obviously not “omnipotent” in the context he operates in. He has rules to respect. He cannot do anything he likes. He may face opposing forces or principles.

  486. In the case of Stonehenge we have a) means, motive and opportunity

    Really Lizzie? You know what these are? Or is it just that you can imagine what they are? Do you appreciate the difference? It’s vital.

  487. Maybe memory?

    That’s the problem, isn’t it. You argue that functional sequences are a subset of possible sequences. OK. let’s follow that.

    Suppose functional sequences are one in a trillion. That would reduce memory requirements from 10^500 to 10^491, using common ID numbers. Is that significant improvement? How about one in a trillion trillion? 10^482.

    Where’s the storage?

    There are certainly intelligent methods to discover it. Both top down and bottom up. They are certainly big shortcuts when compared to a random walk. Or to a random walk + NS.

    Examples? Give us a thought experiment demonstrating a shortcut to protein folding, followed by a shortcut to finding which folds lead to greater reproductive success. Followed by a shortcut to knowing in advance which combinations of neutral or nearly neutral variations will be needed in the future.

  488. I’m afraid I think in terms of storage capacity because I did most of my professional programming back in the 80s, when a thousand bytes was a lot. I had to account for and justify every byte.

    Remember the Y2K problem? That was caused by database designers trying to squeeze as much data as possible into the smallest possible space. That was the world I learned to program in.

    From that I learned that there is always a physical implementation for knowledge, and limits to how much can be stored and how quickly it can be accessed.

    Nothing has changed except the number of zeros available. When you start talking about hundreds of zeros in the exponent, you are up against the resources of the universe.

  489. NS cannot be “simulated”. It must be “implemented”. If you implement true NS, it will bring you nowhere, because a true complex reproductive advantage cannot be achieved in a blind environment by a replicator, not even by a simple computer virus.

    Any physical process can be simulated. H-bombs can be simulated. Earthquakes can be simulated. Even weather can be simulated.

    The environment is not blind. Variation is blind. The environment is both active and passive. It is passive in the sense that biochemical constraints determine what sequences are viable. It is active in that competition determines which viable variants have a reproductive advantage.

  490. We can’t interview the creators of Stonehenge, but we certainly have demonstrated that there are methods of building Stonehenge that require only technology available to the time.

    There’s a video of a single guy moving and planting a Stonehenge sized block unassisted. we know where the stones were quarried. So we have means and opportunity.

    As for motive, we are still building monuments.

  491. That would reduce memory requirements from 10^500 to 10^491, using common ID numbers. Is that significant improvement? How about one in a trillion trillion? 10^482.

    After coffee that looks like it should have been 10^488 and 10^476. Using American billions, not British billions.

    I don’t see that it changes the argument.

  492. 495

    Elizabeth,

    In the case of Stonehenge we have a) means, motive and opportunity

    Why do we have means, motive, and opportunity? What if someone came across it and said, wow, look at this rock formation. Where did this come from? First step – eliminate design.

    We’d still be spinning our wheels with materialistic explanations that never quite add up, and we’d never find out how or why someone did it. Sure, there would be some testable hypotheses supported by data touching on possible geological causes (because that’s how science works!) but nothing very convincing. Certainly someone would mention arches.

    Ridicule and expulsion would face anyone who considered or proposed the possibility of design. Rather than working on the who, how, or why, they would spend their time demonstrating mathematically that giant rocks placed in circles and neatly stacked with astronomical significance are more likely to be created by designers. “Real scientists” would ask why design proponents didn’t just figure out how DruidsDidIt with their hands tied behind their backs because the very concept is considered religious and unscientific.

    But rational heads prevailed back then, or perhaps no one was smart enough to be so stupid. So we investigated the who, how, and why. That is what happens when you follow the evidence where it leads rather than narrowing the search on ideological grounds.

  493. I give up trying to get the number of zeros right. I screwed up again. :)

  494. 497

    Elizabeth,

    My charges that objections to ID are ultimately preferential are supported and warranted.

    You approve when someone infers design in the case of Stonehenge and then goes on to determine who, how, and why.

    In the next case you expect the opposite – determine who, how, and why and then perhaps you can infer design.

    It’s clearly not rational. But that doesn’t make you insane. It just means you like one conclusion more than the other. I like asparagus but I can’t eat tomatoes. I could pile up logical-sounding reasons why asparagus is good and tomatoes are bad and I could debate it for hours, but if someone digs deep enough they’re going to get to the bottom of it.

  495. wow, look at this rock formation. Where did this come from? First step – eliminate design.

    The first step would be to note that it looks like other things known to be built by humans. The second step is to ask whether it is within the capabilities of humans.

    These steps seem to be bypassed by biological design advocates. The only designers we have actually observed are living things. We see people building things. We see birds building things, we see termites and bees building things.

    We haven’t seen any non-living designers at work, so we can’t apply steps one and two.

  496. Elizabeth,

    You are free to choose how to term it. But I am glad we have essentially agreed that anything that cannot be rationally checked is believed. Belief is immanent to science (hence statistics, theory of probability, belief nets, a view of the world maintaining that it is stochastic/uncertain in nature, to name a few manifestations of it). Our life itself is guided by belief. I believe that the chair I am sitting on will not break under me, I believe that my colleagues are honest and responsible scientists, I believe that what I am doing will be helpful to others &c. Belief is central to our being.

