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Oldies but baddies — AF repeats NCSE’s eight challenges to ID (from ten years ago)

In a recent thread by Dr Sewell, AF raised again the Shallit-Elsberry list of eight challenges to design theory from a decade ago:

14 Alan FoxApril 15, 2013 at 12:56 am Unlike Profesor Hunt, Barry and Eric think design detection is well established. How about having a go at this list then. It’s been published for quite a while now.

I responded a few hours later:

______________

>>* 16 kairosfocus April 15, 2013 at 2:13 am

AF:

I note on points re your list of eight challenges.

This gets tiresomely repetitive, in a pattern of refusal to be answerable to adequate evidence, on the part of too many objectors to design theory:

>>1 Publish a mathematically rigorous definition of CSI>>

It has long since been shown, objections and censorship games notwithstanding, that reasonable quantitative metrics for FSCO/I and so for CSI, can be built and have been built. Indeed Durston et al have used such to provide a published list of values for 15 protein families.

>> 2 Provide real evidence for CSI claims >>

Blatant, all around you. But, a man convinced against his will is of the same opinion still.

Just to pick an example {–> from the list}, a phone number is obviously functionally specific (ever had a wrong number call?) and — within a reasonable context [though not beyond the 500 bit threshold] complex.

>> 3 Apply CSI to identify human agency where it is currently not known >>

FSCO/I is routinely intuitively used to identify artifacts of unknown cause, as IIRC, WmAD has pointed out regarding a room in the Smithsonian full of artifacts of unknown purpose but identified to be credibly human.

>> 4 Distinguish between chance and design in archaeoastronomy >>

The pattern of Nazca lines or the like, fit within the nodes-arcs pattern and collectively exhibit FSCO/I similar to other complex drawings. The 500 bit threshold is easily passed. If you want to contrast odds of a marker wandering randomly in a random walk, the difference will be trivial.

In short this is a refusal to use simple common sense and good will.

>> 5 Apply CSI to archaeology >>

Just shown, this is a case or repeating much the same objection in much the same context as though drumbeat repetition is capable of establishing a claim by erasing the underlying fallacies. Being wrong over and over and over again, even in the usual anti-design echo chambers, does not convert long since corrected fallacy into cogent reasoning.

>> 6 Provide a more detailed account of CSI in biology
Produce a workbook of examples using the explanatory filter, applied to a progressive series of biological phenomena, including allelic substitution of a point mutation. >>

There are book-length cogent treatments of CSI as applied to biology [try Meyer's SITC for starts {{ --> . . . I know, I know, this was published 2009, six years after the "challenge," but AF is raising it in 2013, TEN years after the challenge}}], and that is not enough for the objectors, there will never be enough details.

Similarly, the objection starts within an island of existing function and demands a CSI based explanation of a phenomenon known to be well within the threshold of complexity. This is a strawman tactic.

>> 7 Use CSI to classify the complexity of animal communication As mentioned in Elsberry and Shallit (2003: 9), many birds exhibit complex songs. >>

What?

Is there any doubt that bird or whale songs or bee dances for that matter are long enough and complex enough to be FSCI? That they function in communication? That we did not directly observe the origin of the capacities for such but have reason to see that they are grounded in CSI in the genome and related regulatory information expressed in embryological development that wires the relevant nerve pathways?

So, are you demanding a direct observation of the origin of such, which we do not have access to and cannot reasonably expect, when we do have access to the fact that we have indications of FSCO/I and so raise the question as to what FSCO/I is a known reliable, strongly tested sign of as best causal explanation?

>> 8 Animal cognition
Apply CSI to resolve issues in animal cognition and language use by non-human animals. >>

Capacity for language, of course, is biologically rooted, genetically stamped and embryologically expressed. So it fits into the same set of issues addressed under 7 just now.

Repetitive use of fallacies does not suddenly convert them into sound arguments.

Nor, can one reasonably demand solutions to any number of known unresolved scientific problems as a condition of accepting something that is already well enough warranted on reasonable application of inductive principles. That is, it is well established on billions of test cases without significant exception, that FSCO/I is a reliable sign of design as cause.
____________

To suddenly demand that design thinkers must solve any number of unsolved scientific questions or the evidence already in hand will be rejected, is a sign of selective hyeprskepticism and a red herring tactic led away to a strawman misrepresentation, not a case of serious and cogent reasoning. >>

=========

(*And yes, AF, I am modifying French-style quote marks to account for the effect of the Less Than sign in an HTML-sensitive context. No need to go down that little convenient side-track again twice within a few days. Especially, as someone by your own testimony apparently living in a Francophone area.)

NB: BA77′s comment at 17 is worth a look also. Let’s clip in modified French style, that he may clip and run that readeth:

>> Mr. Fox, it seems the gist of your eight ‘questions’ from ten years ago is that you doubt whether or not information, as a distinct entity, is even in the cell? In fact I remember many arguments with neo-Darwinists on UD, not so many years back, who denied information, as a distinct entity, was even in the cell. Is this still your position? If so, may I enlighten you to this recent development???,,,

Harvard cracks DNA storage, crams 700 terabytes of data into a single gram – Sebastian Anthony – August 17, 2012
Excerpt: A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times.,,, Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored.
http://www.extremetech.com/ext…..ingle-gram

That DNA stores information is pretty much the mainstream position now Mr. Fox,,,

Venter: Life Is Robotic Software – July 15, 2012
Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter.
http://crev.info/2012/07/life-is-robotic-software/

That information is a distinct entity in the cell is pretty uncontroversial Mr. Fox, so why the list of eight questions? The only question that really matters is can purely material processes generate these extreme levels of functional information? Perhaps you would like to be the first Darwinist on UD to produce evidence that material processes can produce enough functional information for say the self assembly of a novel molecular machine?>>

The much underestimated and too often derided BA77  continues at 18:

>> Mr. Fox, as to the fact that a cell contains functional information, I would like to, since Dr. Sewell approaches this from the thermodynamic perspective, point out something that gets missed in the definition of functional information in the specific sequences of DNA, RNAs, and proteins. There is a deep connection between entropy and information,,

“Is there a real connection between entropy in physics and the entropy of information? ….The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…”
Siegfried, Dallas Morning News, 5/14/90, [Quotes Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin]

“Bertalanffy (1968) called the relation between irreversible thermodynamics and information theory one of the most fundamental unsolved problems in biology.”
Charles J. Smith – Biosystems, Vol.1, p259.

Demonic device converts information to energy – 2010
Excerpt: “This is a beautiful experimental demonstration that information has a thermodynamic content,” says Christopher Jarzynski, a statistical chemist at the University of Maryland in College Park. In 1997, Jarzynski formulated an equation to define the amount of energy that could theoretically be converted from a unit of information2; the work by Sano and his team has now confirmed this equation. “This tells us something new about how the laws of thermodynamics work on the microscopic scale,” says Jarzynski.
http://www.scientificamerican……rts-inform

And what is particularly interesting about this deep connection between information and entropy is that,,,

“Gain in entropy always means loss of information, and nothing more.”
Gilbert Newton Lewis – preeminent Chemist of the first half of last century

And yet despite the fact that entropic processes tend to degrade information, it is found that the thermodynamic disequilibrium of a ‘simple’ bacteria and the environment is,,,

“a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong
http://books.google.com/books?…..;lpg=PA112

Moleular Biophysics – Information theory. Relation between information and entropy: – Setlow-Pollard, Ed. Addison Wesley
Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz’ deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures.
http://www.astroscu.unam.mx/~a…..ecular.htm

Moreover we now have good empirics to believe that information itself is what is constraining the cell to be so far out of thermodynamic equilibrium:

Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH
Excerpt: It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.
http://journals.witpress.com/paperinfo.asp?pid=420

Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009
Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
http://www.dailygalaxy.com/my_…..ave-t.html

In fact, Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum information/entanglement by the following method:,,,

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 yet, despite all this, we have ZERO evidence that material processes can generate even trivial amounts classical information much less generate massive amounts transcendent ‘non-local’ quantum information/entanglement,,,

Stephen Meyer – The Scientific Basis Of Intelligent Design
https://vimeo.com/32148403

Stephen Meyer – “The central argument of my book is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question.”

Verse and Music:

John 1:1-4
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. In him was life, and that life was the light of all mankind.

The Afters – Every Good Thing – Lyric Video
http://www.youtube.com/watch?v=FY2ycrpbOlw >>

Joe puts in a good knock at 25:

>>Earth to Alan Fox,

Neither you, Shallit, Elsberry nor the NCSE need concern yourselves with CSI. That is because all of you can render CSI moot just by stepping up and demonstrating that blind and undirected processes can account for what we call CSI.

It is that simple- demonstrate blind and undirected processes can produce CSI and our argument wrt CSI, falls.

However seeing that you all are nothing but cowards, you won’t do that because that means actually having to make a positive case. And everyone in the world knows that you cannot do such a thing.

The point being is that your misguided attacks on ID are NOT going to provide positiove evidence for your position. And only positive evidence for blind and undirected processes producing CSI is going to refute our arguments. >>

I picked back up from BA77 at 26:

>> BA77: The connexion between entropy and information is indeed important. I like the expression of it that runs like: the entropy of a body is the average missing info to specify the exact microstate of its constituent particles, that exists if what one knows about the system is the thermodynamic macrostate defined by its macro-level thermodynamic properties. This of course implies the degree of freedom or lack of constraint on the particles, and links to the situation where a rise in entropy is often linked to a rise in disorder, a degradation of availability of energy.  >>

_______________
And, dear Reader, what do you think AF’s answer is, several days later on this the 19th of April in this, The Year of Our Risen Lord, “dos mil trece” [= 2013]?

Dead silence, and heading off to other threads where he thought he could score debate points.

(In short, he raised dismissive talking points and stayed not for an answer. Sad.)

Let us hope that headlining the above will at least allow others who need and want such, to find a reasonable summary answer to the NCSE talking points. END

PS: Dembski and Luskin have responded at one time or another to the S-E team, try here and here (part II here; complete with with AF popping up here at no 3).

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515 Responses to Oldies but baddies — AF repeats NCSE’s eight challenges to ID (from ten years ago)

  1. Before Mr. Fox steps in with his usual obfuscation and denial of the facts already in evidence, I would like to point out that the ‘problem of information’ is far deeper than Mr. Fox, and perhaps many others, realize.,,, Usually ID argues that strings of functional information, such as what we find in DNA, RNAs and proteins, can’t be arrived at by Darwinian, chance and necessity, processes. And this is indeed a VERY powerful argument against neo-Darwinism that has nothing less than a null hypothesis backing up its assertion (Dembski, Marks, Abel). Moreover, as was pointed out recently, the trend in evidence in recent years, has decidedly been against Darwinian processes ever falsifying the null. To recap this trend in evidence (that I went over the other day). It was at first assumed by the ID community, at least as far as I am aware, that the plasticity of proteins was far greater than it is now found to be. And as such far more leeway was granted to Darwinian explanations at that time. With ID, at that time, focused mainly on the origin of proteins and IC molecular machines and systems. But now, in the past few years, the limits for what Darwinian processes can actually accomplish has been found, empirically, to be much greater than what was originally granted to them. Dr. Behe relates that sentiment here:

    Severe Limits to Darwinian Evolution: – Michael Behe – Oct. 2009
    Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
    http://www.evolutionnews.org/2.....n_evo.html

    In 2010 Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke came along and found:

    Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness – May 2010
    Excerpt: Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken.
    http://bio-complexity.org/ojs/.....O-C.2010.2

    Then in 2011 Douglas Axe and Ann Gauger came along and drove the nail home:

    The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway – Ann K. Gauger and Douglas D. Axe – April 2011
    Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth.
    http://bio-complexity.org/ojs/.....O-C.2011.1

    But what does all this mean as to the constraints for neo-Darwinian processes? Well Dr. Gauger lays out the implications here:

    More from Ann Gauger on why humans didn’t happen the way Darwin said – July 2012
    Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
    You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
    Facing Facts
    But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.
    http://www.uncommondescent.com.....rwin-said/

    Moreover, while ID was doing the dirty work that Darwinists refused to do, i.e. finding out what the limits to Darwinian processes actually were/are, from the other end of the spectrum it was/is becoming more and more evident that the supposed genetic similarity between species, particularly between man and apes, was far greater than Darwinists had originally misled the general public to believe. Falling from approximately 99% similarity to now around 85% to 70% or even lower genetic similarity:

    Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% – by Jeffrey P. Tomkins – February 20, 2013
    Excerpt: For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor.
    http://www.answersingenesis.or.....chromosome

    As well please note the conservative nature of the preceding study in this excerpt from materials and methods section of the preceding paper:

    “The definition of similarity for each chimp chromosome was the amount (percent) of optimally aligned chimp DNA (minus ‘N’s). This definition was considered to be quite conservative because it did not include the amount of human DNA absent in the chimp genome nor does it include chimp DNA that could not be aligned to the human genome assembly—a category of chimp DNA termed “unanchored contigs”.”

    But if a person were to ask, “how much DNA is absent between the two species?”, the answer is far larger than most people would have expected. It is now found that a significant percentage of all genomes sequenced, including humans, have completely unique ORFan genes with no traceable evolutionary lineage:

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.
    http://ccsb.dfci.harvard.edu/w.....n_2013.pdf

    Orphan Genes (And the peer reviewed ‘non-answer’ from Darwinists) – video
    http://www.youtube.com/watch?v=1Zz6vio_LhY

    This early study found,,

    Human Gene Count Tumbles Again – 2008
    Excerpt:,, the analysis revealed 1,177 “orphan” DNA sequences.,,, 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

    Even Jerry Coyne, who is certainly not friendly to ID, nor to Christians in general, admitted that,,

    From Jerry Coyne, More Table-Pounding, Hand-Waving – May 2012
    Excerpt: “More than 6 percent of genes found in humans simply aren’t found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps.”
    Jerry Coyne – ardent and ‘angry’ neo-Darwinist – professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics.

    Where will percentage difference between chimps and humans finally end up? Nobody really knows,,,

    Ten years on, still much to be learned from human genome map – April 12, 2013
    Excerpt:,,,”What’s more, about 10 percent of the human genome still hasn’t been sequenced and can’t be sequenced by existing technology, Green added. “There are parts of the genome we didn’t know existed back when the genome was completed,” he said.,,,
    http://medicalxpress.com/news/.....enome.html

  2. But one thing is crystal clear, the trend in evidence is definitely against neo-Darwinism ever being scientifically established as the true explanation for how we got here!

    As is evident thus far, Darwinists have been getting squeezed from both ends over the last few years, from the protein level, the plasticity is just not there for them as it was assumed to be, and on the whole genome level, the gaps are growing wider and wider, to the point of making genetic comparisons completely embarrassing as a Darwinian talking point.

    Moreover with the gaps between humans and apes/chimps growing wider and wider, it is also interesting to point out that it is now known that there is also far more similarity between genomes of widely divergent species than was at first expected by Darwinists:

    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

    First Decoded Marsupial Genome Reveals “Junk DNA” Surprise – 2007
    Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,,
    The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off.
    http://news.nationalgeographic.....m-dna.html

    Moreover,,

    Family Ties: Completion of Zebrafish Reference Genome Yields Strong Comparisons With Human Genome – Apr. 17, 2013
    Excerpt: Researchers demonstrate today that 70 per cent of protein-coding human genes are related to genes found in the zebrafish,,,
    http://www.sciencedaily.com/re.....131725.htm

    Now, at least for me, the percent genetic similarity between apes and humans falling precipitously from the original 99% mark that Darwinists had originally, from a point of forcing evidence into a desired conclusion, misled the general public to believe, as well as the percent genetic similarity being far higher for species that were thought to be widely divergent from humans, should have, by all rights, stopped the molecular reductionism model of neo-Darwinism (DNA makes RNA makes proteins) dead in its tracks, or at least it should have, at least, put a severe pause in the step of many of the neo-Darwinists who come on UD, such as wd400, who continually push the modern synthesis of neo-Darwinism as if none of this crushing evidence has even come to light.,, But aside from dealing the mendacity of the neo-Darwinists who come on UD,,, Joe pointed something out to me that this ‘problem’ has actually been dealt with to some degree by people who hold a evolutionary viewpoint (although apparently they hold it not as dogmatically as the UD Darwinists typically do),,,

    Joe stated,,

    That has all changed thanks to evo-devo. Now it isn’t so much changing genotypes but the way the genotypes are used, especially during development. Same genes used in different ways is now the mechanism for macroevolutionary change – see Shubin “Your Inner Fish”.

    Now evo-devo, as far as I know, tries to explain body plan morphogenesis (macro-evolution) by appealing to mutations in the regulatory sequences of DNA which regulate gene expression. (i.e. as far as I know it is molecular reductionism with a twist!), but, as I pointed out to Joe, Dr. Nelson has addressed this issue,,

    Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth – No Evidence For Body Plan Morphogenesis From Embryonic Mutations (excellent update) – video
    Text from one of the Saddleback slides:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
    2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
    3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
    Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
    http://www.saddleback.com/mc/m/7ece8/

    Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress – Paul Nelson – April 7, 2011
    http://www.evolutionnews.org/2.....45581.html

    Moreover,,,

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,

    http://www.the-scientist.com/?.....plicing%2F

    The mouse is not enough – February 2011
    Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.”
    http://www.the-scientist.com/news/display/57986/

    ,,,Alternative splicing,,, may contribute to species differences – December 21, 2012
    Excerpt: After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns—which determine the segments of those genes included or excluded—vary from species to species.,,,
    The results from the alternative splicing pattern comparison were very different. Instead of clustering by tissue, the patterns clustered mostly by species. “Different tissues from the cow look more like the other cow tissues, in terms of splicing, than they do like the corresponding tissue in mouse or rat or rhesus,” Burge says. Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says,,,
    Excerpt of Abstract: To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified;
    http://phys.org/news/2012-12-e.....wires.html

    Finding widely different ‘alternative splicing codes’ in different species is devastating to neo-Darwinism because of neo-Darwinism’s inability to account for any changes of any fundamental code once it is in place. The reason why drastically different alternative splicing codes between different species is devastating to neo-Darwinian evolution is partly seen by understanding ‘Shannon Channel Capacity’:

    “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
    Donald E. Johnson – Bioinformatics: The Information in Life

    Shannon Information – Channel Capacity – Perry Marshall – video
    http://www.metacafe.com/watch/5457552/

  3. But perhaps the best way to understand the reason why this is so devastating to neo-Darwinian evolution is by taking a look at what Richard Dawkins himself said about what would happen if one were to ‘randomly’ change the genetic code once it is in place:

    Venter vs. Dawkins on the Tree of Life – and Another Dawkins Whopper – March 2011
    Excerpt:,,, But first, let’s look at the reason Dawkins gives for why the code must be universal:
    “The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.” (2009, p. 409-10)
    OK. Keep Dawkins’ claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code).
    Simple counting question: does “one or two” equal 23? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.
    http://www.evolutionnews.org/2.....44681.html

    The bottom line is that if any regulatory code, such as the alternative splicing code, is ‘randomly changed’ in part, then it throws the entire code out of whack and will be ‘instantly catastrophic’ to the organism, to use Richard Dawkins most appropriate words, thus rendering the ‘bottom up’ gradual change of neo-Darwinism impossible. i.e. The entire code must be implemented ‘top down’ when the species was originally created! A code is a all or nothing, take it or leave it, ‘top down’ deal!

    It is also interesting to remember just how hard it was to crack the alternative splicing code for humans:

    Breakthrough: Second Genetic Code Revealed – May 2010
    Excerpt: The paper is a triumph of information science that sounds reminiscent of the days of the World War II codebreakers. Their methods included algebra, geometry, probability theory, vector calculus, information theory, code optimization, and other advanced methods. One thing they had no need of was evolutionary theory,,,
    http://crev.info/content/break.....e_revealed

    Also of note, the genetic code and the ‘species specific’ alternative splicing codes are not the only codes to be discovered in life thus far:

    “In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10].
    Donald E. Johnson – Programming of Life – pg.51 – 2010

    Moreover,,,

    “Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source — from a mind or personal agent.” (Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

    “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.)

    Verse and music:

    John 1:1-4
    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. In him was life, and that life was the light of all mankind.

    Eric Church – Like Jesus Does (Acoustic)
    http://www.youtube.com/watch?v=wuG1rLPjVkk

  4. 1 Publish a mathematically rigorous definition of CSI

    (Side-note, the quotation marks you are using would be correct in Finnish but not in French. Unfortunately I can’t demonstrate as the characters are interpreted as HTML. The opening Guillemet “points” out from the quote, not in.)

    It would seem to be a simple matter, if a mathematically rigorous definition of CSI existed, to reproduce it.

  5. I mean <<like this>>

  6. <<It has long since been shown, objections and censorship games notwithstanding, that reasonable quantitative metrics for FSCO/I and so for CSI, can be built and have been built. Indeed Durston et al have used such to provide a published list of values for 15 protein families.>>

    Now measuring the functional sequence complexity of proteins (if we allow for the sake of argument that Durston can reliably do this) has nothing to do, as far as I can see, with Dembski’s “Complex Specified Information” as set out in “No Free Lunch”. The concept of FSCO/I appears to be KF’s personal invention’ unendorsed by any ID theorist. Does a clear unambiguous definition of CSI exist? If so, what is it?

  7. Alan,

    The following is from “No Free Lunch”:

    Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the same sense required by the complexity-specification criterion (see sections 1.3 and 2.5). The specification of organisms can be crashed out in any number of ways. Arno Wouters cashes it out globally in terms of the viability of whole organisms. Michael Behe cashes it out in terms of minimal function of biochemical systems.- Wm. Dembski page 148 of NFL

    You lose, again, as usual. Now what?

  8. Where’s the definition of CSI, Joe?

  9. AF: Okay, you have got the full quote marks to work, I guess you used the commenting feature, prob being when you copy and paste onwards, trouble I bet. KF

  10. TEST: <> test , test. KF

  11. WHOOPS, AT LEAST NOTHING BROKE. kf

  12. Alan,

    If you read “No Free Lunch” you would read that CSI wrt biology, is biological specification.

    Specified information is just Shannon information with meaning or function. IOW it is information in the normal use of the word.

    I don’t understand your issue with it. You use it every day.

  13. F/N: adequate definitions of CSI and metrics thereof exist, I alluded to the one used by Durston et al c 2007, as that one is the one most closely tied to standard usage in information theory on H, average info per symbol. Follow his discussion on null, ground and functional states and on degrees of redundancy and you will see that. (Cf. discussion in my always linked note here.)

    It also happens to be peer review published, with 15 values for protein families.

    No explicit threshold is listed but the sampling theory “needle in haystack” point about the atomic & temporal resources of the solar system or the observed cosmos and the config space of 500 – 1,000 bits is straightforward and applicable. The implication is that the issue is not increments within islands of function with nicely behaved fitness functions etc, but getting to shores of function in such spaces dominated by gibberish as is inevitable.

    If you want to get into debate games on the Dembski model and metric framework of 2005, the log reduction and deduction here on shows how this can be inserted into reasonable upper limits that boil down to a threshold metric with 500 – 1,000 bits as the threshold. (Someone actually objected to such a metric, but was pointedly reminded that much of Einstein’s Nobel Prize was won on an equation that specified a threshold with fairly similar mathematics.)

    The problem is a matter of selectively hyperskeptically making mountains out of molehills.

    Let me clip the linked:

    _______________

    >> xix: Later on (2005), Dembski provided a slightly more complex formula, that we can quote and simplify, showing that it boils down to a “bits from a zone of interest [[in a wider field of possibilities] beyond a reasonable threshold of complexity” metric:

    X = – log2[10^120 ·p_S(T)·P(T|H)].

    –> X is “chi” and p_ is “phi”

    xx: To simplify and build a more “practical” mathematical model, we note that information theory researchers Shannon and Hartley showed us how to measure information by changing probability into a log measure that allows pieces of information to add up naturally:

    Ip = – log p, in bits if the base is 2. That is where the now familiar unit, the bit, comes from. Where we may observe from say — as just one of many examples of a standard result — Principles of Comm Systems, 2nd edn, Taub and Schilling (McGraw Hill, 1986), p. 512, Sect. 13.2:

    Let us consider a communication system in which the allowable messages are m1, m2, . . ., with probabilities of occurrence p1, p2, . . . . Of course p1 + p2 + . . . = 1. Let the transmitter select message mk of probability pk; let us further assume that the receiver has correctly identified the message [[--> My nb: i.e. the a posteriori probability in my online discussion here is 1]. Then we shall say, by way of definition of the term information, that the system has communicated an amount of information Ik given by

    I_k = (def) log_2 1/p_k (13.2-1)

    xxi: So, since 10^120 ~ 2^398, we may “boil down” the Dembski metric using some algebra — i.e. substituting and simplifying the three terms in order — as log(p*q*r) = log(p) + log(q ) + log(r) and log(1/p) = – log (p):

    Chi = – log2(2^398 * D2 * p), in bits, and where also D2 = p_S(T)

    Chi = Ip – (398 + K2), where now: log2 (D2 ) = K2

    That is, chi is a metric of bits from a zone of interest, beyond a threshold of “sufficient complexity to not plausibly be the result of chance,” (398 + K2). So,

    (a) since (398 + K2) tends to at most 500 bits on the gamut of our solar system [[our practical universe, for chemical interactions! ( . . . if you want , 1,000 bits would be a limit for the observable cosmos)] and

    (b) as we can define and introduce a dummy variable for specificity, S, where

    (c) S = 1 or 0 according as the observed configuration, E, is on objective analysis specific to a narrow and independently describable zone of interest, T:

    Chi = Ip*S – 500, in bits beyond a “complex enough” threshold

    NB: If S = 0, this locks us at Chi = – 500; and, if Ip is less than 500 bits, Chi will be negative even if S is positive.

    E.g.: a string of 501 coins tossed at random will have S = 0, but if the coins are arranged to spell out a message in English using the ASCII code [[notice independent specification of a narrow zone of possible configurations, T], Chi will — unsurprisingly — be positive.

    Following the logic of the per aspect necessity vs chance vs design causal factor explanatory filter, the default value of S is 0, i.e. it is assumed that blind chance and/or mechanical necessity are adequate to explain a phenomenon of interest.

    S goes to 1 when we have objective grounds — to be explained case by case — to assign that value.

    That is, we need to justify why we think the observed cases E come from a narrow zone of interest, T, that is independently describable, not just a list of members E1, E2, E3 . . . ; in short, we must have a reasonable criterion that allows us to build or recognise cases Ei from T, without resorting to an arbitrary list.

    A string at random is a list with one member, but if we pick it as a password, it is now a zone with one member. (Where also, a lottery, is a sort of inverse password game where we pay for the privilege; and where the complexity has to be carefully managed to make it winnable. )

    An obvious example of such a zone T, is code symbol strings of a given length that work in a programme or communicate meaningful statements in a language based on its grammar, vocabulary etc. This paragraph is a case in point, which can be contrasted with typical random strings ( . . . 68gsdesnmyw . . . ) or repetitive ones ( . . . ftftftft . . . ); where we can also see by this case how such a case can enfold random and repetitive sub-strings.

    Arguably — and of course this is hotly disputed — DNA protein and regulatory codes are another. Design theorists argue that the only observed adequate cause for such is a process of intelligently directed configuration, i.e. of design, so we are justified in taking such a case as a reliable sign of such a cause having been at work. (Thus, the sign then counts as evidence pointing to a perhaps otherwise unknown designer having been at work.)

    So also, to overthrow the design inference, a valid counter example would be needed, a case where blind mechanical necessity and/or blind chance produces such functionally specific, complex information. (Points xiv – xvi above outline why that will be hard indeed to come up with. There are literally billions of cases where FSCI is observed to come from design.)

    xxii: So, we have some reason to suggest that if something, E, is based on specific information describable in a way that does not just quote E and requires at least 500 specific bits to store the specific information, then the most reasonable explanation for the cause of E is that it was designed. The metric may be directly applied to biological cases:

    Using Durston’s Fits values — functionally specific bits — from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:

    RecA: 242 AA, 832 fits, Chi: 332 bits beyond
    SecY: 342 AA, 688 fits, Chi: 188 bits beyond
    Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond >>
    _______________

    The Mathematics is straightforward, and the result is intuitively reasonable. On the gamut of our solar system, 500+ bits of FSCO/I is not credibly a product of blind chance and mechanical necessity.

    But intelligence routinely produces such. As for instance, posts in this thread exemplify. And, in the biological context, specification is cashed out as function. Which is what Dembski, Meyer, Johnson, Durston, Trevors and Abel and others all more or less say. FSCO/I is just a summary description for that.

    So, it is quite reasonable and inductively well grounded that if we see FSCO/I beyond that threshold, it is best explained on design.

    Unless, one’s real problem is a priori evolutionary materialism as ideology, or one of the fellow traveller ideologies that are operationally indistinguishable therefrom.

    KF

  14. F/N 2: let me clip my excerpts from Durston et al:

    _____________

    >>Abel and Trevors have delineated three qualitative aspects of linear digital sequence complexity [2,3], Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC). RSC corresponds to stochastic ensembles with minimal physicochemical bias and little or no tendency toward functional free-energy binding. OSC is usually patterned either by the natural regularities described by physical laws or by statistically weighted means. For example, a physico-chemical self-ordering tendency creates redundant patterns such as highly-patterned polysaccharides and the polyadenosines adsorbed onto montmorillonite [4]. Repeating motifs, with or without biofunction, result in observed OSC in nucleic acid sequences. The redundancy in OSC can, in principle, be compressed by an algorithm shorter than the sequence itself. As Abel and Trevors have pointed out, neither RSC nor OSC, or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life [5]. FSC includes the dimension of functionality [2,3]. Szostak [6] argued that neither Shannon’s original measure of uncertainty [7] nor the measure of algorithmic complexity [8] are sufficient. Shannon’s classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that ‘different molecular structures may be functionally equivalent’. For this reason, Szostak suggested that a new measure of information–functional information–is required [6] . . . .

    Shannon uncertainty, however, can be extended to measure the joint variable (X, F), where X represents the variability of data, and F functionality. This explicitly incorporates empirical knowledge of metabolic function into the measure that is usually important for evaluating sequence complexity. This measure of both the observed data and a conceptual variable of function jointly can be called Functional Uncertainty (Hf) [17], and is defined by the equation:

    H(Xf(t)) = -[SUM]P(Xf(t)) logP(Xf(t)) . . . (1)

    where Xf denotes the conditional variable of the given sequence data (X) on the described biological function f which is an outcome of the variable (F). For example, a set of 2,442 aligned sequences of proteins belonging to the ubiquitin protein family (used in the experiment later) can be assumed to satisfy the same specified function f, where f might represent the known 3-D structure of the ubiquitin protein family, or some other function common to ubiquitin. The entire set of aligned sequences that satisfies that function, therefore, constitutes the outcomes of Xf. Here, functionality relates to the whole protein family which can be inputted from a database . . . .

    In our approach, we leave the specific defined meaning of functionality as an input to the application, in reference to the whole sequence family. It may represent a particular domain, or the whole protein structure, or any specified function with respect to the cell. Mathematically, it is defined precisely as an outcome of a discrete-valued variable, denoted as F={f}. The set of outcomes can be thought of as specified biological states. They are presumed non-overlapping, but can be extended to be fuzzy elements . . . Biological function is mostly, though not entirely determined by the organism’s genetic instructions [24-26]. The function could theoretically arise stochastically through mutational changes coupled with selection pressure, or through human experimenter involvement [13-15] . . . .

    The ground state g (an outcome of F) of a system is the state of presumed highest uncertainty (not necessarily equally probable) permitted by the constraints of the physical system, when no specified biological function is required or present. Certain physical systems may constrain the number of options in the ground state so that not all possible sequences are equally probable [27]. An example of a highly constrained ground state resulting in a highly ordered sequence occurs when the phosphorimidazolide of adenosine is added daily to a decameric primer bound to montmorillonite clay, producing a perfectly ordered, 50-mer sequence of polyadenosine [3]. In this case, the ground state permits only one single possible sequence . . . .

    The null state, a possible outcome of F denoted as 0, is defined here as a special case of the ground state of highest uncertainly when the physical system imposes no constraints at all, resulting in the equi-probability of all possible sequences or options. Such sequencing has been called “dynamically inert, dynamically decoupled, or dynamically incoherent” [28,29]. For example, the ground state of a 300 amino acid protein family can be represented by a completely random 300 amino acid sequence where functional constraints have been loosened such that any of the 20 amino acids will suffice at any of the 300 sites. From Eqn. (1) the functional uncertainty of the null state is represented as

    H(X0(ti))= – [SUM]P(X0(ti)) log P(X0(ti)) . . . (3)

    where (X0(ti)) is the conditional variable for all possible equiprobable sequences. Consider the number of all possible sequences is denoted by W. Letting the length of each sequence be denoted by N and the number of possible options at each site in the sequence be denoted by m, W = mN. For example, for a protein of length N = 257 and assuming that the number of possible options at each site is m = 20, W = 20257. Since, for the null state, we are requiring that there are no constraints and all possible sequences are equally probable, P(X0(ti)) = 1/W and

    H(X0(ti))= – [SUM](1/W) log (1/W) = log W . . . (4)

    The change in functional uncertainty from the null state is, therefore,

    delat_H(X0(ti), Xf(tj)) = log (W) – H(Xf(ti)). (5)

    . . . . The measure of Functional Sequence Complexity, denoted as z, is defined as the change in functional uncertainty from the ground state H(Xg(ti)) to the functional state H(Xf(ti)), or

    z = delta_H (Xg(ti), Xf(tj)) . . . (6)

    The resulting unit of measure is defined on the joint data and functionality variable, which we call Fits (or Functional bits). The unit Fit thus defined is related to the intuitive concept of functional information, including genetic instruction and, thus, provides an important distinction between functional information and Shannon information [6,32].

    Eqn. (6) describes a measure to calculate the functional information of the whole molecule, that is, with respect to the functionality of the protein considered. The functionality of the protein can be known and is consistent with the whole protein family, given as inputs from the database. However, the functionality of a sub-sequence or particular sites of a molecule can be substantially different [12]. The functionality of a sub-molecule, though clearly extremely important, has to be identified and discovered . . . .

    To avoid the complication of considering functionality at the sub-molecular level, we crudely assume that each site in a molecule, when calculated to have a high measure of FSC, correlates with the functionality of the whole molecule. The measure of FSC of the whole molecule, is then the total sum of the measured FSC for each site in the aligned sequences. Consider that there are usually only 20 different amino acids possible per site for proteins, Eqn. (6) can be used to calculate a maximum Fit value/protein amino acid site of 4.32 Fits/site [NB: Log2 (20) = 4.32]. We use the formula log (20) – H(Xf) to calculate the functional information at a site specified by the variable Xf such that Xf corresponds to the aligned amino acids of each sequence with the same molecular function f. The measured FSC for the whole protein is then calculated as the summation of that for all aligned sites. The number of Fits quantifies the degree of algorithmic challenge, in terms of probability, in achieving needed metabolic function. For example, if we find that the Ribosomal S12 protein family has a Fit value of 379, we can use the equations presented thus far to predict that there are about 1049 different 121-residue sequences that could fall into the Ribsomal S12 family of proteins, resulting in an evolutionary search target of approximately 10^-106 percent of 121-residue sequence space. In general, the higher the Fit value, the more functional information is required to encode the particular function in order to find it in sequence space. A high Fit value for individual sites within a protein indicates sites that require a high degree of functional information. High Fit values may also point to the key structural or binding sites within the overall 3-D structure.>>

    _____________

    FYI.

    Been there all along, two clicks away.

    KF

  15. F/N 3: Basic defn CSI, repeatedly drawn to AF’s attention:

    ___________

    NFL: >>p. 148: “The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology.

    I submit that what they have in mind is specified complexity [[cf. here below], or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . .

    Biological specification always refers to function . . . In virtue of their function [[a living organism's subsystems] embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways [[through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole] . . .”

    p. 144: [[Specified complexity can be defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ” >>
    __________

  16. OT: Technique Unlocks Design Principles of Quantum Biology – Apr. 19, 2013
    Excerpt: University of Chicago researchers have created a synthetic compound that mimics the complex quantum dynamics observed in photosynthesis and may enable fundamentally new routes to creating solar-energy technologies. ,,,
    The resulting molecules were able to recreate the important properties of chlorophyll molecules in photosynthetic systems that cause coherences to persist for tens of femtoseconds at room temperature.
    “That may not sound like a very long time — a femtosecond is a millionth of a billionth of a second,”
    http://www.sciencedaily.com/re.....120954.htm

    Despite their confident tone that they have matched what is found in nature, it seems they may have a bit more engineering and ‘creating’ to do before they truly match what is found in nature,,

    Life Uses Quantum Mechanics – September 25, 2012
    Excerpt: ,,,it looks as if nature has worked out how to preserve (quantum) entanglement at body temperature over time scales that physicists can only dream about.,,,
    Maintaining the entangled state for 100 microseconds is “an extraordinary figure,” the article states. The best human engineers have achieved is 80 microseconds.,,,,
    http://crev.info/2012/09/life-.....mechanics/

  17. I see that Lizzie is still bellyaching about CSI.

    Earth to Lizzie- if your position had any positive evidence, you wouldn’t need to worry yourself with CSI. So perhaps that is what you should focus on. Attacking ID and CSI will never produce positive evidence for your position.

  18. Lizzie:

    If ID proponents can calculate the probability distribution under a “chance hypothesis that takes into account Darwinian and other material mechanisms”, then, cool.

    Actually Lizzie, you guys can’t even demonstrate a feasibility pertaining to Darwinian and other material mechanisms. The point being is just by saying there may be a probability is giving you guys a benefit of doubt that you do not deserve.

    But until they’ve done that, no matter how many equations they produce, they haven’t given us any definition of CSI that will allow us to detect design in biology,…

    That is your opinion. However it is very noticeable that you still cannot produce any positive evidence wrt biology for a chance hypothesis including Darwinian and other material mechanisms.

    So it appears that all you have left is your whining and your fellow whiners.

  19. And Neil Rickert continues his cluelessness:

    As an example, consider the player pianos that were at one time common. You inserted a roll of paper with punched holes, and the mechanism of the player piano used those holes to trigger the motion of the piano keys. To me, that player roll was never information. It was more like a template. It was something used as part of a causal role.

    Neil, piano rolls were created by an agency using INFORMATION.

    I see DNA as more like the piano roll than like the sheet music.

    Both piano rolls and sheet music are designed, therefor according to Neil, DNA is designed.

    Nice job Neil.

  20. NR (via Joe):

    Has it registered that the old piano rolls were programs, carrying out encoded step by step finite sequences of operations stored in a medium and achieving a definite task based on a code reader connected to effectors (complete with different languages!)?

    Wiki:

    A piano roll is a music storage medium used to operate a player piano, piano player or reproducing piano. A piano roll is a continuous roll of paper with perforations (holes) punched into it. The perforations represent note control data. The roll moves over a reading system known as a ‘tracker bar’ and the playing cycle for each musical note is triggered when a perforation crosses the bar and is read.

    The majority of piano rolls play on three distinct musical scales. The 65-note (with a playing range of A-1 to C#7) format was introduced in 1896 in the USA specifically for piano music. In 1900 a USA format playing all 88-notes of the standard piano scale was introduced. In 1902 a German 72-note scale (F-1, G-1 to E7) was introduced. All of these scales were subject to being operated by piano rolls of varying dimensions. The 1909 Buffalo Convention of US manufacturers standardized the US industry to the 88-note scale and fixed the physical dimensions for that scale.

    Piano rolls were in continuous mass production from around 1896 to 2008,[1][2] and are still available today, with QRS Music claiming to have 45,000 titles available with “new titles being added on a regular basis”.[3] Largely replacing piano rolls, which are no longer mass-produced today, MIDI files represent a modern way in which musical performance data can be stored. MIDI files accomplish digitally and electronically what piano rolls do mechanically. Software for editing a performance stored as MIDI data often has a feature to show the music in a piano roll representation.

    The first paper rolls were used commercially by Welte & Sons in their Orchestrions beginning in 1883.[4]

    For the player piano:

    A player piano (also known as pianola or autopiano) is a self-playing piano, containing a pneumatic or electro-mechanical mechanism that operates the piano action via pre-programmed music perforated paper, or in rare instances, metallic rolls.

    Am I the only one to remember punch card stacks and also eight bit paper tape (with a ninth sprocket hole) as computer program storage media?

    I trust that it is understood that prong height [how a Yale lock key works . . . your keys are physical instantiations of passwords], hole/no hole, dot-dash, etc are all ways to encode data and can be used to encode digital data.

    In short, we have a case of FSCO/I and again a clear instance that it is designed.

    And, save for giving the Wiki cite, this has been said more than once before here at UD.

    KF

  21. EL (via Joe):

    Nope.

    The pivotal issue is sampling theory, not probability distributions.

    In essence, as has been pointed out over and over and over again, but ignored, when one takes a relatively small sample of a large population, one only reasonably expects to capture the bulk, not special zones like the far tails or isolated and highly atypical zones. This is like the old trick of reaching a hand deep into a sack of beans and pulling out a handful or two to get a good picture of the overall sack’s contents.

    When we have config spaces for 500 bits or more, we are dealing with pops of 3.27 * 10^150 and up, sharply up. The atomic resources of the solar system working at fastest chemical reaction rates and for the scope of the age of the cosmos, would only be able to sample as one straw to a cubical haystack 1,000 LY thick, about as thick as our Galaxy.

    The only thing we could reasonably expect to pick up on a blind sample of such scope, would be the bulk. Here, straw, and not stars or solar systems etc.

    Where also, the other thing that you have long, and unreasonably, refused to accept is that once we deal with specifically functional configs of sufficient complexity, the constraints of proper arrangement of the right parts to achieve function confine us to narrow and very unrepresentative zones of the space of possibilities. Islands of function for illustrative metaphor.

    All of this has been accessible long since but you have refused to listen.

    I will simply say that by looking at sampling theory without having to try to get through a thicket of real and imaginary objections to probabilistic calculations, we can easily and readily see why it is unreasonable on the gamut of the solar system (or for 1,000 bits the observed cosmos) to expect to encounter FSCO/I by blind chance and mechanical necessity.

    Where also of course the thresholds of complexity chosen were chosen exactly for being cutoffs where the idea that chance and necessity would be reasonable would become patently ridiculous. It just turns out that even 1,000 bits is 100 – 1,000 times fewer bits than are in the genome for credible first cell based life.

    And, that is the pivotal case as this is the root of the suggested Darwinian tree of life. Where, precisely because the von Neumann self replicator [vNSR] required for self replication is not on the table, cutting off the hoped for excuse of the wonderful — though undemonstrated — powers of natural selection acting on chance variations.

    The only empirically warranted explanation for the FSCO/I pivotal to first life is the same as the only observed source of such: design.

    The problem is not with the logic, it is that the implications run counter to strongly held ideological beliefs. That is why every sort of selectively hyperskeptical dismissal, red herring and strawman argument is resorted to rather than face it.

    And, once design is at the table as of right not sufferance, then there is no good reason to try to exclude it in dealing with major body plans etc. Ideological blinkers don’t count.

    Dembski et al have compiled models that give an analytical context that gives probabilities. As I and others have shown, by putting in reasonable cut-off points based on atomic resources accessible, we can turn this into a practical system good enough for the sort of inference we need.

    Onward, we can indeed go on to do a yardstick comparison with the performance of the on-average blind sample, i.e simple random samples. This is because of the search for a search problem that gives us a cascade of higher and higher level searches that are at least as difficult on average as a simple random search.

    In other words, if a search process is outperforming what flat random search would do, there is active information that has been injected intelligently into it, with all but certainty. The degree of the information added can be estimated from the out-performance of the typical search used as yardstick.

    And, there are sufficient cases accessible in the literature (just review the recent work of Marks and Dembski) to show that.

    All of this has been pointed out to you, years ago now.

    And all of it has been ignored or dismissed and the adequately answered objections have been recirculated over and over again.

    The name for that, sad to say, is going in closed minded circles, hoping for the desired result to come out.

    It may feel good (especially in an ideologically congenial circle), but it is not sound. And that too has long since been pointed out over and over and over.

    It would be funny, if it were not ever so sad.

    KF

  22. Regarding Neil via Joe and KF:

    I just got back about an hour ago from the country’s primary Computer History Museum. We were dropping our son off at a big all-day hacking event for teens, so we took the opportunity to look around the museum. Among all the other great exhibits, I saw several examples of early computers using punch-card based information storage and retrieval.

    Neil’s comment about the player piano punch roll demonstrates that he does not understand computing and does not understand information.

    I’m afraid the design inference will be very difficult for someone to understand if they can’t even recognize information storage when they see it.

  23. EA: They have hacking events for kids???? KF

    PS: Punched paper tape.

  24. Lizzie via Joe @18:

    kf has given an excellent response.

    However, I’m also curious about the “Darwinian and other material mechanisms.” What mechanisms would that be?

    I’m not being facetious. I sincerely would like to know what mechanism is proposed. We have the following fundamental forces: gravity, electromagnetism, the strong and weak nuclear forces. We have the laws of physics. We have subsidiary mechanisms, like chemistry.

    What mechanism is proposed? Darwinism (as Darwin proposed it) certainly doesn’t include any proposed mechanism for biological novelty. At most, what he did was propose a way for biological novelty to be preserved after it is already made. (In fact, natural selection is just a label applied after-the-fact to forces not understood, but we’ll leave that discussion for another time.) Natural selection certainly is not a ‘mechanism’ for producing biological novelty and complex specified information or systems.

    So, which mechanism is being proposed? Pure chemical necessity? Errors in copying nucleotides? These have been pretty well reviewed and we have a good sense as to the probabilities, which is where criticisms of materialistic evolution often rightly focus.

    And don’t try to answer by referring to general concepts like drift, bottlenecks, convergence, punctuation, population genetics, punctuation, and so on. Those are attempts to describe, label or calculate what is going on. But they aren’t the actual mechanisms.

    So, pray tell, what mechanism is proposed as the source of biological novelty?

  25. 25

    Journey Into Information Theory

    It’s well produced and very basic.

    There’s also one for cryptography: Journey Into Cryptography.

  26. kf @23:

    They have hacking events for kids????

    Yeah, back in my misspent youth when I was programming on the early Apple II machines, and later doing PASCAL, and also HexDec programming* on a Burroughs L9911-200 “Mini” Computer** (which used large sheet punch cards, by the way), the word “hacking” always carried a negative connotation. A “hacker” was a bad guy.

    Nowadays it is apparently a good word. A lot of the coding events at the schools and universities are called “hacking” events. :)

    —–

    * Now for those who haven’t tried HexDec programming, that is a tedious job. Natural language source code has been such a huge boon to the whole enterprise of programming. In some ways I feel bad that my kids haven’t had to go through the exercise of poring over HexDec printouts for hours to track down a stray character. There is a lot of value in having to look ‘under the hood,’ so to speak, rather than just operating at a high level.

    ** The Burroughs (so-called) “Mini” was a 5′ long beast that weighed about 1000 lbs and pulled 16.8 amps at 120v. All with an impressive 8kb memory! It had three types of information storage: stripe ledger, cassette tape, and punched paper.

  27. Thanks, Chance. I’ll have to check those videos out.

    One has to be a little careful with Khan about evolution/ID stuff, as it isn’t quite up to speed and perpetuates many of the common misconceptions, but he seems to be pretty good with general math, computing information and so forth. He has certainly done a great service with his academy.

  28. 28

    Eric @27, agreed on both counts. I’ve watched several of the Information Theory videos. They appear to be good material, especially for kids.

  29. And don’t try to answer by referring to general concepts like drift, bottlenecks, convergence, punctuation, population genetics, punctuation, and so on. Those are attempts to describe, label or calculate what is going on. But they aren’t the actual mechanisms.

    Well put, Eric.

    I think you’ve done a great job exposing why neo-Darwinism is doomed. It doesn’t have a mechanism to explain biological diversity. The evolutionists can rant and rave all they want about molecules like DNA and proteins and enzymes, and processes like inheritance and duplication and recombination and mutation, but we all know those things are just nature operating freely. And nature certainly isn’t a mechanism.

    So evolutionists, where’s the mechanism?

    Silence. That’s what I thought. You can’t provide mechanisms because your all atheist-materialist-Darwinists so you don’t believe in them.

  30. 30

    “The evolutionists can rant and rave all they want about molecules like DNA and proteins and enzymes, and processes like inheritance and duplication and recombination and mutation, but we all know those things are just nature operating freely. And nature certainly isn’t a mechanism.”

    There’s the mechanism: right there creationists! And and also here. Who can say we don’t have a mechanism? Machines cause evolution, duh. And if you want proof, evolution caused humans and humans make machines, therefore evolution makes machines, which are the mechanism.

  31. Well, there is an evolutionary mechanism, but I didn’t mention it by name in #24, because I wanted people to think through the issue before coming to a conclusion.

    As we look for a mechanism, I think it is helpful to hark back to the basic forces operating in nature and then work upward to see if we can identify an actual mechanism.

    In evolution’s case (and, yes, Virginia, I am talking about evolution as it is generally understood, meaning purely naturalistic evolution), there is no force of nature, no causal element, that can produce what we see in biology. Thus, the grand, overarching, be-all and end-all evolutionary mechanism is this:

    Chance

    That is it. Once agency is rejected, and given that necessity cannot, by definition, produce the kinds of systems we see in biology, we are left with only one option. Chance.*

    There are a couple of other basic ways to describe the same mechanism:

    Particles bumping into each other.

    Accidental collisions over long periods of time.

