Home » Intelligent Design » DLL Hell, Software Interdependencies, and Darwinian Evolution

DLL Hell, Software Interdependencies, and Darwinian Evolution

In our home we have six computers (distributed among me, my wife, and two daughters): two Macs, two Windows machines, and two Linux (Unix) machines. I’m the IT (Information Technology) or IS (Information Systems) guy in the household — whatever is is.

A chronic problem rears its ugly head on a regular basis when I attempt to update any of our computer systems: Software programs are often interdependent. DLLs are dynamic link libraries of executable code which are accessed by multiple programs, in order to save memory and disk space. But this interdependence can cause big problems. If the DLL is updated but the accessing program is not, all hell will break loose and the program will either severely malfunction or suffer an ignominious, catastrophic, instantaneous death. On the other hand, if the program is updated and the DLL is not, the same thing can happen.

I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell, and how the hypothesized intermediates did not die of asphyxia at the moment of birth (or hatching), without the chance to reproduce.

Of course, we all know that this kind of challenge — no matter how obvious or compelling — presents no problem for the D-Fundies (Darwinian Fundamentalists), who are true believers in the clearly impossible, based on materialistic assumptions in which design could not possibly have played a role.

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271 Responses to DLL Hell, Software Interdependencies, and Darwinian Evolution

  1. 1

    To be picky…

    DLLs are usually designed so that upgrading them should not break old programs. So, in theory, they should be able to be replaced independently of the program that are using them. Of course, in practice, either the old programs depend on bugs in the new version or the new version introduces bug not in the old version causing “all hell to break loose”

  2. Welcome back Gil!

  3. Gil you can overcome dependency hell, but it takes a lot of planning and compensation. apt-get upgrade :)

  4. vpr, for even better overcoming dependency hell I think “aptitude upgrade” will do the job!

  5. 5

    Take your holistic reasoning back to the Dark Ages Gil. We have advanced beyond common sense. Scientists can draw imaginary lines to make a closed system in nature wherever and whenever it is convenient. No need for this “big picture” stuff.

  6. 6
    Granville Sewell

    Gil,

    Yes, welcome back.

    This is one of the main points I made in my Mathematical Intelligencer article.

  7. I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell,

    A great analogy. And then consider that the programming of life is far more sophisticated than even the most advanced OS.

    And then close your eyes, put your hand over your ears and repeat “It all happened by chance. It all happened by chance.

  8. Mr Dodgen,

    First, welcome back to UD!

    Where exactly is your problem with avian lung evolution? With the evolution of the structures or the evolution of the process?

    It seems from your comment about asphixiation that you are concerned about process. However, bi-directional air flow could work in structures that allow uni-directional flow, just less efficiently.

    BTW, you don’t have to figure this out yourself. If you Google “evolution avian lung” you can find plenty of resources to help!

    Again, welcome back!

  9. Flow-through respiration is hypothesized to have appeared in theropod dinosaurs long before there were birds. See, for instance, http://oak.cats.ohiou.edu/~rid.....irsacs.pdf.

    Does intelligent design offer an alternative hypothesis?

  10. We should alert all readers that we do not pay Nakashima to make his comments here. The master of the unnderwhelm and the just so story does it all on his own. The denier of all things reasonable makes his claims out of ether. The magic of Darwinism.

    I am sure we will be treated to all the underwhelming evidence for avian lung development in the near future and the one or two steps necessary for a gene duplication event with an appropriate deletion and reversal to accomplish it all in just one set of gametes.

    It will be fun to watch this simple process unfold before our very eyes just as the slicer and dicer on the boardwalk with his handy dandy gadget make great epicurean delights. I passed one last night but I do not think it was Nakashima.

  11. Mr Jerry,

    We should alert all readers that we do not pay Nakashima to make his comments here.

    What?! I was wondering why the check was slow in arriving. :)

    But seriously, the ad hominem is a poor comeback. PM Erasmus immediately!

  12. Mr Sewell,

    Very nice article! I was struck by this quote:

    When Dr. Behe was at the University of Texas El Paso in May of 1997 to give an invited talk, I told him that I thought he would find more support for his ideas in mathematics, physics and computer science departments than in his own field.

    Given the way his own department treats him, I also think it would be wise for him to appeal to a non-biological audience, especially the math, computer science, and engineering crowd. These are the folks who have a chance to understand the information-theoretical basis for modern ID anyways.

  13. 13

    Hi jerry,

    I am sure we will be treated to all the underwhelming evidence for avian lung development in the near future and the one or two steps necessary for a gene duplication event with an appropriate deletion and reversal to accomplish it all in just one set of gametes.

    Nah. Just evidence that the pulmonary system was probably present in the theropod dinosaurs long before birds:

    O’Connor PM & LPAM Claessens (2005). Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs. Nature 436:253-256

    http://oak.cats.ohiou.edu/~rid.....irsacs.pdf

    I hope the link works

  14. 14

    Your in good company Gil, Michael Denton wonders about the avian lung in this video:

    No Beneficial Mutations – Not By Chance – Evolution: Theory In Crisis
    http://www.youtube.com/watch?v=OdZYguRuzn0

    if we were to get a proper “beneficial mutation’ in a polyfunctional genome of interdependent genes then instead of the infamous “Methinks it is like a weasel” single function information problem for Darwinists, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford.

    S A T O R
    A R E P O
    T E N E T
    O P E R A
    R O T A S

    Which is translated ;
    THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

    This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation.

    This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations.

    The puzzle I listed is only poly-fuctional to 4 elements, as stated earlier the minimum genome is poly-constrained to approximately 382 elements (genes). For Darwinist to continue to believe in random mutations to generate the staggering level of complexity we find in life is absurd in the highest order!

    And in reflection to your computer crashing Gil, Should you not just start randomly changing code until the problem is fixed and you have evolved a OS that is far superior?

  15. However, bi-directional air flow could work in structures that allow uni-directional flow, just less efficiently.

    Nakashima-san, I think the point to consider isn’t that an undirected avian lung evolution is a logical impossibility, but rather an unreasonable assumption considering the issues involved with making changes to already highly related programming work together by those consciencely trying hard to do so per Gil’s example.

  16. Gil,
    I pointed jerry to this open access paper a little while ago.. they again show air sacs present in theropod dinosaurs and present a hypothetical pathway for the evolution of the avian respiratory system using fossil evidence. what part of this proposed pathway do you find unreasonable?

    http://www.plosone.org/article.....ne.0003303

  17. Khan,

    What genes/ DNA sequences are involved?

    IOW how can one objectively test the premise that an accumulation of genetic accidents led to the evolution of the avian respiratory system.

    Hopefully it took less than two specified mutations or your position is in a lot of trouble.

  18. Mr Bornagain77,

    Where does the number 382 come from? There are 12 ways to read a DNA strand, 2 directions X 2 strands X 3 reading frames. While each of these is possible, it does not happen in practice that overlapping readings are used. If it were common, then frameshifts due to indel mutations would not be so harmful. We have already discussed this.

  19. Mr Joseph,

    There is a new book, How To Build A Dinosaur. Some of it is amusing, but it is a start on answering your request for an objective test.

    Hopefully it took less than two specified mutations or your position is in a lot of trouble.

    Luckily, it took more than two, but they were unspecified! :)

  20. Joseph,

    I don’t know. some extant reptiles have air sacs in the tail, so doing some comparative genetics/development between them and reptiles without air sacs and birds might be a good place to start. but the fossil evidence is certainly compelling, and the pathway they propose is plausible and is a good starting point for investigation. or do you disagree? if so, what specifically about the pathway do you think is implausible?

  21. 21

    “There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
    (Dr. John Sanford; Genetic Entropy 2005)

    Moreover, single genes are shown to code for multiple protein products:

    Human genes are multitaskers:
    abstract: Genome-wide surveys of gene expression in 15 different tissues and cell lines have revealed that up to 94% of human genes generate more than one (protein) product.
    http://www.nature.com/news/200......1199.html

    And multiple genes are shown to code for single protein products

    Multiple genes code for high-molecular-mass rhoptry proteins of Plasmodium yoelii
    excerpt: The genes in the family were distributed on 6 chromosomes probably at 9 or more loci.
    http://www.sciencedirect.com/s.....L&

  22. vpr: Gil you can overcome dependency hell, but it takes a lot of planning and compensation. apt-get upgrade

    Yeah, I know. I upgraded one of my Linux boxes from an old Xandros distro to the latest Ubuntu. I spent the entire day working through the problems. One of my favorite apps, the GMP big-number math library, didn’t work after I downloaded GCC and attempted to compile the GMP source with it. The GMP ./configure script gave me error messages, so I went online and found that I had to do a sudo apt-get to fix the problem.

    All is well now.

    Man, that Darwinian stuff sure is amazing. No planning, understanding, or intelligence required. Just add water, random chance, lots of time, and poof: the human mind emerges in 10^17 seconds.

  23. Hmmm… on one side we have scientists of all political persuasions and all religions, all of whom come to the conclusion that evolution is true. Also on that side we have reams of carefully produced and peer-reviewed evidence.

    On the other side we have a group of conservative fundamentalist Christians, some of whom are lawyers, some engineers, and some lay-people who cite “common sense” as the reason they doubt evolution.

    I need to weigh this carefully to determine which side is more likely to be right.

  24. Mr Bornagain77,

    You’ve quoted this section of the book before. It is a laundry list of different possibilities, not a desription of how every possibility applies to the whole genome.

    Is there support for the number 382? I don’t see it.

    As I’ve said before, every time the same protein is produced by multiple genes/loci, there is less poly-constraint on that protein.

  25. Mr Dodgen,

    Man, that Darwinian stuff sure is amazing. No planning, understanding, or intelligence required. Just add water, random chance, lots of time, and poof: the human mind emerges in 10^17 seconds.

    And beetles! Remember, the main product of evolution is bacteria.

  26. 26

    “An earlier study published in 1999 estimated the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382.”
    John I. Glass et al., “Essential Genes of a Minimal Bacterium,” Proceedings of the National Academy of Sciences, USA103 (2006): 425-30.

    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?” – David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8

    On top of the fact that we now know the genetic code of the simplest organism ever found on Earth has a highly advanced algorithmic code that surpasses man’s ability to devise as such, we also know for a fact that no operation of logic ever performed by a computer will ever increase the algorithmic code inherent in a computer’s program, i.e. Bill Gates will never use random number generators and selection software to write highly advanced computer codes:

    “… no operation performed by a computer can create new information.”
    Douglas G. Robertson, “Algorithmic Information Theory, Free Will and the Turing Test,” Complexity, Vol.3, #3 Jan/Feb 1999, pp. 25-34. The Evolutionary Informatics Lab:
    http://www.evoinfo.org/index.html

    Thus evolution is soundly defeated at even the most basic level of what we now know for Functional Information generation, namely it is shown that no sequence of events, in the foundational logic of computer language, can ever produce complex functional information.

    Defeating Evolution With The “Simple Cell” – video
    http://www.youtube.com/watch?v=giO7UmH7Zw4

    Global Organization of Metabolic Fluxes in the Bacterium, Escherichia coli
    Excerpt:
    Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization of individual reactions into metabolic networks is increasingly well understood, the principles governing their global functional utilization under different growth conditions pose many open questions.

  27. Hmmm… on one side we have scientists of all political persuasions and all religions, all of whom come to the conclusion that evolution is true.

    Dear Mr. Legend,

    Where on earth did you get the idea that I don’t believe evolution is true? Of course I believe evolution is true. Living things are not now as they once were, so by definition life has evolved.

    The question is whether or not random changes can accumulate to produce highly complex, functionally integrated, interdependent, information-processing machinery and the information such systems process, given the available probabilistic resources, and even given unrealistically optimistic assumptions.

    These are the kinds of questions engineers, mathematicians, and computer scientists tend to ask. These questions are never asked by pseudo-scientists like Darwinian evolutionists — they just make up stories with no rigorous analysis, and declare the problem solved.

    Those of us who are involved in information theory, computer programming, engineering, mathematics, and other rigorous scientific disciplines tend not to be convinced by hand-waving declarations of consensus.

    In our engineering department we have a saying: “Does it pass the beverage-out-the-nose test?”

    I’ll let you figure out what that means. The Darwinian mechanism does not pass the test.

  28. 28

    Hey Gil,
    I remember a post you did one time a few years back about intelligent design found throughout the universe from the big bang to life…

    Here is a article I am still working on that covers most of the high points of that fact,,There may be a few gems in it you can use, especially towards the end.

    Intelligent Design – The Anthropic Hypothesis

    http://docs.google.com/View?id=dc8z67wz_0hm7ftjfn

    You might like this two:

    Turin Shroud Hologram Reveals The Words “The Lamb” – short video
    http://www.youtube.com/watch?v=7XLcdaFKzYg

    Shroud Of Turin Carbon Dating Overturned By Scientific Peer Review – Robert Villarreal – Concluding statement of Press Release video
    http://www.youtube.com/watch?v=UEJPrMGksUg

  29. 29

    I’ll let you figure out what that means.

    Interesting that you won’t come right out and claim that the people involved in information theory, computer programming, engineering, mathematics, and other rigorous scientific disciplines don’t support the Darwinian theory. Why is that, Gil?

  30. #7:

    A great analogy. And then consider that the programming of life is far more sophisticated than even the most advanced OS.

    #15:

    Nakashima-san, I think the point to consider isn’t that an undirected avian lung evolution is a logical impossibility, but rather an unreasonable assumption considering the issues involved with making changes to already highly related programming work together by those consciencely trying hard to do so per Gil’s example.

    OK, so let me get this straight: The “programming of life” is way beyond the capabilities of any intelligence we know about or can even conceive of. Therefore, life must have been designed by some intelligence.

  31. pubdef– OK, so let me get this straight: The “programming of life” is way beyond the capabilities of any intelligence we know about or can even conceive of. Therefore, life must have been designed by some intelligence.

    Um no. It’s that the programming of life is way beyond the capabilities of any intelligence we know about so we can be confident that it didn’t come about by accident.

    Now, you really didn’t mean to imply that since the programming of life is way beyond the capabilities of any intelligence we know about it means it came about by accident, did you?

  32. Intelligent Design – The Anthropic Hypothesis

    http://docs.google.com/View?id=dc8z67wz_0hm7ftjfn

    You might like this two:

    Turin Shroud Hologram Reveals The Words “The Lamb” – short video
    http://www.youtube.com/watch?v=7XLcdaFKzYg

    Shroud Of Turin Carbon Dating Overturned By Scientific Peer Review – Robert Villarreal – Concluding statement of Press Release video
    http://www.youtube.com/watch?v=UEJPrMGksUg

    That’s some incredible stuff BA!! I’d been cautiously following the coverage on the shroud of Turin for a while now, but these new developments really puts the nail in the coffin! Thanks for sharing!

    Also, that’s an impressive compilation of documents and videos for the Anthropic Hypothesis. I do intend to look through them thoroughly. =)

  33. The question is whether or not random changes can accumulate to produce highly complex, functionally integrated, interdependent, information-processing machinery and the information such systems process, given the available probabilistic resources, and even given unrealistically optimistic assumptions.

    What mechanism is there in nature that actively limits microevolution from changing into macroevolution? This is decidedly the center of the debate, and it’s something the ID camp needs to answer.

    Microevolution and macroevolution are the same process on different scales; it is irrational to say that only one of them exists. When you seek to “refute” macroevolution, all you’re doing is reducing micro to a minimum effect and pushing macro to a maximum effect, when in fact there is a spectrum in between. And since creationist terms are perpetually undefined, it’s remarkably easy to employ a smokescreen and impossible to objectively determine what evidence would be required to support it. So now we’re asking you.

    When do two recently diverged species descendants become sufficiently distinctive that macroevolution has occurred? What is the minimal requirement?

    These are the kinds of questions engineers, mathematicians, and computer scientists tend to ask. These questions are never asked by pseudo-scientists like Darwinian evolutionists — they just make up stories with no rigorous analysis, and declare the problem solved.

    You do realize that mathematics and investigative science are two completely different fields that are handled completely different when it comes to proof? In math, things are provable. In science, things are only provable beyond a shadow of a doubt (I.E., searching the most reasonable explanation with the data given).

    Those of us who are involved in information theory, computer programming, engineering, mathematics, and other rigorous scientific disciplines tend not to be convinced by hand-waving declarations of consensus.

    Perhaps you should ask yourself why they came to a consensus in the first place.

  34. Generally what I see going on around here is a combination of the following:

    1) Dunning-Kruger effect
    http://en.wikipedia.org/wiki/Dunning-Kruger

    Contributors here have HUGE gaps in their knowledge of the science. The deeper one’s ignorance, the deeper one’s unawareness of one’s ignorance, leading one to erroneously conclude that one is more than competent enough to make sweeping judgments about entire fields of science.

    2) Defense mechanisms like denial (no, there really is no evidence) and dismissal (biologists are “psuedo-scientists” and they tell “just-so stories). This mechanism works with number 1 above to keep people from filling in the huge gaps in their knowledge.

    These two are a deadly combination: they turn people into creationists. Luckily the cure is simply education, but unfortunately, people need to stop feeling that the religion is threatened by education. It isn’t.

  35. Legend:

    Kindly help us — apparently in your view, the ignorant, stupid, insane (or possibly wicked) — out by showing how, for instance, the weak Anti-design argument correctives linked above, right, are grossly in error and how such error is compounded by too much ignorance to spot the errors. (If 30+ cases are too many, pick on say the first 4 – 8.)

    Then kindly go into the left hand column and show me how the information and thermodynamics anchored notes I have put up (and which are linked in every post I have made at UD) are similarly riddled by error compounded by malignant ignorance.

    Thanks in advance.

    GEM of TKI

    PS: Remember, the leading ID thinkers are in general PhD level practitioners in relevant fields. And us mere blog commenters and/or posters often have relevant graduate level education and professional experience. That is why we are (a) skeptical of the notion that chance + necessity can account for the evident highly complex designs we see around us, and (b) are confident that there are empirically well-warranted signs of design that point to the design of life and/or the cosmos.

  36. Mr Legendary1,

    These two are a deadly combination: they turn people into creationists. Luckily the cure is simply education…

    That is actually the subject of a significant portion of the Lewontin review of Sagan’s Demon Haunted World, which we are discussing on another thread. Your position is with Sagan. Lewontin does not think it is so simple.

  37. Mr Bornagain77,

    Bill Gates will never use random number generators and selection software to write highly advanced computer codes…

    But these folks will!

  38. “I need to weigh this carefully to determine which side is more likely to be right.”

    You do, but you won’t.

  39. Nakashima-San:

    Genetic algorithms use tightly constrained, goal directed random walks to try to capture higher performing configurations.

    They are not at all properly analogous to spontaneous chance variation plus — upon spontaneously achieving first complex function [!!!] — non-foresighted selection as mechanisms of claimed macroevolution.

    And that’s why GA’s are not created by having a million monkeys bang away at keyboards at random.

    GEM of TKI

  40. Legendary!,

    The theory of evolution is built on ignorance and relies on ignorance so that it is accepted.

  41. Legendary1,

    Generally what I see here is the following:

    1)Darwinist newcomer effect:
    Gotcha!

    In all seriousness I’m not trying to alienate you from the rest of the mostly respectful discourse that ensues here, but if you’re going to off-handedly jump in and slap a set of general judgemental criteria on every ID proponent here then you should at least do so without blatantly expressing the same set of criteria that you underhandedly pin on us.

    If you truly believe that contributors here have such a HUGE gap in their knowledge, then you have some serious catching up to do =P Otherwise, I’ll politely request that you please provide proof for your claim.

    Defense mechanisms like denial… and dismissal… This mechanism works with number 1 above to keep people from filling in the huge gaps in their knowledge.

    Welcome to the debate! We see materialists doing the exact same thing, and then calling it “evolutionary biology.”

    These two are a deadly combination: they turn people into creationists. Luckily the cure is simply education, but unfortunately, people need to stop feeling that the religion is threatened by education. It isn’t.

    As I said, you have a lot of catching up to do.

    Junk DNA

    More on DNA

    The intelligent function of ribosomes

    Scroll down for a series of posts covering alot of what you apparently haven’t read yet.(You especially might want to read the posts concerning the education standards in Texas)

    An article on academic freedom

    On that note you make the claim that religion isn’t threatened by education, and I’d have to agree! Religion IS, however, threatened by a philosophically restricted education that entails a heavy materialistic socio-political bias. =D

    Kinda makes you wonder why Christianity has been on the decline within the past few decades doesn’t it? After all, it’s not like indoctrinating the next generation with philosophically restricted world views through the modern educational system could EVER have any effect on that right? I mean, it’s not like their going to be the ones constituting the majority of the American population at some poi- oh wait…

  42. Before I lock off for now:

    RDK, the big difference between micro and macro-evo is that for us to get to first function we have to successfully cross a huge config space to get to an island of function, by unforesighted chance + necessity.

    Then, one may tinker around and reward differential functionality and reproductive success one’s heart’s content.

    But, there is no credible empirical basis for showing the ability to get to shores of function in large config spaces [1,000 bits or more worth.]

    The empirical evidence on microevo — and too much of even that is misleading or exaggerated in significance (e.g. peppered moths, Darwin’s finches) — relates in general to a few base pairs shifting at random, orders of magnitude short of what is needed for 1st life [~ 600 k bits] or the dozens of novel body plans at eh Cambrian [~ 10's - 100's of m bits].

    And, on Behe’s survey of malaria parasites, even a few base pairs worth of functional mutation is hard to do. And recall, the malaria parasite has in 1 year more reproductive events than all of the mammals would have had across time on any generally accepted timeline; up to the 100+ millions of years.

    The search resources are simply not there to get from micro-evo to macro-evo, RDK

    GEM of TKI

  43. 43

    KF,

    Let us not forget the importance of “active information in all of this.” The difference between man and ape maybe 8% or maybe 1% but ultimately the reason why the effective genetic differences are so great have to do with the functioning of that code. The activity of our genes plays a greater role in “what” we are and thus “what we can come from” than merely the bits of information can reveal.

    A natural mountain with no signs of ID can have just as much information as Mt Rushmore but it is in the unlikelihood of the “specificity” that the improbabilities become unbridgeable.

    This is why ID needs to work out the idea of specificity and activity to come up with a case that correctly defines the greater improbability of active information because active information shows far greater signs of design and working intelligence than now regular non-active or minimally active code does.

    The challenge of active information may or may not pose a serious challenge to universal common ancestry but it in fact does pose an unbridgeable one to Neo DE.

    Wouldn’t you say?

  44. Legendary1:

    Hmmm… on one side we have scientists of all political persuasions and all religions, all of whom come to the conclusion that evolution is true.

    Are you saying no scientists doubt Darwinian evolution?
    ROTFLMAO

    1)This is a mere ad hom.

    2)The underlying assumption on your part? No ‘real’ scientist doubts Darwinism.

    How many more times do we have to put up with such inane codswallop?

    Also on that side we have reams of carefully produced and peer-reviewed evidence.

    Reams of carefully invented speculation (also known as just-so stories) and tons of evidence of micro-evolution is all there is. Wake up and smell the mephitic deficiencies of NDE.

    On the other side we have a group of conservative fundamentalist Christians, some of whom are lawyers, some engineers, and some lay-people who cite “common sense” as the reason they doubt evolution.

    This repeats the underlying BS and foolish, propaganda-based assumptions of your 1st part. “All IDists are ignorant fanatical farmer hillbillies.”?! Yet another Darwinist piece of slander.
    So, guys like Wells, Sternberg, Meyer, Kenyon, Wilder Smith, Dembski, Witt, Nelson and hundreds of others are in fact just unlearned fakes?

    No one will take you seriously if you keep spouting such salient falsehoods instead of bringing actual facts to the table.

    I need to weigh this carefully to determine which side is more likely to be right.

    You ought to weigh the weakness of your own ignorance-based comments here. Hint: you need some artificial gravity since thus far you’re points are weightless.

    While you’re at it, go back a few 100 years and join the flat earth consensus science of that day – you’d fit right in with your kind of swill-based arguments.

  45. Legendary1:

    Generally what I see going on around here … 1) Dunning-Kruger effect

    Indeed, developed by Cornell people. Interestingly the same U that geneticist and ID proponent John Sanford comes from. The guy that wrote the book that’s demolishing NDE.

    This should really be applied to you above the rest. Often the one who brings up such criticism, instead of an actual argument, is the one to whom this type of comment applies.

    Contributors here have HUGE gaps in their knowledge of the science.

    You don’t have a clue who your talking to.

    The deeper one’s ignorance, the deeper one’s unawareness of one’s ignorance, leading one to erroneously conclude that.

    Again, this applies nicely to yourself by the fact that you even bring up such a comment.

    2) Defense mechanisms like denial (no, there really is no evidence) and dismissal (biologists are “psuedo-scientists” and they tell “just-so stories).

    Denial is the name of the game for Darwinists and atheists.

    There is no God and Dawkins is his prophet.

    These two are a deadly combination: they turn people into creationists.

    Well gee that would explain why most of the great scientists in history were creationists!

    Go home and suck your thumb a while child, might help soothe your profound betise.

  46. 46

    “No human investigation can be called true science without passing through mathematical tests.”
    Leonardo Da Vinci

    It is extremely interesting to note that the principle of Genetic Entropy lends itself very well to mathematical analysis by computer simulation:

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances. Using realistic estimates for the relevant biological parameters, we investigate the rate of mutation accumulation, the distribution of the fitness effects of the accumulating mutations, and the overall effect on mean genotypic fitness. Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net
    http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf

    Whereas, evolution has no rigorous mathematical foundation with which we can analyze it in any computer simulation:

    Accounting for Variations – Dr. David Berlinski: – video
    http://www.youtube.com/watch?v=aW2GkDkimkE

    EV Ware: Dissection of a Digital Organism
    excerpt: Ev purports to show “how life gains information.” Specifically “that biological information… can rapidly appear in genetic control systems subjected to replication, mutation and selection.” (We show that) It is the active information introduced by the computer programmer and not the evolutionary program that reduced the difficulty of the problem to a manageable level.
    http://www.evoinfo.org/Resources/EvWare/index.html

  47. Hi kairosfocus

    Nakashima-San:

    Genetic algorithms use tightly constrained, goal directed random walks to try to capture higher performing configurations.

    They are not at all properly analogous to spontaneous chance variation plus — upon spontaneously achieving first complex function [!!!] — non-foresighted selection as mechanisms of claimed macroevolution.

    And that’s why GA’s are not created by having a million monkeys bang away at keyboards at random.

    GEM of TKI

    Actually you have it completely backwards. Reading a bit too much Dembski, eh?

    There are numerous problems with slapping search algorithms into an analogy for evolution. Evolution doesn’t need to work in all possible landscapes

  48. 48

    RDK,

    Above you have proclaimed something but did not support it. Science involved arguments so that we can reach a valid understanding. Unsupported proclamations are the stuff of politics and advertisement.

    Are we to believe that evolution happens within it’s own special universal domain separate from the rest of reality?

    Does that sound like good science to you or a poor synthesis of evolution and it’s place in reality? Are we to say that evolution is to be considered it’s own entity? If so where did it originate from? And what evolutionary process evolved evolved evolution?

    By singleing it out from the rest of the pheneomna of the uiverse you have actually boxed it in- as all independent phenomena require their own facilitator and explanation. To say something exists without an mechanism for its emergence results in a situation that goes beyond contingency, necessity, and chance as explanatory mechanisms. Mechanisms which constitute the exact naturalistic principles from which the theory evolutionary is extended and justified.

    Without universal relationships with all other phenomena one leads oneself to a anti-scientific or supernatural conclusion or result.

    If however you actually look at evolution as it actually is, a part of the acting universe as a whole – then it becomes a process by which makes sense in regard to the greater cosmic whole. And it is in this proper domain we which we call reality that ID is able to challenge and critique DE’s prowess. Nothing can be critiqued if it is kept in it’s own impenetrable conceptual fortress.

    Now ID claims that intelligence is a non-physical explanation for the specified complexity of things. Hence, ID does not need to fallow a materialistic universal synthesis as it never claims this model to be the one true template of intelligence or for scientific inquiry. Intelligence is interwoven throughout the universe and it is the one natural acting force, cause and explanation that can pick and choose how and when it get’s involved. And this constitutes the explanatory benefit that an ID perspective beings to science.

  49. …in fact, it needs to work in one particular set of search spaces (the organism’s present environment, complete with selection pressures, etc.). Evolutionary processes exploit that variable.

    But anyway:

    Before I lock off for now:

    RDK, the big difference between micro and macro-evo is that for us to get to first function we have to successfully cross a huge config space to get to an island of function, by unforesighted chance + necessity.

    Are you asking scientists to completely and flawlessly document every single genetic change that occurred since the beginning of life (and possibly even before that, considering that the first signs of life are probably not what we would today call “life”)? Good luck. Everybody is aware of the tentative nature of science. There are things we can observe directly, and things that can be inferred due to a strong amount of supporting evidence. The relationships of organisms on macroevolutionary scale can be inferred from what we know of microevolution (and you sell it short with claims of hyped evidence; we know quite enough to make such an inference), as well as that pesky fossil record that remains unexplainable to intelligent design.

    Then, one may tinker around and reward differential functionality and reproductive success one’s heart’s content.

    …so basically you’re just questioning how life came about? How it got its first boost? Cool. So am I. But that’s not in the realm of evolutionary biology. That’s a field we call abiogenesis.

    But, there is no credible empirical basis for showing the ability to get to shores of function in large config spaces [1,000 bits or more worth.]

    ID attempts to refute that life came from non-life? A m I reading this correctly? Are you asserting that abiogenesis did not occur?