  497. 500

    Petrushka,

    You’re getting a little warmer.

    The first step would be to note that it looks like other things known to be built by humans.

    First you have to really think through what “looks like” means. If it means that you eyeball something and draw a conclusion, you might be right or not. Perhaps consider similarities rather than a visual inspection. And then start asking what similarities are.

    The only designers we have actually observed are living things.

    You’re absolutely right, and yet here everything is, and we want to explain it. We can use your logic and narrow it down to every known observed cause, but that leaves us with nothing. If that’s not good enough for you, which it isn’t for me, then we must realize that it’s something not yet observed.

    The trouble is that you apply this filter only when it suits you. That’s why I call it a preference.

    You’ll consider something else that no one has observed and cling to every shred of evidence that’s not contradictory.

    In that sense alone both explanations are equal. You object to it in one case but not in the other. It’s not rational. Your thinking is compromised. It happens to all of us. I don’t like tomatoes.

  498. wow, look at this rock formation. Where did this come from? First step – eliminate design.

    The problem with this as a first step is that even following Dembski’s rules, you first have to eliminate natural causes.

    You see a ring of flowers or mushrooms. Designed or natural?

    We know that humans plant things in circles because we have observed them. We know that humans have the capability. But to reach a design inference, we need to eliminate false positives.

    You can’t do this by calculating the odds against seeds or spores falling in a circle. You have to know something about the processes involved.

    The same is true of evolution. You can’t arbitrarily say that structures requiring multiple mutations can’t occur naturally unless you run the experiment.

    I suppose there’s some safety in knowing that such experiments take decades. And in the fact that they can’t approach the results that take millions of years.

  499. 502

    Petrushka,

    You don’t even hear yourself. Read yourself. Whatever.

    The same is true of evolution. You can’t arbitrarily say that structures requiring multiple mutations can’t occur naturally unless you run the experiment.

    You’re admitting that there’s no experimental evidence to support your position. Which is more astounding, that you see that as problem for my position, or that you don’t see it as a problem for yours? Am I actually reading this?

  500. In that sense of the word, Eugene, sure.

    But it’s important not to equivocate between “believe” as in “the balance of the evidence leads me to be confidence that X will not lead to Y” and as in “I believe in one God, father almight, maker of heaven and earth”.

    The second is an act of faith. The first is merely a well-supported working assumption based on good probabilistic evidence.

    To take a less contentious example: believing that homoepathy works is probably essential for it to work at all. Believing that antibiotics work is to accept that statistics are a decent way of estimating confidence in a prediction.

  501. You’re admitting that there’s no experimental evidence to support your position.

    Sure there is. the Lenski experiment required three mutations, one of which was slightly detrimental.

    Malaria has independently evolved multiple mutation resistance to chloroquine several times. Within decades.

  502. 505

    Petrushka,

    You have retreated to safety on this side of the edge of evolution, where people hypothesize and collect data. But here on the reality side the claims become more modest. Bacteria develop resistance, lose it, and regain it. I’m not diminishing it. It’s impressive.

    Did you know that some people can be killed by peanuts while others can’t? Some people die from certain viruses while others are immune. Sometimes it’s hereditary. You’re reading something into it that just isn’t there. You talk about grand evolutionary changes and then produce variations within a very specific bacteria. You’re supposed to talk softly and carry a big stick, not the opposite.

  503. You could reasonable claim that the same result could be achieved naturally, but the claim that it can be achieved intentionally is more surpassingly demonstrated.

    So if Newton studies the behavior of cannonballs and concludes that it is possible to fire one at a velocity that would lead to it orbiting the earth rather than falling to the ground, he has demonstrated that the moon was placed in orbit intentionally, or at least that is the preferred inference?

  504. 61.1.1.1.9

    Elizabeth,

    I see no principal distinction between the two as they are different manifestations of the same basic principle. Neither did the founding fathers of contemporary science (here I am in good company :) It is important to understand that an act of faith is not blind but is also based on evidence and potential opportunity to validate it, albeit by different means. So I cannot agree with your “merely”.

    BTW, it is good that you know the Nicene creed.

  505. Petrushka:

    So, darwinists will go on “simulating” NS by intelligent selection, so that they can lie and affirm that NS can do what it cannot do. A nice trick. And I am tired to repeat it.

    The environment is blind. Nobody sets the environment to achieve evolution.

    A genetic algorithm is not blind. It is a system set up exactly to prove what it will prove. Compliments! From that point of view, no genetic algorithm is better than the infamous Weasel.

    NS cannot do anything. Just implement it in a true informational system, if you have the courage to do that. A replicating advantage, a true, natural replicating advantage, is the most difficult thing to obtain by random variation, in any true natural blind environment, except than in the fantasy of darwinists.

  506. 509

    Petrushka,

    if Newton studies the behavior of cannonballs and concludes that it is possible to fire one at a velocity that would lead to it orbiting the earth rather than falling to the ground, he has demonstrated that the moon was placed in orbit intentionally, or at least that is the preferred inference?

    If you fire a cannonball into orbit, you demonstrate that you can fire a cannonball into orbit.

    Perhaps that wasn’t your intention. Perhaps you’re speculating that a cannonball can fire itself into orbit, and this experiment supports your hypothesis by demonstrating that under the right circumstances a cannonball might enter orbit. And that’s fine. You now have data to support your hypothesis.

