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A Simple Gene Origination Calculation

In this month’s Nature Genetics, there is an article by Zhou, et. al., dealing with the generation of new genes in Drosophila melanogaster—the fruit fly. While only having access to the abstract, I nonetheless was struck by one of their findings: the rate of new functional gene generation. As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

Here’s the link to the abstract.

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218 Responses to A Simple Gene Origination Calculation

  1. 1

    Heh, this should create a little PANDA-moanium.

  2. While I wish I could read the paper in it’s entirety, I must admit that the conclusion they came to is a little disturbing… though it depends on what your prior philosophical commitments are on the origin of life as we know it today.

  3. They make it sound so simple. I wonder how many dead flies had to die before the genome was fully functional.

    Jackanory.

  4. Amazing coincidence, PaV. I was asking myself just a couple hours ago how many new functional genes come from duplicates of other genes and how many are de novo. (I think it was Michael Behe who criticized Kenneth Miller for overemphasizing the role of duplication. But if 44% percent of the new genes shared by Drosophila species arose by duplication, wouldn’t the percentage for a single species be higher?) I still wonder exactly how de novo formation works. And what is a non-functional gene? Does that mean it doesn’t yield a product, or does it mean that the product does not serve a function in the proteome? Does mutation sometimes turn non-functional genes into functional ones?

    Is there a geneticist in the house?

    F2XL, is your problem here that the abstract says indirectly that there are in fact non-coding regions in the genome that don’t serve a function? After all, turning a functional non-gene region into a gene would stop that region from serving its prior function. Are you concerned that this does not jibe with genetic entropy?

    Didn’t Dr. Dembski argue in “Searching Large Spaces” and other writings that even one de novo functional gene is very unlikely to be discovered by random search? Or did he say that base-pair sequences he specified as a target were very unlikely to be hit? The abstract seems to address formation of any new genes that do something, not just genes that do what the researchers had in mind before looking at the genome. Isn’t this a much bigger target than Dr. Dembski considered?

  5. 5
    PannenbergOmega

    Doesn’t this paper’s findings seems to support Darwinian theory?

  6. PO: Current Darwinian thought suggests that so-called ‘gene conversion’ is the process/mechanism by which speciation can occur, and, presumably, up to macroevolutionary changes. However, this mechanism presupposes that duplicated genes have no function, and are therefore free to neutrally evolve–something which is now being questioned since psuedogenes have been found to be involved in gene regulation. Again, without having access to the entire paper, the critical phrase seems to be ‘new function’: that is, the authors are not just talking about the rate of gene duplication, but the rate at which these new genes develop a new function. My ‘simple’ calculation based on this rate points out that the rate which they measure is entirely too slow to account for major taxonomic change—macroevolution.

  7. PannenbergOmega:

    Doesn’t this paper’s findings seems to support Darwinian theory?

    The question is not ID vs. Darwin, the question is to what extent did the designer use the darwinian model — or as Behe so aptly put it, where is the edge of evolution?

    There are two IDish things that glare out of this document.

    1 – If this study establishes a base-line rate (which assumes no agency in the development of the fruitfly) then how did man get to be so genetically different from monkeys?

    2 – The 11.9% De Novo genes, are these statistically reasonable, or are these scratch-marks from the designer’s tools; ie, evidence of agency?

  8. 8
    matthew_ackerman

    This was covered in a commentary on the paper over at PT. (http://pandasthumb.org/archive.....l#comments)

    PaV is confusing various types of genetic change. There simply aren’t thousands of genes that humans have and chimpanzees lack.

    Although PaV doesn’t site a specific study, I suspect he is referring to the number of genes which aren’t EXACTLY the same in humans and chips. Differences between two homologous gene sequence often arise from a single mutation event and usually ave no affect on an organism at all.

    By contrast the drosophila study is measuring the rate of gene origin through a specific mechanism. Creating an entire gene takes significantly longer than making a small change to an existing gene.

    By way of analogy PaV has found out the price of a gallon of water, filled up his car w/ 20 gallons of gas, and is now offering the clerk 2 dollars. This won’t work, because the price of a gallon of water isn’t the price of all other gallons of all liquids.

    I’m surprised that such a simple and obvious error which has been corrected else where is of much interest to anyone.

  9. The implications of this are awesome, and thus they will be entirely and predictably ignored by the Darwinian priesthood. It’s a very big problem not only for the putative hominid evolution line, but for primate and hominoid evolution across the board in all families. It’s worse than that of course (for Darwinians at least) -it’s a problem across the animal kingdom, and most obviously with mammalian evolution in all orders.

    Goes to show just how overly generous Remine is being to the Darwinians in his appraisal of Haldane’s Dilemma. And even with the dice loaded in their favour, they are flummoxed.