    That seems like an odd assertion. We can reasonably assume that there was a time in the universe where there was no life present (before the cooling of the first stars, for example). Today, we do have life. Therefore, life MUST have come from non-life. Unless you’re also going to play the YEC card.

    The empirical evidence on microevo — and too much of even that is misleading or exaggerated in significance (e.g. peppered moths, Darwin’s finches) — relates in general to a few base pairs shifting at random, orders of magnitude short of what is needed for 1st life [~ 600 k bits] or the dozens of novel body plans at eh Cambrian [~ 10's - 100's of m bits].

    Could you please explain why you find the evidence for microevolution to be so misleading? What would it take to convince you? Vestigial structures? Human tails? Veriform appendix? Subterranean populations of animals that lost eyesight due to enough generations living in a lightless environment? Bacteria developing the ability to consume nylon, a man-made substance? Or how about bacteria developing the ability to consume PCP, a highly toxic chemical not known to occur naturally, that has been used as a wood preservative since the 1930′s?

    Sorry if my attempts are a bit underwhelming; it’s kind of hard to appease the rigorous and unending questions posed by creationists who oddly enough don’t seem to press any other scientific field of relative worth with the same amount of vigor. But just what part of microevolution do you find hard to believe?

    In any case, this is exactly what I outlined in my last post. You’re conflating the terms with each extreme end of the spectrum, when in fact there is a whole field in-between. You’re pushing microevolution to a miniscule effect–very sill–and pushing macroevolution to a maximum effect, which is equally silly.

    And, on Behe’s survey of malaria parasites, even a few base pairs worth of functional mutation is hard to do. And recall, the malaria parasite has in 1 year more reproductive events than all of the mammals would have had across time on any generally accepted timeline; up to the 100+ millions of years.

    So the reproductive habits of one strain of parasite disproves the efficacy of the entire process of microevolution? Wow! I wish I could safely apply that to any other field of science!

    But in any case, I’ll say what I said on the evolution fallacies thread: don’t fix what isn’t broken. The malaria parasite is highly specialized, and continues to devastate large numbers of people in areas where medical assistance is scarce. Even if you change the selection pressures, which I doubt Behe did a good job representing, then what incentive is there to change the current modus operandi?

    The search resources are simply not there to get from micro-evo to macro-evo, RDK

    I won’t lie and tell you that I can come up with evidence that will convince you, because it won’t; but the evidence is there; you just have to look hard enough. :)

  50. By singleing it out from the rest of the pheneomna of the uiverse you have actually boxed it in- as all independent phenomena require their own facilitator and explanation. To say something exists without an mechanism for its emergence results in a situation that goes beyond contingency, necessity, and chance as explanatory mechanisms. Mechanisms which constitute the exact naturalistic principles from which the theory evolutionary is extended and justified.

    Knowing that something had a mechanism for its emergence is one thing. Knowing exactly how that happened in detail is another.

    Humour me then: can you rigorously explain, in detail, how the emergence of the intelligence involved in intelligent design came about?

    Now ID claims that intelligence is a non-physical explanation for the specified complexity of things. Hence, ID does not need to fallow a materialistic universal synthesis as it never claims this model to be the one true template of intelligence or for scientific inquiry. Intelligence is interwoven throughout the universe and it is the one natural acting force, cause and explanation that can pick and choose how and when it get’s involved. And this constitutes the explanatory benefit that an ID perspective beings to science.

    Well that’s just too easy isn’t it? :)

    For some reason you think you can still play science and not heed to as scientific mindset. The supernatural has no place in science. If something is not natural–if it cannot be observed or tested–then science has no comment on it. I guess science has no comment on your intelligent designer, since it is literally undistinguishable from naturalistic processes only in the sense that it cannot be detected on its own merit.

    Perhaps we should apply Occam’s Razor and cut out all the unnecessary parts?

    god exists
    god created the universe
    the universe exists

    god exists
    god created the universe
    the universe exists

  51. pubdef– OK, so let me get this straight: The “programming of life” is way beyond the capabilities of any intelligence we know about or can even conceive of. Therefore, life must have been designed by some intelligence.

    Um no. It’s that the programming of life is way beyond the capabilities of any intelligence we know about so we can be confident that it didn’t come about by accident.

    Now, you really didn’t mean to imply that since the programming of life is way beyond the capabilities of any intelligence we know about it means it came about by accident, did you?

    Well, “accident” is not the word I would choose, but I do mean something like “ID seems to require the existence of something for which we really have no evidence.”
    As far as comparing NDE with ID: let’s look at the implications for scientific research. NDE tries to see how something we know something about (mutation, selection, what have you) may be capable of producing what we see. To the extent that “what we know something about” is insufficient, it tries to figure out how other things we can observe and test can help fill in the blanks.
    ID, on the other hand, proposes something we know nothing at all about — an intelligence far superior to anything we have ever experienced. Then, it eschews any desire or responsibility to learn anything about it. (Is there any analogy to this in materialists science? Have you ever heard a scientists say “it is not within the purview of science to say what this is or how it works?” These are not rhetorical questions.)
    One more quick run at what I’m trying to say: You claim that evolution puts way more reliance on chance than it can bear. I’m asking you to consider whether you are doing the same to “intelligence.”

  52. Mr Kairosfocus,

    They are not at all properly analogous to spontaneous chance variation plus — upon spontaneously achieving first complex function [!!!] — non-foresighted selection as mechanisms of claimed macroevolution.

    That appears not to be the case. The whole point of GAs like MESA is that GAs are analogous biological evolution, aka repeated iterations of a population experiencing heritable variation and selection. If Dr Dembski and other ID theorists agreed wth you, they would just declare ev, AVIDA, etc a category mistake and ignore them. Instead, they accept that GAs _are_ evolution, and attempt to use them to demonstrate certain aspects of evolution – for example the need for active information.

    “Evolution” is an abstraction. It doesn’t need DNA, any more than “Flight” needs feathers.

  53. 53

    RDK your only argument was saying ID has it too easy. Well let the facts fall where they may- if ID provides an more easily applicable explanation so be it. Intelligence does operate on a choice basis. We can quickly get into the “what or who designed the designer” debate but I appeal to intelligence as the fundamental force from which all things come. That is we reach a point of infinite intelligence giving life to a sequence of other lesser intelligences. A top down view of specified complexity.

    The idea that you think evolution can only be critiqued where it works it absurd ans clearly shows your agenda which is devout preservation of the theory in crises.

    The fact that you obviously dont know what gave rise to your evolution is not a good reason to accept a promissory note on if and when we can expect and explanation. If the theory does not work find a new theory.

    It makes no sense to accept materialism as your rule book for science but then exempt your theory from having to abide it.
    That is the sign of a religious dogma. If material necessity, chance and contingency operate everywhere in the universe than lets judge they theory as being part of that whole.

    ID thinks the fundamental mechanical force needed to bridge the universal probability gaps is intelligence which is defined as a non material force acting in the physical world and inferred by effects and quantified in bits of information.

    For starters, it’s just that easy. :)

  54. 54

    Everything That begins to exist has a cause;

    The Universe began to exist:

    Therefore the universe has a cause.

    Since the beginning of the universe was an absolute origin of space-time, matter-energy, The cause of the universe must be transcendent of space-time, matter-energy.

    Information is shown to be transcendent and dominate of space-time, matter-energy in quantum teleportation experiments.

    Thus information is the only known candidate to present itself for the creation of the universe.

    John 1:1 In the beginning was The Word (Logos)

  55. Mr Bornagain77,

    Thank you for sharing. As another candidate besides Information, what about Error, or less cynically, Humor?

  56. 56

    RDK:

    Knowing that something had a mechanism for its emergence is one thing. Knowing exactly how that happened in detail is another.

    That’s an accurate statement, although I don’t know what it has to do with ID. Or evolution for that matter. If someone has the “exactly how that happened in detail” part handy I’d love to look it over.
    Science routinely answers some questions while leaving others. A thermometer may accurately measure temperature, and yet it will never determine the source of the heat it measures. It offers no explanation for what it detects.
    It seems like you’re awfully generous in letting evolution off the hook when it comes to details, and unyielding in requiring that ID explain what it never claimed to.

  57. Thank you for sharing. As another candidate besides Information, what about Error, or less cynically, Humor?

    My favorite abstraction is abstraction itself, so that gets my vote.

  58. 58

    Legendary1,

    ——”Hmmm… on one side we have scientists of all political persuasions and all religions, all of whom come to the conclusion that evolution is true. Also on that side we have reams of carefully produced and peer-reviewed evidence.

    On the other side we have a group of conservative fundamentalist Christians, some of whom are lawyers, some engineers, and some lay-people who cite “common sense” as the reason they doubt evolution.

    I need to weigh this carefully to determine which side is more likely to be right.”

    I’m glad ethos works for all your questions, and you feel no need for logos. :),

  59. 59

    bornagain77 (#54) wrote: “Everything That begins to exist has a cause.”

    Isn’t that a hypothesis rather than a fact? Have you proven it?

  60. 60

    Paul, the idea that something cannot exist and not exist in the same cirrcumstance has not been proven either.

    I just love it when conventionalists (ala Popper) turn to irrationality in order to protect their cherished paradigm.

    Sounds very sciency to me.

    Paul, can please provide a list of things that came into existence without a cause?

  61. 61

    I’m glad ethos works for all your questions, and you feel no need for logos. :),

    That seems interesting. Would you kindly translate for the philosophically impaired?

  62. Clive:

    No, logos is important too, hence my reference to the reams of evidence on the one side (which of course the other side is lacking).

    For those who have claimed that I am new hear and thus don’t know what I’m talking about, let me just say that I have been reading this site since before the Dover trial. I have read it faithfully, slogging through Davescott’s marine posts, attempts by O’Leary to equate evolution to Nazism, Gil’s criticism that computer simulations can’t possibly be right and his claims that engineers are in a better position to judge biology than biologists, and Mr. Dembski’s street theater. I have also read Behe’s “Edge of Evolution” and Dembski’s “No Free Lunch.” And yes, the logos (both in terms of evidence and logic) as well as the ethos are on the side of evolution.

    Bornagain77, you said:

    “Everything That begins to exist has a cause”

    That’s a clever attempt to get around the objection that your argument also applies to god. But your argument still fails. How do you know that everything that begins to exist has a cause? By observing things in this universe. So, if you want to be proper, you should say, “Everything that we know of in this universe that begins to exist has a cause.” This is true because of the laws of this universe (we’ll leave aside quantum physics, which has actually called this into question).

    Well, the universe is not inside this universe, now is it? Plus, the laws of this universe break down at the moment of the big bang. So we really cannot say if the universe needed a cause to come into existence. Your argument is bad.

  63. 63

    Does God Exist? Argument From The Origin Of Nature – Kirk Durston

    http://www.youtube.com/watch?v=Ncttu3p0RlY

  64. Legendary “That’s a clever attempt to get around the objection that your argument also applies to god”

    Wrong.

    Legendary “So we really cannot say if the universe needed a cause to come into existence.”

    No of course we cant say that beCAUSE the universe was caused by nothing!!

    Or the universe “poofed” into existence.

    Or the universe “existed before it existed”.

    Or “nothing did it”.

    Or “do you believe in magic?”

    All these are live possibilites. Like the Queen told Alice in so many words when Alice asked about believing impossible things.

    The Queen:”I dare say you haven’t had much practice. When I was your age, I always did it for half an hour a day. Why, sometimes I’ve believed as many as six impossible things before breakfast.”

    Bourne and Upright you just need to practice more.

    Vivid

  65. 65

    Legendary2,

    ——”No, logos is important too, hence my reference to the reams of evidence on the one side (which of course the other side is lacking).”

    The other side is lacking logos. I like arguments by assertion too :D.

    ——”or those who have claimed that I am new hear and thus don’t know what I’m talking about, let me just say…”

    I do claim that you don’t know what you’re talking about, regardless of your time as a lurker.

    And yes, the logos is entirely on the side of the ID folks.

    ——”Bornagain77, you said:

    “Everything That begins to exist has a cause”

    Legendary2 responds:

    ——”That’s a clever attempt to get around the objection that your argument also applies to god.”

    No it doesn’t. There has to be a prime reality, an initial first mover, otherwise you’re in an infinite regress of causes. Maybe you’re comfortable with an infinite regress of causes as an explanation, I’m not. Besides, it is a non sequitur to attribute the same necessary conditions and causes to something supernatural, as we can legitimately attribute the necessary causes to the natural. Never the twain shall meet as far as needing causes; it only applies to natural stuff. Your argument is bad :)

  66. No, sorry.

    We aren’t stuck in an infinite regress, because there only need be an initial cause in OUR universe. We have no idea what the state of things were like before our universe. Something like causation may not have applied. We don’t know. But in any case, it defeats the necessity of a prime mover.

    How did the universe get here? I don’t know. You don’t either. I, however, don’t kid myself that I do.

  67. 67

    Legendary1,

    You do kid yourself, for your negation of any positive explanation can only be a negation if you at least know enough to know that the positive explanation is wrong. It’s fine to be agnostic, but let’s not say that we know that we must be agnostic, for we do not know enough about the unknown to know that it is unknowable, to quote a phrase.

  68. Legend: …Gil’s criticism that computer simulations can’t possibly be right and his claims that engineers are in a better position to judge biology than biologists…

    Dear Mr. Legend,

    You are not only a legend in your own time, but a legend in your own mind. The quote above betrays a hideous misrepresentation of everything I’ve posted at UD.

    I never said that “computer simulations can’t possibly be right.” I write computer simulations that are demonstrably right. What I’ve said is that computer simulations that make extravagant simplifying assumptions can’t be trusted unless they are empirically tested against the reality they attempt to simulate. Even in my areas of expertise — AI, guidance, navigation and control, and transient, nonlinear, dynamic finite element analysis — my sims are never trusted until they are compared with reality.

    I never said that “engineers are in a better position to judge biology than biologists.” I’ve claimed that when evolutionary biologists make claims about the creative power of their proposed mechanism of random variation and natural selection to produce systems that give every indication of being highly engineered technology, they should be required to produce at least some empirical evidence — not declarations of consensus within their incestuous group — that the proposed mechanism is actually capable of producing the technology we observe.

    In no other area of real, hard science would the extravagant, untested, and unverified claims of Darwinists be accepted without challenge.

  69. I don’t, and you aren’t grasping what I am saying.

    Your side is the one positing the necessity of a first cause for the universe (to make your faith in the Christian god seem more rational). I have shown that one has no reason whatsoever to feel that a first cause for the universe is a necessity. Thus your side’s argument falls apart.

    Nowhere did I say we must be agnostic. Implicit in my refutation is also the idea that we have no reason to think there wasn’t a first cause, whatever that might be. We just have no reason to think there was; we can’t decide between the two options. And if we can’t decide between them, clearly we can’t make the first cause argument that Bornagain thinks he can make.

  70. Gil, the systems do not “give every indication of being highly engineered technology.” By smuggling in this assumption you beg the question– you assume what you are trying to prove. Whether or not life looks like engineered technology is the issue under question here. Nice try though.

    Also, there is plenty of empirical evidence, both experimental and otherwise, for evolution. You just choose to ignore it. Unfortunately, there won’t be anything I could say or any evidence I could point out to you that would be able to break through your shell of rationalizations and denial.

    As a side note, Gil, I remember when you wrote an article here claiming that for a computer simulation to properly model random selection, errors would have to be instituted in the “underlying machinery.” You said “both the hardware and the software must be subject to random errors,” i.e the hardware as in the computer itself. I’ve had a great deal of difficulty taking seriously anything you say about computer simulations since I read that.

  71. 71

    Legendary2,

    ——”Your side is the one positing the necessity of a first cause for the universe (to make your faith in the Christian god seem more rational).”

    No one doubts that there must be a cause, in general. What is in question is whether the cause was personal or not. And I don’t hang my Christian hat on this peg, so you can stop with the silly motive mongering game of why folks adhere to a personal first cause. Could it be that a personal first cause just makes good sense? But, I suppose that you reckon no personal first cause, and that the Big Bang occurred on its own after the singularity created itself, and over time here you are, a non-personal thing yourself, just a cloud of atoms, a box of fireworks no different in content or personality than that singularity. As if a thing exploding will one day come to know itself. Makes perfect sense.

  72. 72

    Gil, Legendary3,

    ——”As a side note, Gil, I remember when you wrote an article here claiming that for a computer simulation to properly model random selection, errors would have to be instituted in the “underlying machinery.” You said “both the hardware and the software must be subject to random errors,” i.e the hardware as in the computer itself. I’ve had a great deal of difficulty taking seriously anything you say about computer simulations since I read that.”

    That was a fantastic point Gil. I’ll tuck that one away for future reference. Very well put.

  73. Gil, the systems do not “give every indication of being highly engineered technology.”

    Okay, let me get this straight: A base-four, digitally encoded protein-manufacturing system that folds the manufactured proteins into precise three-dimensional shapes that are required for interactive function with a multitude of other manufactured and precisely folded proteins, and a transport system with lock-and-key verification systems, not to mention error detection and repair algorithms, give no indication whatsoever of engineered technology.

    It is at this point that one must throw up his hands in horror at the capacity of some intellectuals for self-inflicted blindness, and the denial of evidence and logic.

  74. pubdef–“ID seems to require the existence of something for which we really have no evidence.”

    As opposed to pinning it’s hopes on the expectation of the spontaneous generation of life? What evidence do we have for that?

    Anyway, it’s not so much “no evidence” it’s that there is no certainty — at least no measurable certainty — which is true of anything involving the unknown.

    With regard to evidence, in which direction do the scales tip? The expectation that highly complex things can form at random or via unknown necessities that would violate a fundamental biological axiom, or the understanding that there must be an uncaused cause not affected by the laws of physics and the observation that life is highly analogous to things of known design?

  75. 75

    –Legendary (ha!) “Your side is the one positing the necessity of a first cause for the universe (to make your faith in the Christian god seem more rational). I have shown that one has no reason whatsoever to feel that a first cause for the universe is a necessity. Thus your side’s argument falls apart.”

    Are you actually staring into space when you write this stuff? (alright, whatever…)

    Anyway, let me understand this; (Our) side, is positing the necessity for a first cause for the universe, and (We) are doing it to make a case for, presumably, (O)ur beliefs.

    Please enlighten me; what are the names of these Christians who dragged science into believing that everything has a material cause leading back to the beginning of space and time? What an evil plot, these Christians. They’ve fooled the scientists into believing that the Big Bang was the start of things. Then, those crazy scientists started mapping everything backwards – insisting cause upon cause – into the very core of the shockwave that started it all. It’s almost like causes came to be expected, even necessary. No one even suggested they stop looking.

    –Legendary (ha!) Nowhere did I say we must be agnostic. Implicit in my refutation is also the idea that we have no reason to think there wasn’t a first cause, whatever that might be. We just have no reason to think there was; we can’t decide between the two options. And if we can’t decide between them, clearly we can’t make the first cause argument that Bornagain thinks he can make.

    Somebody help me out here; what is the opposite of a fish out of water?

    By your reasoning, we think for some unknown reason, that there must be one final cause right before there are no more causes to look for…and since we can’t assume there are any more causes after the last one we found – it must mean there isn’t any. Therefore believing there isn’t is more correct than believing there is?

    Makes perfect sense if you say it fast enough.

  76. Upright: “Makes perfect sense if you say it fast enough”

    Legend AKA Alice: “If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn’t. And contrary wise, what is, it wouldn’t be. And what it wouldn’t be, it would. You see?”

    Vivid

  77. Clive Hayden @ 72:
    “Gil, Legendary3,

    ——”As a side note, Gil, I remember when you wrote an article here claiming that for a computer simulation to properly model random selection, errors would have to be instituted in the “underlying machinery.” You said “both the hardware and the software must be subject to random errors,” i.e the hardware as in the computer itself.”

    That was a fantastic point Gil. I’ll tuck that one away for future reference. Very well put.”

    Changing the hardware in a computer that’s running a computer simulation would be like changing the laws of physics in the universe that’s running the phenomena being simulated.

  78. Nakshima-San:

    I am well aware that GA’s are alleged to mimic evolution. New World Enc makes a very relevant distinction, in its discussion of algorithms:

    Genetic algorithms attempt to find solutions to problems by mimicking the theory of biological evolution, in which cycles of “random mutations” are thought to yield successive generations of “solutions.” This process is likened to the concept of “survival of the fittest.” In genetic programming, the algorithm is regarded as a “solution” to a problem.

    In short, we must make a distinction between the actual state of the world and the models propounded by evolutionary biologists etc.

    Similarly, in Wiki’s intro to its GA article, that materialism-leaning site makes a very telling acknowledgment:

    A genetic algorithm (GA) is a search technique used in computing to find exact or approximate solutions to optimization and search problems. Genetic algorithms are categorized as global search heuristics. Genetic algorithms are a particular class of evolutionary algorithms that use techniques inspired by evolutionary biology such as inheritance, mutation, selection, and crossover (also called recombination).

    Evo bio is of course a field of study with a particular dominant theoretical paradigm, not a state of the world. (Science is inherently provisional and all that.) But more directly, observe that we are dealing with a search technique, one that is intelligently directed and set up.

    The crucial first challenge remains that in the prebiotic world as imagined under evolutionary materialist scenarios, there were no intelligences to direct whatever chemical formations may have occurred, so the search space challenge to get to shores of function thence enabling differential success of competing functions, and optimising by hill climbing. Also, observed independently living unicellular life is subject to autodisintegration of functionality below DNA complexity of a bit over 300,000 base pairs; which specifies a configuration space that is vastly beyond the search resources of the observed cosmos.

    (NB: RDK’s “must have” is a matter of deduction within a circle of Lewontinian materialistic assumptions as addressed in my always linked note, Section E. Nor, are all alternatives to evo mat scenarios equivalent to Young Earth Creationism. Nor, is YEC properly to be brushed aside with a dismissive sneer, without cogently answering not just the perceived weaker issues they raise but the central and far more difficult to address ones too — the ones that just happen to overlap with the very different — and far older [it goes back to being immemorial in the days of Plato . . . ] — movement of thought, Intelligent Design. Strawmen and ad hominems leading to sneering prejudices and dismissals will not do; at least, not here at UD.)

    Similarly, on macroevolution, the need of body plan origination and transmission from generation to generation poses the challenge that, credibly, 10′s – 100′s of mega bits of bioinformation has to be embryologically feasible before a novel body plan can come into existence to find and compete in an ecological niche.

    Worse, in the case of earth, on the usual timelines, the Cambrian is a window of 5 – 10 MY or so. In that window, on the fossil evidence — and this has been in material part known since Darwin’s day — there is a “sudden” wide bursting out of dozens of phylum and subphylum level branches on the body plans of animals.

    So, on evo mat premises, 100′s – 1,000′s or mega bits of bio-information have to originate in this one small planet in a very tight time window, by chance + necessity. Simply the scope of the information explosion is beyond the probabilistically credible reach of the observed cosmos, much less 5 – 10 MY or even 4 – 5 BY on this one small planet.

    By contrast, we have the observation hat intelligent designers routinely create FSCI-rich systems, with this or larger scopes of functional algorithmic, coded digital information. And, in every case of such information, where we independently directly know the origin, it is produced by intelligence.

    So, intelligent design is a very reasonable explanation for the origin and body plan level diversity of life. One that — Lewontinian a priori marterialist impositins notwithstanding — is supported by the exact same type of induction that underlies ever so much of our scientific reasoning. So, it has every reason to be treated as a scientifically based inference, noises by today’s evolutionary materialist de facto magisteria notwithstanding.

    GEM of TKI

    PS: RDK: First, a note: kindly, note that that every post I make here is linked to an extensive discussion of the issues you have made. Consult these before making further ad hominem laced assertions.

  79. Gil, 68:

    when evolutionary biologists make claims about the creative power of their proposed mechanism of random variation and natural selection to produce systems that give every indication of being highly engineered technology, they should be required to produce at least some empirical evidence — not declarations of consensus within their incestuous group — that the proposed mechanism is actually capable of producing the technology we observe.

    Spot on — just one reason why I am glad to see you back.

    GEM of TKI

    PS: The allusions to ethos, pathos and logos are to the three classes of persuasion in rhetoric, e.g. in Aristotle’s the Rhetoric, Bk 1 Ch 2:

    Of the modes of persuasion furnished by the spoken word there are three kinds. The first kind depends on the personal character of the speaker [ethos, more or less to [perceived credibility or authority]; the second on putting the audience into a certain frame of mind [pathos -- emotions]; the third on the proof, or apparent proof, provided by the words of the speech itself [logos - fact and logic, real or perceived]. Persuasion is achieved by the speaker’s personal character when the speech is so spoken as to make us think him credible . . . Secondly, persuasion may come through the hearers, when the speech stirs their emotions. Our judgements when we are pleased and friendly are not the same as when we are pained and hostile . . . Thirdly, persuasion is effected through the speech itself when we have proved a truth or an apparent truth by means of the persuasive arguments suitable to the case in question . . . .

  80. Clive:

    No one doubts that there must be a cause, in general. What is in question is whether the cause was personal or not. And I don’t hang my Christian hat on this peg, so you can stop with the silly motive mongering game of why folks adhere to a personal first cause. Could it be that a personal first cause just makes good sense? But, I suppose that you reckon no personal first cause, and that the Big Bang occurred on its own after the singularity created itself, and over time here you are, a non-personal thing yourself, just a cloud of atoms, a box of fireworks no different in content or personality than that singularity. As if a thing exploding will one day come to know itself. Makes perfect sense.

    Good argument, Clive! I hadn’t considered that things always do have the properties and intentionalities of the mechanisms that created them. That’s why swords made in forges by blacksmiths remain burning hot like the fires they were forged in, and they are as intelligent as the smith, while crystals formed from chaotic magma show no structure whatsoever. Good show.

    That was a fantastic point Gil. I’ll tuck that one away for future reference. Very well put.

    You should tuck that away and quote it as much as possible. It will gain you great respect. And remember, if you ever want to simulate anything to do with airspeed or something like that, you should throw your computer out the window.

    Gil:

    Okay, let me get this straight: A base-four, digitally encoded protein-manufacturing system that folds the manufactured proteins into precise three-dimensional shapes that are required for interactive function with a multitude of other manufactured and precisely folded proteins, and a transport system with lock-and-key verification systems, not to mention error detection and repair algorithms, give no indication whatsoever of engineered technology.

    You can couch it in computer engineering jargon all you want, but the fact remains that DNA and the other structures of life are not computerized. They just show order. You can’t beg the question and simply say, “well, I used a lot of technological terms to describe them, so isn’t it obvious that they are designed?” No, it isn’t, especially when a proven non-design related mechanism has been shown to exist, your denial notwithstanding.

    Upright biped:

    By your reasoning, we think for some unknown reason, that there must be one final cause right before there are no more causes to look for…and since we can’t assume there are any more causes after the last one we found – it must mean there isn’t any. Therefore believing there isn’t is more correct than believing there is?

    No, that isn’t my argument at all, although I know it’s easier to knock down a scarecrow than a real life man who can resist and knock you down instead. Go back and read what I wrote, and try to follow along. We posit the necessity of causes based on our observations of things in this universe and the laws of nature of this universe. This universe, strangely enough, did not exist before it existed. What was the state of things before this universe? We don’t know.

    Put another way, causation (which involved priority– one thing coming before another) is dependent on time. Time and space came to be at the start of this universe. If time did not exist, what can it mean to say that something needed a cause. Before had no meaning, thus cause had no meaning, thus there is no way one can hold onto the necessity of causation when causation has no meaning whatsoever in a pre-universe state.

    Now bring on the strawmen arguments!

  81. “You can couch it in computer engineering jargon all you want, but the fact remains that DNA and the other structures of life are not computerized. They just show order. You can’t beg the question and simply say, “well, I used a lot of technological terms to describe them, so isn’t it obvious that they are designed?” No, it isn’t, especially when a proven non-design related mechanism has been shown to exist, your denial notwithstanding.”

    Well, quite a stupid statement. DNA, computer programming and language are similar phenomena, though not exactly identical. There is nothing else like them except intelligently designed.

  82. I should have clarified my previous statement and said the DNA, transcription, translation process. DNA can and does exist in certain instances and is quite unremarkable just as are crystals and snow flakes.

  83. 83

    Legendary1:

    You can couch it in computer engineering jargon all you want, but the fact remains that DNA and the other structures of life are not computerized. They just show order.

    They “just” show order. It sounds so simple. How does one arrange such things in order?
    If using technical terms to describe them is just a smokescreen to make them seem more complex than they are, then try accurately describing them without technical terms.
    BTW, “protein manufacturing,” “three dimensional,” “precisely folded,” and “transport systems” are not computer jargon.

  84. PPS: Legend. Sorry to have to say this, but I see no signs — despite your self-reported longterm lurker status — of a serious engagement on the merits on your part. Please, do not fall into the trap of being wise in your own eyes, unconscious of being a prisoner in a manipulative, modern-day Plato’s cave world of manipulative shadow-shows. (To show that you have not fallen into that trap, the best answer would be to engage at least a good cross section of issues on the merits, and soundly show why the design alternative is an inferior explanation to your preferred evolutionary materialist one. Just as, I have taken the time to put my more complete thoughts down as a briefing note, and link them through every post I make. You may disagree with the conclusions I have drawn, but I would think that the always linked will show that I have reasons and evidence for my conclusions, not just empty-headed repetitions of someone else’s ideas. For instance you will see why I think there is a link from thermodynamics to information [including the fact of controversy on it, and why I think Brillouin and Jaynes et al have a valid point], and why I think that FSCI is a good and reliable sign of intelligence; including a rule of thumb metric for the threshold where this comes into play. Thence, you will see how this relates to OOL, OO body plan diversity, and extending to the issue of finetuning, to cosmology. You will also see why I consider that something is rotten in the state of early C21 science and science education on origins, something that — with the help of colleagues and partners — I intend to do something about; on an INDEPENDENT basis. History and economics both tell us that there is nothing like a little free competition to fix the problems of hubris-laced monopoly.)