    But it also demonstrates that you can fire a cannonball into orbit. And it supports the hypothesis that you can fire a cannonball into orbit even better than the one that a cannonball can fire itself into orbit.

    Allow me to repeat. You can do something deliberately to demonstrate that it can happen accidentally. But in doing so, you demonstrate even more convincingly that you can do it deliberately.

    It’s all in those two sentences. It’s simple logic. Talking about the moon won’t change it.

  507. The environment is blind. Nobody sets the environment to achieve evolution.

    No sir. The environment is not blind. Every living thing competes against predators, parasites and other organisms, for food and resources. In addition, biochemistry places constraints on what variations can maintain metabolism and reproduction.

    There is nothing blind about the environment or about selection.

  508. But in doing so, you demonstrate even more convincingly that you can do it deliberately.

    So all you have to do to demonstrate that design is possible is to design a protein coding sequence from scratch, without using a randomly generate library that has been selected for sequences that fold.

    If you use selection, you are using evolution.

  509. I’m curious if you disagree with Newton:

    The qualities of bodies, which admit neither intensification nor remission of degrees, and which are found to belong to all bodies within the reach of our experiments, are to be esteemed the universal qualities of all bodies whatsoever.

  510. Petrushka:

    The environment is not blind. Every living thing competes against predators, parasites and other organisms, for food and resources. In addition, biochemistry places constraints on what variations can maintain metabolism and reproduction.

    Are you suggesting that biochemistry was set up to favour the evolution of complex replicators? Or that predators are intentionally trying to evolve compexity in their victims?

    There is nothing blind about the environment or about selection.

    Maybe the only blind entity here is your reasoning.

  511. Are you suggesting that biochemistry was set up to favour the evolution of complex replicators?

    That’s the belief of a lot of ID proponents, including Michael Denton. Personally I don’t know if it was “set up,” but it does work that way.

    As for predators, it has long been noted that predators and prey evolve complex relationships. Same with parasites and hosts.

    Do you deny that predators actively select the weaker of their prey?

  512. OK.

    First of all, I would like to clarify that I do believe that consciousness in its essence is transcendental, independent of physical interface, and that it has a fundamental property that can be described as both cognition and feeling. In pure form, those aspects of consciousness are not tied to specific representations. In our experience of human consciousness, however, we usually represent what arrives to us through the interfece (for instance, the brain), but the cognitive and sentimental value of those representations are essentially a product of consciousness itself.

    So yes, intelligence can be completely separated from specific representations and form the interface. In us humans, intelligence works mainly through the brain interface, and uses its computing structures, but every meaning, purpose, sense of good and evil, pleasure and pain, are properties of consciousness, not of the physical computing apparatus.

    I’m curious as to what you think the “computing structures” are used for, if all the other things are done independently of it.

    What, in your view, could this independent entity do, without the physical interface? What would be missing from its capability if the brain ceased to exist (as brains do), or the interface went black?

    Not exactly. I believe that my “disembodied mind” (the designer’s) does exactly what my own “disembodied mind connected to a physical brain” (my personal mind) does all the time: it interacts continuously in both directions with a physical structure (the brain, and in particular the neurons). In the case of the designer, the physical structure would not be a personal brain, but possibly the cells of biological beings to be designed for further evolution.

    So it seems that you posit these disembodied minds as physical forces, capable of moving ions through ion channels and, by the same token, molecules into interaction with other molecules.

    Presumably you are aware that there are well-described physical forces that also do this? The electromotive force, for instance. Do you envisage that your “disembodied minds” counteract these forces if they see them pushing things in an unwanted direction? If so, wouldn’t this be detectable? Would you not observe a bias in the probability distributions of such events? How could they control “key aspects of the neuronal work without violating any known physical laws. “? How could it be that “the special nature of of quantum reality allows that”? Quantum predictions may be statistical, but that doesn’t mean you can slip a bias under the wire and hope that no-one notices. To take a very different example: Harold Shipman thought that a few extra old ladies dying a bit earlier than they otherwise would would escape detection as being a mere statistical fluctuation, but it didn’t. Given enough data, even tiny effects give rise to detectable signal in the statistical noise.

    As I understand your position, it is that there is enough random jitter in the physical world that a major additional set of entities, namely disembodied intelligent minds, can exert substantial forces on it and yet produce no statistically detectable effects at the physical level, except, presumably, the otherwise unaccountable phenomena of biological beings and moral behaviour.

    Do I have this approximately right?

    If so, I’d still like to know what you think our disembodied minds use our brains for :)

    If not, perhaps you could clarify further.

    Cheers

    Lizzie

  513. 516

    Perhaps someone else can chime in – not necessarily agree or disagree with what I’m saying, but to indicate that you understand it. Because it’s so simple that I can state it in two sentences.

    Then, Petrushka, I will understand whether you are evading the point or whether I’m not making it as clearly as I think I am. None of your illustrations even address the logic of it.

    I repeat,

    You can do something deliberately to demonstrate that it can happen accidentally. But in doing so, you demonstrate even more convincingly that you can do it deliberately.