    Or as I have often summarized many alleged evolutionary ‘explanations:’

    Stuff Happens.

    —–

    * We could have an interesting angels-on-the-head-of-a-pin discussion about what is meant by “chance” and whether “chance” really means “necessity in ways that we don’t understand.” Regardless, the only available alternative is what is typically known as chance. There is nothing more.

  32. The TSZ ilk are moaning about some alleged “slight of hand” wrt calculating probailities, when in fact their entire position is nothing but slight of hand as it obvioulsy doesn’t have any evidentiary support.

    And nice to see they still can erect strawman after strawman:

    Remember that the Creationist Model holds that everything was poofed in a single atomic event. All mass, energy, physics and chemistry and everything — including life, which has not changed since it all got poofed up 6000 years ago.

    Leave it to a dork named “Flint” to come up with that garbage. And as is typical “Flint” doesn’t reference that bit of crap.

  33. Joe (& TSZ):

    There is no sleight of hand involved.

    Sampling theory is well known and is routinely used to characterise distributions on the known properties of such sampling in light of the law of large numbers [i.e. a large enough sample, often 25 - 30 in cases relevant to bell type distributions -- the far tails are special regions and tend not to be picked up, we have had the discussion about dropping darts from a ladder to a paper cut-out long since (years and years ago . . . ), you are just not going to easily hit the tail by chance with reasonable numbers of "drops" . . .] and related results.

    Indeed, this theory and its needle in the haystack result is what lies behind the statistical form of the second law of thermodynamics.

    The basic point is a simple as the point of the proverb about (blindly) searching for needles in haystacks.

    Namely, if there is ever so much stack and ever so little needle, it is going to be very hard to find the needle in the stack.

    In this case, with the known rate of fast chemical reactions [taking down to ~ 10^-14 s for ionic rxns], the known scope of the solar system [~ 10^57 atoms, ~ 10^17 s as a reasonable acceptable per argument lifetime to date, etc] we can see how much searching can be done, and the sample size is extremely generous as a result. But 2^500 possibilities for 500 bits [coins will do as one coin is a 2-sided die in effect, storing 1 bit of info in which face is up] is well beyond this, 3.27 * 10^150 possibilities.

    By way of rough illustration, a one straw sized sample to a cubical haystack as thick as our galaxy.

    Sampling theory tells us the overwhelmingly likely — all but certain — result of a blind sample on this scope: we have only a right to expect to see a reflection of the bulk of the distribution, not very unusual items. Think, a very large sack of beans, in which there is just one golden bean. Stick in hand at random, and pull out a handful. Do you EXPECT to see the golden bean?

    Not if you are rational.

    That is, what is strictly logically possible may be so deeply isolated in the field of possibilities, that it is effectively empirically unobservable. This in fact, at far less compelling level, is the basic logic behind the classic statistical hyp testing approach that infers that far tails are special regions unlikely to come up in reasonable sized sample. So, if we see what would be far tail popping up when it should be unobservable, we have reason to infer that this is not by chance alone.

    This brings us back to the basic problem of Darwin’s warm little pond or the like.

    We know the physical and chemical forces and statistics that are at work, well understood for coming on 100 years now. Where, there are no signs of physics and chemistry being programmed to assemble life molecules and arrange them in requisite patterns relevant to cell based life function. (Where, if there were, that would be a strong clue that he cosmos was designed, for the best explanation of such an astonishing result would be that the laws of the cosmos would embed a life program. It’s bad enough that to get the sort of cosmos we have that is a suitable stage for C-chemistry aqueous medium cell based life, we are looking at astonishing fine tuning.)

    And, the components and structures required to get you even close to code using self-replicating, metabolising, cell based life with encapsulation just simply are a golden bean search on steroids.

    Nor can gleefully jumping up and down and shouting Hoyle’s “fallacy” help.

    The threshold problem comes way way way before we get to what Hoyle used as a striking example.

    Sir Fred spoke of tornadoes assembling Jumbo jets from aerospace junkyards, by way of rhetorical flourish.

    He could as well have spoken of assembling one d’Arsonval galvanometer based instrument on the panel on the flight deck. As a matter of fact, getting the right nut and bolt together and bolting it up to the right torque in the right place in a pile of galvanometer parts is already a stiff challenge for the tornado. And I would never trust an electrical “circuit” assembled by a tornado!

    Such examples are scaled up to macro-level familiar forces and components. The real challenge is at molecular level, but the point still holds.

    To correctly clump and assemble the right components for complex, functionally specific molecular nanotech systems relevant to cell based life — which I must remind, are code using [with code storage based on molecular sequences in D/RNA] — must address serious issues of high contingency, energetically unfavourable components, cross-interference, chirality, and more.

    Absent a priori evolutionary materialism backed up by the heavy hand of censorship and expulsion, the reasonable person would long since have concluded that the best explanation (per the empirically reliably known source of the FSCO/I involved) for something like what we see in the living cell is design.

    Like it or lump it, design sits at the table as of right, not grudging sufferance.

    KF

  34. Flint (via Joe):

    At this stage, to erect that sort of strawman in the teeth of easily accessible and abundant evidence to the contrary is not only a loaded strawman argument but one rooted in willful disregard for duties of care to truth and fairness; in the hope of profiting by a misrepresentation or outright untruth being perceived as true.

    In one sharp, short word: lying.

    Are you even willing to face the point that the reason why 500 bits is chosen as the FSCO/I threshold is rooted in the search capacity of a solar system of 10^57 atoms, and 10^17 s, which is of the order of the typical timeline proposed since the big bang. (And many YEC’s don’t like that either, though Humphreys [sp?] has a model in recent years of a 15 BY cosmos with a young earth.)

    Immoral rhetorical stunts like you just pulled go to character at this point, and add to the cumulative picture that is building up regarding the patterns of behaviour of far too many objectors to design theory.

    And, other denizens of TSZ and similar sites, harbouring such tactics (and worse) and letting them stand by failing to police yourselves, is enabling behaviour.

    KF

  35. Kairosfocus posted this:

    There is no sleight of hand involved.

    The sleight of hand involves continuing to offer various reformulations of CSI, all of which have a fatal flaw built in.

    When will you face up to the problem that scientists have been pointing out to IDists for the past ten years: unless you can specify the frequency distribution of the population you are sampling, then you can draw no valid conclusions about the probability of a “tail” event.

  36. Well the TSZ ilk are still all in a tither wrt CSI. Unfortunately for them they STILL don’t have any evidence to support the claims of their position.

    They are satisfied attacking a caricature of CSI and ID. That is because they are either too dishonest, ignorant or stupid to try to support their position.

    My apologies for dragging their tripe back to UD.

  37. But it is nice to see keiths bring up his oft-refuted diatribe and say that we have no response to it.

    Earth to keiths- you were corrected in the thread you linked to, loser.

  38. So Flint lies like a rug and the TSZ ilk attack kairosfocus for calling him out.

    Lizzie’s lozers are just total wastes of skin…

  39. timothya:

    The sleight of hand involves continuing to offer various reformulations of CSI, all of which have a fatal flaw built in.

    Your entire position is a fatal flaw as it doesn’t even deserve probability considerations as you can’t demonstrate a feasibility.

    Does it really bother you guys so much that unlike you, ID actually has a methodology for making determinations?

  40. timothya:

    Two questions:

    1. Are you suggesting that we have to know the exact, precise, unequivocal probability of event X occurring by purely natural processes before we can draw an inference that event X did not occur by purely natural processes?

    2. On what basis do forensics experts and archaeologists draw an inference to design? Must they first lay out a precise formulation of all possible probabilities of the item in question having been produced by purely natural processes?

  41. TA:

    Do, tell us specifically, on evidence, the relevant flaw?

    Let’s start from a simple contrast, a la Abel & Trevors and harking back through Thaxton et al to Orgel and Wicken:

    1: OSC/Order: ftftftftftftftft . . .

    2: RSC/Randomness: ygd46eyvyfduhudcuftdc . . . .

    2: FSC/Organisation: this is a sequence of characters in English . . .

    Do you wish to imply that there is no material, describable distinction across the three? Kindly, explicitly justify such a notion. (The sound you hear is laughter on the part of onlookers. BTW, as through nodes and arcs net lists, we can reduce any describable structure to strings, so the above is WLOG.)

    Next, let us examine Dembski’s basic definition, from NFL:

    p. 148: “The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology.

    I submit that what they have in mind is specified complexity [[cf. here below], or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . .

    Biological specification always refers to function . . . In virtue of their function [[a living organism's subsystems] embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways [[through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole] . . .”

    p. 144: [[Specified complexity can be defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ”

    Now, I actually do think there is a minor flaw here, the need to clarify the limits. That is why I use 500 bits as a solar system limit; for 10^57 atoms, 10^17 s and chem rxn times ~ 10^-14 s. For the observed cosmos, I square this, and am assured that the needle in haystack challenge is even deeper. That is, the 10^80 atoms of the observed cosmos working for 10^25 s and at PLANCK-time rates rounded down to 10^-45 s, cannot sample as much as 1 in 10^150 of the space.

    This is a needle in a haystack blind search challenge on skyrockets.

    Next, we can look at the Dembski quantification of 2005, and see how reducing logs and making reasonable upper limits gives us, for the solar system:

    Chi_500 = Ip*S – 500, where once Chi goes positive on a solar system scope (our practical cosmos for chemical interactions, absent invention of a warp drive) we can be assured blind search is all but utterly certain to fail. A practical impossibility.

    So, I think your bluff that all definitions of complex specified info are flawed, fails.

    And BTW, in the world of information systems, the normal stuff we use, buy and create, is FSCI, in bits.

    It is high time to put that talking point out to pasture.

    KF

  42. PS: Flint and other TSZ denizens, I did not invent the short, sharp little word or the meaning: speaking with disregard to the truth, hoping to profit by the misrepresentation or outright untruth being perceived as true. Nor did I create the fact that you, Flint, spoke in just that way by so willfully misrepresenting design theory as Young Earth Creationism, with the onward intent to infer or imply — the subtext is quite obvious — attempted imposition of an imagined right wing theocratic tyranny on science and culture; which is a slander, even of young earth creationists as a whole. The very concept, that there is a 500 bit FSCI threshold, is in the context of the usual models of solar system formation, and much of the context of cosmological fine tuning is that of a cosmos of some 13.7 BY in light of a big bang cosmological model. For years, there have been the WAC’s to correct those willing to pay attention, right here at UD, so there is no excuse at this stage for someone who resorts to such slander tactics. And those who harbour or try to defend such are indulging in enabling and upholding in wrong. Where also if you want to try an immoral equivalency game observe that when Mr Arrington learned that he had been in error he corrected it and apologised. (There seems to be some sort of technical problem with the UD mobile site, which I did not even know existed previously. [I thought the purpose of those nice fat tablets was to be able to access web sites normally? Or, is this for those who want cell phones to play at being miniature computers? My advice is go get a tablet.]) After years of smears, outright vicious lying and web stalking, outing tactics, cruel mockery and threats against my family, I do not find any widespread willingness to acknowledge wrong and apologise, much less retract and seek to make amends for injury and insult done. Instead, I find a tide of Alinskyite amoral nihilism that takes malicious glee in creating poison and polarisation, and read from that, that such are a menace to our civilisation and a sign of what lies ahead if the madness is not stopped short of the cliff. KF

  43. EA: There is no need for exact probability calcs or estimates. All we need are circumstances that sampling theory will let us see are of the needle in haystack variety, where is is simple to see that by its nature, the bulk of possible configs in a relevant situation will be gibberish. KF

  44. CSI wrt biology = biological specifcation. Biological specifcation always refers to function.

    That is more proof that Lizzie did NOT create CSI with her algorithm- no function created/ observed (and it starts with the very function that needs to be explained-> reproduction).

  45. EA @22:

    We were dropping our son off at a big all-day hacking event for teens…

    My bank account just went to zero dollars.

    Could you talk to your son for me?

    Thanks

  46. Eric Anderson posted two questions:

    1. Are you suggesting that we have to know the exact, precise, unequivocal probability of event X occurring by purely natural processes before we can draw an inference that event X did not occur by purely natural processes?

    2. On what basis do forensics experts and archaeologists draw an inference to design? Must they first lay out a precise formulation of all possible probabilities of the item in question having been produced by purely natural processes?

    1. No. Though you do need to have a clear idea of how natural processes work before rejecting the no-design null hypothesis. That is to say, you should have a well-specified (and well-populated) frequency distribution for your attribute before tossing the null overboard.

    2. On the basis of frequency distributions of designed events observed to occur in the past. In other words, the real work involved is constructing a frequency distribution for the attribute of interest against which any new event can be compared.

    It is dangerous, as well as unscientific, to simply assume what that frequency distribution looks like until the legwork has been undertaken. Constructing frequency distributions for attributes at the genomic, biochemical, physiological and population levels is what biologists, archaeologists, forensic scientists and insurance actuaries generally do via observations and experiment.

  47. F/N: TA, do you understand that far tails of bell or similar distributions are but one rather peculiar example of the broader case of separately and “simply” describable narrow — i.e. unrepresentative of the typical members of W — zones of interest T in large config spaces W? [Where as the W standing in for omega hints, the antecedents of interest lie in statistical thermodynamics and the warrant for results, including the statistical underpinnings of the second law of thermodynamics and why entropy of a system tends to increase. Cf. here on.]

    1: Do you understand the generality of sampling theory results on capturing gross and typical patterns of a population without needing to know details of its generating factors, forces and resulting mathematical distributions?

    2: As in, do you understand that with a large sack of beans that you have in hand, a couple of hands full from deep in the sack, can be utterly telling?

    3: But, if there is a single gold bead or a lost wedding ring in the sack, you have a challenge to find it that way?

    4: What then happens when the sack is so large that you cannot pour it out to search more than a tiny, tiny fraction, regardless of the number of gold beads, once they are sufficiently rare that feasible samples are utterly unlikely to pick them up?

    5: Do you now see the significance of the base definition being offered by WmAD in NFL, and of the developments over the past decade or so? Namely, why it is that random search, in a world of search for search [S4S], becomes the typical search [which BTW is a good example of why the Bernoulli-Laplace principle of indifference is so often a useful default . . . ], and why if a search is outperforming it, that is a sign that it was tuned to the distribution in some way, indicative of intelligence and injection of active information, which can be measured by the degree of over-performance relative to the expected result of the typical search?

    6: That people may object to something does not mean that the thing objected to is thereby falsified — the error of selective hyperskepticism. And,

    7: even where there are problems, we can learn to keep the baby and discard the bath water or even the dirty diaper.

    8: As has been shown, the basic concept of CSI is sound, the distinctions between OSC, RSC and FSC are objective, and the matter can be reduced to metric models that consistently show a track record of performance that FSCO/I is consistently seen to come form just one source, intelligence.

    9: Where, chance and necessity, on reasonable models, will fall below the threshold or reasonable observability, something that is being abundantly confirmed by the experience of billions of test cases all around us.

    KF

  48. ‘The much underestimated and too often derided BA77…’

    By crystallising the animus against Philip of his ‘bottom-feeder’ critics, KF, you are inadvertently dignifying their inchoate howling, giving aid comfort to ‘our friends’ across the epistemological chasm – the enemies of reason – in however nugatory a measure and elliptical manner. Pardon my presumption, as a 22 carat ‘dogsbody’ nescientist, in bringing this to your notice.

  49. ‘Specified information is just Shannon information with meaning or function. IOW it is information in the normal use of the word.

    I don’t understand your issue with it. You use it every day.’

    Neither does Alan, Joe. He’d have to go back to primary school, and start learning from scratch again. He’s got lost. What should be reason is a maze to him.

  50. Kairosfocus posted this, with my answers interpolated in his approved manner:

    F/N: TA, do you understand that far tails of bell or similar distributions are but one rather peculiar example of the broader case of separately and “simply” describable narrow — i.e. unrepresentative of the typical members of W — zones of interest T in large config spaces W? [Where as the W standing in for omega hints, the antecedents of interest lie in statistical thermodynamics and the warrant for results, including the statistical underpinnings of the second law of thermodynamics and why entropy of a system tends to increase. Cf. here on.]

    No I don’t understand anything in that paragraph. Particularly obscure is any connection between standard statistical sampling from biological populations and statistical analysis of physical entropy.

    1: Do you understand the generality of sampling theory results on capturing gross and typical patterns of a population without needing to know details of its generating factors, forces and resulting mathematical distributions?

    What is “the generality of sampling theory”? I do know about sampling theory and I know it works well if you already know the form of the population distribution being sampled.

    2: As in, do you understand that with a large sack of beans that you have in hand, a couple of hands full from deep in the sack, can be utterly telling?

    Or not utterly telling, depending on the frequency distribution of the beans with respect to the attribute you are investigating. Can you specify what hypothesis you are investigating about the nature of the beans?

    3: But, if there is a single gold bead or a lost wedding ring in the sack, you have a challenge to find it that way?

    In that case it isn’t a bag of beans. Your null hypothesis has been invalidated. Try again. For example: what is the likelihood of finding a wedding ring in a sack of beans sampled at random from a bean factory?

    4: What then happens when the sack is so large that you cannot pour it out to search more than a tiny, tiny fraction, regardless of the number of gold beads, once they are sufficiently rare that feasible samples are utterly unlikely to pick them up?

    In that case you have invalidated your sample design again (you can’t “adequately” sample an infinitely large bag of beans). Please, please, please get your statistical definitions straight, and then stick to them.

    5: Do you now see the significance of the base definition being offered by WmAD in NFL, and of the developments over the past decade or so? Namely, why it is that random search, in a world of search for search [S4S], becomes the typical search [which BTW is a good example of why the Bernoulli-Laplace principle of indifference is so often a useful default . . . ], and why if a search is outperforming it, that is a sign that it was tuned to the distribution in some way, indicative of intelligence and injection of active information, which can be measured by the degree of over-performance relative to the expected result of the typical search?

    Invalid argument if you are addressing biological processes (biological processes do not involve cosmological-scale searches. They “search” the specific genomic options offered by mutation.

    6: That people may object to something does not mean that the thing objected to is thereby falsified — the error of selective hyperskepticism. And,

    Agreed. Your arguments are falsified by evidence, not because I happen to disagree with them.

    7: even where there are problems, we can learn to keep the baby and discard the bath water or even the dirty diaper.

    Agreed. The bath water of cosmic-scale “blind search” can safely be discarded in relation to the behaviour of biological systems.

    8: As has been shown, the basic concept of CSI is sound, the distinctions between OSC, RSC and FSC are objective, and the matter can be reduced to metric models that consistently show a track record of performance that FSCO/I is consistently seen to come form just one source, intelligence.

    You are simply restating the same circular argument. To calculate the CSI/(insert any other preferred version) of an object, you have to know in advance what designed objects look like. How do we know such a thing? Why, because we know how humans design stuff! To borrow your own terminology, you are smuggling in the answer via your premises.

    9: Where, chance and necessity, on reasonable models, will fall below the threshold or reasonable observability, something that is being abundantly confirmed by the experience of billions of test cases all around us.

    Wrong. We do not have “billions of test cases”. There is only one known cause of intentional design: humans. With a sample of one, you can freely construct a regression curve of any shape that floats your boat.

    Well actually, we might reasonably extend a capability of design to a range of species related to humans – primates, beavers, birds of paradise, bees, lichens. Though whether our cousins in the rest of nature are exercising intentional design is a good question.

  51. Axel posted this:

    By crystallising the animus against Philip of his ‘bottom-feeder’ critics, KF, you are inadvertently dignifying their inchoate howling, giving aid comfort to ‘our friends’ across the epistemological chasm – the enemies of reason – in however nugatory a measure and elliptical manner. Pardon my presumption, as a 22 carat ‘dogsbody’ nescientist, in bringing this to your notice.

    Pardon me, but what is a “nescientist”?

  52. @ Eric Anderson:

    In case Timothy A doesn’t find time to respond, Dr Liddle has posted an answer at TSZ

    Eric asks timothya:

    timothya:

    Two questions:

    1. Are you suggesting that we have to know the exact, precise, unequivocal probability of event X occurring by purely natural processes before we can draw an inference that event X did not occur by purely natural processes?

    No.

    2. On what basis do forensics experts and archaeologists draw an inference to design? Must they first lay out a precise formulation of all possible probabilities of the item in question having been produced by purely natural processes?

    No (assuming that by “natural” you mean “unintended”, or something similar).

    Look: Dembski proposed a formula – a metric – for inferring design, based on Fisherian hypothesis testing, that involves determining that the candidate pattern is in the rejection region of a probability distribution under the null of non-design. So, clearly, to, calculate that metric we need the probability distribution under the null. Dembski provides no way of calculating that distribution that does not involve first knowing what non-design processes can do. And if we knew that, he wouldn’t need his calculation. So his entire argument is circular.

    That doesn’t mean that inferring design from a pattern isn’t possible; what it does mean is that CSI, and its relatives, are useless for doing so.

    There are several other comments that might be of interest. Just to mention the “needle-in-a-haystack” analogy beloved by Kairosfocus. Unless you know there is only one needle (and all evidence points to the contrary) and you can work out the size of the haystack, the analogy is inapt.

  53. Axel quoting Joe

    ‘Specified information is just Shannon information with meaning or function. IOW it is information in the normal use of the word.

    I don’t understand your issue with it. You use it every day.’

    The point at issue is whether CSI is a measurable quantitiy. If it were, I would have thought someone could explain how to measure the CSI of something, anything. Of course, then, I would be inclined to ask, what can you then show from the result of such a calculation. But, first things first.

  54. Alan Fox:

    The point at issue is whether CSI is a measurable quantitiy.

    It is and we have told you how to measure it. OTOH you cannot provide any support for the claims of your position- not even any methodology.

  55. It is and we have told you how to measure it.

    Forgive me for being dubious, Joe, but, if this were the case, this would establish “Intelligent Design” as having a possible theory which would, I would have thought, been shouted from the rooftops. If someone can indeed calculate the CSI of something …anything… why don’t they want to demonstrate the procedure?

    If there is some calculation that I have overlooked, by all means draw it to my attention. “It’s been done” as a bald statement without reference to what, when and where something has been done is insufficient (to put it mildly).

  56. Alan Fox:

    Forgive me for being dubious, Joe, but, if this were the case, this would establish “Intelligent Design” as having a possible theory which would, I would have thought, been shouted from the rooftops.

    Seeing that your head is [snip, language], I doubt that you would hear it anyway.

    If someone can indeed calculate the CSI of something …anything… why don’t they want to demonstrate the procedure?

    We have. OTOH your position has yet to demonstrate anything beyond bald assertions.

    If there is some calculation that I have overlooked, by all means draw it to my attention.

    I have. Again your willful ignorance means nothing here.

    But anyway-

    When discussing information some people want to know how much information does something contain?

    If it is something straight-forward such as a definition, we can count the number of bits in that definition to find out how much information it contains.

    For example:

    aardvark: a large burrowing nocturnal mammal (Orycteropus afer) of sub-Saharan Africa that has a long snout, extensible tongue, powerful claws, large ears, and heavy tail and feeds especially on termites and ants

    A simple character count reveals 202 characters which translates into 1010 bits of information/ specified complexity.

    1010 bits > 500, therefor CSI is present.

    Now wrt biology each nucleotide has 2 bits.

    _______

    CALC: 7 bits per ASCII character (not 5 per Baudot character) * 202 characters = 1414 bits.

    Functionally specific, so S = 1.

    Chi_500 = 1414 * 1 – 500 = 914 bits beyond the solar system threshold.

    Designed.

    KF

  57. Longer version:

    The causal tie between an artifact and its intended character — or, strictly speaking, between an artifact and its author’s productive intention — is constituted by an author’s actions, that is, by his work on the object.- Artifact

    When discussing information some people want to know how much information does something contain?

    If it is something straight-forward such as a definition, we can count the number of bits in that definition to find out how much information it contains.

    For example:

    aardvark: a large burrowing nocturnal mammal (Orycteropus afer) of sub-Saharan Africa that has a long snout, extensible tongue, powerful claws, large ears, and heavy tail and feeds especially on termites and ants

    A simple character count reveals 202 characters which translates into 1010 bits of information/ specified complexity.

    Now what do we do when all we have is an object?

    One way of figuring out how much information it contains is to figure out how (the simplest way) to make it.

    Then you write down the procedure without wasting words/ characters and count those bits. The point is that you have to capture the actions required and translate that into bits. That is if you want to use CSI. However by doing all of that you have already determined the thing was designed Now you are just trying to determine how much work was involved.

    But anyway, that will give you an idea of the minimal information it contains- Data collection and compression (six sigma DMAIC- define, measure, analyze, improve, control).

    CSI is a threshold, meaning you don’t need an exact number. And it is a threshold that nature, operating freely has never been observed to come close to. Once CSI = yes you know it was designed.

    On Shannon Information and measuring biological information:

    The word information in this theory is used in a special mathematical sense that must not be confused with its ordinary usage. In particular, information must not be confused with meaning.- Warren Weaver, one of Shannon’s collaborators

    Is what Weaver said so difficult to understand?

    Kolmogorov complexity deals with, well, complexity. From wikipedia:

    Algorithmic information theory principally studies complexity measures on strings (or other data structures).

    Nothing about meaning, content, functionality, prescription. IOW nothing that Information Technology cares deeply about, namely functional, meaningful, and useful information. Not only Information Technology but the whole world depends on Information Technology type of information, ie the type of information Intelligent Design is concerned with.

    And both Creationists and IDists make it clear, painfully clear, that when we are discussing “information” we are discussing that type of information.

    And without even blinking an eye, the anti-IDists always, and without fail, bring up the meaningless when trying to refute the meaningful. “Look there is nature producing Shannon Information, you lose!”- ho-hum.

    Moving on-

    Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the same sense required by the complexity-specification criterion (see sections 1.3 and 2.5). The specification of organisms can be crashed out in any number of ways. Arno Wouters cashes it out globally in terms of the viability of whole organisms. Michael Behe cashes it out in terms of minimal function of biochemical systems.- Wm. Dembski page 148 of NFL

    In the preceding and proceeding paragraphs William Dembski makes it clear that biological specification is CSI- complex specified information.

    In the paper “The origin of biological information and the higher taxonomic categories”, Stephen C. Meyer wrote:

    Dembski (2002) has used the term “complex specified information” (CSI) as a synonym for “specified complexity” to help distinguish functional biological information from mere Shannon information–that is, specified complexity from mere complexity. This review will use this term as well.

    In order to be a candidate for natural selection a system must have minimal function: the ability to accomplish a task in physically realistic circumstances.- M. Behe page 45 of “Darwin’s Black Box”

    With that said, to measure biological information, ie biological specification, all you have to do is count the coding nucleotides of the genes involved for that functioning system, then multiply by 2 (four possible nucleotides = 2^2) and then factor in the variation tolerance:

    from Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling, Vol. 4:47 (2007):

    [N]either RSC [Random Sequence Complexity] nor OSC [Ordered Sequence Complexity], or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life. FSC [Functional Sequence Complexity] includes the dimension of functionality. Szostak argued that neither Shannon’s original measure of uncertainty nor the measure of algorithmic complexity are sufficient. Shannon’s classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that “different molecular structures may be functionally equivalent.” For this reason, Szostak suggested that a new measure of information—functional information—is required.

    Here is a formal way of measuring functional information:

    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak, “Functional information and the emergence of biocomplexity,” Proceedings of the National Academy of Sciences, USA, Vol. 104:8574–8581 (May 15, 2007).

    See also:

    Jack W. Szostak, “Molecular messages,” Nature, Vol. 423:689 (June 12, 2003).

    original posts can be found here, here and here

  58. Joe posted this:

    It is and we have told you how to measure it. OTOH you cannot provide any support for the claims of your position- not even any methodology.

    Joe is claiming that CSI is measurable. Could he please provide a published example of the CSI value of an actual object?

    Note: I am asking for a published example of the CSI of an actual object, not an explanation of how to do it.

    Just the facts, Ma’am.

  59. AF:

    You have been around UD for at least eight years.

    You full well know there are good and public, published answers to your pretended points of objection.

    It is public record that both Dembski and Durston et al have published metrics, the latter building on work by Szostak which in turn is in the context of Shannon’s H-metric of average info per symbol in a comms system. Abel has published a warrant for a set of plausibility bounds, from earth to solar system to observed cosmos, consistent with what has been in use for years. That is, 500 bits is a very good solar system threshold for what is well beyond the credible reach of blind chance and mechanical necessity.

    All this, if you really don’t know, it is because you have willfully shut your eyes to what you full well should have long since noted and acknowledged and instead insist on continued misrepresentation.

    And yes, at this stage I fully intend what that implies; this is now going to character, not merely an issue of disagreement as the facts are patent, easily seen and have been repeatedly presented to you, but willfully ignored the better to sustain a misrepresentation in hopes of that being perceived as truth.

    In any case, the actual simplified Dembski 2005 metric is easy to understand and see its warrant, save to those who refuse to do so, on the pretence that any objection they can repeat drumbeat style is fatal.

    The best answer to this is to ask of you, show us a case where on actual observation, something that Chi_500 = Ip*S – 500 passes as credibly designed, is known to be the product of blind chance and mechanical necessity.

    To this date, after years on this and other ways to measure much the same that come down to being equivalent in effect, all that comes up is a string of hopeful cases that on closer inspection support the point that FSCO/I is reliably observed to be the product of design.

    This is multiplied by literally billions of cases in point, growing with every post in this thread including yours, on how intelligence is the known source of such FSCO/I.

    In short the truth is that you are playing a game of pretending that a burden of warrant that has long since been met to any reasonable standard is not met. Obviously, because of the implications that are so patently unwelcome to you and ilk.

    Furthermore, what is increasingly evident — has been clear for months now — is that you are simply here to spout dismissive talking points and ignore evidence that does not suit your agendas, not to seriously or fairly engage matters on the merits.

    Duly noted, to your utter discredit.

    For shame!

    KF

    PS: Onlookers who may not know the actual facts, for just a start, cf. here on.

  60. A simple character count reveals 202 characters which translates into 1010 bits of information/ specified complexity.

    1010 bits > 500, therefor CSI is present.

    Let me see if I have this right. For your example of text, you work out the probability of a particular letter (1 in 26) and then multiply up for the number of letters in a piece of text. The result, if it exceeds a threshold of 500 bits, is “designed”. How does your calculation show the difference between meaningful text and jumbled letters? BTW the comment section in those blogposts of yours should be recommended to everyone here who’d like to get a better understanding of human communication. ;)

  61. You full well know there are good and public, published answers to your pretended points of objection.

    I know no such thing.

    If I am mistaken, then it should be no problem to direct me to the source of a genuine calculation of the CSI of something… anything. Or do you endorse Joe’s risible response?

  62. Alan Fox:

    The result, if it exceeds a threshold of 500 bits, is “designed”.

    Not quote. The if 500 bits is met then CSI is present.

    How does your calculation show the difference between meaningful text and jumbled letters?

    It doesn’t. It isn’t supposed to. Meaning/ function is an OBSERVATION.

    And yes the comment sections of my blog demonstrates the vacuuity of the evos’ position. Nice call Alan.

  63. AF:

    If I had thought you a naive newbie, I would be patient. But I know better.

    You full well know that the Chi_500 metric incorporates a parameter, S, that reflects the objective evaluation of functional specificity, which can be identified per the approach of Dembski in NFL, 141 – 8, namely a separate, independent specifying description that puts you in a zone T in W where T is such that on relevant accessible resources, blind chance and mechanical necessity are maximally unlikely to access T, for the reasons of the gold bead in the sack of beans or the needle in the haystack or the large number of monkeys typing at random.

    All of this, you know or should know.

    All of this you routinely use in a world of just such functionally specific digital information.

    KF

  64. ?= –log2[10120 · ?S(T)·P(T|H)]

    (Sorry, doesn’t display correctly)

    Or are you talking about Dembski’s formula that Dr Liddle eviscerates at TSZ?

  65. Alan Fox:

    Or are you talking about Dembski’s formula that Dr Liddle eviscerates at TSZ?

    LoL! Lizzie hasn’t “eviscerated” anything. Like you, she doesn’t even appear to understand science.

  66. Kairosfocus posted this:

    You full well know that the Chi_500 metric incorporates a parameter, S, that reflects the objective evaluation of functional specificity, which can be identified per the approach of Dembski in NFL, 141 – 8, namely a separate, independent specifying description that puts you in a zone T in W where T is such that on relevant accessible resources, blind chance and mechanical necessity are maximally unlikely to access T, for the reasons of the gold bead in the sack of beans or the needle in the haystack or the large number of monkeys typing at random.

    If S is a simple thing to understand, can you please write it down in simple declarative statements instead of endless subordinate clauses? It is very difficult to follow what you mean from this sentence.

  67. AF:

    All EL has done for years is to try to obscure the matter. Just as others before her. You are appealing to the presumed authority of objectors when the evidence is there in front of you to address. (And you are dodging he diverse approach of Durston et al, which gives much the same result, save that it uses the tricks and techniques of info theory.)

    The matter becomes instantly clear once you do the log reduction on Dembski’s result and then use a reasonable upper limit on search and observation resources, here the solar system’s 10^57 atoms and ~10^17 s.

    That boils down to saying every atom every 10^-14 s (the speed of ionic chem rxns) takes an observation of a possible state from the config space of 500 bits, which is far too generous already but nothing will satisfy the determined objector, that is what you and others are showing.

    After all that, for the lifespan of the solar system (and more actually) it is still so far short of the scope of the space that it is comparable to taking a one straw sized sample from a cubical haystack as thick as our galaxy. Superpose such a notional haystack on our galactic neighbourhood, and with all but certainty, such a sample will reliably come up straw and nothing else.

    That is a simple result of sampling theory for the same basic reason why a gold bead in a truck-load of beans will be all but impossible to find on taking a single at random handful.

    That is what you need to address.

    And then you need to show us a case within the resources of the solar system that shows us blind chance and mechanical necessity reliably producing FSCO/I without intelligent intervention.

    That is the inductive challenge.

    Which many tries have been made at, all fatally flawed as you doubtless saw, over the course of years.

    Stop the red herring and strawman games, and the improper appeals to imagined authority of objectors; who are playing much the same games.

    Address the matter on the merits, or else stand exposed as one playing at continued willful misrepresentation in the teeth of every opportunity to correct the distortion.

    KF

  68. So, just to be clear, Kairosfocus:

    Are you saying that for something …anything… if we can count the number of “whatevers” and establish that it passes some (as far as I can see – arbitrarily chosen) threshold related to all possible “whatevers” then it must be “designed”. Which seems to suggest everything above the complexity of a short text, whether of meaningful or jumbled letters, is, in fact, “designed”? And Dembski says this, too?

    Regarding “whatevers”, I am not sure what property is the thing that is counted with respect to something or anything. What phusical property of a subject of a CSI calculation is used as CSI?

  69. F/N: Let me pause to show the fatal flaw in the objection EL makes, in brief:

    EL: And there’s your belling problem, right there. Dembki’s entire solution to the problem of detecting design absolutely depends on the proper calculation of the distribution of probabilities under his null hypothesis.

    Which of course she pretends breaks the problem.

    1 –> First problem, there is no good reason to see that OOL, the origin of the cell based life, is amenable to Darwinian mechanisms. That is the problem is first to provide the encapsulated, gated metabolising molecular nanotech automaton with a built in code based self replication facility from blind physics and chemistry, not from some imagined power of differential reproductive success. Where also the imagined self replicator — never mind the usual stories put up — is just that, a materialist bed time fairy tale every inch as much as the one about belling cats.

    2 –> There is no good reason to believe that the imagined tree of life has good empirical, fossil life record warrant for its root, trunk and main branches, i.e there is no good reason to imagine that the world of life exists in a continent of closely connected incrementally improved functional states traversible in a tree pattern of descent.

    3 –> Nor has such been observed in the lab or the current world. For example, Axe’s results show that protein folds are isolated to like 1 in 10^64 or 10^77. That is isolated islands of function on steroids, from the molecules on up.

    4 –> The imagined observed power of Darwinian mechanisms collapses.

    5 –> Similarly the key to the claimed mechanisms is chance variation plus differential reproductive success leading to descent with (cumulative, unlimited) modification. Where the NS part is a SUBTRACTER of info, not an adder. It is chance variation that must be the source of info. Which runs headlong into the FSCO/I th5reshold and islands of function issues.

    6 –> Moreover, usually in physical modelling or analysis situations there is a long hard way and there is an easier rough and good enough one for practical purposes. This is one of them. Flailing away at the former does not answer to the latter, and ends up as a strawman fallacy.

    7 –> Namely, you can sit all day and object away at the problems of calculating probabilities of darwinian pathways (which is itself a damaging admission of what has not been done). But there is no way that you are going to be beyond the search resources of a solar system or the observed cosmos, and the difficulty of surmounting 500 – 1,00 bits, which for OOL is 1,000 times too small, and for OO body plans is 100,000 times too small. So, the FSCO/I threshold challenge holds.

    8 –> The only real sound answer would be to conclusively show in lab or field or fossil record that there is a continuous continent of viable configs that makes a smoothly incremental tree starting from the first warm little pond or the like, possible. That is not happening, has not happened, and is utterly unlikely to happen, for myriads of reasons some outlined in brief above.

    9 –> So the real case is that there is an arbitrary question begging imposition of a priori materialism under the misleading name of a mere methodological constraint, and there is an a priori framework that converts the slightest things convertible into just so stories into evidence alleged to make the whole molecule to Mozart just so story seem as certain as the falling of an apple or the orbit of the planets around the sun.

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

    If you put on rosy-tinted glasses, don’t be surprised to see that everything looks rosy.

    KF

    PS: In a world of bits, you pretend that bits are not reasonable elements? (Where BTW, there are two approaches, one on log a priori and a posteriori calcs, the other on directly observing contingent states and possibilities. A latching light switch such as in your room, stores 1 bit. a byte of info, 8. a USB stick has its capacity marked on it, and so forth.) Ludicrous. Go do your basic homework about IT literacy and then come back.

  70. kairosfocus,

    Alan Fox is just obtuse. Nothing anyone says will ever be good enough, which is strange given the fact that Alan’s position is totally untestable and useless.

    The point being is that Alan cannot provide anything tat even approaches CSI as a methodology for his position. His position doesn’t have any methodology beyond bald declarations.

  71. And if evidence turns up that primitive lifeforms – unrelated to anything on Earth – once existed on Mars. There would be another needle. You don’t know how many needles for OOL and you don’t know how many needles for protein function.

  72. Alan’s position is totally untestable and useless.

    Arguments from incredulity don’t advance the cause of other explanations. Explanations must stand on their own merits. “Design” arguments invariably go no further than “evolution could not have…”. Get your own hypothesis!

  73. Alan Fox:

    And if evidence turns up that primitive lifeforms – unrelated to anything on Earth – once existed on Mars.

    IF that happens your position will be unable to explain it also.

    You don’t know how many needles for OOL and you don’t know how many needles for protein function.

    YOU don’t know Alan and that is why your position is totally bogus.

  74. Alan Fox:

    Arguments from incredulity don’t advance the cause of other explanations.

    All you have are arguments from incredulity, Alan. You sure as hell don’t have any evidence.

    Explanations must stand on their own merits.

    ID does. Your position doesn’t.

    “Design” arguments invariably go no further than “evolution could not have…”.

    And that just further exposes your ignorance. Nice job.

    1- ID is NOT anti-evolution

    2- ALL design inferences MANDATE that necessity and chance be eliminated before reaching a design inference

    3- Unguided evolution can’t even muster a testable hypothesis

    You lose, again, as usual

  75. Joe: that is why I am outright calling his bluff. I suggest that he goes here and reads the draft backgrounder unit I just put together on basics of ICTs, so he can know what he is talking about. KF

  76. Joe asserts:

    ID is NOT anti-evolution

    Well, I agree of course! But what then is ID? It’s not science. doesn’t have any theories or hypotheses. Makes no testable predictions. The method of calculating “CSI” is a secret not to be divulged but only “it’s been done”. What is ID, other than theologically driven bad philosophy?

  77. And until Kairosfocus collected works receive some sort of endorsement from other known ID proponents, he should not expect people to take his personal inventions such as FSCO/I (or whatever) seriously. Anyone with an internet connection can start a blog, KF; there is no peer-review and no guarantee of quality.

  78. I think what Alan Fox et al have are arguments from infinite credulity; there is no sound reason (outside of ideology) to think that random & lawful interactions of matter, on their own and unguided by intelligence, can create significant amounts of FSCO/I.

    Back in Darwin’s day, they thought a cell was made of a very simple set of primordial substances. They thought that some innate, lawful quality of this “protoplasm”, when clumped together, would simply generate organic constructs on its own. They thought it was simpler and simpler all the way down.

    They had absolutely no expectation that there would be any kind of complex machinery inside the cell – certainly not the landscape of manufacturing and programming nano-technology we have found in astounding quantities every cell.

    Reasonable people immediately, intuitively recognize that there is no reasonable expectation that such things can be generated via chance & necessity. It is only the unreasonable madness of commitment to ideology that blinds these people to the blatantly obvious.

    You cannot point out the blatantly obvious to the willfully blind.

  79. AF said:

    And until Kairosfocus collected works receive some sort of endorsement from other known ID proponents, he should not expect people to take his personal inventions such as FSCO/I (or whatever) seriously. Anyone with an internet connection can start a blog, KF; there is no peer-review and no guarantee of quality.

    IOW, AF goes completely by “endorsements” and “authority”, and is incapable of understanding the arguments on his own and reaching his own conclusions. Instead of simply admitting that he doesn’t understand any of this and recuse himself from commenting on that which he cannot understand, his ideology commits him to cheerleading his “side” and rhetorically antagonizing those he disagrees with.

    If you don’t understand the arguments KF presents, AF, you should simply refrain from commenting about them. Otherwise, all you are is a barking dog, you comments bereft of all but rhetorical substance.

  80. It is only the unreasonable madness of commitment to ideology that blinds these people to the blatantly obvious.

    So blatantly obvious (what is, by the way,) that explanations such as how to calculate CSI can be dispensed with; ;)

  81. AF:

    Why do you repeat already answered canards as though they have not long since been answered? This is willfully continued untruthful misrepresentation by now.

    Your behaviour is now beyond excuse.

    As in for record again:

    a: in the literature, published several times, we see addressing of functional sequence complexity, by Abel, Trevors, Durston et al in a context involving Szostak et al. This is essentially the same point.

    b: As has been cited to you but ignored, both Meyer and Dembski make it plain that functionally specific complexity is a proper application of the CSI concept to the biological world, just read here on for clips.

    c: The log reduction and derivation of Chi_500 from the Dembski 2005 work is there for anyone with High School Algebra (assuming that still teaches people about general logarithms) to follow. And

    d: the numbers for solar system and cosmos used in thresholds have been discussed in the literature coming on four years ago now by Abel, cf here.

    In short, insistently repeated willful misrepresentation on your part.

    Pull up your socks.

    KF

  82. AF goes completely by “endorsements” and “authority”

    The only published papers claiming some property of things called “CSI” is William Dembski. Until KF publishes something, there is little point in expending energy. Does Dembski agree with KF about his FSCO/I? To date, there has been no comment.

  83. …both Meyer and Dembski make it plain that functionally specific complexity is a proper application of the CSI concept to the biological world…

    And do either of them perform a calculation to demonstrate how it is done? Is that an unreasonable request to ask where such a demonstration may be looked at?

  84. Alan Fox:

    But what then is ID? It’s not science.

    How would you know? You don’t know what it is and you don’t seem to understand science.

    ID is based on our knowledge of cause and effect relationships. It can be tested and falsified, just as with all design inferences.

    As I said, you don’t seem to understand much of anything.

    And for predictions, please tell us of the predictions that unguided evolution makes- what is a testable hypothesis wrt unguided evolution? Or just shut up because it will be obvious that you are just another belligerent mud-slinger.

    As for CSI, you use it every day. So again, what is your issue?

  85. Earth to Alan Fox-

    There aren’t any published papers wrt unguided evolution actually producing something. So why the double-standards?

    AGAIN, you use CSI every day. Communication would be impossible without it.

    All you are doing is proving that nothing will ever satisfy you.

  86. AF:

    In this very thread, you have seen a simple case of a calculation for FSCO/I, the relevant form of CSI, that shows how it is calculated, on ASCII and Baudot code premises.

    You have seen why the complexity threshold is set at 500 bits, and that has been explained on needles in haystacks, truckloads and sacks of beans with gold beads and an allusion to statistical thermodynamics. In the face of this, you try to deny what is there in front of your eyes because it is inconvenient.

    You even tried to deny the reality of bits.

    You refuse to look at basic applications of high school algebra but pretend to dismiss information theory results. You pretend — never mind how some of your ilk in trying to deride and dismiss inadvertently showed that I have exactly the relevant background to speak from knowledge — that I am any and anybody setting up a blog to spout off.

    If I am so ignorant as that, kindly pull your copy of Taub and Schilling and your copy of Connor show my citations on how we get to bits as an info metric false.

    You can go to my always linked summary note (based on a simplification of what I taught students), here on, and show that I don’t know what I am talking about in outlining info th basics. Try here on on the thermodynamics issues as well. (Onlookers, this note is linked from every comment I have ever made at UD.) Then come back and show that the work through from Dembsky 2005 already linked fails the test of High School Algebra, and that the related threshold, needle in haystack calcs make no sense. None of this you have done to date, yet you pretend to be in a position to debate the matters. I suggest that you go and do your basics before pretending to be able to do more than play at puerile rhetorical games.

    As in, you have patently flunked at pons asinorum but insist on continuing misrepresentations and blind appeals to modesty in the face of alleged authorities when facts and evidence were in play. That speaks, tellingly.

    KF

  87. And Alan, at least we have a methodology. And that is something you cannot say about your position.

    Ya see, if your position had any methodology at all you would present it and demonstrate how CSI (and its variants) just doesn’t measure up. But all we get from you and your ilk is that CSI (and its variants) are deficient and the reasoning is based on a caricature.

    So do you have anything beyond your whining about something that you use every day?

  88. F/N: Clipping Dembski and Meyer again to AF, severalth time in several days, counting clips by others. This shows the link between CSI, function in a generally biological context and FSCO/I. It will also show that AF is simply spouting talking points and not engaging substance, because he cannot or will not but insists on pushing “his” side:

    __________

    WmAD, NFL: >> p. 148: “The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology.

    I submit that what they have in mind is specified complexity [[cf. here below], or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . .

    Biological specification always refers to function . . . In virtue of their function [[a living organism's subsystems] embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways [[through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole] . . .”

    p. 144: [[Specified complexity can be defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ” >>

    SCM, reply to Falk: >> The central argument of my book is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). [--> notice how this is substantially equivalent to [digitally coded] functionally specific complex information] Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question . . . . In order to [[scientifically refute this inductive conclusion] Falk would need to show that some undirected material cause has [[empirically] demonstrated the power to produce functional biological information apart from the guidance or activity a designing mind. Neither Falk, nor anyone working in origin-of-life biology, has succeeded in doing this . . . . >>

    ___________

    In short, here we see the demand for endorsement being met. Of course we know the reply above, “that’s just Dembski.”

    That is the objection is selectively hyperskeptical and no amount of evidence will suffice, ever. The problem is not facts and reasoning but a willfully closed mind. One that is perfectly willing to respond on merits and endlessly recycle adequately answered objections. (Which was also a problem with EL.)

    KF

  89. But amidst all this sound and fury, there is a slight omission. How to calculate CSI. What metric do you choose as the raw data for the calculation?

    And if the methodology is just to compare the result against some arbitrarily chosen threshold, what on Earth can it do, other than sort all real things into two categories; above and below the threshold. So how does this give us any insight on any particular object, other than a “sciency” way of saying “sure looks designed to me!”

  90. What metric do you choose as the raw data for the calculation?

    You don’t use a metric. You use the nodes employed by the medium for the function in question. In text, that means letters. In proteins, that means ATGC binding sites required for the functionality of the protein. In chemistry, that means chemical bindings necessary for the construction of a von-neumann self-replicating machine. In structural engineering, it means shape (necessary geometric point configuration) x fit x number of objects in place for the function. Etc.

    And if the methodology is just to compare the result against some arbitrarily chosen threshold…

    The threshold isn’t arbitrary. It’s a comparison of the potential chance arrangements of the nodes in the media (the search space, or straw in the haystack) and the arrangements that have function (the needle) against the available computational resources (how much time & materials available for chance interactions to produce any of the functional constructs).

    But, all this has been explained to you countless times.

  91. wjm: and the arrangements that have function (the needle)

    how and when is the determination made for the number of sequences that have function?

    seems to me that unless you have a grasp of how many needles there actually are in the stack the you cannot make any meaningful calculation(s).

  92. Alan Fox:

    But amidst all this sound and fury, there is a slight omission. How to calculate CSI.

    We have told you how. So why the dishonesty?

    And Alan, at least we have a methodology. And that is something you cannot say about your position.

    Ya see, if your position had any methodology at all you would present it and demonstrate how CSI (and its variants) just doesn’t measure up. But all we get from you and your ilk is that CSI (and its variants) are deficient and the reasoning is based on a caricature.

    So do you have anything beyond your whining about something that you use every day?

  93. franklin:

    how and when is the determination made for the number of sequences that have function?

    Umm, your position needs to know that too. However you can’t tell us how and when your position makes any determination.

    Strange that doesn’t bother you.

  94. so, joe, has ID determined the number of sequences that have function (which appears to be a requirement for your calculations) or does it come up completely empty on this front?

  95. So franklin, has your position determined anything, anything at all, scientifically? If it has what has it determined and how?