  85. PPPPS: Legend (and SA): I see selective hyperskepticism is alive and wellt his morning at UD, on the DNA- RNA- Ribosome- Enzyme algorithmic, 4-state digital code controlled protein manufacturing system. (Don’t get me started on routing to destinations in the cell using headers and transport networks . . . )

    Let me just draw on materialism-leaning Wiki, in its article on the genetic code, citing the lead to the article:

    The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences, called codons, and amino acids. A triplet codon in a nucleic acid sequence usually specifies a single amino acid (though in some cases the same codon triplet in different locations can code unambiguously for two different amino acids, the correct choice at each location being determined by context)[1]. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. Thus the canonical genetic code is not universal. For example, in humans, protein synthesis in mitochondria relies on a genetic code that varies from the canonical code.

    It is important to know that not all genetic information is stored using the genetic code. All organisms’ DNA contain regulatory sequences, intergenic segments, and chromosomal structural areas that can contribute greatly to phenotype but operate using distinct sets of rules that may or may not be as straightforward as the codon-to-amino acid paradigm that usually underlies the genetic code (see epigenetics).

    In the article on epigenetics, we may read:

    In biology, the term epigenetics refers to changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence, hence the name epi- (Greek: over; above) -genetics. These changes may remain through cell divisions for the remainder of the cell’s life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism;[1] instead, non-genetic factors cause the organism’s genes to behave (or “express themselves”) differently.[2] The best example of epigenetic changes in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo which in turn become fully differentiated cells. In other words, a single fertilized egg cell – the zygote – changes into the many cell types including neurons, muscle cells, epithelium, blood vessels et cetera as it continues to divide. It does so by activating some genes while inhibiting others.[3] . . . .

    The molecular basis of epigenetics is complex. It involves modifications of the activation of certain genes, but not the basic structure of DNA. Additionally, the chromatin proteins associated with DNA may be activated or silenced. This accounts for why the differentiated cells in a multi-cellular organism express only the genes that are necessary for their own activity. Epigenetic changes are preserved when cells divide. Most epigenetic changes only occur within the course of one individual organism’s lifetime, but some epigenetic changes are inherited from one generation to the next.[9] Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.

    This is food for thought for one snack for us members of the Clapham Bus Stop society.

  86. Mr Kairosfocus,

    It is remarkable that so much quotation worthy research was done without involving a design hypothesis!

  87. Legend–What was the state of things before this universe? We don’t know.

    Well, we do know some things. We know our laws of physics couldn’t have applied else the universe would not have come into existence.

    If time did not exist, what can it mean to say that something needed a cause.

    Well, time does exist now so that means something had to have occurred to have caused our particular set of circumstances to come about.

    And can you see the irony in what you are espousing? :-)

  88. 88

    Sometimes upon re-reading, I see that the direction of my posts can easy to miss. Something to work on.
    But I’m not in the hyperskeptical camp. My point was that to refer to DNA and its reproduction as “order” is a gross oversimplification. And that it is a union of information and physical mechanisms which cannot be reduced to “computer jargon.”

  89. 89

    –Legend: “No, that isn’t my argument at all, although I know it’s easier to knock down a scarecrow than a real life man who can resist and knock you down instead. Go back and read what I wrote, and try to follow along. We posit the necessity of causes based on our observations of things in this universe and the laws of nature of this universe.”

    Sorry there Legend, but when you posit there are traceable causes back to a point where there are no more causes, then I have accurately described your position. Sorry if you don’t like the implications of your position, but you can amend it any time.

    Secondly, no one is trying to look beyond or outside this Universe. It is the very observations within this universe that cannot be explained by material causes.

    I see you understand this point, or you would’nt be trying so hard to rid yourself of the facts.

  90. 90

    By the way Legend,

    Genetic information is not like something with meaning – it is something with meaning.

    Codons are not like symbols in a symbol system – they are symbols in a symbol system.

    Nucleic sequencing is not like prescriptive digital information – it is prescriptive digital information.

    Genetic transcription and translation is not like a physically-inert language – it is a physically-inert language.

    There is nothing in the laws that govern this universe that says genetic information has to exist the way it does. In fact, as far as the physical laws of the universe are concerned, it doesn’t even have to exist at all. Yet it exists, without physical laws to explain it.

    So…when you are tracing those physical causes of observable phenomena inside this universe, you won’t run out of road at the Big Bang, you’ll run out of road at the point that information organizes inanimate matter into living tissue.

  91. pubdef–“ID seems to require the existence of something for which we really have no evidence.”

    As opposed to pinning it’s hopes on the expectation of the spontaneous generation of life? What evidence do we have for that?

    I think you’re not comparing apples to apples. I’m raising a basic concept of ID, the bedrock principle that “intelligence” can provide an explanation that is superior to material-based explanations. You’re rebutting with a specific question that you apparently think materialistic science has a problem answering. In this light, I think it’s inapposite to talk about “pinning its hopes,” for two reasons. First, a materialistic theory of evolution does not have to answer every question, especially in an area (abiogenesis) which is not, strictly speak, in its purview. Second, even if we’re looking at materialistic science as a whole, the question of abiogenesis is the subject of exploration; there are scientists who are trying to learn about it. Are there ID-oriented scientists who are trying to understand the nature of an intelligence that would be capable of creating life?
    So, which paradigm (ID or materialism) requires the bigger step outside of the empirical data?

  92. #80:

    DNA, computer programming and language are similar phenomena, though not exactly identical. There is nothing else like them except intelligently designed.

    “Not exactly identical” — one point of divergence is that we know how computer code is designed and who (what kind of being) designs it. Now, if you have two things that might be designed, and you know exactly what kind of being designed one of them and you have no idea whatsoever who or what designed the other (in fact, have never observed anything remotely capable of such design), are they equally likely to have been designed? Is the first only a little more likely?

  93. 93

    pubdef:

    Now, if you have two things that might be designed, and you know exactly what kind of being designed one of them and you have no idea whatsoever who or what designed the other (in fact, have never observed anything remotely capable of such design), are they equally likely to have been designed?

    Given an object of unknown origin, how does increased complexity (we have never observed anything capable of design it) reduce the likelihood of design?
    From where do you draw such an inference, that vast complexity is evidence against design?

  94. 94

    Legend,

    1) Evolution has nothing to do with it. (strawman)

    2) I don’t deny evolution per se. (another strawman)

    3) You have yet to back up any material explantion whatsoever with evidence of any naturally occuring (non-agency) digitally encoded algorythm being communicated between physical objects anywhere in the universe. (empirical evidence needed)

  95. 95

    Legendary4,

    ——”Kairosfocus: I have to give it to you, you are an intellectual heavyweight on this site. In terms of intelligence, I would say you outrank Dembski by some degrees, Gil by more, Clive by even more than that, and O’Leary and bornagain by leagues and leagues.”

    This is insulting and inappropriate. If you want to play this game, I think you’re a total moron.

  96. Legendary1,

    Of all the philosophical naturalists that have participated on this blog, you are among the easiest to write off.

    So far your overly generous contributions of broad, general, and judgemental claims that are backed up with no evidence whatsoever is astounding.

    You, like many other Darwinists only prove our points by brightly radiating typical attacks on credibility, fabricating weak conceptual arguments, making unbased blanket statements about the validity of perfectly rational ID proposals in regard to religious motives, dismissing said proposals off-handedly and pointing fingers at said motives for justification, dismissing said proposals after a rigorous amount of research and evidence have been presented, and also dismissing the negative arguments against your position. Notice how almost every response to your original post by ID proponents here have included citations, links, documents, and evidential claims.

    You’re the one here making some pretty outrageous positive arguments, so guess where the burden of proof lies? If you think you’re above the bar of accounting for such a burden, or if you feel your “legendary” status reduces such scientific requirements into a mere triviality, then either you’re begging to be dismissed, here to be a troll, you’re simply here to prove the points that I made above, or you’re here to prove what the new philosophically restricted inquiry known as “science” has become. Personally I’d choose almost all of the above, but then again the burden lies upon you to prove me wrong.

  97. #93:

    Given an object of unknown origin, how does increased complexity (we have never observed anything capable of design it) reduce the likelihood of design?
    From where do you draw such an inference, that vast complexity is evidence against design?

    There’s an implied “surely you don’t mean that” tone in your questions, but yes, that’s pretty much exactly what I mean. I’m questioning the apparent ID assumption that if something seems way too complex for any intelligence we know of to have made it, all that is needed is more and more intelligence. I’m saying, instead, that if something is outside of the abilities of any intelligence we know of, it may well be wise to see whether something else may be capable of producing it.
    Here’s an analogy I’m working on. Imagine an object that we can tell is thousands of years old. Suppose the “design filter” (Dembski’s or generic) is inconclusive; it’s a genuine close case. Now suppose that we are convinced that construction of the object is way outside the technological resources of the people of that time. Is that relevant at all to your conclusion about whether the object is designed? Suppose it is not such a close case; it really seems a lot more specified and complex, but you still have absolutely no plausible explanation for how Fred Flintstone and his crew could have constructed it. Are you going to conclude that some other kind of intelligent being put it there?

  98. Clive,

    ——”Kairosfocus: I have to give it to you, you are an intellectual heavyweight on this site. In terms of intelligence, I would say you outrank Dembski by some degrees, Gil by more, Clive by even more than that, and O’Leary and bornagain by leagues and leagues.”

    “This is insulting and inappropriate.”

    Not only that Clive, but it’s completely inaccurate. The persons whom he deems to dwell at the bottom of his pretend intellectual hierarchy could run circles around him, and one of them has already proven it with arguments that are actually useful and documentation to back it up.

  99. 99

    PaulN,

    ——”Not only that Clive, but it’s completely inaccurate. The persons whom he deems to dwell at the bottom of his pretend intellectual hierarchy could run circles around him, and one of them has already proven it with arguments that are actually useful and documentation to back it up.”

    Of course. I took that to be a given.

  100. Mr Lengendary1,

    Your last post was pointless and completely ad hominem. Believe it or not, not all Internet discussion is a race to the bottom. Please don’t start down that road.

  101. 101

    LegendaryNone,

    I have put you in moderation, but I have not blacklisted you. Partly to give you an opportunity to straighten up, and partly because I want the satisfaction of deleting your nonsense if you don’t.

  102. 102

    pubdef:

    There’s an implied “surely you don’t mean that” tone in your questions, but yes, that’s pretty much exactly what I mean. I’m questioning the apparent ID assumption that if something seems way too complex for any intelligence we know of to have made it, all that is needed is more and more intelligence.

    Ok, surely you do mean it.
    If something is so complex that no intelligence known to us could have designed it, then how is less intelligence a better explanation?
    No one is saying all that is needed is more intelligence. Perhaps more intelligence, more experience, more knowledge, more resources, more time, even more designers.

    Now suppose that we are convinced that construction of the object is way outside the technological resources of the people of that time. Is that relevant at all to your conclusion about whether the object is designed? Suppose it is not such a close case; it really seems a lot more specified and complex, but you still have absolutely no plausible explanation for how Fred Flintstone and his crew could have constructed it. Are you going to conclude that some other kind of intelligent being put it there?

    You’ve answered your own question by indicating that it would require technology to ‘construct.’ Can there be technology without intelligence?
    We might figure out who made it, we might not. But I wouldn’t waste time wondering if natural forces accidentally simulated intelligence and wielded technology in order to produce a seemingly manufactured result.

  103. pubdef–I’m raising a basic concept of ID, the bedrock principle that “intelligence” can provide an explanation that is superior to material-based explanations.

    But you are offering a faith-based explanation, not a material-based one.

    OTOH, we do know “intelligence” (design, planned action etc) exists as an influence on the material — namely creative force can take unrelated objects that would never have otherwise been joined and use them for an effective purpose.

    And since intelligence exists we know it can be objectified so a methodology can be developed to confidently ascertain design.

    The problem with arbitrarily rejecting intelligence (which is not supernatural, btw) as a factor in the development of life is that would end up with a false understanding of nature if it should be that intelligence is a factor in the development of life.

  104. pubdef (#98)

    Congratulations. You got to the crux of the problem. To quote your last paragraph,

    Here’s an analogy I’m working on. Imagine an object that we can tell is thousands of years old. Suppose the “design filter” (Dembski’s or generic) is inconclusive; it’s a genuine close case. Now suppose that we are convinced that construction of the object is way outside the technological resources of the people of that time. Is that relevant at all to your conclusion about whether the object is designed? Suppose it is not such a close case; it really seems a lot more specified and complex, but you still have absolutely no plausible explanation for how Fred Flintstone and his crew could have constructed it. Are you going to conclude that some other kind of intelligent being put it there?

    Let’s supply a real-world example for your analogy. Take Stonehenge. It is complex and specified. I think we all agree that it looks designed. Supposing that we were to determine that early humans in Britain were simply not up to the job of creating the structure with the technology they had. We then have a choice. We can hypothesize that nature made it unassisted, or that this is evidence for non-human intelligence. If the human hypothesis failed, would your fallback hypothesis really be icebergs and floods, or tornadoes? Or would you give a second thought to the alien hypothesis?

    That is precisely the question that is being asked with regard to the intricate organization of life. If it is beyond our present technology, and we were not there at its inception, is that evidence that nature must have done it somehow, or evidence that some non-human (and superhuman up to now) intelligence designed it and implemented the design?

    Do you see that as a stupid question, or one on which reasonable people can differ?

  105. Upright Biped said recently:

    “Genetic transcription and translation is not like a physically-inert language – it is a physically-inert language.”

    Um, actually, there is interesting and excellent positive experimental evidence that supports the hypothesis that the code that underlies translation is in fact not inert. Rather, there is a decided and demonstrable chemical basis for this code (that we all call the genetic code).

    Dave Wisker already pointed this discussion to a good review that discusses this evidence.

  106. #103:

    You’ve answered your own question by indicating that it would require technology to ‘construct.’ Can there be technology without intelligence?
    We might figure out who made it, we might not. But I wouldn’t waste time wondering if natural forces accidentally simulated intelligence and wielded technology in order to produce a seemingly manufactured result.

    OK, I guess I made it too complicated. Let me go back to my original hypo, and sharpen it a little.

    We have an object, and it’s a tossup whether it is designed or not, but it clearly could not have been constructed by people who lived at any time close to the age of the object. Given that you have no clear indication that it is or is not designed, would you consider it relevant that the only “designers” we know anything about (humans) could not have done it?

    My point is very simple: to reliably detect intelligent design, you have to consider whether there are any plausible candidates for the intelligent designer (i.e., is there anything or anyone intelligent enough to have designed it?). If there is not, you can either imagine a greater intelligence (or more experience, knowledge, resources, what have you), or you can consider whether there is something that you can learn something about that could produce complexity.

  107. 107

    Gil @68

    I never said that “engineers are in a better position to judge biology than biologists.” I’ve claimed that when evolutionary biologists make claims about the creative power of their proposed mechanism of random variation and natural selection to produce systems that give every indication of being highly engineered technology, they should be required to produce at least some empirical evidence — not declarations of consensus within their incestuous group — that the proposed mechanism is actually capable of producing the technology we observe.

    In no other area of real, hard science would the extravagant, untested, and unverified claims of Darwinists be accepted without challenge.

    Meanwhile, the National Academy of Engineering is Celebrating the Achievements of Charles Darwin

    Gil, since you feel so strongly about this, you really should contact the NAE and straighten them out. Please let us know what they say.

  108. #104:

    But you are offering a faith-based explanation, not a material-based one.

    I’ve quickly gone over my posts and I really can’t see that anything I’ve said can be interpreted as “offering a faith-based explanation.” In fact, I don’t think I’ve offered an “explanation” at all, but rather (1) argued that scientific investigation within a materialist paradigm does not require any more of an assumption than ID, (2) argued that the plausibilty of an intelligent designer is at least relevant to a calculus of design detection, and (3) asked a couple of questions, which, by and large, seem to have gone unanswered (e.g., in #51, “Have you ever heard a scientist say “it is not within the purview of science to say what this is or how it works?”).
    And let me ask one more question before I go off to play — what does “nonmaterialist science” look like? After you “detect design,” what do you do next? (OK, that’s two questions.)

  109. 109

    Arthur,

    I am aware of the research posted. I am also aware of other studies that fundamentally dispute the claim. This stands against the backdrop of a slew of OOL researchers that are not looking to solve the issue (of the informational organization of organic matter) through chemical affinities. They’ve already been there. The speculative counter claim you’ve suggested is a piddle of an idea at the foot of a mountain of contrary evidence.

    The nature of the patterns within nucleic sequencing did not come about because it physically had to.

    I will be happy to debate you on this point if you like. (pack your lunch)

  110. I realize it might be a waste of time after 110 posts to go back to the OP, but I just saw this news item disputing the bird-dinosaur link.

    Ruben has been a big holdout against the “birds are theropod dinosaurs” classifiers. Still publishes in peer reviewed journals, though.

  111. 111

    We have an object, and it’s a tossup whether it is designed or not, but it clearly could not have been constructed by people who lived at any time close to the age of the object. Given that you have no clear indication that it is or is not designed, would you consider it relevant that the only “designers” we know anything about (humans) could not have done it?

    My point is very simple: to reliably detect intelligent design, you have to consider whether there are any plausible candidates for the intelligent designer (i.e., is there anything or anyone intelligent enough to have designed it?).

    I really don’t mean to nitpick, but one of the conditions of the scenario is that a degree of intelligence would have been required to design the object in question. (This condition is added by asking whether anyone was intelligent enough to have designed it.) If the scenario specifies that intelligence was required, then it was required.
    I understand what you mean, and what you’re asking.
    But if the evidence points to design, and yet we don’t know of any intelligence great enough to design it, what of it? So there’s something we don’t know yet. Would that be the first time, or the last?

    I think we can all agree that if something contains a certain degree of complex, specified information (Alice In Wonderland, for example) that intelligence is the best explanation.
    How does increasing the complexity and function shift us toward blind natural forces as the best explanation, when such forces have no track record for producing anything much simpler? We must accept the evidence, even if it leaves us with unanswered questions.

  112. 112

    djmullen,

    ——”Changing the hardware in a computer that’s running a computer simulation would be like changing the laws of physics in the universe that’s running the phenomena being simulated.”

    Why?

  113. Hi Upright Biped,

    You said:

    “I am aware of the research posted. I am also aware of other studies that fundamentally dispute the claim.”

    I don’t suppose you’d care to share?

    “This stands against the backdrop of a slew of OOL researchers that are not looking to solve the issue (of the informational organization of organic matter) through chemical affinities. They’ve already been there.”

    Actually, everyone who works on RNA aptamers – many more people than work on other aspects of the OOL – are exploring exactly this issue, in one way or another. Every new aptamer sheds light into the ways by which the chemical properties of RNA shaped the evolution of the genetic code.

    “The speculative counter claim you’ve suggested is a piddle of an idea at the foot of a mountain of contrary evidence.”

    With all due respect, I’m willing to hazard the guess that you cannot provide any positive experimental evidence that argues against the hypothesis that the chemical properties of RNAs played a direct role in the evolution of the genetic code.

    “The nature of the patterns within nucleic sequencing did not come about because it physically had to.”

    Nothing has to occur. But it is hard to make an evidence-based argument that the genetic code is entirely arbitrary and disconnected fom the chemical properties of RNA. Because there isn’t any evidence that supports this position.

    “I will be happy to debate you on this point if you like. (pack your lunch)”

    If yer really interested, drop a note to one of the recent entries on my blog and I’d be glad to set up a discussion there. I’m not very comfortable with the delay that moderation here causes, and I’m a tiny bit concerned that, as happened before, when things get dicey for the ID side, I will again be blacklisted. That would put a crimp in any discussion.

  114. #111:

    really don’t mean to nitpick, but one of the conditions of the scenario is that a degree of intelligence would have been required to design the object in question. (This condition is added by asking whether anyone was intelligent enough to have designed it.) If the scenario specifies that intelligence was required, then it was required.

    I think we can agree that a degree of intelligence is required to design anything; this is not really germane to the scenario, where the problem can equivalently be stated as “is the object designed?” or “did the object require intelligence to come into being?” If there is nothing inherent about the object to tilt the answer one way or another, you could reasonably decide that it more likely was not designed if you have no designer candidates, or more likely was designed if the time period and location of the object was just swarming with eligible designers.

    But if the evidence points to design, and yet we don’t know of any intelligence great enough to design it, what of it? So there’s something we don’t know yet. Would that be the first time, or the last?

    OK as far as it goes, but two points: (1) the degree of evidence that we would accept as “pointing to design” varies with our knowledge, or lack thereof, of a capable intelligence; (2) a good faith, scientific, response to “something we don’t know yet” is to investigate further, which would be incompatible with any disavowal of inquiry into the nature and methods of the designer/intelligence.

    I think we can all agree that if something contains a certain degree of complex, specified information (Alice In Wonderland, for example) that intelligence is the best explanation.

    I’m tempted to agree, solely on the ground that “a certain degree” is no specific quantity, and CSI has no established definition, but on reflection, I’ll have to say — no, I don’t agree. I don’t think that any degree of CSI would convince me to simply ignore the other side of the question — is there any evidence at all of a plausible designer/intelligence? (I know I’m leaving myself open to a charge of dogmatism, but so be it.)

    How does increasing the complexity and function shift us toward blind natural forces as the best explanation, when such forces have no track record for producing anything much simpler?

    Well, I’m sure you realize that evolutionary biologists do not concede the point of your last clause. Short of devoting years of study to the subject, I can’t evaluate their claims independently, but my minimal toe-dipping into arguments on both sides leads me to give them some credence.

    Having said that, my answer to the meat of your question (“How does increasing the complexity and function shift us toward blind natural forces as the best explanation”) is: if increasing complexity and function moves out of the range of plausible designers/intelligence, then it seems reasonable to consider the alternatives.

  115. #103:

    The problem with arbitrarily rejecting intelligence (which is not supernatural, btw) as a factor in the development of life is that would end up with a false understanding of nature if it should be that intelligence is a factor in the development of life.

    The problem with rejecting anything as an explanation is that we would end up with a false understanding if it turned out to be a factor.
    Sounds a bit like Pascal’s Wager, to me.

  116. pubdef–But you are offering a faith-based explanation, not a material-based one.

    You are claiming that biodiversity can solely be attributed to random genomic changes fixed by natural selection. Correct me if I’m wrong.

    Regardless, this can’t be demonstrated.

    argued that scientific investigation within a materialist paradigm does not require any more of an assumption than ID,

    That would depend on what is being investigated and what is being concluded.

    (2) argued that the plausibilty of an intelligent designer is at least relevant to a calculus of design detection, and

    Which it looks like you have backwards — if the calculus indicates design, a designer is not merely plausible but likely

    (3) asked a couple of questions, which, by and large, seem to have gone unanswered (e.g., in #51, “Have you ever heard a scientist say “it is not within the purview of science to say what this is or how it works?”).

    Yes

    And let me ask one more question before I go off to play — what does “nonmaterialist science” look like?

    It wouldn’t look like ID. How does ID involve the nonmaterial?

    After you “detect design,” what do you do next? (OK, that’s two questions.)

    Declare design has been detected which is rather similar to what one would do if one determined an event to have occurred by chance.

  117. pubdef –The problem with rejecting anything as an explanation is that we would end up with a false understanding if it turned out to be a factor.

    Which is why you shouldn’t reject anything a priori such as by declaring ID out of bounds solely because it doesn’t identify a designer.

    It’s really no different than saying Darwinism may not be considered because it contradicts Genesis.

    And it has nothing to do with Pascal’s Wager.

  118. 118

    Arthur Hunt,

    ——”I’m a tiny bit concerned that, as happened before, when things get dicey for the ID side, I will again be blacklisted.”

    I’ll only blacklist you if you’re rude.

  119. Clive @ 112:
    “djmullen,

    ——”Changing the hardware in a computer that’s running a computer simulation would be like changing the laws of physics in the universe that’s running the phenomena being simulated.”

    Why?”

    Diffaxial has answered that question pretty well in post #5 in the “A More Realistic Computer Simulation of Biological Evolution” thread.

    An real life evolving population depends on the laws of physics staying the same. If they change, nothing may work. For instance, if you cut the strength of the strong nuclear force in half, every atom in the universe will explode and both the evolving creatures and the rest of the world will cease to exist.

    If you change the ADD instruction in the computer hardware to act like a SUB, your program will also explode, taking the simulated evolving creatures and their simulated environment with it.

    If you want to mimic Darwinian evolution, you have to restrict your mutations to the parts of the program that represent the evolving critter’s DNA because that’s what changes in evolution.

    In the new thread, Gil also seems to think that DNA mutations that might kill the simulated organism are prohibited, which is definitely not the case!

  120. Pubdef, 97:

    Suppose the “design filter” (Dembski’s or generic) is inconclusive . . .

    PD, the causal factor explanatory filter rests on looking at aspects of an entity or process, and then it identifies low/high contingency relative to similar starting circumstances. On low seeing contingency regularities for an aspect, it looks for a lawlike model, along lines of Newton’s mechnics as an exemplar of explantion by natural law.

    On seeing high contingency for an aspect, the DEFAULT is chance, showing itself in stochastic scatter of outcomes. It is only on strong positive evidence of signs of intelligence — i.e of directed, purposeful contingency — that the filter would infer to ART, not nature.

    So, the suggested inconclusivity is not a relevant issue.

    In praxis, if we see less than something like 500 – 1,000 bits of functional i9nformation that exhibits a clear border between function and non-function, the inference will be to chance, stochastic, undirected contingency. (The possibility of incorrectly ruling against design in such cases is cheerfully accepted, as the issue is to be clear on unambiguous cases.)

    GEM of TKI

  121. AH, 105:

    there is interesting and excellent positive experimental evidence that supports the hypothesis that the code that underlies translation is in fact not inert. Rather, there is a decided and demonstrable chemical basis for this code (that we all call the genetic code).

    Insofar as the DNA/RNA molecule is code-bearing, it is free to vary its monomers in particular positions of the code.

    For instance, all 64 possible three-letter combinations have a functionally relevant meaning, and occur. That is, the code does not forbid or restrict sequences unduly. And, if it did — i.e. if the sequences of A, G, C, T/U were determined by chemical forces — then it could not be information-bearing.

    What is chemically and physically driven is the complementarity of the two strands in a DNA sequence, and of course the sugar-phosphate links are the snap-together parts that make chaining possible. But, just like snap-together toy letters, this chaining does not specify which letters go in what sequence.

    DNA is about information storage in a four-state digital code.

    GEM of TKI

  122. 122

    pubdef:

    (2) a good faith, scientific, response to “something we don’t know yet” is to investigate further, which would be incompatible with any disavowal of inquiry into the nature and methods of the designer/intelligence.

    (2) a good faith, scientific, response to “something we don’t know yet” is to investigate further, which would be incompatible with any disavowal of inquiry into the nature and methods of the designer/intelligence.I agree. But no one had disavowed further investigation. ID just isn’t the means to do it. It’s like fingerprint analysis. It tells us who held the gun, but not why or what they did with it. But that first piece of information tells us where to point the investigation next.

    my answer to the meat of your question (”How does increasing the complexity and function shift us toward blind natural forces as the best explanation”) is: if increasing complexity and function moves out of the range of plausible designers/intelligence, then it seems reasonable to consider the alternatives.

    That’s true, if we factor in the assumption that there can’t be any intelligence we don’t already know about, which is an unusual response to evidence that it exists.
    Remember, if we identify intelligence as the cause, then natural means are ruled out.

  123. 123

    I butchered the first part of that.

    (2) a good faith, scientific, response to “something we don’t know yet” is to investigate further, which would be incompatible with any disavowal of inquiry into the nature and methods of the designer/intelligence.

    I agree. But no one had disavowed further investigation. ID just isn’t the means to do it. It’s like fingerprint analysis. It tells us who held the gun, but not why or what they did with it. But that first piece of information tells us where to point the investigation next.

  124. #116:

    How does ID involve the nonmaterial?

    I don’t know for sure. What does this mean?

  125. #122:

    I agree.

    Cool.

    But no one had disavowed further investigation. ID just isn’t the means to do it. It’s like fingerprint analysis. It tells us who held the gun, but not why or what they did with it. But that first piece of information tells us where to point the investigation next.

    I’m not sure that “no one” has disavowed further investigation. I was pretty sure I had seen someone (Luskin, perhaps) say “the identity of the designer is not a scientific question,” but I can’t find it right now. And speaking of “right now,” I’m signing off this thread at this point — any of you can have the last word, and I’ll see you next time.

  126. What does this mean?

    That you screwed up your HTML :-)

  127. pubdef,

    I’m still waiting for your answer to my questions in #104. According to #106, #108, and #115 you have read *103, and according to #114 you have read #111, so I know you have had time.

    In #114 you say,

    I don’t think that any degree of CSI would convince me to simply ignore the other side of the question — is there any evidence at all of a plausible designer/intelligence?

    If you insist for each instance that there is no evidence at all of a plausible designer/intelligence, and so therefore the object in question must not be designed, do you not cut yourself off from any possibility of ever seeing a designer/intelligence where evidence may be all over the place, simply because you treat each instance as the first?

    You say,

    I know I’m leaving myself open to a charge of dogmatism, but so be it.