    I apply this principle directly to OOL research in which they, for example, create some fatty vesicles and state that such fatty vesicles, possibly a step toward early life, could occur naturally under these conditions. Without disputing that, I add, quite simply, that the same results can also be produced intentionally by repeating the experiment, and with even greater certainty than that it might happen “in the wild.” If this is not the case then the experiment is not repeatable and loses significance.

    I’ll be back later tonight prepared to break it down sentence by sentence if what I’m saying is the least bit unclear. You don’t need to come up with “what if” scenarios because I’ve already given you one. That is the scenario. If I’m wrong, tell me why.

  514. You’ve made your point over and over and over and over and over and over, and I’ve agreed with it each time.

    What you haven’t done is relate it to the discussion of evolution vs ID.

  515. 518

    Results seem to fall right in line with the fairly flat distribution rate of rm+ns evidenced by lenski e-coli.

    Lenski e-coli: 15 +-5 fixed mutations -> 5*10^4 generations
    corn: 15 fixed mutations -> 10^4 generations

    Where predicted (based on lenski) would have fixed mutations <=5 within the first 10^4 generations. With the corn's fixed mutation variance (2) attributed to intelligent selection.

    Same observed wall over and over

  516. Scott, there is an important misunderstanding here that needs clearing up.

    I don’t think anyone (or many people) think that the fact that something can occur “naturally” (without intention) means that it cannot occur “artificially” (by intention).

    We could have a completely compelling account of OOL and all life forms and it would not rule out the possibility that it was all nudged along by an Intelligent Designer. Indeed, as Christopher Hitchens points out, the chances that people would evolve is vanishingly small, and the chances even that a species as intelligent as us would have evolved by now is probably also quite small.

    So even if it all happened as Darwin says, in no way does that rule out a gentle nudge in some Intelligent Designer’s intended direction.

    Just because something can happen naturally doesn’t mean it did.

    So please don’t level at Darwinists the charge that they are trying to demonstrate that their was no Designer. We are not. We are merely pointing out that biology can be explained, as most other phenomena can be explained, in terms of natural forces.

    Whether an Intelligent Designer conceived those natural forces, forseeing that we might come to exist, is a matter of faith, and nothing in science rule it out. But neither does anything in science, IMO, rule it in. In fact, my own theological position is that a supernatural agent that was ruled in by science would be an oxymoron.

  517. 520

    We are merely pointing out that biology can be explained, as most other phenomena can be explained, in terms of natural forces.

    I am still looking forward to you applying that standard to the observable physical entailments as described in post #49.

  518. The input of information is therefore driving the output production, but as in all other forms of information, the input and the output never physically interact.

    This seems to be a paraphrase of the “central dogma of molecular biology.”

    What kind of response are you waiting for?

  519. Are there observable things that we can generalize to other forms of information, for instance?

    Probably not. Information is an abstraction, and you can’t reason backwards from an abstraction to the properties of a physical instance, because abstractions shed detail.

  520. I don’t see the problem, Upright BiPed, or rather, I think the problem is a spurious one arising from your insistence that mechanisms in which a pattern in one medium gives rise to a corresponding pattern in another is “abstract” or “symbolic”, and thus somehow mysterious.

    You take the example of a musical box, which is obviously a human artefact, and say that the nubs on the cylinder “represent” the notes that emerge. I think this is a misuse of the word “represent”. Yes, a skilled musician and musical box expert could probably “read” the cylinder as “symbols” and reproduce the melody in her head (I probably could, actually) but in the context of the musical box itself, there is no abstract layer. The melody that emerges can of course be explained simply “in terms of natural forces”.

    Same with DNA – there is no abstract layer, merely a sequence of molecules whose chemical interactions are predictable and well-understood.

    The interesting question, of course, is: how did it come about that a self-replicating molecule, like DNA, acquired a sequence in which other molecules, formed chemically as a result of the DNA sequence, catalyse the production of certain proteins that themselves enhance the probability that the whole system, DNA sequence included, will self-replicate.

    And we don’t know, exactly, but what we do know is that any sequence that enhances the whole thing’s chances of self-replication will become more frequently represented in the population of self-replicators (logic dictates this), and so while we do not know the exact historical pathway by which these sequences came about, we can infer that in the proto-cell’s ancestry, certain sequences produced reproductively advantageous results.

    Interestingly, gpuccio’s fascinating proposal for the mechanisms by which an Intelligent Designer could facilitate this, would be completely consistent with any OOL scenario, requiring the Designer only to work below the statistical radar, ensuring that certain sequences, on the pathway to the Intelligent Designer’s desired endpoint, otherwise equiprobable with other sequences, did, in fact, occur.

    But if the ID is working below the statistical radar, then we aren’t going to be able to infer his/her contribution to the process by any scientific means.

  521. There’s nothing to refute, UBP. Physical systems can transmit information, as you point out.

    The origin of the information might be an intelligent agent, such as a musical box manufacturer, or it might be information accumulated over many generations of self-replicators replicating within a hazardous environment with limited resources.

    There is no “abstract” level, except in our own descriptions of the process, which is not surprising as we are creatures capable of abstract descriptions. Molecules are not.

  522. Elizabeth:

    I’m curious as to what you think the “computing structures” are used for, if all the other things are done independently of it.

    It is used exactly to do what it can do: to compute. Exactly as we humans use a computer to compute.

    But it is perfectly true that “every meaning, purpose, sense of good and evil, pleasure and pain, are properties of consciousness, not of the physical computing apparatus.”