  96. Folks: In the teeth of the actual worked out examples given and analysis as also linked we see further recirculation of silly objections. Either someone is not even reading before commenting, or else does not care about the truth or to actually do anything beyond recirculate objections. It seems at least one objector does not even understand what the basic unit of information is, the bit. The amount of info in an on/off switch or a coin that may be heads or tails up, i.e that for a two-state choice. That speaks volumes. On the subject of probability calculations, all we need is credible reason to know that functional configurations are rare in the space of all possibilities, which is a result of functional specificity and is backed up starting from rarity of fold domains in AA possibility space and going on up from there. Once that is so, as has been outlined and linked, sampling theory will show that a sample exhausting the atomic and temporal resources of the cosmos will be so far below the scope of possibilities for 500 bits (2^500 ~ 3.27 * 10^150) that we have only a reasonable expectation that we will pick up the overwhelming bulk, gibberish. The example of the comparison of pulling a one-straw sized sample from a cubical haystack as thick as our galaxy, shows why. There is no need to have any specific knowledge of the numbers of stars and planets etc, just that they are rare relative to the bulk. And with 1,000 bits — 100 times too small for OOL and 10,000 times too small for OO body plans — the atomic resources of the observed cosmos would be predictably fruitlessly exhausted by being able only to sample 1 in 10^150 of the possibilities. (Such BTW is very close to the rationale behind the second law of thermodynamics on statistical thermodynamics.) The thresholds chosen are not arbitrary — picked out of a hat, pulled out of the air, they are based on the number of chemical rxn states or the number of Planck time atomic states possible for our solar system or the observable cosmos [the objector has plainly not even read the discussion by Abel]. In short the objectors have not done their homework, on the charitable interpretation for the newbie, who should ask rather than assert. AF does not even have that much excuse. KF

  97. franklin,

    Not every triplet codes for an amino acid. And even a fully coded sequence may not ever fold into a functional protein. That has the been the issue for genetic engineering. Sure insulin did well but not many successes after that. Most transferred sequences refused to find a functional shape even though they were transcribed.

  98. how and when is the determination made for the number of sequences that have function?

    Scientifically. That’s work that Douglas Axe and others have done.

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: 2004
    Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, 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.ncbi.nlm.nih.gov/pubmed/15321723

  99. You see, Franklin and AF, this is not all that complicated. Each medium in question has arrangements of nodes that either produce a function, or they do not. The group of functional arrangements of nodes vs the group of non-functional arrangements of nodes (whatever particular nodes/material is in question) will probably always result in a vast amount of non-functional arrangements vs a tiny number of [functional] arrangements.

    Even with a node material specifically designed to produce complex, functional arrangements of nodes – language – the potential non-functional arrangements (straw) is exponentially larger than the relatively tiny space of functional arrangements (needle) shown via the infinite monkey theorem, and random rearrangements of the letters of language can only be statistically relied upon to produce meaningless sequences in long strings.

    They do not produce “Hamlet” or even a post of the length you’re reading here. Thus, reliably, only intelligence is known to produce functional CSI over 500 bits in node arrangements of any material.

    It’s only difficult to understand if you are protecting yourself from the implication – that intelligence is the only thing currently known to generate such functional, specified, complex node arrangements in any material.

  100. joe: So franklin, has your position determined anything, anything at all, scientifically? If it has what has it determined and how?

    I’ll take that as a resounding no from the ID camp!

  101. wjm: Scientifically. That’s work that Douglas Axe and others have done.

    I’m sure you noticed, william, that the paper you cite is quite a bit of theory/estimates but lacking much in the way of experimental confirmation (4 experiments according to the author) which makes it interesting but far from the definitive word on the world of proteins.

    but let’s use a real life example. How many functional sequences have the ID research camp determined can bind oxygen?

  102. Well, Timothya, it’s an arbitrarily-coined derivative of the noun, ‘nescience’, ‘absence of knowledge’, ‘ignorance’, in which, as regards science, I abound – like so many atheist scientists, except that they may be extremely erudite in their field or fields, yet lacking in the will to identify correct assumptions, hypotheses, etc., on which to base their perhaps otherwise flawless logic.

    As Keynes indicated of Hayek, in that case, however delicate, extensive and profound the filigree of such a person’s logical edifice, built on such erroneous foundations, it cannot but lead to anywhere but the mad-house.

    With the advent of the quantum paradigm, science has advanced by an all but infinite order of magnitude, because under the mechanistic paradigm, it was a deliberately, because necessarily, extremely pedantic, incremental process of building a picture of reality as perceived and empirically-tested, straining out all non-essential considerations, aspects, etc.

    True enough, the methodology remains, but theoretical physicists of merit, necessarily theists, will realise and acknowledge to themselves, that they are approaching the final bounds of potential physical discovery, at both extremes of the scale, since the paradoxes necessarily and manifestly proliferate at an ever greater rate. And crucially, paradoxes in most people’s lexicon are mysteries which, a priori, absolutely defy logic. So physics becomes increasingly the management of paradoxes – what Christians call, ‘mysteries’.

    The mutton-headed scientismificists, instead, remain confident of the value of their ‘promissory note’. ‘One day, my son,’ (with a broad sweep of the arm…) ‘understanding the least detail of this whole, vast universe will be gained by man, by you or your children, maybe.’

    Unfortunately, this requirement for a reductionist pedantry has led to a situation in which the partisans of scientism, are like the invisible ‘fifth gunner’ in, an erstwhile, gun crew of the Royal Artillery (Senior Regiment, Right of the Line).

    We had a wonderful character in the UK, called Sir John Harvey-Jones, who had been the CEO of ICI, and spent his latter years trouble-shooting SMEs for a television programme. (He was appalled by Thatcher’s decimation of manufacturing industry by the way).

    I can’t remember why he was studying a gun-crew in operation, but he noticed one man in the crew who never actually did anything. He asked why this was so, and eventually it was discovered that the fifth man who did nothing, used to hold the horse’s reins…!

    So, scientism’s finest cannot come to terms with the fact that at no time have they, or anyone else, ever understood the mystery of life, animal and vegetable – or indeed, as Planck observed, inorganic matter.

    They yearn for a non-existent past, a past in which Darwinism and the atheism it propped up were the unassailable, the ultimate biological, even cosmological paradigm. Except that they never had that horse in the past, whose imaginary reins they still insist on holding.

    Scientism, evolution, the multiverse, whatever crackpot dream they can conjure up, can never be anything but profoundly deceitful chimaeras. Not that evolution was ever even a plausible candidate for study via the scientific method – instead, surely, constituting the most farcically-favoured phenomenon in empirical science’s long history of regressive obstructionism by the ruling authorities in their various fields. But then when the multinationals pay the piper, Mammon rules with an iron fist.


  103. So franklin, has your position determined anything, anything at all, scientifically? If it has what has it determined and how?

    I’ll take that as a resounding no from the ID camp!

    No, franklin. I am looking for what you would accept before I bother with you.

    How many functional sequences have the ID research camp determined can bind oxygen?

    You cannot present any experimental confirmation that demonstrates blind and undirected chemical processes can produce any sequence capable of binding oxygen. :razz:

    Heck can your position even account for oxygen? Nope.

    I’m sure you noticed, franklin, that all “evolutionary” papers are quite a bit of theory/estimates but lacking much in the way of experimental confirmation, which makes it interesting but far from the definitive word on the world of biology.

  104. joe: No, franklin. I am looking for what you would accept before I bother with you.

    I thought I was quite clear in what I was asking. As you and wjm indicate the IDist (or anyone attempting their calculation) needs to know how many needles are in the haystack. If you don’t have this information then you obviously (by your and wjm’s knowledgement) cannot make the calculation that you claim to be able to make.

    So, joe, if the specified function is oxygen binding how many sequences are there that can meet this specification?

  105. I thought I have been quite clear. It doesn’t matter how many needles are in the haystack as blind and undirected processes cannot produce any of them.

    For once I would say the evolutionists are correct. Evolutionism does not posit a blind search. It isn’t a search at all. Stuff happens and what works (at the time and place) gets kept. Anything found is pure happenstance.

    The point being is even if there was a haystack full of needles, blind and undirected processes may never even stumble upon it nor know what it was or what to do when that happened.

  106. joe:It doesn’t matter how many needles are in the haystack as blind and undirected processes cannot produce any of them.

    if you haven’t examined and applied the ID explanatory filter to each and every individual sequence that fits the criteria, e.g., ability to bind oxygen, on what foundation are you making your assertion? You’ve made it clear that you aren’t making the determination based on any evidence since you rule out sequences before you even know what they are.

  107. franklin:

    if you haven’t examined and applied the ID explanatory filter to each and every individual sequence that fits the criteria, e.g., ability to bind oxygen, on what foundation are you making your assertion?

    On the grounds that neither you nor anyone else has ever demonstrated blind and undirected chemical processes producing such a thing- including oxygen. IOW there isn’t any evidence, that is the whole point.

  108. franklin @91:

    . . . seems to me that unless you have a grasp of how many needles there actually are in the stack the you cannot make any meaningful calculation(s).

    This is a rational question, but at the end of the day it is not a reasonable refutation of the design inference, nor does it allow us to hand wave away the design inference.

    First of all, we cannot, without omniscience, know the exact number of functional states. So a demand for knowledge of all states would in effect be a demand for omniscience (in effect saying we cannot know if something was designed unless we know everything). However, that is not how science works. We can and do draw reasonable inferences all the time in all areas of science. We can draw reasonable conclusions based on what we do know.

    In addition, there are people who have looked into this, and the number of functional proteins is realistically estimated to be indeed very small compared with all possible amino acid configurations.

    Further, once you have one portion of, say, a protein complex that requires a specific complementary protein, the number of needles available to fill that role draws close to one. This situation is not an isolated incident; it is rampant in biology.

    In addition, it is not adequate to take the facile approach that some do of saying that locating any old function will do. Life is here. We are trying to explain how it got here. We are trying to explain how the specific systems we see arose. So we are dealing with specificity at each level.

    Finally, just based on common-sense everyday experience, a moment’s reflection is sufficient to remind us that the number of functional configurations of matter is a tiny droplet in the vast sea of non-functional configurations. Indeed, the number of non-functional states approaches, what for practical purposes, is nearly infinite. This is true not only at the microscopic level, but at the macroscopic level as well.

  109. You know what? I get the objections to how CSI is calculated. At least to a certain extent. The role of “specification” in the formula seems critical to the outcome, but how do you measure it? It seems like it would almost have to be a binary thing (either it is a recognized specification or not), and its determination will be based purely on the recognition of the observer. I think this is where its detractors get their, “well it looks designed” characterization. Recognizing a specification could be confused with recognizing design, particularly if one wanted to be confused, and perhaps even if they did not.

    But there seems no shortage of folks who really want to be confused. Yet I suspect that if I were to sit down with these same CSI detractors for a few hands of poker, and if I happened to keep ending up with Royal Flushes each hand, all of the confusion would fade away, and in a burst of clarity, these same folks would make a design inference. They would accuse me of cheating (though they might not know how) and of cheating quite badly that I would be so obvious about it. Any clear-thinking, unbiased observer KNOWS there is something to the ability to infer design, and when I see someone nitpicking the current formulation while not offering up solutions, I start to suspect that that person might not actually WANT answers to be found, which, whatever else it might say about them, would seem to disqualify them as any sort of real scientist.

    Honestly, I also get the objection about not knowing (even approximately) how many needles (variations that are functional) are in the haystack affecting the odds of one being in a random sampling. But why don’t we know this? Why have Darwinists been content to merely assume there are needles everywhere? Where are the rigorous studies that demonstrate this is true? Don’t evolutionary biologists WANT to know whether there are islands of functionality, how much distance is between them, and how much this scales with complexity? Why is it only ID scientists who must look for these kinds of answers?

    I just see lots of accusations of ignorance directed toward ID when the ones pointing fingers are at least as much in the dark and quite evidently satisfied to remain there.

  110. eric: This is a rational question, but at the end of the day it is not a reasonable refutation of the design inference, nor does it allow us to hand wave away the design inference

    It does allow us to handwave away any calculations that require that information for the determination as per wjm’s assertions.

    ,

    However, that is not how science works. We can and do draw reasonable inferences all the time in all areas of science. We can draw reasonable conclusions based on what we do know.

    when doing any analysis within a science framework it is always essential to recognize where the specific calibration/calibrators reside. Extrapolating outside the range of a standard curve of any type is not accepted nor should it be. With the design inference (basically a guess) the highest level calibrator ‘you’ have are human designers who’s technology is far below most of chemistry let alone biochemistry. When you posit a designer for life and/or the universe you are far afield of of your standard curve in the realm where the error bars are exceedingly high.. Most scientist recognize this yet here it seems to be an accepted methodology.

    eric: In addition, there are people who have looked into this, and the number of functional proteins is realistically estimated to be indeed very small compared with all possible amino acid configurations.

    I think the data refutes your assertion here.

    eric: Further, once you have one portion of, say, a protein complex that requires a specific complementary protein, the number of needles available to fill that role draws close to one. This situation is not an isolated incident; it is rampant in biology.

    here it seems you are either ignoring the history of the organism/system or just assuming it ‘poofed’ into existence intact with no intermediates.

    Locating and identifying ‘any old function’ is certainly prudent when addressing assertions that protein function is rare. That biochemistry on Earth does not use all possible functional sequences makes no difference especially since no one claims that it (life) does.

  111. 111

    WJM’s comment at #98 is apropos. Even if we were to grant that any properly folded protein constituted a relevant functional selection, we would only have at most 1 in 10^64 such proteins by Axe’s estimate. This is extremely generous yet it demonstrates the problem of functional isolation. Before a protein can even be considered for function in a given context, it must fold. There are an extremely small number of sequences that will render a stable fold (10^-64). For a 150 residue sequence, there are 20^150 possible sequences, or around 10^195. Considering those ratios we can estimate 10^131 stable folding configurations for a 150 amino sequence. But how many of those proteins can provide a specific required function (such as DNA polymerization)? There’s no way to tell for sure, but even if a generous number is supposed, like one-trillion-trillion trillion, the search is still prohibitive.

    An illustration might be of some help. For a gray scale image of 1024 pixels squared, there’s a search space of 2^28 possible configurations. This number is diminutive next to the above number of 10^195, yet still provides a vast landscape of images over which it is possible to traverse. For example, there are a nearly inestimable amount of configurations that could yield a recognizable rendering of Albert Einstein’s face. Yet it follows that this can only be a tiny proportion of all possible configurations, because where there may be a million ways to render Einstein’s face in a recognizable way, there must also be numerous ways to render any one of billions of other faces. And then we must also be able to render objects which are not faces at all, but any one of numerous other abstract or specific representations — cars, planes, trains, bicycles, motorcycles, cows, horses, donkeys, cats, dogs, planets, galaxies, chairs, tables, houses, skyscrapers, grass, trees, grapes, etc. — each in their personal identities (Saturn or Jupiter, Nero or Spot, Triumph or Harley, Ford Model T or Maserati MC12, etc). The images of all imaginable objects must be able to occupy the same configuration space of 1024×1024 pixels and 256 shades of gray in different configurations which must each differ substantially from Einstein.

    Such is likely the case with proteins. After considering the noisy, non-folding sequences, specific biological functions must narrowly exist in the overall search space, because the space must also account for every type of possible function. I don’t think it’s reasonable to presume that ubiquitous functions such as ATP synthase, the ribosome, and the various polymerases are not required for “other” types of life. We don’t know such organisms can exist. It seems likely that, as with images of Einstein that are specific to a singular man, these biological subsystems are specific to a singular phenomenon in the known universe.

    Even so, objections to specific functional necessities notwithstanding, traversing the noise is practically prohibitive. Just as generating random permutations in a 1024^2 gray scale image shouldn’t practically be expected to produce a recognizable image of Einstein, neither should random mutations effectively stumble on a functional sequence of amino acids, regardless of whether such a sequence could contribute to function in a constrained and complex operational system.

  112. Franklin #91

    “However many ways there may be of being alive, it is certain that there are vastly more ways of being dead”
    Richard Dawkins

  113. 113

    Correction to #111.

    “there’s a search space of 2^28 possible configurations.”

    I believe this should be

    “there’s a search space of around 2^8*10^6 possible configurations.”

    :oops:

  114. 114

    I could have used a much smaller sample space, such as 16 shades of grey on a 256^2 image. :)

  115. chance: WJM’s comment at #98 is apropos. Even if we were to grant that any properly folded protein constituted a relevant functional selection, we would only have at most 1 in 10^64 such proteins by Axe’s estimate

    Axe conducted 4 experiments with a single protein. It is quite the leap to generalize that these limited data are representative and apply to all protein sequences.

    given the number of possible sequences how would a designer go about picking which one to use? In our ‘intelligent agent’ experience the only way is trial and error. We (as intelligent agents) cannot predict function from sequence alone. Are there any ID inferences on how this is accomplished?

    Another question I have seen that I think is very interesting is how would a disembodied entity interact with atoms and molecules and cause changes. In our ‘intelligent agent’ experience this is quite impossible unless of course you believe the likes of Uri Geller.

  116. Eric Anderson said:

    In addition, there are people who have looked into this, and the number of functional proteins is realistically estimated to be indeed very small compared with all possible amino acid configurations.

    franklin said:

    I think the data refutes your assertion here.

    What data?

    The only research into this area that I’m aware of was conducted by Robert Sauer in the late 1980′s and by Douglas Axe more recently – in fact, Axe built upon Sauer’s work.

    Sauer concluded that there was at best 1 chance in 10^63 of getting a functional protein. He showed that proteins are highly specified, meaning that there could be very little variance in the amino acid sequence before there was a loss of function.

    Axe followed up on Sauer’s work, and his findings were published in the most prestigious journals in his field. His research showed that in the case of a single 150-sequence protein, of all 150-sequence proteins, only 1 in 10^77 could do the job. He estimated the likelihood of finding any functional protein with a sequence of 150 amino acids at 1 in 10^74.

    These are peer-reviewed conclusions published in the most prestigious science journals.

    Since these kinds of proteins are necessary for life itself – the simplest cell, requiring maybe 250 different proteins with an average of 150 sequences – one wonders about the odds of such functional proteins being generated by chance not from Darwinian error mechanisms, which already have proteins in place to play around with, by simply by amino acids bumping around happenstance in a pool of chemicals.

    Meyer places the odds of a functional 150-sequence protein coming into existence by chance in a pool of amino acids (using only peptide bonds and left-handed acids) at 1 in 10^164.

    There is no competing data, that I’m aware of. There is no data that indicates otherwise. If there is, please refer to it. Otherwise, you are just barking in service of your ideology.

  117. 117

    Franklin, if you have a better estimate than Axe’s, by all means go with it. Who’s doing such research anyway? Regarding disembodied intelligence, it’s not germane. ID is about design detection.

    As to how designers design, we may indeed use trial and error, but we don’t produce designs this way. We improve them this way. These two processes are complementary, but not comparable. How intelligence is able to abstractly model functional configurations of matter or abstract mathematical ideas has nothing to do with trial and error.

    Regarding predicting function based on sequence, we also can’t reasonably predict how a complex program will behave based on the sequence of instructions, but that doesn’t prohibit us from writing working code. We invent processes which help us manage and provide abstractions for such complexity. Surely you’re not suggesting that in principle it is impossible to predict any function from any sequence, but more likely you are appealing to our current level of ignorance about the complexities of the 3D spatial relationships involved in protein folding. However even this problem appears more amenable to intelligence than raw computation; see Foldit.

    Online Gamers Achieve First Crowd-Sourced Redesign of Protein

    How random mutations can achieve such feats remains to be seen. It doesn’t even appear remotely plausible.

  118. Axe conducted 4 experiments with a single protein. It is quite the leap to generalize that these limited data are representative and apply to all protein sequences.

    And yet, it is the only data available – along with Sauer’s work, that showed the same thing. Here’s the problem – the only research data available indicates that chance is not a plausible explanation for the generation of functional proteins, and is certainly not a plausible explanation for the generation of the 250 proteins necessary for rudimentary life to begin, when those complex, integrated, functional proteins had to clump together by chance from a pool of chemicals, and all present at the same time in the proper configuration for a self-replicating machine to “manifest”.

    That’s 250 different functional proteins, on average 150 sequences long, and on average each having to be formed from chemical scratch where any introduction of a right-handed amino acid or a non-peptide bond ruins the mix, and each one having an estimated functional variance of 1 in 10^77.

    What the current data supports, whether one quibbles with whether or not it is “definitive”, is that the idea that protein functionality can be accomplished “by chance” is a materialist fairy tale.

    Perhaps when you have data to the contrary, you can offer something other than ideological obstinance.

  119. Here’s a question for you, franklin:

    Do you really think it is reasonable that in a pool of chemicals, ONLY left-handed amino acids happen to clump together form a folded tool that HAPPENS to fit perfectly with 249 other similarly happenstance folded tools that HAPPEN to only use peptide bonds that all happen to coincidentally exist and resist easy degradation in the same time frame to put together a self-replicating machine?

    Is your credulity infinite in service of your ideology? Will you draw the line anywhere and demand evidence before you continue believing? Do you really think it plausible without any supporting evidence that a pool of chemicals happened to produce a finely-tuned, 250-piece self-replicating machine?

    What you believe here, without evidence, is nothing short of a materialist miracle. Surely you realize this? Are you that devoted to your ideology?

  120. franklin:

    With the design inference (basically a guess) the highest level calibrator ‘you’ have are human designers who’s technology is far below most of chemistry let alone biochemistry. When you posit a designer for life and/or the universe you are far afield of of your standard curve in the realm where the error bars are exceedingly high.

    And with human design, including biochemical work and nanotechnology work, we know for a fact that the number of non-functional states vastly outnumbers the number of functional states. It is a simple fact of matter, and has nothing to do with whether the function came about due to design or pure chance — that is a separate question.

    There may be some error bars, but reasonable estimates have been made — in contrast to what essentially amounts to a bald, unsupported assertion on your part that there are lots of functional states. Unless you’re not saying that, in which case, what is your point?

    Furthermore, when estimating the probabilities of things like OOL, design proponents have bent over backwards to give chance every possible advantage in the calculations. We are not dealing with a situation in which design proponents make very aggressive assumptions and the answer could go either way with just a 5-10% difference in the assumptions used. Design proponents are extending every opportunity for chance to do its work (assuming all particles in the entire solar system or even the known universe, for example, as a resource to chance), and the calculations demonstrate that chance doesn’t have a chance. The clear answer is not a close call that will be affected by just a slight tweak of the numbers here or slight adjustment of a percentage there. We’re talking many, many orders of magnitude.

    The idea that functionally integrated living systems can come about as a result of particles randomly bumping into each other has to rank as perhaps the most preposterous idea ever proposed — certainly in recent memory.

  121. Franklin is hitting on a point that has already been covered- if any ole sequence will do then it ain’t so darn specified. We agree, Franklin.

    Anything else?

  122. It bears repeating that Axe et al. (that would be the rest of the ID vanguard) do not properly represent the matter of the fraction of protein sequence space that is functional. As I explain here, Axe’s experiments fail utterly to accurately assess the situation, and his one belated response to my essay avoided (ducked) the major criticism of his work entirely.

    Anyone who relies on Axe to argue in favor of CSI and ID has already lost the argument, I am afraid.

  123. 1 in 10^12 is the low end estimate for finding a functional protein from evolutionists. But would 1 in a trillion be helpful?

    How Proteins Evolved – Cornelius Hunter – December 2010
    Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
    http://darwins-god.blogspot.co.....olved.html

    Moreover, the 1 in 10^12 estimate for functional proteins was arrived at by ignoring some fairly glaring problems (as is usual for Darwinists:

    A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells – 2009
    Excerpt: “Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division.”
    http://www.plosone.org/article.....ne.0007385

    Thus the supposed 1 in 10^12 functional proteins of Darwinists are actually found to be useless for life.

    Here are some more estimates which are in the same ballpark as Axe’s figure:

    Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein – Cornelius Hunter – Dec. 1, 2012
    Excerpt: In one study evolutionists estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit was 10^43. The lower limit was 10^21.
    http://rsif.royalsocietypublis.....5/953.long
    These estimates are optimistic for several reasons, but in any case they fall short of the various estimates of how many attempts would be required to find a small protein. One study concluded that 10^63 attempts would be required for a relatively short protein.
    http://www.ncbi.nlm.nih.gov/pubmed/2199970
    And a similar result (10^65 attempts required) was obtained by comparing protein sequences.
    http://www.sciencedirect.com/s.....9377900443
    Another study found that 10^64 to 10^77 attempts are required.
    http://www.ncbi.nlm.nih.gov/pubmed/15321723
    And another study concluded that 10^70 attempts would be required. In that case the protein was only a part of a larger protein which otherwise was intact, thus making the search easier.
    http://www.plosone.org/article.....ne.0000096
    These estimates are roughly in the same ballpark, and compared to the first study giving the number of attempts possible, you have a deficit ranging from 20 to 56 orders of magnitude. Of course it gets much worse for longer proteins.
    http://darwins-god.blogspot.co.....1503051454

    Thus no matter how you slice it, even using the most optimistic figure from Darwinists, the numbers simply do not crunch!

  124. 124

    BA77 @122, great info, thanks! :D

  125. given the number of possible sequences how would a designer go about picking which one to use?

    Given the number of possible sequences available from a 26 letter + punctuation alphabet, and given that the vast majority of such combinations are gibberish, how is your average person able to put together long strings of coherent, functional, meaningful prose?

    Given the number of possible shapes and arrangements of matter, the vast majority of which produce nothing of functional consequence, how can engineers build a fullly functioning battleship?

    Isn’t a battleship, compared to the possible chance arrangements of the matter comprising the battleship, just as much needle in the haystack as a function protein?

    Can chance & necessity build a battleship, franklin? or write War & Peace?

  126. wjm: What data?

    The only research into this area that I’m aware of was conducted by Robert Sauer in the late 1980?s and by Douglas Axe more recently – in fact, Axe built upon Sauer’s work.

    Well then you aren’t very aware of much of the pertinent literature available on this subject.

    for example among the many publications on this topic is this:
    Searching sequence space for protein catalysts
    Sean V. Taylor*, Kai U. Walter*, Peter Kast, and Donald Hilvert†
    PNASv vol. 98 no. 19: 10596–10601

    more importantly is that Axes work falls within the values generated by other researchers….10^10-10^63

    I’m sure you are also aware that Axe used a mutated version of the native protein. As I’m sure you are also well aware the protein he used is renowned for its multi-functionality. However, for whatever reason Axe only looked at a single function of this enzyme and ignored screening for the other known functions of this enzyme. How does he know that function was not enhanced for these other activities? He also did not screen for any new, novel function. You cannot make the extreme extrapolations from this very limited data set to protein domains in general….unless of course you choose to remain ignorant others work in this field.

    wjm: And yet, it is the only data available

    Hardly. Are you using your ignorance of available research as a barking point to service to your ideology?

  127. eric: The idea that functionally integrated living systems can come about as a result of particles randomly bumping into each other has to rank as perhaps the most preposterous idea ever proposed — certainly in recent memory.

    it sure is a good thing that no one actually posits your strawman construct!

    eric:There may be some error bars, but reasonable estimates have been made

    May be? surely you jest! How can any reasonable estimate be made for a process with which you have no idea not only if but how it could possibly be implemented. As I stated before you are very far afield of any calibrator you can lay your hands on.

    As for functional sequences and rarity…literature values indicate the higher range for functional sequences at 10^10. Given about 250 gallons of pond water typically containing 10^12 bacteria the probability of a functional sequence arising approaches_______________. You can fill in the blank.

  128. wjm: Can chance & necessity build a battleship, franklin?

    to make your tortured analogy fit the biological/biochemistry realm what would be the mass to charge ratios of the various components of the battleship?

  129. I wasn’t employing an analogy, franklin. I asked a straightforward question. Can chance and necessity build a battleship?

    Yes or no.

  130. wjm: The only research into this area that I’m aware of was conducted by Robert Sauer in the late 1980?s and by Douglas Axe more recently – in fact, Axe built upon Sauer’s work.

    Do you think Sauer and Axe were operating in a vacuum? That they cited no related literature to support their methods and results let alone put those results in perspective? Have you even perused the references cited in Axe’s paper (they are usually found at the end of the published article especially ones published in such a prestigious journal)?

  131. Well I’m sure glad you aren’t trying to compare biochemical processes where mass and charge are critical with human building activities…so no, wjm, for all we know people build battleships.

    here is a straight forward question for you: How does a disembodied entity interact with atoms and molecules to push them together and cause a desired outcome?

  132. franklin:

    My construct is indeed the foundational “explanation” of materialism. Stuff bumps into other stuff, some of the stuff sticks together, add time, and viola, life. It doesn’t sound too believable when we strip away all the fancy language, does it? But that is very much in essence what is being proposed.

    Why do you think mass and charge have anything to do with it? Are you suggesting that the particles come together by necessity to form life? Other particles besides those in biochemistry also have mass and charge. Yet we never, ever, see complex functional systems coming together through purely natural processes. Referring to mass and charge as though it somehow helps explain how particles could come together in functional groups is irrational and/or a bluff.

    And what is this disembodied question you keep bringing up? What does that have to do with the design inference we are discussing? Talk about strawmen . . .

  133. eric: and what is this disembodied question you keep bringing up? What does that have to do with the design inference we are discussing? Talk about strawmen . . .

    a bit of a thought experiment on one possible Designer category and feasability of concept.

    eric: My construct is indeed the foundational “explanation” of materialism. Stuff bumps into other stuff, some of the stuff sticks together, add time, and viola, life. It doesn’t sound too believable when we strip away all the fancy language, does it?

    If that is your understanding of chemistry, physics, biochemistry, ect. that explains a lot.

    Eric, describe for me, if you could, with some detail preferably, any biochemical/chemical process that does not involve particles with mass and charge.

  134. franklin:

    Eric, describe for me, if you could, with some detail preferably, any biochemical/chemical process that does not involve particles with mass and charge.

    What does that have to do with anything? We are talking about the odds of a functional protein arising through purely natural processes. Then you start talking about mass and charge. Is it an attempt to derail the discussion, or is there a point to bringing up mass and charge?

    As for functional sequences and rarity…literature values indicate the higher range for functional sequences at 10^10. Given about 250 gallons of pond water typically containing 10^12 bacteria the probability of a functional sequence arising approaches_______________. You can fill in the blank.

    What is your reference for 10^10? And what is the basis of the calculations? For what length of amino acid chain?

    Also, what do bacteria have to do with the calculation? Meyer is talking about functional proteins forming from amino acids on prebiotic Earth.

  135. eric: What does that have to do with anything?

    I asked because I was curious if you could actually make your charicature work in describing chemical/biochemical processes.

    eric: Then you start talking about mass and charge. Is it an attempt to derail the discussion, or is there a point to bringing up mass and charge?

    well if I recall it went something along the lines of battleships and war and peace and chance and necessity. I, at first, thought wjm was trying to make an analogy between human shipbuilding activities and chemical/biochemical processes.

  136. Phinehas:

    Why have Darwinists been content to merely assume there are needles everywhere?

    Keeping the focus on proteins, as some ID proponents appear to think that something can be ascertained about a particular protein from the number of residues. There is even the explicit assertion that any protein sequence above a certain number of residues cannot have come about by evolutionary processes. The argument relies on the idea that evolutionary processes must perform an exhaustive search and that functionality is rare and isolated in the set of all theoretically possible protein sequences.

    Now scientists have not been content to make such assumptions. Here is a paper giving some idea of the problems. Keefe & Szostak have done some interesting work by looking at one function (ATP binding) and the work continues. But currently there is no reliable method of ascertaining the possible function a novel protein might have, other than synthesizing it and experimenting with it in as many situations as can be contrived, a process of trial-and-error that can be carried out by flasks of bacterial broth and natural selection much more effectively, as Richard Lenski has demonstrated. And the process that occurs in Lenski’s flasks is not blind or exhaustive search. It is stumbling upon functional sequences that are related to existing sequences, as is postulated to happen with evolutionary sequences in vivo.

    Performing arithmetical calculations simply on the number of residues tells us nothing about how that protein will fold and what enzymatic or other activity it might have in any particular cellular setting. ID proponents will have to do better than “it sure looks designed to me”.

  137. Another paper discussing protein function and sequence space. Douglas Axe gets a mention, as does Shannon entropy.

  138. Franklin #126: As for functional sequences and rarity…literature values indicate the higher range for functional sequences at 10^10.

    First, what is your reference for 10^10?
    Secondly, what does functional mean? Are we searching for a protein with a specific function A – or will any function do? Function surely cannot be viewed upon without context. If for instance a ‘primitive’ cell is in need for a protein with a specific function A it has no use for an array of proteins with other functions in other contexts – e.g. proteins with functionality in higher organisms.

  139. Mr. Fox, if you haven’t noticed, Szostak’s 1 in 10^12 estimate for functional protein sequences was refuted here:

    A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells – 2009
    Excerpt: “Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division.”
    http://www.plosone.org/article.....ne.0007385

    i.e., the supposed 1 in 10^12 functional proteins of Darwinists are actually found to be useless for life.

    Moreover even if it were true it would be no hope for your preferred atheistic worldview,,,

    How Proteins Evolved – Cornelius Hunter – December 2010
    Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
    http://darwins-god.blogspot.co.....olved.html

    Szostak, a Darwinist as far as I know, did make an interesting comment here:

    The Origin of Life on Earth
    Excerpt: Every living cell, even the simplest bacterium, teems with molecular contraptions that would be the envy of any nanotechnologist. As they incessantly shake or spin or crawl around the cell, these machines cut, paste and copy genetic molecules, shuttle nutrients around or turn them into energy, build and repair cellular membranes, relay mechanical, chemical or electrical messages—the list goes on and on, and new discoveries add to it all the time.
    It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from nonliving matter around 3.7 billion years ago.
    Dr. Jack Szostak – Nobel Laureate
    http://www.scientificamerican......e-on-earth

  140. But hey Mr. Fox, does it not strike you as extremely strange that we are talking about evolution ‘hypothetically’ producing a functional protein, instead of examining any actual proteins? Why don’t you, as a Darwinist, have any actual examples of neo-Darwinism producing proteins Mr. Fox?

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations which is approx. equivalent to 1 million years of supposed human evolution)
    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

    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

  141. CR: Your image space point is excellent. KF

  142. Alan Fox:

    ID proponents will have to do better than “it sure looks designed to me”.

    IF that were true it would still be more than your position has, Alan. :razz:

  143. Earth to franklin-

    Do YOU have any evidence that blind and undirected chemical processes can produce a functional protein?

    If not then please stuff it already…

  144. Bornagain77 #139: (..) does it not strike you as extremely strange that we are talking about evolution ‘hypothetically’ producing a functional protein, instead of examining any actual proteins?
    I couldn’t agree more Bornagain77. That’s what I’m talking about in #137: where is the context? And without context what does functional mean? Are we searching for proteins which theoretically can have a function – any function? Surely a functional protein in context A is not functional – or even detrimental – in another context.

  145. Surely a functional protein in context A is not functional – or even detrimental – in another context.

    Well, one could assume that. However the only way currently available to researchers of discovering what proteins do is to observe the functions of those proteins that exist in vivo and in vitro. There is as yet no way to predict what function a novel protein might possess in a particular context without synthesizing it and trying it (as happens in RM + NS). Some kind of predicting tool or program would be immensely useful in medicine in developing new antibiotics, for example.

  146. Alan Fox:

    There is as yet no way to predict what function a novel protein might possess in a particular context without synthesizing it and trying it (as happens in RM + NS).

    Please present the evidence that demonstrates that is what RM + NS actually does this. Just saying it doesn’t make it so. First tell us how it was determined the mutations were random/ chamce events.

    Good luck with that…

  147. Please present the evidence that demonstrates that is what RM + NS actually does this.

    Lenski!

  148. First tell us how it was determined the mutations were random/ chamce events.

    This is why theists can be comfortable with evolution. There is the irrefutable possibility that God could be directing evolution by loading the dice in some immeasurable way. Non-theist sees random mutation. Theist sees hand of God. Same evidence. It’s only fundamentalists who want to indulge in virtuoso believing such as a 6,000 year old Earth , a literal flood and so on that seem not to see things for what they are rather than how they wish them to be.


  149. Please present the evidence that demonstrates that is what RM + NS actually does this.

    Lenski!

    Please reference the paper that demonstrates RM + NS were responsble.


  150. First tell us how it was determined the mutations were random/ chamce events.

    This is why theists can be comfortable with evolution. There is the irrefutable possibility that God could be directing evolution by loading the dice in some immeasurable way. Non-theist sees random mutation. Theist sees hand of God. Same evidence. It’s only fundamentalists who want to indulge in virtuoso believing such as a 6,000 year old Earth , a literal flood and so on that seem not to see things for what they are rather than how they wish them to be.

    OK so you have no idea how it was determined. Do you really think that your bloviation means something?

  151. Box #143: Surely a functional protein in context A is not functional – or even detrimental – in another context.

    Alan Fox #144: Well, one could assume that.

    The point being that context extenuates the domain of so called functional proteins. It’s the context – the whole organism – that decides what is functional. To speak of ‘functionality’ without reference to the actual organism as a whole is nonsensical. Functionality – of proteins and other parts – means being subordinate to the whole.

  152. E. coli Long-term Experimental Evolution Project Site home page. I invite everyone to have a look at this very informative resource.

  153. Lenski has no idea how to determine if the mutations were random/ chance events.

  154. It’s the context – the whole organism – that decides what is functional.

    No. In the terms of the whole organism, it’s the niche environment that decides what is functional, on a comparative basis. That’s the “natural selection” aspect of evolution. Phenotypes that outlive their rivals get to pass on and spread their genotype.

  155. Alan Fox:

    In the terms of the whole organism, it’s the niche environment that decides what is functional, on a comparative basis.

    No. Environments do NOT decide. And natural selection does NOT select. And outreproducing your rivals does NOT = a designer mimic.

  156. To speak of ‘functionality’ without reference to the actual organism as a whole is nonsensical. Functionality – of proteins and other parts – means being subordinate to the whole.

    Well of course. That’s why I said “in a particular context” in respect of proteins. Haemoglobin makes sense packed into human red blood cells (and in the bodies of Riftia tube worms).

  157. Alan,

    Your position can’t account for haemoglobin….

  158. No. Environments do NOT decide. And natural selection does NOT select. And outreproducing your rivals does NOT = a designer mimic.

    That may be Joe’s view. My view is the niche is the designer. One reason I prefer the scientific theory of evolution is that one theory explains both the diversity of life and where and when it is found with its overarching nested hierarchy . Evidence against evolution would be finding organism and niche out of step and outside the hierarchical arrangement predicted by evolutionary theory. “Rabbits in the Cambrian”!

  159. Mr. Fox, you invite people to look at Lenski’s long term evolution experiment. Dr. Behe did just that and found,,,

    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

    Moreover,,,

    Rose-Colored Glasses: Lenski, Citrate, and BioLogos – Michael Behe – November 13, 2012
    Excerpt: Readers of my posts know that I’m a big fan of Professor Richard Lenski, a microbiologist at Michigan State University and member of the National Academy of Sciences. For the past few decades he has been conducting the largest laboratory evolution experiment ever attempted. Growing E. coli in flasks continuously, he has been following evolutionary changes in the bacterium for over 50,000 generations (which is equivalent to roughly a million years for large animals). Although Lenski is decidedly not an intelligent design proponent, his work enables us to see what evolution actually does when it has the resources of a large number of organisms over a substantial number of generations. Rather than speculate, Lenski and his coworkers have observed the workings of mutation and selection.,,,
    In my own view, in retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski’s work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient — that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism.
    http://www.evolutionnews.org/2.....66361.html

  160. Joe @ 149

    The statement that mutations are random is both profoundly true and profoundly untrue at the same time. The true aspect of this statement stems from the fact that, to the best of our knowledge, the consequences of a mutation have no influence whatsoever on the probability that this mutation will or will not occur. In other words, mutations occur randomly with respect to whether their effects are useful. Thus, beneficial DNA changes do not happen more often simply because an organism could benefit from them. Moreover, even if an organism has acquired a beneficial mutation during its lifetime, the corresponding information will not flow back into the DNA in the organism’s germline. This is a fundamental insight that Jean-Baptiste Lamarck got wrong and Charles Darwin got right.

    However, the idea that mutations are random can be regarded as untrue if one considers the fact that not all types of mutations occur with equal probability. Rather, some occur more frequently than others because they are favored by low-level biochemical reactions. These reactions are also the main reason why mutations are an inescapable property of any system that is capable of reproduction in the real world. Mutation rates are usually very low, and biological systems go to extraordinary lengths to keep them as low as possible, mostly because many mutational effects are harmful. Nonetheless, mutation rates never reach zero, even despite both low-level protective mechanisms, like DNA repair or proofreading during DNA replication, and high-level mechanisms, like melanin deposition in skin cells to reduce radiation damage. Beyond a certain point, avoiding mutation simply becomes too costly to cells. Thus, mutation will always be present as a powerful force in evolution.
    — Loewe, L. (2008) Genetic mutation. Nature Education 1(1)

    Re: lack of correlation between mutations and their usefulness c.f. the fluctuation test (Luria & Delbruck 1943) and the replica plating test (Ledeberg & Ledeberg 1952).

    However, the above quote is not 100% correct – we know that some organisms can generate certain types of mutation in reaction to particular situations that they are repeatedly exposed to – e.g. hypervariability of surface proteins in an African trypanosome. Nonetheless, such cases appear to be very rare.

  161. Mr Fox states;

    I prefer the scientific theory of evolution

    Mr. Fox, neo-Darwinian evolution is not a ‘scientific’ theory for the simple fact it if it were true it would undermine trustworthiness of our cognitive faculties.

    Alvin Plantinga – Evolutionary Argument against Naturalism – video
    http://www.youtube.com/watch?v=r34AIo-xBh8

    If you don’t believe Plantinga, how about Pinker and Dawkins?

    Scientific Peer Review is in Trouble: From Medical Science to Darwinism – Mike Keas – October 10, 2012
    Excerpt: Survival is all that matters on evolutionary naturalism. Our evolving brains are more likely to give us useful fictions that promote survival rather than the truth about reality. Thus evolutionary naturalism undermines all rationality (including confidence in science itself). Renown philosopher Alvin Plantinga has argued against naturalism in this way (summary of that argument is linked on the site:).
    Or, if your short on time and patience to grasp Plantinga’s nuanced argument, see if you can digest this thought from evolutionary cognitive psychologist Steve Pinker, who baldly states:
    “Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not.”
    Steven Pinker, evolutionary cognitive psychologist, How the Mind Works (W.W. Norton, 1997), p. 305.
    http://blogs.christianpost.com.....ism-12421/

    Why No One (Can) Believe Atheism/Naturalism to be True – video
    Excerpt: “Since we are creatures of natural selection, we cannot totally trust our senses. Evolution only passes on traits that help a species survive, and not concerned with preserving traits that tell a species what is actually true about life.”
    Richard Dawkins – quoted from “The God Delusion”
    http://www.youtube.com/watch?v=N4QFsKevTXs

    supplemental notes:

    Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013
    Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated?
    http://www.uncommondescent.com.....e-details/

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003)


  162. No. Environments do NOT decide. And natural selection does NOT select. And outreproducing your rivals does NOT = a designer mimic.

    That may be Joe’s view.

    It is the only view that is supportable.

    My view is the niche is the designer.

    Good, now go find some support for it and you will have somnething.

    One reason I prefer the scientific theory of evolution is that one theory explains both the diversity of life and where and when it is found with its overarching nested hierarchy

    There isn’t any scientific theory of evolution and you don’t know what a nested hierarchy is.

  163. @ Phil

    You should have a look at what Dennis Venema (a theist and former creationist), writing at Biologos, has to say about Behe’s comments on the ongoing Lenski experiment.

    Part 1

    Part 2

  164. Clavdivs-

    No one has any idea if mutations are chance events. The lack of correlation between mutations and their usefulness doesn’t do it.

  165. Alan,

    Lenski’s experiment has NOT produced any new proteins, no new functions and definitely no new body plans. Lenski is proving that evolution is very limited. Very limited.

    Thanks Lenski.

  166. CLAVDIVS are you actually quoting papers from 1943 qand 1952 to support your preferred position that mutations are random? Let me welcome you to the 21st century:

    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

    Shapiro on Random Mutation:
    “What I ask others interested in evolution to give up is the notion of random accidental mutation.”
    http://www.huffingtonpost.com/.....11144.html

    Non-Random and Targeted Mutations (Epigentics to the level of DNA) – video
    http://www.youtube.com/watch?v=qTChu5vX1VI

    Antibiotic Resistance Is Prevalent in an Isolated Cave (4 million year old) Microbiome – April 2012
    Excerpt: ‘Antibiotic resistance is manifested through a number of different mechanisms including target alteration, control of drug influx and efflux, and through highly efficient enzyme-mediated inactivation. Resistance can emerge relatively quickly in the case of some mutations in target genes and there is evidence that antibiotics themselves can promote such mutations [43], [44], [45], [46]; however, resistance to most antibiotics occurs through the aegis of extremely efficient enzymes, efflux proteins and other transport systems that often are highly specialized towards specific antibiotic molecules.’
    http://www.plosone.org/article.....ne.0034953

  167. And let me invite you Mr. Fox, to see how misleading Venema can be to what the evidence actually says:

    Intelligent Design and the Origin of Biological Information: A Response to Dennis Venema By: Casey Luskin – October 3, 2011
    http://www.discovery.org/a/17571

    Responding to Venema’s Response to Meyer’s Response to Venema’s Response to Meyer’s Signature in the Cell: The Last in a Series (We Promise!) – Casey Luskin – October 22, 2011
    http://www.evolutionnews.org/2.....52061.html

  168. There isn’t any scientific theory of evolution and you don’t know what a nested hierarchy is.

    One of the predictions of the theory of evolution (a scientific theory must make testable predictions capable of falsification) is that speciation and reproductive isolation will lead to increasing diversity in a pattern of successive bifurcations. Find a fossil out of context and evolution will have some ‘splainin’ to do.

    Of course the pattern could just be the whim of the disembodied designer. But so could any other pattern. Only evolution must fit the nested hierarchy, which it does without observed exception.

    There is no other theory that explains the diversity of life. ID is no such theory.”Evolution can’t explain ____*(insert favourite argument from incredulity) is not a theory with any explanatory or predictive power.

  169. Mr. Fox pulls out the neo-Darwinian canard that a pre-Cambrian rabbit would falsify evolution. Would it really Mr. Fox?

    “nobody to date has yet found a demarcation criterion according to which Darwin(ism) can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote was as stated in 1973 LSE Scientific Method Lecture

    “In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history’s inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike “harder” scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture.”
    ? Jerry A. Coyne – professor of evolution at the University of Chicago

    “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli (pp. 27-28) –

    Punctuated Equilibrium and Patterns from the Fossil Record – Casey Luskin
    Excerpt: “The Cambrian Explosion is by no means the only “explosion” in the fossil record. One evolutionist concedes that for the origin of fishes, “this is one count in the creationists’ charge that can only evoke in unison from paleontologists a plea of nolo contendere [no contest].” Plant biologists have called the origin of plants an “explosion,” saying, “the … radiation of land (plant) biotas is the terrestrial equivalent of the much-debated Cambrian ‘explosion’ of marine faunas.” Vertebrate paleontologists believe there was a mammal explosion because of the few transitional forms between major mammal groups: “There are all sorts of gaps: absence of gradationally intermediate ‘transitional’ forms between species, but also between larger groups — between, say, families of carnivores, or the orders of mammals.” Another study, “Evolutionary Explosions and the Phylogenetic Fuse,” found a bird (as well as a mammal) “Early Tertiary ‘explosion’” because many bird and mammal groups appear in a short time period lacking immediately recognizable ancestral forms. Finally, others have called the origin of our own genus Homo, “a genetic revolution” where “no australopithecine (ape) species is obviously transitional” leading one commentator to call it, like others called the Cambrian Explosion, a “big bang theory” of human evolution.”
    http://www.ideacenter.org/cont.....hp/id/1232

  170. The unscientific hegemony of uniformitarianism – David Tyler – May 2011
    Excerpt: The pervasive pattern of natural history: disparity precedes diversity,,,, The summary of results for phyla is as follows. The pattern reinforces earlier research that concluded the Explosion is not an artefact of sampling. Much the same finding applies to the appearance of classes. These data are presented in Figures 1 and 2 in the paper.
    http://www.arn.org/blogs/index.....niformitar

    Creation and Evolution: The Biological Evidence – Dr. Marc Surtees – Disparity precedes Diversity – video
    http://www.youtube.com/watch?v.....age#t=402s

  171. Alan Fox:

    One of the predictions of the theory of evolution (a scientific theory must make testable predictions capable of falsification) is that speciation and reproductive isolation will lead to increasing diversity in a pattern of successive bifurcations. Find a fossil out of context and evolution will have some ‘splainin’ to do.

    Please reference this alleged theory of evolution and its predictions. Your word means nothing, Alan.

    Creation predicted reproductive isolation.

    And again Alan, ypou don’t know what a nested hierarchy is. Linnean taxonomy displays a nested hierarchuy and it has nothing to do with evolution.

    And Army is a nested hierarchy and has nothing to do withn evolution.

    Your ignorance is not an argument, Alan.

  172. Mr. Fox pulls out the neo-Darwinian canard that a pre-Cambrian rabbit would falsify evolution. Would it really Mr. Fox?