  10. Just one minor quibble with this blog entry (or perhaps major). Darwin’s theory of evolution does not claim that man evolved from the monkey. It claims that man and monkeys both evolved from a common ancestor which no longer exists. So the observation about how long it would take for man to evolve from the monkey is not relevant to the discussion.

  11. Is a simple mathematical extrapolation of data obtained from an abstract really worthy of posting at Uncommon Descent?

    This seems to be the intellectual equivalent of doing a movie review based on a trailer.

    I wish people would stop using religious terminology (zephr) to insult Darwinists. Does that not reflect badly on religion?

    Does calling atheism a “religion” really hurt atheism or does it hurt religion even more by associating the negative connotations of atheism with it?

    The idea of a “Darwinian priesthood” is asinine. Who are you trying to insult here? Darwinists or priests?

    I’m sorry but some of you people really need to think about what you’re saying and not just fly off the handle trying to insult atheists and Darwinists. It is more likely to hurt your cause than help it.

  12. Off Topic: ID skeptic D’Souza rebuts Dawkins following Al Jazeera “debate”: http://townhall.com/columnists.....al-jazeera

  13. PaV, thank you for sending me off to read about pseudogenes. As I understand it, a pseudogene is a DNA sequence that looks much like a known gene but does not function as a gene. Do you suppose a gene is called de novo if it isn’t a good match for any other known gene in the Drosophila species group? What I’m guessing is that all new genes not considered de novo arose through mutation of existing genes (changing function) or mutation of pseudogenes (introducing gene function). Does that make sense?

    Biologists say that the rate of evolutionary innovation differs considerably from one species to the next. Would you please explain your rationale for extending the observed rate of appearance of new genes in a particular species subgroup to quite a different species?

    I’m guessing that a small genetic change may yield a crucial first step into a new (maybe extended) niche. There may be many payoffs for genetic change in the new niche that are not available in the old niche. My un-expert hunch is that the rate of gene formation is related to the time a type has occupied its niche. This leads me to ask how long fruit flies have occupied their niche(s)?

    Many people know that the rate of genetic change in humans is high. Relatively few know that it is also high in chimps (which are apes, not monkeys).

  14. Again I ask, is there a geneticist in the house?

    I used to have a reminder taped to the monitor of the computer I programmed: “Don’t guess!” It takes less time to look up the answer to something you’re not sure about or to write a little test program to see how things actually work than to guess and straighten things out later with debugging.

    I feel kind of bad about guessing in my comments. I’m not lazy. The problem is that it takes some knowledge of a field to look up answers to questions in the field. I hope someone knowledgeable will point me in the right direction.

  15. jdmack, we are not children here. We all actually understand the concept of the common ancestor.

    matthew_ackerman, it is my understanding that the latest count of genes unique to humans, and without apparent source (de novo) is around 50. (I read that on this blog or at TT recently, but don’t have a citation.) 50 de novo genes in no more than 5 million years is a pretty good pace. Especially, consider that the lineage between man and CA probably had a generation rate of about 10 years, where the fruit fly’s generation rate is a few days.
    1 – We’ve been evolving at quite a clip.
    2 – Even the fruit fly’s rate of development of de novo genes seems awfully fast. I question whether its pace can be supported by statistical analysis.

  16. The Zhou et al. abstract was discussed at the Panda’s Thumb on June 25. Some people there were concerned about the low rate of appearance of new genes. But according to biologist Ian Musgrave, who seems to have dug into Haldane’s Dilemma, there are no known de novo genes when chimps and humans are compared. See his comment for the explanation of what the differences are.

    This also led me to Recent acceleration of human adaptive evolution, which appeared in the Proceedings of the National Academy of Sciences in December 2007. This is an extraordinary case where you not only get full-text for free, but can read an accessible explanation by the lead author, paleoanthropologist John Hawks.

    Our evolution has recently accelerated by around 100-fold. And that’s exactly what we would expect from the enormous growth of our population.

    His prefatory remarks make me feel not too dumb with my guessing and questioning above.

    [A] very small fraction of the mutations in any given population will be advantageous. And the longer a population has existed, the more likely it will be close to its adaptive optimum — the point at which positively selected mutations don’t happen because there is no possible improvement. This is the most likely explanation for why very large species in nature don’t always evolve rapidly.

    Instead, it is when a new environment is imposed that natural populations respond. And when the environment changes, larger populations have an intrinsic advantage, as Fisher showed, because they have a faster potential response by new mutations.

    From that standpoint, the ecological changes documented in human history and the archaeological record create an exceptional situation. Humans faced new selective pressures during the last 40,000 years, related to disease, agricultural diets, sedentism, city life, greater lifespan, and many other ecological changes. This created a need for selection.