    That’s fine as long as you admit it up front. But then it would seem that you have no reason to complain if someone else points out that you are offering a faith-based explanation, not an evidence-based one.

  128. BTW, for the record, it should be noted that pubdef was not kicked off of this thread because things got dicey for ID, as was alleged to happen consistently by Arthur Hunt in #113.

  129. 129

    Upright:

    I am aware of the research posted. I am also aware of other studies that fundamentally dispute the claim. This stands against the backdrop of a slew of OOL researchers that are not looking to solve the issue (of the informational organization of organic matter) through chemical affinities. They’ve already been there. The speculative counter claim you’ve suggested is a piddle of an idea at the foot of a mountain of contrary evidence.

    I for one would love to see this mountain of contrary evidence. Just citations would be fine for now.

  130. Paul,
    In answer to 104, why don’t we skip the speculative stuff about Stonehenge and talk instead about a real-world example. There have been several documented cases of cattle mutilation that remain unsolved. Variously,the cow is completely drained of blood, the internal organs removed with no apparent point of entry and surgical incisions appear to have been made with lasers. in some cases the cow is found dumped far from its field with no tracks leading to or from it. An FBI investigation said that several of these cases remain inexplicable by conventional means. now of course it’s possible that some rogue surgeons with access to laser tools and a helicopter did this. but some people may also say it was aliens. is this a point on which reasonable people can differ?

  131. meant to add, of course there’s also the third possibility that all the “mutilation” was the result of predation and decomposition.

  132. Khan (#129,130),

    In answer to 104, why don’t we skip the speculative stuff about Stonehenge and talk instead about a real-world example.

    I’m sorry. I was under the mistaken impression that Stonehenge was a real-world example. I’ll try to avoid such speculative examples in the future :P .

    There have been several documented cases of cattle mutilation that remain unsolved. Variously,the cow is completely drained of blood, the internal organs removed with no apparent point of entry and surgical incisions appear to have been made with lasers. in some cases the cow is found dumped far from its field with no tracks leading to or from it. An FBI investigation said that several of these cases remain inexplicable by conventional means. now of course it’s possible that some rogue surgeons with access to laser tools and a helicopter did this. but some people may also say it was aliens. is this a point on which reasonable people can differ?

    meant to add, of course there’s also the third possibility that all the “mutilation” was the result of predation and decomposition.

    Assuming the facts are as you state, particularly that “the internal organs [were] removed with no apparent point of entry and surgical incisions appear to have been made with lasers”, then I would tend to discount predation. I don’t know of too many carnivores with lasers in their teeth, and most of the time when a carnivore removes an organ it leaves a pretty large rip in the carcass. Having said that, it would take further study to determine whether psychotic surgeons, aliens, or demons (I would discount angels) are the most likely explanation. And I would want reasonable proof that the facts are as you say. But yes. At some point it would be reasonable to say that some kind of intelligence did this. Or would you disagree?

  133. 133

    I read the Wikipedia entry for Cattle Mutilation. It suggested several possible natural explanations for the apparent incisions, missing organs, etc. I doubt there’s anything there that ID would quantify as clear-cut evidence of intelligence.
    Now if the dead cows were arranged to spell “ET WAS HERE” from space, that would be different.

  134. Paul,
    I called Stonehenge speculative bc no one has shown that creating it was beyond the technology of humans living at that time. it is also a distant analogy bc it is not a living organism.

    as far as cattle mutilations go, can you describe a test that would properly distinguish between demons and aliens? personally, i don’t discount the idea of an intelligent agent at work but I would limit it to the one agent we have direct, objective experience with, namely ourselves.

  135. Khan (#135),

    I agree with you that Stonehenge hasn’t been conclusively demonstrated to be outside of the technology of ancient humans. It certainly was outside the knowledge and technology that many people attributed to ancient humans, but that is another matter.

    It seems to me like the analogy is from the weaker to the stronger. Humans have been observed moving massive stones into monuments. Humans have not (yet) created life, nor has unassisted nature been observed to do so. It is arguable that life is more difficult to create than stonehenge.

    As far as cattle mutilations go, there is a test which might provide evidence one way or another. It is not easy, and cannot be guaranteed to work. But planned or fortuitous video could give some evidence whether the intelligent agent were an alien or a demon, and hopefully could distinguish between both of them and psychotic surgeons. But some questions may simply not be answerable with assurance in this life.

  136. ScottAndrews (#133),

    You’re right. It would prove that the intelligent agent understood English. :)

  137. Footnote:

    Re DW, 129: I for one would love to see this mountain of contrary evidence. Just citations would be fine for now.

    1 –> Mr Whisker needs to start with the basic fact that the protein-coding part of the genome uses all 64 three-letter combinations of A, G, C, T/U that are mathematically possible.

    2 –> Thus, we see that the chemistry of chaining does not determine the sequence, and that the sequences are meaningful in the sense of specifying a particular action to be taken by the Ribosome-centred machinery: read-codon, start, read next codon [using tRNA anticodon-bearing molecule], add AA to chain, . . . , stop and detach.

    3 –> Thereafter, headers guide dispatching (and are snipped off as appropriate), and the protein folds, may agglomerate and/or incorporate activating atoms or functional groups etc. [NB on the significance of prions -- not event he folding is deterministic, and misfolding is not only possible but results in destructive snowballing effects.]

    4 –> This onward functionality is NOT a product of the chemistry of the chaining, or the chemical properties of the side-groups in the A, G, C, T/U monomers in D/RNA.

    5 –> It is a (highly complex) product of the energy patterns in the AA chain, and its 3-D key-lock fitting that enables active sites etc. All, in a complex, integrated whole that uses hundreds of proteins.

    6 –> thus, we see an algorithmic, digital information processing step by step sequence, which uses stored information in DNA chains that is well beyond the reasonable search resources of the observed cosmos to find islands of first function through chance to create initial or elaborated functional patterns.

    7 –> Nor is it the result of the physical and chemical forces at work as such — indeed, many of the monomers would be hard indeed to form under spontaneous warm pond conditions, much less survive and combine in a small enough compass to spontaneously assemble the machinery and the code then execute them. (Even the idea that all this would spontaneously find itself in a bilipid layer micelle of about 10 microns size that finds itself with ports and sensors that stick out into the surrounding medium is dubious.]

    8 –> Notice, the chemistry of the DNA system is plainly tightly controlled and algorithmically managed chemistry, and typically the reactions are heavily endothermic. That is, absent the algorithmic control we observe, very different reactions would spontaneously occur.

    GEM of TKI

  138. 138

    Kairosfocus:

    Footnote:

    Re DW, 129: I for one would love to see this mountain of contrary evidence. Just citations would be fine for now.

    1 –> Mr Whisker needs to start with the basic fact that the protein-coding part of the genome uses all 64 three-letter combinations of A, G, C, T/U that are mathematically possible.

    2 –> Thus, we see that the chemistry of chaining does not determine the sequence, and that the sequences are meaningful in the sense of specifying a particular action to be taken by the Ribosome-centred machinery: read-codon, start, read next codon [using tRNA anticodon-bearing molecule], add AA to chain, . . . , stop and detach.

    First of all, Mr Kairosfocus needs to keep in mind that it is illogical to take the code as it exists today and draw the conclusions about the stereochemical hypotheses that he does. If he had read the articles which I have cited (especially Yarus et al), he would have clearly seen that the authors did not fall into that trap. Instead, they present hypotheses which deal with the the building of the code over time. Not all of the process is governed by biochemical affinities now, as Yarus et al acknoweldge:

    Nevertheless, it seems that many chemical attractions, manifested as binding affinities, still are reflected in the modern coding table

    One should not assume that all of the features present (or the forces which influence now) in the extant process of protein synthesis were there or had an influence on it at the beginning.

    Now, how about that mountain of contrary evidence?

    PS–Please note that my last name does not contain an ‘H’

  139. 139

    Dave Wisker:

    Instead, they present hypotheses which deal with the the building of the code over time.

    Does it make a difference? Name something complex that would require intelligence to create, but which requires no intelligence to build step-by-step over time? If each individual step were to be functional on its own, that process would require more planning and forethought, not less.

  140. 140

    Hi Scott,

    Dave Wisker:

    Instead, they present hypotheses which deal with the the building of the code over time.

    Does it make a difference? Name something complex that would require intelligence to create, but which requires no intelligence to build step-by-step over time? If each individual step were to be functional on its own, that process would require more planning and forethought, not less

    That is not what I was responding to. Kairos was trying to say the current system is not determined chemically, and I was simply pointing out that the sterochemical hypothesis doesn’t assume the prebiotic association of entities resembles the current one. That leads me to ask you, why would each step have to be “functional” on its own? The stereochemical affinities of the original components could have produced the initial association without any “function” being necessary. Expecting each step to have “function” is an extraneous, unnecessary assumption.

  141. Dave Wisker, (#140)

    You’re right, of course. Each step need not have function. But in that case natural selection cannot select for function, and the staggering improbabilities that people use to argue against abiogenesis, or against a massive increase in complexity in life itself, are perfectly justified.

    There are four defenses I can see against this argument. First is to argue that the probabilities are not that low. Good luck with that.

    Second is to argue that there really is a way with functional intermediates, but we just haven’t found it yet. Because the evidence for it is lacking, that is, of course, faith-based argumentation. If that’s your faith, fine, just so we’re clear about it.

    Third is to argue that there really is a way with functional intermediates, and at least in these three cases we know what it is, or at least could be. This is the evidence that jerry has been waiting for, and never seen, nor, with the possible exception of color vision, have I. We’d be quite interested if you have any.

    Fourth is to demonstrate that the process cannot be that impossible, because it happens periodically, probabilities to the contrary notwithstanding. For example, add ammonia, phosphoric acid, methane, montmorillonite clay, and some other specified sterile ingredients, zap with electricity, and you get bacteria in 3 years. To my knowledge, the experiment has not been done successfully. Or perhaps go to a distant planet and find life on it, which would suggest that life is not that hard to evolve given enough time.

    In a way, this, I suspect, is where you really come down. Life as we know it is here, there can’t have been any designer, and thus what we see is a demonstration of what unassisted nature can do.

    Of course, arguing that way begs the question of whether there was a designer or not. It requires an anti-designer presupposition, which must include and anti-interventionist-God presupposition. It is basically religious. The scientific evidence we see suggests design to the unprejudiced observer (and even to some prejudiced ones). Thus we have here a classic case of science versus religion, except the reverse of what is claimed by naturalistic scientists.

    I would not deprive you of your religious presuppositions. I just think that they should be recognized for what they are.

  142. 142

    Hi Paul;
    Dave Wisker, (#140)
    You’re right, of course. Each step need not have function. But in that case natural selection cannot select for function,

    Sorry, Paul, but this is a massive non sequitur. My point is simply that some steps may not have adaptive value with which natural selection can manifest itself. This is hardly news; even Darwin understood the concept of selectively neutral variation, and how it behaves. Gould and Lewontin in their famous paper on spandrels discuss features that may not be adaptive at all but arise as byproducts of other adaptive traits. Even much of the genomic architecture of eukaryotes may be due primarily to neutral evolution: that at least is one hypothesis by geneticist Michael Lynch (which I have mentioned here before). In other words, neutral steps in a pathway does not mean you can logically draw the conclusion you just did.

    and the staggering improbabilities that people use to argue against abiogenesis, or against a massive increase in complexity in life itself, are perfectly justified.
    Of course, the stereochemical hypothesis isn’t about abiogenesis, if you are defining abiogenesis as the theory of the origin of life itself. As the paper by Yarus et al which I have mentioned before states:

    This underscores the notion that the origin of the genetic code is a different and later event than the origin of life; it employed amino acids that lie at the end of what must have been highly evolved anabolic pathways. These pathways must have evolved before the code, and ribozymes are obvious candidates for their catalysis.

    So, do you have any evidence that calculates the staggering improbabilities of the stereochemical hypothesis for origin of the genetic code specifically? Preferably arguments with some experimental results we can evaluate?

    There are four defenses I can see against this argument. First is to argue that the probabilities are not that low. Good luck with that.
    Actually, Art Hunt discussed some of that beforehand with jerry (I presume you missed it) . I will continue with Yarus et al’s.discussion of the size of the basic minimum pool of random sequence RNA’s needed for the RNA world and the stereochemical hypothesis for the genetic code. They write (emphasis mine):

    Heuristic methods for estimating pairing probability can be used to show that real motifs like the isoleucine aptamer (29, 32) and the hammerhead ribozyme (41b), corrected for folding, should appear among several times 10^9 to 10^10 randomized RNAs. This corresponds to nanograms of 100-mer RNAs, which we now estimate as the minimal pool size required to initiate an RNA world (30). These quantities are 10,000- to 100,000-fold smaller than those used in modern selection experiments. Therefore, an RNA world is more accessible than might have been thought.

    They also discuss further experimental work suggesting additional ways that active RNA synthesis can occur:

    In addition to the quantitative problems of RNA synthesis, new experiments also make clear that the qualitative aspects of active RNA synthesis are subject to fewer constraints than once thought. For example, both strands of a completely complementary hybrid helix can be nucleic acid enzymes, as in the combination of a DNA ribonuclease strand and a hairpin RNAse strand (42). Furthermore, a moderately active ligase ribozyme can be built using just two nucleotides, 2,6-
    diaminopurine and uracil (43).

    Now, perhaps you can put up those experimental results that actually contradict any of this. To borrow your smug phrase, good luck with that.

    In a way, this, I suspect, is where you really come down. Life as we know it is here, there can’t have been any designer, and thus what we see is a demonstration of what unassisted nature can do.

    You suspect wrong, which doesn’t surprise me. I’m used to Iders and creationists trying to tell me what I really think. I’ll give you a chance to save face, though: please show where I have ever said there cannot be a designer. Otherwise, I’d save the amateur psychologizing for those more easily impressed by it.

  143. Dave Wisker (#142),

    I am quite pleased to hear that my suspicion was wrong. Suspicions should be rebuttable with evidence just like any other belief. Thank you for giving some evidence.

    You’re right, of course. Each step need not have function. But in that case natural selection cannot select for function,
    Sorry, Paul, but this is a massive non sequitur. My point is simply that some steps may not have adaptive value with which natural selection can manifest itself.

    I’m not sure what the significant difference is between what I said and your correction. If a step does not change function, it cannot be naturally selected. In that case, natural selection cannot act as a multiplier to increase the odds of the organism, or proto-organism, surviving in large enough numbers to make reasonably probable the next step.

    Now it could be claimed that in a 6-step pathway, only steps 2 and 6 conferred natural advantages, in which case they could be naturally selected. But that means that at steps 1, 3, 4, and 5 natural selection cannot manifest itself. Natural selection does not apply to neutral changes. That seems pretty obvious.

    Gould and Lewontin in their famous paper on spandrels discuss features that may not be adaptive at all but arise as byproducts of other adaptive traits.

    But spandrels are in fact selected for, precisely because of their linkage to adaptive traits. They are not examples of neutral mutations or even neutral variations, which was what the rest of your paragraph discussed. (And of course, the original spandrels were clearly designed, which means that the existence of spandrels does not provide good evidence against design.)

    Of course, the stereochemical hypothesis isn’t about abiogenesis, if you are defining abiogenesis as the theory of the origin of life itself. As the paper by Yarus et al which I have mentioned before states:

    This underscores the notion that the origin of the genetic code is a different and later event than the origin of life; it employed amino acids that lie at the end of what must have been highly evolved anabolic pathways. These pathways must have evolved before the code, and ribozymes are obvious candidates for their catalysis.

    So, do you have any evidence that calculates the staggering improbabilities of the stereochemical hypothesis for origin of the genetic code specifically? Preferably arguments with some experimental results we can evaluate?

    Now wait just a minute. You want me to give evidence that calculates the staggering improbabilities of the stereochemical hypothesis for the origin of the genetic code? Preferably arguments with some experimental results?

    Your request doesn’t make much sense. Evidence doesn’t calculate. And arguments aren’t evidence. But I’ll try to understand.

    Perhaps you meant that I should be able to show, using arguments with experimental evidence, that calculations regarding the improbabilities of the stereochemical hypothesis for the origin of the genetic code are accurate.

    This seems a little bizarre to me. According to the theory, “the origin of the genetic code is a different and later event than the origin of life”. That would seem to imply that there was life without a genetic code. Of what did this life consist? Let me turn the question around; do you have any experimental evidence of any life without a DNA code? If not, why are you asking for experimental evidence that the theory is wrong?

    The paper goes on to say, “it [presumably life] employed amino acids that lie at the end of what must have been highly evolved anabolic pathways. These pathways must have evolved before the code”. What’s all this “must have” stuff? We know this how? Is there any actual evidence for “highly evolved anabolic pathways” existing without DNA control? Or are you asking me to criticize a theory with no experimental evidence for it, and then wondering if I can give experimental evidence against it?

    Well, I think I can. It’s not probative evidence; it doesn’t slam the door on the logical possibility that Yarus et al. might be right. But as you know, we rarely if ever get that in science. Basically, it goes like this. We have not yet observed the spontaneous origin of life anywhere; not on Earth, not on Mars, not on Titan, not in laboratories, and not in commercially canned food. That doesn’t mean it can’t happen. But it does mean that it isn’t easy, and we can reasonably suspect that it can’t happen. We have never observed “highly evolved anabolic pathways” without either design, or life. Again, it doesn’t prove it can’t happen, but it is evidence consistent with the hypothesis that it doesn’t happen.

    Now you may complain that that isn’t much evidence. But I would submit that it is at least evidence. To go beyond that evidence is to go on faith; either faith with the evidence, or faith against the evidence. Take your pick.

    You quote Yarus et al. describing the hammerhead ribozyme and the isoleucine aptamer and noting that “an RNA world is more accessible than might have been thought.” That is good news. We should soon get some actual experimental evidence that should help us to know whether an RNA world is experimentally viable. There is still the small matter of making the roughly 100 mer RNA’s themselves, but hey, one thing at a time.

    You object to what you call my “smug phrase”. I think you have misunderstood. If you claim that before DNA, or at least before RNA that had the coded information in it for whatever ribozymes and/or proteins that were necessary for known life, there was some kind of stereochemical pathway where the intermediate steps survived and reproduced because of their relative stereochemical advantages, then you are not actually pursuing my defense #1. You are actually pursuing defense #2 (without experimental evidence) or defense #3 (with experimental evidence). It sounds like you are claiming that there is some stereochemical advantage to certain intermediates. Therefore my “Good luck with that” doesn’t apply. In that case, please don’t take it personally.

    But I would be interested in whether you have enough data to suggest a specific pathway from ammonia, water, phosphate, methane (hey, I’ll give you the methane and keep the molecular oxygen away to boot) to any specific viable organism. Do you even have a specific pathway, with reasonable yields for each step, from a mixture of roughly 100 mer RNA’s to life itself? Or are you still forced to use defense #2 (I take it you reject defense #4).

    P.S. I did miss the discussion between Art Hunt and jerry. I found a brief exchange between Arthur and Upright BiPed, without a lot of specifics. Perhaps you have the link to the conversation to which you referred.

  144. Mr Wisker:

    I think Mr Giem 9143) responds aptly to several of your points.

    In particular — and relevant to my own point — he aptly observes that:

    According to the theory, “the origin of the genetic code is a different and later event than the origin of life”. That would seem to imply that there was life without a genetic code. Of what did this life consist? Let me turn the question around; do you have any experimental evidence of any life without a DNA code? If not, why are you asking for experimental evidence that the theory is wrong?

    The paper goes on to say, “it [presumably life] employed amino acids that lie at the end of what must have been highly evolved anabolic pathways. These pathways must have evolved before the code”. What’s all this “must have” stuff? We know this how? Is there any actual evidence for “highly evolved anabolic pathways” existing without DNA control? Or are you asking me to criticize a theory with no experimental evidence for it, and then wondering if I can give experimental evidence against it?

    I add, that he inference to “must have” reflects the assumption that scientific investigation of the possible origins of life could only work on the implicit premise that life has to have originated by blind mechanical necessity and chance. In short,t eh underlying issue is a priori imposition of Lewontinian metaphysical evolutionary materialism, by which the empirically demonstrated source of functionally specific complex information is excluded a priori, as that just might allow a Divine Foot in the door.

    Now, on the particular issue that I responded to earlier, here is the key cite, from AH at 105:

    . . . there is interesting and excellent positive experimental evidence that supports the hypothesis that the code that underlies translation is in fact not inert. Rather, there is a decided and demonstrable chemical basis for this code (that we all call the genetic code).

    By citing the well-known fact that all 64 logically possible three-letter codons exist and have meaning, I have pointed out that the code as we see it is not chemically determined (that is, as to sequences of letters in the codons).

    Furthermore, only if there is room for contingency can there be a code: chains of symbols by definition per their function, communicate information by being intrinsically improbable, apart from being an act of intent.

    Moreover, a major function of these codes in OBSERVED life [as opposed to speculative reconstructions] is to program the step by step construction of proteins that then fold and agglomerate to form components in highly complex protein macromolecule based systems in the cell. Given that proteins are very thermodynamically uphill, such a step by step process with energy fed in suggests purposeful art, not spontaneous chance. (Kindly provide evidence that a prebiotic soup — of whatever kind –would naturally occur and that it would long preserve itself, creating circumstances where it would be credibly probable that clusters of molecules in that pond or comet head or hydrothermal vent would come together in micelles or on clay or whatever at about 20 microns separation to spontaneously start up the various activities of cell based life. [Here, my point is that the metabolism first and the RNA first scenarios for OOL are running into the adverse classical and statistical thermodynamics issues Sir Fred Hoyle raised by speaking of tornadoes forming 747's in junkyards, reflection on which is in fact the technical root of the modern design movement, as can be seen in Thaxton et al, Chs 7 - 9 TMLO.])

    If you are suggesting that the genetic code’s assignments and existence are the secondary, chemical forces-driven result of that process, you first need to show good reason on empirical data to accept that the original metabolic and no-DNA process is factually well founded.

    Thereafter, you will need to show that a functioning process then spontaneously created — stepwise, with functional advantages selectable by natural selections — an algorithmic process to replicate itself, inventing a language along the way as well as the algorithms and the machines that carry it out.

    I will speak as one who has had some experience in creating language based algorithmic functional entities. For, the difficulties of getting algorithms and code right the first time — or the umpteenth time for that matter — even when they are very close to right — atre such that no claimed spontaneous process would be credible.

    Finally, if the laws of chemistry and thermodynamics somehow have “life” written into them, what would that tell us about the nature of a universe in which such is the case?

    GEM of TKI

  145. PS: I see I forgot: pardon my dyslexic eyes.

  146. 146

    Hi Paul,

    This seems a little bizarre to me. According to the theory, “the origin of the genetic code is a different and later event than the origin of life”. That would seem to imply that there was life without a genetic code. Of what did this life consist? Let me turn the question around; do you have any experimental evidence of any life without a DNA code? If not, why are you asking for experimental evidence that the theory is wrong?

    First of all, the stereochemical hypothesis for the origin of the genetic code arose from other work which suggested that the genetic code as we see it today is not what life used in its very earliest forms. Secondly, when I say this or that hypothesis has experimental backing, I’m not saying (as the wording of your question implies), that this primordial life has somehow been recreated in a test tube. That, frankly, is a naïve expectation (at least at this point), and if that is the only kind of experimental evidence you will accept in order to discuss the hypothesis seriously, please speak up now and save us both the effort. Instead, I’m saying the hypothesis has experimental results which support many of its central tenets. For example, the stereochemical hypothesis predicts the genetic code relies on interactions which should be observable and reproducible today. Yarus et al’s review paper summarizes much of that experimental backing. That doesn’t mean the hypothesis is free of highly speculative aspects, however. Far from it. But of the many hypotheses floating around out there, I like this one because it does have many elements which are conducive to experimental examination and for which there is a rich literature (RNA aptamer work, upon which the hypothesis is built, is being done by many labs, as Art Hunt pointed out). So, I was asking for positive experimental evidence which contradicts any of the reported empirical bases for the hypothesis.

    I suppose I should step in here and say something about what I don’t believe. I don’t believe the stereochemical hypothesis is true. It’s one of many hypotheses coming out of the overarching RNA World idea. But I like it better than others because, as I pointed out above, it has elements conducive to experimental examination. I hope that makes my position a bit clearer.

    Since I hate reading long individual posts myself, I will spare you a long one and address the rest of your reply later, if that’s ok (I much prefer discussion board format than blog comments for this kind of thing).

  147. I have a general comment and that is that speculation is treated as fact in the evolution debate at the level of the common person. Many of us often remark that evolutionary biology is the only science where imagination is treated as evidence. But the average person on the street does not have this impression. They are under the impression that the evidence is overwhelming and so it is for the small stuff.

    But when we get to the real issues at hand we are treated to speculation at best. I have no problem with investigating the most outlandish concepts but only if it is admitted that they are probably not true. And admitted in the textbooks and in the curriculum. But such is not the case in evolutionary biology and is beginning to be the case in cosmology where the multiverse must be invoked to get away from the fine tuning problem.

    What upsets me in not the science or the speculation but the hypocrisy and double standards that are current in these areas. And the typical person on the street hasn’t a clue about it and thinks ID is nonsense and the scientists are honest brokers of reality.

    By the way the very small discussion that Art Hunt had with me was on the probability of a random protein being useful. He believes that a useful protein pops up at the rate of 1 in 10^10 or 1 in a billion. That might make a useful debate but I do not have the expertise to assess it. What I have after working in academia, business, government and the military and seeing how each works and having a science education is to know the bs meter of an argument. The needle for the meter is off the scale in the evolutionary biology field.

  148. 148

    jerry,

    If you don’t have the expertise to assess an argument, how do you know how to apply your bs meter to it?

  149. jerry,
    can you provide a specific example from the peer-reviewed evolutionary biology literature where imagination is treated as evidence or speculation is treated as fact?

  150. 150

    Hi Paul,
    To continue our discussion,

    The paper goes on to say, “it [presumably life] employed amino acids that lie at the end of what must have been highly evolved anabolic pathways. These pathways must have evolved before the code”. What’s all this “must have” stuff? We know this how? Is there any actual evidence for “highly evolved anabolic pathways” existing without DNA control? Or are you asking me to criticize a theory with no experimental evidence for it, and then wondering if I can give experimental evidence against it?

    As you are well aware, scientific papers discussing hypotheses commonly assume the hypothesis is true for argument’s sake, and then outline what conditions must also be true in order for the hypothesis to work, as well as for making predictions. That is what the authors are doing here. Surely this isn’t controversial, especially since the genetic code is not being suggested to have appeared at the point in which life itself originated. I noticed you seem to be assuming anabolic pathways require DNA control. Why? What conceptually prevents RNA from performing a similar role? And if we consider RNA as a precursor to DNA as genetic material, what questions/obstacles about the origin of translation are made simpler and easier to achieve under a strictly biological paradigm (assuming we can set aside any pre-existing paradigm preferences for the moment)? Doing this may indeed solve some problems, but it also may bring up others which in the end might be insurmountable. Should the former happen, then the hypothesis itself may need to be abandoned. In a later comment, I will point out some thinking on the precursor conditions for the stereochemical hypothesis, which will at least address your question about life not needing the genetic code as we see it today.

    Well, I think I can. It’s not probative evidence; it doesn’t slam the door on the logical possibility that Yarus et al. might be right. But as you know, we rarely if ever get that in science. Basically, it goes like this. We have not yet observed the spontaneous origin of life anywhere; not on Earth, not on Mars, not on Titan, not in laboratories, and not in commercially canned food. That doesn’t mean it can’t happen. But it does mean that it isn’t easy, and we can reasonably suspect that it can’t happen. We have never observed “highly evolved anabolic pathways” without either design, or life. Again, it doesn’t prove it can’t happen, but it is evidence consistent with the hypothesis that it doesn’t happen.

    Of course, we haven’t seen life designed in the laboratory either, and even if we did, all that would show is that humans can design life—usually after careful study of how nature does it. So frankly, I don’t find this particular argument especially compelling. But I am not insisting the genetic code had to have arisen the way Yarus et al’s hypothesis suggests, so design may very well be the answer. It sure would be nice, though, if you could point out some experimental evidence specifically contradicting the experimental evidence claimed to support the stereochemical hypothesis. That would be the most effective way to knock it out of the running, IMHO.

  151. “If you don’t have the expertise to assess an argument, how do you know how to apply your BS meter to it?”

    Human nature. People act in different ways depending upon the type of evidence they present or the arguments they use. I watch what you and anyone else presents and it is an indictment of the lack of evidence for your position. If you had firm evidence, you and the others would behave differently.

    I have never seen a coherent argument for macro evolution (origin of complex novel capabilities) and I have read a lot of pro naturalistic evolution books. Hence, I suspect such an argument does not exist or else it would be presented. If it did exist it would be standard fare in every discussion. And then there is Provine admitting it was faith that led him to believe in naturalistic evolution. A faith in something he has never seen.

    I keep pointing you to the Brosious article and its lack of examples or hard evidence. It was meant as an up to date review of macro evolution and it is mostly speculation. If there was chapter and verse supporting his beliefs do you not think he would have presented them. So there is a way of applying the BS meter without having the detailed background on something.

    There is are various levels of expertise and after a certain point no more is necessary to assess certain aspects of an issue. The lack of expertise I was pointing to was the knowledge on the functionality of proteins. One does not have to be an expert on protein biology/chemistry to understand many or most of the issues. What I was referring to is that I do not have the information to make a good judgment on what is possible and what is not at the moment to make a functional protein that will work with another functional protein to create a situation that is more functional than either working independently.