    Yes. It is a central tenet of evolutionary theory that the increasing diversity of life forms a branching nested hierarchy with all non-extinct life-forms kinked back to the universal common ancestor by unbroken chains of viable intermediates. Evidence that contradicted the pattern that is found, so far without exception, would indeed deal the theory a mortal blow. Of course, it would not affect the credibility of any alternative theory. Theories stand on their own merits and the observed fit with data.

  173. Alan Fox:

    It is a central tenet of evolutionary theory that the increasing diversity of life forms a branching nested hierarchy

    You don’t know what a nested hierarchy is. And prokaryotes do NOT fit into a nested hierarchy. No what?

  174. And STILL no reference for the alleged “evolutionary theory”.

    Unguided evolution can’t even muster a testable hypothesis…

  175. Mr. Fox,,

    Materialism predicted it took a very long time for life to develop on earth. Theism predicted life to appear abruptly on earth after water appeared on earth (Genesis 1:10-11) – We find evidence for complex photo-synthetic life in the oldest sedimentary rocks ever found on earth -

    Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. Theism predicted complex and diverse life to appear abruptly in the seas in God’s fifth day of creation. – The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short “geologic resolution time” in the Cambrian seas. -

    Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record – Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record, then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. -

    Materialism predicted animal speciation should happen on a somewhat constant basis on earth. Theism predicted man was the last species created on earth – Man himself is the last generally accepted major fossil form to have suddenly appeared in the fossil record. -

  176. Please reference this alleged theory of evolution and its predictions. Your word means nothing, Alan.

    If my word means nothing to you, Joe, what would be the point of me giving you references to the theory of evolution. Moreover, this site claims to be about “Intelligent Design”. Surely we should be discussing its strengths and weaknesses. Attacking ToE will not get ID a free pass.

    Besides, the literature available on evolutionary matters is vast. The internet has original papers and there are popular analyses for the interested amateur. Popular books abound. Over the years, I have contacted many scientists seeking further information, a PDF of a paper unavailable without a subscription or explanation on various points and have almost invariably had helpful responses. I find it sad, not that you reject evolution per se, but that you are so incurious, almost triumphalist in your ignorance.

  177. Alan Fox:

    If my word means nothing to you, Joe, what would be the point of me giving you references to the theory of evolution.

    If you reference it then it wouldn’t be your word, duh.

    Moreover, this site claims to be about “Intelligent Design”. Surely we should be discussing its strengths and weaknesses. Attacking ToE will not get ID a free pass.

    What ToE? Also your ignorance of science is duly noted as all design inferences must go through necessity and chance.

    Besides, the literature available on evolutionary matters is vast.

    Vast and nothing to do with unguided evolution. Most of it is just lip service to evolution.

    And I do NOT reject evolution, Alan. And I bet I know more about it than you do.

    IOW YOU appear to be triumplalist in YOUR ignorance.

  178. So Alan canNOT reference this alleged theory of evolution but he is sure that it exists.

    Pathetic…

  179. bornagain @ 165

    I know you like regurgitating quotes from your vast Google docs repository, but I note that not a single word you posted contradicts what I wrote – or even seriously engages with it. Please read for comprehension next time. Thanks.

  180. Materialism predicted it took a very long time for life to develop on earth.

    Well, I would say that the observed and extrapolated rates of evolution require sufficient time to happen. Scientific measurement and experiment has established the age of the Earth at around 4.7 billion years and the first liquid water at perhaps 4 billion years. Evidence of cyanobacteria shows up at around 3.5 billion years. So there does seem to be enough time for evolution to work on primitive life. The origin of life is still an open question.

  181. Mr. Fox, you appeal to mystical evidence that you have never produced and then call Joe ignorant. This is all the more ironic in that your preferred atheistic worldview demands epistemological failure. i.e. IGNORANCE!

    Metaphysical Naturalism is reducto ad absurdum on (at least) these eight following points:

    1. The argument from the intentionality (aboutness) of mental states implies non-physical minds (dualism), which is incompatible with naturalism
    2. The existence of meaning in language is incompatible with naturalism, Rosenberg even says that all the sentences in his own book are meaningless
    3. The existence of truth is incompatible with naturalism
    4. The argument from moral praise and blame is incompatible with naturalism
    5. Libertarian freedom (free will) is incompatible with naturalism
    6. Purpose is incompatible with naturalism
    7. The enduring concept of self is incompatible with naturalism
    8. The experience of first-person subjectivity (“I”) is incompatible with naturalism

    I strongly suggest watching Dr. Craig’s presentation, that I have linked, to get a full feel for just how insane the metaphysical naturalist’s position actually is.

    Is Metaphysical Naturalism Viable? – William Lane Craig – video
    http://www.youtube.com/watch?v=HzS_CQnmoLQ

  182. And I bet I know more about it than you do.

    How much are you thinking of betting?

  183. Alan Fox:

    Scientific measurement and experiment has established the age of the Earth at around 4.7 billion years…

    Only if the assumptions made are true. Ya see Alan HOW the Earth was formed directly impacts its age. And only IF the earth was entirley molten- no crystals at all could exist- does the dating method even have a chance of working.

  184. Actually Mr. Fox we have evidence of photosynthetic bacteria in the oldest sedimentary rocks ever found on earth:

    The Sudden Appearance Of Photosynthetic Life On Earth – video
    http://www.metacafe.com/watch/4262918

    When Did Life First Appear on Earth? – Fazale Rana – December 2010
    Excerpt: The primary evidence for 3.8 billion-year-old life consists of carbonaceous deposits, such as graphite, found in rock formations in western Greenland. These deposits display an enrichment of the carbon-12 isotope. Other chemical signatures from these formations that have been interpreted as biological remnants include uranium/thorium fractionation and banded iron formations. Recently, a team from Australia argued that the dolomite in these formations also reflects biological activity, specifically that of sulfate-reducing bacteria.
    http://www.reasons.org/when-di.....pear-earth

    Does the Chemistry of the Cell Point to Its Origin in Darwin’s “Warm Little Pond”? – February 23, 2012
    Excerpt: Studies have indicated that the earliest life may be older than the oldest known rocks, which are dated at 4 billion years old.
    http://www.evolutionnews.org/2.....56641.html

    Life – Its Sudden Origin and Extreme Complexity – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4287513

    Moreover, as if that wasn’t bad enough you have no prebiotic chemical signatures to appeal to.

    Dr. Hugh Ross – Origin Of Life Paradox (No prebiotic chemical signatures)- video
    http://www.metacafe.com/watch/4012696

  185. Alan Fox:

    How much are you thinking of betting?

    Well I won that bet so I could wager another $10,000

  186. CLAV, I directly contradicted you. You stated in regards to directed mutations:

    “Nonetheless, such cases appear to be very rare.”

    I showed you to be completely wrong per Shapiro!

  187. Mr. Fox, you appeal to mystical evidence that you have never produced and then call Joe ignorant.

    Joe is clearly ignorant of evolutionary theory, as are many others, yourself included. That’s your choice. It does baffle me that evolutionary theory (and the perennial misunderstandings and misrepresentations) is argued about so much on a site that purportedly advances the idea that there is a theory of “Intelligent Design”. As I keep saying, claiming that ToE is wrong or non-existent does not improve the claim that a theory of “Intelligent Design” exists. It is almost as if ID proponents don’t have a scientific theory, so reluctant is everyone to elaborate on it.

  188. Alan Fox:

    Joe is clearly ignorant of evolutionary theory, …

    Alan Fox is clearly a lying loser.

    Does it make you feel big to lie about other people, Alan?

    And Alan, unlike unguided evolution, ID actually has a methodology. So go pound sand, loser.

  189. Now Now Mr. Fox projecting your obvious weakness onto others is not the way to go! :)

  190. Ya see Alan HOW the Earth was formed directly impacts its age. And only IF the earth was entirley molten- no crystals at all could exist- does the dating method even have a chance of working.

    Interesting!

    So what does the evidence indicate for the age of the Earth, Joe, in your view?

  191. Alan Fox:

    So what does the evidence indicate for the age of the Earth, Joe, in your view?

    We have to know HOW it was formed, Alan. Just as I said.

    Are you happy being an obtuse arse?

  192. Mr. Fox, Do you believe the formation of the earth was completely happenstance?

    Linked from Appendix C from Dr. Ross’s book, ‘Why the Universe Is the Way It Is’;
    Probability for occurrence of all 816 parameters ? 10^-1333
    dependency factors estimate approx. 10^324
    longevity requirements estimate approx. 10^45
    Probability for occurrence of all 816 parameters ? 10^-1054
    Maximum possible number of life support bodies in observable universe ? 10^22

    Thus, less than 1 chance in 10^1032 exists that even one such life-support body would occur anywhere in the universe without invoking divine miracles.
    http://www.reasons.org/files/c....._part3.pdf

    Hugh Ross – Evidence For Intelligent Design Is Everywhere (10^-1054) – video
    http://www.metacafe.com/watch/4347236

  193. Michael Denton – We Are Stardust – Uncanny Balance Of The Elements – Fred Hoyle Atheist to Deist/Theist – video
    http://www.metacafe.com/watch/4003877

    “Dr. Michael Denton on Evidence of Fine-Tuning in the Universe” (Remarkable balance of various key elements for life) – podcast
    http://intelligentdesign.podom.....3_59-07_00

    The Place of Life and Man in Nature: Defending the Anthropocentric Thesis – Michael J. Denton – February 25, 2013
    Summary (page 11)
    Many of the properties of the key members of Henderson’s vital ensemble —water, oxygen, CO2, HCO3 —are in several instances fit specifically for warm-blooded, air-breathing organisms such as ourselves. These include the thermal properties of water, its low viscosity, the gaseous nature of oxygen and CO2 at ambient temperatures, the inertness of oxygen at ambient temperatures, and the bicarbonate buffer, with its anomalous pKa value and the elegant means of acid-base regulation it provides for air-breathing organisms. Some of their properties are irrelevant to other classes of organisms or even maladaptive.
    It is very hard to believe there could be a similar suite of fitness for advanced carbon-based life forms. If carbon-based life is all there is, as seems likely, then the design of any active complex terrestrial being would have to closely resemble our own. Indeed the suite of properties of water, oxygen, and CO2 together impose such severe constraints on the design and functioning of the respiratory and cardiovascular systems that their design, even down to the details of capillary and alveolar structure can be inferred from first principles. For complex beings of high metabolic rate, the designs actualized in complex Terran forms are all that can be. There are no alternative physiological designs in the domain of carbon-based life that can achieve the high metabolic activity manifest in man and other higher organisms.
    http://bio-complexity.org/ojs/.....O-C.2013.1

    The Role of Elements in Life Processes
    http://www.mii.org/periodic/LifeElement.php

    The vastness, beauty, orderliness, of the heavenly bodies, the excellent structure of animals and plants; and the other phenomena of nature justly induce an intelligent and unprejudiced observer to conclude a supremely powerful, just, and good author.
    — Robert Boyle (1627 – 1691), father of experimental chemistry

    Periodic Table – Interactive web page for each element
    http://www.mii.org/periodic/MiiPeriodicChart.htm

  194. Now Mr. Fox projecting your obvious weakness onto others is not the way to go!

    I don’t see ignorance as an insoluble problem. I am certainly ignorant of a positive scientific theory of “Intelligent Design”. I would like to learn about such a theory or confirmation that no such thing exists. Joe and you have the same opportunities with evolutionary theory.

  195. Tell you what Mr. Fox, let’s please forget all the name calling you have started in on and just get back to the supposed overwhelming evidence for evolution. Could you please show us where it is?

    Neo-Darwinists claim that evolution is an observed fact on par with the observed fact of gravity. But very contrary to their claims, the plain fact of the matter is that there are ZERO observed instances of neo-Darwinian evolution:

    Where’s the substantiating evidence for neo-Darwinism?

    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).)

    Four decades worth of lab work is surveyed here, and no evidence for neo-Darwinian evolution surfaces:

    “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/

    How about the oft cited example for neo-Darwinism 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 doesn’t seem to be helping! 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 doesn’t seem to be helping either! 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).)

    Now that just can’t be right!! 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!!!

    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 something is going terribly wrong here!!! Tell you what, let’s just forget trying to observe evolution in the lab, I mean it really is kind of cramped 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, who believe in Intelligent Design, 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

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    - Michael Behe – The Edge of Evolution – page 146

    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.....20071.html

    Now, 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!!! It is as if the whole neo-Darwinian theory, relentlessly sold to the general public as it was the gospel truth, is nothing but a big fat lie!!!

  196. bornagain @ 186

    Show where Shapiro proves that correlations between mutations and their usefulness to the organism – in terms of survival, reproduction, etc – are other than rare.

    Don’t bother with canards about mutations being correlated with “stimuli” and “regulation” – totally different, and already acknowledged in my quote. Please try and keep up!

  197. Alan Fox:

    I don’t see ignorance as an insoluble problem. I am certainly ignorant of a positive scientific theory of “Intelligent Design”. I would like to learn about such a theory or confirmation that no such thing exists. Joe and you have the same opportunities with evolutionary theory.

    I have taken advantage of my opportunities, Alan. That is why it is a safe bet that I understand evolution better than you- or at least I portray it better than you do.

    I learned about evolution by reading Mayr, Gould, Darwin, Dawkins, Shubin, Carroll, Jones (Darwin’s Ghost), Shapiro, Coyne, biology textbooks, etc. So if I have some misunderstanding- something that neither you nor anyone else has been able to demonstrate BTW- perhaps it is the fault of those references.

    So instead of being a coward and just falsely accuse me of being ignorant of evolution, perhaps you can actually provide some evidence to support your BS.

    I dare you.

  198. Tell you what Mr. Fox, let’s please forget all the name calling you have started in on…

    I started name-calling? Pointing out your and Joe’s ignorance of evolutionary theory is not name calling. Would you not think calling someone a lying loser or an obtuse arse was more in that vein.?

    …and just get back to the supposed overwhelming evidence for evolution. Could you please show us where it is?

    But why should I need to? There are lots of sites dedicated to promoting evolutionary theory and lots of popular books. Dawkins has several. “The Greatest Show on Earth” is a tour de force on evidence for evolution and includes a huge bibliography. Now I predict that you will reject Dawkins out of hand. I could refer you to Talk Origins, I could solicit recommendations from fellow commenters at TSZ. I have already referenced the Lenski experiment and linked to the Lenski Lab website. None of this will interest you. Are you a gardener? Try an experiment. Clear a patch of ground, say a couple of meters square and do nothing else to it (or you might find a fire-damage clearing nearby) and observe the recolonisation over the growing season.

    Now, reciprocate. Tell me about the theory of “Intelligent Design”…

  199. Joe @ 164

    You are muddying the waters that I attempted to clarify.

    We do have an idea that mutations are not correlated with their effect on phenotypic usefulness – from empirical experiments.

    Of course mutations are correlated with a variety of biomolecular processes, and mutations do not just occur at any position in the genome with equal probability. But this is not the same thing as mutations being correlated with their consequences for the organism in its environment.

  200. It appears that everyone is ignorant of a positive scientific theory of “unguided evolution”. I would like to learn about such a theory or confirmation that no such thing exists.

    There are many ideas on evolution, but none that really constitute a scientific theory, let alone a scientific theory of unguided evolution. Unguided evolution can’t muster a testable hypothesis, and that is required first.

    Even James Shapiro recognizes that unguided evolution is just an ideology, not a theory.

    If there were such a theory then we would something to compare ID with to see if it measures up or not. Then people like Alan couldn’t flail around just to muddy the waters.

    Just like CSI- give us something we can compare it to and then we will take your “criticisms” seriously.

    Attacking ID will not provide positive support for unguided evolution.

  201. Clavdivs:

    We do have an idea that mutations are not correlated with their effect on phenotypic usefulness – from empirical experiments.

    That does NOT mean they are random/ chance events.

  202. WJM asked:

    Can chance & necessity build a battleship, franklin?

    franklin said:

    no, wjm, for all we know people build battleships.

    Since you said “no” to the question of “can chance & necessity build a battleship”, and then add that people build them, it must then be your position that humans somehow operate (when building a battleship) outside of what can be explained via the categories of chance and necessity.

    Are humans not material entities generated by and bound to behavior that is ultimately explicable via the fundamental causal categories of material interaction – necessity (law) and chance? You answer indicates that humans can operate via some other categorical description, something besides chance and necessity. What causal category would that be, franklin?

    here is a straight forward question for you: How does a disembodied entity interact with atoms and molecules to push them together and cause a desired outcome?

    I have no idea what a “disembodied entity” would be, or how it would interact with anything. It sounds like a contradiction in terms to me.

  203. HMM CLAV you cite references from 1943 and 1952 and then you ask ME to keep up??? :)

    Are Mutations Random? – video
    http://www.youtube.com/watch?v=D720rzuIuv8

    A brief look into the history of the “random mutation” hypothesis and why current data about the genome no longer support the idea that most mutations are random.

    This is actually a preparation video I made for a talk I gave at Ignite Tulsa last year. Unfortunately, Ignite Tulsa messed up the videography, so the event never got uploaded to YouTube.

    The references were hard to read, so here there are listed out:

    Kondrashov. 1995. Contamination of the Genome by Very Slightly Deleterious Mutations: Why Have We Not Died 100 Times Over? Journal of Theoretical Biology 175(4):583-594.

    Templeton. 2006. Population Genetics and Microevolutionary Theory.

    Orgel and Crick. 1980. Selfish DNA: The Ultimate Parasite. Nature 284:604-607.

    Chuang and Li. 2004. Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions of the Human Genome. PLoS Biolog 2(2)e29.

    Hall. 1999. Transposable Elements as Activators of Cryptic Genes in E. Coli. Genetica 107:181-187.

    Market and Papavasiliou. 2003. V(D)J Recombination and the Evolution of the Adaptive Immune System. PLoS Biology 1(1):e16.

    Papavasiliou and Schatz. 2002. Somatic Hypermutation of Immunoglobulin Genes: Merging Mechanisms for Genetic Diversity. Cell 109:S35-44.

    Fondon and Garner. 2004. Molecular Origins of Rapid and Continous Morphological Evolution. PNAS 101:18058-18063.

    Barry. 2006. Implicit Information in Eukaryotic Pathogens as the Basis of Antigenic Variation. In “The Implicit Genome”, Oxford University Press.

    Non-Random and Targeted Mutations
    http://www.youtube.com/watch?v=qTChu5vX1VI

    Emerging research suggests beneficial mutations can be non-random, stress-induced, and target specific regions of the genome.

    De novo genetic variation revealed in somatic sectors of single Arabidopsis plants 2013
    http://f1000research.com/articles/2-5/v1

    An environmentally induced adaptive insertion event in flax 2009

    Non-random mutation: The evolution of targeted hypermutation and hypomutation 2013

    Changes to DNA methylation and homologous recombination frequency in the progeny of stressed plants 2013

  204. Alan [SNIP]:

    Pointing out your and Joe’s ignorance of evolutionary theory is not name calling.

    It is seeing that you cannot support your claim.

    Dawkins doesn’t provide any way to test his blind watchmaker thesis.

    Lenski has proven that evolution is very, very limited. And he didn’t demonstrate that the changes were random/ chance events.

    IOW Alan, you appear to be just another clueless tool, and apparently proud of it.

  205. Alan Fox:

    There are lots of sites dedicated to promoting evolutionary theory and lots of popular books.

    A scientific theory needs to be published in a scientific peer-reviewed journal.

    Websites and popular books do NOT cut it.

    Are you really that dense, Alan?

  206. Joe @ 201

    Of course they’re not random/chance events Joe. No biologist is saying they are, because they’re known to be correlated with various biomolecular processes – as I just said!

  207. So Mayr wasn’t a biologist? “What Evolution Is” was total BS?

  208. And computer signals are known to be connected with various electrical processes.

  209. Mr. Fox I know you pride yourself on your superior intellect, and I appreciate you taking the time to humble yourself to try to show us ignorant IDiotards the error of our ways, but when I request specific evidence for evolution, say a protein or a molecular machine, and I am told to clear a piece of ground instead, I really have to wonder if you have both oars in the water as to what it takes to prove your claim scientifically! :)

  210. bornagain @ 203

    As expected: another regurgitation of totally irrelevant quotes. You’ve not presented the tiniest shred of evidence that mutations are correlated with usefulness to the organism in its environment – except in rare cases.

    And you failed to show where Shapiro refuted this point in the original cite. Because he didn’t, did he?

    And you’ve raised the ridiculously fatuous non sequitur about empirical experiments being somehow irrelevant or unimportant because they’re old. Why don’t we go jump of a cliff because Galileo and Newtons experiments on gravity were just so long ago!!!! Please address the substance of the fluctuation and replica plating tests next time around, if you can.

  211. Mr. Fox I know you pride yourself on your superior intellect, and I appreciate you taking the time to humble yourself to try to show us ignorant IDiotards the error of our ways, but when I request specific evidence for evolution, say a protein or a molecular machine, and I am told to clear a piece of ground instead, I really have to wonder if you have both oars in the water as to what it takes to prove your claim scientifically!

    Not a gardener then, Phil. The reason I suggest you might like to look at how wild plants recolonise a cleared patch or waste ground is because the processes of natural selection such as intra-species and inter-species competition are so beautifully demonstrated. Granted, it take s little effort and time. What do mean by “specific evidence for evolution, say a protein or a molecular machine”? There are plenty of descriptions of the relatedness of organisms that can be observed via molecular phylogenetics but I guess you’ll wave that away too. I note you ignored my point about some reciprocity on information supplying. No further comment on name calling either? I begin to suspect you are not a fair interlocutor.

  212. Joe @ 208

    And computer signals are known to be connected with various electrical processes.

    Is that a response to me? If so, so what? Cheese is correlated with various dairy processes too.

    The point still stands that empirical studies show that mutations are not correlated with phenotypical usefulness, except in rare cases.

  213. Oops

    takes a little effort

  214. Molecular phylogenetics say nothing of a mechanism, Alan. And inter-species competetion does not explain the species in the first place.

    As for name calling, mine are just observations. And obvioulsy I was correct as you have FAILED to support your false accusations.

    Sp perhaps you should address your personal issues before posting.

  215. CLAV, are you insane? The fact that the programming and machinery of the cell is what is changing the genome is what refutes the fact that the mutations are not truly ‘random’ in the Darwinian sense. Are you, against all reason, trying to maintain that the sophisticated machinery and programming of the cell randomly evolved to induce random mutations in a Darwinian sense? Well by golly if you believe that just sign me up next to the rubber room next to yours! :) You’ve got to be kidding me if you want me to swallow that garbage!

  216. Calvdivs:

    The point still stands that empirical studies show that mutations are not correlated with phenotypical usefulness, except in rare cases.

    So what? That still doesn’t mean they are due to blind and undirected chemical processes

  217. And inter-species competetion does not explain the species in the first place.

    For the umpteenth time, the theory of evolution is an attempt to explain the diversity of life on Earth. It has nothing to say about the origin of life on Earth.


  218. And inter-species competetion does not explain the species in the first place.

    For the umpteenth time, the theory of evolution is an attempt to explain the diversity of life on Earth. It has nothing to say about the origin of life on Earth

    For the umteenth time if it cannot say how the OoL came about then it cannot say anything about its subsequent diversity because the two are connested. OoL = design then the inference is they were designed to evolve and evolved BY DESIGN.

    Also:

    1- I did NOT say anything about the OoL on Earth. Obvioulsy you still have those many personal issues.

    2- Those species, Alan. the species that are to re-colonise, duh

  219. And trying to bring the thread back on topic:

    1.Publish a mathematically rigorous definition of CSI

    Elsberry and Shallit still have no response to their challenge of 2003. Ten years, guys!

  220. We say that we have done such a thing, Alan. And we have asked you guys for something from your position to compare it to so you cannot keep flailing like little sissies.

  221. So Mr. Fox, still no novel protein or molecular machine as requested? You did bring up molecular phylogenetics,,, OKIE DOKIE now we are getting somewhere:

    Orphan Genes (And the peer reviewed ‘non-answer’ from Darwinists) – video
    http://www.youtube.com/watch?v=1Zz6vio_LhY

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,,
    The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.
    http://ccsb.dfci.harvard.edu/w.....n_2013.pdf

    Bothersome Bats and Other Pests Disturb the “Tree of Life” – Casey Luskin – December 5, 2012
    Excerpt: Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.
    (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, “Understanding phylogenetic incongruence: lessons from phyllostomid bats,” Biological Reviews of the Cambridge Philosophical Society, Vol. 87:991-1024 (2012).)
    http://www.evolutionnews.org/2.....67121.html

    Nature Article Finds MicroRNAs are “Tearing Apart Traditional Ideas about the Animal Family Tree”

    Casey Luskin June 29, 2012
    Excerpt: When Peterson started his work on the placental [mammal] phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn’t cooperate. If the traditional tree was correct, then an unprecedented number of microRNA genes would have to have been lost, and Peterson considers that highly unlikely. “The microRNAs are totally unambiguous,” he says, “but they give a totally different tree from what everyone else wants.”,,, Maybe the reason that different genes yield different evolutionary trees is because there isn’t a single unified tree of life to be found. In other words, perhaps universal common ancestry is simply wrong.
    http://www.evolutionnews.org/2.....61471.html

    micro-RNA and Non-Falsifiable Phylogenetic Trees – (Excellent Research) video
    http://www.youtube.com/watch?v=qv-i4pY6_MU

    Gene tree discordance, phylogenetic inference and the multispecies coalescent – 2009
    Excerpt: Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates.
    http://www.sciencedirect.com/s.....4709000846

    The universal ancestor – Carl Woese
    Excerpt: No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.
    http://www.pnas.org/content/95/12/6854.full

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

  222. Phil 221

    Sorting wheat from chaff:

    Please don’t expect me to watch videos, I haven’t the bandwidth.

    Please don’t expect me to treat the writings of Casey Luskin on science as a useful source of information.

    What is it in the New Scientist article by Helen Pilcher that is anti-evolution?

    Don’t expect me to purchase papers for 37 dollars.

    What is it in the paper by Woese that is anti-evolution?

    What is it in the New Scientist article by Ruth Williams that is anti-evolution?

  223. Oh and Phil,

    Any information to offer on a possible theory of intelligent design?

  224. Alan Fox- all chaff.

    Intelligent Design Evolution is OK with evolution, Alan.

    You would think that a person who has followed this debate since 2005 would at least know the basics. Nothing says that Alan is willfully ignorant more than his willful ignorance.

  225. Alan Fox:

    Any information to offer on a possible theory of intelligent design?

    As with the alleged theory of evolutipn it’s in various websites and popular books- S Meyer, Behe, Dembski, Gonzales, ENV, etc. It’s all there if you dare.

  226. Mr. Fox, so you see nothing at all contrary to Darwinian thinking in pervasive phylogenetic incongruence? Not even a hint? Is pervasive phylogenetic incongruence what you expected? If so well by golly I think you can call the physicists up and tell them to stop looking for you have finally discovered the ‘Theory Of Everything’! :)

    Who would have thought that it would be biologists that came up with the first Theory of Everything?

    Biological divergence? Evolution. Biological convergence? Evolution. Gradual variation? Evolution. Sudden variation? Evolution. Stasis? Evolution. Junk DNA? Evolution. No Junk DNA? Evolution. Tree of life? Evolution. No tree of life? Evolution. Common genes? Evolution. Orfan genes? evolution. Cell with little more than a jelly-like protoplasm? Evolution. Cell filled with countless, highly-specified nano-machines directed by a software code? Evolution. More hardy, more procreative organisms? Evolution. Less hardy, less procreative organisms? Evolution.
    Evolution explains everything. -
    William J Murray

  227. Mr. Fox, so you see nothing at all contrary to Darwinian thinking in pervasive phylogenetic incongruence? Not even a hint? Is pervasive phylogenetic incongruence what you expected? If so well by golly I think you can call the physicists up and tell them to stop looking for you have finally discovered the ‘Theory Of Everything’!

    What I am seeing are your lack of responses.

    You throw a long cut-and-paste out but show no evidence of having read the material you link to. you can prove me wrong by responding to the points I raised. Here they are again:

    What is it in the New Scientist article by Helen Pilcher that is anti-evolution?

    What is it in the paper by Woese that is anti-evolution?

    What is it in the New Scientist article by Ruth Williams that is anti-evolution?

  228. As well, MR. Fox, contrary to Darwinism, at least ID does have a falsification criteria to demarcate it,

    Dembski’s original value for the universal probability bound is 1 in 10^150,

    10^80, the number of elementary particles in the observable universe.

    10^45, the maximum rate per second at which transitions in physical states can occur.

    10^25, a billion times longer than the typical estimated age of the universe in seconds.

    Thus, 10^150 = 10^80 × 10^45 × 10^25. Hence, this value corresponds to an upper limit on the number of physical events that could possibly have occurred since the big bang.

    How many bits would that be:

    Pu = 10-150, so, -log2 Pu = 498.29 bits

    Call it 500 bits (The 500 bits is further specified as a specific type of information. It is specified as Complex Specified Information by Dembski or as Functional Information by Abel to separate it from merely Ordered Sequence Complexity or Random Sequence Complexity; See Three subsets of sequence complexity)

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    http://www.tbiomed.com/content/2/1/29

    This short sentence, “The quick brown fox jumped over the lazy dog” is calculated by Winston Ewert, in this following video at the 10 minute mark, to contain 1000 bits of algorithmic specified complexity, and thus to exceed the Universal Probability Bound (UPB) of 500 bits set by Dr. Dembski

    Proposed Information Metric: Conditional Kolmogorov Complexity – Winston Ewert – video
    http://www.youtube.com/watch?v=fm3mm3ofAYU

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

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

    Here is a general overview of the predictions for Intelligent Design:

    A Positive, Testable Case for Intelligent Design – Casey Luskin – March 2011 – several examples of cited research
    http://www.evolutionnews.org/2.....45311.html

    A Response to Questions from a Biology Teacher: How Do We Test Intelligent Design? – March 2010
    Excerpt: Regarding testability, ID (Intelligent Design) makes the following testable predictions:

    (1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

    (2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

    (3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

    (4) Much so-called “junk DNA” will turn out to perform valuable functions.
    http://www.evolutionnews.org/2.....rom_a.html

    On the Origin of Protein Folds – Jonathan M. – September 8, 2012
    Excerpt: A common objection to the theory of intelligent design is that it makes no testable predictions, and thus there is no basis for calling it science at all. While recognizing that testability may not be a sufficient or necessary resolution of the “Demarcation Problem,” my article, which I invite you to download, will consider one prediction made by ID and discuss how this prediction has been confirmed.
    http://www.evolutionnews.org/2.....64081.html

    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

  229. Mr. Fox, I understand what they are saying perfectly and know for a fact that they, and you, don’t have any mechanism to explain the drastic differences they are finding. So once again I ask you “Is pervasive phylogenetic incongruence what you expected?”

    Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008
    Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.
    Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.
    http://www.icr.org/i/pdf/techn.....Theory.pdf

  230. Is pervasive phylogenetic incongruence what you expected?

    You first need to demonstrate that phylogenetic incongruence is indeed pervasive. This paper suggests that phylogenetic incongruence among bacteria can be explained by recombination.

  231. Alan Fox:

    What I am seeing are your lack of responses.

    Nice projection.

    And phylogenetic analysis doesn’t say anything about unguided evolution. So why the deception?

  232. PS @ Phil

    Please don’t expect me to take seriously material sourced from the Institute for Creation Research.

  233. Typical coward- attack the website not the evidence.

  234. Alan Fox,

    You first need to demonstrate that phylogenetic incongruence is indeed pervasive.

    Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.
    (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, “Understanding phylogenetic incongruence: lessons from phyllostomid bats,” Biological Reviews of the Cambridge Philosophical Society, Vol. 87:991-1024 (2012).)

    Then you state

    This paper suggests that phylogenetic incongruence among bacteria can be explained by recombination.

    But alas Mr Fox, even bacteria will not cooperate with your preferred atheistic/materialistic worldview:

    The Dictionary of Life | Origins with Dr. Paul A. Nelson – video
    http://www.youtube.com/watch?f.....vCo#t=760s

    The essential genome of a bacterium – 2011
    Figure (C): Venn diagram of overlap between Caulobacter and E. coli ORFs (outer circles) as well as their subsets of essential ORFs (inner circles). Less than 38% of essential Caulobacter ORFs are conserved and essential in E. coli. Only essential Caulobacter ORFs present in the STING database were considered, leading to a small disparity in the total number of essential Caulobacter ORFs.
    http://www.ncbi.nlm.nih.gov/pm.....201158.pdf

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

    Estimating the size of the bacterial pan-genome – Pascal Lapierre and J. Peter Gogarten – 2008
    Excerpt: We have found >139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered.
    http://www.paulyu.org/wp-conte.....genome.pdf

    Thus once again I ask:

    “Is pervasive phylogenetic incongruence what you expected?”

  235. Mr Fox sniffs:

    Please don’t expect me to take seriously material sourced from the Institute for Creation Research.

    I guess you’re right, that’s almost as silly as taking Genesis seriously:

    The best data we have [concerning the Big Bang] are exactly what I would have predicted, had I nothing to go on but the five books of Moses, the Psalms, the bible as a whole.
    Dr. Arno Penzias, Nobel Laureate in Physics – co-discoverer of the Cosmic Background Radiation – as stated to the New York Times on March 12, 1978

    “Certainly there was something that set it all off,,, I can’t think of a better theory of the origin of the universe to match Genesis”
    Robert Wilson – Nobel laureate – co-discover Cosmic Background Radiation
    http://www.evidenceforchristia.....38;id=3594

    “There is no doubt that a parallel exists between the big bang as an event and the Christian notion of creation from nothing.”
    George Smoot – Nobel laureate in 2006 for his work on COBE

    “Now we see how the astronomical evidence supports the biblical view of the origin of the world. The details differ, but the essential elements in the astronomical and biblical accounts of Genesis are the same: the chain of events leading to man commenced suddenly and sharply at a definite moment in time, in a flash of light and energy.”
    Robert Jastrow – Founder of NASA’s Goddard Institute – Pg.15 ‘God and the Astronomers’

    ,,, ‘And if you’re curious about how Genesis 1, in particular, fairs. Hey, we look at the Days in Genesis as being long time periods, which is what they must be if you read the Bible consistently, and the Bible scores 4 for 4 in Initial Conditions and 10 for 10 on the Creation Events’
    Hugh Ross – Evidence For Intelligent Design Is Everywhere; video
    http://www.metacafe.com/watch/4347236

    “I now believe that the universe was brought into existence by an infinite intelligence. I believe that the universe’s intricate laws manifest what scientists have called the Mind of God. I believe that life and reproduction originate in a divine Source. Why do I believe this, given that I expounded and defended atheism for more than a half century? The short answer is this: this is the world picture, as I see it, that has emerged from modern science.”
    Anthony Flew – world’s leading intellectual atheist for most of his adult life until a few years shortly before his death
    The Case for a Creator – Lee Strobel (Nov. 25, 2012) – video
    http://www.saddleback.com/mc/m/ee32d/

  236. franklin:

    more importantly is that Axes work falls within the values generated by other researchers….10^10-10^63

    As we look at the origin of life, let’s use for a moment, just for purposes of discussion, the extremely optimistic 1 in 10^10 probability you have asserted for a stable, functional fold of, say, 150 amino acid positions.

    That is just for getting a stable, functional fold. This does not mean that the fold would occur spontaneously under natural conditions. Many (perhaps most) proteins do not spontaneously fold to their correct functional configuration, but require cellular machinery to correctly fold. (The cell also includes review and repair/destruction systems for defectively folded proteins, but we’ll leave that aside for a moment.)

    In addition, it does not address critical issues like interfering cross reactions or degradation. I presume it also does not address chiralty, although it wasn’t clear from the information you provided.

    Further, proteins generally do not function in a vaccuum, but instead in a complex of multiple proteins. We can understand this easily if we look at the simplest form of protein, say, one that simply binds to a particular molecule. Then what? That function may do something, but without other machinery involved, the “function” is no more meaningful than any non-organic chemical bonding to another. In life, proteins are typically grouped together to form machines, or act as switches, regulators, and catalysts for each other in a controlled way.

    Imagine that a stable functional protein were to arise on the early Earth under your 1 in 10^10 probability, say a protein that binds some particular molecule. Then what? In order to get another protein that works in conjunction with our first protein we cannot just rely on our 1 in 10^10 probability to come up with any old function. Rather, we would need a protein that has some ability to interact with the first protein or at least with the relevant bound molecule to do some additional function. In other words, the second protein has a much higher requirement of specification. The probability of that protein arising, even under the optimistic estimates, is not even close to 1 in 10^10. It is orders of magnitude less likely.

    So, even with your most optimistic estimate, it quickly becomes evident that if we add a couple more proteins to the mix (as is absolutely necessary for any from of life) we are quickly in the range of the 1 in 10^74+ estimates that are closer to Axe’s number.

    The reality is that there is plenty of room to haggle over specific numbers and percentages and estimates and still not alter the overall conclusion one bit:

    Given the resources of the known universe there is no reasonable way that the complex specified functionality for even a simple organism could arise through purely natural means.

    To believe it is possible is not science.

    It is just another miracle story.

  237. This does not mean that the fold would occur spontaneously under natural conditions. Many (perhaps most) proteins do not spontaneously fold to their correct functional configuration, but require cellular machinery to correctly fold.

    I think you are wrong here. Most proteins (especially up to 100 residues or so) will spontaneously fold to a specific (crystallizable) conformation immediately as they are being synthesized in vivo and a the appropriate pH and osmotic pressure in vitro

  238. Oops

    …at the appropriate pH…

  239. Just wondering, Eric. Your experience would be in engineering, wouldn’t it?

  240. Eric Anderson #236
    Thank you for your powerful discourse. I made some weak attempts to address the same issue in several postings during this thread. I’m glad to see that someone did a convincing job.

  241. AF:

    At this stage it is sadly clear you are only spewing talking points on a subject you have little understanding of or interest in understanding.

    Count one, the root of the tree of life is OOL. That makes it highly relevant, and this is why OOL appears in any number of biology textbooks that address evolution.

    It just turns out that the aspect is the one that most directly exposes the failures of the whole system.

    As a result the only known, empirically grounded source of FSCO/I is at the table as of right not grudging sufferance: design.

    As to your talking point on failed to give “rigorous” definitions, in fact models are not about mathematical rigour but empirical adequacy and correspondence with reality. Including metric ones. The “rigour game” as an objection is often just a disguise for selective hyperskepticism. (If you doubt me come up with a rigorous proof from first principles in axiomatic Zermelo-Frankel set theory for 3 + 2 = 5.)

    By any reasonable standard FSCO/I is a common and measured quantity it is what appears in file sizes all the time, such as a PDF doc of 158 kB. The capital B means bytes, eight bits together in a cluster. The k here means strictly 2^10 or 1024.

    In short you are belabouring a commonplace revealing your intentions to be dismissive rather than serious.

    As for the expressions, it is readily obvious that the 2005 Dembski metric can be converted into the form Chi_500 = Ip*S – 500, and that objective criteria can be established for evaluating function, such as in a PDF document, or in DNA for a protein etc. The Durston metric, in functional bits, fits, is based on the Shannon H metric with adjustment for observed biofunction and variability of places in AA sequences in protein families.

    In short it takes into account redundancies, which reduce the actual degree of info.

    In short your attempts above have discredited you as willfully dismissive without good reason and out of depth.

    I sent you to where you can look at a 101 on basics about info, I hope you at least will start from there after eight years hanging around dismissively in UD’s columns. (If your real underlying prob is high school algebra, I think Khan Academy may be of help.)

    KF

  242. eric: As we look at the origin of life, let’s use for a moment, just for purposes of discussion, the extremely optimistic 1 in 10^10 probability you have asserted for a stable, functional fold of, say, 150 amino acid positions.

    If you want to speculate about the origin of life we should rather focus on what is the minimal amino acid alphabet that can form functioning peptides and proteins. Are you familiar with any of the research in this area?

    eric: Further, proteins generally do not function in a vaccuum, but instead in a complex of multiple proteins

    While this is mostly true for current life as we observe it does not necessarily apply to the origin of the first replicators which were likely much simpler than life forms of today.

    eric: Rather, we would need a protein that has some ability to interact with the first protein or at least with the relevant bound molecule to do some additional function.

    the first function of a biomolecule could have been as simple as ‘bind oxygen’ which would certainly act prevent oxidative degradation or even ‘bind protons’ or ‘bind a atom of a metal’ which could act as a buffer in the former case or as a means of generating a catalyst. There are a great many scenarios where simple binding of any number of substrates can lead to more complex molecular chemistry.

  243. bornagain @ 215

    Are you deliberately missing the point?

    If by “Darwinian sense” you mean in the “atheistic materialistic sense”, then I have no idea whether anything is or is not “random” in that sense — I’m not an atheistic materialist and I’m not talking about metaphysics I’m talking about science.

    If by “Darwinian sense” you mean “as understood by the modern scientific theory of biological evolution” then I’ve already explained multiple times that according to modern biological science:

    1. Mutations are correlated with various biomolecular processes, so mutations are not “random” in the specific sense that they do not appear at any location in the genome with equal probability.

    2. Mutations are not correlated with usefuless to the organism in its environment (with rare exceptions), so mutations are “random” in the specific sense that their benefit or detriment to the phenotype does not affect their probability of occurrence.

    You, my friend – whether deliberately or due to a profound confusion of thoughts – are conflating these two very different concepts of randomness with regard to mutations. Everyone seems to agrees with the first meaning; but you have yet to even acknowledge the second meaning.

    Do you agree that empirical evidence gives good reason to believe that (with rare exceptions) mutations are not correlated with usefulness to the organism in its environment?

  244. Franklin:

    What you need to do is to show on observation not speculations, how a chemical stew — racemic is energetically favoured — becomes able to give us chiral based, structural molecules working as nanomachines to implement a C-chemistry, encapsulated, gated, metabolising automaton with code based self-replication.

    Absent that you are spinning just so stories and materialist origins myths with no relevance to the real world.

    KF

  245. This does not mean that the fold would occur spontaneously under natural conditions. Many (perhaps most) proteins do not spontaneously fold to their correct functional configuration, but require cellular machinery to correctly fold.

    I think you are wrong here. Most proteins (especially up to 100 residues or so) will spontaneously fold to a specific (crystallizable) conformation immediately as they are being synthesized in vivo and a the appropriate pH and osmotic pressure in vitro

    alan is quite correct here. Protein folding in many cases is extremely rapid requiring no other conditions outside of those that act to denature proteins, i.e., disrupt hydrogen binding. Numerous in vitro experiments underscore this known chemical phenomena.

  246. Count one, the root of the tree of life is OOL. That makes it highly relevant, and this is why OOL appears in any number of biology textbooks that address evolution.

    For the gadzillionth time. Evolutionary theory does not address the origin of life on Eaeth. Evolutionary theory is an attempt to explain life’s diversity, not its origin.

  247. Claudius:

    Relevant mutations are chance based, in the sense that there is no credible correlation between changes and onward functionality, and there are no natural forces that program the emergence of life forms by necessity. And if there were, that would be as strong a proof of design — laws of nature programmed to produce life — as you could muster. In short that is barking up the wrong tree.

    In fact the relevant molecules are highly contingent and the chaining chemistry is not connected directly to the means by which they store info or fold and function. Those are at 90 degrees. Indeed, to store info we need as much flexibility to get strings of characters as we can get. For proteins, we need to be able to get sequences that give us a vast array of possible folds and funcitons.

    And,t eh real world still highlights that the relevant fold and function patterns are exceedingly rare int he space of all possible chains. That is before we look at the problem of racemic forms as the normal pattern of formation in an extra biological context, and it is before we look at interfering cross reactions etc.

    Yes I know I know you want to stay as far from Darwin’s little pond as possible but that is exactly what grounds the problem most directly.

    Remember OOl is the ROOT of the tree of life. No root, no trunk no branches etc.

    Where also, playing pretty little parsing games with definitions of “random” are not going to do more than chase away after red herrings.

    KF

  248. franklin:

    While this is mostly true for current life as we observe it does not necessarily apply to the origin of the first replicators which were likely much simpler than life forms of today.

    Really? How likely? On what are you basing this likelihood? And how does this compare to the likelihood that these replicators exist outside the imagination? Is this statement of likelihood a scientific one? Or faith-based?

  249. kf: Absent that you are spinning just so stories and materialist origins myths with no relevance to the real world.

    there are numerous published data that support all of what Alan and I are speaking about from the chemical perspective including work on minimalist amino acid libraries and generation of functional peptides and proteins.

    Can you supply us with the details of the first replicator and how a disembodied D/designer might act on atoms and molecules to put them together to achieve the desired configurations?…lacking those levels of detail that I think your ‘just so story meme’ applies equally well to you and your position.

  250. By any reasonable standard FSCO/I is a common and measured quantity…

    Hogwash! I give you credit for coining the acronym. It is scientifically vacuous and useless. You can’t tell me how to measure the data related to any real entity on which to base a calculation of CSI or its variants.

  251. …the chaining chemistry is not connected directly to the means by which they store info or fold and function.

    Good grief! Folding follows sequence like night follows day. It’s an emergent property.

  252. Phinehas: Really? How likely? On what are you basing this likelihood? And how does this compare to the likelihood that these replicators exist outside the imagination? Is this statement of likelihood a scientific one?

    I get the impression that you are unaware of the body of data concerning RNA nucleotide generation and polymerization. Based on your understanding of the chemistry what different conditions promote, not only nucleotide formation, but polymerization of those nucleotides into RNA. All the while recalling that RNA catalytic activity can be achieved with as little as five nucleotides.

  253. AF: You can spew that talking point till you are blue in the face, it remains the case that the OOL is the root of the relevant tree. And it is the case that this is why it is addressed in any number of textbooks etc. In short there is a major question being begged at the outset, one that when properly addressed shows the breakdown of the whole system from the beginning. KF

  254. t eh real world still highlights that the relevant fold and function patterns are exceedingly rare int he space of all possible chains.

    You have no way of knowing this and what evidence there is currently suggests otherwise. Plus nobody is saying that proteins pop up de novo. RM + NS will only explore sequence space adjacent to already viable sequences.

  255. Evolutionary theory is an attempt to explain life’s diversity, not its origin.

    For some, evolutionary theory is an attempt to be intellectually fulfilled without allowing a divine foot in the door. And IF these folks, at around 7:59 EST tomorrow morning, suddenly had the ability to replace pure speculation and towering doubt with some sort of evidence pointing to the existence of self-replicating molecules or the like, I’m betting that by 8:00am EST, they wouldn’t be nearly as concerned about the boundaries of evolutionary theory.

  256. …it remains the case that the OOL is the root of the relevant tree.

    I don’t have an explanation for the origin of life on Earth; Do you?

  257. franklin:

    Let’s go with your impression. Will that help you answer my questions?

  258. Like it or not, Phinehas, evolutionary theory still doesn’t attempt to explain life’s origin. Behe should have dumped the flagellum and raised OOL at Harrisburg.

  259. AF, stop playing strawman games. The chaining chemistry is essentially independent of the sequence. The side branches that bear the active components are at in effect right angles. And that is why proteins, RNA and DNA are informational macromolecules. The sequencing needs to be explained, and the link between instructing a particular chain of codons in mRNA that is the tape for assembling a protein in the ribosome based on tRNA’s being loaded at a universal CCA coupler with the right AA, and the resulting chained protein that when folded then functions based on side chain interactions, is informationally connected. The design of a special string that will fold into a knot and function in special ways is not a trivial design problem and is not solved by the chemistry of chaining. KF

  260. 260

    KF,

    “Your image space point is excellent.”

    Thanks much. :) I think it needs some refinement, but in general it makes sense. It may be best to use a much smaller pixel and color space, such as 16-color gray and 64 pixels squared, which would still provide a gigantic image space (16384 bits) while keeping enough detail to produce distinct faces at disparate ages and facial expressions, etc., as well as distinct models of automobile, species of animal, and so on. Anything smaller risks necessary detail, and anything larger may be superfluous.

  261. AF: Still insisting on refusing to look at the logic of the roots of the tree of life I see. Rhetorically convenient, until the begged questions are highlighted. KF

  262. CR, I intend to headline it on the morrow, DV. I will add a few comments. KF

  263. AF, stop playing strawman games. The chaining chemistry is essentially independent of the sequence. The side branches that bear the active components are at in effect right angles. And that is why proteins, RNA and DNA are informational macromolecules. The sequencing needs to be explained, and the link between instructing a particular chain of codons in mRNA that is the tape for assembling a protein in the ribosome based on tRNA’s being loaded at a universal CCA coupler with the right AA, and the resulting chained protein that when folded then functions based on side chain interactions, is informationally connected. The design of a special string that will fold into a knot and function in special ways is not a trivial design problem and is not solved by the chemistry of chaining. KF

    This is sheer gobbledegook. You appear to have a total miscomprehension of basic biochemistry!

  264. phinehas: Let’s go with your impression. Will that help you answer my questions?

    Why should I bother if your lacking in knowledge of pertinent data and the literature on the subject? That is where your answers lie.

  265. AF: Cf the discussion here on on OOL and the particular importance of FSCO/I in that, with particular reference to code based self replication. Where of course your predictable next objection will be to the implication of codes: LANGUAGE. KF

  266. This is sheer gobbledegook. You appear to have a total miscomprehension of basic biochemistry!

    that seems to be a common theme here at UD.