    Larger population sizes allowed the rapid response to selection — more new adaptive mutations. Together, the the two patterns of historical change have placed humans far from an equilibrium. In that case, we expect that the pace of genetic change due to positive selection should recently have been radically higher than at other times in human evolution.

  17. By the way, don’t discount the Hawks et al. article out of hand because of the fluffiness of what I cut and pasted from Hawks’ blog. They actually began by making predictions based on genetic theory, and then analyzed a large amount of genetic data. They tested their claim that human adaptive evolution has accelerated against a null hypothesis, and clearly rejected the null.

  18. CEC09: (#4):

    I believe that a “non-functional” gene is one that is known to be transcribed—that is, m-RNA is being formed, but for which no active protein function is known to exist. So, as you allude, it’s gene product is not part of the proteome.

    M_ackerman: (#8):

    Here is a citation from a Scientific American article from two years ago: “The group estimated that humans have acquired 689 new gene duplicates and lost 86 since diverging from our common ancestor with chimps six million years ago. Similarly, they reckoned that chimps have lost 729 gene copies that humans still have.”

    This isn’t the one or two a.a. differences between primates and mankind’s genes. These are new, functional genes, present in the human genome, and nowhere to be found in the chimpanzee genome. New calculation: 689/~8 newly functional gene duplicates/million years= 86 million years.

    jdmack (#10): It is estimated that humans and chimps diverged 6 million years ago. That means that their LKCA lived 6 million years ago. I just calculated 86 million years as the needed time to account for the gene difference between apes and man. Obviously the rate published by Zhou, et. al. is problematic for Darwinists when it results in this kind of calculation.

    Dave1968: (#11):

    “Is a simple mathematical extrapolation of data obtained from an abstract really worthy of posting at Uncommon Descent?”

    It is when such a simple mathematical calculation doesn’t jive with what is known to have happened.

    The whole gene duplication process, and de novo gene origination, is/are a process/es that are not fully understood. And if part of this/these process/es involve non-coding DNA, then we might be dealing with a mechanism that has very little to do with chance, and little to do with true novelty. In the meantime, prescinding from this kind of critical view, the numbers simply don’t work! That’s worth pointing out—even if it causes Darwinists to cringe.

    CEC09: I’ll take a look at what Ian Musgrave has to say, but let’s be realistic: just because Musgrave says there are no de novo genes separating apes and mankind, that doesn’t mean he’s right, or that his reasoning is right. Secondly, it is one thing for mutations to occur within genes themselves; it’s an entirely different thing to have ‘new genes’ develop since new genes involve such a great increase in information, information coding for possibly hundreds of amino acids, and not just one or two amino acids here and there.

  19. CEC09: From what I can see, in asserting that there are no de novo gene differences between apes and humans, Ian Musgrave seems to be giving us no more than his opinion.

    Notice this: the authors of the paper under discussion were working with species of fruit flies. How did they arrive at a figure for 5-11 million years for a functionally new gene to appear unless they found differences between various species of the fruit fly? Should we thus conclude that whereas species of fruit flies are separated by whole genes either being present or not, this isn’t the case when it comes to apes and men. Does this sound reasonable at all?

  20. jdmack, (10)

    You said,

    Darwin’s theory of evolution does not claim that man evolved from the monkey. It claims that man and monkeys both evolved from a common ancestor which no longer exists. So the observation about how long it would take for man to evolve from the monkey is not relevant to the discussion.

    It is true that standard evolutionary theory assumes that chimpanzees and humans (or monkeys and humans, for that matter) descended from a common ancestor which was not a modern chimpanzee. However, until the ancestor is found, it remains hypothetical, and the ancestor could be essentially a modern chimpanzee, or the ancestor, the modern chimpanzee, and the modern human could be genetically equidistant.

    Even in the best-case scenario, where the ancestor is genetically precisely between modern chimpanzees and modern humans, the genetic distance between modern humans and the ancestor would still be half of that between modern humans and modern chimpanzees. Thus, the statement that “the observation about how long it would take for man to evolve from the monkey is not relevant to the discussion” is incorrect even if we replace “monkey” with “chimpanzee”. The observation does not eliminate the problem; it only decreases its magnitude by half at the most.

    This objection reminds me of the claim that calculations cannot be made regarding the origin of life. Those making such a claim are simply trying to keep anyone from even attempting a calculation. They know that if such a calculation is attempted, their theory will appear ridiculous. Thus the spin that this area of science is beyond calculation. I guess that in these areas of science, only just-so stories are acceptable.

  21. 21

    “They know that if such a calculation is attempted, their theory will appear ridiculous.”