    Art Hunt makes an assertion and he may be right or it may be couched in some restrictions that I have no idea about at the moment. Over time a discussion on this would get at the issues. There have been others on this site who have indicated that the odds of finding a suitable protein island of proteins is much rarer than what was given by Art. Hence, I do not have the knowledge or expertise to assess this at the moment. But I suspect that there are others out there who do have this information.

    The main thesis of the Edge of Evolution was that these proteins are rare and there is no evidence that they exist in any great number. And funny how none of the reviews called Behe on this. Instead they debated irrelevant issues. Why? The BS meter is detecting something.

    One thing that sets off the BS meter like a Geiger counter in an uranium mind is an attempt to hide behind obscure scientific data. If it was relevant it would have been brought front and center long ago.

  152. jerry,
    to summarize,
    your conclusion that there is no evidence for macroevolution is based on one article in a book that you cite incessantly and the behavior of some people on a website.
    the problem is, whenever someone presents evidence for macroevolution, you either say you don’t know enough to make a judgement or ignore it. for example, art presented some nice evidence showing that two mutations can turn a herbaceous plant into a woody one (think: dandelion to oak). you said you didn’t know enough about plants to make a judgement. have you learned enough in the meantime? and if you’re dissatisfied with the lack of examples in the Brosius article, here’s one:

    http://mbe.oxfordjournals.org/...../24/9/1982

    the authors show that the d-globin gene (encoding a subunit of hemoglobin that allows for greater oxygen affinity) in amniote vertebrates arose through duplication and divergence of an embryonic globin-like gene. this additional was one of the factors that enables the diversification of tetrapods, so it’s a very significant change.

  153. “Art Hunt makes an assertion and he may be right or it may be couched in some restrictions that I have no idea about at the moment. Over time a discussion on this would get at the issues.”

    I agree. But ID proponents choose to avoid substantive discussion.

    ” There have been others on this site who have indicated that the odds of finding a suitable protein island of proteins is much rarer than what was given by Art. “

    To pick up on a theme of yours, jerry, these “others” are using imaginary arguments that are not grounded in chemical or experimental reality. My assertions are backed up by direct experimental measurement and by some pretty obvious and simple chemistry.

    Hence, I do not have the knowledge or expertise to assess this at the moment. But I suspect that there are others out there who do have this information.

    You suspect incorrectly.

    The main thesis of the Edge of Evolution was that these proteins are rare and there is no evidence that they exist in any great number. And funny how none of the reviews called Behe on this. Instead they debated irrelevant issues. Why? The BS meter is detecting something.”

    jerry, I have called Behe on this. Heck, I even gave Behe an opportunity to review and comment on my Pandas Thumb entry before I posted it. He declined, I suspect because he knows that I am a working biochemist and that my arguments gut the very core of his thesis. He has no response to my various essays because there is no ID- or Behe- friendly one.

    (Oh, and what does “there is no evidence that they exist in any great number” mean? Are you claiming that there are not very many proteins in the biosphere? Maybe some clarification is in rder.)

  154. khan,

    Whenever I need reassurance, khan provides. He says:

    “that there is no evidence for macroevolution is based on one article in a book that you cite incessantly”

    Are you trying to impugn me or Brosius with this sentence?

    I use the Brosius article because of who chose it, the context in which it is used and what it says. You use an interesting choice of words and it is one of my cues that there is no evidence. You would not waste a second with what I said and instead present the overwhelming evidence.

    I thank you for the article on hemoglobin and in time I will read it. I believe hemoglobin is often used as an example of gene duplication and its usefulness and also in common ancestry. But as I have asked you before, why don’t you lay out the evidence in the article in layman’s language so all might learn.

    As an aside, do you think that two mutations that turn a dandelion into an oak is the type of explanation that would explain how microbes turned into man. If it isn’t, then why mention it? If it is, then why is such an explanation not in the books on evolution? I keep on wondering why the experts on evolutionary biology don’t emphasize them or how they missed it.

    PS – Allen MacNeill pointed me to the Vrba and Eldredge book which is titled “Macroevolution.”

  155. jerry,
    another great ad hominem coupled with a substance-free non-reply. your stock and trade.

    I thank you for the article on hemoglobin and in time I will read it.

    great, I look forward to that. just like I look forward to you eventually learning about mitochondria, plants, protein formation, etc. you keep saying you don’t know enough about these evidences for macroevolution to make a judgement, yet you never bother to learn about them and then continue in with your assertions that there is no evidence for macroevolution. why is that?

    But as I have asked you before, why don’t you lay out the evidence in the article in layman’s language so all might learn.

    if you look in 152, it’s right there at the bottom.

    As an aside, do you think that two mutations that turn a dandelion into an oak is the type of explanation that would explain how microbes turned into man.

    behe extrapolates from malaria to everything else in Edge. you seem to accept that logic. why don’t you accept the same logic here?

    If it is, then why is such an explanation not in the books on evolution?

    perhaps bc the paper is from 2008 and textbooks don’t move that fast.

  156. 156

    Jerry,

    I have never seen a coherent argument for macro evolution (origin of complex novel capabilities) and I have read a lot of pro naturalistic evolution books. Hence, I suspect such an argument does not exist or else it would be presented.

    Since you use a very idiosyncratic definition of macroevolution, I assume you don’t look in the macroevolution sections of the books for answers. Here, however, you have been given several concrete examples that address your concerns. Art Hunt gave you the plant examples, and I gave several that addressed some of the ones you specifically suggested, i.e, insect wings, multichambered hearts, and the avian oxygen transport system. Yet, to my recollection, you never responded. Instead, here you are waving a bs meter. I know you saw Art’s examples. Since I was under moderation at the time, there is a good chance you missed mine: they can be found in the “human-evolution-the-spin-machine-in-top-gear” thread.

    I keep pointing you to the Brosious article

    And I keep asking you what is so new and special about exaptations.

    It was meant as an up to date review of macro evolution and it is mostly speculation.

    Actually, it was a discussion of retronuons and exaptations. Again, what makes this article so important? Exaptations are nothing new (they are simply mutations with deferred selective value) and fall easily under modern evolutionary theory. They challenge none of its essential tenets.

    If there was chapter and verse supporting his beliefs do you not think he would have presented them.

    Maybe some of his beliefs aren’t so well supported– I noticed he seemed to side with Gould and the “species selection” crowd. That group has never really made much of a case for their point of view.
    Yet here we are, trying to engage you with nice juicy examples to tear into. And what do we get in return? a bs meter reading!

    There is are various levels of expertise and after a certain point no more is necessary to assess certain aspects of an issue. The lack of expertise I was pointing to was the knowledge on the functionality of proteins. One does not have to be an expert on protein biology/chemistry to understand many or most of the issues. What I was referring to is that I do not have the information to make a good judgment on what is possible and what is not at the moment to make a functional protein that will work with another functional protein to create a situation that is more functional than either working independently.

    Yet you have declared Behe’s book the “definitive work” on the subject. How on earth would you know, if you don’t have the knowledge to come to an informed opinion?

    Art Hunt makes an assertion and he may be right or it may be couched in some restrictions that I have no idea about at the moment. Over time a discussion on this would get at the issues.

    Are you planning on engaging in a discussion with him on it?.

    There have been others on this site who have indicated that the odds of finding a suitable protein island of proteins is much rarer than what was given by Art. Hence, I do not have the knowledge or expertise to assess this at the moment. But I suspect that there are others out there who do have this information.

    Funny, the only one actually talking numbers from wet bench experiments has been Art. That sets my BS claxon squawking, to tell you the truth.

    The main thesis of the Edge of Evolution was that these proteins are rare and there is no evidence that they exist in any great number. And funny how none of the reviews called Behe on this. Instead they debated irrelevant issues. Why? The BS meter is detecting something.

    None? How about Ian Musgraves review at The Panda’s Thumb?

    http://pandasthumb.org/archive.....s-rib.html

    One thing that sets off the BS meter like a Geiger counter in an uranium mind is an attempt to hide behind obscure scientific data.

    How would you know if it was “obscure” or not? Or are you simply assuming it is obscure because you haven’t heard about it?

  157. “I have never seen a coherent argument for macro evolution (origin of complex novel capabilities)”

    Ouch! Talk about a slam! That’s worth a five minute major, IMO. (Aside – nice job, Pens!)

    Help me out, jerry. Send me along questions so that my essay that others have linked to here can be improved, so that readers such as yourself can follow and understand it better.

  158. khan,

    You present possible sources of macro evolution (I will continue to use our definition because it is the issue under debate). The question is what actually happened and how.

    To me you are presenting speculation and I question the speculation and the mechanism behind your claims. To get past the speculation phase one has to present evidence to show how something happened. So far I claim that no one has done that.

    Has Dawkins done it? Has Ayala done it? Has Carroll done it? Has Ken Miller done it? Has Coyne done it? Has Henry Gee done it? Has Provine done it? Has Allen MacNeill done it on his web site?

    I have not seen it in these so called experts on evolution. If you disagree then you will have to make a much better argument then they have made.

    I ask you to lay out in layman’s language the arguments and you say you did such and as your example you point to the end of comment #152. I am sorry but those few general sentences don’t do it. I suggest you clear your thoughts and make a long comment summarizing your arguments maybe using the hemoglobin article as a starter. Indicate what is hard fact, what is suspected to be true and how it relates to your thesis on how macro evolution (our definition) happened.

    If you cannot do that then we are at an impasse. You see I have not seen it done with all the authors I have mentioned and you and Dave referencing articles don’t accomplish it.

    Prepare you defense of naturalistic evolution and use as much space as you want. You might want to lay it out in a series of comments so that it is easier to read. Until then all I see is some wishful speculation and the pointing to an occasional study. If it is well thought out and full of logic and facts then it will be read and can be used for future discussions.

  159. Jerry:

    Let me scoop out a couple of estimates on protein formation, from Bradley’s fairly recent presentation, using point 9 in my first appendix the always linked:

    ______________

    Recently, Bradley has done further work on this, using Cytochrome C, which is a 110-monomer protein. He reports, for this case (noting along the way that Shannon information is of course really a metric of information-carrying capacity and using Brillouin information as a measure of complex specified information, i.e IB = ICSI below), that:

    >>Cytochrome c (protein) — chain of 110 amino acids of 20 types

    If each amino acid has pi = .05, then average information “i” per amino acid is given by log2 (20) = 4.32

    The total Shannon information is given by I = N * i = 110 * 4.32 = 475, with total number of unique sequences “W0” that are possible is W0 = 2^I = 2^475 = 10^143

    Amino acids in cytochrome c are not equiprobable (pi ? 0.05) as assumed above.

    If one takes the actual probabilities of occurrence of the amino acids in cytochrome c, one may calculate the average information per residue (or link in our 110 link polymer chain) to be 4.139 using i = – ? pi log2 pi [TKI NB: which is related of course to the Boltzmann expression for S]

    Total Shannon information is given by I = N * i = 4.139 x 110 = 455.

    The total number of unique sequences “W0” that are possible for the set of amino acids in cytochrome c is given by W0 = 2^455 = 1.85 x 10^137

    . . . . Some amino acid residues (sites along chain) allow several different amino acids to be used interchangeably in cytochrome-c without loss of function, reducing i from 4.19 to 2.82 and I (i x 110) from 475 to 310 (Yockey)

    M = 2^310 = 2.1 x 10^93 = W1

    Wo / W1 = 1.85 x 10^137 / 2.1 x 10^93 = 8.8 x 10^44>>

    Recalculating for a 39 amino acid racemic prebiotic soup [as Glycine is achiral] he then deduces (appar., following Yockey):

    >>W1 is calculated to be 4.26 x 10^62

    Wo/W1 = 1.85 x 10^137 / 4.26 x 10^62 = 4.35 x 10^74

    ICSI = log2 (4.35 x 10^74) = 248 bits . . . .

    Two recent experimental studies on other proteins have found the same incredibly low probabilities for accidental formation of a functional protein that Yockey found

    1 in 10^75 (Strait and Dewey, 1996) and

    1 in 10^65 (Bowie, Reidhaar-Olson, Lim and Sauer, 1990).>>
    ________________

    In short, there is good reason, coming from serious calculation by serious and in some cases even eminent workers, to infer that AH’s estimates on the odds of functional proteins forming by chance are rather too optimistic.

    As well, the issue of what function is comes into force: unless the relvant proteins are integrated with other relevant macromolecules in a matrix ont eh scope of about 20 microns, they will have no function — part, wholes and organisation are all implicated.

    Sir Fred Houyle’s 747 in a junkyard remark — which I elaborate on in the same appendix — brings this to the fore. That is, even when the proper parts are present, their organisation into a functional, complex whole then needs to be reckoned with. For that, we must face the fact that the configuration space on that is generally well beyond the reach of the search resources of the cosmos we observe.

    No wonder evolutionary materialistic origin of life theories are at a conundrum.

    GEM of TKI

  160. “In short, there is good reason, coming from serious calculation by serious and in some cases even eminent workers, to infer that AH’s estimates on the odds of functional proteins forming by chance are rather too optimistic.”

    These “serious calculations” would lead one to insist that proteins such as that discussed in this essay cannot possibly exist.

    When a calculation fails so badly to agree with observation and experimental result, the proper thing to do is to toss the calculation, or at least examine the math to figure out where and why the calculation is so badly in error.

  161. Hi Dave,

    Thanks for your replies. You even, IIUC, answered some of my questions, albeit indirectly. I asked,

    do you have any experimental evidence of any life without a DNA code?”

    Your reply was,

    Secondly, when I say this or that hypothesis has experimental backing, I’m not saying (as the wording of your question implies), that this primordial life has somehow been recreated in a test tube. That, frankly, is a naïve expectation (at least at this point), and if that is the only kind of experimental evidence you will accept in order to discuss the hypothesis seriously, please speak up now and save us both the effort.

    I take it that the short answer to my question is “No.”

    If the answer is “no”, that in itself is evidence against the theory. The theory requires that we have life before DNA, or at least before the current (majority) DNA code. Just as the existence of life without a DNA code would be evidence for the hypothesis of Yarus et al. (HY), the non-existence of life without a DNA code is evidence against HY.

    You may object that this is very weak evidence, and susceptible to being overturned at a moment’s notice, and I would agree that this evidence is the kind backing the “all swans are white” assertion; one black swan effectively refutes it. But you don’t have the right to insist that I stop calling it evidence. And it is evidence suggesting that HY is wrong, because it suggests that one of HY’s fundamental premises is wrong.

    You precede this answer with the statement,

    First of all, the stereochemical hypothesis for the origin of the genetic code arose from other work which suggested that the genetic code as we see it today is not what life used in its very earliest forms.

    Suggested to whom and for what reason? This is beginning to sound like my defense #4: Life must have arisen naturally, the genetic code could not reasonably have been anywhere near its present form if life arose spontaneously, therefore the genetic code must have arisen in a different form. There is experimental evidence for the second clause, and therefore there is experimental evidence suggesting HY. But that is only true if one starts with the premise that life must have arisen naturally.

    You defend HY by saying,

    I’m saying the hypothesis has experimental results which support many of its central tenets.

    That may be true. But if one of its central tenets has no evidence for it, and the extant evidence is against it, if that central tenet should fail, the truth of any or all of the other tenets would not save the theory. The theory that GWB’s invasion of Iraq caused 9/11 may have evidence supporting many of its central tenets. But the simple fact that the invasion didn’t happen until after 9/11 means that all those considerations are irrelevant. It doesn’t matter if some Muslims hate GWB for what he did. It doesn’t matter if we find private journals from the hijackers saying, “Bush’s invasion of Iraq must be avenged.” The theory is false. Just so, if there was no life without a DNA code, HY is false. Period. Evidence against life without a DNA code is evidence against HY, and your asking for “experimental evidence” has been fulfilled.

    You started out by asking,
    Preferably arguments with some experimental results we can evaluate?

    Now, you are asking for something else;

    I was asking for positive experimental evidence which contradicts any of the reported empirical bases for the hypothesis.

    The problem I have with HY is not with its empirical bases. It is with the “highly speculative aspects”, to use your phrase. So why should I be asked to provide experimental evidence against the parts that I don’t particularly question?

    You seem to recognize the weakness of HY, for you say,

    I suppose I should step in here and say something about what I don’t believe. I don’t believe the stereochemical hypothesis is true. It’s one of many hypotheses coming out of the overarching RNA World idea. But I like it better than others because, as I pointed out above, it has elements conducive to experimental examination. I hope that makes my position a bit clearer.

    Yes, I think that does make your position clearer. Now if you will clarify one other point, it will be helpful. Robert Shapiro, in Origins: A Skeptic’s Guide to the Creation of Life on Earth,

    Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin for life have failed unequivocally. Further, new geological evidence may indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. In such a case, some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.

    Would you, if all the evidence overwhelmingly pointed to an intelligent designer, join Shapiro in his search for non-intelligent explanations for life, or are you prepared to give this search up at some point, however difficult that point might be to reach?

    You will be pleased to know that I do not have time right now to combine replies to your last two posts, and so will approximately halve the length of this post, responding only to #146. The response to #150 will have to wait for now.

  162. Can entities that grow, divide, evolve, respond to external stimuli, and are capable of rudimentary metabolism arise from simple beginnings, and without DNA?

    Sure enough!

  163. Folks:

    Busy this morning, so I simply point to TMLO online [click the picture to do a download -- FAT] where one may read ch 10 which in part goes into protocell worlds as are imagined by many,including Fox’s microspheres, coacervates, proteinoids etc.

    I refer to a document from 25 years ago to point out that this is nothing really new, and it is not a real answer on OOL dilemmas of evo mat paradigms.

    GEM of TKI

  164. 164

    Hi Paul,

    That may be true. But if one of its central tenets has no evidence for it, and the extant evidence is against it, if that central tenet should fail, the truth of any or all of the other tenets would not save the theory. The theory that GWB’s invasion of Iraq caused 9/11 may have evidence supporting many of its central tenets. But the simple fact that the invasion didn’t happen until after 9/11 means that all those considerations are irrelevant. It doesn’t matter if some Muslims hate GWB for what he did. It doesn’t matter if we find private journals from the hijackers saying, “Bush’s invasion of Iraq must be avenged.” The theory is false. Just so, if there was no life without a DNA code, HY is false. Period. Evidence against life without a DNA code is evidence against HY, and your asking for “experimental evidence” has been fulfilled.

    We have zero empirical evidence that intelligence has designed and created life ( no created life in any test tubes, as far as I know). It doesn’t matter if we devise hypotheses involving information and irreducible complexity, probability and such– the fact is, we have no empirical demonstrations that intelligence has even done it once. Without this, the truth of the rest of the tenets of the ID hypothesis cannot save it. If there are no clearly demonstrable instances of intelligence designing and creating life, then the ID hypothesis is false. Period. Have you informed the ID community about this? If not, why not?

    i>The problem I have with HY is not with its empirical bases. It is with the “highly speculative aspects”, to use your phrase.

    That’s fine with me, as long as you consistently apply the same skepticism to intelligent design.

    Would you, if all the evidence overwhelmingly pointed to an intelligent designer, join Shapiro in his search for non-intelligent explanations for life, or are you prepared to give this search up at some point, however difficult that point might be to reach?

    I’d probably choose the route that has the most viable research program (Baby needs shoes, after all). ;)

    Seriously, though, it would depend on just how much positive evidence there was for the other side. The scenarios posited above by Shaprio involve 100% negative evidence. Frankly, I’m wary of arguments built entirely on that. If that were all of the “overwhelming” evidence for ID, then I would be driven to suspect that research on neither side would be fruitful.

  165. Dave Wisker:

    We have zero empirical evidence that intelligence has designed and created life ( no created life in any test tubes, as far as I know).

    The ONLY evidence we have demonstrates that life comes from life.

    Anything else is science fiction.

    BTW there isn’t any data that demonstrates living organisms arose from non-living matter via unguided processes. That goes against all observations.

  166. I refer to a document from 25 years ago to point out that this is nothing really new, and it is not a real answer on OOL dilemmas of evo mat paradigms.

    KF, you clearly don’t understand why I cited my essay. Paul Giem asked Dave Wisker for experimental evidence for life without a DNA code. I interrupted (with belated apologies) gave him some. Many here will protest that Fox’s pets were/are (a few labs work on similar systems today) not alive, but these arguments boil down to circular reasoning and are thus self-refuting. And they are to boot irrelevant. What is quite clear is that one does not need any sort of DNA code to attain any of the life-like characteristics I listed.

  167. Mr hunt:

    You haver it precisely backwards. As Thaxton et al summarised in chs 9 & 10 of TMLO — all of 25 years ago — Fox’s proteinoids (which are not proteins) and microspheres (which are not cytoplasm-containing bilipid layer-enclosed cells) only very superficially resembled life, and even proteins. (Not to mention, as others objected at the time: where did all those optically active pure amino acids come from to be heated to form the non-protein bonded proteinoids in a plausible pre-life world?)

    These entities undergo no step-by step controlled biochemical metabolic processes, and what is called “growth” and “reproduction” is a matter of simple physical processes. Insofar as proteinoids are chemically active as catalysts, much of that is rooted int eh activity of amino acieds, and they bear no resemblance to the activity level or complex key-lock fitting structures of enzymes.

    To proffer such long since adequately rebutted superficial lists still as in any way comparable to life, is to show the utter bankruptcy of the evolutionary materialist origin of life paradigm that they were suggested for in the first place.

    And that conclusion is neither circular reasoning nor self-refuting.

    It is a simple pointing out of the obvious differences between globules of molecules and well-known processes and characteristics of living cells.

    GEM of TKI

  168. Onlookers:

    Re Mr Wisker, 164:

    We have zero empirical evidence that intelligence has designed and created life ( no created life in any test tubes, as far as I know). It doesn’t matter if we devise hypotheses involving information and irreducible complexity, probability and such– the fact is, we have no empirical demonstrations that intelligence has even done it once. Without this, the truth of the rest of the tenets of the ID hypothesis cannot save it. If there are no clearly demonstrable instances of intelligence designing and creating life, then the ID hypothesis is false. Period.

    1 –> This is of course a turnabout rhetorical resort: not having any good evidence that mechanical necessity and chance can give rise fo FSCI, per the information origination and thermodynamics issues that arise, the attempt is to shift rthe burden odf proof.

    2 –> In fact, cell based life is from a category of systems that we know very well: finely-tuned, multi-part complex entities that exhibit algorithmic step by step processes that use functionally specific complex coded information.

    3 –> Common examples of such systems include PCs and cell phones. And, as these names suggest, we know that such entities are the routine product of intelligent designers. Going further, we are able to identify, following Von Neumann in the ’40′s, the architectural requisites of a self-replicating automaton; which we observe being met in the cell — blueprint and replicating factory must be incorporated in the entity. that is, we see that we need to move up to a higher level of complexity; just we have not been technically able to do so as yet from scratch. (Mind you, post Ventner and post recombinant DNA, intelligent design of life forms is a FACT, not a speculation.]

    4 –> Furthermore, in ALL cases of FSCI-rich systems where we know the origin directly and independently, we see that these are the product of intelligent designers.

    5 –> On consulting the issues of getting to isolated islands of fucntion in vast configuration spaces, we see that chance based random walks, regardless of the presence of hill-climbing rewards, first have to get to the shores of function, before hill climbing selection processes can have any impact.

    6 –> But, routinely, intelligences using understanding and creaticity, develop such functional entities.

    7 –> So, FSCI etc are reliable signs of intelligent design, and on the same inductive grounds that we used to get to the generally accepted laws of nature, we have every right to treat FSCI etc as reliable signs of intelligence in action.

    8 –> Therefore, let us not allow ourselves to be distracted: the real unmet empirical evidence challenge is the one to show that with reasonable odds of success, FSCI etc can be produced by blind chance + mechanical necessity through random walks that get us to shores of function.

    9 –> That, after weeks, months and years of putting up this challenge at UD, the anti-design advocates still resort to turnabout rhetorical tactics and the like, tells us most eloquently, that they cannot meet the spontaneous information origination by chance plus necessity only challenge.

    10 –> So, we have every reason to be confident that the inference to design on reliable signs such as FSCI etc, is a good one.

    GEM of TKI

  169. 169

    Mr kairos:

    1 –> This is of course a turnabout rhetorical resort:

    That is exactly what it was, to show Paul a problem with his argument.

  170. “You haver it precisely backwards. As Thaxton et al summarised in chs 9 & 10 of TMLO — all of 25 years ago — Fox’s proteinoids (which are not proteins) and microspheres (which are not cytoplasm-containing bilipid layer-enclosed cells) only very superficially resembled life, and even proteins.”

    KF, if you don’t read and understand my essay, you really won’t be able to make any substantive contribution to this discussion, I’m afraid.

    I am not claiming that Fox’s proteinoids were the geneological precursor to proteins as we know them. But that’s irrelevant when it comes to the place of Fox’s critters in the OOL.

    Of course, this does make another point that ID proponents have a hard time swallowing – not only do the basic properties of life not require DNA, they don’t even require proteins as we know them. That’s two very big strikes against the need for a code in these processes.

    “(Not to mention, as others objected at the time: where did all those optically active pure amino acids come from to be heated to form the non-protein bonded proteinoids in a plausible pre-life world?)”

    Similar protocells can be had from Urey-Miller-type mixtures. Which makes this objection irrelevant as well.

    “These entities undergo no step-by step controlled biochemical metabolic processes, and what is called “growth” and “reproduction” is a matter of simple physical processes.”

    In other words, many of the features of living things are “matter(s) of simple physical processes”. Thank you for making my point.

    No code. Just chemistry. We’re making some progress here.

    “Insofar as proteinoids are chemically active as catalysts, much of that is rooted int eh activity of amino acieds, and they bear no resemblance to the activity level or complex key-lock fitting structures of enzymes.”

    Another irrelevant objection. As I explain in my essay.

    “To proffer such long since adequately rebutted superficial lists still as in any way comparable to life, is to show the utter bankruptcy of the evolutionary materialist origin of life paradigm that they were suggested for in the first place.”

    KF, I would argue that your unwillingness to even begin to address any of the issues I raise in my essay shows that this essay in fact makes some points that are very threatening to the ID perspective.

    “And that conclusion is neither circular reasoning nor self-refuting. “

    You don’t get it. But I’ll keep trying to epxlain.

  171. Mr Wisker:

    As I jut pointed out in steps, we have seen designers and have warranted signs of design; e.g. FSCI. (For simple working purposes, take this as: as a case of functionally specific information, especially algorithmic or linguistic information, comprising at least 500 – 1,000 working bits. [More formal definitions exist but this is good enough for practical purposes. this post is good enough as it passed 143 7-bit ASCII alphanumeric characters.] )

    There is no case of observed chance + necessity spontaneously giving rise to FSCI, on a base of literally millions of test cases.

    It is those who assert or assume that C + N (“lucky noise” as I have termed it; cf the Welcome to Wales exercise) can reasonably give rise to FSCI who have a burden of proof to meet. If met, it would knock the central pillar out from Design theory.

    Just as, a perpetuum mobile — if credibly demonstrated — would destroy thermodynamics.

    The ball is in your court.

    GEM of TKI

  172. 172

    Hi kairos,

    You still haven’t rescued Paul from declaring ID false by his own argument. There is zero evidence of any intelligence ever having designed and created life. No matter how convincing or plausible any inferences and probability calculations are, ID is false because there is no evidence for one of its central tenets.

  173. 173

    Dave W, perhaps this capsule version will help:

    If life could be created by scientists / designers can create life / therefore ID.

    If life could not be created by scientists / life is more than chemistry / therefore ID.

    See how easy that is? ID no matter what.

  174. Onlookers:

    The just above by Mr Wisker is an unfortunately apt illustration of refusing to accept that circumstantial evidence of a typical variety encountered in science is evidence, and that induction on the balance of the empirical evidence is the fundamental method of science. (Insofar as science can be said to have a method as such.)

    It therefore manifests selective hyperskepticism, and leads to the improper attempt to turn around the burden of proof and to dismiss that which would otherwise be manifestly well warranted.

    Without simply repeating what has already been pointed out, let us note:

    1 –> We have identified that life forms exhibit FSCI.

    2 –> It is known (on millions of instances) that the only observed source of FSCI is intelligence.

    3 –> It is also known on the search space and statistical weight reasons that ground say the 2nd law of thermodynamics, that there will be maximally low probability that chance processes will be able to get us tot he shores of islands of such complex functionality; on the gamut of our observed universe.

    4 –> On inference to best explanation per observed evidence, intelligence is the best explanation for the FSCI we see in life.

    5 –> This conclusion is of course provisional: should someone succeed in showing that FSCI is credibly and with reasonable probability produced by undirected mechanical necessity and chance, then the postulated clam will be withdrawn. (Note: where probabilities are sufficiently low, that which is logically possible is often not empirically credible; which is the foundation of the statistical mechanical form of the 2nd law of thermodynamics.)

    6 –> And, that holds, whether or not we have directly observed such intelligences actually in the act of creating life de novo.

    7 –> That instead of putting up a case where lucky noise creates complex, functionally specific information, we see an attempted — but improper — turnabout of the burden of proof in the teeth of massive empirical observation, simply shows that the true burden of proof has not been met, and that we are not up against a scientific issue, but a worldview commitment.

    GEM of TKI

  175. PS: Onlookers, again, the case of proteinoids and protocells etc 9as raised again in mr Wisker’s essay) was already solidly answered 25 years ago, as summarised by thaxton et al in TMLO. Cf Chs 9 – 10 here. Proteinoids, microspheres et al only very superficially resemble the realities and processes of recognisable life; in particular the step by step programmed processes of metabolism and of reproduction of cells simply find no parallel in the simplistic bullet points Mr Wisker lists. (And If I were wrong on the point, Mr Wisker could very easily refute point by point. But, as a look at he linked work will illustrate,a nd as a basic knowledge of cell processes of say protein formation and cell division will illustrate, I am not)

    That such superficialities and equivocations should still be trotted out 25 years later, tells us a lot, and not in the favour of those who advocate such.