  267. Well CLIV, if you are not arguing for a Darwinian viewpoint of randomness then what’s your point of arguing that the mutations are random to need? And if molecular machinery controlled by sophisticated software, that we have yet to understand, is driving the vast majority of changes to the genome then why in blue blazes mislead people that they are ‘random’ mutations when you have no clue what is really going on? For instance, this paper that came out yesterday uncovered another level of complexity and certainly argues for a ‘top down’ view of ‘controlled randomness’ i.e. exactly how did bottom up Darwinian randomness engineer the following?:

    Researchers study code that allows bacteria to either bet on the present or travel in time – April 22, 2013
    Excerpt: Experimental studies have revealed dozens of regulatory genes, signaling proteins and other genetic tools that cells use to gather information and communicate with one another.
    “Bacteria don’t hide their intentions from their peers in the colony,” said study co-author José Onuchic, co-director of CTBP, Rice’s Harry C. and Olga K. Wiess Professor of Physics and Astronomy and professor of chemistry and biochemistry and cell biology. “They don’t evade or lie, but rather communicate their intentions by sending chemical messages among themselves.”
    Individual bacteria weigh their decisions carefully, taking into account the stress they are facing, the situation of their peers, the statistics of how many cells are sporulating and how many are choosing competence, Onuchic said. Each bacterium in the colony communicates via chemical “tweets” and performs a sophisticated decision-making process using a specialized complex gene network comprised of many genes connected via complex circuitry. Taking a physics approach, Onuchic, Ben-Jacob and study co-authors Mingyang Lu, Daniel Schultz and Trevor Stavropoulos investigated the interplay between two components of the circuitry—a timer that determines when sporulation occurs and a two-way switch that causes the cell to choose competence over sporulation.
    “We found that the sporulation timer and the competence switch work in a coordinated fashion, but the interplay is complex because the two circuits are affected very differently by noise,” said Schultz, a postdoctoral fellow at Harvard Medical School and a former graduate student at CTBP.
    Noise results from random fluctuations in a signal; every circuit—whether genetic or electronic—responds to noise in its own way. In the case of B. subtilis, noise is undesirable in the sporulation timer but is a necessity for the proper function of the competence switch, the researchers said.
    “Our study explains how the two opposite noise requirements can be satisfied in the decision circuitry in B. subtilis,” Onuchic said. “The circuits have a special capacity for noise management that allows each individual bacterium to determine its fate by ‘playing dice with controlled odds.’”
    Ben-Jacob said the timer has an internal clock that is controlled by cell stress. The noise-intolerant timer typically keeps the competence switch closed, but when the cell is exposed to stress over a long period of time, the timer activates a decision gate that opens brief “windows of opportunity” in which the competence switch can be flipped.
    Thanks to its architecture, the gate oscillates during the window of opportunity, he said. At each oscillation, the switch opens for a short time and grants the cell a short window in which it can use noise as a “roll of the dice” to decide whether to escape into competence.
    “The ingenuity is that at each oscillation the cell also sends ‘chemical tweets’ to inform the other cells about its stress and attempt to escape,” said Ben-Jacob, the Maguy-Glass Professor in Physics of Complex Systems and professor of physics and astronomy at Tel Aviv University. “The tweets sent by others help regulate the circuits of their neighbors and guarantee that no more than a specific fraction of cells within the colony will enter into competence.”
    http://phys.org/news/2013-04-code-bacteria.html

  268. AF: it is you who are patently ignorant or willfully dismissive. You know or should know the chaining of R/DNA chains, and you should know the chaining of proteins. You should know that the biological activity rests on side branches. You should know that the sequence is basically independent of the chaining reactions. You should know that the information in D/RNA is stored in contingent sequences. You should know that protein function depends on contingent chaining, leading to deep isolation of folds in AA sequence space, etc etc. KF

  269. Franklin: the just above holds for you too. KF

  270. kf: AF: Cf the discussion here on on OOL and the particular importance of FSCO/I in that, with particular reference to code based self replication.

    self-replication requires nothing more than templating. no code analogies required.

  271. Alan Fox:

    For the gadzillionth time. Evolutionary theory does not address the origin of life on Eaeth. Evolutionary theory is an attempt to explain life’s diversity, not its origin.

    Stuff it Alan. The two are directly linked. How life started is how it evolved. If it started by design then it has evolved by design.

    Alan Fox:

    Folding follows sequence like night follows day. It’s an emergent property.

    No, that is false. There is a reason why there are chaperones- precisely because the chains do not just fold, especially the longer chains.

    Then there is a timing issue that effects the fold- as in so-called silent mutations ain’t so silent. The arrival time of the tRNA at the ribosome effects the fold.

    Then there are prions- invading proteins that alter the configuration of their “sister” chains.

    So it ain’t as Alan said.

  272. @ franklin

    It does feel like a dialogue with the deaf. Maybe we should just leave them to it. I do have some tiles to grout that I’ve been neglecting.

  273. franklin, perhaps you can straighten this guy’s basic chemistry out:

    Top Ten Most Cited Chemist in the World Knows That Evolution Doesn’t Work – James Tour, Phd. – video
    http://www.youtube.com/watch?v=WCyAOCesHv0

  274. joe: If it started by design then it has evolved by design.

    or the designer(s) realized they made a faulty product and abandoned the project and what we see is the end result of that initial broken design. No evolution by design necessary.

  275. franklin:

    self-replication requires nothing more than templating.

    Prove it. I would say you need a template and catalysts. Then a way to separate the strands.

    All the while recalling that RNA catalytic activity can be achieved with as little as five nucleotides

    It is a very limited catalyst- not a do-everything molecule. Buy a vowel and calm down.

  276. Alan Fox:

    It does feel like a dialogue with the deaf.

    Yes it does, Alan. You are incapable of understanding anything.

  277. …especially the longer chains.

    It’s true that chaperone proteins prevent mis-folding and aggregating in larger proteins and also act as heat shock proteins. They do not confer any additional information on how folding ensues.


  278. If it started by design then it has evolved by design.

    or the designer(s) realized they made a faulty product and abandoned the project and what we see is the end result of that initial broken design.

    Broken or not, it is still evoltion by design.

  279. 279

    Alan Fox,

    “You appear to have a total miscomprehension of basic biochemistry!”

    This tactic is common for you. Just announce, “You don’t know what you’re talking about!” and then leave it at that, as if the comment itself offers a correction.

    So please tell us why the sequence of aminos is not significant, or why mRNA codons don’t need to be matched with the corresponding tRNA, or why tRNA doesn’t need to be charged with the correct amino, or why the side chain interactions of residues are not relevant, etc. ;)

  280. Alan Fox:

    It’s true that chaperone proteins prevent mis-folding and aggregating in larger proteins and also act as heat shock proteins. They do not confer any additional information on how folding ensues.

    The chains wouldn’t fold without them. Genetic engineering has had only limited success, for example with insulin. Other transferred genes weren’t so lucky because the chains did not fold (Sermonti “Why is a Fly Not a Horse?”).

  281. My BAD-

    The chains wouldn’t fold without them.

    Fold properly- ie take the shape required for their function.

  282. And if you can straighten out his basic chemistry franklin here are a few more you can work on:

    Dr. Charles Garner on the problem of Chirality in nature and Origin of Life Research – audio
    http://intelligentdesign.podom.....1_16-07_00

    Origin Of Life – No Realistic Explanations – Charles Thaxton PhD. – video
    http://www.metacafe.com/watch/5222490/

    The Origin Of Life Requires Intelligence – Kirk Durston PhD – 2013 video
    http://www.metacafe.com/w/10335610

    The Origin of Life – Lecture On Probability – John Walton – Professor Of Chemistry – short video
    http://www.metacafe.com/watch/4012749

    The following is a very interesting ‘origin of first self-replicating molecule’ interview with one of the top chemists in America today:

    On The Origin Of Life And God – Henry F. Schaefer, III PhD. – video
    http://www.metacafe.com/watch/4018204

    Intelligent Design or Evolution? Stuart Pullen
    The chemical origin of life is the most vexing problem for naturalistic theories of life’s origins. Despite an intense 50 years of research, how life can arise from non-life through naturalistic processes is as much a mystery today as it was fifty years ago, if not more.
    http://www.arn.org/arnproducts.....php?id=106

    “The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!”
    (Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University)

    In fact Dean Kenyon, who was a leading Origin Of Life researcher as well as a college textbook author on the subject in the 1970s, admitted after years of extensive research:

    “We have not the slightest chance for the chemical evolutionary origin of even the simplest of cells”.

    Origin Of Life? – Probability Of Protein And The Information Of DNA – Dean Kenyon – video
    http://www.youtube.com/watch?v=9VhR2BHhxeo

    Life What A Concept! – Robert Shapiro – video
    http://www.youtube.com/watch?&v=ku9wUbbPVYg#!

    Professor Robert Shapiro~ quote from preceding video
    “I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.
    I’m always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words “To be or not to be, that is the question,” that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn’t be functional until it attained a certain length and could copy itself — appearing on the Earth.”
    Robert Shapiro was professor emeritus of chemistry at New York University. He is best known for his work on the origin of life, having written two books on the topic: Origins, a Skeptic’s Guide to the Creation of Life on Earth and Planetary Dreams.

    etc.. etc..

  283. So please tell us why the sequence of aminos[acids] is not significant

    ???

    The sequence of residues in a protein is paramount!

  284. Robert Shapiro was professor emeritus of chemistry at New York University.

    I was privileged to have some personal email correspondece with Professor Shapiro at about the time of the Dover trial. One thing he assured me of was that he was by no means a creationist. I endorse his book, “Planetary Dreams” as a good read.

  285. *signs off*

  286. joe; Prove it. I would say you need a template and catalysts. Then a way to separate the strands.

    well of course you need the template but not any catalyst. As far as separating strands a thermal gradient would work nicely.

    joe: It is a very limited catalyst- not a do-everything molecule.

    Where did I say it was a do-everything molecule? These discussions would proceed much better if you refrained from making stuff up and trying to attribute your fabrication to me or anyone else. As for limited activity much like Lenski’s bacteria weak function can (and has) led to greater function via evolutionary processes.

  287. 287

    Alan @283, you were referring to gobbledegook at #259. Care to elucidate? And thanks for the pedantry, my comment was totally indecipherable without your correction.

    The sequence of residues in a protein is paramount!

    Of course it is, as is the mapping between mRNA codons and their corresponding tRNA anticodons, as is the charging of tRNA by aaRS.

    *signs off*

    C’mon Alan, one more drink before bedtime — it can only make you funnier. :P

  288. chance: why mRNA codons don’t need to be matched with the corresponding tRNA

    what process do you think is involved in tRNA binding and why one binds and not another? do you think there are little hands in there sorting through the soup of all tRNAs to find the correct one? or is it more likely it has to do with binding kinetics…perhaps even something along the lines of the kinetics of competitive binding.

  289. 289

    franklin, feel free to straighten me out. You seem to know quite a bit about biochemistry. How does the ribosome perform the matching? Is there a chemical necessity at work that doesn’t require a complex arrangement of proteins and RNA in the ribosome? I’m not being facetious, I’m interested. How does aaRS match an anticodon with an amino acid? What’s the necessity relationship there?

  290. Alan Fox:

    The sequence of residues in a protein is paramount!

    But not sufficient- meaning it takes more than just the sequence to get the proper spatial configuration.

  291. 291

    Footnote to #289,

    Open questions, some restatement, etc.

    Is the mapping between codon and anticodon in the ribosome by direct necessity, or does it require a contingent and complex arrangement internally? Moreover, could the mapping be changed by a configurational change in the ribosome?

    The same question would apply with aaRS (aminoacyl tRNA synthetase). Is the mapping contingent? Could a different charging outcome be produced by reconfiguring key parts of the aaRS?

    It’s the contingency — the potential arbitrary mapping — that’s of interest here. I don’t imagine invisible hands, but complex arrangements of matter for a purpose, supposing that different arrangements would produce different results, similar to any machine or computational environment.

  292. Mr Fox you state:

    I was privileged to have some personal email correspondece with Professor Shapiro at about the time of the Dover trial. One thing he assured me of was that he was by no means a creationist.

    And yet after the trial, and after his book, in the video shortly before he passed away, he stated:

    “I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.

    Go figure, nature didn’t do it, and he is not a creationist,,, is there a third option? Perhaps Dawkins aliens?? :)

  293. CLIV, perhaps you would be interested in this video I found a while back:

    Learning from Bacteria about Social Networking (Information Processing) – video
    Excerpt: I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers.
    http://www.youtube.com/watch?v=yJpi8SnFXHs

  294. Franklin, I suggest you learn about self replication based on coded stored information, joining a self replication facility to a metabolic automaton. The notion that there is some magical self-replicating molecule out there that does it all has no serious empirical foundation. The last one tried here at UD, the Polymerase chain rxn, simply revealed the need for the enzyme as is implied by the name. Oops. KF

  295. Joe, not only do you have chaperoned folding, but prions that fold to more stable, propagating states that — due to non-function — create destructive diseases. Indeed there has been suspicion this is part of the Alzheimer’s story. KF

  296. Franklin: How blatant is it when we see a refusal to acknowledge that a code is a code. Object code FYI is code. KF

  297. chance: How does the ribosome perform the matching?

    On a serious not if you don’t understand how this works or at least have a basic grasp of chemistry there is no way you can evaluate much in this debate.

    chance, it’s chemistry all the way down. All tRNAs can bind, and likely do, but they don’t all bind with equal affinity in the presence of any given codon. the weaker binding tRNA is easily displaced by one with greater kinetic affinity to form the complex that ultimately results in a conformational change with the end result of the amino acid being incorporated into the growing chain. It is this chemical process (binding affinity) that ‘selects’ the correct tRNA for any given codon.

    Have you ever wondered or explored how hemoglobin works? How (and why) it unloads carbon dioxide at the lungs/gills and binds oxygen at the lung/gills. or how hemoglobin ‘knows’ to deliver oxygen and pick up protons and carbon dioxide at metabolically active tissue? It is all chemistry which, in the case of hemoglobin, results in conformational changes (via chemistry through both active site and allosteric binding of substrates) which trigger a change in binding affinities for the various substrates.

  298. “I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.

    ba77 I don’t think the quoted sentence means what you think it means. Try reading it again with care this time.

  299. 299

    franklin, it’s not just chemistry all the way down, it’s chemistry and contingency. This is apparent in the myriad valid sequence arrangements of DNA codons. I’m asking if the mapping of codon to anticodon is contingent upon the configuration of the ribosome. I’m asking if charging tRNA is contingent upon the configuration of aaRS. I’m asking if it’s possible to change the mapping with another contingent arrangement of some internal parts. If you don’t know the answer, just say so; don’t try to make my lack of expertise the basis for your not going into details. If you have details, produce them. If you don’t, I won’t hold it against you, or make claims that you shouldn’t be discussing such things.

    Grandfather clocks are physics all the way down, until you try to get at the relationship between pendulum oscillations and hand movements. Then it’s not just physics, but contingent arrangements of highly specific parts designed for a purpose to convert mechanical energy into a timekeeping apparatus.

  300. current data suggest that the primary role for chaperone proteins is not solely to assist protein folding but to prevent protein aggregation prior to protein folding. This mechanism is also the reason partially denatured proteins (e.g., heat shock) are associated with upregulation of HSP but associated complexes of the chaperone:damaged protein. Many diseases are not so much associated with misfolded proteins (although they do occur) but as a result of protein aggregates.

  301. chance: franklin, it’s not just chemistry all the way down, it’s chemistry and contingency

    No, it is not. Your lack if expertise is showing.

  302. Folks:

    We are now down to chemistry issues. And there is need to understand that the chaining and the information are at what for simplicity I have called right angles.

    Let’s do the simpler one, proteins.

    By and large, in life forms, amino acids are grouped around a key C -atom, which (as in organic chemistry generally) has four bonds. One to a carboxylic acid, COOH. One to an amine, NH2. One to H, and one to a side group, which we can represent as R.

    Formula: H2N – CHR – COOH

    The chaining is effectively generic, as COOH and NH2 from two Aa’s react, eliminating H2O. Any of the 20 main AAs of life (there are a lot of others) can chain to any of the others.

    This is part of the high contingency.

    The key to interesting behaviour is the R groups. From this we get folding patterns as AA’s chain and may be chaperoned. The chaining is based on codons from DNA via RNA. It is not driven by the chaining chemistry that would force AA A to be followed by B then C etc. No information carrying capacity, and no flexibility as a class of biopolymers based on particular sequence.

    D and RNA are based on chaining in a similar string: -*-*-*- . . .

    Here, the key thing is a PO4 group and a sugar, ad this allows the chain to form. Again the chain and the side groups are “at right angles.” (And no this is not intended to say anything about actual 3-D geometry, it is for simplification.)

    What happens in effect is that the sequence can store coded information at 4 states per position. Up to 2 bits.

    Which is where we get 64 3-letter codons, which code for start, elongate with particular AA’s, and stop. In the ribosome, that allows the production of proteins based on converting 64 codes to start/stop and add particular AA’s, about 20.

    All of this is well known, and it its known that the chaining is such that GCAT/U can follow in the string in any succession.

    The actual elongation happens through tRNA’s,and it is the case that such have a coupler end that through CCA at the 3′ end, is a “universal” connector to the AAs.

    So it is inherently possible to reprogram, using up codes for different purposes, indeed that has been done with some of the stop codons. Specialised enzymes load the tRNA’s, based on general configuration, but the coupler is standard.

    What is happening above is that the chemistry is being highlighted in a way that distracts from the associated places where contingency is significant. Contingency is critical to information bearing character.

    Hence the summary: string structures, where the chaining chemistry is at effective “right angles” to the informational part that leads to function.

    KF

  303. 303

    There’s no contingency in sequence arrangements in DNA? I think that’s your bias showing.

    Just to note, it seems more clear that codon to anticodon matching has more to do with necessity than contingency. This appears to make sense after browsing some articles and rereading frankin’s comment at #297.

    Thanks for your congeniality. ;)

  304. F/N: see what I mean about how important it is to understand that the chaining and the side branches are “at right angles”? Here we have someone posing as knowledgeable, “correcting” those who correctly point to the significance of the distinction between the chaining and the contingency of what succeeds what in the chains, and then using this to suggest that the informational character of D/RNA is not real, and thus also of proteins. Yes, chemistry is used in the process, but the chemistry is used in ways that are similar to how magnetic domains are used to store information in a magnetic tape, or how the prongs along a Yale lock key’s spine store info on how high or low, in what combination. KF

  305. Actually franklin since he was talking about DNA and RNA, it is you who is misreading.

    OOL (Origin Of Life) on the Rocks:
    Excerpt: An important survey of the origin-of-life (OOL) field has been published in Scientific American. Robert Shapiro, a senior prize-winning chemist, cancer researcher, emeritus professor and author of books in the field, debunks the Miller experiment, the RNA World and other popular experiments as unrealistic dead ends. Describing the wishful thinking of some researchers, he said, “In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry.”
    Shapiro had been explaining that millions of organic molecules can form that are not RNA nucleotides. These are not only useless to life, they get in the way and clog up the beneficial reactions. He went on to describe how extrapolation from the Miller Experiment produced an unearned sense of euphoria among researchers: “By extrapolation of these results, some writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case,” he warned in a section entitled, “The Soup Kettle Is Empty.” He said that no experiment has produced amino acids with more than three carbons (life uses some with six), and no Miller-type experiment has ever produced nucleotides or nucleosides, essential for DNA and RNA.
    Shapiro described in some detail the difficult steps that organic chemists employ to synthesize the building blocks of RNA, using conditions highly unrealistic on the primitive earth. “The point was the demonstration that humans could produce, however inefficiently, substances found in nature,” he said. “Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA.” Here, for instance, is how scientists had to work to create cytosine, one of the DNA bases:

    I will cite one example of prebiotic synthesis, published in 1995 by Nature and featured in the New York Times. The RNA base cytosine was prepared in high yield by heating two purified chemicals in a sealed glass tube at 100 degrees Celsius for about a day. One of the reagents, cyanoacetaldehyde, is a reactive substance capable of combining with a number of common chemicals that may have been present on the early Earth. These competitors were excluded. An extremely high concentration was needed to coax the other participant, urea, to react at a sufficient rate for the reaction to succeed. The product, cytosine, can self-destruct by simple reaction with water. When the urea concentration was lowered, or the reaction allowed to continue too long, any cytosine that was produced was subsequently destroyed. This destructive reaction had been discovered in my laboratory, as part of my continuing research on environmental damage to DNA. Our own cells deal with it by maintaining a suite of enzymes that specialize in DNA repair.

    There seems to be a stark difference between the Real World and the imaginary RNA World. Despite this disconnect, Shapiro describes some of the hype the RNA World scenario generated when Gilbert first suggested it in 1986. “The hypothesis that life began with RNA was presented as a likely reality, rather than a speculation, in journals, textbooks and the media,” he said. He also described the intellectual hoops researchers have envisioned to get the scenario to work: freezing oceans, drying lagoons, dry deserts and other unlikely environments in specific sequences to keep the molecules from destroying themselves. This amounts to attributing wish-fulfillment and goal-directed behavior to inanimate objects, as Shapiro makes clear with this colorful analogy:

    The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

    Realistically, unfavorable molecules are just as likely to form. These would act like terminators for any hopeful molecules, he says. Shapiro uses another analogy. He pictures a gorilla pounding on a huge keyboard containing not only the English alphabet, but every letter of every language and all the symbol sets in a typical computer. “The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne.” That’s why Gerald Joyce, Mr. RNA-World himself, and Leslie Orgel, a veteran OOL researcher with Stanley Miller, concluded that the spontaneous appearance of chains of RNA on the early earth “would have been a near miracle.”
    Boy, and all this bad news is only halfway through the article. Does he have any good news? Not yet; we must first agree with a ground rule stated by Nobel laureate Christian de Duve, who called for “a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry.” That rules out starting with complex molecules like DNA, RNA, and proteins (see online book).
    http://www.creationsafaris.com.....#20070215a

    But Shapiro did go on the propose a miracle laden metabolism first scenario:

    From that principle, Shapiro advocated a return to scenarios with environmental cycles involving simple molecules. These thermodynamic or “metabolism first” scenarios are only popular among about a third of OOL researchers at this time. Notable subscribers include Harold Morowitz, Gunter Wachtershauser, Christian de Duve, Freeman Dyson and Shapiro himself. Their hypotheses, too, have certain requirements that must be met: an energy source, boundaries, ways to couple the energy to the organization, and a chemical network or cycle able to grow and reproduce. (The problems of genetics and heredity are shuffled into the future in these theories.) How are they doing? “Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them,” Shapiro admits. “In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle.” In addition, “An understanding of the initial steps leading to life would not reveal the specific events that led to the familiar DNA-RNA-protein-based organisms of today.” Nor would plausible prebiotic cycles prove that’s what happened on the early earth. Success in the metabolism-first experiments would only contribute to hope that prebiotic cycles are plausible in principle, not that they actually happened.
    Nevertheless, Shapiro himself needed to return to the miracles he earlier rejected. “Some chance event or circumstance may have led to the connection of nucleotides to form RNA,” he speculates. Where did the nucleotides come from? Didn’t he say their formation was impossibly unlikely? How did they escape rapid destruction by water? Those concerns aside, maybe nucleotides initially served some other purpose and got co-opted, by chance, in the developing network of life. Showing that such thoughts represent little more than a pipe dream, though, he admits: “Many further steps in evolution would be needed to ‘invent’ the elaborate mechanisms for replication and specific protein synthesis that we observe in life today.”
    Time for Shapiro’s grand finale. For an article predominantly discouraging and critical, his final paragraph is surprisingly upbeat. Recounting that the highly-implausible big-molecule scenarios imply a lonely universe, he offers hope with the small-molecule alternative. Quoting Stuart Kauffman, “If this is all true, life is vastly more probable than we have supposed. Not only are we at home in the universe, but we are far more likely to share it with unknown companions.”
    Update Letters to the editor appeared in Science1 the next day, debating the two leading theories of OOL. The signers included most of the big names: Stanley Miller, Jeffrey Bada, Robert Hazen and others debating Gunter Wachtershauser and Claudia Huber. After sifting through the technical jargon, the reader is left with the strong impression that both camps have essentially falsified each other. On the primordial soup side, the signers picked apart details in a paper by the metabolism-first side. Concentrations of reagants and conditions specified were called “implausible” and “exceedingly improbable.”
    Wachtershauser and Huber countered that the “prebiotic soup theory” requires a “protracted, mechanistically obscure self-organization in a cold, primitive ocean,” which they claim is more improbable than the volcanic environment of their own “pioneer organism” theory (metabolism-first). It’s foolish to expect prebiotic soup products to survive in the ocean, of all places, “wherein after some thousand or million years, and under all manner of diverse influences, the magic of self-organization is believed to have somehow generated an unspecified first form of life.” That’s some nasty jabbing between the two leading camps. 1Letters, “Debating Evidence for the Origin of Life on Earth,” Science, 16 February 2007: Vol. 315. no. 5814, pp. 937 – 939, DOI: 10.1126/science.315.5814.937c.

    Thank you, Robert Shapiro, for unmasking the lies we have been told for nearly a century. The Miller Experiment, the RNA World, and all the hype of countless papers, articles, popular press pieces and TV animations are impossible myths. We appreciate your help revealing why it’s all been hyped bunk. Now finish the job and show that yours is no better.
    You know you cannot stay with small molecules forever. You have not begun to bridge the canyon between metabolic cycles with small molecules to implausible genetic networks with large molecules (RNA, DNA and proteins). Any way you try to close the gap, you are going to run into the very same criticisms you raised against the RNA-World storytellers. You cannot invoke natural selection without accurate replication (see online book).

  306. 306

    KF @304, yes, we get that often here — the suggestion that chemistry is sufficient for biology. That’s simply not demonstrable. Physics isn’t sufficient for mechanical clocks, and silicon and electricity are not sufficient for computation. Each requires a highly contingent component, but this simple fact is not readily admitted even though apparent. We’re supposed to assume that everything we observe is an emergent property of matter, but the complex and contingent nature of biology, mechanical apparati, and electronics forcefully suggests otherwise.

  307. As to how far OoL researchers have actually gotten, I think the following is about the best:

    Yarus has been a strong proponent of the “RNA World” hypothesis. The team’s findings argue that RNA enzymes (ribozymes) did not have to be as complex at first to have a function. He said, “If there exists that kind of mini-catalyst, a ‘sister’ to the one we describe, the world of the replicators would also jump a long step closer and we could really feel we were closing in on the first things on Earth that could undergo Darwinian evolution.” He refers to the fact that Darwinian evolution by natural selection cannot be invoked till there is a replicator – a system able to duplicate its parts accurately. Yarus admitted, “the tiny replicator has not been found, and that its existence will be decided by experiments not yet done, perhaps not yet imagined.”
    But does this work support a naturalistic origin of life? A key question is whether the molecule would form under plausible prebiotic conditions. Here’s how the paper described their work in the lab to get this molecule:

    RNA was synthesized by Dharmacon. GUGGC = 5’-GUGGC-30 ; GCCU – 5’P-GCCU-3’ ; 5’OH-GCCU = 5’-GCCU-3’ ; GCCU20dU = 5’-GCC-2’-dU; GCC = 5’-GCC-3’ ; dGdCdCrU = 5’-dGdCdCU-3’ . RNA GCC3’dU was prepared by first synthesizing 5’-O-(4,4’- Dimethoxytrityl)3’-deoxyuridine as follows: 3’-deoxyuridine (MP Biomedicals; 991 mg, 0.434 mmol) was dissolved in 5 mL anhydrous pyridine and pyridine was then removed under vacuum while stirring. Solid was then redissolved in 2 mL pyridine. Dimethoxytrityl chloride (170 mg, 0.499 mmol) was dissolved in 12 mL pyridine and slowly added to 3’-deoxyuridine solution. Solution was stirred at room temperature for 4 h. All solutions were sequestered from exposure to air throughout.
    Reaction was then quenched by addition of 5 mL methanol, and solvent was removed by rotary evaporation. Remaining solvent evaporated overnight in a vacuum chamber. Product was then dissolved in 1 mL acetonitrile and purified through a silica column (acetonitrile elution). Final product fractions (confirmed through TLC, 1.1 hexane:acetonitrile) were pooled and rotary evaporated. Yield was 71%. Dimethoxytrityl-protected 30dU was then sent to Dharmacon for immobilization of 30-dU on glass and synthesis of 5’-GCC-3’-dU.
    PheAMP, PheUMP, and MetAMP were synthesized by the method of Berg (25) with modifications and purification as described in ref. 6. Yield was as follows: PheAMP 85%, PheUMP 67%, and MetAMP 36%.

    Even more purification and isolation steps under controlled conditions, using multiple solvents at various temperatures, were needed to prevent cross-reactions. It is doubtful such complex lab procedures have analogues in nature.
    http://www.creationsafaris.com.....#20100302a

    color me unimpressed!

  308. kf, your use of contingency amounts to little more than stating that the correct chemical structure/environment needs to be present or a specific reaction will not occur. Nowhere have you replaced the basic chemical nature of all of these processes by using the word ‘contingency or contingent’. If I pressed you for details this much would become immediately obvious to anyone.

  309. chance, in your clock example where does the physics stop? Certainly not with the counterweights and pendulum and not the gearing…these are all firmly set in physics. So my question to you is what, specifically, is the non-physics portion of the clock?

  310. franklin did you know that there is a ‘non-chemical’ component to DNA?

    Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009
    Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
    http://www.dailygalaxy.com/my_.....ave-t.html

    The re4ason why it is doing this ‘chemically impossible’ action is because of quantum entanglement:

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Quantum Information/Entanglement In DNA – Elisabeth Rieper – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement between the electron clouds of nucleic acids in DNA – Elisabeth Rieper, Janet Anders and Vlatko Vedral – February 2011
    http://arxiv.org/PS_cache/arxi.....4053v2.pdf

    finding Quantum entanglement in DNA on a massive scale is no small matter:

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

    The falsification for local realism (materialism) 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

    Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012)
    Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed.
    Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can’t stay hidden, or they must have infinite speed.,,,
    The remaining option is to accept that (quantum) influences must be infinitely fast,,,
    “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,,
    http://www.sciencedaily.com/re.....142217.htm

  311. No one is claiming either the physics or the chemistry stops, only that they are not sufficient as explanations.

    As to:

    Why should I bother if your lacking in knowledge of pertinent data and the literature on the subject?

    No particular reason, other than that some might wonder why, after having made a bald assertion about the probability of something, and after having had your bluff called, you chose to fold. That’s not what someone usually does when they are confident about their hand.

  312. 312

    franklin,

    “chance, in your clock example where does the physics stop? Certainly not with the counterweights and pendulum and not the gearing…these are all firmly set in physics. So my question to you is what, specifically, is the non-physics portion of the clock?”

    The non-physics portion is the contingent arrangement of specifically shaped, interacting parts — gears, pullies, weights — to translate mechanical motion into a symbolic system of timekeeping. This aspect of the clock cannot be accounted for by physics. Clocks are not emergent properties of matter. They require something which physics cannot provide.

    Physics is necessary, not sufficient, for mechanical clocks.

  313. kairosfocus @ 247

    What a pleasure to be in agreement with you on this occasion.

    Yes, mutations are chance based in the sense that there is no credible correlation between changes and onward functionality. This is what I’ve been pointing out all along to those on this thread who continue to befog the issue with the conflationary blanket claim “mutations are not random”.

  314. phinehas:No particular reason, other than that some might wonder why, after having made a bald assertion about the probability of something, and after having had your bluff called, you chose to fold.

    Here is the statement I made:
    While this is mostly true for current life as we observe it does not necessarily apply to the origin of the first replicators which were likely much simpler than life forms of today.

    hardly a bald assertion or probability. speculation for sure as is all of ID…after all an inference to design is nothing more than a speculation. Also a caution given the rising complexity we see in the fossil record (for whatever reason) certainly supports the development of the more complex from the simpler. So, hopefully, now you can see why it is hard for me to take you seriously given your misrepresentations of our communications.

  315. chance: Physics is necessary, not sufficient, for mechanical clocks.

    so it all boils down to you need a human (err intelligent agent) to build the clock. It seems we agree that all the workings of the clock are entirely based on physics.

    Who made the claim that clocks are and emergent property of matter?

  316. bornagain @ 267

    Well CLIV, if you are not arguing for a Darwinian viewpoint of randomness then what’s your point of arguing that the mutations are random to need?

    I notice you didn’t answer the question – here it is again:

    Do you agree that empirical evidence gives good reason to believe that (with rare exceptions) mutations are not correlated with usefulness to the organism in its environment?

    The point of arguing this has got nothing to do with “Darwinism” aka atheistic materialism.

    The point is to bring clarity and enlightenment about what modern biological science has discovered based on empirical evidence about the nature of mutations, and to counterract obfuscatory rhetoric that deceptively confuses the two senses of “random” with respect to how mutations work, and thus advance the discussion and, hopefully, the understanding of participants and onlookers.

    What’s your point in continuing to argue that mutations are non-random with respect to a uniform probability — something that everyone agrees with, and which is completely irrelevant to my point that the empirical evidence shows mutations are random with respect to usefulness to the organism?

  317. 317

    franklin,

    so it all boils down to you need a human (err intelligent agent) to build the clock. It seems we agree that all the workings of the clock are entirely based on physics.

    It all boils down to physics being insufficient as a cause for an entire category of contingent arrangements of matter, such as mechanical systems. Informational systems qualify here too, software and programmable microprocessors, vehicles, manufacturing processes, and so on. There are an entire category of physical objects which cannot be explained by appeals to physical necessity. They have certain properties, among them contingency.

    You asked where the physics stops. I obliged.

    Who made the claim that clocks are and emergent property of matter?

    It’s implied in your question: “So my question to you is what, specifically, is the non-physics portion of the clock?”

    The non-physics portion of the clock is its construction — the origin of a system which requires, but is not brought about by, physical necessity.

  318. CLAV, I disagree that the empirical evidence gives warrant for the blanket statement that you hold. I believe the organism is always, via sophisticated programming, making minute adjustments to maintain its extreme disequilibrium with the environment. The two references I’ve already cited for you give a tip of the iceberg view of this sophisticated programming and a glimpse of the constant minute adjustments being made with the cell. Underestimating the sophistication of what is going on within the cell has always been the number 1 mistake of people when they approach the cell (especially Darwinist)

  319. chance, from my perspective it is a ridiculous point. Humans building things (things that don’t replicate with variation) isn’t really an Earth shattering or ‘aha’ moment for me but perhaps it is to you.

    If that was the whole point of your exercise I have only myself to blame for wasting my time.

  320. Alan Fox:

    I think you are wrong here. Most proteins (especially up to 100 residues or so) will spontaneously fold to a specific (crystallizable) conformation immediately as they are being synthesized in vivo and a the appropriate pH and osmotic pressure in vitro.

    I’m not sure that is true. We are talking about whether an amino acid chain of reasonable length in an OOL context would fold to a stable functional state.

    It is of course true that when moderated by cellular machinery (even in the most basic case where the moderation simply consists of a residue-by-residue construction sequence, which by its very nature exponentially constrains the possible folds) most proteins will fold properly. However, we do know that many proteins require more significant moderation. More to the point, without any cellular machinery in place (the amino acids coming together in a primordial soup example) the likelihood of a stable and functional spontaneous fold is proportionally decreased.

  321. eric: I’m not sure that is true. We are talking about whether an amino acid chain of reasonable length in an OOL context would fold to a stable functional state.

    Outside of it being absolutely true why do you think it is not true?

    The major problem with proteins folding in vivo is the high concentration of proteins in the cellular environment which tend to aggregation given the opportunity. Outside of the cell, in vitro low concentration of proteins, protein folding is rapid and even after you denature the protein once the denaturing agent is removed, e.g., via dialysis, the protein will immediately (microseconds) folds into its native state. There is a lot of published work on this aspect of proteins.

    Eric, have you given any thought to what the minimal amino acid library requirements would be to obtain functional proteins?

  322. franklin @242:

    I will simply note that in response to all the concrete things I listed that we do know about what is required for the simplest forms of life that exist, you have simply responded with vague speculations about theoretical, hypothetical and unconfirmed possibilities about simpler forms of life that might have existed.

    Furthermore, your speculations don’t contain any engineering level information for why we should think first life was so incredibly simple, just a “well, it could have been a lot simpler” approach.

    People more experienced than you and me have looked at this issue for years. The theoretical lower limit for any kind of self-reproducing life form is many dozens, if not hundreds, of distinct (and carefully specified) proteins.

  323. Alan @246:

    For the gadzillionth time. Evolutionary theory does not address the origin of life on Eaeth. Evolutionary theory is an attempt to explain life’s diversity, not its origin.

    So I take it you would be willing to seriously consider the possibility that first life on Earth was purposely designed? If so, what kinds of criteria would you employ to determine whether it was designed or not?

  324. eric: we do know about what is required for the simplest forms of life that exist

    OK, what is the simplest possible life form?

    And I hope you wouldn’t try to provide any ‘ vague speculations about theoretical, hypothetical and unconfirmed possibilities about the simplest forms of life’ since I assume from your 322 that you have something concrete that we can work with.

    One of the major problems I see you facing is that the life you describe (dozens and possibly hundreds of proteins, require sufficient oxygen for the production of said proteins. All evidence points to life forming prior to a oxygen rich environment. How do you get around that problem?

  325. 325

    franklin @319,

    “chance, from my perspective it is a ridiculous point. Humans building things (things that don’t replicate with variation) isn’t really an Earth shattering or ‘aha’ moment for me but perhaps it is to you.

    If that was the whole point of your exercise I have only myself to blame for wasting my time.”

    Your attitude all along suggests that you thought you were wasting your time.

    If you agree that a category of physical reality exists which is not amenable to explanations by physical processes, then this is indeed progress, at least in my estimation. You should just extend it to OOL. Since DNA nucleotide arrangements are contingent, and the proteins they code for (among other things) are complex and specific, they require an explanation that does not have its root in physical necessity.

    But believe me, I’m not holding out hope that you’ll confess that biology is not explainable in terms of physics and chemistry. However the point needed to be made. When we observe certain arrangements of matter, specific and contingent arrangements, we infer design because we can detect purposeful configurations that serve a purpose or perform a task which cannot be explained by pure physicality. It’s not like ID proponents just produce the notion out of thin air — biological systems look designed, and they look designed because they share properties in common with things we know to be designed: manufacturing systems, information storage and processing, code translation. quality control, materials synthesis, signalling systems, and all other manner of teleological phenomena. Not too many people take the position these things don’t look designed, not even somebody like Dawkins; rather they claim that one needn’t invoke design because there is a well-understood physical process which accounts for its illusory nature.

    But neither one of us is expecting to convince the other, are we? At least, I don’t have an expectation that you’ll “come around”. Rather, I comment to test ideas, improve my knowledge, sharpen my arguments, and even more so, for the benefit of those looking on who may be trying to decide if the apparent design in nature is real or illusory. I suspect you have your own motives that don’t involve my edification. I just happen to think that when the concept of design is compared to the notion of chemical necessity being responsible for living systems, that it becomes clear pretty quickly that spontaneous emergence of life from non-living matter doesn’t hold up.

  326. Chance @289:

    The more basic question is why there is need for a ribosome in the first place?

    The fact is that the process must be controlled and moderated. We keep getting told that it “just happens” by chemistry. That is the lazy, engineering-naive person talking.

    The “it’s chemistry all the way down” kind of talk with respect to cellular mechanics is eerily similar to the naive “necessity” folks who think that life just comes about automatically due to chemical necessity. Different level of organization; same kind of thinking.

  327. If you agree that a category of physical reality exists which is not amenable to explanations by physical processes, then this is indeed progress, at least in my estimation. You should just extend it to OOL

    On what basis would I justify that? the components of your clock have no mass and charge (granted the matter that makes up the parts does but the gears and pendulum don’t) so why would I ever think that the parts would/could ‘get together’. This isn’t the case with atoms and molecules and it is comparing apples to spiderwebs to try and do so.

    your only calibrator for designed objects are what humans produce (at least for the highest levels of technology). You are speculating far beyond your standard curve which is fraught with error.

  328. franklin seems to think that just because some things can stick together (with their charge) it becomes possible for marvelous functional specified structures to emerge through purely natural causes. This is nonsense.

    There are other kinds of molecules that stick together, such as resins, magnetically attracted particles, adhesives, and so forth, and we never see any of them coming together to form functional complex specified structures.*

    Gotta hand it to him though. This whole red herring down the rabbit hole of particles having “charge” was a distraction from the real issues that I hadn’t come across before. Amazing what folks will come up with to try to explain away the appearance of design.

    —–

    * Ironically, this sticking together of atomic and molecular particles cuts both ways. One of the big open problems in OOL research is the problem of interfering cross reactions.

  329. eric, your chemistry-naivity is showing for all to see!

    that you think the bonds formed between atoms and molecules are analogous to glue and other adhesives is quite telling. Did you ever take a chemistry course of any sort?

    Take a look at the chemistry found in the eutectic phase of water and the functional structures that have been generated as an example of what non-enzymatic chemistry can produce.

    Are you familiar at all with the Periodic Table and why it is organized the way it is?

    You are correct in that it is only an ‘appearance of design’ that is the issue and if you want to coherently discuss biology, evolution, and even the origin of life issues a lack of a background/understanding of chemistry is going to be large impediment to any progression of knowledge.

  330. 330

    franklin @327

    “the components of your clock have no mass and charge (granted the matter that makes up the parts does but the gears and pendulum don’t) so why would I ever think that the parts would/could ‘get together’. This isn’t the case with atoms and molecules and it is comparing apples to spiderwebs to try and do so.”

    So you have necessity acting at the level of atoms and molecules. How does that necessity produce complex and contingent arrangements of matter — specific and complex components which must all be present and function together for a purpose? How does necessity account for DNA replication and error correction, which require discrete arrangements of interdependent material parts, each specified and complex? How does it account for signalling systems, transport systems, motors of multiple types, materials synthesis pathways, and so on and so forth?

    I’m not asking how you account for their operation, I’m asking how to explain their existence. It won’t do to simply point out that atoms and molecules stick together. There are multiple interdependent nanotech subsystems in living cells which, like the internal parts of any machine are contingent, and together are irreducibly complex. Its numerous instances of nanotechnology that your idea of chemical necessity needs to explain. You need to tell us why biochemistry looks and functions like advanced technology.

  331. 331

    Eric @328, It would seem that a chemistry class is all that stands between any man and OOL mastery. I hear that chemists pretty much have the problems sorted out. ;)

    “Ironically, this sticking together of atomic and molecular particles cuts both ways. One of the big open problems in OOL research is the problem of interfering cross reactions.”

    Here’s a quote from an article at EnV about RNA world, which makes reference to a paper by Gerald Joyce:

    But other problems quickly mount. There’s no natural selection without self-replication, and copies must be accurate enough to avoid error catastrophe. In addition, harmful cross-reactions tend to gunk up the works. (These problems were all described 28 years ago in the early ID book by Thaxton, Bradley and Olsen, The Mystery of Life’s Origin.) Joyce writes:

    In the laboratory one can prepare milligram quantities of random-sequence RNA molecules containing 40 or more subunits. One can provide an endless supply of activated nucleotide building blocks and control all aspects of the reaction conditions. Stacking the deck in this way, why haven’t we witnessed the origin of RNA life experimentally? Because even a lucky milligram of RNA is insufficient. In order for a seed copy of replicating RNA to germinate, it must produce additional copies of itself faster than the existing copies become degraded, and it must operate with sufficient fidelity that the accurate copies are not overwhelmed by error copies. The requisite rate and fidelity of replication might reasonably be achieved in a pure reaction system that contains only the replicator and its corresponding building blocks. However, in a complex mixture of almost entirely mismatched parts, what process singles out the rare matching components? Darwinian evolution can enrich one molecule in a milligram, but before the onset of Darwinian evolution there would be only chemistry, and the chemistry of complex mixtures of cross-interacting molecules is very messy.

    When You Wish Upon a Star

    Perhaps there’s a good reason why DNA replication is ubiquitous in all known self-replicating life. It appears to be necessary.

  332. To revisit CLAV’s assertion:

    (with rare exceptions) mutations are not correlated with usefulness to the organism in its environment

    whereas to the contrary I hold:

    the cell is always monitoring the environment and, via sophisticated programming and molecular machinery, is always making minute adjustments within the cell to maintain its extreme thermodynamic disequilibrium with the environment.

    Here are a few references to back up my position:

    Demonic device converts information to energy – 2010
    Excerpt: “This is a beautiful experimental demonstration that information has a thermodynamic content,” says Christopher Jarzynski, a statistical chemist at the University of Maryland in College Park. In 1997, Jarzynski formulated an equation to define the amount of energy that could theoretically be converted from a unit of information2; the work by Sano and his team has now confirmed this equation. “This tells us something new about how the laws of thermodynamics work on the microscopic scale,” says Jarzynski.
    http://www.scientificamerican......rts-inform

    For calculations of the information content of a cell, from the thermodynamic perspective, please see the following site:

    Moleular Biophysics – Information theory. Relation between information and entropy: – Setlow-Pollard, Ed. Addison Wesley
    Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz’ deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures.
    http://www.astroscu.unam.mx/~a.....ecular.htm

    Moreover,,

    “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong

    Moreover to maintain this extreme thermodynamic disequilibrium we find that,,,

    Life Leads the Way to Invention – Feb. 2010
    Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale.
    http://creationsafaris.com/cre.....#20100226a

    and,,

    Making the Case for Intelligent Design More Robust – April 2010 – Dr. Fazale Rana
    Excerpt: The sum total of metabolic processes represents a complex, reticulated web of chemical reactions, each one catalyzed by an enzyme. Poor biochemistry students are expected to know each chemical transformation (and the enzymes that catalyzes them) for each pathway in the cell—not to mention how the various pathways interconnect! ,,,

    Map Of Major Metabolic Pathways In A Cell – Diagram
    http://www.sigmaaldrich.com/im.....17_04_.pdf

    ,,,Given the dynamic environment of the cell, fluctuations in the levels of metabolites are bound to happen. When these unintended variations occur, they will travel throughout the networks. Some processes in the cell are sensitive to metabolite concentrations and will be negatively affected as a result. To combat these affects, metabolic systems have regulatory systems in place (based on engineering principles) that dampen concentration bounces, keeping them within tight bounds. In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites.
    http://www.reasons.org/article.....ore-robust

    ExPASy – Biochemical Pathways – interactive schematic
    http://web.expasy.org/cgi-bin/.....mbnails.pl

    As well,

    Learning from Bacteria about Social Networking (Information Processing) – video
    Excerpt: I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers.
    http://www.youtube.com/watch?v=yJpi8SnFXHs

    Researchers study code that allows bacteria to either bet on the present or travel in time – April 22, 2013
    Excerpt: Experimental studies have revealed dozens of regulatory genes, signaling proteins and other genetic tools that cells use to gather information and communicate with one another.,,,
    Each bacterium in the colony communicates via chemical “tweets” and performs a sophisticated decision-making process using a specialized complex gene network comprised of many genes connected via complex circuitry.,,,
    “The ingenuity is that at each oscillation the cell also sends ‘chemical tweets’ to inform the other cells about its stress and attempt to escape,”,,, “The tweets sent by others help regulate the circuits of their neighbors and guarantee that no more than a specific fraction of cells within the colony will enter into competence.”
    http://phys.org/news/2013-04-code-bacteria.html

    etc.. etc..

  333. Franklin #297: it’s chemistry all the way down.
    Franklin #288: do you think there are little hands in there sorting through the soup of all tRNAs to find the correct one?

    I’ll give you something to laugh about: for me ‘little hands’ is a very real possibility. There are countless activities in the cell that we cannot explain bottom-up.
    For instance, how does the cell keep the strings of DNA from getting hopelessly tangled? One of the players addressing the problem are enzymes called “topoisomerases” whose task is to help manage the spatial organization of chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of genes or regions of the chromosome, and prevent a hopeless mass of knots. How can we explain this with chemistry mr. Franklin?

    A more general question would be: how does the epigenome work? What directs genes to produce the intricately sculpted and differentiated form of a complex organism, and how can this directing agency be governed by the very genes that it directs?

    Allow me one last example: world’s toughest bacterium Deinococcus radiodurans.
    Excerpt: An efficient system for repairing DNA is what makes the microbe so tough. High doses of radiation shatter the D. radiodurans genome, but the organism stitches the fragments back together, sometimes in just a few hours. The repaired genome appears to be as good as new.

    “When subjected to high levels of radiation, the Deinococcus genome is reduced to fragments,” they write in Proceedings of the National Academy of Sciences. “RecA proteins may play role in finding overlapping fragments and splicing them together.”

    The question is Franklin, without the help of invisible hands, how do RecA proteins ‘know’ the correct sequence of the DNA?

  334. F/N:

    It is sadly amusing to see the old watches don’t reproduce strawman that fails to even see that Paley addressed just that point in Ch 2 of his work. That is, just after noting how on observing the FSCO/I of the watch found in a field [or if you will the Antikythera mechanism, of unknown cause and much speculated purpose], we will naturally infer to an intelligent designer as its best explanation, he went on to address what would properly happen, why, if we were to in addition note that the found watch in the course of its movements formed another like unto it (and talk about clues . . . ):

    Suppose, in the next place, that the person who found the watch should after some time discover that, in addition to all the properties which he had hitherto observed in it, it possessed the unexpected property of producing in the course of its movement another watch like itself — the thing is conceivable; that it contained within it a mechanism, a system of parts — a mold, for instance, or a complex adjustment of lathes, baffles, and other tools — evidently and separately calculated for this purpose . . . .