    Given appropriate assumptions, one can make any theory look ridiculous.

  22. Mr King:

    First, kindly inform us as to how calculations such as those summarised here are premised on dubious assumptions.

    Next, let us look at PaV’s deductions above, as a back- of- the- envelope style, order of magnitude estimate:

    As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

    Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 [NB: 8 is mid-point to [5, 11]] new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

    So, kindly explain: where are the dubious assumptions in the above, and why are they dubious?

    GEM of TKI

  23. Nitpicking “monkey” is nothing more than pedantry. Monkey in the context of ancestor to man is a simple, recognizable, one-word term used to describe a common primate ancestor. Given artists’ renderings of what these primate ancestors looked like “monkey” doesn’t seem to be particularly inaccurate. Ape-like might be a better term but who knows – the appearance of these creatures is an imaginary extrapolation from tiny bone fragments and the actual ancestry is no more than an educated guess based on age, location, and perceived similarity of bone fragments.

  24. PaV, I believe that de novo genes are genes that are not modifications of pre-existing genes. For instance, a duplication could make an additional gene, but it would not be de novo. There are a variety of patterns — insertions, reversals, etc., which make new genes, but genes that are not de novo. If some non-coding “junk” DNA suddenly got incorporated as a working gene (not infeasible, it just needs a mutation to make a start marker, and it needs to make some functional sense) then we would have a de novo gene.

    However, this article says that in fruit flies about 11% of the new genes are of the de novo variety. If humans have 689 new genes, the fruit fly experience would imply that we have about 75 de novo genes. Other sources suggest that we have between 50 and 100 de novo genes. The report that we have NO de novo genes would be quite surprising in light of other reports and in light of the fruit fly study.

  25. Should we thus conclude that whereas species of fruit flies are separated by whole genes either being present or not, this isn’t the case when it comes to apes and men. Does this sound reasonable at all?

    Yes. There are many more Drosophila than humans at present, and the human population has exploded only recently. It seems safe to say that the number of Drosophila has been huge throughout the past 6 million years. Furthermore, if you accept the generation rates someone gave above of 3 days for Drosophila and 10 years for humans, Drosophila have gone through about 1200 more generations over the past 6 million years than humans have. The Hawks et al. paper I linked to above would lead us to expect many fewer beneficial genetic changes in humans than in Drosophila, and it is “reasonable at all” to extend this to new genes.

  26. Actually, I’m not taking into account the environmental shift of humans, and the presumably stable environment of fruit flies. This doesn’t change my statement that it would be reasonable, given what we know, for there to be no de novo genes when humans and chimps are compared. It simply means that you definitely cannot take rates and percentages from one species group and use them to make estimates for a species under quite different circumstances.

  27. CEC09, (25)

    You did mean 1200 times more generations for fruit flies than for humans, I hope.

    Daniel King, (21)

    You said,

    Given appropriate assumptions, one can make any theory look ridiculous.

    That depends on how you define “appropriate”. If you mean assumptions chosen to embarrass a theory, that is debatable, but just barely possible for the theory of gravity and its more sophisticated relative, the general theory of relativity. Origin of life theory, however, can be embarrassed even by using rather straightforward, and even generous assumptions, as I noted here. (Comment 49. Note: read carefully before replying, to avoid personal embarrassment.)

  28. CEC09:

    I read the abstract, and I really think that it is impossible to comment on it without reading the whole paper, which I can’t.

    I will therefore make a few remarks about the above discussion, and especially about some of the many points you raised.

    You say (#4):

    “I still wonder exactly how de novo formation works”.

    Nobody knows how it works. We just know that we find in species genes which have no significant homology with other known genes, even in a very general way. Those are named “de novo genes”. Nobody knows how they arise. They are certainly vastly beyond any probabilistic resource. In essence, any kind of gene must have been, in the beginning, a “de novo” gene. Then, gene families are observed, where homologies can be found between the components of the same family. But nobody knows how “de novo” genes first arise, and in reality nobody knows how and why genes which have some homology are related. Even accepting some form of descent from one gene to the other, in most cases the mechanism of change is not known. The proposed mechanism of random variation and some form of selection is comnpletely impotent to generate those kinds of effects, as demonstrated by all the various calculations we have often discussed here at UD.

    You say:

    “And what is a non-functional gene? Does that mean it doesn’t yield a product, or does it mean that the product does not serve a function in the proteome?”