    IOWs, no subjective representation exists in the computing apparatus (the brain). All subkective representations of the brain content and computations take place in consciousness, and not in the physical machine of the brain.

    What, in your view, could this independent entity do, without the physical interface? What would be missing from its capability if the brain ceased to exist (as brains do), or the interface went black?

    At death consciousness survives, and continues to represent things. Those things will be different things, and no more the physical computations of the brain. But it still consciousness that represents. NDE experiences are good empirical examples of that.

    So it seems that you posit these disembodied minds as physical forces, capable of moving ions through ion channels and, by the same token, molecules into interaction with other molecules.

    It is a possibility, as I have said. But if you read carefully my posts, you will see that that is not my favourite option.

    My favourite model is that consciousness interacts with matter at quantum level, probably causing specific “wave function collapses” that, while apparently respecting possible probabilities inherent in the wave function, are in reality informationally configured by consciousness.

    IOWs, consciousness just acts on “configurable switches”, inputting information where pure randomness would normally be present. For the probabilistic nature of quantum wave function collapse, that needs not violate any physical laws., especially if it happens at specific levels, like neuronal discharge, or intracellular critical events, including mutations.

    The only “anomaly” we could observe would be the emergence of functional information without any reasonable probabilistic explanation.

    The possibility that consciousness could design without exerting a specific force, however, has already been discussed, I believe by Dembski, in one of his books.

    Presumably you are aware that there are well-described physical forces that also do this? The electromotive force, for instance.

    See above. Consciousness acts at quantum level, not in a deterministic way. It is not a force, but the output of a transcendental “I” endowed with free will.

    Quantum predictions may be statistical, but that doesn’t mean you can slip a bias under the wire and hope that no-one notices.

    Yes, it means exactly that. Quantum experiments are not usually accomplished taking into account the contribution of cosnciousness. And anyway, if one looks correctly, one can detect something. Some data exist in that direction. You can find some of them in the book “The spiritual brain”, for instance.

    It is a new field of investigation, but it will progress rapidly, especially if the reductionist prejudice of strong AI will not be any more the religion of academic science.

    Moreover, to detect the “anomaly” one certainly needs the concepts of ID theory, and especially the concept of dFSCI.

    Given enough data, even tiny effects give rise to detectable signal in the statistical noise.

    It depends. First of all the signal noise ratio must be in the range of the research methodology. And you must know what to look for. The real anomaly would be the functional arrangements of the pseudorandom events, and only the tools of ID can really show that anomaly. The general probabilistic distribution could well not be violated, unless evaluated in terms of functional information.

    Do I have this approximately right?

    Yes, if you take into account my further clarifications in this post. But if you have other questions, I will be happy to answer them

  523. Thanks! Here is my first question:

    Elizabeth:

    I’m curious as to what you think the “computing structures” are used for, if all the other things are done independently of it.

    It is used exactly to do what it can do: to compute. Exactly as we humans use a computer to compute.

    But it is perfectly true that “every meaning, purpose, sense of good and evil, pleasure and pain, are properties of consciousness, not of the physical computing apparatus.”

    IOWs, no subjective representation exists in the computing apparatus (the brain). All subkective representations of the brain content and computations take place in consciousness, and not in the physical machine of the brain.

    But what does the brain compute? As humans we use computers to give us answers to questions we present it with. But the content of those questions is based on our observations and perceptions of the external world.

    And we know that the brain itself (or do you dispute this?) is responsible for taking in data from the external world and parsing it into predictions about what will happen next.

    In the absence of such a mechanism, how would your disembodied mind even know what to ask its “computer” to do?

    Your analogy just isn’t working for me! Without a brain, surely the disembodied mind is blind, deaf, and anaesthetised.

    Or, if not, what are these brain networks doing?

  524. GPuccio,

    Yours are very good posts with much food for thought. I always enjoy reading them even though something appears questionable to me (such as things on consciousness, but as yet I am very far from putting my questions not even objections into words, I am just in the stage of accumulating info on this for myself). A big thank-you for your time here at UD.

  525. Agreed :)

  526. Chewing these over and taking them in turn:

    At death consciousness survives, and continues to represent things. Those things will be different things, and no more the physical computations of the brain. But it still consciousness that represents. NDE experiences are good empirical examples of that.

    Well, leaving aside how good NDEs are of out-of-brain phenomena (I’m not convinced), descriptions of them suggest that the out-of-body person can see and hear (but not, oddly, touch) the world. So what do you think the brain is doing when we see and hear – if the disembodied mind can do both, surely we don’t need our visual and auditory systems, yet we seem to have them. Also they often mislead us. How can this be, if the mind is in control of the brain, and has its own perceptual faculties?

    In fact, how, in your model, can we account for mental illness, or neurological disability?

    My own view, of course, is that mind is what the brain does. That they are not different things, but different aspects of the same thing. Indeed, the foundation of functional brain imaging is the correlation of mental events with neural events – what is experience by the person with what is observed in their neurons (or at

    My favourite model is that consciousness interacts with matter at quantum level, probably causing specific “wave function collapses” that, while apparently respecting possible probabilities inherent in the wave function, are in reality informationally configured by consciousness.