    The first effect would be to increase his admiration of the contrivance, and his conviction of the consummate skill of the contriver. Whether he regarded the object of the contrivance, the distinct apparatus, the intricate, yet in many parts intelligible mechanism by which it was carried on, he would perceive in this new observation nothing but an additional reason for doing what he had already done — for referring the construction of the watch to design and to supreme art [--> an allusion to Plato in The Laws, Bk X on chance and necessity vs art] . . . . He would reflect, that though the watch before him were, in some sense, the maker of the watch, which, was fabricated in the course of its movements, yet it was in a very different sense from that in which a carpenter, for instance, is the maker of a chair — the author of its contrivance, the cause of the relation of its parts to their use.

    In short, for generations, there has been a pounding away at a strawman Paley.

    And in fact, there has been a subsequent vindication of Paley’s thought, as von Neumann from c. 1949 on conceived the nature of such a mechanism, with the advantage of information processing technology in hand. Namely, the von Neumann [kinematic] self-replicator. (vNSR]

    Such a device uses:

    (i) an underlying storable code to record the required information to create not only (a) the primary functional machine [[here, for a "clanking replicator" as illustrated, a Turing-type “universal computer”; in a cell this would be the metabolic entity that transforms environmental materials into required components etc.] but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility;

    (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with

    (iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling:

    (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by

    (v) either:

    (1) a pre-existing reservoir of required parts and energy sources, or

    (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.

    Also, parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral von Neumann universal constructor.

    That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [[Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).]

    Where may we see such a wonder?

    All around us, the living cell effects such a vNSR as a key component of what it is, an encapsulated, gated, metabolising automaton that uses stored coded information [in D/RNA] in driving construction processes linked to a self-replication process.

    This is a key part of why OOL is so pivotal, and why the attempt to rhetorically sever the root from the trunk and branches of the tree of life metaphor/analogy used from Darwin on, is so telling. It is an admission of the decisive gap in the whole account. For not least, unless there is a viable replication “system of parts” [and associated step by step processes] that couples self replication to the metabolic mechanism and encapsulation with gating, etc, there is no reproduction of a metabolic automaton to feed the chance variation and differential reproductive success mechanisms that are claimed to be able to achieve the body plan origination transformations being claimed.

    And, likewise there is another hole, in the notion that blind random walks are able to get us to coded, complex, functionally specific information and associated structures and mechanisms. The need to cross seas of gibberish to find islands of function makes the search for needles in haystacks by blind chance look like child’s play.

    In addition to all this, in the name of announced corrective knowledge of our alleged ignorance on the relevant chemistry [it is applied organic chemistry and polymer science for Pete's sake! . . . O level and A level . . . first College Chemistry, I suppose, should be adequate to follow . . . ] we are being fed blatant misinformation.

    It is the patent case that he chemistry of chaining of proteins and DNA or RNA, is distinct form the informational things that occur “at right angles” to the chain. We have here a string data structure implemented by chaining monomers: . . . -*-*-*-*- . . .

    At each link, we have monomers that have a form where there is a chain of links, whether sugar-phosphate, or carboxyllic acid-amine. That forms a standard coupler much like the one in the railways. A train of monomers can form, but there is nothing in the chaining that determines which must succeed which. That is why in fact DNA is used as a primary information store in the cell: G|C|A|T in the same string, are such that any of the four may follow any of the four. Indeed, that is why all 64 states are used in the code that is first transcribed to RNA — where U goes in place of T, then matured, transferred to a ribosome then translated into a sequence of amino acids [AA's] that forms a protein. mRNA serves as a control tape very much similar in purpose to the old punched paper tape of computing a generation ago. (That sort of tape is what probably lies behind the ideas in Turing’s computing machines, though he envisioned erasable tapes. magnetic tape then followed, and in my young days, the usual image of a computer at work was the refrigerator sized tape machines spinning the tapes — dinner-plate sized reels — away].)

    The information in the string of R/DNA is no more determined by the chemistry of chaining than is the informational content of the paper tape or the mag tape reel determined by the relevant physics and chemistry of its component parts. These materials and forces of nature (part of the classic definition of engineering . . . ) simply enable/constrain the design of such a system, they do not design it. Nor is blind chance and mechanical necessity a good explanation of contrivance, given the evident needle in haystack on steroids challenges, not to mention the need to explain the origin of codes which implies LANGUAGE. (Never mind attempts to brush that aside, what we are looking at there is ideological resistance, not a fair minded assessment of say the origin and explanation of firmware or other object code — directly executable, machine-specific code — in computers.)

    When it comes to proteins, we are looking at an almost Robe Goldbergian assembly system of parts and components used to carry out a step by step procedure, i.e. an algorithm. Try this video and this one that is a bit more instructional, for a reminder that will help clear away the rhetorical fog being smoked up from the burning of strawmen.

    We have not gone into details about geometric handedness of many relevant molecules, or how the basic thermo-chemistry is not affected by the issue of being a mirror image. That’s why a 50-50 L/R handed mixture is t5he normal product of organic reactions, save in settings where handedness is set up. We have not highlighted how in a realistic prebiotic context, there would be major problems with concentration, with interfering molecular species and the likely formation of a useless, hindering tar, the bane of such exercises. The stability issues in aqueous medium have not been addressed, but note that Miller-Urey used trapping out which makes use of Le Chetalier’s principle of rxns moving to relive the imposed stress, by removing products leading to formation of more product rather than equilibrium that is very much against significant, durable quantities of the substance.

    In short, the OOL chaos is the fundamental context that decisively undermines the neat mechanistic-materialistic view of origin of life and body plans.

    Before I conclude, one last t point.

    Predictably, there is snide dismissiveness on the possibility of intelligence at relevant times in the past of origins. This is little more than willful bias. We have no good reason to imagine that we humans exhaust the scope of intelligence. Indeed something as simple as beavers show what we can see as intelligence, albeit limited, in dam designs. So long as intelligence relevant to design is POSSIBLE at the point of origins, the inductive evidence on the only known adequate source of FSCO/I should be allowed to speak as what it is a reliable sign.

    The willful contentiousness of the determined objector should not be allowed to detain us from reasonable conclusions.

    (The same attitude was very evident in the days of marxism as the avant garde view, a generation past. Clever, determined arguments and all the rhetoric that billions spent on agitprop could muster were brought to bear, stubbornly, to make a fundamentally flawed and unworkable scheme seem plausible. Unfortunately, millions paid with their lives for that. And, as it came apart and collapsed, we saw nary an apology or retraction from those who had been so busily contending for the system. [I will give the Russians credit here: they sent a delegation to Jamaica in 1990, to apologise for what they had done to us.] They spun on a penny and went off on new tangents. Many of which, if one looks closely, are little more than repackaged marxist subversion. Neo-marxisms, in short. And of course, because there has not been proper eduction and much of the major media have been complicit in allowing the history to be largely forgotten or never learned, many are falling for what in the old days would have been instantly spotted as subversive front operations. Right now, it looks to me much like the wheels are beginning to come off our civilisation. And if you dare to point out the problem YOU are the problem. Classic shoot- the- messenger agit-prop tactics. Wake up and smell the rapidly rising tide of disaster, folks. First, MASSIVE Geo-Strategic failure, duly covered up by the dominance of political correctness in the major media. Right now, I think Iran’s sprint across the nuke line to join North Korea and Pakistan may be the decisive point. What are the same voices that fiddled while our civilisation burned, going to say on the fine morning when we wake up and go to work, to see not a few planes crashing into buildings but nuke suicide bomb attacks, probably across North America and Europe? Or, a devastating EMP pule wipeout of electrically related technologies? Or something like that? Or simply the closing of the Straights of Hormuz backed up by nuke blackmail, etc? What excuse will we hear [or not hear in the event of an EMP attack]? [And BTW, on 9/11, a subtext was, fear of just such a nuke attack.] I will not now go on and on on how the rise of social, familial, sexual, drugs end so on chaos, is feeding the matrix of ever rising real and imagined crises from which the media halo anointed political messiahs will come. I am sick to the stomach of the manipulations of the Plato’s cave media world in which we now so plainly live. As for what is being done under false colours of science education, feeding the materialist ideologies that undermine knowledge, morals, impulse control and the like, as Plato warned against in his The Laws Bk X, all I will say is that the door is being opened for nihilism. Wake up! And instead of brushing aside such a warning from someone who lived through a marxist subversion attempt that ended up in a mini civil war that cost me a much loved “auntie” — the victim of murder motivated by propaganda smear, I suggest you begin by looking at this note on media spin games and thinking soberly about what is really going on in our world.)

    The tactics that have been resorted to above, are utterly telling on the real balance on the merits.

    KF

  335. Well, I guess I must resign myself to not seeing any sensible response to Elsberry and Shallit and their eight challenges. We don’t even manage to address CSI or get any inkling about what data go in to the calculation or how to manipulate it.

    To be fair, Kairosfocus gamely tries to bolster his own personal concept of FSCO/I but the challenge is for Dembski’s CSI and unless Dr. Dembski wants to endorse KF’s invention as the same as CSI, it remains a red herring (maybe not soaked with oil of ad hominen but it still won’t do).

  336. Mr. Fox, since I can never seem to get you to provide JUST ONE EXAMPLE example of a molecular machine that was arrived at purely Darwinian processes, perhaps I can get you to provide JUST ONE EXAMPLE of a falsification for this null hypothesis:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    Is Life Unique? David L. Abel – January 2012
    Concluding Statement: The scientific method itself cannot be reduced to mass and energy. Neither can language, translation, coding and decoding, mathematics, logic theory, programming, symbol systems, the integration of circuits, computation, categorizations, results tabulation, the drawing and discussion of conclusions. The prevailing Kuhnian paradigm rut of philosophic physicalism is obstructing scientific progress, biology in particular. There is more to life than chemistry. All known life is cybernetic. Control is choice-contingent and formal, not physicodynamic.
    http://www.mdpi.com/2075-1729/2/1/106/

    “Nonphysical formalism not only describes, but preceded physicality and the Big Bang
    Formalism prescribed, organized and continues to govern physicodynamics.”
    http://www.mdpi.com/2075-1729/2/1/106/ag

  337. Phil

    Answer some of the outstanding questions you haveignored in this thread and I may be more inclined to respond to your questions. I want them to be your questions, though. No cutting and pasting. And NO videos!

    Ball’s in your court.

  338. Alan Fox:

    Well, I guess I must resign myself to not seeing any sensible response to Elsberry and Shallit and their eight challenges.

    Their “challenges” prove that they are totally clueless.

    If they really wanted to rid the world of ID then all they have to do is step up and provide positive evidence for blind and undirected processes producing CSI. But they cannot so they are forced to act like little babies.

    And Alan you obvioulsy do NOT understand Dembski’s CSI so you cannot say it isn’t the same as kairosfocus’ FSCI/O- hint- the are the same, duh.

    So I guess we IDists will have to resign ourselves to the fact that our opponents will just make stuff up and act like it means something.

  339. Alan Fox:

    Answer some of the outstanding questions you haveignored in this thread …

    We are waiting on you to do that, Alan. Ya see so far all you have is to act like a little baby and say “that isn’t good enough”. Yet your position doesn’t have anything that even measures up to CSI.

    So until you and your ilk actually ante up and tell us what you would accept- by providing proper examples that support your position’s claims, then we have nothing to discuss as you will just do your typical cowardly maneuver as seen in comment 335.

  340. And Alan you obvioulsy do NOT understand Dembski’s CSI so you cannot say it isn’t the same as kairosfocus’ FSCI/O- hint- the are the same, duh.

    So does Joe Gallien speak for Bill Dembski, now?

  341. So until you and your ilk actually ante up and tell us what you would accept- by providing proper examples that support your position’s claims, then we have nothing to discuss…

    Well, that’s true. Nobody seems able to come up with a meaningful definition of CSI in response to Elsberry and Shallit, whose 2003 challenge is the subject of this thread.

    Plenty of folks seem to want to change the subject, though. You,Phil,Eric, Chance etc.

  342. Alan Fox:

    So does Joe Gallien speak for Bill Dembski, now?

    Not required. Unlike Alan Fox I can actually comprehend what I read.

  343. Alan Fox:

    Nobody seems able to come up with a meaningful definition of CSI in response to Elsberry and Shallit, whose 2003 challenge is the subject of this thread.

    Just because YOU are too dense to understand what we have told you, that doesn’t mean that you haven’t been told.

    CSI is better defined than anything your position has to offer, Alan. And I understand that bothers you so much that you have to lie.

  344. So I guess we IDists will have to resign ourselves to the fact that our opponents will just make stuff up and act like it means something.

  345. Alan Fox:

    So does Joe Gallien speak for Bill Dembski, now?

    Not required. Unlike Alan Fox I can actually comprehend what I read.

    I didn’t think so.

  346. Alan Fox:

    I didn’t think so.

    You are incapable of thought, Alan. And you sure as hell cannot demonstrate any difference between CSI and FSCI/O.

  347. CSI is better defined than anything…

    And that definition of CSI is…?

    You keep saying stuff like this but what is the definition?

  348. Alan Fox:

    You keep saying stuff like this but what is the definition?

    CSI is Shannon information that has meaning/ function and is at least 500 bits in length.

  349. You use CSI every day, Alan. Communication would be impossible without it.

    IOW you are serious mental issues and are apparently proud of it.

  350. And you sure as hell cannot demonstrate any difference between CSI and FSCI/O.

    You’re damn right! Nobody else can either because there is no clear definition of FSCO/I and no clear definition of CSI.


  351. And you sure as hell cannot demonstrate any difference between CSI and FSCI/O.

    You’re damn right!

    There isn’t any difference, Alan.

    Nobody else can either because there is no clear definition of FSCO/I and no clear definition of CSI.

    Perhaps you think so. But then again you are a proven arse.

  352. CSI is Shannon information that has meaning/ function and is at least 500 bits in length.

    If that is so then CSI is a trivial, useless and arbitrary concept. It merely divides all entities into two sets, divided by the arbitrarily chosen constant.

  353. CSI for Dummies, ie Alan Fox:

    CSI stands for Complex Specified Information

    Complex meaning it is not simple. Complex meaning it is intricate. And complex because it contains many parts or facets.

    (Wm. Dembski takes that meaning and gives it a mathematical form. He does so, because like Galileo before him, he sees science as incomplete without the mathematics. You put something in mathematical form and then someone else can check it. But dummies can’t understand this and that is why I created this post)

    Specified meaning something is indicated or defined, in detail. A good set of assembly instructions specifies what part goes where and as well as the order to put them together.

    Information meaning it is communicated data.

    IOW complex specified information is a term to differentiate between Shannon Information and information that has a specific meaning.

    Shannon information does not care about content or meaning, ie it does not care about specification. All the weight goes to the number of characters transmitted.

  354. Oops, sounds misleading

    for divided read decided


  355. CSI is Shannon information that has meaning/ function and is at least 500 bits in length.

    If that is so then CSI is a trivial, useless and arbitrary concept.

    Perhaps to you. But then again you don’t seem to understand anything.

    It merely divides all entities into two sets, divided by the arbitrarily chosen constant.

    So you say yet cannot support. How is the constant arbitrary? What are the two sets?

  356. Shannon information does not care about content or meaning, ie it does not care about specification.

    Exactly!

    Fine for telecommunications etc where bandwidth is of primary concern. Useless in biology.


  357. Shannon information does not care about content or meaning, ie it does not care about specification.

    Exactly!

    Fine for telecommunications etc where bandwidth is of primary concern. Useless in biology.

    That is why there is CSI- to differentiate- are you this much of an ass in person?

  358. So Alan is given a definition of CSI and as predicted he acts like a little cry-baby.

    Nice job, Alan.

  359. How is the constant arbitrary? What are the two sets?

    I can’t believe you need to ask this! Your 10 to the 150 or other arbitrarily chosen constant separates any entity into either set A for those below and set B for those above the threshold. If you think there is any point whatsoever in performing such a trivial calc. well I am sure most others can follow my thoughts; ;)

  360. That is why there is CSI- to differentiate- are you this much of an ass in person?

    Round we go in circles. You now need to tell me how you are calculating your CSI.

  361. Alan Fox:

    Your 10 to the 150 or other arbitrarily chosen constant separates any entity into either set A for those below and set B for those above the threshold.

    1- It isn’t arbitrary

    2- It does not separate. Stuff below the threshold can still be designed as blind and undirected processes don’t appear to be capable of producing even 100 bits of SI.

    The point of the calc is to determine design, Alan. And that is a major determination and effects all future research.

  362. Alan Fox:

    You now need to tell me how you are calculating your CSI.

    How many times, Alan? You have been told many times already. And as predicted you are just flailing like the sissy that you are.

    CSI is measured by counting the bits. I even gave you an example that you choked on.

  363. The point of the calc is to determine design, Alan. And that is a major determination and effects all future research.

    What calc? You can’t show me a calculation, can you?

  364. Alan Fox:

    What calc? You can’t show me a calculation, can you?

    I gave you an example you dimwitted twit.

    Do you really think that being an asshole helps your case?

  365. CSI is measured by counting the bits.

    So, that falls back to the trivial and merely picking things as conaining CSI or not according to some arbitrary threshold. Useless.

  366. Mr. Fox, perhaps I would be less perplexed by your continued dogmatic claim that purely material processes can produce the unfathomed levels of complex functional information we find in the cell if you were to ever actually cite a specific example of sophisticated function arising de novo in the cell. i.e. a molecular machine should do the trick!! You see Mr. Fox, despite your belittling of anyone who doubts your claim as ignorant, the fact of the matter is that, despite the cell being packed with molecular machines,,,

    Venter: Life Is Robotic Software – July 15, 2012
    Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter.
    http://crev.info/2012/07/life-is-robotic-software/

    ,,,despite this,, we have no evidence that Darwinian processes can produce any molecular machines whatsoever,,

    Molecular Machines: – Michael J. Behe
    Excerpt: JME is a journal that was begun specifically to deal with the topic of how evolution occurs on the molecular level. It has high scientific standards, and is edited by prominent figures in the field.,,,
    In the past ten years JME has published 886 papers. Of these, 95 discussed the chemical synthesis of molecules thought to be necessary for the origin of life, 44 proposed mathematical models to improve sequence analysis, 20 concerned the evolutionary implications of current structures, and 719 were analyses of protein or polynucleotide sequences. There were zero papers discussing detailed models for intermediates in the development of complex biomolecular structures. This is not a peculiarity of JME. No papers are to be found that discuss detailed models for intermediates in the development of complex biomolecular structures in the Proceedings of the National Academy of Science, Nature, Science, the Journal of Molecular Biology or, to my knowledge, any journal whatsoever.
    http://www.arn.org/docs/behe/mb_mm92496.htm

    Yet we have evidence that Intelligence can do as such,,

    Whether Lab or Cell, (If it’s a molecular machine) It’s Design – podcast
    http://intelligentdesign.podom.....3_41-08_00

    I know that you, as an atheist, probably think this is a minor inconsequential detail that can be safely ignored, because it is brought up by IDiots, but I would beg to differ. What is to separate your claim that purely material processes can easily produce these molecular machines from a bald face lie if you don’t ever actually produce an example of them doing as such?

  367. I gave you an example you dimwitted twit.

    Unless we are talking about counting bits, you didn’t. And if you are just counting bits, you are back with trivial and useless.

  368. Alan Fox:

    So, that falls back to the trivial and merely picking things as conaining CSI or not according to some arbitrary threshold. Useless.

    Useles to you, perhaps. Then again you are useless.

    And why do you think the threshold is arbitrary? Especially seeing taht it has been explained amny times why that threshold was chosen?

    Do you really think that your ignorance means something? Really?

  369. I gave you an example you dimwitted twit.

    Unless we are talking about counting bits, you didn’t. And if you are just counting bits, you are back with trivial and useless.

    Just because you, a proven imbecile, can say it is trivial and useless, that doesn’t make it so, Alan. You actually have to make a case and you can’t.

  370. Mr. Fox, perhaps I would be less perplexed by your continued dogmatic claim…

    I’m making no claims here. I’m asking if there is a way of calculating Dembski’s CSI. Are you able to address the topic or do you want to continue derailing?

  371. Alan Fox does know about trivial and useless because that is his entire position- trivial and useless.

  372. Just because you, a proven imbecile, can say it is trivial and useless, that doesn’t make it so, Alan. You actually have to make a case and you can’t.

    But still no calc!

  373. Alan Fox:

    I’m making no claims here.

    Yes Alan, you don’t have to keep reminding us that you are a coward.

    I’m asking if there is a way of calculating Dembski’s CSI.

    Dembski has written how to do that. I have also, as have others.

    Again your willful ignorance means nothing here.

  374. So Alan’s questions have been answered and now all he has is belligerence.

    Nice job, Alan.

  375. Dembski has written how to do that. I have also, as have others.

    If that were the case you would be able to show me where these calculations are. Where are they? They’re not trivial and useless, by any chance, are they? They do exist, don’t they? You didn’t imagine them, did you?

  376. The causal tie between an artifact and its intended character — or, strictly speaking, between an artifact and its author’s productive intention — is constituted by an author’s actions, that is, by his work on the object.- Artifact

    When discussing information some people want to know how much information does something contain?

    If it is something straight-forward such as a definition, we can count the number of bits in that definition to find out how much information it contains.

    For example:

    aardvark: a large burrowing nocturnal mammal (Orycteropus afer) of sub-Saharan Africa that has a long snout, extensible tongue, powerful claws, large ears, and heavy tail and feeds especially on termites and ants

    A simple character count reveals 202 characters which translates into 1010 bits of information/ specified complexity.

    Now what do we do when all we have is an object?

    One way of figuring out how much information it contains is to figure out how (the simplest way) to make it.

    Then you write down the procedure without wasting words/ characters and count those bits. The point is that you have to capture the actions required and translate that into bits. That is if you want to use CSI. However by doing all of that you have already determined the thing was designed Now you are just trying to determine how much work was involved.

    But anyway, that will give you an idea of the minimal information it contains- Data collection and compression (six sigma DMAIC- define, measure, analyze, improve, control).

    CSI is a threshold, meaning you don’t need an exact number. And it is a threshold that nature, operating freely has never been observed to come close to. Once CSI = yes you know it was designed.

    On Shannon Information and measuring biological information:

    The word information in this theory is used in a special mathematical sense that must not be confused with its ordinary usage. In particular, information must not be confused with meaning.- Warren Weaver, one of Shannon’s collaborators

    Is what Weaver said so difficult to understand?

    Kolmogorov complexity deals with, well, complexity. From wikipedia:

    Algorithmic information theory principally studies complexity measures on strings (or other data structures).

    Nothing about meaning, content, functionality, prescription. IOW nothing that Information Technology cares deeply about, namely functional, meaningful, and useful information. Not only Information Technology but the whole world depends on Information Technology type of information, ie the type of information Intelligent Design is concerned with.

    And both Creationists and IDists make it clear, painfully clear, that when we are discussing “information” we are discussing that type of information.

    And without even blinking an eye, the anti-IDists always, and without fail, bring up the meaningless when trying to refute the meaningful. “Look there is nature producing Shannon Information, you lose!”- ho-hum.

    Moving on-

    Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the same sense required by the complexity-specification criterion (see sections 1.3 and 2.5). The specification of organisms can be crashed out in any number of ways. Arno Wouters cashes it out globally in terms of the viability of whole organisms. Michael Behe cashes it out in terms of minimal function of biochemical systems.- Wm. Dembski page 148 of NFL

    In the preceding and proceeding paragraphs William Dembski makes it clear that biological specification is CSI- complex specified information.

    In the paper “The origin of biological information and the higher taxonomic categories”, Stephen C. Meyer wrote:

    Dembski (2002) has used the term “complex specified information” (CSI) as a synonym for “specified complexity” to help distinguish functional biological information from mere Shannon information–that is, specified complexity from mere complexity. This review will use this term as well.

    In order to be a candidate for natural selection a system must have minimal function: the ability to accomplish a task in physically realistic circumstances.- M. Behe page 45 of “Darwin’s Black Box”

    With that said, to measure biological information, ie biological specification, all you have to do is count the coding nucleotides of the genes involved for that functioning system, then multiply by 2 (four possible nucleotides = 2^2) and then factor in the variation tolerance:

    from Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling, Vol. 4:47 (2007):

    [N]either RSC [Random Sequence Complexity] nor OSC [Ordered Sequence Complexity], or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life. FSC [Functional Sequence Complexity] includes the dimension of functionality. Szostak argued that neither Shannon’s original measure of uncertainty nor the measure of algorithmic complexity are sufficient. Shannon’s classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that “different molecular structures may be functionally equivalent.” For this reason, Szostak suggested that a new measure of information—functional information—is required.

    Here is a formal way of measuring functional information:

    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak, “Functional information and the emergence of biocomplexity,” Proceedings of the National Academy of Sciences, USA, Vol. 104:8574–8581 (May 15, 2007).

    See also:

    Jack W. Szostak, “Molecular messages,” Nature, Vol. 423:689 (June 12, 2003).

    original posts can be found here, here and here


  377. Dembski has written how to do that. I have also, as have others.

    If that were the case you would be able to show me where these calculations are.

    I have, Alan. Again your ignorance and lies mean nothing to me.

    They’re not trivial and useless, by any chance, are they?

    Not to educated people.

  378. CSI is a threshold, meaning you don’t need an exact number.

    And there you have it, folks. Joe is merely sorting stuff into two piles. Trivial and useless.

  379. And Alan Fox belongs to both piles as he is not only trivial but very useless.

  380. Mr. Fox, The claim of ID is very specific, namely that Darwinian processes are grossly inadequate to produce functional information. Do you reject this very specific claim or support it? Being a atheist I hold that you reject it. If you indeed do reject it please stop playing these stupid games and show me the exact falsification of Abel’s null or a exact example of a molecular machine by arising by Darwinian processes. Else-wise, why should you be considered anything more that a dogmatic Atheist who is willing to do anything it takes, with any deceptive means at his disposal, to protect his faith

  381. I see in another thread, KF states:

    Chi = Ip*S – 500, in bits beyond a “complex enough” threshold

    Joe appears to be correct. He and KF are both sorting entities into two sets, according to an arbitrary threshold. If this is all CSI is, then it is trivial and useless.

  382. Mr. Fox, perhaps you would like to be the first atheistic Darwinist in the history of UD to show an example of this ‘trivial and useless’ threshold of 500 bits being broken by purely material processes?

    Book Review – Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.
    Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren’t chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.
    So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it’s a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.
    http://www.fourmilab.ch/docume.....k_726.html

  383. Yes Alan, we get it. CSI is trivial and useless to illiterate punks like you.

    That’s fine. However we notice that your psoition doesn’t have anything that even measures up to CSI. And that means, by your “logic” that your position isn’t even trivial and worse than useless.

    Nice job.

  384. The claim of ID is very specific, namely that Darwinian processes are grossly inadequate to produce functional information. Do you reject this very specific claim or support it?

    I get that ID proponents reject evolutionary theory. I don’t think we have an adequate or complete picture of the evolutionary processes that resulted in the pattern of extant and extinct life we observe but it is the only theory we have that fits the evidence and continues to progress in line with developments in the biological sciences. ID brings nothing to the table. I don’t accept that ID proponents have raised any valid objections to the ToE other than scientists are already aware of. This is obvious from the way a new paper with controversial findings is often hailed as a problem for Darwinism when it is the scientists working in the field who are modifying and adding to the theory as more evidence and data accumulate.

    Now, Phil, are you going to have the courage to respond to those questions addressed to you or do you think you think communication is only one-way?

  385. …your psoition doesn’t have anything that even measures up to CSI.

    Of course not! How could anyone? We don’t know how to measure CSI of something … anything … because nobody can tell us how!

    =========

    AF, why do you insist on a continued willful misrepresentation in the teeth of the evident truth presented to you any number of times, including above in this thread?

    Your remarks just above are 123 ASCII characters in standard English [clearly objectively recognisable], at 7 bits per character.

    This gives us I*S = 861 * 1 = 861 functionally specific bits.

    Applying the Chi_500 metric that AF tries to imagine does not exist or is unusable:

    Chi_500 = 861 = 500 = 361 bits beyond the solar system threshold

    This is a second live demonstration in several days to AF.

    Let us see his next excuse for — sadly, predictably — dismissing and misrepresenting it.

    KF

  386. Alan Fox:

    I get that ID proponents reject evolutionary theory.

    Nope, we cannot reject that which does not exist.

    ID brings nothing to the table.

    How would you know? You can’t even find the table.

    We don’t know how to measure CSI of something … anything … because nobody can tell us how!

    I have told and shown you how to measure CSI you lying sack.

    Does it make you feel good to lie, Alan?

  387. Natural selection- trivial and useless

    genetic drift- trivial and useless

    random mutations- not defined and undetermined

    Yup Alan understands all about trivial and uselessness.

  388. Mr. Fox, other than dodging my request for a specific example of Darwinian processes producing the functional information that you claim they can, and then dogmatically claiming that evolution is science, even though you can provide no example, is ‘science’ (it is not!) you have honestly addressed my question how exactly? You are being purposely misleading and obtuse!

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003)

    Whereas Darwinism has no identifiable falsification criteria (at least no criteria that a Darwinist will accept), one can easily falsify ID:

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

  389. F/N: AF has just been corrected on his continued misrepresentations of FSCO/I and CSI, at 385 above. KF

  390. I have told and shown you how to measure CSI you lying sack.

    Well, you say you can count the bits of something … anything … and if greater than 2^500 or 10^150 it must be designed and if not it still might be. Trivial and useless. And unendorsed, so far. Would any other ID proponent like to confirm that Joe’s CSI is Dembki’s CSI?

  391. Mr. Fox, why don’t you quit wasting everybody’s time and just produce an example? Why the charade? Are you that dense?

  392. You are being purposely misleading and obtuse!

    I don’t regard you as a fair interlocutor and you have not reciprocated by responding to questions that I have addressed to you. The ball is still in your court.

  393. AF: You have again been corrected at 385 above. Your behaviour at this point is so outrageous, that I have refrained from snipping Joe, even though I do not like the words he has used. (Though I am even more suspicious of the second word he used, that in this sense is not in my vocabulary, I hope it is not one of those really nasty American idioms.) Your willful misrepresentation is indeed a form of deliberate falsehood intended to mislead. Please stop it. KF

  394. Mr. Fox, why don’t you quit wasting everybody’s time and just produce an example? Why the charade? Are you that dense?

    Ignore my comments then. In fact, you do anyway! You have never given an honest reply to any question I have addressed to you.

  395. franklin seems to think that we cannot bring in our knowledge of human design to help inform us about biological systems because human designs don’t have “charge” and don’t stick together like atoms and molecules do.

    Those tens of thousands of people who work in fields such as nanotechnology, biotech, and pharmaceuticals? We were all just imagining them. They don’t exist.

    —–

    Look, this whole “But, but particles have mass and charge” nonsense is a complete red herring. Whenever you’re ready to address the real issues, franklin, let us know.


  396. have told and shown you how to measure CSI you lying sack.

    Well, you say you can count the bits of something

    I said more than that you lying sack.

    Geez Alan you are just a pathetic little imp and no one regards you as a fair interlocutor.

    So perhaps you should crawl back to your swamp and wallow in its stench.

  397. Alan Fox:

    Ignore my comments then.

    That is what you do, Alan- ignore comments. And then you act as if your ignorance means something. Strange, that…

  398. AF: You know full well that the sense of specification that has been defined since NFL has to do with an independent description that allows us to recognise that a case E is or is not in T, separate from simply listing members of T in W. 123 characters in standard English counts. The case just given is CSI, it is specific in the functional sense and it is dFSCI, as it is in a standard digital code, ASCII. Your behaviour at this point is willful and willfully misleading, hoping to profit by making misrepresentations appear to be truth or from sowing confusion in the minds of onlookers. This is beyond the pale of reasonable and civil discussion. Stop it. KF

  399. It is useless to discuss anything with Alan without a moderator to keep him honest. And it is even doubtful that a moderator would help. The mod would just get pissed off and say Alan is a lost cause…

  400. AF is corrected here. KF

    +++++++++

    You have again been corrected at 385 above.

    I have told you that pasting edits into past comments is a disreputable way to attempt dialogue. You can do better than that. Please stop it.

    Your behaviour at this point is so outrageous, that I have refrained from snipping Joe, even though I do not like the words he has used. (Though I am even more suspicious of the second word he used, that in this sense is not in my vocabulary, I hope it is not one of those really nasty American idioms.)

    Your incapacity to honestly moderate your own blog posts had already been noted. Joe’s childish insults just make me smile. They and your inability to deal with them must probably reflect badly on you, but that’s your problem.

    Your willful misrepresentation is indeed a form of deliberate falsehood intended to mislead. Please stop it.

    Why I am allowed to post here is beyond me. You know I think ID is dangerously political nonsense. I have never posted anything here that I knew was not true I am not going to gratuitously insult anyone here but I will post what I think without caution as and when I feel like it unless Barry or anyone else cancels my account. That again is their choice.

    ++++++++++

    AF is corrected here, KF

  401. Alan Fox:

    Why I am allowed to post here is beyond me.

    That is beyond me too. You definitely don’t have anything to offer, not even a valid criticism.

    And again, I did not insult you. I have just made observations. It is not my fault that you act the way that you do and say the crap that you say.

  402. Alan Fox

    I have told you that pasting edits into past comments is a disreputable way to attempt dialogue.

    And who are you to make such a claim? Your incapcity to engage in an honest discussion proves that you are just a belligerent waste of skin.

  403. AF is corrected here. KF
    +++++++

    KF’s insertion:

    AF, why do you insist on a continued willful misrepresentation in the teeth of the evident truth presented to you any number of times, including above in this thread?

    Your remarks just above are 123 ASCII characters in standard English [clearly objectively recognisable], at 7 bits per character.

    This gives us I*S = 861 * 1 = 861 functionally specific bits.

    Applying the Chi_500 metric that AF tries to imagine does not exist or is unusable:

    Chi_500 = 861 = 500 = 361 bits beyond the solar system threshold

    This is a second live demonstration in several days to AF.

    Let us see his next excuse for — sadly, predictably — dismissing and misrepresenting it.

    KF

    So you seem to be confirming that CSI is merely a count in bits, in the case of letters as a 1 in however many possibilities (I guess 2^7)times the number of letters. For a protein the 1 in 20 times number of residues. Above the threshold, … Design! I get that, I really do. And the process seems to me trivial and useless. This cannot be all that Dembski means when he talks about CSI, really? Sorting things into two piles?

  404. Alan,

    Determining design is huge. That you cannot understand that just demonstrates that you are scientifically illiterate.

  405. Archaeology, two piles- designed or not

    Forensic science, two piles- designed or not

    Geez the two pile method seems to work just fine within science.

  406. kf @334:

    The “self-reproducing” canard is such an absurd response to the challenges facing a purely natural creation story. You have done a great job of addressing this issue.

    However, I think it is important to keep in mind that self-reproduction is, logically, irrelevant to the substantive question at hand. There are mutations going on regularly in organisms. You and I each have more mutations now than we did when we were born. There is no logical reason, on Darwinian principles, why we don’t see individual organisms evolve into something else over their lifetime, other than the question of time.

    Imagine there were an organism that lived for millions of years. Would it eventually turn into something else? On Darwinian principles, why not?

    There are a few things that self-reproduction does bring to the table in support of the evolutionary story: it (i) keeps an organism (in the sense of a lineal descent line of organisms) alive for millions of years, allegedly long enough for some of the mutations to add up to something novel, (ii) provides additional copies so that there are more possible opportunities for mutation (in the population as a whole, that is, not necessarily in any specific line), (iii) provides more opportunities for extraneous copies of genetic material, mistakes, and other mutations during the reproduction process, and (iv) in the case of sexual reproduction, allows for recombination.

    At the end of the day, however, all of these are simply ways to get more opportunities, more resources for mutation to do its creative work. It tells us precisely nothing about whether mutations can in fact create the biological systems we see in nature.

    So the self-reproducing refrain often trotted out is at most a way to get more mutation opportunities, though, unfortunately, all those additional opportunities are still swallowed up as but a rounding error in the vast probability space. More importantly, it does nothing to address the substantive issue at hand: the creation of functional biological systems.

  407. AF is corrected here. KF
    +++++++

    Joe:

    Archaeology, two piles- designed or not

    Hmm. I doubt many archeologists count bits when they attempt to distinguish a human-made stone arrow head from a frost-flaked chip of rock. Are there any papers on distinguishing artefacts by assessing CSI?

    Forensic science, two piles- designed or not

    Pattern-matching whether DNA, fingerprints, tyre-tracks fibres from clothing is pretty well-established. Difficult to say more about a DNA sample or a clothing fibre without a sample to compare it to. How is CSI used in forensics?

  408. Alan, you know, or should know, that the design inference is not just a count of bits. There has to also be an observable function, or specification, if you will.

    Counting bits is the easiest, most objective and obvious way to establish a complexity threshold. And yes, that aspect, is quite simple. If you think it is trivial, fine. We also think it is pretty elementary. Yet it is an important aspect because it allows the elimination of false negatives. I suspect you already know this, though.

    Ironically, the fact that many people fight tooth and nail in opposition to this very basic point speaks volumes about how important it is and how challenging it is to their a priori philosophical framework.

  409. AF is corrected here. KF

    However, I think it is important to keep in mind that self-reproduction is, logically, irrelevant to the substantive question at hand.

    Indeed. Evolution does not address the issue of where the first living organisms came from. It assumes life as a given. Evolution needs self reproducing, imperfectly replicating, self-sustaining organisms before it can do its work.

    There are mutations going on regularly in organisms.

    .Indeed. Somatic mutations can result in cancers, especially where tissue is turning over rapidly such as in epithelial cells and sex organs.

    You and I each have more mutations now than we did when we were born. There is no logical reason, on Darwinian principles, why we don’t see individual organisms evolve into something else over their lifetime, other than the question of time.

    Here you are in complete misunderstanding. The only mutations that matter to evolution are mutation in your genome. The genome that you inherited from your parents resulted in you developing into you. The genetic information that you pass on to your offspring is a result of a process called meiosis where genes can be shuffled during crossover and recombination. It is also possible (statistically almost certain) that there will be some variation from the genome that grew you caused by mutations. Your offspring’s genome will be a mix of you and the other parent’s genes. They will inherit some mutations (which in all likelihood will be neutral. Mutations to not cause changes during the lifetime of an individual. It is when genes containing mutations are passed on and affect the development of the offspring that the changes in alleles that selection can work on occur. Genomes, as far as the lifetime of any one organism is concerned, are fixed.

  410. AF is corrected here. KF

    ++++++++

    Alan, you know, or should know, that the design inference is not just a count of bits. There has to also be an observable function, or specification, if you will.

    OK.

    So how is function quantified? And how does that quantity enter into the calculation?

  411. Alan Fox:

    I doubt many archeologists count bits when they attempt to distinguish a human-made stone arrow head from a frost-flaked chip of rock.

    Non-sequitur. Two piles, Alan. Please TRY to stay focused and not try to change the subject.

    Are there any papers on distinguishing artefacts by assessing CSI?

    They assess artefacts via counterflow or work. And CSI = counterflow and work.

    Pattern-matching whether DNA, fingerprints, tyre-tracks fibres from clothing is pretty well-established.

    Cause and effect relationships. Very good, Alan

    How is CSI used in forensics?

    TWO PILES, Alan. Two piles- YOU brought it up, now choke on it.

  412. Alan Fox:

    Evolution does not address the issue of where the first living organisms came from.

    Then it cannot say anything about its diversity as the two are directly connected.

    Evolution needs self reproducing, imperfectly replicating, self-sustaining organisms before it can do its work.

    Umm, Alan, you are equivocating as ID is OK with evolution by design- genetic algorithms are examples of this.

  413. eric: Alan, you know, or should know, that the design inference is not just a count of bits. There has to also be an observable function, or specification, if you will.

    I agree with Alan’s question about function. Do proteins binding protons and acting as intra & extracellular buffers count as an observable function? If yes, how many proteins can function in this regard? If no, why do you consider a non-bicarbonate buffering systems (most vertebrates) as being a non-funcitonal aspect of protein function?

  414. Alan Fox:

    So how is function quantified?

    Function is an observation. Once observed we can see how specified the function is.

  415. Alan mentions meiosis above. That is strange because his position can’t account for that either.

  416. eric: Those tens of thousands of people who work in fields such as nanotechnology, biotech, and pharmaceuticals? We were all just imagining them. They don’t exist.

    Yeah, eric, I’m sure the fields of biotech and pharmaceutical (pharmacology and its related field toxicology) aren’t the least bit concerned with chemistry and how molecules bind to a receptor and with what affinities or even how they might elicit a biological response? Then there is the issue concerning what metabolites(and if they are reactive or not) are produced when a drug or non-therapeutic compound is administered or contacts a organism. I mean common sense and a bit of reflection should be all that is needed to determine this information so you in this field would need any knowledge of chemistry outside of stuff bumps into each other and some sticks together.

  417. OK so the two pile methodology is good in science (see archaeology, forensic science and SETI) except when it comes to Intelligent Design- is that right, Alan?

    Do you ever get tired of holding up those double-standards?

  418. I wonder if franklin and Alan realize that the only reason we are even discussing Intelligent Design is because their position has proven to be useless, trivial and most of its claims are either flase or untestable.

    I guess that would bother me to the point of belligerence too.

  419. AF is corrected here. KF

    ++++++++

    OK so the two pile methodology is good in science (see archaeology, forensic science and SETI) except when it comes to Intelligent Design- is that right, Alan?

    I don’t accept for one moment that any archaeological dig just sorts things into two piles, except perhaps when riddling possible artefacts like small potsherds and other fragments from spoil. Extracting artefacts from substrate and accretions is only the precursor to detailed examination and recording context is also a crucial element of any dig.

    I doubt forensic science investigations end up with two piles. They might perhaps sweep an area for clues such as cartridge cases etc.

    SETI is another matter and one apparently misunderstood by you. SETI do not know what is out there. The search for extra-terrestrial intelligent life is speculative and is looking for anything unusual. But there is no pattern to match or any of idea what a signal from ET might look like. The work will start once and if an anomaly is found. Then the process of deciding if it indeed an attempt at communication from ETs can begin. What that might involve, would seem pointless to speculate until there is something to work with. Echos of Jocelyn Bell and the pulsar signals that were initially designated “LGM” (little green men).

    Now I can see that at some level of analogy an ID proponent could claim to be thought experimenting in the same way as SETI researchers, niether having a pattern to guide them in what to look for but SETI are looking for anomalous signalsat in the electromagnetic spectrum – real phenomena. ID “research” appears to be looking for imaginary phenomena.

  420. Alan Fox:

    I don’t accept for one moment that any archaeological dig just sorts things into two piles,

    Well they do- one for possible artifacts and another for dirt and rocks.

    I doubt forensic science investigations end up with two piles.

    They do- crimes and non-crimes

    SETI is another matter and one apparently misunderstood by you.

    Your faklse accusations mean nothing, coward.

    SETI do not know what is out there.

    They depend on knowledge of cause and effect relationships, just as with ID.

    Archaeology, forensic science, SETI and ID all depend on our knowledge of cause and effect relationships.

    OTOH your position depends on ignoring that and pressing on regardless.

  421. Again, for Alan:

    Archaeology, two piles- designed or not

    Forensic science, two piles- designed or not

    Geez the two pile method seems to work just fine within science.

    Two piles. The same two piles that ID makes, according to Alan.

  422. AF is corrected here. KF

    ++++++++

    Well they do- one for possible artifacts and another for dirt and rocks.

    Things are much more sophisticated than that. Context is hugely important (where the artefact was found) so likely artefacts are never plonked in a pile on current scientific digs.Fragments that are found together are kept together and separate from fragments found elsewhere.

    They do- crimes and non-crimes

    That’s just silly, like your pile of rocks. If evidence suggests an unexplained death was from natural causes such as a heart attack due to underlying medical condition, then further forensic investigation might be considered unnecessary but there is much more to forensics than just deciding if a crime has been committed or not.

    They [SETI] depend on knowledge of cause and effect relationships, just as with ID.

    SETI (receiving no public finance) depend on donations! And they are speculating. They do not know what they are looking for because there is no precedent, no pattern to know what to look for. But they are not claiming the existence of invisible, disembodied, imaginary designers. And, as I said, they are processing signals in the electromagnetic spectrum for anything that seems anomalous. Until they have something odd to look at there is no more to be usefully said.

  423. Alan Fox:

    Things are much more sophisticated than that. Context is hugely important (where the artefact was found) so likely artefacts are never plonked in a pile on current scientific digs.Fragments that are found together are kept together and separate from fragments found elsewhere.

    What a jerk. Two piles- designed or not. It does not matter if there are many piles of designed objects for any one site.

    Alan Fox:

    If evidence suggests an unexplained death was from natural causes such as a heart attack due to underlying medical condition, then further forensic investigation might be considered unnecessary but there is much more to forensics than just deciding if a crime has been committed or not.

    Umm first they have to make that decision, Alan. The entire investigation depends on that decision- design/ crime or not.

    As for SETI- they have said what they are looking for and explained it. Again that you think your ignorance means something is funny, but that is it.

  424. 424

    @Alan Fox:

    SETI works this way:
    1. Specify a pattern.
    2. Look for the pattern.
    3. If pattern found, test whether there are natural explanations for the pattern.
    4. If no natural explanation found, conclusion: aliensdidit.

    I think that’s exactly the activity-flow kairosfocus posted for detection of intelligent design.

  425. AF is corrected here. KF

    ++++++++

    SETI works this way:
    1. Specify a pattern.
    2. Look for the pattern.
    3. If pattern found, test whether there are natural explanations for the pattern.
    4. If no natural explanation found, conclusion: aliensdidit.

    No. That’s completely wrong. SETI have no pattern or specification. They are monitoring the EM spectrum and looking for anomalies. What they can say about any anomaly will have to wait until something anomalous is found. Their search is purely speculative. I doubt anyone is going to be convinced by a default explanation – “We can’t explain this signal, so it must be aliens” – but until there is something anomalous to examine, it’s all imagination.

  426. And Alan knows about imagination because his position relies on it. Somehow, when we ain’t lookin’, natural selection allegedly does some amazing stuff.

    Again SETI works by understanding cause and effect relationships- they know what nature does and the know what takes an agency to produce.

  427. 427

    @Alan Fox:
    Patterns are not anomalies. However anomalies ARE patterns.

    I doubt anyone is going to be convinced by a default explanation

    I’m in no position to judge the validity of SETI.
    SETI = Search for Extraterrestrial Intelligence. They are using the specified patterns (you call them anomalies) to search for intelligence. To me this means that SETI is at the very least as scientific as intelligent design.

  428. Destructing Alan:

    Things are much more sophisticated than that.

    Yes, Alan, as with Intelligent Design. However it is you that went down this road. I am here to beat you with it.

    Context is hugely important (where the artefact was found) so likely artefacts are never plonked in a pile on current scientific digs.Fragments that are found together are kept together and separate from fragments found elsewhere.

    Yes, that is how Intelligent Design proceeds. There are different piles for differnt areas of investigation. The design inference from physics has it piles. The design inference from biology has its piles. The design inference from chemistry has it piles. The design inference from cosmology has its piles.

    Its piles and piles of design inferences, Alan.

    That’s just silly, like your pile of rocks.

    YOU brought up the piles. And you mangled your analogy in the process.

    If evidence suggests an unexplained death was from natural causes such as a heart attack due to underlying medical condition, then further forensic investigation might be considered unnecessary but there is much more to forensics than just deciding if a crime has been committed or not.

    Exactly how ID proceeds. We have looked and are still looking for materialistic answers, but given what we know the design inference is the best explanation to date.

    We haven’t closed the door but seeing that all you have all bald assertions and false accusations, we ain’t expecting anything of substance from you any time soon.

  429. AF: Functionally specific information — as is stipulated — has functional specificity [which you seem bound and determined to ignore], which distinguishes it from mere information carrying capacity; what so-called Shannon info measures. You will note that I identified the use of info capacity to achieve a function, in your case an expression in English. That functionality and specificity, joined to complexity that puts us into islands of function that are beyond the search capacity of the solar system since its founding, are where the outcome rests. Intelligence routinely and easily produces such, blind chance plus necessity has such a challenge to do so that it is not a credible explanation on the gamut of our solar system. (Our effective cosmos if you look and see the recent Nat Geog article on suggestions on interstellar flight.) KF

  430. F/N: here comes the predictable rhetorical attempt to pretend that function is some vague, fuzzy meaningless entity. Text in asci code in English has function. The DNA , RNA and proteins in the living cell have function, all of which happens as well adapted components are put together in specific ways that achieve an observable end or carry out a process. Function is an observable, and often a measurable feature. So, it is reasonable to insist that we are looking at function and function that depends on specific configuration. Where that is not clearly the case, out of an abundance of caution the Chi_500 metric specificity variable goes to 0, its default value. This of course means it will miss cases, but that is not a problem given its purpose. And, the cases of DNA, RNA and proteins are not in any way dubious or fuzzy. red herrings and strawmen again. As is so sadly usual. KF

  431. AF is corrected here. KF

    ++++++

    They are using the specified patterns (you call them anomalies) to search for intelligence.

    They don’t know what any EM signal sent by ETs would look like. There is no precedent so nothing to base a specification on. They are assuming that deliberate signals would be sent on a narrow band which makes it easier to distinguish from things like pulsars that emit EMR on a wide spectrum. But it is all assumption. With no previous experience of ET, or indeed whether they exist near enough in time and space to be spotted (and if they are signalling) it is all speculation.

    To me this means that SETI is at the very least as scientific as intelligent design.