    Usually we call “gene”, or more precisely “protein coding gene”, those DNA sequences which have the characteristics of being transcribed and translated. That can be an inference from the structure of the DNA sequence, or we can have the evidence of the transcription and translation (in other words, we can know the mRNA or the protein). But the number of genes is often merely deducted by the analysis of the DNA sequence, and many studies about homologies are conducted in the same way. Obviously, when the protein is known, and so its function, the gene can be studied in a more realistic way.
    Pseudogenes are genes which are very similar to functioning genes, but are no more functional. I think that usually they are neither transcripted nor translated, but I would not take anything for granted in this very difficult subject: anything we actually know about non coding DNA (including pseudogenes) is in my opinion highly provisional.
    Finally, I am not sure, but I don’t think we have evidence of translated proteins which have no function in the proteome, and which are there, waiting to be magically transformed by random mutations to acquire a purpose. Usually, a cell is a very crowded place, and each protein has its role.

    You say:

    “F2XL, is your problem here that the abstract says indirectly that there are in fact non-coding regions in the genome that don’t serve a function? After all, turning a functional non-gene region into a gene would stop that region from serving its prior function.”

    I don’t think the abstract says that. There was a thred some time ago about a much more specific work about the formation of a de novo gene (I don’t remember the name of the thread or of the article), and the possibility was discussed that a de novo gene originared by mutations from a segment of non coding DNA. The interesting thing is that the supposed “progenitor” sequence seemed to be transcribed and functional. So, your question is legitimate, and indeed it is the same question which i made in that thread: if the original non coding DNA was transcribed and functional, what happens when it gives rise to a protein coding gene? (In the case discussed, there was no evidence of duplication of the original sequence).
    Moreover, the results of the ENCODE project seem to show that practically all the genome is transcribed. That does not prove that it is functional, but it is a good step in that direction.

    You say:

    “Didn’t Dr. Dembski argue in “Searching Large Spaces” and other writings that even one de novo functional gene is very unlikely to be discovered by random search?”

    Yes, he did, and it is. If we really find de novo genes in species, and we do find them, and will find them ever more, that is only a good reason to ask ourselves how those genes ever did arise. The only reasonable answer is design (see next point).

    You say:

    “Or did he say that base-pair sequences he specified as a target were very unlikely to be hit? The abstract seems to address formation of any new genes that do something, not just genes that do what the researchers had in mind before looking at the genome. Isn’t this a much bigger target than Dr. Dembski considered?”

    That’s a very important and pertinent question, and often a cause of misunderstanding. The subject is vast, but I will just outline some aspects:

    a) Nobody really knows how big the target of functional proteins is, but we have all the reasons to think that it is very, very small compared with the immense search space of all possible protein sequences. Let’s make an example, amd take the generic search space of all proteins of 100 aminoacids (which are indeed very small proteins). The whole search space is about 10^130. That’s something!
    But how many of these proteins can be functional? Nobody really knows, but even if we take “functional” in a very big sense, that is “able to have some useful function in some kind of living being”, still we have to remember that there are a lot of constraints, some known, some unknown, to that result: proteins have to be able to fold, and to fold in some ordered way, usually corresponding to some fundamental 3D structure. The folded protein must have domains, and active sites, which can exert some function, usually interacting with other proteins or with other organic molecules. In other words, there are all kinds of arguments, some of them also experimental (see for instance the interesting field of protein enineering), to believe that only a minor subset of proteins can be functional.

    But how minor? We have to realize that, with a search space of 10^130, even a very big number is really minor. Let’s pretend, just to discuss, that 10^30 proteins of 100 aminoacids are in some way functional: they can fold in some orderly way, and they can have some biologic function, as enzymes or in other ways. 10^30 molecules would seem a very big target, and it really is. But, in a search space of 10^130 sequences, there would still be a probability of only 10^30/10^130, that is of 1:10^100, of finding that kind of target by chance in a random search. And that is still a probability vastly beyond any reasonable biologic resource (yes, I know, that’s not beyond Dembski’UPB, but we have to be realistic: that kind of UPB is only an extreme reference, useful in a theorical discussion, but if we discuss real life and biological systems, probably any level around 10^30 or 10^40 is more than enough).

    b) But the above reasoning about “any protein which could have some function” is still only an extreme, theorical argument. In reality, given a biological context, only a very minor subset of generically functional proteins can have an “useful” function. In other words, the more a context is complex, the more a new function becomes difficult to find by chance. Let’s remember that most proteins, in a cell, are functional only because they interact precisely in complex, and I would say irreducibly complex, networks of other proteins, and many of those networks are really abstract in nature: they transmit information from cell to cell or inside a cell, they regulate other functions in very finely tuned ways, and so on. Inserting a new element in such complex and finely tuned contexts really requires a very precise choice of functional proteins.
    So, the problem is not that a cell should give rise to any possible functional protein (which, as shown at point a) would anyway be impossible), or to the protein Dr. Dembski or anybody else defines. The cell has to find some specific functional protein which can be useful in the context of the existing biological network. A protein which can be useful in a species will not be useful in another one, and even minor differences can create enormous losses of functionality.
    So, given that, would you still believe that a specific organism, in a specific context, can really choose in a target of 10^30 functional proteins of 100 aminoacids (which was in itself a very generous exaggeration)? Or should we reduce the target to 10^10, or to 10^6?