  176. 176

    Onlookers, two things:

    1)Had kairosfocus read the comments between Paul Giem and me more carefully, it would be obvious he should be having this conversation with Paul.

    2) Had kairosfocus read subsequent posts more carefully he would not be so thoroughly confusing me with Art Hunt.

  177. Um…

    “1 –> We have identified that life forms exhibit FSCI.”

    Actually, no one anywhere has actually ever established, by direct experimental measurement, that FCSI (or CSI, or whatever) actually exists, in nature or in biology. Rather, those experimental measurements that have been done pretty clearly establish that FCSI (or CSI, or whatever) is a fictional concept.

    As I have indicated in this thread, what ID proponents have done is roll out calculations that have no basis in biological or physical reality. This is a big stumbling block for ID – math that is disconnected from reality is no way to explore the nature of something.

  178. Onlookers

    Passed back for a moment.

    Simply look above for yourself, and then follow the link to Mr Wisker’s blog post. Esp consder the remarks in his linked blog post that:

    Ask a high school bio student (e.g., perform a sort of “toddler test”) if these [I add: excerpted below . . . ] characteristics would qualify something as being alive, and the answer very likely would be yes. But in spite of this, OOL research has largely (but not entirely) moved on from these “creatures”. Why is this, if we are so close to (or even at) the point of having created cellular life from little more than amino acids? The answer is simple – there isn’t a very good conceptual link between protocells and life as we know it – e.g., the “DNA+RNA+protein” world.

    What’s the list?

    He claims that these microspheres show:

    electrotactism (the ability to sense an electrical field)

    aggregation (the ability to collect into colonies)

    mobility (the ability to move more or less at will)

    osmosis (the ability to absorb material from the environment)

    permselectivity (the ability to selectively pass materials across a semi-permiable barrier)

    fission (the ability to break about into smaller functional units)

    reproduction (the ability to create functional copies)

    conjugation (the ability to join directly to another)

    communication (the ability to pass information directly to another)

    excitability (the ability to generate and utilize energy, especially electrical fields)

    This list is based on a most patently superficial comparison to real life cells, in turn through a lot of equivocation of key terms and meanings.

    Of the above list “ability to move AT WILL” are “reproduction” are the most tellingly misleadingly equivocative, I think.

    So, the problems I have highlighted clearly relate to BOTH Mr Hunt and Mr Wisker.

    Onlookers, you will get a much clearer idea by simply reading TMLO chs 9 – 10, from 25 years ago.

    Sad, really.

    But instructive — oh, ever so instructive — on just how absent the tap root of the evolutionary materialist account of the origins of life is.

    GEM of TKI

  179. I have made the comment several times before. There are no accepted definitions of life, intelligence, species and science. People cannot agree on just what each is.

    As regards to life, I do not think anyone in ID holds that the current DNA based system is the only possible form of life. But life is like obscenity, we will know it when we see it but really cannot define it. We have speculated here on silicon based life but someone said it was rejected because silicon does not form as many molecules as carbon does.

    Is HAL in 2001 a life form even if he could not reproduce? Most of us would agree that the Christian God if He exists would be a life form. So what is life is problematic.

  180. 180

    Arthur Hunt,

    ——”As I have indicated in this thread, what ID proponents have done is roll out calculations that have no basis in biological or physical reality.”

    As ID has indicated, what evolutionist proponents have done is roll out hypotheses that have no basis in calculations.

  181. Hi Dave,

    I was a little rushed on the last comment, as evidenced by my missing a blockquote and not ending the italics appropriately. I now have more time to continue our discussion, so will take up #150 with this comment. I’ll come to your attempted logical judo later.

    You said,

    I noticed you seem to be assuming anabolic pathways require DNA control. Why?

    Because it only appears that way to you. I don’t start by assuming that anabolic pathways require DNA control. It is indeed theoretically possible that RNA could control those pathways, or even that they need no control or that they control themselves. But never having seen “highly evolved [understood as complex specified] anabolic pathways” without DNA control, it does seem reasonable that the existence of such an entity, if not impossible, is at least problematic. You yourself later recognize that, as far as the possibility of RNA functioning where DNA now is,

    Doing this may indeed solve some problems, but it also may bring up others which in the end might be insurmountable. Should the former happen, then the hypothesis itself may need to be abandoned.

    Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such “highly evolved anabolic pathways” without DNA control will turn out to be not realistically feasible?

    I tend to be a little more careful the way I phrase things. Maybe the authors were too, and they are quoted out of context in this regard. But I would have preferred to say something like, “If our hypothesis is correct, then life . . . employed amino acids that lie at the end of what must have been highly evolved metabolic pathways. . . .” Otherwise, the “must have” switches from a testable consequence of the theory, and a potential liability, to an assertion about reality. But now that I know, I’ll be more careful about accepting conclusions drawn from the paper. I can adjust.

    You say,

    Of course, we haven’t seen life designed in the laboratory either, and even if we did, all that would show is that humans can design life—usually after careful study of how nature does it.

    Note the implicit assumption that “nature” did it, without any help. You really have a hard time letting go of your assumptions. Or maybe you just misspoke, for you go on to say,

    But I am not insisting the genetic code had to have arisen the way Yarus et al’s hypothesis suggests, so design may very well be the answer.

    You then finish with

    It sure would be nice, though, if you could point out some experimental evidence specifically contradicting the experimental evidence claimed to support the stereochemical hypothesis. That would be the most effective way to knock it out of the running, IMHO.

    I’m not sure it would. For practically any theory, one can find supportive evidence. As I noted above (#161), the best way to destroy the theory that GWB’s invasion of iraq did not cause 9/11 is not to argue that GWB did not make any Muslims mad. It is to concentrate on the time issue. Just so, for any theory, it is not the evidence that supports the theory that is likely to be most vulnerable; it is the evidence about the “highly speculative aspects” that is most likely to destroy the theory. That’s why I do not concentrate on “the experimental evidence claimed to support the stereochemical hypothesis.”

    I take it by your silence that you are agreeing that my statement that in a given evolutionary pathway,

    Each step need not have function. But in that case natural selection cannot select for function,

    is accurate, as long as the last clause is understood as meaning “for that step”, and are withdrawing your previous objection that what I said is “a massive non sequitur.

  182. 182

    Hi Paul,

    Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such “highly evolved anabolic pathways” without DNA control will turn out to be not realistically feasible?

    I don’t think so, given the state of the research now being done. We haven’t really explored that yet– there is another interesting review by Yarus discussing what he suggests are the precursors to organisms using the genetic code. I was hoping to discuss that in a later comment.

    I tend to be a little more careful the way I phrase things. Maybe the authors were too, and they are quoted out of context in this regard. But I would have preferred to say something like, “If our hypothesis is correct, then life . . . employed amino acids that lie at the end of what must have been highly evolved metabolic pathways. . . .” Otherwise, the “must have” switches from a testable consequence of the theory, and a potential liability, to an assertion about reality. But now that I know, I’ll be more careful about accepting conclusions drawn from the paper. I can adjust.

    That’s cool. I’m just not used to having to explain what is usually recognized as a given. Suffice it to say that the researchers clearly recognize theer are certain conditions upon which the sterochemical hypothesis depends.

    You say,
    Of course, we haven’t seen life designed in the laboratory either, and even if we did, all that would show is that humans can design life—usually after careful study of how nature does it.
    Note the implicit assumption that “nature” did it, without any help. You really have a hard time letting go of your assumptions. Or maybe you just misspoke, for you go on to say,

    No implicit assumption is being made here. I’m simply saying that if humans ever manage to design or create life, much of their practical design inspiration will come from examining how living things (i.e ‘nature’) are today. I certainly did not misspeak.

    I’m not sure it would. For practically any theory, one can find supportive evidence. As I noted above (#161), the best way to destroy the theory that GWB’s invasion of iraq did not cause 9/11 is not to argue that GWB did not make any Muslims mad. It is to concentrate on the time issue. Just so, for any theory, it is not the evidence that supports the theory that is likely to be most vulnerable; it is the evidence about the “highly speculative aspects” that is most likely to destroy the theory. That’s why I do not concentrate on “the experimental evidence claimed to support the stereochemical hypothesis.”

    I’m afraid I disagree. Were there any clear experimental evidence unequivocably contradicting the empirical support for the stereochemical hypothesis, it would be abandoned. That is the quickest, surest way for an hypothesis to bite the dust. At least in science it is.

    I take it by your silence that you are agreeing that my statement that in a given evolutionary pathway,
    Each step need not have function. But in that case natural selection cannot select for function,
    is accurate, as long as the last clause is understood as meaning “for that step”, and are withdrawing your previous objection that what I said is “a massive non sequitur.

    Yep. That is much clearer.

  183. Hi Dave (#164)

    I agree with you that negative evidence is always inherently weaker than positive evidence. If that was all I had to offer, then the case for ID in the origin of life would be weaker than it is.

    That criticism does not apply in the same way to the creation of functional genetic code. We know that humans can create and insert into organisms functional genetic code, and so it is not unreasonable to postulate entities with human-like intelligence to explain apparently sudden increases in genetic information.

    It is also important to note that this weakness of minimalist ID theory would not make it significantly worse than the hypothesis of Yarus et al. It would simply mean that they would face the same kind of evidentiary challenge.

    It should also be noted that you have significantly sharpened the argument in your parallel in two ways. First, I asked for any evidence, even if only suggestive, for life without DNA. In your parallel, you asked for “empirical demonstrations” and “clearly demonstrable instances”, a much higher standard. Second, I spoke of there being “Evidence against life without a DNA code”, and you spoke of how

    Without this [empirical evidence that intelligence has designed and created life], the truth of the rest of the tenets of the ID hypothesis cannot save it. If there are no clearly demonstrable instances of intelligence designing and creating life, then the ID hypothesis is false. Period.

    That is, your supposed parallel would strengthen “evidence against HY” to “the ID hypothesis is false. Period“.

    But, being as I believe in a variant of ID, I do not have to play by the minimalist rules. And the fact is, we do have evidence for the production of life from non-living material by an apparently superhuman agency. There are several instances recorded, two of which are quite convincing if one takes the record(s) at face value, and one of which was convincing enough that several witnesses were so strongly persuaded that they were willing to die for what they professedly believed to be the truth of the matter. I am speaking, of course, of the resurrection of Jesus.

    Now, I know that there have been multiple attempts to discredit the testimony of those who shared their experience. So i will not argue that we have a logically airtight case, and you simply must assent. I don’t even believe that. This is particularly true with this short presentation of the evidence. It is meant to be evocative rather than probative.

    And I know that some would say that this is “religious” rather than “scientific” evidence. But this misunderstands the questions involved. For the believer in naturalism, there is no ultimate distinction between history and biology, just as there is no ultimate distinction between biology and chemistry and none between chemistry and physics. So history is just very very complicated physics. On the other hand those who believed in the resurrection of Jesus were quite firm in the belief that it was a historical event. If you like, it took place at least partly in the physical world, and had physical effects

    The evidence for the resurrection being at least partly physical is fairly clear from several passages. The passages I am citing are not being cited as sacred scripture to which if you do not assent, you are bound for hell. They are being cited as evidence of what the belief of those who had the experiences in question was. But it does seem fair to mention them as a witness to their belief. Some of the passages in question are 1 Cor 15 (the whole chapter, especially verses 5-8 and 12-19), Luke 24:36-43, John 20:24-29, and referring to a slightly different context, 2 Peter 1:16-18.

    Again, I am not offering those texts to prove that the Resurrection happened. I am simply offering them as evidence of what those who had been there believed, and claimed to believe upon good evidence.

    So I think that it is arguable that there is indeed positive evidence suggesting a superhuman entity that is able to give life to non-living matter. This would mean that your attempted parallel between ID and the hypothesis of Yarus et al. (HY) would fail to be convincing, as on the crucial point of positive evidence for a supporting prerequisite for the theory, there is a difference. HY does not at present have any positive evidence for life without DNA, and at least one variant of ID has at least some evidence, however weak, for a superintelligent entity that can create living matter our of non-living matter.

    I see that you are wary of arguments based on negative evidence. Hopefully positive evidence will be a little more to your taste.

  184. 184

    Hi Paul,

    Many thanks for your last reply. Among other things, it certainly can be presented as a concise rebuttal to the “all religious faith is irrational” argument.

    I’m afraid I will have little time for comment today, but to your request for “any evidence, even if only suggestive, for life without DNA”, I suggest two sources. The simplest one is to go back through this thread and read the comments by Art Hunt on protocells– he is on moderation, so his responses to our discussion are often buried back in the thread. The second source is another review by Yarus on the evidence he sees for the existence of cells using RNA before the genetic code (they are called ribocytes):

    Yarus M (2002). Primordial genetics: phenotype of the ribocyte. Ann. Rev. Gen. 36: 125-151.

    From the abstract:

    The idea that the ancestors of modern cells were RNA cells (ribocytes) can be investigated by asking whether all essential cellular functions might be performed by RNAs. This requires isolating suitable molecules by selection-amplification when the predicted molecules are presently extinct. In fact, RNAs with many properties required during a period in which RNA was the major macromolecular agent in cells (an RNA world) have been selected in modern experiments. There is, accordingly, reason to inquire how such a ribocyte might appear, based on the properties of the RNAs that composed it. Combining the intrinsic qualities of RNA with the fundamental characteristics of selection from randomized sequence pools, one predicts ribocytes with a cell cycle measured (roughly) in weeks. Such cells likely had a rapidly varying genome, composed of many small genetic and catalytic elements made of tens of ribonucleotides. There are substantial arguments that, at the mid-RNA era, a subset of these nucleotides are reproducibly available and resemble the modern four. Such cells are predicted to evolve rapidly. Instead of modifying preexisting genes, ribocytes frequently draw new functions from an internal pool containing zeptomoles (<1 attomole) of predominantly inactive random sequences.

  185. Onlookers:

    A footnote, re AH at 177:

    no one anywhere has actually ever established, by direct experimental measurement, that FCSI (or CSI, or whatever) actually exists, in nature or in biology. Rather, those experimental measurements that have been done pretty clearly establish that FCSI (or CSI, or whatever) is a fictional concept.

    As I have indicated in this thread, what ID proponents have done is roll out calculations that have no basis in biological or physical reality. This is a big stumbling block for ID – math that is disconnected from reality is no way to explore the nature of something.

    In fact, this is a capital example of dismissive rhetoric, driven by selectively hyperskeptical thinking that seeks to brush aside — rather than face squarely — a key DESCRIPTIVE and empirically well warranted concept. One that by the way traces to leading scientists at he turn of the 1970′s, and which is by no means a strictly design theoretic concept. (Had AH et al simply read the weak argument correctives in the RH column above, they would not be stuck in such an elementary error.)

    Let us begin with remarks by Prigogine et al, 1972:

    The point is that in a non-isolated system there exists a possibility for formation of ordered, low-entropy structures at sufficiently low temperatures. This ordering principle is responsible for the appearance of ordered structures such as crystals as well as for the phenomena of phase transitions. Unfortunately this principle cannot explain the formation of biological structures. The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly-ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred. [[Ilya Prigogine, Gregoire Nicolis & Agnes Babloyants, "Thermodynamics of Evolution," Physics Today, (Vol. 25, November 1972) p. 23. (Emphasis added.)]

    Then, the next year, Orgel went on record:

    “[L]iving 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 which 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.” [[Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall, 1973). (Emphases added.)]

    Clearly we see here a description of functionally specific, complex information as a distinguishing characteristic of life, and the implication of such being in life forms at molecular level: FSCI is maximally improbable to originate by undirected contingency-based processes, without active information that cuts down the search spaces.

    Going further, in steps:

    1 –> DNA/RNA are based on a four state digital component, taking values A/ G/ C/ T (or U). One digit therefore specifies four possible configurations. When two are present, for each state of the first, four different possibilities exist for the second. So, for N four-state digits, there are 4^N possible configurations, or equivalently 2^2N. (N four-state elements are equivalent to 2N binary digits, in terms of basic information storage capacity.)

    2 –> Following the Koonin estimate, a minimally complex unicellular organism would therefore use a DNA of capacity equivalent to roughly 600,000 – 1,000,000 bits. That is, a configuration space of ~ 9.94 *10^180,617 to ~ 9.90 *10^301,029.

    3 –> To create a comparative yardstick, 500 bits specifies ~ 3.27 *10^150 configurations, and 1,000 bits, ~ 1.07 *10^301 configurations. But, the ~ 10^80 atoms of our observed cosmos, changing state every Planck time [[~10^-43s], and for 10^25 s [[~ 3*10^17 y] would cycle through less than 10^150 configurations. So, hitting on a unique state specified by 500 bits at random would be comparable to finding just one of the possible states of the atoms on a one-shot try. And, with 1,000 bits, if the atoms of our observable universe were to be converted into a random walk search engine runing for a thermodynamically “reasonable” lifetime, it would not be able to search 1 in 10^150 of the possible configurations. [[For, 2^1,000 is of course the SQUARE of 2^500.]

    4 –> So, if a fairly specifically functional, coded digital string uses more than 500 – 1,000 bits, it is reasonable to see that it is not empirically feasible to discover such a string by a random-walk search procedure.

    [ . . . ]

  186. 5 –> Or, using an illustration, we may imagine the digitally coded configuration space as being a vast digital pacific ocean, dotted with islands and archipelagos of function. If a search-raft were to begin at an arbitrary location, and with resources limited to 10^150 possible steps, were to now move about on the ocean at random, if the space of the ocean were to be specified by 1,000 or more bits, the search could not cover as much as one part in 10^150 of the map. (In short, such a “lottery” is empirically — as opposed to logically — unwinnable.)

    6 –> But now, for Koonin’s [2000] minimally complex micro-organism, we are at least 600 to 1,000 times the bit depth of the limit of feasible random walk based search on the gamut of the credible search resources of our cosmos. (And, it bears noting that the genetic code table shows that all sixty-four mathematically possible three-letter combinations are used in protein codes as codons for amino acids or as start/stop codes. So, there is no chemical constraint that forbids any of the possible sequences of the letters {A, G, C, T/U}.)

    7 –> Then, when we observe the Gerhart et al count of the number of base pairs for a modern arthropod, 180 * 10^6, we see the further search space vs search resources challenge to get to body plan innovation level macro-evolution. For, if we take 10 – 100 million base pairs as a reasonable estimate, we see that this range corresponds to ~ 8.19 *10^ 6,020,599 to ~ 1,36 *10^ 60,205,999 possible configurations. (And, worse, the search space is now constrained to our home planet [[~ 6*10^21 tonnes, and perhaps up to 3.8 - 4.6 BY (ignoring the Cambrian limit of ~ 600 MY!)], not the cosmos as a whole.)

    8 –> Consequently, simple chance on the gamut of our observed cosmos is not a credible source of the fundamental functional innovations that have given rise to first life and to the perhaps 30 – 40 major phylum or sub-phylum level body plans in the current world and in fossil forms.

    9 –> Now, the issue here is the arrival of the initially functional: such initial functionality is the premise of any onward variation and selection process that may help improve functionality through Darwinian-type evolutionary mechanisms. Indeed, a second look at Darwin’s closing summary in Ch 15 of origin will again highlight that Darwin begins his theory with pre-existing life:

    >>It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.>>

    10 –> In the days when “protoplasm” was imagined to be a fairly simple mixture of organic and inorganic compounds, this may have sufficed. But now, we know that life crucially depends on complex, functionally specific step by step algorithmically implemented digital information, stored in DNA strings that start out at ~ 600,000 bits for independently existing unicellular life forms. We therefore need a reasonable account for the origin of such functionally specific, complex information, including not only for first life but also, for body-plan innovations.

    11 –> On best, empirically anchored explanation, the best alternative is simple: in every case where we directly know the origin, complex functional digital strings that have information capacity of at least 1,000 bits, are invariably the product of intelligence. So, FSCI is a reliable sign of intelligence, and we may confidently infer from FSCI as observed, to intelligence as its causal origin.

    12 –> The reason for the sort of dismissals above is then quite simple: FSCI cuts clean across the attempt to account for the origins of our cosmos, and of life and its diversity including ourselves, on chance + mechanical necessity only in a postulated materialistic cosmos. So, it will be stoutly resisted by those who are committed to such agendas, and their fellow travellers.

    _____________

    Clearly, despite Mr Hunt’s confident declarations to the contrary, the FSCI concept is based on the relevant physics and biology, and is a well observed phenomenon. Indeed, using the 1,000 bit threshold, this or any other ASCII string of length at least 143 characters, is a case of FSCI.

    Neither Mr Hunt nor any other evo mat advocate here at UD can identify a case of known origin that credibly is the result of chance + necessity, as opposed to intelligence.

    thee is a whole Inernet full of cases in point on how FSCi is routinely teh product of intelligence. Libraries, Offices bookshops and many other cases provide further instantiation, amounting to literally billions of known cases,with no counter instances.

    In short,the inference from FSCI to intelligence as its best explanation is one of the best- supported, empirically warranted inferences we make.

    GEM of TKI

  187. Arthur Hunt:

    Actually, no one anywhere has actually ever established, by direct experimental measurement, that FCSI (or CSI, or whatever) actually exists, in nature or in biology. Rather, those experimental measurements that have been done pretty clearly establish that FCSI (or CSI, or whatever) is a fictional concept.

    1- If you don’t like CSI nor FCSI then all YOU have to do is when an IDist says this is CSI/ FCSI is to demonstrate that nature, operating freely, can account for it.

    IOW all YOU have to do is to actually support YOUR position!

    However you have proven that the theory of evolution is a fictional concept.

    No measurements or calculations on how many mutations it takes to get a novel protein machinery.

    No measurements or calculations on anything.

    Heck no one even knows if the transformations required for universal common descent can even be produced by an amount of mutatioal accumulation.

    IOW you should stop complaining about ID and focus on your position.

    THAT is how you refute ID by demonstrating nature, operating freely can account for it.

    But you cannot so you have to complain about ID.

    Too bad your position doesn’t have anything as well defined as CSI or IC.

    Then perhaps we could test it.

  188. Hi Dave,

    In #182 you say,

    Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such “highly evolved anabolic pathways” without DNA control will turn out to be not realistically feasible?

    I don’t think so, given the state of the research now being done. We haven’t really explored that yet– there is another interesting review by Yarus discussing what he suggests are the precursors to organisms using the genetic code. I was hoping to discuss that in a later comment.

    Whoa. I’ll wait for the discussion. But in the meantime, are you saying that if someone comes up to me and asks whether life arose spontaneously, I am supposed to say, “I have no idea”? I can’t say, “I don’t know for sure, but at present it looks to me like it didn’t”? No conclusions, however tentative and open to revision, are allowed?

    Does that also apply to the Privileged Planet hypothesis also? If so, have you written to the Iowa State faculty about the gross injustice of closing down the debate prematurely? Or is it only ID adherents who are not allowed to draw any conclusions?

    You move from the phrase “how nature does it” to “how living things (i.e ‘nature’) are today”. In the one case it seems to imply that nature is an active agent, and could easily imply that nature does it as opposed to an intelligent designer. The second way of saying it does not carry those implications. But if you didn’t mean them, that’s cool.

    It looks like we’ll have to disagree for now regarding your comments on the quickest, surest way to dispatch the hypothesis of Yarus et al. But that’s okay. We don’t have to agree at present.

    I’m glad we have reached agreement on whether, in an evolutionary pathway, if a given step does not have a function, that step cannot be influenced by natural selection.

  189. 189

    Hi Paul,

    Whoa. I’ll wait for the discussion. But in the meantime, are you saying that if someone comes up to me and asks whether life arose spontaneously, I am supposed to say, “I have no idea”? I can’t say, “I don’t know for sure, but at present it looks to me like it didn’t”? No conclusions, however tentative and open to revision, are allowed?

    Of course not. Where did you get the idea I think that? If that is the impression my posts are giving, then maybe I need to polish my communication skills.

    Does that also apply to the Privileged Planet hypothesis also? If so, have you written to the Iowa State faculty about the gross injustice of closing down the debate prematurely? Or is it only ID adherents who are not allowed to draw any conclusions?

    How exactly did the Iowa State faculty close down the debate prematurely? I haven’t followed that story very closely, apparently, although I did read som things about Gonzalez’s tenure, but as far as I know that is a separate issue. And I have looked at the book in question briefly, but didn’t see much in it of substance that added to or improved on the basic Anthropic Principle, which has been floating around in astrophysics circles for some time. Did the Iowa State faculty shut down all debate on the Anthropic Principle as well?

    You move from the phrase “how nature does it” to “how living things (i.e ‘nature’) are today”. In the one case it seems to imply that nature is an active agent, and could easily imply that nature does it as opposed to an intelligent designer. The second way of saying it does not carry those implications. But if you didn’t mean them, that’s cool.

    Right. The original example I had in mind when I wrote it was the basic design of the aircraft wing, which originally used the shape of bird wings as a starting point. The main point I was trying to make was, even if man eventually manages to create life, that doesn’t conclusively show that life has to have intelligence to create it. It will be the first actual empirical example of intelligence creating life. But if it used nature as inspiration for much of its design ideas, all we can really say is, intelligence can create life if it bases much of the design on nature (which may or may not require intelligence for its designs). It would still require substantially more work to establish that life itself needs intelligence for its creation. That was the reason I brought up thge steochemical hyoptehsis in the first place: somebody here (I forget who at the moment) stated as a premise that information requires intelligence for its generation, the genetic code being one. My whole point was that this premise is false, since conceptually the stereochemical hypothesis which shows that many of the associations between entities that make up the code could be explained by chemical affinity, without intelligence as a necessary prerequisite. Just how plausible the hypothesis is remains to be determined, for some of the reasons you and I have been discussing. But the flat, absolute statement that information
    requires intelligence is false.

    It looks like we’ll have to disagree for now regarding your comments on the quickest, surest way to dispatch the hypothesis of Yarus et al. But that’s okay. We don’t have to agree at present.

    We don’t have to agree at all, actually ;)

    I’m glad we have reached agreement on whether, in an evolutionary pathway, if a given step does not have a function, that step cannot be influenced by natural selection.

    To put it in flowery evo-language, the evolutionary path to a fitness peak can include neutral steps, and can,in some cases, include steps in which fitness is reduced.

  190. Mr Kairosfocus,

    Since you have many times referred to the size of the problem to be solved in terms of millions of bits, I thought you would be interested in this slide presentation on gigabit optimization using genetic algorithms. Apparently it was possible to search such spaces to optimality for 33-Mbit problems in 2005, using less resources than the known universe.

    ID advocates may be especially interested in slide 31. Dr Goldberg argues there that to pass proof of concept gigabit optimization and apply the technique to engineering problems (including computational protein cemistry), it will be necessary to use evolutionary methods to build very large cognitive models, something he analogizes to human cognitive capacity.

  191. Nakashima-San

    Please play a little game, called “spot the active information.”

    of course one can pick out a winneer in a much bigger config space than 1,000 bits. We do it allt he time when we compose messages based on intelligent activity.

    GA’s are inherently intelligently designed, and in the cases in view are set up to optimise [or quasi-optimise, heuristics and all that] to a target. they are foresighted search.

    This is just the opposite of blind necessity and undirected contingency.

    Just think: if the entire program and PC in question running the algor you link were subjected to significant random variation, what would happen real fast, why?

    GEM of TKI

  192. PS: You should be able to see some of what is going on from this summary at Wiki:

    ________________

    Genetic algorithms are implemented in a computer simulation in which a population of abstract representations (called chromosomes or the genotype of the genome) of candidate solutions (called individuals, creatures, or phenotypes) to an optimization problem evolves toward better solutions. Traditionally, solutions are represented in binary as strings of 0s and 1s, but other encodings are also possible. The evolution usually starts from a population of randomly generated individuals and happens in generations. In each generation, the fitness of every individual in the population is evaluated, multiple individuals are stochastically selected from the current population (based on their fitness), and modified (recombined and possibly randomly mutated) to form a new population. The new population is then used in the next iteration of the algorithm. Commonly, the algorithm terminates when either a maximum number of generations has been produced, or a satisfactory fitness level has been reached for the population. If the algorithm has terminated due to a maximum number of generations, a satisfactory solution may or may not have been reached.
    ___________________

    Recall, the key challenge for origin of life and of body plan lecvel biodiversity is to get TO shores of function that have even initial functionality.

    That term “fitness function” is all too revealing that this is like the physicist the Engineer and the economist on a desert island with cans of food, but no opener.

    Cutting the joke short — and, my dad is an Economist — the economist says: “first, postulate a can opener . . . “

  193. Mr Kairosfocus,

    As easy as this problem is, the fitness function does not present the population with a single target.

    A burst of cosmic rays passing through the machine would cause it to reboot or perhaps fail permanently. Pace to Mr Dodgen, the active information in the cosmic rays have not added anything to the simulation. Your point?

  194. Mr Kairosfocus,

    This is indeed why so many people make a strong distinction between OOL and ToE. Evolution is the can opener of diversity. Since you consistently refer to the complexity of body plan FCSI in the 10-100 Mbit range, that is the relevant comparison to a 33 Mbit GA operating using evolution.

  195. Macro-evolution in action! Speciation based on a one base pair mutation event

    The comment to that story is also worth reading.

  196. 196

    Nakashima,

    ——-”Macro-evolution in action! Speciation based on a one base pair mutation event”

    Ummmm, different colored feathers doesn’t constitute a new species anymore than my brother and I having different hair color constitutes us as being two different species.