    I certainly think the search is scientific. I can’t say the same for the ID movement.

  432. AF is corrected here. KF

    The DNA , RNA and proteins in the living cell have function, all of which happens as well adapted components are put together in specific ways that achieve an observable end or carry out a process.

    I’d start to be a little bit impressed if your method could distinguish between a protein that had function with a protein that did not. At present we can only test proteins we can find in the wild or that we synthesize. Telling us what we already know about existing proteins is no use at all.

  433. AF is corrected here. KF

    ++++++++

    …islands of function…

    This is an analogy that just does not approach reality. Do you want to go through this again? Would a separate thread not make more sense? There are threads on TSZ making clear the objections to this favourite canard of yours.

  434. AF:

    Indeed SETI is all speculation. But IF they received a narrow band signal, and IF that signal had a recognizable specification (prime numbers, pi, etc.), and IF that signal was sufficiently complex (first 50 prime numbers, 50 digits of pi, etc), what do you suppose would happen then, Alan? Care to speculate?

  435. Alan,

    Seth Szostak from SETI disagrees with you.

    I’d start to be a little bit impressed if your method could distinguish between a protein that had function with a protein that did not.

    You still don’t understand science, Alan. We make OBSERVATIONS and attempt to explain them. We OBSERVE proteins functioning and try to explain them- what they do, how they came to be, etc.

    The WHOLE WORLD would be impressed if people like you ever supported the claims of your position. But all you have is “That ain’t designed” and hurl false accusations.

  436. Alan Fox:

    There are threads on TSZ making clear the objections to this favourite canard of yours.

    Those threads are all EVIDENCE-FREE, Alan. That means those “objections” don’t amount to jack.

  437. AF is corrected here. KF

    ++++++

    Indeed SETI is all speculation. But IF they received a narrow band signal, and IF that signal had a recognizable specification (prime numbers, pi, etc.), and IF that signal was sufficiently complex (first 50 prime numbers, 50 digits of pi, etc), what do you suppose would happen then, Alan? Care to speculate?

    Much more money would become available for a much closer look at the signal. But if it turned out to be genuine, that gives OOL theories a huge boost via the Drake equation. A huge “if” but still worth looking, in my view.

  438. AF:

    Much more money would become available for a much closer look at the signal.

    Do you think a closer look would be merited? Why do you suppose that is?

    Much more money? For science? You don’t think such a discovery would be a real science stopper? You don’t think it would be trivial and uninteresting? You don’t think we’d be merely sorting signals into two piles?

  439. AF (cont):

    Interestingly, my proposed specification and level of complexity were rather arbitrary and not rigorously set out in peer-reviewed mathematical formulas. How much CSI did the aforementioned signal contain, Alan? Are you suggesting that we might just throw money(!), much more money(!!), toward a closer look at the signal before we’d figured out exactly how much CSI it contained?

  440. AF is corrected here. KF

    ++++++++++

    Why do you suppose that is?

    My answer was in the comment.

    How much CSI did the aforementioned signal contain

    CSI is an incalculable concept. It bears as much meaning as a couple of other words bandied around here, “design” and “intelligence”.

  441. Alan Fox:

    But if it turned out to be genuine, that gives OOL theories a huge boost via the Drake equation.

    The Drake equation has what to do with the OoL?

  442. Alan Fox:

    CSI is an incalculable concept.

    And yet I have showed you how to do so, complete with an example. Why do you insist on being the fool?

    It bears as much meaning as a couple of other words bandied around here, “design” and “intelligence”.

    In context, those words mean quite a bit, Alan. They have a great deal of significance in science. Strange that you have issues with them.

  443. Phinehas,

    Please keep your SETI signals out of my pile! ;) But please keep piling it on Alan.

    Alan of the one pile- he maketh the pile, he eateth from it and cometh hither to try to shareth.

  444. AF is corrected here. KF

    ++++++++

    AF: CSI is an incalculable concept.

    And yet I have showed you how to do so, complete with an example.

    Ah yes, The Aadvark.I wonder if you repeat the text and have two “piles” of text, do we have double the CSI? One kind of mutation is a gene duplication. Does that double the CSI? If possible, please show your working.

  445. AF is corrected here. KF

    ++++++++

    The Drake equation has what to do with the OoL?

    You’re just funnin’ with me, Joe. Without other examples of life elsewhere, we could be the only pile of people. But two piles, two independent piles… Does away with our uniqueness. From your point of view: one pile, good; two piles, bad.

  446. Alan,

    You are sadly mistaken, again, as usual. The only way there is life on other planets is if Intelligent Design is correct.

  447. Alan Fox:

    I wonder if you repeat the text and have two “piles” of text, do we have double the CSI?

    Nope. Dembski covered that, as have many others.

    One kind of mutation is a gene duplication.

    And just how did you determine a gene duplication is a blind and undirected chemical process?

    Does that double the CSI?

    Why would it?

  448. AF is corrected here. KF

    ++++++++

    The only way there is life on other planets is if Intelligent Design is correct.

    That seems a very odd thing to say, even for you. If there is life on other planets, there is life on other planets. What connects ID to other planets? There is no mention of other planets and other lifeforms being created elsewhere in the universe in the Bible, as far as I am aware.

  449. AF is corrected here. KF

    +++++

    Does that double the CSI?

    Why would it?

    I thought proteins and their DNA codings contained CSI above a certain threshold. If CSI is a numerical property it is, presumably, additive. Or do special rules apply?

  450. The only way there is life on other planets is if Intelligent Design is correct.

    That seems a very odd thing to say, even for you.

    It’s actually covered in “The Privileged Planet”- chapter 16:

    14) You haven’t shown that ETs don’t exist.

    “This is true, but we did not intend to. In fact, ironically, design might even improve the possibility of ETs.”

    If there is life on other planets, there is life on other planets. What connects ID to other planets?

    ID says the universe is designed. Other palnets are in that universe.

    There is no mention of other planets and other lifeforms being created elsewhere in the universe in the Bible, as far as I am aware.

    ID doesn’t have anything to do with the Bible. However there are plenty of UFOs and visitations in it.

  451. Alan Fox:

    I thought proteins and their DNA codings contained CSI above a certain threshold.

    Perhaps. So what?

    If CSI is a numerical property it is, presumably, additive.

    It can be. It depends on the CONTEXT. Two copies of the same book does NOT double the CSI.

  452. AF:

    Do you think a closer look would be merited? Why do you suppose that is?

    My answer was in the comment.

    The part about giving OOL theories a big boost? I didn’t realize that you were interested in OOL theories. You know…since they are outside the theory of evolution and all.

    C’mon Alan. You were being so open and forthcoming there for a brief moment. Why go back to being coy all of a sudden? Why would you be loathe to admit that, given the scenario I outlined, much more money would be thrown at studying the signals because a design inference would be warranted?

    I note that a number of my questions went unanswered:

    You don’t think such a discovery would be a real science stopper?
    You don’t think it would be trivial and uninteresting?
    You don’t think we’d be merely sorting signals into two piles?
    Are you suggesting that we might just throw money(!), much more money(!!), toward a closer look at the signal before we’d figured out exactly how much CSI it contained?

    Any speculation as to why these were ignored I leave to the reader.

  453. And just how did you determine a gene duplication is a blind and undirected chemical process?

  454. AF is corrected here. KF

    ++++++

    You don’t think such a discovery would be a real science stopper?

    No! The reverse!!!

    You don’t think it would be trivial and uninteresting?

    No! The reverse!!!

    You don’t think we’d be merely sorting signals into two piles?

    No.

    Are you suggesting that we might just throw money(!), much more money(!!), toward a closer look at the signal before we’d figured out exactly how much CSI it contained?

    No (as phrased). CSI is a bogus concept so it would not figure in anyone’s calculations.

  455. Alan Fox:

    CSI is a bogus concept so it would not figure in anyone’s calculations.

    So bogus that the internet would be impossible without it. The lives we live would be impossible without that bogus concept.

    Alan one pile, just say anything.

    And Alan, what Phinehas is driving at is the design inference wrt biology would also be “The reverse!” from what you think it would do.

  456. AF:

    I think you might be confused on your last answer. (Or maybe I’m the one confused?) If CSI is a bogus concept that would not figure into anyone’s calculations, then I would think your answer would be, yes, we would throw much more money toward a closer look at the signal without paying attention to CSI.

    In any case, I appreciate your candid answers. Here’s a follow-up question:

    Is it your position that, in the SETI scenario I outlined, an inference to intelligent design played no role of any significance?

  457. AF is corrected here. KF

    ++++++

    I think you might be confused on your last answer. (Or maybe I’m the one confused?)

    Judging by your follow-up, neither of us are confused.

    …yes, we would throw much more money toward a closer look at the signal without paying attention to CSI.

    I predict that if SETI finds an EMR source that looks suspicious (though what sort of signal would arouse suspicion is impossible to guess), interest would be huge and donations would pour in to fund further investigation.

    Is it your position that, in the SETI scenario I outlined, an inference to intelligent design played no role of any significance?

    Yes. “Intelligent Design” is nothing more than an empty catchphrase. “Intelligent Design” inferences don’t work in practice. Nobody has shown what CSI is in any consistent way and nobody can show how to apply the various bit-counts to any real situation. If “ID” inference operates as described by Joe or KF, then it only tells us what we already know. As soon as an unknown parameter is allowed in (as it must with ET) then you might as well use a crystal ball.

  458. I simply can’t follow Alan’s logic:

    “Yes. “Intelligent Design” is nothing more than an empty catchphrase. “Intelligent Design” inferences don’t work in practice.”

    How can we not look at certain objects and infer design? And why is it not possible to work out the complexity involved in that design?

    To me this just seems obscure, therefore, if Alan is correct, what am I not understanding? (if indeed I am even understanding his position correctly)

    Can someone please help me out here.

    Thanks :)

  459. AF:

    Why do you insist on continuing willful misrepresentations, in the hopes of making such seem true? Do you not recognise that at this point they go to character?

    FYI’s (or at least for the sake of onlookers who might think your remarks have any merit whatsoever):

    1 –> CSI is an observable and measurable entity, as can be seen, again, by a very simple example of three different strings:

    1] OSC/ mechanical order (like in a crystal of NaCl): wewewewewewe . . .

    2] RSC/chance strings (such as may happen with a rock matrix):iw3ertujshkjsdbvhsdv . . .

    3] FSC/organised functionally specific strings (such as may happen in an informational polymer like RNA/protein): this string is a case of functionally specific information . . .

    2 –> FSC depends crucially on the specific configuration of matched components, which drastically constrains the number of possibilities, relative to the configuration space of possible arrangements, scattered or clumped of same components. [Think about how many ways the parts of a car engine can be arranged in working order, vs the number of ways such could be clumped or scattered that would not work.] This is why the concept of an island of function [T] in a much larger sea of non-functional gibberish [W - T], out of the field of possibilities W, makes sense.

    3 –> Your repeated verbal dismissals of such basics just show closed mindedness and selective hyperskepticism, because evidently you do not wish to go where such points and the easiest way to object is to willfully distort and dismiss basic concepts. But after a certain point it is no more misunderstanding, it is willfully continued misrepresentation, sadly, with all that this implies.

    4 –> You have actually been corrected in this thread several times and have simply ignored correction in order to further spew out your talking points.

    5 –> In addition, a focus on strings is WLOG, as complex arrangements can be reduced to clusters of nodes and connecting arcs, leading to a string that describes the list. Indeed, that is more or less how something like AutoCAD, etc works.

    6 –> You objected that CSI cannot be quantified. On being confronted with a correction, more than once in this thread, you have ducked and dodged. For instance, contrast:

    AF, 385: . . . We don’t know how to measure CSI of something … anything … because nobody can tell us how!

    KF, ed note to 385: AF, why do you insist on a continued willful misrepresentation in the teeth of the evident truth presented to you any number of times, including above in this thread?

    Your remarks just above are 123 ASCII characters in standard English [clearly objectively recognisable], at 7 bits per character.

    This gives us I*S = 861 * 1 = 861 functionally specific bits.

    Applying the Chi_500 metric [--> Chi_500 = I*S - 500, bits beyond the solar system threshold] that AF tries to imagine does not exist or is unusable:

    Chi_500 = 861 = 500 = 361 bits beyond the solar system threshold

    This is a second live demonstration in several days to AF.

    Let us see his next excuse for — sadly, predictably — dismissing and misrepresenting it.

    AF, 390 to Joe: you say you can count the bits of something … anything … and if greater than 2^500 or 10^150 it must be designed and if not it still might be. Trivial and useless. And unendorsed, so far. Would any other ID proponent like to confirm that Joe’s CSI is Dembki’s CSI?

    AF, 400: [KF:] You have again been corrected at 385 above.

    [AF:] I have told you that pasting edits into past comments is a disreputable way to attempt dialogue. You can do better than that. Please stop it . . .

    7 –> Willful distortions, evasions and red herrings led away to such strawmen soaked in ad hominems and set alight. In this case, it is entirely in order to correct a willfully obtuse objector who continues to distort and misrepresent in the teeth of correction by exposing that fact, right there in his comment. Especially after there has been adequate notification and correction. And the personal attack that I am dishonest in moderating Joe is laughable. He slips off the wagon from time to time, but at least tries. That speaks volumes by contrast.

    8 –> And here is your sentence at this point: this correction is going to be linked or appended in this thread so soon as you show yourself playing the drumbeat talking point misrepresentation game again.

    9 –> You tried to then raise the issue that has been addressed for years, of duplication of information. Does duplication create new info de novo? Nope, from its very name. However, the duplicating mechanism may indeed be further FSCO/I as can be seen from a photocopier or the highly complex DNA transcribing mechanism in the living cell.

    10 –> In addition, there may be post copying adjustments that point to further CSI — such as in the maturation of mRNA with snipping and possible rearrangements, addition/stripping of headers etc. [Cf here the ISO OSI 7-layer comms model and how similar mechanisms do appear in the living cell.]

    11 –> Where also (contrary to your just counting bits caricature) it has been carefully specified right there in the name, that the issue is a joint specificity- complexity criterion; as has been pointed out by Dembski et al for years and indeed as traces back to Orgel’s distinctions in 1973 and to Wicken’s identification of functionally specific complex organisation in 1979 that you also ignore. (Cf. here for the cites and comments that have been repeatedly pointed out, linked and/or cited to you, and which you willfully ignored the better to continue willful misrepresentations.)

    12 –> One that may as Durston et al show, be adjusted for redundancy that comes up in the code or possible substitutions.

    13 –> Where also — as you full well know or should know — that joint between complexity and specificity [especially functional specificity] is a crucial distinction from mere info carrying capacity, aka info in the Shannon sense.

    14 –> Your bland declaration that the construct FSCO/I has not been “endorsed” is a bit of dismissive ad hominem, in a context where on being challenged to show yourself competent to address basic info theory [by contrast with the undersigned who has had to teach such in the context of teaching telecomms . . . cf. again a basic intro in my always linked briefing note through my handle here on] has repeatedly been corrected by reference to not only Orgel-Wicken but also Dembski and Meyer (cf clip here on; Dembski in the often used cite from NFL pp. 144 and 148 in discussing CSI’s nature and definition, points out that in biological contexts, specification is cashed out as FUNCTION.) as well as Abel, Trevors, Durston et al. in their use of OSC/RSC/FSC, and its quantification tracing to work by Szostak and onwards to the significance of Shannon’s H metric of average info per symbol in light of redundancies leading to non-uniform distribution of symbols; e.g. e is about 1/8 of typical English text and Q is most often followed by U, save with things like Iraq or QANTAS.

    15 –> It is by now well known or should full well be known that the log reduction of the 2005 Dembski equation that then sets limits based on the 10^57 atoms of our solar system acting as searching agents for the lifespan of the system, at a rate equal to that of the fastest chemical rxns, gives a quantification that yields bits beyond the threshold of a needle in haystack search that per sampling theory, makes it maximally implausible that blind chance and mechanical necessity could act together or separately to find shorelines of islands of function in the sea of gibberish implied by the FSCO/I in something beyond 500 bits of complexity: Chi_500 = I*S – 500.

    16 –> Let me clip from the linked briefing, where it discusses the quantification by Durston et al. 2007. Pardon length, it is needed at this point, making substitutions for non-English symbols:

    11 –> Durston, Chiu, Abel and Trevors provide a third metric, the Functional H-metric in functional bits or fits, a functional bit extension of Shannon’s H-metric of average information per symbol, here. The way the Durston et al metric works by extending Shannon’s H-metric of the average info per symbol to study null, ground and functional states of a protein’s AA linear sequence — illustrating and providing a metric for the difference between order, randomness and functional sequences discussed by Abel and Trevors — can be seen from an excerpt of the just linked paper. Pardon length and highlights, for clarity in an instructional context:

    Abel and Trevors have delineated three qualitative aspects of linear digital sequence complexity [2,3], Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC). RSC corresponds to stochastic ensembles with minimal physicochemical bias and little or no tendency toward functional free-energy binding. OSC is usually patterned either by the natural regularities described by physical laws or by statistically weighted means. For example, a physico-chemical self-ordering tendency creates redundant patterns such as highly-patterned polysaccharides and the polyadenosines adsorbed onto montmorillonite [4]. Repeating motifs, with or without biofunction, result in observed OSC in nucleic acid sequences. The redundancy in OSC can, in principle, be compressed by an algorithm shorter than the sequence itself. As Abel and Trevors have pointed out, neither RSC nor OSC, or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life [5]. FSC includes the dimension of functionality [2,3]. Szostak [6] argued that neither Shannon’s original measure of uncertainty [7] nor the measure of algorithmic complexity [8] are sufficient. Shannon’s classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that ‘different molecular structures may be functionally equivalent’. For this reason, Szostak suggested that a new measure of information–functional information–is required [6] . . . .

    Shannon uncertainty, however, can be extended to measure the joint variable (X, F), where X represents the variability of data, and F functionality. This explicitly incorporates empirical knowledge of metabolic function into the measure that is usually important for evaluating sequence complexity. This measure of both the observed data and a conceptual variable of function jointly can be called Functional Uncertainty (Hf) [17], and is defined by the equation:

    H(X f(t)) = -[SUM]P(X f(t)) logP(X f(t)) . . . (1)

    where X f denotes the conditional variable of the given sequence data (X) on the described biological function f which is an outcome of the variable (F). For example, a set of 2,442 aligned sequences of proteins belonging to the ubiquitin protein family (used in the experiment later) can be assumed to satisfy the same specified function f, where f might represent the known 3-D structure of the ubiquitin protein family, or some other function common to ubiquitin. The entire set of aligned sequences that satisfies that function, therefore, constitutes the outcomes of X f. Here, functionality relates to the whole protein family which can be inputted from a database . . . .

    In our approach, we leave the specific defined meaning of functionality as an input to the application, in reference to the whole sequence family. It may represent a particular domain, or the whole protein structure, or any specified function with respect to the cell. Mathematically, it is defined precisely as an outcome of a discrete-valued variable, denoted as F={f}. The set of outcomes can be thought of as specified biological states. They are presumed non-overlapping, but can be extended to be fuzzy elements . . . Biological function is mostly, though not entirely determined by the organism’s genetic instructions [24-26]. The function could theoretically arise stochastically through mutational changes coupled with selection pressure, or through human experimenter involvement [13-15] . . . .

    The ground state g (an outcome of F) of a system is the state of presumed highest uncertainty (not necessarily equally probable) permitted by the constraints of the physical system, when no specified biological function is required or present. Certain physical systems may constrain the number of options in the ground state so that not all possible sequences are equally probable [27]. An example of a highly constrained ground state resulting in a highly ordered sequence occurs when the phosphorimidazolide of adenosine is added daily to a decameric primer bound to montmorillonite clay, producing a perfectly ordered, 50-mer sequence of polyadenosine [3]. In this case, the ground state permits only one single possible sequence . . . .

    The null state, a possible outcome of F denoted as ø, is defined here as a special case of the ground state of highest uncertainly when the physical system imposes no constraints at all, resulting in the equi-probability of all possible sequences or options. Such sequencing has been called “dynamically inert, dynamically decoupled, or dynamically incoherent” [28,29]. For example, the ground state of a 300 amino acid protein family can be represented by a completely random 300 amino acid sequence where functional constraints have been loosened such that any of the 20 amino acids will suffice at any of the 300 sites. From Eqn. (1) the functional uncertainty of the null state is represented as

    H(X 0(ti))= – [SUM] P(X 0(ti)) log P(X 0(ti)) . . . (3)

    where (X 0(ti)) is the conditional variable for all possible equiprobable sequences. Consider the number of all possible sequences is denoted by W. Letting the length of each sequence be denoted by N and the number of possible options at each site in the sequence be denoted by m, W = m N. For example, for a protein of length N = 257 and assuming that the number of possible options at each site is m = 20, W = 20257. Since, for the null state, we are requiring that there are no constraints and all possible sequences are equally probable, P(X 0(ti)) = 1/W and

    H(X 0(ti))= – [SUM](1/W) log (1/W) = log W . . . (4)

    The change in functional uncertainty from the null state is, therefore,

    Delta-H(X 0(ti), X f(t j)) = log (W) – H(X f(ti)). (5)

    . . . . The measure of Functional Sequence Complexity, denoted as z, is defined as the change in functional uncertainty from the ground state H(X g(ti)) to the functional state H(X f(t i)), or

    z = delta H (X g(ti), X f(tj)) . . . (6)

    The resulting unit of measure is defined on the joint data and functionality variable, which we call Fits (or Functional bits). The unit Fit thus defined is related to the intuitive concept of functional information, including genetic instruction and, thus, provides an important distinction between functional information and Shannon information [6,32].

    Eqn. (6) describes a measure to calculate the functional information of the whole molecule, that is, with respect to the functionality of the protein considered. The functionality of the protein can be known and is consistent with the whole protein family, given as inputs from the database. However, the functionality of a sub-sequence or particular sites of a molecule can be substantially different [12]. The functionality of a sub-molecule, though clearly extremely important, has to be identified and discovered . . . .

    To avoid the complication of considering functionality at the sub-molecular level, we crudely assume that each site in a molecule, when calculated to have a high measure of FSC, correlates with the functionality of the whole molecule. The measure of FSC of the whole molecule, is then the total sum of the measured FSC for each site in the aligned sequences. Consider that there are usually only 20 different amino acids possible per site for proteins, Eqn. (6) can be used to calculate a maximum Fit value/protein amino acid site of 4.32 Fits/site [NB: Log2 (20) = 4.32]. We use the formula log (20) – H(Xf) to calculate the functional information at a site specified by the variable X f such that X f corresponds to the aligned amino acids of each sequence with the same molecular function f. The measured FSC for the whole protein is then calculated as the summation of that for all aligned sites. The number of Fits quantifies the degree of algorithmic challenge, in terms of probability, in achieving needed metabolic function. For example, if we find that the Ribosomal S12 protein family has a Fit value of 379, we can use the equations presented thus far to predict that there are about 1049 different 121-residue sequences that could fall into the Ribsomal S12 family of proteins, resulting in an evolutionary search target of approximately 10^-106 percent of 121-residue sequence space. In general, the higher the Fit value, the more functional information is required to encode the particular function in order to find it in sequence space. A high Fit value for individual sites within a protein indicates sites that require a high degree of functional information. High Fit values may also point to the key structural or binding sites within the overall 3-D structure.

    11[a] –> Thus, we here see an elaboration, in the peer reviewed literature, of the concepts of Functionally Specific, Complex Information [FSCI] (and related, broader specified complexity) that were first introduced by Orgel and Wicken in the 1970′s. This metric gives us a way to compare the fraction of residue space that is used by identified islands of function, and so validates the islands of function in a wider configuration space concept. So, we can profitably go on to address the issue of how plausible it is for a stochastic search mechanism to find such islands of function on essentially random walks and trial and error without foresight of location or functional possibilities. We already know that intelligent agents routinely create entities on islands of function based on foresight, purpose, imagination, skill, knowledge and design.

    17 –> Particularly note:

    The measure of Functional Sequence Complexity, denoted as z, is defined as the change in functional uncertainty from the ground state H(X g(ti)) to the functional state H(X f(t i)), or

    z = delta H (X g(t i), X f(t j)) . . . (6)

    The resulting unit of measure is defined on the joint data [--> i.e. complexity based on number of informational elements] and functionality [--> based on observed biofunction] variable, which we call Fits (or Functional bits). The unit Fit thus defined is related to the intuitive concept of functional information, including genetic instruction and, thus, provides an important distinction between functional information and Shannon information [6,32] . . . .

    In general, the higher the Fit value, the more functional information is required to encode the particular function in order to find it in sequence space.

    17 –> Durston et al do not discuss a specific threshold of reasonable search resources, but the needle in haystack threshold for the solar system already given is reasonable. Durston’s metric brings in the redundancy of the actual code used [as opposed to the distribution that is chemically possible] and so we may freely insert it into the Chi_500 metric expression, as was done in the IOSE and in discussion threads here at UD before that, some years back now . . . with AF doubtless looking on:

    Using Durston’s Fits values — functionally specific bits — from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:

    RecA: 242 AA, 832 fits, Chi: 332 bits beyond
    SecY: 342 AA, 688 fits, Chi: 188 bits beyond
    Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond

    xxiii: And, this raises the controversial question that biological examples such as DNA — which in a living cell is much more complex than 500 bits — may be designed to carry out particular functions in the cell and the wider organism.

    18 –> So, not only is it a matter of reasonable description, modelling and quantification, but this is closely linked to serious work that has appeared in the peer reviewed literature, for some years now. AF, you are willfully misrepresenting what you do or should know better than. That, sir, FYI — as you know or full well should know, is willfully deceptive and in defiance on your part of duties of care to truth, accuracy and fairness.

    19 –> There is also some discussion of SETI and whether there is specification involved in assessing the use of narrowband, evidently modulated or at least evident carrier, signals. The answer to this is obvious. To maintain a steady carrier at a narrowband transmission and to modulate it with an intelligence bearing signal that is recognisable, would be signs of functional specificity. Unfortunately, the more likely forms of transmission for an advanced culture going about its business, broadband coded frequency hopping signals or the like will only appear as an increment of noise, save to those who have the code to pull it out of the apparent sea of noise. In short the SETI is looking for what we can, in the context of maybe someone is saying hi, here we are.

    20 –> At the same time, as natural oscillators are possible, the presence of a case of a narrowbad signal or periodic one that is explicable on natural factors, would not count. Pulsars do not count as signs of intelligence, though if one were to be found with a coding on the signal, that would be a different story. That’s why Sagan’s Contact used a modulated signal in a pattern that is quite specific and unlikely to be “natural,” the sequence of primes.

    21 –> In short SETI does in fact show that it is understood that coded information in a functionally specific complex organised context, would be a sign of design by intelligence. It also shows that – per willingness to spend a fair sum of money — it is generally accepted that humans do not exhaust the set of potential intelligences. So much for that particular strawman tactic.

    ++++++++++

    So, AF, you have been duly corrected on your main errors, and this summarises the corrections. Now, I would advise you to attend to such correction and amend your ways.

    KF

    PS: In some of his remarks, AF makes reference to ID being a dangerous political movement and to the Bible. It is evident from this that he is in material part motivated by the ID = Creationism smear pushed by the NCSE et al. His behaviour above and elsewhere in and around UD for the past eight years, should thus be understood as that of an ideologue who supports the evolutionary materialist scientism agenda that likes to fly the false colours of “science” in our day [whether as an actual atheistical materialist or as a fellow traveller makes but little difference . . . ], seeking to oppose what he perceives to be an opposed political movement by “any means deemed necessary,” and too often using subtler forms of Alyinskyite tactics of misrepresentation, polarisation and attempting to discredit. Hence the refusal to actually engage substance on science, especially where he patently has gaps in his understanding. Hence we can understand the resort to attempted drumbeat repetition of sloganeering talking points meant to dismiss what he obviously cannot cogently address on the merits. Hence the enabling behaviour of quietly going along with those who use more blatant forms of neo-marxist tactics, though outright abuse. He believes that all the angels are on his side, and only devils and fools or incompetents on this. It is therefore fair comment to summarise per the patterns that have been evident: he projects unto us or is willing to go along with the projection to us, of an imagined hidden right wing fundamentalist theocratic nazi-like tyrannical agenda that threatens “progress” illuminated by the light of “science” and “reason.” In short, he is playing at dirty, deeply polarised politics, not genuine discussion of science at a table of civility. He is posting drumbeat talking points here to enable the dismissal of what is said here, and to try to make us look like idiots [note the common school-yard taunt on this . . . ] or evil, ignorant and incompetent hypocrites. No wonder he almost never takes up the actual discussion on merits beyond dismissive talking points or snippets he can wrench to fit into his talking points. In first reply, he is hereby pointed to the UD weak argument correctives from here on that address the “creationism in a cheap tuxedo” and onward linked slanderous, loaded talking points. He is pointed here, to highlight that in fact Fascism, which he — doubtless following a common error — imagines is right wing, is actually an ideology of nihilistic, superman as political saviour, messianic statism, on the left end of the political spectrum. It is indeed to the right of Stalin’s Communism, but that is the only sense of “right” that is relevant. In addition, any species of political messianism is an attempt to substitute a political order and leader for loyalty to God our Saviour, and is both idolatrous and profoundly anti- [= counterfeit] Christian. So it is unsurprising to see a visual demonstration here — NB the discussion to go with it — that Hitler and his National Socialist German Worker’s Party in particular were Anti-christian. And finally, AF and ilk would be well advised to heed Plato’s warning on the question-begging imposition of evolutionary materialism on a culture’s trend-setters and where it leads to historically, radical relativism o knowledge and morals, multiplied by the rise of nihilist factions who are taught to think that the highest right is might, leading onwards to chaos and to attempt to restore order, open or veiled tyranny:

    [[The trendy philosophers, teachers and artists c. 400 BC] say that the greatest and fairest things are the work of nature and of chance, the lesser of art [[ i.e. techne] . . . They say that . . . The elements are severally moved by chance and some inherent force according to certain affinities among them-of hot with cold, or of dry with moist, or of soft with hard, and according to all the other accidental admixtures of opposites which have been formed by necessity. After this fashion and in this manner the whole heaven has been created, and all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only . . . .

    [[T]hese people would say that the Gods exist not by nature, but by art, and by the laws of states, which are different in different places, according to the agreement of those who make them; and that the honourable is one thing by nature and another thing by law, and that the principles of justice have no existence at all in nature, but that mankind are always disputing about them and altering them; and that the alterations which are made by art and by law have no basis in nature, but are of authority for the moment and at the time at which they are made.- [[Relativism, too, is not new; complete with its radical amorality rooted in a worldview that has no foundational IS that can ground OUGHT.] These, my friends, are the sayings of wise men, poets and prose writers, which find a way into the minds of youth. They are told by them that the highest right is might [[ Evolutionary materialism leads to the promotion of amorality], and in this way the young fall into impieties, under the idea that the Gods are not such as the law bids them imagine; and hence arise factions [[Evolutionary materialism-motivated amorality "naturally" leads to continual contentions and power struggles], these philosophers inviting them to lead a true life according to nature, that is, to live in real dominion over others [[such amoral factions, if they gain power, "naturally" tend towards ruthless tyranny; here, too, Plato hints at the career of Alcibiades], and not in legal subjection to them . . .

  460. PJ: I hope the just above will be of help. KF

  461. Joe: You are reminded to get back up on the wagon, and also of a certain message. KF

  462. Alan Fox:

    Intelligent Design” is nothing more than an empty catchphrase.

    Is it? Good luck proving that bit of tripe, Alan.

    Do you really think that your bald spewage means something?

    “Intelligent Design” inferences don’t work in practice.

    Yes they do. Your ignorance means nothing here, Alan.

    If “ID” inference operates as described by Joe or KF, then it only tells us what we already know.

    So we already know that the universe and living organisms are designed? Then why aren’t we teaching that in schools?

    I see Alan is still upset because his position has absolutely nothing.

    Natural selection? Proven to be impotent.

    Genetic drift? Always known to be impotent

    So all Alan has to attack ID like a belligerent little child.

  463. So CSI is a “bogus” concept that the world cannot live without.

    How does that work, Alan?

  464. AF: You have a false accusation of fraud — not merely a claim of error — on the table to deal with. KF

  465. 1: AF is corrected here. KF

    2: AF: You have a false accusation of fraud — not merely a claim of error — on the table to deal with. KF
    3: Functional sequence complexity speaks of strings – . . . -*-*-*-* – . . . – which are functionally specific, and complex enough to be relevant to CSI & FSCO/I. Where also, such is WLOG as anything reducible to a set of nodes and arcs can be reduced to a network list thus strings. Attempts to sweep functional sequence complexity off the table are ill-informed or ill-intentioned. KF

    +++++++

    Quick response to Kairosfocus in comment # 459.

    I’ll try and work with your bullet points.
    I’m not going to respond to the following numbered points:

    2. (FSC is irrelevant to this thread)
    3. ad hominem
    4. ditto
    5. irrelevant
    7. ad hominem
    8. Juvenile
    10. Garbled
    12. Durston does not talk about CSI so irrelevant
    16. ditto
    17. ditto
    18. ad hominem
    and the bafflegab in the PS

    So, to the remaining points:

    1.

    CSI is an observable and measurable entity…

    So you keep saying. But you fail to explain how to measure it for any meaningful example. Try the nine residue polypeptide, oxytocin. As it was the first polypeptide to be sequenced and synthesized, it seems an appropriate example. Compare it with the hypothetical (at least I made it up) polypeptide whose sequence is RHHRKST. I’m especially interested if you get a different numerical result for the two entities.

    6.

    You objected that CSI cannot be quantified.

    I wouldn’t put it as strongly as that. CSI may be a measurable quantity. We have yet to see a meaningful definition or a clear reproducible way of calculating this (let’s say) alleged property of an entity.

    9.

    You tried to then raise the issue that has been addressed for years, of duplication of information. Does duplication create new info de novo? Nope, from its very name.

    Right so all entities that are identical only contain one measurable quantity of CSI. So CSI literally doesn’t add up. If you have a gene duplication event followed by drift mutations in the redundant gene does that then have more CSI?

    11.

    Where also (contrary to your just counting bits caricature) it has been carefully specified right there in the name, that the issue is a joint specificity- complexity criterion

    In reply to a comment by Eric Anderson, who asserted:

    Alan, you know, or should know, that the design inference is not just a count of bits. There has to also be an observable function, or specification, if you will.

    I asked “So how is function quantified? And how does that quantity enter into the calculation?”

    This remains unanswered.

    13.

    Where also — as you full well know or should know — that joint between complexity and specificity [especially functional specificity] is a crucial distinction from mere info carrying capacity, aka info in the Shannon sense

    See 11. I asked for clarification and as yet remain unanswered.

    14. I’m sorry, sometimes your stream-of-consciousness verbal diarrhoea masks any possible kernel of content.

    15.

    It is by now well known or should full well be known that the log reduction of the 2005 Dembski equation that then sets limits based on the 10^57 atoms of our solar system acting as searching agents for the lifespan of the system, at a rate equal to that of the fastest chemical rxns, gives a quantification that yields bits beyond the threshold of a needle in haystack search that per sampling theory, makes it maximally implausible that blind chance and mechanical necessity could act together or separately to find shorelines of islands of function in the sea of gibberish implied by the FSCO/I in something beyond 500 bits of complexity: Chi_500 = I*S – 500.

    Needles in haystacks and islands of function are repackaged arguments from incredulity. And you seem to be back to bit counting.

    19. You seem to be agreeing with me about SETI

    20. ditto

    21.

    In short SETI does in fact show that it is understood that coded information in a functionally specific complex organised context, would be a sign of design by intelligence.

    If ETs showed up they’d be real entities. Maybe we could get them to perform intelligence tests to see how intelligent they were. This semantic trick with “intelligence” becomes tiresome.

    It also shows that – per willingness to spend a fair sum of money — it is generally accepted that humans do not exhaust the set of potential intelligences.

    Obscure to the point of inscrutability!

    So much for that particular strawman tactic.

    :rolleyes:

    Finally:

    So, AF, you have been duly corrected on your main errors, and this summarises the corrections.

    Absolute nonsense. All you have done is repeat the same old bafflegab. No demonstration of how to calculate CSI, just words to obscure the paucity of your response.

    Finally, finally:

    I told you to stop editing into past comments. The practice is unethical. Yet, when corrected, you persist and I shall therefore not be making any further responses to you via this website until you mend your ways.

    Good day, Sir.

  466. 1: AF is corrected here. KF

    2: AF: You have a false accusation of fraud — not merely a claim of error — on the table to deal with. KF
    3: Functional sequence complexity speaks of strings – . . . -*-*-*-* – . . . – which are functionally specific, and complex enough to be relevant to CSI & FSCO/I. Where also, such is WLOG as anything reducible to a set of nodes and arcs can be reduced to a network list thus strings. Attempts to sweep functional sequence complexity off the table are ill-informed or ill-intentioned. KF

    +++++

    If franklin and CLAVDIVS are still checking in, could I ask if they would like to visit TSZ here

  467. AF:

    I can’t say I’m following you. Frankly, I’m not really interested at the moment in whether or not CSI, as currently formulated, is a valid concept. As pointed out earlier, it wasn’t included in my outlined scenario in any sort of explicit way. To review what we’ve established so far (and BTW, I totally agree with your answers to my questions, though I must confess that whatever point you are making with that last one is still too subtle for me to grasp):

    Given the following scenario.

    A. SETI receives a narrow band signal from space.
    B. The signal had a recognizable specification (prime numbers, pi, etc.).
    C. The signal was sufficiently complex (first 50 prime numbers, 50 digits of pi, etc.).

    The response would be.

    D. Much more money!

    Could you please walk me through exactly how you got (rather emphatically) to D without making any sort of inference to design whatsoever?

  468. Alan Fox,

    What do you think about trying to run through a relatively straightforward example of the very thing you are looking for folks such as kairosfocus to provide?

    In other words, you provide the meaningful definition of CSI and way of calculating it.

    Now, I understand that this has you doing the work that others should have done — and they say they have done already — and I also understand that one of your points is that no meaningful definition or unambiguous method has yet been given.

    Nevertheless, I hope you’ll agree that simply trying may prove educational for all of us. Sometimes, with some people, the best way to show the car is broken is to try starting the ignition and driving the thing.

  469. AF: You have been caught out in a flat case of false accusation of fraud — “bogus,” and have taken no heed. You have given no indication of correcting willful, continued misrepresentations of facts, patiently and repeatedly pointed out to you in correction (from multiple sources and I suspect across the course of eight years), and at the end, you have twisted about reluctantly given, well-justified corrections on your behaviour into further false accusations of personal attacks. These substantiate the concerns that you are showing yourself the closed minded ideologue and propagandistic rhetor using “any means deemed necessary.” (Which I will further document in a moment, as a lesson for the onlooker, as obviously you will pay no heed to correction.) Now at length you want to take up your ball and run home, on the pretence that it is I who need to amend my ways. Sadly, utterly revealing. Pull up your socks, man! KF

    ++++++++

    Could you please walk me through exactly how you got (rather emphatically) to D without making any sort of inference to design whatsoever?

    I am disinclined to comment further here until Kairosfocus mends his ways and stops editing into other peoples past comments. It’s unethical and unacceptable. Did you ever find your way over to The Skeptical Zone? (Ah, I see you registered) I could start a thread there if you like.

  470. Sometimes, with some people, the best way to show the car is broken is to try starting the ignition and driving the thing.

    But I can’t even see the damn car!

  471. AF:

    That’s too bad. If you do decide to return, my questions will be waiting for you. ;)

    Unfortunately, the atmosphere at TMZ wasn’t particularly to my liking, though Liz was a generous enough host.

  472. Ah well, never mind, Phinehas.Here is an article that might help clarify where I was going. I especially like the mention of context. ;)

    Bye

  473. Phinehas, AF,

    I read through the above link from AF and found a few problems with it.

    It’s no wonder therefore that AF is as confused as he is.

    What do others think?

    :)

  474. AF:

    That’s an interesting and informative article. Thanks for sharing it.

    However, I’m not sure I see how it relates to the scenario I outlined. That SETI is looking for simplicity as an indication of “artificiality” has no bearing on whether specified complexity could indicate the same. In fact, you’ve agreed that the scenario I outlined, which did not consist of a simple tone or green square, would likely provoke a similar reaction. Supposing otherwise would stretch the bounds of credulity.

    So are you now saying that the scenario I outlined would not merit a similar inference?

  475. Earth to Alan Fox-

    FSC is the same thing as CSI wrt biology. Just because you choose to be willfully ignorant of this that isn’t a refutation.


    CSI is an observable and measurable entity…

    So you keep saying. But you fail to explain how to measure it for any meaningful example.

    You are just lying now.

    Try the nine residue polypeptide, oxytocin. As it was the first polypeptide to be sequenced and synthesized, it seems an appropriate example. Compare it with the hypothetical (at least I made it up) polypeptide whose sequence is RHHRKST. I’m especially interested if you get a different numerical result for the two entities.

    My goodness, you are just ignorant as to how science operates. CONTEXT Alan. We don’t just see polypeptides floating around.

    That said, 9 residues maps back to 27 nucleotides. 27 x 2 = what, Alan?

    Then we check for specificity. If any ole 9 residues or sequence order will do, then it ain’t specified.

    So, 9 residues has an information carrying capacity, ie Shannon information, of 54 bits, Alan. Then it matters if there is some function as to if that information is A) specified and B) just how specific is it.

  476. In SETI and Intelligent Design, SETI researcher Seth Shostak wants to assure everyone that the two don’t have anything in common.

    However it is obvious that Seth doesn’t completely understand ID’s argument, and he misrepresents the anonymous quote he provided.

    Seth on ID:

    The way this happens is as follows. When ID advocates posit that DNA–which is a complicated, molecular blueprint–is solid evidence for a designer, most scientists are unconvinced. They counter that the structure of this biological building block is the result of self-organization via evolution, and not a proof of deliberate engineering. DNA, the researchers will protest, is no more a consciously constructed system than Jupiter’s Great Red Spot. Organized complexity, in other words, is not enough to infer design.

    Yes specified complexity is used as evidence for design. Not mere complexity and not organized complexity. A hurricane is an example of organized complexity. DNA is an example of specified complexity.

    Seth on IDists on SETI:

    “upon receiving a complex radio signal from space, SETI researchers will claim it as proof that intelligent life resides in the neighborhood of a distant star. Thus, isn’t their search completely analogous to our own line of reasoning–a clear case of complexity implying intelligence and deliberate design?” anonymous IDist(s)

    (No IDist claims complexity implies intelligence so methinks Seth made it all up)

    What does Seth say about his made-up quote?:

    In fact, the signals actually sought by today’s SETI searches are not complex, as the ID advocates assume.- S Shostak

    1- All that quote said was about RECEIVING, not searching.
    2- And if you did RECEIVE a signal of that nature you would claim it as such
    3- By ID’s standards of complexity is related to probability your narrow band meets the complexity criteria

    An endless, sinusoidal signal – a dead simple tone – is not complex; it’s artificial.- Shostak

    Not if we use the word complexity in terms of (im)probability then that sine wave would meet the criteria.
    However Seth does add some insight:

    Such a tone just doesn’t seem to be generated by natural astrophysical processes. In addition, and unlike other radio emissions produced by the cosmos, such a signal is devoid of the appendages and inefficiencies nature always seems to add –

    Exactly! And if natural astrophysical processes can be found that generate such a tone then you would have to search for something else. Something that natural astrophysical processes cannot account for.

  477. Aaln Fox:

    If ETs showed up they’d be real entities.

    There is more evidence for ETs then there is for your position, Alan. Does that bother you too?

    And if meeting the designer(s) is the only way to get you to accept Intelligent Design, then it is clear that you don’t give a damn about science- clearer.

  478. OK to recap-

    Alan is OK with archaeology, forensic science and SETI using two piles. But he is against ID doing so (the two piles are designed or not), for reasons he never divulges. :roll:

    Then Alan talks about CONTEXT because when it suits him, context is important. After he talks about context Alan pulls polypeptides from his butt, ie NO CONTEXT, and asks us to measure their information. :roll:

    And finally Alan still plays obtuse wrt CSI even though he uses CSI every day and the world couldn’t get by without it. :roll:

    Is that about right, Alan?

    :razz:

  479. Onlookers (attn AF, EL & ilk at TSZ, etc):

    Over the past few days, AF has unfortunately shown just why after eight years he has made no progress in understanding or soundly interacting with design theory or thinkers. This has come to a head in his remark at 454 above, where he stated:

    CSI is a bogus concept so it would not figure in anyone’s calculations.

    That is a flat out false accusation of sustained fraud by the design theory movement and associated thinkers, and when he has been confronted with cases in point, including taken from his own comments, he has only been evasive or dismissive, returning to some variant of this false accusation or concepts pretty directly tied to it. However, in his mind he thinks himself justified in his behaviour — a typical problem with ideologues. Why is that? This can be seen from what he has further plainly stated at 400 above:

    I think ID is dangerously political nonsense. I have never posted anything here that I knew was not true . . .

    In short, first he imagines himself to be defending the materialist orthodoxy from some dangerous attack, an attack by what others elsewhere have called — by way of false accusation — “Creationism in a cheap tuxedo.” This can be seen from his further remark at 448 that plainly reflects this assumption that the framework for design thought is Bible-based fundamentalism (by way of irrelevantly injecting a reference to the Bible projected unto design theory supporters, into a discussion on SETI):

    There is no mention of other planets and other lifeforms being created elsewhere in the universe in the Bible . . .

    Now, such attacks have long since been corrected and pointed out to him, but he is not listening, he is too full of his ideological frame of thought and the pattern of thinking and arguing that has led him so far astray.

    But isn’t he sincere, never speaking that which he knows to be false, as he also declared in the cited snippet?

    I am afraid, however, duties of care to truth, accuracy and fairness go beyond merely not speaking what one KNOWS is not true.

    They include not speaking that which one SHOULD KNOW is not true. And particularly, they require refraining from manifestly false accusations (how many slanderers imagine they are speaking the truth?!!) and from refusing to attend to or heed correction. Of which unfortunately we have all too much evidence of in hand, even just in this thread.

    I simply again point to the UD weak argument correctives again (which were already linked and are accessible on this and every UD post), on the attempt to politicise what design theory is about and the related attempts to conflate it with the already successfully smeared creationists. Let it further suffice to note that the creationists themselves make it plain that they differ fundamentally with design thinkers. The WAC’s make plain why: creationism in the usual sense is about starting with scripture held to be accurate record of origins from the Creator, and adjusting science to fit that record. Design theory is about what can be inferred on tested reliable inductive sign that indicates cause across chance, necessity and design. The antecedents of design thought lie in those Bible thumping fundies — NOT — Plato [cf. here on The Laws, Bk X c. 360 BC], Cicero and co.

    All of this is in the easily accessible corrective record, but AF has chosen to refuse to heed his duties of care to seek the truth before speaking in reflection of what is well warranted as true. On being corrected, he has either ignored it or has resorted to some of the worst debate tactic comebacks that distort, dismiss, evade or twist about the truth.

    That is, he has plainly, repeatedly spoken in willful defiance of duties of care to truth, fairness and warrant, hoping to profit from what is false or what is a misrepresentation or what is a false accusation being perceived as true. Such, sadly, is willfully deceptive. (Cf. definition here.) And at length when corrected, he has sought to twist about the matter, projecting falsehood and misrepresentation to others as if that justifies his behaviour.

    Now, let us — in steps of thought, proceed to correct some key points in his comment at above, by way of record:

    1 –> Observe his opening tactic in comment 465 above [the main focus for this response], responding to a step by step presentation in above that lays out facts, develops rational argument on such facts and then draws up corrective conclusions and calls, after many days of repeated, unheeded correction of falsehoods:

    I’m not going to respond to the following numbered points:

    2. (FSC is irrelevant to this thread)
    3. ad hominem
    4. ditto
    5. irrelevant
    7. ad hominem
    8. Juvenile
    10. Garbled
    12. Durston does not talk about CSI so irrelevant
    16. ditto
    17. ditto
    18. ad hominem
    and the bafflegab in the PS

    So, to the remaining points:

    2 –> First, foremost he begins by willfully ignoring the baseline directly presented fact in comment 459 no 1, which lays out the contrast of FSCO/I with random strings and strings that reflect order, and thus also DEMONSTRATES the existence of CSI . . . complex, AND specified information. That is, CSI (regardless of merits and demerits of any particular metric model) cannot be “bogus” — fraudulent — as it is objectively and readily shown to be an actual observable phenomenon:

    1 –> CSI is an observable and measurable entity, as can be seen, again, by a very simple example of three different strings:

    1] OSC/ mechanical order (like in a crystal of NaCl): wewewewewewe . . .

    2] RSC/chance strings (such as may happen with a rock matrix):iw3ertujshkjsdbvhsdv . . .

    3] FSC/organised functionally specific strings (such as may happen in an informational polymer like RNA/protein): this string is a case of functionally specific information . . .

    3 –> So, if one shuts ones eyes to patent facts again presented in correction, then one begins on the wrong foot.

    4 –> He then proceeds to the key step of arbitrarily dismissing remark 2 of 459, on the fact that functional sequence complexity speaks to strings that exhibit FSCO/I and thus Complex Specified Information. Note no 2 from 459, which AF dismisses with the bland — and obviously false– assertion that “FSC is irrelevant to this thread”:

    2 –> FSC [--> as was directly exemplified in 1 of 459, just cited] depends crucially on the specific configuration of matched components, which drastically constrains the number of possibilities, relative to the configuration space of possible arrangements, scattered or clumped of same components. [Think about how many ways the parts of a car engine can be arranged in working order, vs the number of ways such could be clumped or scattered that would not work.] This is why the concept of an island of function [T] in a much larger sea of non-functional gibberish [W - T], out of the field of possibilities W, makes sense.