    The real fact is that it doesn’t matter. A search of 1:10^100, for all practical purposes, is as impossible as a search of 10^130, if we don’t incorporate information about the desired result in the search. And the only principle which can incorporate that kind of information is design.

  29. CEC09:

    you definitely cannot take rates and percentages from one species group and use them to make estimates for a species under quite different circumstances.

    I fail to follow your reasoning here. While I would agree that you cannot use the rate of evolution of one species to determine the rate of evolution of another species down to multiple decimal places. However, we are discussing orders of magnitude here. We should be able to get some sense of orders of magnitude accross different genetic lines. This idea that we can know nothing from evidence extrapolation is just as silly as the idea that we can determine with precision via extrapolation. We need to get beyond this simple black and white thinking.

  30. bFast, extrapolation is regarded as highly dangerous throughout science, not to mention statistics. There are many examples of the errors it leads to.

    One of the reasons I introduced the Hawks et al. paper to the discussion is that it gives very strong evidence that the rate of human evolution has accelerated by TWO orders of magnitude in recent times as a consequence of the population explosion and shifts in living conditions. In other words, extrapolation of the human present to the human past, or vice versa, leads to grossly incorrect conclusions.

    When within-species extrapolation of the rate of genetic innovation is so strongly contraindicated for humans, and has been shown to be strongly related to population size, how can you possibly defend extrapolating results for a species group with populations that have long been much larger than the present human population to the human species?

    My objection to extrapolation of the numbers in the Zhou et al. abstract is not merely a matter of principle. Rigorous scientific study of the human genome clearly tells us not to extrapolate. This is not just one of my unexpert guesses.

  31. You did mean 1200 times more generations for fruit flies than for humans, I hope.

    Thanks, Paul Giem. I was a bit rushed. Ten years is about 1200 times as long as 3 days.

    Even in the best-case scenario, where the ancestor is genetically precisely between modern chimpanzees and modern humans, the genetic distance between modern humans and the ancestor would still be half of that between modern humans and modern chimpanzees.

    I’m glad you brought this up. It’s more reasonable, though somewhat simplistic, to think of chimps and humans as separated by 12 million years than by 6 million years.

  32. I’d like to see the whole paper.

    Maybe someone who knows more about fruit fly research can tell me if any “new functional genes” have actually been observed to arise in all the generations of Drosophila studied?

    If even one has been observed, it seems that a rate could be calculated, rather than having to be estimated.

    I none has been observed, how do we know it ever happens?

  33. 33

    Paul Giem #27:

    “(Comment 49. Note: read carefully before replying, to avoid personal embarrassment.)”

    Thanks for the warning. That is such a kindness. You are a Christian in the best sense.

  34. CEC09:

    the rate of human evolution has accelerated by TWO orders of magnitude in recent times as a consequence of the population explosion and shifts in living conditions.

    1, how recently has there been a significant shift in living conditions for human/humanoid species? 10,000 years? Even a 100 times increase in evolution means little with this much time accounting for it. The vast lions share of the 6 million years of interest is at the slower pace. What of the fruit fly, has its environment not been affected by modern farming practices. I’m sure they love fruit orchards.

    We also see that population (which until about 10,000 years ago was miniscule for the human lineage) benefits evolution. Fruit flies vastly outnumber us, don’t they? They certainly vastly outnumbered our ancestors 1/2 million years ago. Every which way you turn, evolution should be happening vastly more slowly in humans than in fruit flies.

    My calculations suggest that, per generation, humans have evolved over 4 orders of magnitude faster than fruit flies. That, in light of the fact that there are many more fruit flies than humans (especially averaged out over the 6 million years.)

    # generations in 6 million years:
    Human 600,000. Fruit fly 600,000,000.

    # new genes during this time:
    Fruit fly: 50 (8 per mil * 6)
    Human: 689

    # new genes in human during this time if they evolve at fruit fly’s rate (per generation) 0.05

    Difference in pace: about 14,000 to 1.

    dacook, “I none has been observed, how do we know it ever happens?”

    If one species of fruit fly has a gene that all other species don’t have, a new gene must have come from somewhere. It does not require observing the new gene appearing to determine this. However, this observation does not give us the cause — was the new gene the product of dumb luck or of an active agent.

  35. The real fact is that it doesn’t matter. A search of 1:10^100, for all practical purposes, is as impossible as a search of 10^130, if we don’t incorporate information about the desired result in the search. And the only principle which can incorporate that kind of information is design.