    IOWs, consciousness just acts on “configurable switches”, inputting information where pure randomness would normally be present. For the probabilistic nature of quantum wave function collapse, that needs not violate any physical laws., especially if it happens at specific levels, like neuronal discharge, or intracellular critical events, including mutations.

    OK, let’s take a neuron, firing stochastically. Every time it fires, it slightly changes the polarisation of the post-synaptic neuron. For that post-synaptic neuron to fire, many depolarising signals need to be received from a whole population of other neurons within a certain time-window. And let’s say, that at quantum level, the disembodied brain nudges certain electrons so that an ion travels in direction x instead of direction y, thus tipping the balance of one of the presynaptic neurons into firing a fraction earlier than it would otherwise have done, thus just making the critical time-window of the post-synaptic neuron and causing it to fire when it would not other wise have done.

    In this way, a tiny quantum nudge by the disembodied mind is amplified, just like the butterfly in Peking, into a cascade of neural events and behaviours that would not otherwise have happened, but which is the intended output of the disembodied mind.

    Is that the kind of thing you have in mind?

    The only “anomaly” we could observe would be the emergence of functional information without any reasonable probabilistic explanation.

    But not in the case I have outlined above. We know that Hebbian learning occurs, and we know that it results in coordinated behaviour. You are saying that our disembodied minds can nudge that behaviour one way or the other (or at least I think you are saying that), which is a reasonable view (indeed I held it once myself :)). However, firstly, the unnudged brain is not going to produce detectably different behaviour to the nudged brain (or I don’t see how, unless you are arguing that brains unnudged would be completely chaotic, and I see no reason for that, given what we know about how neural networks work), and so observing the output isn’t going to tell us whether they were nudged or not. Did you put the money into the charity shop because you were nudged, or would you have done it anyway? Did you fail to put the money into the charity shop because your disembodied mind “chose” not to do the right thing (why? Why would it?) when, left to its own devices, the brain would have caused you to put the money in?

    And on what basis would the disembodied mind make the decision? What data does it use, and, when the data collection system is offline (as in an NDE or OBE), where do the data come from?

    The thing is, that I can see the attraction of the idea, but on inspection it seems to collapse – every attribute we want to give the disembodied mind seems either duplicative or powerless, and, where powerless, the missing power is possessed by the brain.

    However, if we posit (as I do) that mind is what the brain does, there is no such difficulty. We make our decisions based on the data we collect from our sensory organs, parsed by the brain into objects, and people, and goals, and abstractions, and act on the basis of that information, simulating the likely results of our action, and feeding back those results into the decision-making process. Without a brain, I don’t see how moral and creative decisions can be made, or, if they can be, what is all that moral and creative decision-making machinery in the brain for, and why, when it goes wrong (as it often, sadly, does), does our disembodied mind not simply over-ride it?

    The possibility that consciousness could design without exerting a specific force, however, has already been discussed, I believe by Dembski, in one of his books.

    Can you summarise? It seems to me to be a pretty important point!

  527. Sounds like vitalism revisited to me.

  528. Eugene: Scientific method rests on believing that

    (a) objective reality exists, and
    (b) we can establish a coherent understanding of the world.

    This is a belief. It is not possible to prove or refuiute this.

    Nonsense. Every time we put our coffee cup down and it’s still there to pick up 5 minutes later, we add credibility to the belief that there’s an objective reality and we have established a coherent understanding of at least a part of it. If it turned into a lizard and crawled away we would have strong evidence refuting the existence of objective reality.

    You’ve fallen into the “equivocation fallacy” trap where you use different meanings for “believe” in different parts of your argument and thus reduce your argument to absurdity.

    Scientific beliefs, along with most everyday beliefs such as “the sun rises in the east” or “this road goes to Laredo” are the type that can be strengthened or refuted by the evidence. Either the sun rises in the east, adding confirmation to your belief or it doesn’t, refuting it. The road either goes to Laredo or somewhere else.

    The religious beliefs you talk about are the type where you believe any darn thing you want to despite the lack of evidence for them or even against the evidence. You can see a Designer. The person standing next to you sees nothing.

  529. You are declaring “Design!” with no trace of a Designer and ignoring all the rats chewing matches which account perfectly well for the fire.

    You insist that an incredibly unlikely Designer made the life we see while completely ignoring evolution which accounts very well for the life we find around us.

  530. Rats, matches and people are all known to exist. Rats and matches will account for the fire. People can’t account for the fire because investigation has shown there were none around at the time. Yet you insist the fire was arson.

  531. You talk about grand evolutionary changes and then produce variations within a very specific bacteria.

    There’s more divergence separating bacteria from each other than there is separating one animal from another.

  532. 535

    Elizabeth,

    You are also entirely missing the point of what I am saying.

    I don’t think anyone (or many people) think that the fact that something can occur “naturally” (without intention) means that it cannot occur “artificially” (by intention).

    I am not suggesting that. That has nothing to do with what I am saying.

    I am saying, in very simple words, that by demonstrating that something can occur naturally by means of a repeatable experiment you even more conclusively demonstrate that it can occur deliberately.

    Before I used two sentences. That’s one. I can’t break it down any more. If a simple sentence can’t express a simple thought than an illustration is even more likely to be misunderstood.

    The objection is raised repeatedly that abiogenesis, even not well-defined, is supported by hypotheses and data, while no one bothers to do any such research with regard to design.