  197. Mr hayden,

    Yes, that is the “in action” part of the story. There seems to be some mate selection preference for similarly colored birds, so depending on your species concept they could be called separate species when they stop interbreeding significantly.

    Preference for self similarity is quite functional, and is a basic driver of speciation from single celled creatures onward.

  198. 198

    Nakashima,

    ——”Yes, that is the “in action” part of the story. There seems to be some mate selection preference for similarly colored birds, so depending on your species concept they could be called separate species when they stop interbreeding significantly. Preference for self similarity is quite functional, and is a basic driver of speciation from single celled creatures onward.”

    Well then it’s too early to call it speciation. And we could call mate selection a “preference”, like I prefer brunettes, but that wouldn’t mean that blondes are a different species.

  199. 199

    Well then it’s too early to call it speciation.

    Most evolutionary biologists would agree with you, and call it “incipient” speciation.

  200. 200

    Dave Wisker @199:
    Given that no one knows whether the birds will speciate, it seems the term “incipient speciation” could only be used retrospectively.

  201. 201

    Hi Scott,

    The term is used to describe a situation in which reproductiove isolation is beginning to develop. Reproductive isolation is an essential element of the speciation process. So no, it is not a term that can only be used retrospectively.

  202. 202

    Dave Wisker @201:
    I had read that it was the early stage of speciation, which would be difficult to know unless speciation occurred.
    But I’ll concede that the comment was hair-splitting, non-productive, and probably inaccurate.

  203. Mr Hayden,

    Since they live on separate islands, I think there are other factors that will push them to speciation. Unfortunately the news item does not say how strong the mate preference is today, but does say it will be a long difficult process to set up such experiments.

  204. 204

    Hi Scott,

    The process of speciation doesn’t always end up with two species– in some cases the reproductive isolation fails to be maintained and the two once-diverging populations begin to merge again. In addition, the building up of isolation and genetic divergence can be observed and tracked before the actual species are formed. Incipient species are really just populations in the process of diverging, before the barriers are irreversible. They can be identified as such without an actual speciation ‘event’ occurring.

    But I’ll concede that the comment was hair-splitting, non-productive, and probably inaccurate.

    I wouldn’t say that. It sparked my interest (of course, how populations begin to differentiate genetically is my are of interest). So it got geek points from me at least ;)

  205. A couple of things for the queue:

    1. I don’t know about 500 bits, but, for random biological processes, 200 bits of FCSI (according to KF’s calculations, that, as the following shows, is out of touch with reality) is like falling out of bed. I don’t think 500 bits is any less accessible.

    2. According to Dembski, Behe, Durston, Axe, and every other real ID theorist, the quantity of functional information is computed by deriving the fraction of all possible proteins (or nucleic acids, or sequences) that can satisfy a given biological or biochemical function. This is a value that can be experimentally measured (as opposed to estimated by calculation). Simply prepare a large population of random polymers (polypeptides or polynucleotides, typically) and ask how many of the population can satisfy a given biological or biochemical function.

    This sort of measurement is inadvertently done on a routine basis. Anyone who does phage display with random libraries, anyone who uses mRNA display to discover new functional sequences, they all do this measurement. And they all routinely reach the same answer – functional sequences are relatively frequent occurrences (if 1 in 10^10 or so is frequent). ID theory, including KF’s numbers, insists that random combinatorial approaches can never, ever work. Every time that such an experiment works (and it does all the time), it’s yet another stake in the heart of ID.

  206. Nakashima-San:

    The problem with assuming that minor changes on a hill slope that lead up to the top of the hill through a hill-climbing algorithm adequately model leaps across seas of non-function to create novel body plans, should be plain.

    1 –> Consider on a hardware store that like both your archipelago and mine, is subject to hurricanes. Do we expect to ever see a hurricane passing over such a store and spontaneously assembling a livable three-bedroom house with all the trimmings?

    2 –> Such is of course logically possible, but is so maximally improbable that it is empirically unobservable on the gamut of our observed universe.

    3 –> Underlying is the key problem with GA’s as I highlighted earlier: they assume that functionality comes in a smoothly varying “continental” landscape, with local hills and valleys. On such a functionality/ fitness landscape, hill climbing through modest variation of already somewhat functional entities and promotion of the more successful will work to get you to peaks.

    4 –> in the real world, the landscape is more like a vast sea of non-function [which would be a flat zero on a functionality metric] with isolated islands of function. So, teh challenge is to first get to shorelines of function, before hill climbing can occur.

    5 –> this manifestly holds for origin of life (which you wish to concede then wall off), which BTW directly implies that the Darwinian tree of life is lacking its taproot. [It therefore has no basis for ever getting evolution of biodiversity started. That is already a failure to get our the starting gate in the race . . . ]

    6 –> But, the same challenge also holds for body plan level macro-evolution (which is the relevant issue, not micro-evolution within the islands of function.)

    7 –> The Cambrian fossil life revolution is a good illustrative case: perhaps 38 phyla and subphyla, with no evident precursors, in a context where unicellular life forms maybe are independently viable at 300 – 500 k base pairs, but to get to novel body plans you have to account for novel cell types, tissues, organs and organisation, requiring a due set of proteins and enzymes and other regulatory mechanisms. All of which calls for increments in DNA. On the evidence of modern arthropods, 10 – 100 mega bits is a reasonable estimate of the novelty that has to happen dozens of times over.

    8 –> Moreover, once we are dealing with body plans, we have to create new arrangements of the embryo or basic developing organism,not at late developmental stages, but in early stages, where odds against getting a viable change at random exponentiate. [A mutation that changes how many digits appear is one thing, one that fiddles with the spine or central nervous system, or that creates such etc are a wholly different other.]

    9 –> In short, given the abundant evidence for isolated islands of function is a wide sea of non function for complex digitally encoded information, one cannot simply assume or assert that macro-evo is just cumulative micro-evo. (And, onlookers, notice the latest exchange over bird feather colouration!)

    10 –> Worse, the fossil record, however one interprets it, is the only direct access to the world of life in the remote past. And its “almost unmanageably rich” evidence [250k+ fossil species, billions of actual fossils] gives a clear testimony: sudden appearance, stasis and disappearance or continuation into the present world are the overwhelmingly dominant features of that record (especially when one duly reckons with the implications of observed mosaic lifeforms like the platypus).
    ______________

    In short, the immeasurably better explanation of the leaps in FSCI we see in body plan level biodiversity is the only directly known source of FSCI: intelligence.

    GEM of TKI

  207. 207

    Nakashima,

    ——”Since they live on separate islands, I think there are other factors that will push them to speciation.”

    And since I live on a different continent than Asia, eventually we will be different species.

  208. 208

    Hi Clive

    If reproductive isolation is maintained long enough, speciation is inevitable.

  209. 209

    Dave Wisker,

    ——-”If reproductive isolation is maintained long enough, speciation is inevitable.”

    That’s the very question at hand isn’t it? Since it is the question it also cannot be your conclusion or else you’re arguing in a circle.

  210. 210

    Its not the “very” question, Clive. Populations that exchange genes are more alike genetically than those that do not. An empirically verified fact. Reproductive isolation results in genetic divergence of populations, and the divergence grows the longer the isolation is in place. This is another empirically verified fact. Populations that differ enough genetically will not produce fertile offspring. This is still another empirically verified fact (the level of genetic divergence necessary for this to happen can vary, however).

    No question about it: if reproductive isolation is maintained long enough, speciation is inevitable

  211. 211

    Dave Wisker,

    ——”No question about it: if reproductive isolation is maintained long enough, speciation is inevitable”

    You can keep repeating the mantra, it doesn’t make it true. Rote does not make right.

  212. 212

    Clive,

    Ignoring what I wrote supporting it and implying I am just repeating the same sentence undermines the credibility of your point dramatically.

  213. 213

    Dave Wisker,

    There is no evidence for it, how about that?

  214. 214

    Clive,

    Dave Wisker,

    There is no evidence for it, how about that?

    Are you saying that there is no evidence for population divergence under reproductive isolation? That there is no evidence that this isolation results in enough genetic divergence that interfertility is impaired?

  215. 215

    Dave,

    There is no evidence of speciation by virtue of sexual preference or sexual isolation.

  216. 216

    This also leads me to wonder about the apparent coordination between punctuated evolutionary changes and speciation.
    As it is, we have many species of related animals in a recognizably similar state of evolution*. That is, we can recognize birds, cats, and dogs all over the world, similar enough that we can tell what they are.
    But in each case it appears that they speciated after they completed their transitions to being birds, cats and dogs.
    Given entire populations of animals, all at a sufficient state of fitness to have been selected in their current states, it seems odd that they would wait to speciate until they achieved some significant change in form.
    Where are the descendants of the species that branched from their intermediates? Shouldn’t we see more of them today?
    *For the sake of discussion.

  217. 217

    I think the question makes more sense if I turn it around.
    If we envision the tree of life as a series of intermediates branched by speciation, why do the majority of living examples of speciation appear to spring from so few points along the tree of life? Why are there dozens of species of whale, and no species of any of the nearest predecessors not recognizable as whales? It suggests that they didn’t speciate until they were finished “becoming” whales.

  218. 218

    I neglected to mention the obvious, that the other species descended from intermediates could all be extinct, but why would dozens of species of whale survive and not one pre-whale?

  219. 219

    Clive, theer ius very good evidence for sexual selection maintaining strong reproductive isolation between two otherwise genetically compatible species:

    Boughman JW (2001). Divergent sexual selection enhances reproductive isolation in sticklebacks. Nature 411: 944-948.

  220. 220

    Dave Wisker,

    Of course isolation produces reproductive isolation. The question is whether this produces speciation by virtue of the isolation.

  221. I happened to be reading a book my daughter left on a recent visit, and came across a reference in it to another book entitled The descent of man, and selection in relation to sex. Geoffrey Miller (The Mating Mind) suggests Darwin’s discussion of human’s descent from ape ancestors was not the main issue of the book, rather it was sexual selection.

  222. 222

    Dave Wisker, I don’t think Clive believes speciation ever happens. That’s not, strictly speaking, and ID position, but it’s a position of something else from which ID, errr, speciated.

  223. 223

    David Kellogg,

    I like your humor.

  224. 224

    David Kellogg,

    Ahh…well, there will always be those who demand every dropped Japanese bomb be accounted for before admitting the Japanese actually attacked Pearl Harbor.

  225. 225

    DW, Yes. Or like the holocaust denier who will only accept accounts from those who actually died in the gas chambers (cf Jean-Francois Lyotard, The Differend).

  226. 226

    Explanation: I don’t think IDers are at all comparable to such deniers. That’s just the limit case that Lyotard examines in his book about certain kinds of argumentative impasses.

  227. Mr ScottAndrews,

    I neglected to mention the obvious, that the other species descended from intermediates could all be extinct, but why would dozens of species of whale survive and not one pre-whale?

    They no longer fit the ecological niches that exist today as well as their descendant species.

  228. Hi Dave,
    Thanks for your note (#184). And thanks for the compliment.

    On life without DNA, if we are to use Art Hunt’s “protocells” we need to define life. I’ll discuss that below. On Yarus, I will have to read the entire article before commenting, and do not have immediate access to it. However, in the next few days I should be able to do so, probably Tuesday or Wednesday. Hopefully we can have a good discussion then.

    In the meantime, if Art Hunt is correct in his claim, protocells are life without DNA. So how does he define life? In #157 he links to an essay of his with very little description. The essay is apparently on 2 mutations changing a plant from a herbaceous annual to a woody perennial. In #160 he links to another essay apparently attempting to refute Behe’s The Edge of Evolution. In 162, he links to another essay, and this time lists several properties that it looks like he is suggesting is life (or perhaps protolife):
    Growth
    Division
    Evolution
    Response to external stimuli
    Possession of rudimentary metabolism.
    In #166 he pointed back to his previous post, presumably #160. In #170 he again refers to “my essay” (the one linked in #160, linked 3 times) and to “Fox’s critters”.

    I looked at his essays. They seem a little short on documented detail. They are probably reassuring to one who starts out agreeing with him but wavering. But they are less helpful to someone who starts out skeptical and wants evidence rather than assertions. In particular, the claim is made that “the information content of proteins is inherently low.” I would appreciate evidence and citations, rather than this assertion that is found halfway through his article. He also posits the frequency of simple nucleotidyltransferases at 10^-14, again without explaining where that figure came from. Hopefully, he has some rationale behind these statements.

    In the paper he lists several properties of protocells (see #178 for the exact quotes):
    The ability to sense an electrical field
    Aggregation
    Mobility
    Osmosis
    The ability to selectively pass materials across a semi-permeable membrane
    Fission
    Reproduction
    Conjugation
    Communication
    Excitability

    This list contains some redundancies. It seems to me that if protocells undergo fission, they have to undergo reproduction. Osmosis is one specific example of the ability to selectively pass materials across a semi-permeable membrane.

    The list also contains some properties that are not well-defined. It is not clear how we know that the protocells have the ability to sense an electrical field. Does that simply mean that they can be demonstrated to react to an electrical field? I shall assume that this is what he really means, and he can correct me if I am wrong.

    The same is true for communication, which is defined as the ability to pass information directly to another. Presumably this means another protocell. It is not clear what kind of information is being passed. It seems to be something vague, like passing a molecule with a particular enzymatic activity to another protocell. I am not sure why this would not be considered as an enzyme moving from one protocell to another, rather than a protocell communicating with another. For now, until this property is better explained, I shall ignore it.

    Finally, excitability is not a clear-cut concept. Capacitors can store and discharge energy. An example of how protocells generate electrical fields is not given, or what form of energy is converted into electrical fields, or for what purpose protocells “utilize” (a word that means put to use and implies purpose) elecrical fields. Again, in the absence of further information, I will consider this to mean that protocells can convert other forms of energy to electrical energy, and then convert electrical energy into other forms of energy. Again, Art can correct me if I misunderstood.

    Thus our new modified list looks like this: Protocells can
    react to an electrical field, and transform other forms of energy into electrical energy and electrical energy into other forms of energy,
    aggregate,
    move,
    pass materials across a semi-permeable membrane,
    split apart, and
    fuse.
    Compare this with your list, and we should add
    grow
    evolve (change?)
    Response to external stimuli, and
    possess a rudimentary metabolism.

    Art states,

    Ask a high school bio student (e.g., perform a sort of “toddler test”) if these characteristics would qualify something as being alive, and the answer very likely would be yes.

    But this, rather than supporting his thesis, illustrates the poor quality of biological teaching in the US.

    Let me explain. The above are properties of most life. But they do not come close to adequately defining life, or getting close to its essence. And they are philosophically unsatisfying. A good definition uses crucial properties, and as few as possible to differentiate the objects included by the definition from those excluded by the definition. Thus the ability to pass materials across a semipermeable membrane is a poor criterion, because non-living membranes have this property, and because although all living things have this property, it does not reach to the core of life. If computers ever become sophisticated enough to be considered alive, they will not have this property, so it is conceivable that life would not have this property.

    The same goes for fusing. Many living things do not fuse, Soap bubbles fuse. Fusion is not near the core of life. Responding to external stimuli is a poor differentiator, as is movement, aggregation, responding to electrical energy, transforming electrical energy into other forms, and creating electrical energy (thunderstorms, anyone?). Growth is not a criterion, or every adult mammal would be considered dead. Growth is indeed a property of life as we know it, but if we found a living organism that never grew, we could not thereby assert that it was not alive. The same is true for reproduction. Several close relatives of mine can no longer reproduce, and one of them has never reproduced. I would hesitate to call them not alive. Although reproduction is a requirement for living things to continue to exist where death is a reality, philosophically the requirement that the essence of life is reproduction seems misguided. And soap bubbles can fission with the right wind currents; I’ve seen it happen.

    Perhaps the most misguided criterion is that life evolves. Change happens to non-living things. The morphology of algae has apparently not changed significantly in 3+ billion years according to standard interpretations. If the genome has also not changed, algae would still be alive. Stasis in the fossil record is not evidence that the organisms are dead. If we somehow developed an organism that had perfect genetic repair, the organism would still be alive.

    Frankly, I suspect the last one is an attempt to define evolution into life. Perhaps someone was so thrilled with Dobzhansky’s statement that he/she tried to define life sot that it would make sense in the light of evolution. Or perhaps someone wanted a definition to knock down those pesky intelligent design creationists. Whatever the reason, it was a lousy definition.

    It is instructive to note that, other than the membrane properties, none of the above criteria are capable of differentiating life from fire. Fire can react to an electrical field, create and transform electrical energy, aggregate, move, split apart, fuse, grow, evolve, and respond to external stimuli. Fire even possesses a rudimentary metabolism. Chemists familiar with Bunsen burners know that part of the flame is typically oxidizing, and part is typically reducing. There are distinct “metabolic zones.” Any definition of life that does not differentiate between fire and life is a failure.

    However, there is one property that clearly differentiates between life and non-life, and it does not appear in this list. It is organization with the result that the organism imposes a complex order on what it receives from the environment, so that the environment serves the organism rather than vice versa. Food is organized into humans, or pine trees, or bacteria, rather than vice versa That’s why we call them organisms. They are organized, and they organize. As kairosfocus (#185) quotes Orgel as saying, “living organisms are distinguished by their specified complexity.”

    He goes on to say,

    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 which 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.”

    If computers ever do deserve the epithet “living”, it will be because they have mastered the science of organizing their environment to serve their purposes, including their own preservation, and are able to impose their particular brand of complexity on the relatively simple raw materials they intake, rather than because they can evolve, or fission, or aggregate, or any or all of the other properties Art and you have listed.

    It is fascinating to note that neither your list nor that of Art recognizes this aspect of life. Don’t feel too bad; the biology textbooks I have read don’t either. You may have picked your definition up from them. The high school biology students Art appealed to probably got their definition from the textbook also, and Art’s “toddler test” is therefore about as useful as asking an actual toddler.

    It is interesting to note that the hypothesis of Yaris et al. required that “highly evolved anabolic pathways” somehow arose without DNA control. It would be reasonable to propose RNA control for these pathways. But it is totally unreasonable to propose that they arose without any control whatsoever. The point is that life requires control. That’s what the membrane is about—control. That’s what the DNA code is about. That’s what the anabolic pathways are about—controlling the form of what comes in so that it becomes changed into an integral part of the organism.

    And that is why it is difficult, and may be impossible, for RNA to be the control molecule. One needs a way of clearly differentiating the backup from the working copy. If RNA is serving both purposes, it is hard for the cells degradative enzymes to figure out which is which and destroy the working copies when they are no longer needed without destroying the backup copy. DNA solves that problem. I’m still waiting to see evidence that RNA actually does the job in specified circumstances rather than theoretical partial justifications of how it might have happened.

  229. 229

    Hi Paul.

    However, there is one property that clearly differentiates between life and non-life, and it does not appear in this list. It is organization with the result that the organism imposes a complex order on what it receives from the environment, so that the environment serves the organism rather than vice versa.

    I would argue that the beginning of this is the containment of a semi-permeable membrane– a way of creating a more limited internal environment as opposed to be subjected completely to the vagaries of the environment as a whole.

  230. Hi Dave,

    My original comment and your answer were,

    Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such “highly evolved anabolic pathways” without DNA control will turn out to be not realistically feasible?

    I don’t think so, given the state of the research now being done. We haven’t really explored that yet– there is another interesting review by Yarus discussing what he suggests are the precursors to organisms using the genetic code. I was hoping to discuss that in a later comment.

    My next comment was,

    Whoa. I’ll wait for the discussion. But in the meantime, are you saying that if someone comes up to me and asks whether life arose spontaneously, I am supposed to say, “I have no idea”? I can’t say, “I don’t know for sure, but at present it looks to me like it didn’t”? No conclusions, however tentative and open to revision, are allowed?
    Does that also apply to the Privileged Planet hypothesis also? If so, have you written to the Iowa State faculty about the gross injustice of closing down the debate prematurely? Or is it only ID adherents who are not allowed to draw any conclusions?

    The first part of your reply was,

    Of course not. Where did you get the idea I think that? If that is the impression my posts are giving, then maybe I need to polish my communication skills.

    That being the case, the questions I asked about the Privileged Planet hypothesis are mostly irrelevant. If tentative conclusions can be drawn, then the faculty at ISU were within their rights to conclude that Gonzalez was wrong on this issue (whether they were correct in fact, or whether their actions were justified if he were wrong, are separate issues).

    BTW, Gonzalez made one advance from the typical anthropic principles arguments. He introduced the concept that the earth was designed not only for the existence of life but for scientific discovery, which of course has no survival value. This feature, if truly present, is difficult to account for on the basis of either natural selection or an atheistic view of the anthropic principles. It also is positive evidence. Finally, it implies a designer of a particular type; one who is powerful enough and intelligent enough to create a world where scientific discovery is easier than what one would expect from chance, and one who apparently wishes us to engage in scientific discovery. That is, minimalist ID is superseded here.

    Your translation into flowery evolutionary language is interesting. How many neutral steps and/or how many temporarily deleterious steps can one reasonably allow before a postulated evolutionary pathway becomes unfeasible? In other words, where is the edge of evolution in terms of neutral or deleterious mutations? Are there either calculations or experimental evidence that can help us here? I gather you are not too happy with Behe’s answer. Do you have your own, and why?

  231. “If computers ever do deserve the epithet “living”, it will be because they have mastered the science of organizing their environment to serve their purposes, including their own preservation, and are able to impose their particular brand of complexity on the relatively simple raw materials they intake, rather than because they can evolve, or fission, or aggregate, or any or all of the other properties Art and you have listed.”

    Fox’s protocells “are able to impose their particular brand of complexity on the relatively simple raw materials they intake”.

    Not that the debate about what is really living is all of what my argument is about. There seems to be a tenuous agreement that the properties I list, that protocells are observed to possess, are also characteristics seen in living cells. What this means is that a DNA code (or whatever “information” the ID proponent wishes to invoke) is quite unnecessary when it comes to the origination and maintenance of these characteristics.

    “It is interesting to note that the hypothesis of Yaris et al. required that “highly evolved anabolic pathways” somehow arose without DNA control. It would be reasonable to propose RNA control for these pathways. But it is totally unreasonable to propose that they arose without any control whatsoever. The point is that life requires control. That’s what the membrane is about—control.

    Control is an inherent property of chemistry. For example (one quite apart from all that has been discussed in this thread – it’s just a simple illustration), consider a 4-step series of irreversible first order chemical reactions that leads from A to B to C to D to E. It turns out that, no matter how you change the rate constants of the second and third reactions, you don’t change the overall flux thru the pathway at the steady state. That’s quite exquisite control, a simple and strong robustness that we don’t see in engineered systems.

    There’s no reason to claim that prebiotic chemistry was without control. We’re talking chemistry, not primitive engineering.

    And that is why it is difficult, and may be impossible, for RNA to be the control molecule. One needs a way of clearly differentiating the backup from the working copy.

    Why? RNA viruses do this just fine. (Remember this conversation next time you come down with a cold.)

    If RNA is serving both purposes, it is hard for the cells degradative enzymes to figure out which is which and destroy the working copies when they are no longer needed without destroying the backup copy.

    As long as one copy survives, life goes on.

    Life is about RNA, ribosomal RNA to be specific. This is the central player in the cell – the bulk of the RNA is rRNA, most of the rest “services” rRNA, and the majority of cellular metabolism is geared towards rRNA function. DNA is little more than “the back-up copy” of the rRNA. Any code, control, or other aspect informational aspect that one might see in DNA is actually a reflection of the functioning of rRNA.

    DNA solves that problem. I’m still waiting to see evidence that RNA actually does the job in specified circumstances rather than theoretical partial justifications of how it might have happened.”

    I think I told Paul Nelson this fictional anecdote – if a very advanced alien species did a quick fly-by analysis of life on Earth, their conclusion would run along the lines of “well, rRNA sure has found a lot of interesting ways to propagate itself on this planet”. Life is, at its core, all about RNA. Ribosomal RNA. Understand its origins and one understands the OOL.

    (Heck, if ID proponents weren’t so religiously stubborn in their opposition to any and all suggestion that the OOL can actually be studied and understood, I believe they might seize on and study this OBVIOUS candidate for this possible designoid that lies at the core of life as we know it. But that ain’t gonna happen. For obvious reasons.)

  232. Art states,

    Ask a high school bio student (e.g., perform a sort of “toddler test”) if these characteristics would qualify something as being alive, and the answer very likely would be yes.

    But this, rather than supporting his thesis, illustrates the poor quality of biological teaching in the US.

    Um, the “toddler test” was something that Mike Gene introduced me to. If you don’t like it that this ID tool actually takes one places where one is predetermined never to tread, blame him. Not me, nor our schools.

  233. About my essays:

    I looked at his essays. They seem a little short on documented detail.

    I’m sorry. This unsupported assertion is just not true. My essays focus on a few interesting aspects of life, and my claims and conclusions are supported by reference to actual experimentation. (I’ll admit that one may have to follow a trail through several essays. But laziness is no reason to misrepresent things so.)

  234. Mr Hunt:

    Just a reminder:

    1] Prigogine et al, 1972:

    The point is that in a non-isolated system there exists a possibility for formation of ordered, low-entropy structures at sufficiently low temperatures. This ordering principle is responsible for the appearance of ordered structures such as crystals as well as for the phenomena of phase transitions. Unfortunately this principle cannot explain the formation of biological structures. The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly-ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred. [Ilya Prigogine, Gregoire Nicolis & Agnes Babloyants, "Thermodynamics of Evolution," Physics Today, (Vol. 25, November 1972) p. 23. (Emphasis added.)]

    2] Orgel, 1973:

    “[L]iving 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 which 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.” [[Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall, 1973). (Emphases added.)]

    Onlookers, the above exchange with P Giem simply underscores to me how desperately modern biology needs to listen tot he point being made by design thinkers.

    GEM of TKI

  235. 235

    Nakashima:

    They no longer fit the ecological niches that exist today as well as their descendant species.

    I considered that. But doesn’t it seem unusual that these ecological niches could be so discriminating that they permit whales but not the descendants of nearby branches, and yet permit so many varieties of whales? And the pattern appears to repeat within so many other types of creatures?
    I don’t know that the observation itself means anything, but it seems that speciation should branch at occasional intervals, not just radiate from single points.

  236. Hi Dave (#229),

    I would argue that the beginning of this is the containment of a semi-permeable membrane– a way of creating a more limited internal environment as opposed to be subjected completely to the vagaries of the environment as a whole.

    I would almost agree with you. A semi-permeable membrane is a requirement for all known life, for the reason you stated. Whether it is the “beginning” depends on how literally we interpret beginning, and whether life in fact evolved with the first step being a semi-permeable membrane. If you substitute “a presently foundational requirement” for “the beginning of this”, I would agree with you.

  237. 237

    Hi Paul,

    Actually, when I said ‘beginning’, I was referring to the beginning of the development of complex order.

  238. 238

    Hi Paul,

    Your translation into flowery evolutionary language is interesting. How many neutral steps and/or how many temporarily deleterious steps can one reasonably allow before a postulated evolutionary pathway becomes unfeasible? In other words, where is the edge of evolution in terms of neutral or deleterious mutations?

    The answer to that depends entirely on the genetic and ecological context of the situation. For example, how stable is the environment? If it is changing relatively quickly, then the adaptive problem (which defines the “end’ of the sequence of steps) may require more steps to achieve, may render the achievement impossible, or may eliminate the original adaptive problem altogether. So I think the idea of establishing some limit is, in the end, a pointless arbitrary exercise.

  239. Mr ScottAndrews,

    But doesn’t it seem unusual that these ecological niches could be so discriminating that they permit whales but not the descendants of nearby branches, and yet permit so many varieties of whales?

    I don’t understand the distiction you are making between “varieties of whales” and “descendants of nearby branches”. All the varieties of whales _are_ the descendants of nearby branches.

  240. 240

    Nakashima @239:
    Without going into too much about whales, they all have blowholes and blubber. Somewhere a long the way were creatures with no blowholes and no blubber (and perhaps other features common to all whales.) They wouldn’t be considered whales.
    They must have existed for some time. And yet the only descendants appeared to be whales.
    If dozens of whale species branched off after that point, why are there no living descendants from anything further back in the transition?
    And why does that pattern seem to appear in so many life forms? Even between amphibians, reptiles, and mammals?
    I’m not claiming some great knowledge of taxonomy – I might be wrong on every detail. But widespread variations on a relatively smaller number of classifications strikes me as inconsistent with speciation from a number of gradual transitions.

  241. 241

    Hi Scott,

    I don’t mean to just jump in here, but I’d like to offer some ideas for consideration. First of all, when we look at extant species, there is an interesting pattern: older lineages tend to have less species diversity than younger, more recent lineages. This is primarily due to extinction– the older lineages have had more time for competition and natural selection to take their toll. Secondly, consideration must be given to the number of marine niches available. That is because, as a general rule, a niche is occupied by only one species. Two species can do so usually only for a limited time before one either moves away or becomes extinct, or both species ‘partition’ the niche in some way to avoid directly competing (both species may specialize in non-ovelapping diets, for example). What this means is, without ecological opportunity (i.e, available niches), speciation will not usually occur. So one has to figure out how many actual available niches there are (or were) before expecting how many species of a particular type of organism should have existed. Finally, looking at the fossil record and the conditions required for fossilization, it must always be kept in mind just how few organisms ever get fossilized at all. If we find large numbers of a particular species, that is probably a good indication of just how successful that species was. Less succcessful species (in terms of numbers) may never have been fossilized at all, or are buried in rocks we haven’t seen or to which we have no access. to.

  242. Mr ScottAndrews,

    What you are describing is a statistical effect. As time goes on, chance leads to extinction, and species thin out. The same thing happens with individuals, families go extinct.