    If your assumptions were right it would be unlikely that your very own immune system would ever generate any functional antibody.
    BTW, you may read a little bit on immunoglobulin gene diversification in birds that heavily relies on pseudogenes and gene conversion. You will find out that birds and those mammals that employ the same mechanism to generate antibody diversity can indeed produce antibodies against antigens that they or their ancestors never encountered before.

  36. gpuccio:

    Those are named “de novo genes”. Nobody knows how they arise. They are certainly vastly beyond any probabilistic resource.

    How can you establish a very low upper bound on the probability of an event when nobody knows its cause(s)?

  37. Moderators:

    Re Mr King at 33 above.

    He has no permission to use my personal name in this blog or elsewhere. This is relevant first as there is a known asymmetry between ID supporters and opponents, given the issues raised in e.g. Expelled. Mr King either knows, or should know that.

    Secondly, in my case, I have found that use of my personal name and/or contact opens up to spam attacks. (I have retained in my personal site, ways to find my name and contact, but that is for responsible behaviour. What was done above is at minimum grossly irresponsible, and highly disrespectful.)

    I must therefore ask Mr King, on pain of further, more serious appeal to the Moderators, to cease and desist.

    GEM of TKI

  38. sparc:

    First of all, I really believe that my assumptions are right, and I invite you to tell where they should be wrong. In a sense, they are not assumptions at all, but very simple facts about probability.

    Regarding the immune system, the scenario is completely different. Primary antibody diversification is a process which uses random variation very intelligently targeted to generate a repertoire of basic antibody specificities to cover, at a low specificity level, a search space which is very big, but not immense, referring to possible epitopes in nature (an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen). Even so, the basic repertoire is very unspecific, and can ensure only a low level interaction with possible epitopes. Antibody maturation “after” primary response, instead, is a typical process which utilizes random variation very intelligently targeted plus very intelligent selection to increase the specificity of the immune response. Indeed, the process utilized here is the same as used in modern protein engineering: the results of targeted random variation are “measured” against the original epitope, and intelligent selection takes place (obviously, here selection includes very specific informatioon about the target, that is the epitope itself, and is therefore very efficient).

    So, as you can see, there is nothing in what we know about antibody generation which is inconsistent with my “assumptions”. Antibody generation is a perfect example of intelligent engineering using the realistic resources of probability. It is therefore perfectly natural and reasonable that the immune system of birds or mammals can “produce antibodies against antigens that they or their ancestors never encountered before”.

  39. CEC09:

    “How can you establish a very low upper bound on the probability of an event when nobody knows its cause(s)?”

    It’s very simple. The probability of an event is calculated for the hypothesis that a random process of variation is the cause. That is the assumption in darwinian evolution, or whatever you want to call it.

    If the cause is not random variation, but some other causative process (like laws of necessity or design), no calculation of probabilities makes sense. Probabilities are calculated for random events. For events which have a specific cause (necessity) the probability is always 1 (the event has to happen). The point is, as we have often discussed here at UD, the kind of information we observe in biological systems (CSI, or FSCI) simply “cannot” be the result of laws of necessity. So, if you can exclude random processes as a cause (and that’s why we calculate their probabilities), then design is the only known causal process which gan give that kind of result.

    So, to sum up: we don’t know how a new gene originates: we are not sure about the causal mechanism and we certainly don’t know the details of the process. But, about the mechanism, we can make some sound inferences:

    a) It cannot be the result of necessity (as often discussed, necessity cannot give that kind of complex information).

    b)It cannot be the result of random variation (probabilities are absolutely against that).

    c) It can, definitely, be the result of intelligent design (we see that happening every day in human artifacts).

    That’s why, as we always say, design is at present and by far the best explanatory theory for CSI in biological beings.

  40. gpuccio:

    From the perspective of most geneticists and evolutionary biologists, “evolutionary search” is an oxymoron. The term search immediately suggests a goal, contradicting their belief that biological evolution is non-teleological. As Norbert Wiener pointed out in Cybernetics, evolutionary adaptation is much like learning in individuals and in cultures. But it’s easier if we stick with terms familiar to you, provided no one uses them to beg the question of teleology.

    10^30 molecules would seem a very big target, and it really is. But, in a search space of 10^130 sequences, there would still be a probability of only 10^30/10^130, that is of 1:10^100, of finding that kind of target by chance in a random search.