    5 –> That is, I have given an example of FSCI in 1 of 459, pointing out that it exhibits functional sequence complexity and have tied it directly to Dembski’s definition of CSI in NFL, pp. 144 and 148, which AF should be aware of. Let me cite that definition as it has long sat in the IOSE introsummary page that AF has openly brushed off with a wave of his hand:

    p. 148: “The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology.

    I submit that what they have in mind is specified complexity [[cf. here below], or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . .

    Biological specification always refers to function . . . In virtue of their function [[a living organism's subsystems] embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways [[through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole] . . .”

    p. 144: [[Specified complexity can be defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ”

    6 –> In short, CSI is directly connected to function, is manifested in patterns that restrict acceptable configurations to narrow zones T in the wider space of possibilities W ["islands of function"] and so functional sequence complexity per Abel, Trevors, Durston et al is directly relevant to the concerns of this thread. Demonstrated by fact and reasoning, to be further warranted in the end at 16 and 17[b!] of 459 by extensively citing from a 2007 paper just how Durston et al deduced the following directly relevant cases of FSC that then fit in the Chi_500 metric model reduced from the Dembski 2005 expression, namely: Chi_500 = Ip*S – 500, bits beyond the solar system threshold; and — by simply using the fact of function of protein families to see that S = 1 and taking up the I value they deduce from Shannon’s H as extended in the paper cited in detail at point 14 of 459 for the functional state, yield that:

    17 –> Durston et al do not discuss a specific threshold of reasonable search resources, but the needle in haystack threshold for the solar system already given is reasonable. Durston’s metric brings in the redundancy of the actual code used [as opposed to the distribution that is chemically possible] and so we may freely insert it into the Chi_500 metric expression, as was done in the IOSE and in discussion threads here at UD before that, some years back now . . . with AF doubtless looking on:

    Using Durston’s Fits values — functionally specific bits — from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:

    RecA: 242 AA, 832 fits, Chi: 332 bits beyond
    SecY: 342 AA, 688 fits, Chi: 188 bits beyond
    Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond

    xxiii: And, this raises the controversial question that biological examples such as DNA — which in a living cell is much more complex than 500 bits — may be designed to carry out particular functions in the cell and the wider organism.

    18 –> So, not only is it a matter of reasonable description, modelling and quantification, but this is closely linked to serious work that has appeared in the peer reviewed literature, for some years now. AF, you are willfully misrepresenting what you do or should know better than. That, sir, FYI — as you know or full well should know, is willfully deceptive and in defiance on your part of duties of care to truth, accuracy and fairness.

    7 –> So, AF is willfully ignoring the actual presentation of facts, reasoning and evidence that warrants the conclusions, the better to snip and snipe points where corrections are specifically made on the long record of willfully ignoring such facts and evidence, to pretend that such are ad hominem attacks. That is already the proper explanation for the dismissive remarks he makes on points 3, 4, & 7 & 8 etc. Indeed, we see such a warranted correction at 18, which he dismissed “ad hominem.” As for the PS to 459, it directly responded to his prior willful politicisation of and false accusations regarding the matter in defiance of the facts and evidence in record long since. He may brush it aside with a clever quip but it is unfortunately well warranted and corrective of a major political smear he seems to have bought into.

    8 –> So we see the consistent tactics of willfully ignoring facts and evidence, in order to snip out points where after many attempts to correct on facts and evidence, it has had to be directly put that there is a willful falsehood and continued misrepresentation problem at work.

    9 –> To which AF replied by making further dismissals of evidence and further willfully false accusations. Compounded by the rhetorical tactic of twisting about the problem and projecting the blame to the one correcting. Shoot the messenger instead of deal with the message.

    10 –> Point 10 of 459 is dismissed as “garbled.” Let us see, in context:

    10 –> In addition, there may be post copying adjustments that point to further CSI — such as in the maturation of mRNA with snipping and possible rearrangements, addition/stripping of headers etc. [Cf here the ISO OSI 7-layer comms model and how similar mechanisms do appear in the living cell.]

    11 –> This is particularly revealing of underlying refusal to address material evidence that Af should know about if he is to comment with knowledge on CSI, FSCO/I and FSC. In the context of discussing duplication (of strings of info) — raised as an intended objection by AF and before him by Mr May, P, in the sock-puppet persona of MathGirl — and why it does not in itself increase the CSI stock of the cosmos, it had been pointed out at 9 of 459, immediately preceding — note the “In addition” a the start of 10 — that:

    . . . Does duplication create new info de novo? Nope, from its very name. However, the duplicating mechanism may indeed be further FSCO/I as can be seen from a photocopier or the highly complex DNA transcribing mechanism in the living cell.

    12 –> So, the immediate context is the making of mRNA, and it is pointed out that on completion of transcription, mRNA is subject to processing, snipping and possible rearrangements. It is also noted that headers may appear in bio-molecules similar to the same pattern in the well known OSI seven layer info system model that underlies the Internet.

    13 –> Surely, such processing transforms a mere duplicate into something else and points onwards to something else that has the functionally specific complex organisation to do this, and to do it correctly on a reliable basis.

    14 –> So, far from being “garbled,” what is on display here is AF’s willful ignorance — these things have been pointed out to him, and/or he has had access to research them by making simple web searches — that was then covered over by making a rhetorical dismissal.

    15 -> This is a patent case of speaking in willful disregard of duties of care to accuracy, truth and fairness, as well as of defiance of correction, in the interests of a continued willful misrepresentation.

    16 –> the is a similar pattern in response to point 12 of 459. Let us cite 11 – 13 as this gives context:

    11 –> Where also (contrary to your just counting bits caricature) it has been carefully specified right there in the name, that the issue is a joint specificity- complexity criterion; as has been pointed out by Dembski et al for years and indeed as traces back to Orgel’s distinctions in 1973 and to Wicken’s identification of functionally specific complex organisation in 1979 that you also ignore. (Cf. here for the cites and comments that have been repeatedly pointed out, linked and/or cited to you, and which you willfully ignored the better to continue willful misrepresentations.)

    12 –> One that may as Durston et al show, be adjusted for redundancy that comes up in the code or possible substitutions.

    13 –> Where also — as you full well know or should know — that joint between complexity and specificity [especially functional specificity] is a crucial distinction from mere info carrying capacity, aka info in the Shannon sense.

    17 –> It is simply not true that Durston et al do not discuss CSI, the whole 2007 paper is on measuring the information in FUNCTIONALLY specific bio-molecule sequences that are complex. let us note the title and the methods section of the abstract:

    Measuring the functional sequence complexity of proteins

    Kirk K Durston1*, David KY Chiu2, David L Abel3 and Jack T Trevors4 . . . .

    We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families. Considerations were made in determining how the measure can be used to correlate functionality when relating to the whole molecule and sub-molecule. In the experiment, we show that when the proposed measure is applied to the aligned protein sequences of ubiquitin, 6 of the 7 highest value sites correlate with the binding domain.

    18 –> That is why they discuss functional sequence complexity — in a context where from NFL we can see that the issue is functional info in biological contexts and that specificity in that context is cashed out in terms of function in the biological context. Where, proteins are notoriously the workhorses of the cell. Durston et al then use Shannon’s H in null, ground and functional states of long sequences of chained bio-monomers to quantify its information content, and this built on a base where they discussed it across several peer-reviewed papers over the course of years.

    19 –> If this is “misunderstood,” it is misunderstood in a context where AF has been repeatedly corrected on the point, but has consistently defiantly ignored or brushed it aside. Such behaviour, in a context of associated false accusations of fraud ["bogus"], is willful and irresponsible relative to his manifest duties of care to truth, accuracy, warrant and fairness.

    20 –> Not least, this is a specific case that — in a patently biological context (protein families that function across the world of life) — demonstrate FSCO/I in measurable action, and thus also CSI in measurable action. So at this point AF’s case has collapsed and he has no cause for complaint that he has had to be brought up short for irresponsible misbehaviour in the teeth of repeated, easily accessible correction.

    21 –> So, how does he address the explicit, detailed citation and summary on the relevance of FSC to FSCO/I and CSI in the world of life, as I gave in points 16 and 17 of 459? He simply compounds the problem by saying ditto twice, i.e he refuses to attend to direct evidence of his error presented in detailed correction. This is willful and it is fair comment to say it is closed minded and a case of continued misrepresentation compounded by false accusations of fraud (“bogus”)in the teeth of adequate correction.

    22 –> A this point the substantial issue has been settled, but let us continue on at least a snippet basis (ignoring further twist-about accusations or insinuations, ad hominems and personalities for the moment), to see how AF continues to try to brush aside the correction that he has rejected.

    23 –> The first detail point begins:

    [KF:] CSI is an observable and measurable entity [--> NB: with a textual snippet from AF and and biological examples given, with links to the derivation of the metric for Chi_500, and with the Durston case highlighted] …

    [AF:] So you keep saying. But you fail to explain how to measure it for any meaningful example.

    24 –> Willfully misleading falsehood and continued misrepresentation.

    25 –> AF then introduces a novel case, demanding that I address it (it was in fact already taken up by Joe):

    Try the nine residue polypeptide, oxytocin . . .

    26 –> AF knows or should know that 9 AA’s are represented by 27 mRNA bases, and come form a space of 20^9 possibilities for relevant protein space, where the maximum number of bits per 20-state element (disregarding redundancies) is 4.322, yielding ~ 39 bits as carrying capacity; well within the 500-bit limit for FSCO/I. He also knows that it is bio-functional. So, on a simple model of informational capacity adequate for this purpose, we already know that oxytocin is not beyond the threshold where design would be inferred. Chi_500 = 39 – 500; i.e. we are 461 bits short of the relevant threshold of exceeding the search capacity of the solar system’s 10^57 atoms.

    27 –> His attempt to dismiss point 6 of 459 is revealing, given what we have already seen — which includes not only a correction that shows just how CSI is quantifiable and measurable in general and in cases relevant to the biological world, but also AF’s unjust and slanderous assertion that CSI is “bogus” i.e. fraudulent:

    [KF:] You objected that CSI cannot be quantified.

    [AF:] I wouldn’t put it as strongly as that. CSI may be a measurable quantity. We have yet to see a meaningful definition or a clear reproducible way of calculating this (let’s say) alleged property of an entity.

    28 –> I think this is an unacknowledged, unapologetic retraction in part. AF probably realises that the accusation of fraud he has made will not wash, so he sneaks in a modification without accounting for his false accusation. But this will not wash, as in fact meaningful definition and actual calculations both simple and sophisticated have been presented, just willfully ignored.

    29 –> This is continuing misrepresentation, with all that that means given duties of care to truth, accuracy, fairness and warrant ignored by AF as already pointed out.

    30 –> Notice the artfully placed snip-off (do I dare say “quote mining” . . nah, we all know that only those wretched “creationists” do such . . . ) that cuts out the justification again given above in this comment, i.e. my point that duplication itself is not creating novel FSCO/I but that the duplicating mechanism may well be more FSCO/I and further processing will likely inject FSCO/I:

    [KF:] You tried to then raise the issue that has been addressed for years, of duplication of information. Does duplication create new info de novo? Nope, from its very name.

    [AF:] Right so all entities that are identical only contain one measurable quantity of CSI. So CSI literally doesn’t add up. If you have a gene duplication event followed by drift mutations in the redundant gene does that then have more CSI?

    31 –> See how, by quote mining, a strawman has been set up and pummelled? And, how the problem of crossing a sea of gibberish to reach relevant novel body plans on a new island of function has been ducked? In a context of assumed junk DNA where there would be no natural selection pressure of differential reproductive success to filter for function, i.e. we are here looking at a pure random walk? Notice, utter absence of observed, empirical warrant for novel body plans emerging by such “drift”?

    32 –> Let’s just say: just-so story.

    33 –> Nor should we forget the underlying issue: why should copying information to a new site or medium be even imagined to be creation of novel — never before existing — information? That is why I pointed out that duplication already tells us that nothing new is appearing at this stage. But mature the mRNA by snipping up and rearranging etc, push in headers on informational molecules when assembled to dispatch them and snip off for use or the like, or do much the same with information in the Internet and we are dealing with transformation, thus new information.

    34 –> Notice, how AF tries to brush aside the evidence from all around us that when we need specific arrangements of well matched parts to function, it leads to narrow zones in the space of possible configurations, and it then leads to the challenge of search and the question that with limited atomic & temporal resources [10^57 atoms and 12 - 14 bn years in our effective universe, absent discovery of warp drive] we are only reasonably warranted in expecting to pick up the bulk of the distribution, not the narrow special zones:

    Needles in haystacks and islands of function are repackaged arguments from incredulity. And you seem to be back to bit counting.

    35 –> Of course, immediately, when one counts functionally specific bits, one is not merely counting bits, as has been repeatedly pointed out to AF but willfully ignored in the rush to make up strawman targets. Right from the beginning with Orgel in 1973 it has been recognised that the joint between specificity [which may be based on function] and complexity is pivotal in distinguishing organisation from the mere order of a repetitive, low information necessity-shaped crystal structure and chance based mixtures of polymers in a tar or the like:

    . . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity. [[The Origins of Life (John Wiley, 1973), p. 189.]

    35 –> But, AF cannot resist the temptation of a willful misrepresentation that sets up a strawman target.

    36 –> This continues into the attempt to dismiss the inference on what is known from sampling theory into a supposed fallacious appeal to personal incredulity. (Of course, one has a perfect epistemic right to be incredulous in a scientific context where there is an absence of empirical evidence of FSCO/I arising by blind chance and mechanical necessity but plenty of it arising from intelligent action.)

    37 –> But it is in fact well known that blind samples tend to represent the bulk of a distribution, and that as a result when one has the equivalent of a truck full of beans with some few gold beads in it by comparison on steroids, a blind sample made by pulling out a handful will overwhelmingly be likely to only pick up beans. (The calculated comparison is that of using up the resources of our solar system to take a one straw sized sample of a cubical haystack as thick as our galaxy. Even if that were somehow superposed on the galaxy in Earth’s neighbourhood, with overwhelming likelihood the only expected result of such a sample will be straw and nothing else, not suns not planets etc.)

    38 –> Strawman tactics continue:

    I asked “So how is function quantified? And how does that quantity enter into the calculation?”

    This remains unanswered.

    39 –> Function in the world of life — as was pointed out to AF but predictably ignored in the interests of setting up and knocking over strawmen — is of course observed (which gives it objective character) and may be measured in many cases, e.g. the degree of activity of a candidate enzyme in promoting a relevant reaction.

    40 –> This is implicit in functional specificity, which appears in the Chi_500 expression as S [which based on observation and resulting objective warrant takes up values of 0 -- not functionally specific as default, and 1 when such is shown to be present]. Let us remind ourselves, by again clipping the relevant part of the IOSE intro-summary that AF has brushed aside:

    chi is a metric of bits from a zone of interest, beyond a threshold of “sufficient complexity to not plausibly be the result of chance,” (398 + K2). So,

    (a) since (398 + K2) tends to at most 500 bits on the gamut of our solar system [[our practical universe, for chemical interactions! ( . . . if you want , 1,000 bits would be a limit for the observable cosmos)] and

    (b) as we can define and introduce a dummy variable for specificity, S, where

    (c) S = 1 or 0 according as the observed configuration, E, is on objective analysis specific to a narrow and independently describable zone of interest, T:

    Chi = Ip*S – 500, in bits beyond a “complex enough” threshold

    NB: If S = 0, this locks us at Chi = – 500; and, if Ip is less than 500 bits, Chi will be negative even if S is positive.

    E.g.: a string of 501 coins tossed at random will have S = 0, but if the coins are arranged to spell out a message in English using the ASCII code [[notice independent specification of a narrow zone of possible configurations, T], Chi will — unsurprisingly — be positive.

    Following the logic of the per aspect necessity vs chance vs design causal factor explanatory filter, the default value of S is 0, i.e. it is assumed that blind chance and/or mechanical necessity are adequate to explain a phenomenon of interest.

    S goes to 1 when we have objective grounds — to be explained case by case — to assign that value.

    That is, we need to justify why we think the observed cases E come from a narrow zone of interest, T, that is independently describable, not just a list of members E1, E2, E3 . . . ; in short, we must have a reasonable criterion that allows us to build or recognise cases Ei from T, without resorting to an arbitrary list.

    A string at random is a list with one member, but if we pick it as a password, it is now a zone with one member. (Where also, a lottery, is a sort of inverse password game where we pay for the privilege; and where the complexity has to be carefully managed to make it winnable. )

    An obvious example of such a zone T, is code symbol strings of a given length that work in a programme or communicate meaningful statements in a language based on its grammar, vocabulary etc. This paragraph is a case in point, which can be contrasted with typical random strings ( . . . 68gsdesnmyw . . . ) or repetitive ones ( . . . ftftftft . . . ); where we can also see by this case how such a case can enfold random and repetitive sub-strings.

    Arguably — and of course this is hotly disputed — DNA, protein and regulatory codes are another. Design theorists argue that the only observed adequate cause for such is a process of intelligently directed configuration, i.e. of design, so we are justified in taking such a case as a reliable sign of such a cause having been at work. (Thus, the sign then counts as evidence pointing to a perhaps otherwise unknown designer having been at work.)

    So also, to overthrow the design inference, a valid counter example would be needed, a case where blind mechanical necessity and/or blind chance produces such functionally specific, complex information. (Points xiv – xvi above outline why that will be hard indeed to come up with. There are literally billions of cases where FSCI is observed to come from design.)

    xxii: So, we have some reason to suggest that if something, E, is based on specific information describable in a way that does not just quote E and requires at least 500 specific bits to store the specific information, then the most reasonable explanation for the cause of E is that it was designed.

    41 –> In turn this is reflected in Dembski’s CSI-defining remarks as already cited from NFL, that in the biological context specificity is cashed out as function, and it appears in the work of Durston et al as functional sequence complexity. There is no justification whatsoever for the strawman tactic.

    42 –> This one takes the cake for setting up and knocking over strawmen through quite mining in the interests of Alinskyite rhetoric of ridicule:

    [KF:] It also shows that – per willingness to spend a fair sum of money — it is generally accepted that humans do not exhaust the set of potential intelligences.

    [AF:] Obscure to the point of inscrutability!

    43 –> What was left off? Just, the context of noting that if people are spending millions on searches for signals from extraterrestrials, then they obviously do not think that humans exhaust the list of possible intelligences. (It being a well known objection tactic that an objector pretends that only human intelligence can be considered as reasonable and empirically justified so the design inference is out of order somehow.)

    ++++++++

    Such a context of willful, persistent misrepresentation in the teeth of duties of care to truth, evidence, fairness, warrant etc more than justifies taking strong measures to notify the unwary onlooker that something is seriously amiss with what is going on in the comments. Especially after many attempts to correct have been willfully ignored and dismissed. Especially, in the further context of a willful false accusation of fraud, that has not been acknowledged, retracted openly and apologised for.

    Indeed, this case more than merits headlining — as a capital example of what is not to be done in discussing design theory.

    I intend to do so shortly, for record and in hopes that in future this will not ever happen again.

    KF

  480. AF’s tactics exposed and headlined for record, here. KF

  481. So Alan posts a challenge, has it answered and then runs back to TSZ to spew more BS about UD?

    Typical for a coward.

  482. Alan Fox:

    One may not start out by questioning authority but when each new experience demonstrates authority’s assertions don’t gel with reality and one starts examining the basis of those assertions, faith is a common casualty.

    Exactly! I questioned the evolutionary authorities and found their assertions do NOT gel with reality! That is when my faith in evolutionism became a casualty.

    Good call, Alan.

  483. Joe:

    If that is so, then this is now a test of EL and the rest of the TSZ crowd.

    For, if they make themselves willing harbourers and enablers of and accessories to slander, willful continued misrepresentations held on to in the teeth of step by step correction then they remove themselves from the circle of civil discussion, period.

    AF has openly — on demonstrated false accusation — stated that CSI is “a bogus concept.” In the teeth of simple examples and more sophisticated ones, involving metrics relevant to the origin of life and of major body plans, he has tried to suggest that it is useless for calculation, that it is not measurable, and that it is part of some nefarious Creationist, fundamentalist, right-wing theocratic plot to subvert science and civilisation alike.

    When he has been corrected, step by step, point by point, he has doubled down on misrepresentations, showing himself to be guilty of willfully continued misrepresentations. As well as the slander by false accusation and malicious insinuation already seen. (And recall this is in a context where not so long ago there was an attempt at TSZ tracing to OM and RTH — enabled by the TSZ crowd including EL the blog owner — to suggest that I am a Nazi by invidious association; which BTW EL I am pretty sure is actionable in British law . . . American law on tort being currently in a first class mess on matters linked to defamation.)

    So, now we have come to the point where TSZ will need to step up to the plate and show its true colours.

    I, for one, on track record, am not holding my breath in hopes that the leadership will come down on the side of basic civility.

    KF

  484. F/N: I see some disparaging remarks above concerning “faith” and its alleged roots in blind adherence to authority.

    It seems AF et al need to first understand the logic of worldview roots and adherence to first plausibles.

    Namely, that for any claim A that we see as needing to be “proved,” we may ask, why should we accept it. From this we see that there is a pattern of further argument or observations and reasoning etc, B that leads us to see A as warranted. That leads on to C, D , etc.

    So, we have the choice of infinite regress, an absurdity: turtles, all the way doooown. Or else, question-begging circularity at some point, where we loop back. Or else we take a framework of first plausible points, F, as credibly true without further “proof.”

    F is our faith point, our worldview.

    It can only escape infinite regress or circularity by being:

    a: partly self evident (e.g first principles of right reason)

    b: partly held to be so on trust in our collective experience of the world, with

    c: a further context of comparative difficulties — across factual adequacy, coherence and explanatory power . . . elegant simplicity without simplisticness [notice, the reference to in effect a grand inference to best explanation] — among alternate “live option” start points F1, F2, F3 . . . Fn.

    So, the proper question is not to imagine that faith is equated to blind adherence to some authority or other. Instead, we have no choice but to walk by faith, as the basis for all else, including faith in reason and in credible testimony and expertise or authorities, starting with the dictionary, teachers etc. Of course to have reasonable faith we then need to go through the chain above, and it is reasonable to audit authorities as I am currently doing with orthopedic surgeons. (De Yahd-man is at the head of the pack.)

    I am fairly sure (having taken time to investigate) that, if given a fair hearing — as opposed to being subjected to self-refuting and self-serving selective hyperskepticism as we saw too much of in the thread above, the historic NT Christian Faith of Apostles, martyrs, confessors, and ecumenical creeds, will pass with flying colours.

    I am also quite certain, on good reason, that he trendy evolutionary materialist scientism and associated so-called new atheism etc of our day will at once collapse so soon as its account of the human mind and its capability to know, reason and make moral judgements is soberly examined. never mind how it loves to dress up in the holy lab coat and fly the flags of science, with a brazen confident manner. A view of the world that radically undermines reason, knowledge and morality is not even a starter.

    When it comes to the core design inference, the matter is quite simple in the end, as was aptly stated by Stephen Meyer in reply to an objector to his SITC:

    The central argument of my book is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question . . . . In order to [[scientifically refute this inductive conclusion] Falk would need to show that some undirected material cause has [[empirically] demonstrated the power to produce functional biological information apart from the guidance or activity a designing mind. Neither Falk, nor anyone working in origin-of-life biology, has succeeded in doing this . . . .

    [W]e do know of a cause—a type of cause—that has demonstrated the power to produce functionally-specified information. That cause is intelligence or conscious rational deliberation. As the pioneering information theorist Henry Quastler once observed, “the creation of information is habitually associated with conscious activity.” And, of course, he was right. Whenever we find information—whether embedded in a radio signal, carved in a stone monument, written in a book or etched on a magnetic disc—and we trace it back to its source, invariably we come to mind, not merely a material process. Thus, the discovery of functionally specified, digitally encoded information along the spine of DNA, provides compelling positive evidence of the activity of a prior designing intelligence. This conclusion is not based upon what we don’t know. It is based upon what we do know from our uniform experience about the cause and effect structure of the world—specifically, what we know about what does, and does not, have the power to produce large amounts of specified information . . .

    The matter, in the end, is a s simple as that.

    And yes, despite what the advancers of many silly objections and demands for “endorsement” thereby imply, Meyer is openly using a formulation that is essentially the same as my own functionally specific complex organisation and associated information, with particular reference to the digital, coded, algorithmically functional information to be found in DNA in cell based life.

    The time has come to stop the silly rhetorical games, objectors, and to make a sober and honest, informed and open minded assessment of what is on the table in front of us all.

    Starting with the realities of cell based life such as DNA, mRNA, tRNA, ribosomes and protein manufacture and the conundrum for materialist views, of the origin of life.

    KF

  485. …to suggest that I am a Nazi by invidious association…

    That is a very serious allegation that I suggest you substantiate or withdraw.

  486. AF:

    It seems that if you think the shoe is on the other foot, you know how it pinches.

    That incident of invidious association with Nazis happened at TSZ at the hands of OM with RTH coming up in rapid support, as I discussed here.

    (I guess you have ever so soon forgotten the “tour of shame” issue I raised in a post of April 2nd here, in objection to what was being harboured at TSZ. For sadly good reason, I have not. Remember, I have he screen shots posted here at UD.)

    So far as I am aware there has been no retraction only a pretence that nothing was done that was uncivil and improper. Multiplied by the further pretence that I am being obscure or worse in speaking about it. (Your subtext in trying to suggest garbling on my part, is duly noted.)

    FYI, I am pretty sure that when one is explicitly associated with nazis on a matter where there is a matter of principled opposition to a questionable socio-cultural agenda on the part of a quite broad range of people and movements, that is a case of invidious association intended to tar through the well known fallacy and psychological effect guilt by association.

    Methinks, on evidence laid out above and elsewhere, it is you who need to apologise and retract some pretty serious false accusations and willful misrepresentations sustained int eh teeth of step by step correction and before that corrections from many sources for a quite long time.

    KF

  487. Ah! Your link is to one of your “comments-are-closed” diatribes. Tell you what. Promote the thread, open comments and let’s argue your case.

  488. AF:

    You are upholding wrongdoers in evil, and as usual you are dismissing devastating facts with an epithet.

    The screen shots, links and citations do not lie, and they go back to the TSZ thread, which I assume has not been taken down. between OM and RTH, I was plainly invidiously associated with Nazism, and with an alleged right wing theocratic agenda for our civilisation that wants to bring back witch hunts and worse.

    Which, BTW are very familiar-sounding, in the context of some of your allusions and tactics I corrected above.

    I have already pointed out the facts,and can rest content that no fair minded person will see me as wrong to call out OM and RTH for what hey did, and the TSZ crowd for enabling behaviour in the face of uncivil conduct.

    I find this sudden concern for your own reputation and those of your ilk very interesting, also in the teeth of the above where you have indulged in willful misrepresentation, insisted on continuing it in the teeth of repeated well-warranted correction, and compounded it all with an outright accusation of fraud that at minimum would at first level involve Wm Dembski, Stephen Meyer and others. And in the immediate circle of discussion, it would directly imply that I am at least an accessory to the fact to fraud.

    Where it is patent that the accusation is false, is mischievous, is sustained in the teeth of calls for correction and retraction, and indeed is utterly without merit.

    I think there is a need on your part to stop and do some serious reflection on what you have been doing, sir.

    GEM of TKI

  489. The comment that offends you so much is still there, plain to see. There is nothing there that is not fair comment, in my view, especially in contrast to some of the name-calling and other bad behaviour that you condone on this site. But I am prepared to argue the case if you want to promote and open the thread to comments.

  490. Alan Fox:

    Promote the thread, open comments and let’s argue your case.

    Yes Alan. We know we will never be arguing your case because you are too afraid to even make one.

    However you are very good at rejecting other people’s arguments just with your say-so. So what’s the point?

  491. Alan Fox:

    So, Kairosfocus seems to be agreeing with my take that a CSI calculation for a protein sequence merely depends on a count of nucleotides residues. This is an analysis that results in two sets of proteins; shorter or longer than an arbitrary threshold. This would seem to be trivial and useless, merely telling us one thing we already know.

    We already know that living organisms were intelligently designed? Then why all of the fuss?

    And just how is determining living organisms are designed “trivial and useless” when even Richard Dawkins says it would change everything?

    That’s right Alan. Saying something is the result of agency involvement is an investigation changer.

    And as Elsberry has emphasized with the now apparently redundant explanatory filter, you can’t rule out unknown possibilities and default to “design”.

    And Alan is STILL having issues with the word “default”.

    We do NOT default to design, Alan. All known non-design mechanisms are given thorough consideration. Not only that the design criteria still has to be met. THAT is the opposite of “default”.

    So agin- we have Alan A) holding up double-standards B) refusing to grasp that CSI is something he uses every day C) not understanding the meaning of words and D) making a mess just because he can.

    I agree with Elsberry and Shallit. There is no valid concept known as complex specification that can be used to distinguish designed from undesigned entities.

    Thankfully neither of you three stooges conducts investigations that require your two piles.

  492. AF:

    Thanks for letting us all know that in your twisted books, invidious association with Nazis on subjects where such outrageous guilt by association accusations are being used to try to shut down serious principled discussion, and accusations without evidence of intent to carry out witch hunts is fair comment. (The very same, who on seeing that I pointed out to such invidious associations was demanding retractions, it is there just scroll up folks. Double standards indeed.)

    You have explained to us all we need to know to see why you have behaved as you did in this thread and in others.

    Well did Plato warn us of the likes of such, with Alcibiades in mind as Exhibit A.

    As in might and manipulation make ‘right.’

    Good day

    GEM of TKI

    PS: With the direct corrections just a scroll up above, you are back to trying to pretend that joint criteria of specificity and complexity as a basis to infer design, amounts to “counting bits.” Your respect for truth is about as high as your respect for others. I would suggest to you that if you are down in a hole and care to get out, stop digging in further for a start.

    PPS: And if you want to debate points, this thread and others are open. But as at now you hold two strikes against you: you have a track record of disrespect for truth and you have a track record of disrespect for others. I trust that sensible onlookers will therefore have a yardstick for calibrating the credibility and/or soundness or otherwise of what you say.

  493. Alan Fox @409:

    Mutations to not cause changes during the lifetime of an individual. It is when genes containing mutations are passed on and affect the development of the offspring that the changes in alleles that selection can work on occur. Genomes, as far as the lifetime of any one organism is concerned, are fixed.

    Alan, you missed the point of my thought experiment, as well as the broader issue. The evolutionary story is that mutations can build complex functional structures. The primary element here is time, as you acknowledge in referring to the lifetime of one organism.

    When thoughtful individuals express skepticism about the powers of mutations to produce novel biological systems, a very common retort from evolutionists is that once you have a self-reproducing organism then anything is possible, it changes the game. kf has given a very thoughtful and detailed response.

    In addition to kf’s points, I am simply noting the additional fact that the self-reproducing aspect does not mean that somehow the improbable now becomes probable. And reproduction is not, as often portrayed, an answer to thoughtful questions about the source of biological novelty.

    1. If asexual reproduction were to occur with complete fidelity, then the only difference reproduction would make is adding more time. That is why I highlighted the time aspect.

    2. If reproduction occurs without complete fidelity, then you have time, plus potential mutations due to the reproduction process.

    3. If reproduction also occurs sexually, then you also get to add to the mix things like recombination.

    Yet the only thing those latter two forms of reproduction do is add more opportunities for mutations to do something (or to mess something up). They do not in any way change the fundamental proposal: that random mutations in the molecules of an organism can change the organism into a different functional organism. The only things imperfect and/or sexual reproduction do is (i) add a few more ways for mutations to arise and (ii) keep the organism alive (in the sense of a line of descendants) for long enough for some wonderful biological novelty to eventually arise.

    Thus, reproduction itself is not any kind of answer to how functional complexity can actually arise. All it says is, “Well, we’re increasing the number of possible chances.”

    Unfortunately, any increase in odds due to reproduction-related mutations, recombination and the like are but a rounding error against the awful probabilities that beset the theory.

  494. Alan Fox:

    Regarding CSI, kf has given you a calculation that helps with the complexity side of the determination. As you yourself have noted, this is very basic and straight forward.

    As for your demand for a mathematical calculation of the function/specification side of the determination, please answer the following:

    1. Does a piano have a function? If so, what is the mathematical calculation that demonstrates that function?*

    2. Does a computer have function? If so, please provide a precise mathematical calculation for that function.*

    3. Does the ribosome have a function? If so, please describe for us the mathematical calculation that led you to this conclusion.*

    After you have thought about this for a while, there are two possibilities:

    1. You will recognize that, unlike the Shannon bit calculation that can often be used to confirm complexity, it is rarely, if ever, possible to provide a mathematical calculation to prove that something has function. Yet, we regularly recognize function nonetheless. If you get to this point, then we can press forward and have a rational discussion about the design inference.

    2. You will continue to refuse to accept that anything has function if there is not a rigorous mathematical calculation of the function — notwithstanding that you cannot provide such a calculation (indeed, cannot even articulate why any such calculation should be possible or required) for objects that you know have function from objective observation. In this case, you will have demonstrated your lack of objectivity and refusal to consider the evidence and follow it where it leads, in which case, further attempts at discourse are likely futile.

    I trust you will seriously consider the above, if you are sincere in your desire to learn about intelligent design and engage in productive discourse.

    —–

    * Note: We are not looking for a physical description of the object and its various pieces (although in some cases an object’s physical description may give us clues about its function). Rather — as you have demanded — we are looking for a precise mathematical calculation that will yield a conclusion of function.

  495. Folks:

    This is the conclusion I have been forced to after having dealt with what we have been seeing.

    Namely that Plato’s warning is playing out, not just in the openly crude and nasty, but among the more genteel or refined, and the more dangerous for that as such will beguile many into thinking that all is well when the knife is up a sleeve to be slid in at the back if one gets too close.

    It has been a long time now that I pointed out how we need to start from basics in morality. Such as, that it is immoral, self evidently immoral to torture, rape or kill a little child. Remember, how we dealt with people who had ever so hard a time acknowledging even something as patent as that?

    (And, it seems that we are having a sadly live case playing out now, with the abortionist Gosnell. The image of that little baby in the bowl struggling for its life as it is flushed away as unwanted, disgusts me beyond words. Now, notice, the gatekeepers in ever so many media houses were perfectly willing to quash such a report, let it disgust too many people. Forget the excuses proffered, we are dealing with people who care not for truth or right, only for their agenda and what they can get away with. So, let us be direct, they sought to manipulate us, only it has partly broken through the disgusting spin games. Same for the recent events surrounding abuse of pressure cookers of all things. [And there is no movement for pressure cooker control.])

    So, it is a little time for real fair comment.

    Such as that:

    a –> unless your worldview foundation has in it an IS that can bear the weight of OUGHT, you are left with no foundation for ethics, however your present tastes and preferences may play out. Those who covered up Gosnell will play any game gambit they think they can get away with.

    b –> In particular, the evolutionary materialist worldview that likes to wrap itself in a lab coat and fly the flag of science and progress, is such a view. If unchecked, in the end, it will further any misrepresentation, it will outright lie if it can get away with it, it will suppress any unwelcome truth by any means deemed advantageous, it will slander and besmirch any who dare cry out NO.

    c –> And this is the world we now live in; a world dominated by such. Welcome to a foretaste of hell, that is going to get a lot worse before it gets better, IF it can be turned around.

    d –> Labels and iconic cases are important, as they will allow us to describe and explain what we are dealing with. let us start with Provine’s vision (which he tries to pretend is an improvement):

    Naturalistic evolution has clear consequences that Charles Darwin understood perfectly. 1) No gods worth having exist; 2) no life after death exists; 3) no ultimate foundation for ethics exists; 4) no ultimate meaning in life exists; and 5) human free will is nonexistent . . . .

    The first 4 implications are so obvious to modern naturalistic evolutionists that I will spend little time defending them. Human free will, however, is another matter. Even evolutionists have trouble swallowing that implication. I will argue that humans are locally determined systems that make choices. They have, however, no free will . . .

    e –> See the consequences of turning from God, the one who is the IS who is inherently good and so grounds OUGHT, calling us to the standard so ably summed up by “the judicious [Anglican Canon Richard] Hooker” and cited by Locke in his 2nd essay on Govt when he set out to ground liberty and justice?

    f –> Let me cite the contrast, as Hooker speaks foundationally to liberty, justice and genuine freedom in the community:

    . . . if I cannot but wish to receive good, even as much at every man’s hands, as any man can wish unto his own soul, how should I look to have any part of my desire herein satisfied, unless myself be careful to satisfy the like desire which is undoubtedly in other men . . . my desire, therefore, to be loved of my equals in Nature, as much as possible may be, imposeth upon me a natural duty of bearing to themward fully the like affection. From which relation of equality between ourselves and them that are as ourselves, what several rules and canons natural reason hath drawn for direction of life no man is ignorant . . . [[Hooker then continues, citing Aristotle in The Nicomachean Ethics, Bk 8:] as namely, That because we would take no harm, we must therefore do none; That since we would not be in any thing extremely dealt with, we must ourselves avoid all extremity in our dealings; That from all violence and wrong we are utterly to abstain, with such-like . . . ] [[Eccl. Polity,preface, Bk I, "ch." 8, p.80]

    g –> What then follows from Provine’s vision taking the place of that of Locke and Hooker? Much, pivoting on the rejection of our freedom and responsibility to act based on moral choice. Here is how I recently summed it up:

    Without freedom of choice, however, our ability to think and decide reasonably and to the good collapses, crash.

    Duty, now overwhelmed by inability to think and the force of impulses driving our feelings follows, crash.

    Morality, having no supporting foundation, now becomes a matter of the push and counter-push of the factions in the community, leading to radical relativism and “might makes right” nihilism a la Nietzsche, crash.

    Civility and civil society follow in the collapse, crash.

    Anarchy and chaos follow, crash.

    And, then the magical political messiah appears to save us from our woes amidst a media halo, and we end up in veiled or open tyranny, crash.

    Those who retain principles or the memory and feelings of principles soon find themselves isolated and scapegoated then persecuted, crash.

    Freedom is now gone — and to recover such is always a long, arduous and costly, likely bloody, process — crash.

    Our civilisation has been lost to a new barbarianism, crash.

    A LOT is at stake.

    h –> It is obvious from the above that the process is well underway.

    i –> And, we have a label that — courtesy Wikipedia testifying against interest — will work for the people who have thus been morally benumbed and endarkened in heart, and in mind by destructive, manipulative ideologies now running riot across our civilisation:

    Machiavellianism (or machiavellian mask) is, according to the Oxford English Dictionary, “the employment of cunning and duplicity in statecraft or in general conduct”, deriving from the Italian Renaissance diplomat and writer Niccolò Machiavelli, who wrote Il Principe (The Prince) and other works. The word has a similar use in modern psychology where it describes one of the dark triad personalities, characterised by a duplicitous interpersonal style associated with cynical beliefs and pragmatic morality . . . .

    In the 1960s, Richard Christie and Florence L. Geis developed a test for measuring a person’s level of Machiavellianism. Their Mach – IV test, a twenty-statement personality survey, became the standard self-assessment tool of Machiavellianism. People scoring high on the scale (high Machs) tend to endorse statements such as, “Never tell anyone the real reason you did something unless it is useful to do so,” (No. 1) but not ones like, “Most people are basically good and kind” (No. 4), “There is no excuse for lying to someone else,” (No. 7) or “Most people who get ahead in the world lead clean, moral lives” (No. 11). Using their scale, Christie and Geis conducted multiple experimental tests that showed that the interpersonal strategies and behavior of “High Machs” and “Low Machs” differ.[6] Their basic results have been widely replicated.[7]

    Motivation

    A 1992 review described Machiavellian motivation as related to cold selfishness and pure instrumentality, and those high on the trait were assumed to pursue their motives (e.g. sex, achievement, sociality) in duplicitous ways. More recent research on the motivations of high Machs compared to low Machs found that they gave high priority to money, power, and competition and relatively low priority to community building, self-love, and family concerns. High Machs admitted to focusing on unmitigated achievement and winning at any cost.[1]

    Abilities

    Due to their skill at interpersonal manipulation, there has often been an assumption that high Machs possess superior intelligence, or ability to understand other people in social situations. However, research has firmly established that Machiavellianism is unrelated to IQ. Furthermore, studies on emotional intelligence have found that high Machiavellianism actually tends to be associated with low emotional intelligence as assessed by both performance and questionnaire measures. Both empathy and emotion recognition have been shown to have negative correlations with Machiavellianism. Additionally, research has shown that Machiavellianism is unrelated to a more advanced theory of mind, that is, the ability to anticipate what others are thinking in social situations. If high Machs actually are skilled at manipulating others this appears to be unrelated to any special cognitive abilities as such.[1]
    Relations with other personality traits

    Machiavellianism is one of the three personality traits referred to as the dark triad, along with narcissism and psychopathy. Some psychologists consider Machiavellianism to be essentially a subclinical form of psychopathy,[9] although recent research suggests that while Machiavellianism and psychopathy overlap, they are distinct personality constructs.[1][10] Machiavellianism has been found to be negatively correlated with the Agreeableness (r = -.47) and Conscientiousness (r = -.34) dimensions of the Big Five personality model (NEO-PI-R).[10] However, machiavellianism correlates more highly with the Honesty-humility dimension of the six-factor HEXACO model than with any of the Big Five dimensions.[1] Machiavellianism has also been located within the interpersonal circumplex, which consists of the two independent dimensions of agency and communion. Agency refers to motivation to succeed and to individuate the self, whereas communion refers to motivation to merge with others and to support group interests. Machiavellianism lies in the quadrant of the circumplex defined by high agency and low communion.[1] Machiavellianism has been found to lie diagonally opposite from a circumplex construct called self-construal, a tendency to prefer communion over agency. This suggests that people high in machiavellianism do not simply wish to achieve, they wish to do so at the expense of (or at least without regard to) others.[1]

    =========

    Welcome to the brave new evolutionary materialist world.

    Alcibiades — as Plato warned 2350 years ago — rides again.

    KF

  496. Joe @476:

    Of course Shostak is desperately trying to distance himself from those flat-earth, neanderthal, knuckle-dragging, bible-thumping IDists. The funny thing is, his approach is less rigorous than ID.

    An endless, sinusoidal signal – a dead simple tone – is not complex; it’s artificial.

    He sees something that is not known to be produced by natural causes and simply concludes: it isn’t natural, therefore it is artificial.

    Incidentally, that is not an outrageous approach. One could look at something like DNA and make a very similar argument: it is not known to be produced by natural causes, therefore it is artificial. A reasonable tentative conclusion; just as good as SETI’s acknowledged “scientific” approach.

    But ID is more careful and more stringent. It looks not only at known natural causes, but presents a reasonable complexity threshold to help avoid false positives. In other words, it contains an additional objective criterion beyond what is needed for Shostak to accept a signal as created by an intelligence.

    —–

    Note, having met and talked with Shostak briefly, I think he a nice fellow and, personally (unlike some folks who post here), I think SETI is an interesting project and that positive results from SETI would be a most remarkable discovery.

    I suspect, however, that he doesn’t know that much about intelligent design and keeps getting asked by evolutionists “What do you have to say to those nefarious IDists who claim that SETI is a form of design detection?” Hopefully someday he’ll take time to think through the issues a bit more carefully or will be less swayed by the winds of popular evolutionary thought.

  497. Eric,

    SETI is id (lower case). And ID (upper case) is something or other blah, blah, Gregory, blah.

    :)

  498. Alan spews:

    Eric, you seem to misunderstand the core of evolutionary theory which is reiterative steps of variation and selection.

    Nope, we understand it very well. We also understand that there isn’t any EVIDENCE that accumulations of genetic accidents can do anything constructive.

    And BTW both ID and baraminology are OK with variation and selection. YOUR position requires all the variation to be due to chance/ happenstance. And yet you have no way of even making that determination.

    And that is what forces you to be a cowardly equivocator.

    Alan sez:

    The piano, especially, makes me think of evolution.

    It makes every one else think of DESIGN.

    So Alan doesn’t understand ID and he equivocates and oversells evolutionism.

    Pathetic but typical.

  499. Alan Fox:

    My simple point was, however you manipulate the figures, to pretend to be able to predict functionality of unknown sequences is the bogus element.

    That’s not the claim, Alan

    On the other hand, if that is not the claim, then the process becomes trivial.

    Perhaps to you and some other evos, but to the rest of the world determining design from not is a game changer.

  500. Alan Fox:

    The continually varying and multi-dimensional nature of the niche environment is something that some ID proponents find difficult to grasp.

    Nice false accusation. And if you had some EVIDENCE to support your tripe we would be able to grasp what you say. However you do not and that must bother you.

  501. Lack of curiosity and lack of respect for people who have different views was certainly my impression gleaned from interactions at TSZ and other evo sites.

    ;)

  502. F/N: It is worth noting another dark triad/Alinskyite rhetorical trick being used by AF above. Observe, how he speaks when he refers to an outrageous and utterly unwarranted invidious association with nazism and witch hunts being made in a poison the well tactic used by OM and RTH at TSZ, with enabling all around there:

    The comment that offends you so much is still there, plain to see. There is nothing there that is not fair comment, in my view, especially in contrast to some of the name-calling and other bad behaviour that you condone on this site.

    1 –> The key trick is to project blame and turn about the issue to try to create moral confusion and evade responsibility: it is I who am being thin-skinned in response to “fair comment.” (As in, blame the victim and shoot the messenger.)

    2 –> In fact there is no warrant for such an invidious association. For simpler instance, there is no reason to believe that I or any significant number of Christians in our day would wish to pursue witch hunts; which were premised on the false but formerly widespread belief that witches really could harm people or kill them, and were responsible for crop failures and the like that threatened the whole community. In short,they were treated as perceived menaces to society, and were subjected to defective legal procedures that have long since been found to be wrong and corrected, with Christians including clergymen involved in such reforms in light of Biblical principles of the duty to justice and to avoid harm and injustice to neighbour, which are explicitly taught in the Bible. Those are public facts of history, law and theology, easily accessed though unfortunately not usually taught in the sort of circles that promote the notion of Christians as seeking to restore witch hunts or the like. To top off, there is no acknowledgement that when I had occasion to write a systematic theology survey that is intended to train Christians in my region, one of twelve main units of the semester length course is about: THE SINS OF CHRISTENDOM, and addresses just that subject. Something I have repeatedly drawn attention to. (Contrast that with the career busting and stereotypical scapegoating, well-poisoning tactics that are routinely used today to target Christians, coming from secularists. Which was the context of complaint.) Let me cite the major quote from the great Jewish scholar Bernard Lewis from his epochal 1990 essay on the Roots of Muslim Rage, a cite that I did actually endorse as a major context for discussion:

    . . . The accusations are familiar. We of the West are accused of sexism, racism, and imperialism, institutionalized in patriarchy and slavery, tyranny and exploitation. To these charges, and to others as heinous, we have no option but to plead guilty — not as Americans, nor yet as Westerners, but simply as human beings, as members of the human race. In none of these sins are we the only sinners, and in some of them we are very far from being the worst. The treatment of women in the Western world, and more generally in Christendom, has always been unequal and often oppressive, but even at its worst it was rather better than the rule of polygamy and concubinage that has otherwise been the almost universal lot of womankind on this planet . . . .

    In having practiced sexism, racism, and imperialism, the West was merely following the common practice of mankind through the millennia of recorded history. Where it is distinct from all other civilizations is in having recognized, named, and tried, not entirely without success, to remedy these historic diseases. And that is surely a matter for congratulation, not condemnation. We do not hold Western medical science in general, or Dr. Parkinson and Dr. Alzheimer in particular, responsible for the diseases they diagnosed and to which they gave their names.

    3 –> So, right off the bat, this whole exercise by AF and others he has chosen to endorse as making fair comment, is a smear in defiance of duties of care to truth, accuracy and fairness; one that again willfully continues a misrepresentation in the teeth of opportunities to correct it. Pure and simple.

    4 –> Now the context used to invidiously associate me with Nazis is dual. First, I had, to draw out a point that needs to be heard, pointed out how ordinary Germans living near concentration camps were forced to tour the camps after the defeat in 1945, to witness what they had enabled by their silence since 1933. I also highlighted the indictment of the White Rose — Christian — martyrs, who in pamphlets 2 and 4 exposed the holocaust and indicted the German people as a whole for enabling behaviour. When I raised this in a discussion thread here at UD, AF professed ignorance, and OM sought to twist this into my calling the objectors to design theory who have been spending years in denial of the expulsion phenomenon, Nazis.

    5 –> Thus, we see the first stage of a twist-about, blame the victim manipulative rhetorical tactic.

    6 –> In the next step, the extraneous notion was raised that Nazis and I share a common attitude: objection to homosexuality.

    7 –> Note the poisonous twist at work.

    8 –> In the wider context, in the name of “rights” and “equality” an historically unprecedented legal shift is being pushed on what is literally the foundational institution of the community, marriage and family, with implications for sexual identity, freedom of conscience and expression and more. I happen to be one of a vast number of people who view this latest politically correct radical push as ill-advised at best and highly destructive to the stability of our civilisation. People who would join with me in that point would include the likes of Pope John Paul II (whom I, an open and principled protestant have publicly called, The Great), Pope Benedict XVI, Pope Francis, Mother Teresa of India had she been around, Chuck Colson — who until h