    That is why “mitochondrial Eve” is so close to the present, why so many of the bauplans of the Burgess Shale are not around, why so many of the original Dow Jones Industrials no longer exist. The pattern of radiation and extinction is seen over and over.

  243. 243

    Mr. Nakashima,

    It’s entirely possible that the explanation is there and I’m just missing it.
    But when chance leads to extinction and species go out, why do multiple species of whales remain while any speciations from their transitional predecessors do not?
    Those predecessors must have been fit, as they remained long enough to produce the “mitochondrial whale.” What line could be drawn that kills off everything on one side and permits the rest to continue? If it were an environmental anomaly, what explains the repetition of that pattern? The environment permits all sorts of creatures in the sea – why not the variations of those intermediates?
    Thanks for indulging my half-baked question.

  244. Arthur Hunt (#237),

    Fox’s protocells “are able to impose their particular brand of complexity on the relatively simple raw materials they intake”.

    Your comment completely misses the point of my comment, and is arguable incorrect as well. First, protocells do not have a brand of complexity. It could be argued that they have an organization, as they form into rough spheres. It could be argued that they have complexity, as the proteinoids (they are not really proteins, for several reasons) do have multiple parts that are not strictly repeating as the parts of crystals or certain forms of nylon are. But the irrregularly recurring repeats have no overall pattern to which they conform, and thus the proteinoidss, and the protocells, do not have a particular brand of complexity. Not having a particular brand of complexity, they cannot impose it on anything.

    Furthermore, the “raw materials they intake” are not relatively simple. They consist of multiple amino acids linked by peptide and other bonds, and may be hundreds of mers long, with side branching. The protocells simply take these complexes and aggregate them into spheres, with little or no modification. If you wanted to argue that this is a possible first step toward life (not counting the creation, purification, and polymerization of the amino acids themselves), then I might be able to buy it. But arguing that this is a close parallel to what is done by life is a particularly poor example of argument from analogy.

    Not that the debate about what is really living is all of what my argument is about. There seems to be a tenuous agreement that the properties I list, that protocells are observed to possess, are also characteristics seen in living cells. What this means is that a DNA code (or whatever “information” the ID proponent wishes to invoke) is quite unnecessary when it comes to the origination and maintenance of these characteristics.

    Nobody is arguing that “these characteristics” require DNA, or information, or organization. The question is whether DNA, or information, or organization, are necessary for life. You haven’t answered that yet.

    Control is an inherent property of chemistry. For example (one quite apart from all that has been discussed in this thread – it’s just a simple illustration), consider a 4-step series of irreversible first order chemical reactions that leads from A to B to C to D to E. It turns out that, no matter how you change the rate constants of the second and third reactions, you don’t change the overall flux thru the pathway at the steady state. That’s quite exquisite control, a simple and strong robustness that we don’t see in engineered systems.

    You are using “control” in a way that is novel to me. Control means that some entity, usually the organism itself, decides that (or is programmed to act so that) a process happens in a way, in particular at a rate, that is advantageous for the organism. The lack of change in the rate of formation of the end product is the precise opposite of control.

    I’m also having trouble understanding your series of “irreversible” reactions. Most reactions are reversible, and most effectively irreversible reactions are degradative, and the ones that are not are almost always catalyzed by enzymes. Whether enzymes are engineered is precisely what is in question. One cannot use them in contrast to engineered systems without begging the question.

    Perhaps you can give me a specific example of this A to B to C to D to E system so what you mean can be understood better.

    There’s no reason to claim that prebiotic chemistry was without control. We’re talking chemistry, not primitive engineering.

    From an ID point, I agree. What I don’t understand is how you can claim that from a non-ID standpoint. Who or what controlled, and how?

    And that is why it is difficult, and may be impossible, for RNA to be the control molecule. One needs a way of clearly differentiating the backup from the working copy.

    Why? RNA viruses do this just fine.

    Yes, one can use RNA to perform both functions, as long as the need for backup is limited. When one can obtain complex preformed “raw materials” from a cell, such as ribozymes to translate proteins, T-RNA’s, aminoacyl transferases, metabolic intermediates, and all the free ATP one wants, one can use a stripped-down version of information and code it all in RNA which will serve both as the information storage device and the working copy. But when one cannot depend on another cell to produce such things, and the first cell could not, then the problem of preserving information while using it becomes much more complex. Presumably this is why we have not yet discovered cells whose information storage function is performed by RNA. The statement that RNA can do this perfectly well is at present a faith statement against the weight of evidence. If that’s your faith, fine. Just so we’re clear on it.

    Life is about RNA, ribosomal RNA to be specific. This is the central player in the cell – the bulk of the RNA is rRNA, most of the rest “services” rRNA, and the majority of cellular metabolism is geared towards rRNA function. . . .

    That’s a rather parochial attitude. One could just as easily say, “life is about enzymes. RNA is little more than the way the cell produces enzymes.” Or, “life is just about DNA. RNA and enzymes are there simply to protect, reproduce, and service DNA.” In fact, I think I recall someone talking about selfish DNA. Dawkins or something like that. Life is really a whole coordinated package where all the pieces play their part in a master plan.

    I think I told Paul Nelson this fictional anecdote – if a very advanced alien species did a quick fly-by analysis of life on Earth, their conclusion would run along the lines of “well, rRNA sure has found a lot of interesting ways to propagate itself on this planet”.

    I am really impressed. You say that you told Paul Nelson a fictional anecdote? How much more authoritative can you get than that!

    I missed the significance of your last paragraph.

  245. Arthur Hunt (#232),

    Um, the “toddler test” was something that Mike Gene introduced me to. If you don’t like it that this ID tool actually takes one places where one is predetermined never to tread, blame him. Not me, nor our schools.

    I gave reasons why your particular “toddler test” was invalid. You fail to challenge any of those reasons, instead resorting to the claim that Mike Gene uses “toddler tests”, and therefore so can you. If you don’t want to defend against my specific line of reasoning, then at least explain why Mike Gene’s use of the “toddler test” was valid, and why your use paralleled his closely enough so that it is reasonable to consider yours as valid as well.

  246. Arthur Hunt (#233)

    About my essays:

    I looked at his essays. They seem a little short on documented detail.

    I’m sorry. This unsupported assertion is just not true. My essays focus on a few interesting aspects of life, and my claims and conclusions are supported by reference to actual experimentation. (I’ll admit that one may have to follow a trail through several essays. But laziness is no reason to misrepresent things so.)

    Okay, then I’ll support my assertion. In particular, your comments on the protocell mention Nakashima, and didn’t have any other references. And most of the assertions don’t even claim that Nakashima supported them. I think that qualifies as “a little short on documented detail.”

    Now, if I had said “undocumentable detail”, or “false detail”, you might have had reason to complain. You may or may not be able to support your claims from the literature, and it would be unfair of me to claim that you could not without knowing all of the literature. But when I read that particular work, I could have done just as well, and possibly better, simply by reading Nakashima, as your synthesis as presented looks like Nakashima warmed over. In that case, why not simply link to Nakashima rather than your own essay, other than self-aggrandizement?

    This scorn for others, the “look it up yourself and I’m not telling you where I found it, and if you object you’re just lazy” attitude, is not calculated to actually persuade those who may disagree with you at present but are open. It would be much more helpful if you were clearer about what authority stands behind your statements.

    This gets into the philosophy of science. Science usually claims that there is no pope, or college of cardinals, who can discover scientific truth infallibly, and that the only true authorities are experience, including controlled experience, otherwise known as experiments, and logical inferences from the data produced by those experiences. Neither one of these sources are in principle reducible to personal authority. This is in contrast to a political authority, where what the king, or the president, or the judge, says, or the Congress votes, goes, and the less challengeable the decision is, the greater the political authority.

    There are authorities in science. But they are authorities precisely because, and to the extent that, they transmit data accurately and their logic is transparent. Anyone who claims authority in science because “I have studied the situation carefully and I say . . .” is abusing his or her authority. That means that if you want to be truly a scientific authority, and have us take your essays seriously, you will be clear on where you got your data (unless they are commonly known, in which case if someone does not know them you can still show where they came from), and your argumentation will be clear as to how you are using the data and the legitimacy of your inferences. Outside of this kind of support, nothing you say (or I or anyone else says) has any kind of legitimate authority.

    That means that having to follow a trail through several essays, especially unmarked essays, to understand your support is a defect, not an excuse to blame others for laziness. Be careful here, or this could turn out to be projection on your part.

  247. Hi Dave,

    In #237 you clarify that you did mean beginning in the way with which I disagreed. It looks like this is another area where we disagree. I can live with that.

    In #238 you argue that there is no such thing as an edge to evolution. Perhaps you misunderstand. The argument is not so much that anything is off limits to evolution given enough time and enough organisms. Rather, the argument is that probabilistic resources make certain transformations for practical purposes impossible given time and population constraints.

    You actually agree with this, even though you may not recognize it. If you take a Petri dish with E. coli and put it under a hood, and come back the next morning and find a cockroach crawling in it, you do not hypothesize that the cockroach evolved from the E. coli overnight. You assume that it must have gotten in from the outside somehow. In fact, if you started with E. coli, and the next morning you have Serratia marcescens, you assume that someone switched plates. That is, you believe in an edge to evolution also. The disagreement is not over whether an edge exists. The disagreement is over what it is.

    And the argument about environmental influence is a smokescreen. One can postulate all environments, or all reasonable environments, and find the maximum expected variation, and that would constitute the edge of evolution. We could be fooled into thinking that the edge is smaller than it is by failing to take the environment into account. But that does not demonstrate that the limit does not exist, or that attempting to find it is, ” in the end, a pointless arbitrary exercise.”

    That way of arguing seems anti-scientific, of the same kind that ID adherents are accused of when they suggest that attempts to find a naturalistic origin of life may be ultimately fruitless. Only this time there may be more justification in the charge.

  248. Whoops! In #244, I should have referred to #231 rather than #237.

  249. 249

    Paul,

    Actually, my point was, determining this “edge of evolution” using Behe’s criteria is arbitrary and pointless. I’m not saying a limit to what evolution can do does not exist. That one exists is intuitively obvious: the paths evolution takes in lineages is primarily determined by historical contingency, that is, the adaptive challenges and how they were solved in the past often limit what future changes in the lineages can be. Some can be irreversible: highly specialized coadaption, as we see in some plant species and their animal pollinators. So, deriving a general limit when so many variables haven’t even been considered makes it arbitrary and pointless, though you may not realize it.

    And the argument about environmental influence is a smokescreen. One can postulate all environments, or all reasonable environments, and find the maximum expected variation, and that would constitute the edge of evolution. We could be fooled into thinking that the edge is smaller than it is by failing to take the environment into account. But that does not demonstrate that the limit does not exist, or that attempting to find it is, ” in the end, a pointless arbitrary exercise.”

    Again, jumping to a general conclusion without taking the time and effort to actually consider such vital variables is arbitrary and pointless.

  250. 250

    Dave Wisker:

    So, deriving a general limit when so many variables haven’t even been considered makes it arbitrary and pointless, though you may not realize it.

    If the lack of specific information available precludes understanding the limitations of evolution, wouldn’t it also preclude understanding its capabilities? If we haven’t considered the variables, isn’t it also arbitrary and pointless to conclude what natural evolution can accomplish?

  251. 251

    Paul,

    To clarify a bit more, I my original point was that “establishing” a general limit is arbitrary and pointless, mainly because much of what limits a particular lineages is due to unique circumstances. We might be able to attempt establishing what we may or may not expect a particular lineage will be able to accomplish in terms of adaptations, and even come to some broad conclusions. For example, we might be able to predict the fate of an orchid pollinated only by a species of hawkmoth with an extremely long proboscis if the hawkmoth suddenly becomes extinct. If the range of variation in the width and length of the nectary isn’t enough to attract and allow another insect or bird access, then the fate of the plant may very well follow the moth.

    There are some interesting examples of plant species today that may have depended on the Pleistocene megafauna to disperse their seed, and which now face an uncertain future since the extinction of those animals. An interesting popular book on the subject is The Ghosts of Evolution by Connie Barlow. Obviously, for these plants, the limits to what they can do are different from those plants who don’t specialize. In addition, for plants who don’t specialize, they present challenges to the different organisms that must compete for the fruit or nectar, adding even more variables to consider when establishing limits for them.

    The challenge to establishing a general limit are enormous, but maybe not insurmountable, given enough paleoecological, current ecological, and genetic research, and especially with a very broad base of data from many taxa. I don’t see anybody even approaching that depth of research and analysis yet. And there is always the question, “how much is enough?”, coupled with “what exactly does a ‘general limit’ tell us” To be honest, I don’t know the ultimate answer to either one. But I’m pretty sure (for the above reasons) it will take far more than what I’ve seen presented by Behe.

  252. 252

    Hi Scott,

    If the lack of specific information available precludes understanding the limitations of evolution, wouldn’t it also preclude understanding its capabilities? If we haven’t considered the variables, isn’t it also arbitrary and pointless to conclude what natural evolution can accomplish?

    Scott, we actually know quite a bit what evolution can and cannot accomplish (see my examples as just a small subset of what we do know). Coming to very general conclusions– as in setting some overall limit, or declaring there is no limit at all– is pointless and arbitrary if one has not considered the variables involved.

    Many topics of current evolutionary research (a simple browsing of some journals like Evolution or Molecular Ecology will show you) involve establishing just what limits evolution in populations. How much variation does the subject population possess? How much of a role does natural selection vs genetic drift take in influencing gene frequencies? What about landscape features, mating strategies, levels of intra-and inter species competition, geology, etc?

    On the other hand, we have a growing evidence base for the generation of variation, and how little genetic change can produce dramatic phenotypic change. We also see how much variation can be generated by mobile genetic elements (such as retrotransposons). Just browse a few issues of the journal Molecular Biology and Evolution for a tiny fraction of the work being done on that front. Or consider the variation that can occur in “promiscuous” proteins, that is, proteins with additional activity and functions that can absorb many mutations without affecting the primary function of the protein. Mutations affecting these promiscuous functions have been observed to generate novel functionality. The bottom line is, we are seeing more and more evidence for sources of variation. Additional sources of variation only increase the capabilities of evolution, in my view. Does it make the capabilities endless? No, I don’t think so. But it certainly damages the arguments I’ve seen trying to establish a general limit.

  253. 253

    Dave Wisker:

    How much variation does the subject population possess? How much of a role does natural selection vs genetic drift take in influencing gene frequencies? What about landscape features, mating strategies, levels of intra-and inter species competition, geology, etc?

    What strikes me as odd is that one reading such factors listed might conclude that their effect on major evolutionary changes had been observed and documented. In fact, when looking at fossils, we can only guess at what effect the landscape or competition may have had. There isn’t any real observation that we could apply to any forward speculation.

  254. 254

    Scott,

    What strikes me more odd, is that one can observe all of these factors in extant populations, and somehow assume, just because we can’t observe the actual factors at work in the fossil populations, that they didn’t apply then.

    Must we assume they had different genetics? That mutaions occurred any more or less different,y than they do today? That they didn’t sexually reproduce? That they didn’t have ancestors or leave descendants? That they didn’t have to adapt to environmental changes?

    This is selective hyperskepticism, in my opinion.

  255. 255

    Dave Wisker @254:

    What strikes me more odd, is that one can observe all of these factors in extant populations, and somehow assume, just because we can’t observe the actual factors at work in the fossil populations, that they didn’t apply then.

    There are no observations of macroevolution resulting from landscape changes or competition. So when you use such factors to explain past evolution, it’s a guess. And to list those factors and then use expressions like “expected variation” is a bit ridiculous.
    Refusing to accept a guess as fact is not hyperskepticism.

  256. 256

    Scott,

    We have plenty of observed evidence from numerous taxa that even large morphological changes are possible by very few corresponding genetic changes. We have extensive evidence that landscape (i.e., ecological) and competive forces change the gentic structure of populations and, coupled with reproductive isolation, result in divergence and increased diversity. There is no good scientific reason to deny inferring that the capabilities for variation and forces rthat mold it occurred to organisms in the past. An educated inference is not a guess. And to deny that such an inference can be reasonably made suggest two things:

    1) That the body of evidence we see in extant populations is anadequate to explain the diversity of life, and thus

    2) Other mechanisms and forces were involved.

    You seem completely comfortable with 1) & 2), despite the fact that actual empirical evidence supporting either one is almost negligible.

    I think that more than qualifies selective hyperskepticism on your part.

  257. Mr ScottAndrews,

    It’s entirely possible that the explanation is there and I’m just missing it.
    But when chance leads to extinction and species go out, why do multiple species of whales remain while any speciations from their transitional predecessors do not?

    I think this issue is developed nicely at the end of Gould’s Wonderful Life. There he is treating it at the level of entire taxa, but the form of the argument is the same.

    I will try to catch up with the thread!

  258. Mr Wisker,

    Did you really like Barlow’s Ghosts of Evolution? I liked the exposition of the material on the megafauna and the relationship plants can have with animals to accomplish seed dispersal. Even the work on how modern animals introduced by humans (cattle and pigs) could substitute for extinct species. But a lot of the intervening material about ghosts seemed to go to far to be just literary affect. And it got boring.

  259. 259

    Mr Nakashima,

    I liked it for the exact same reasons you did.

  260. 260

    Dave Wisker:

    There is no good scientific reason to deny inferring that the capabilities for variation and forces rthat mold it occurred to organisms in the past.

    What you are describing is not an inference, but an extrapolation. We all know that small things don’t always scale. You can’t build the Empire State Building out of Legos. You assume that microevolution scales, but how could you possibly know that? What is your test?
    Add that to the uncertainty over which mechanisms may or may not effect such changes and there’s not much left to be hyperskeptical about. I respect everyone’s right to put faith in whatever they wish.

  261. 261

    Scott,

    An extrapolation is an inference.

  262. 262

    Dave,

    Zing! You got me. That’s a nice diversion from the question of how we know that microevolution scales to macroevolution.
    How does one test if A scales to B, when one has never seen B, and one isn’t even sure what A is made of?
    That’s why I derive amusement from paragraphs that describe how factor X and factor Y are likely to cause evolutionary effect Z, unless mitigated by circumstance Q. Someone reading them might think they are drawn from repeated observations. They would never guess that it’s all speculation extrapolated from instances of microevolution.
    Your inference is so weak it can only loosely be called such.

  263. Mr ScottAndrews,

    i’m not trying to begin a definitional red herring with this question, but what are you holding to as a definition of macro-evolution?

    Micro-evolution doesn’t scale to macro-evolution in the sense that one day a jellyfish gives birth to a lobster. There is only speciation, happening further and further in the past. We’ve talked recently on several threads about speciation, whether from reporoductive isolation, or from small genetic changes leading to larger phenotypical changes.

  264. 264

    Nakashima,

    I’m glad, because I couldn’t be that precise. Macroevolution, as I understand it, means that all birds are descended from something that was not a bird. Or that the giraffe, with all its physiology enabling it to survive with a long neck, had as its ancestor a creature with neither the a long neck nor the giraffe’s vascular system.
    Rather than harp on my own disbelief that microevolutionary changes add up to such distinctions over time, I’ll just point out that extrapolation is only hypothetical. No one knows if lots of A gets us B.

  265. 265

    After an unexpected and long delay, I have returned to answer a claim that was made earlier in this thread.

    To recap: I had made the comment that the genetic code was “physically inert”. Mr. Hunt chimed in with the familiar refrain that stereochemistry provided a reason to believe otherwise. He stated there “is a decided and demonstrable chemical basis for this code”. To which I replied that there was an overwhelming amount of information which “fundamentally dispute(s)” his claim, and also, that the “nature of the patterns within nucleic sequencing did not come about because it physically had to.” He then replied that “Nothing has to occur. But it is hard to make an evidence-based argument that the genetic code is entirely arbitrary and disconnected from the chemical properties of RNA.”

    I know the conversation has moved on, and I see that Paul Giem, KF, and others have responded to the issues, but I would like to reply anyway.

    Mr. Hunt, the bottom line of your position equates to the inevitability of life existing in an environment such as that provided by the Earth (which by the way, exists in a scientifically inexplicable Universe). You seem certain of this because you are just as certain that Life is a property of matter itself. Apparently Life is inevitable because (given enough time in the right environment) the matter that makes up living things will become functionally organized into living things by means of the containment and transfer of symbolic information (which is what we observe today). Your explanation will never vary from what can be explained by the properties of matter, along with the influence of chance. In other words, it would happen anyway.

    Your position is an unjustifiable abrogation of empirical evidence (as has been pointed out).

    In questions such as these, science and scientist have a public obligation to speak within respectfully modest boundaries as to what is actually known. Suggesting that stereochemistry supports the idea that Life is an inherent and inevitable chemical property of matter (acted upon by chance) is a suggestion that flies in the face of reason (and a mountain of contrary evidence).

    Such claims are based on prior assumptions which are ideologically motivated at their core. They are not a manifest part of the institution of (S)cience itself. The fact that (S)cience allows, and indeed perpetuates, such misleading public claims is an indictment of an institution that is ignoring its responsibilities in the same way it ignores the contrary evidence. Stereochemistry has absolutely nothing to do with the actual sequencing of the nucleic acids in DNA. Why? Because it provides no explaination along the linear axis of nucleic sequencing (where the information and organization is).

    But we need not dottle over science shucking its public responsibilities; we can just address your claim instead.

    You say “nothing has to occur”. I don’t wish to take any big issue with this statement; however it is completely and utterly wrong. The fact that things must occur is the bedrock foundation of empirical science. We rely on it. A dropped apple must fall to the ground on earth, starlight must bend around the sun, and Miller-Urey must create amino acids. To suggest anything different is to instantly remove our ability to know anything at all.

    You then say “it is hard to make an evidence-based argument that the genetic code is entirely arbitrary and disconnected from the chemical properties of RNA.”

    What I find interesting in this sentence is the choice of the words “entirely arbitrary”. No one is suggesting that the genetic code is somehow divorced from the physics that underlies its function in biology – no more than anyone is suggesting that the radial tires on your car are entirely arbitrary and disconnected from the chemical properties of rubber. Why should we make radial tires out of water, or light bulbs out of peat moss?

    What stereochemistry tells us is that the design (strongly inferred by the ignored but logical evidence of agency involvement) appropriately works with its constituent parts – however, that fact does not negate the evidence of agency involvement (no more than the properties of rubber lends doubt as to where radial tires come from).

    I am tickled to death that there are men and women who make it their concern to study stereochemistry and its associated studies, but the suggestion that the findings explain the source of the genetic algorithms and organization inherent in living systems is so far off the mark it does little more than illuminate how ideological assumptions can pollute the claims made by science.

  266. Mr ScottAndrews,

    If I live in Tokyo, I can walk across my apartment, I can walk across town, I can walk to Mt Fuji. I can walk up Mt Fuji. I can walk to Hiroshima. I can Google hundreds of pictures of people walking between those places. So even if I haven’t personally walked all the way to Fuji-san, I can extrapolate based on evidence that it is possible.

    If you want to have a fuller discussion of macro-evolution and speciation there are some good online resources, even books such as Levinton’s Genetics, Paleontology, and Macroevolution, 2nd Edition.

  267. 267

    Mr. Nakashima:
    It’s easy to follow that we can infer one possibility from a very similar possibility. But that’s not what we’re talking about.
    Rather than waste time on an elaborate analogy, a better comparison is this: If you can walk to Hiroshima, can you extrapolate that one could walk to any place where people have ever been, and beyond?
    I’m not saying it’s a pointless hypothesis. But it’s up in the air. It is nowhere near to being established.

  268. Mr ScottAndrews,

    Yes, that is why i said i had Googled all those pictures. I was pretty confident I could get to Hiroshima on that basis. The pictures are analogy to the fossils we have been talking about. I have no evidence I can walk to the Moon, or even San Francisco. So I don’t think I can. ;)

  269. Dave (#249, #251),

    It looks like we agree that there is an edge beyond which evolution cannot reasonably be expected to go (I suspect that we agree that the edge moves with time, and varies somewhat depending on the environment). That means that the underlying premise behind Behe’s attempt to find an edge is valid; there is an edge somewhere.

    You seem to strongly disagree with Behe’s attempt to find an edge. For reasons we discussed, it can’t be that an edge doesn’t exist. So with what in his strategy and/or tactics do you disagree? I’m not necessarily trying to defend him (although, if it seems to me that he is right on a point, I will), but primarily trying to understand why you think his procedure is “arbitrary and pointless.”

    One point that, IMO, needs to be considered is that the limit that Behe sees is not primarily a problem with natural selection. It is a problem of how fast mutations can create the genetic code for a given structure if there is no natural selection for the intermediate steps, or if the intermediate steps are selected against. In other words, the problem limiting the speed of evolution is not so much what mutations can do assisted at each step by natural selection, as what it can do without the assistance of natural selection.

    I can think of three reasonable ways to attack Behe’s theory for where the edge of evolution is located. First is to show that his calculations are off given his premises. One is to show that his premises are faulty, for example by showing that there are no pathways that require long strings of non-selected or deleterious mutations. And one is to show that experimentally we can routinely exceed what he says is the edge, in terms of neutral or deleterious mutations.

    I gather that you are not particularly challenging the calculations themselves. So the challenge has to be to the premises, either theoretically or experimentally.

    It is important to note what is not a legitimate challenge. It is not legitimate to say that natural history demonstrates that evolution has progressed much faster than Behe’s proposed edge, and that therefore he has to have made some mistake. That argument can only be made with the assumption that no design input happened at any stage, and that therefore earth history is a natural experiment demonstrating that Behe is wrong.

    That argument begs the question. The whole point of intelligent design is that we see in nature things that are inexplicable on the basis of natural law and chance and their various combinations alone, that are explicable if there is a designer. Evidence that experimental evolution is not as fast as natural history requires is evidence for some other kind of process, which could be directed intervention. The only way one can trump this evidence is to assume, on a theological basis, that either there cannot be a God, or that God would never act in nature except in accordance to laws which are impersonal and which we understand. Those are theological positions.

    (One must also assume that intelligent aliens are not an option. But while the ID position may not necessarily entail a pro-God position, the anti-ID position necessarily entails an anti-interventionist-God position.)

    I assume, since previously you have allowed for ID as a theoretical possibility, you are not prepared to give a challenge of the sort that “evolution has been demonstrated to work much faster in the fossil record than Behe’s edge, so he must be wrong somehow.” So do you have experimental evidence that he is wrong, or do you find that in multiple cases his premises are wrong, specifically with regard to the need for neutral or deleterious mutations in a given pathway, or do you live by faith that one or both of these will happen without having proof yet?

  270. 270

    Hi Paul,

    Just a note to say I haven’t forgotten our discussion, just haven’t had time to work on it. Probably this weekend.

  271. 271

    Hi Paul,

    I’m going to be addressing Behe’s book (which I own and have read, btw) in stages.

    It looks like we agree that there is an edge beyond which evolution
    cannot reasonably be expected to go (I suspect that we agree that the edge
    moves with time, and varies somewhat depending on the environment).

    Actually, it varies a lot depending on both the environment and amount of
    variation and potential variation possessed by the population in question.
    It is therefore highly contextual.

    That means that the underlying premise behind Behe’s attempt to find
    an edge is valid; there is an edge somewhere.

    I think it is far more fruitful to look for an ‘edge’, if you want to
    call it that (though I think everyone here knows what is really meant by ‘edge’ is ‘limit’) on a case by case basis.

    You seem to strongly disagree with Behe’s attempt to find an edge. For
    reasons we discussed, it can’t be that an edge doesn’t exist.

    For reasons we have discussed, it is clear that any limits are dependent
    on a lot of variables.For instance, how much variation does the population possess at the outset? What is the mutation rate? How much variation is generated by recombination? What is the strength of selection for the adaptive problem at hand? Is the adaptive value of the genotype in question constant or variable? And that is just for one population. If one were trying to establish some general limit, given the large number of variables, then it seems reasonable to examine limits over a wide variety of taxa,environments,and adaptive problems. That, unfortunately, is not what Behe has done.


    with what in his strategy and/or tactics do you disagree? I’m not
    necessarily trying to defend him (although, if it seems to me that he is
    right on a point, I will), but primarily trying to understand why you think
    his procedure is “arbitrary and pointless .

    One point that, IMO, needs to be considered is that the limit that Behe
    sees is not primarily a problem with natural selection. It is a problem of how fast mutations can create the genetic code for a given structure if there
    is no natural selection for the intermediate steps, or if the intermediate
    steps are selected against. In other words, the problem limiting the speed
    of evolution is not so much what mutations can do assisted at each step by
    natural selection, as what it can do without the assistance of natural
    selection.

    Behe is looking only at the limits on multiple mutations occurring simultaneously to solve a particular adaptive problem. We know this because the example from which he derives his limit is one of an extremely harsh selective regime. Under the selective pressure of chloroquine, the only way an
    organism can adapt is for both required mutations to occur at once: any organisms that possess only one of them are eliminated. The adaptation cannot, therefore, occur in steps.

    So, can we derive any general principles about evolution from Behe’s example? Well, the most pertinent question is, are most selective regimes in nature as harsh as this? Do most of the adaptive problems in nature require multiple specific mutations to occur simultaneously in one step? If the answer is “no”, then all Behe has done is find a limit for a very small subset of the kinds of adaptive problems organisms face. Literature on the strength of natural selection in the wild tells us that the strength of selection can vary widely, with very harsh regimes such as chloroquine being on the extreme end of the distribution. So Behe’s limit is inapplicable to most situations in nature. That would rule it out as some metric by which to judge evolution in general, in my opinion.

    I’ll comment later on other aspects of Behe’s book.

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