    My point is not to dispute the abiogenesis research. I am saying, as simply as I can, that the abiogenesis research is the design research.

    Let me repeat this because everyone who responds seems to seize something else and miss the central point. If I could make the font bigger I would.

    Abiogenesis research such as Szostak conducts is design research. While demonstrating what might occur naturally he even more convincingly demonstrates what can be done intentionally.

    I’ve said it perhaps ten times, and no one has objected while also indicating that they understand what I am saying.

  533. Thank you, Eugene and Elizabeth!

  534. 537

    dmullenix,

    We’re so often reminded that OOL and evolution are not the same thing. Has something changed?

    You are declaring “Design!” with no trace of a Designer…
    while completely ignoring evolution which accounts very well for the life we find around us.

    If I asked how evolution explains life ten people would jump on it and object that evolution doesn’t explain life. But you boldly declare the very exact opposite for the sake of rhetoric.

    Here is a news flash: There is no “trace” of anything. There is just life. Show me a trace of chemical abiogenesis. Do you agree that we should stop looking for that as well?

    That your arguments are based on preference rather than reason is naked and exposed. That places them at a diagonal opposite from science.

  535. Elizabeth:

    No, the idea is different. Consciousness interacts with the outer world through the brain (and the body). That’s correct. It collects information, processes it, and outputs actions, and all that goes through the interface.

    Without the brain activity, cosnciousness remains active, but will represent and cognize other things. That rarely happens clearly in the cosncious state, because consciousness is so focused on brain acticity. I have given you the example of NDEs as a model for conscious activity not connected to brain activity (I know you will dispute that, but I am absolutely convinced that it is the truth). I give you another model: the experiences of the mystics. Here, again, we have experience of an inner world usually not accessible to common experience, and completely independent of connections with the outer world.

    A whole inner life can be experienced which arises from the depths of human consciousness, and of its relationship with the divine. And that relationship, even at simple or low level, is beautiful, harmonious, cognitively satisfying, simple, and full of love.

    Believe me, the disembodied mind is everything but blind, deaf, and anaesthetised.

    You will probably try to explain all that with some smart strong AI concoction. OK, who cares? :)

  536. Hi, Scott:

    You are also entirely missing the point of what I am saying.

    OK. It does happen, and I am trying :)

    I don’t think anyone (or many people) think that the fact that something can occur “naturally” (without intention) means that it cannot occur “artificially” (by intention).

    I am not suggesting that. That has nothing to do with what I am saying.

    I am saying, in very simple words, that by demonstrating that something can occur naturally by means of a repeatable experiment you even more conclusively demonstrate that it can occur deliberately.

    Well, I’m not disputing that, at all, as I said explicitly in another post.

    Before I used two sentences. That’s one. I can’t break it down any more. If a simple sentence can’t express a simple thought than an illustration is even more likely to be misunderstood.

    The objection is raised repeatedly that abiogenesis, even not well-defined, is supported by hypotheses and data, while no one bothers to do any such research with regard to design.

    My point is not to dispute the abiogenesis research. I am saying, as simply as I can, that the abiogenesis research is the design research.

    Let me repeat this because everyone who responds seems to seize something else and miss the central point. If I could make the font bigger I would.

    Abiogenesis research such as Szostak conducts is design research. While demonstrating what might occur naturally he even more convincingly demonstrates what can be done intentionally.

    Yes. But if he shows that it can be done naturally, there is no reason to infer that it was done intentionally, even if it could have been.

    The parsimonious conclusion, absent any direct evidence of an intentional agent with the physical means to do it, is that it happened naturally.

    I’ve said it perhaps ten times, and no one has objected while also indicating that they understand what I am saying.

    Well, I understand that that must be frustrating. But I think people have understood it – clearly if something can be done in a lab, it can be done intentionally. But nobody that I know of is saying that it can’t have been done intentionally. They are saying that it could also have been done naturally, and given the absence of evidence for an intentional agent, “naturally” is the more parsimonious conclusion.

    By the way, there’s a good review article on OOL research in last month’s New Scientist that seems to be open access:

    http://www.newscientist.com/ar.....tml?page=1

    As you imply, achieving OOL in the lab would certainly demonstrate that it could be done intentionally!

    To show it could have happened naturally, one would have to show that the lab conditions pertained on early earth. Nonetheless, seeing a life form start to evolve from scratch spontaneously under lab conditions would certainly suggest that no molecular level tinkering is required, just provision of the initial “Goldilocks” conditions for a Darwinian-capable self-replicator.

    For which an ID may well have been responsible, but the argument for a design inference from complexity would be refuted, wouldn’t you say?

    Still, it hasn’t been done yet :)

  537. 540

    Elizabeth,

    You have it precisely backwards.

    Yes. But if he shows that it can be done naturally, there is no reason to infer that it was done intentionally, even if it could have been.

    The exact opposite has occurred. He has shown that it can be done intentionally and is inferring that it can be done naturally.

  538. Elizabeth:

    Well, leaving aside how good NDEs are of out-of-brain phenomena (I’m not convinced), descriptions of them suggest that the out-of-body person can see and hear (but not, oddly, touch) the world. So what do you think the brain is doing when we see and hear – if the disembodied mind can do both, surely we don’t need our visual and auditory systems, yet we seem to have them. Also they often mislead us. How can this be, if the mind is in control of the brain, and has its own perceptual faculties? In fact, how, in your model, can we account for mental illness, or neurological disability?

    The mind in the human state is strongly connected to its physical interface. Therefore, it vastly has to be influenced by the interface itself. Seein or hearing inputs from the outer world needs inputs for the outer world, and those inputs are received and processed through the brain. In NDEs, like in mystical experiences, the mind is partially or completely freed from its connection to the body and brain. Therefore, it can easily perceive other things.

    But, indeed, all power of representation, including seeing and hearing, is ultimately of consciousness, not of the brain. The brain passes to consciousness what will be represented, and the flow of information from ouer reality is soi strong that usually cosnciousness cannot perceive other realities.

    A consciousness strongly connected to the brain is strongly limited in its representations when the brain is damaged. That does not mean that its potentials are forever compromised.

    OK, let’s take a neuron, firing stochastically. Every time it fires, it slightly changes the polarisation of the post-synaptic neuron. For that post-synaptic neuron to fire, many depolarising signals need to be received from a whole population of other neurons within a certain time-window. And let’s say, that at quantum level, the disembodied brain nudges certain electrons so that an ion travels in direction x instead of direction y, thus tipping the balance of one of the presynaptic neurons into firing a fraction earlier than it would otherwise have done, thus just making the critical time-window of the post-synaptic neuron and causing it to fire when it would not other wise have done. In this way, a tiny quantum nudge by the disembodied mind is amplified, just like the butterfly in Peking, into a cascade of neural events and behaviours that would not otherwise have happened, but which is the intended output of the disembodied mind. Is that the kind of thing you have in mind?

    Yes! You said it very well. Thank you for the cooperation :) .

    For the remaining discussion, you should probably read some of my older posts about free will, but I have not the link now, nor the time to write it all again for the moment.

    In brief, just to start the discussion, I believe that free will is always present as the possibility of reacting differently, sometimes very slightly differently, to the existing outer and inner conditions at every moment.

    IOWs, whatever our instant situation, we can always react differently. Sometimes that difference is only inner, sometimes it can change our outer actions.

    The free choice is based on an inner intuition of the moral value of the different possibilities, however tiny the difference may be. IOWs, consciousness has always an inner connection, totally intuitive, with a “moral field”: some reaction to the present condition are “better” (morally), others are “worse” (morally).

    The cumulative effect of our moment by moment use of free will influences our future conditions (IOWs, determines to which situation, inner or outer, we have to react).

    We usually call “freedom” the range of possibilities that our free will can access, at a certain moment. We can have greater freedom or lesser freedom (that is a preexisting condition at each moment), but our free will is always there to be exerted for good or for bad.

    However, if we posit (as I do) that mind is what the brain does, there is no such difficulty. We make our decisions based on the data we collect from our sensory organs, parsed by the brain into objects, and people, and goals, and abstractions, and act on the basis of that information, simulating the likely results of our action, and feeding back those results into the decision-making process.

    In strong AI, there is no true I, no true consciousness. There is no true free will, because we don’t choose anything. Compatibilism is a gross fraud. If everything is determined, either by outer or inner conditions, there is no free will, and we cannot in any way change our destiny. Our destiny is already written by “forces” that we cannot control. Indeed, we ourselves don’t exist.

    Without a brain, I don’t see how moral and creative decisions can be made, or, if they can be, what is all that moral and creative decision-making machinery in the brain for, and why, when it goes wrong (as it often, sadly, does), does our disembodied mind not simply over-ride it?

    The brain does not “decide”. The brain elaborates. Some output, indeed many of them, are simply elaborated, and consciousness has no real control on them. But, if a true decision is made, it is made by cosnciousness through free will, in the context of the possibilities elaborated by the brain.

    A purely compulsive output of the brain is not a decision (although it is often called that way).

    Well, I have no more time now. I will be back.

  539. No, the idea is different. Consciousness interacts with the outer world through the brain (and the body). That’s correct. It collects information, processes it, and outputs actions, and all that goes through the interface.

    Without the brain activity, cosnciousness remains active, but will represent and cognize other things. That rarely happens clearly in the cosncious state, because consciousness is so focused on brain acticity. I have given you the example of NDEs as a model for conscious activity not connected to brain activity (I know you will dispute that, but I am absolutely convinced that it is the truth). I give you another model: the experiences of the mystics. Here, again, we have experience of an inner world usually not accessible to common experience, and completely independent of connections with the outer world.

    But I think you’ve missed my point. Let’s accept NDE experience for the sake of argument now: as reported they are not of “other things” but of every day worldly things – the operating theatre, the child in the room next door, the window ledge outside etc. All things that brains normally collect and, in your model, present to the disembodied mind. So, if the disembodied mind can see, and hear, when the brain is offline, what it that the brain does for it when it is online? As far as I can see, the one thing the brain does do is provide touch sensation (the disembodied mind seems unable to touch the world); however, apart from that advantage, it seems mostly to restrict the mind – tethers the point-of-view (literally) to the body, instead of letting it roam free.

    So why does the disembodied mind even bother with the body? And what about that duplication of sensory input?

    A whole inner life can be experienced which arises from the depths of human consciousness, and of its relationship with the divine. And that relationship, even at simple or low level, is beautiful, harmonious, cognitively satisfying, simple, and fu