    The 100-amino-acid protein is a very old example, predating Dembski. No one claims that there has been a search of 100-amino-acid proteins. No one even claims that there has been a search of length-306 strings of nucleotides (I’m including START and STOP codons). Evolutionary search is on the space of genomes (and even that is a modeling fiction, ignoring epigenetic information). Furthermore, “random search” is highly misleading in suggesting “uniform sampling with replacement.” In fact, the nucleotide mutation rate is quite low. Genomes tend to grow, not shrink, in size due to such phenomena as gene duplication and retrotransposition. And these introduce new genetic regions that are anything but initialized uniformly at random. They start out with much or all of the information of functioning genes. Other interesting biases in the search arise from the fact that some amino acids are coded for by as many as six codons, and some are coded for by just one. AUG codes for both START and methionine, with interpretation according to context.

    These are just a few aspects of genetic change tossed off by a computer geek too tired to see straight. But they’re enough to make analysis incredibly difficult for a Rip Van Einstein on his second cup of coffee.

    A key problem, in my mind, is that we know very little about the topology of the set of functional genes. Do functional genes tend to cluster, in some sense, in the space of nucleotide sequences? What is the probability that a short, functional gene homologous to none other will grow into a slightly longer functional gene? This could happen if an AUG codon arrived, by mutation or some other cause, just ahead of the existing start-AUG, changing the original start-AUG into methionine-AUG. What I’m driving at is that you cannot fix the length of codon sequences in your analysis. If I recall correctly, there are 10-amino-acid artificial proteins.

    Another important consideration is that the search over genomes may produce new genes in many overlapping regions. To get the flavor of what I’m talking about, compare these two questions: What is the probability that four tosses of a fair coin will yield the outcome HTHH? Now what is the probability that sixteen tosses will yield an outcome with HTHH as a subsequence? The regions of the genome that might give rise to genes are much longer than genes, so the analysis should look more like an answer to the latter question than the former (though, again, the sequence length should not be fixed, and sampling is not uniform). In other words, if you restrict your focus to a certain subsequence of nucleotides, you greatly underestimate the probability that a functional gene of a certain length will arise.

  41. CEC09:(25)

    [PaV]: “Should we thus conclude that whereas species of fruit flies are separated by whole genes either being present or not, this isn’t the case when it comes to apes and men. Does this sound reasonable at all?”

    [CEC09]:

    “Yes. There are many more Drosophila than humans at present, and the human population has exploded only recently. It seems safe to say that the number of Drosophila has been huge throughout the past 6 million years……”

    You seemed to have missed the point. Are we to assume that de novo gene origination takes place when it comes to two types of flies that are hardly distinguishable from one another, and yet it hasn’t taken place at all when we’re now dealing with the huge differences that separate humans and chimpanzees? Again, does that sound reasonable to you?

    CEC09: (30)

    “When within-species extrapolation of the rate of genetic innovation is so strongly contraindicated for humans, and has been shown to be strongly related to population size, how can you possibly defend extrapolating results for a species group with populations that have long been much larger than the present human population to the human species?

    My objection to extrapolation of the numbers in the Zhou et al. abstract is not merely a matter of principle. Rigorous scientific study of the human genome clearly tells us not to extrapolate. This is not just one of my unexpert guesses.’

    It appears that you are “bloviating” here: “Rigourous scientific study of the human genome clearly tells us not to extrapolate.” Really?

    You seem to want to argue that what applies to flies, doesn’t apply to humans. To do so, you suggest, is to engage in wrongful extrapolation. We shouldn’t be applying the rates found in flies to that found in humans.

    Well, OK, let’s try to fix this problem. You tell us along the way that flies generate 1200 times faster than humans. Well, does that then mean that the rate of “newly functioning gene formation” in humans should be 1200 times less than that of flies? Oh, but you say that humans are “evolving” twice as fast as other organisms. So, then, the rate in humans should only be 600 times less, making it 5-11 “newly functioning genes” per 600 million years. Doesn’t this mean that chimps and humans should have exactly the same compliment of genes? This is what Musgrave claims, and this might be why he is claiming it, but there are studies suggesting that we have 689 genes that are not found in chimps. So, then, how do you explain this if “newly functioning genes” arise every 600 million years?

    You see, “extrapolating” fly data to human/chimp data makes it easier to explain the genetic difference between humans and chimps, not harder. But you seem to prefer the harder way. I don’t suggest it.

  42. kairosfocus, I deleted Mr King’s post containing your first name. Let’s hope this practice is not repeated.

  43. Now, on matters of substance:

    1] “Assumptions”

    Mr King, we are dealing with a known context, not an abstract discussion of logico-mathematical method.

    In that context, you have invited by pretty direct inference, the conclusion that the sort of calculation above by PaV and/or the design thinkers more broadly, is unwarranted. Above, I therefore challenged you to substantiate — which is plainly not an act of pride but of asking for the reasons for YOUR hope.

    In response, sadly,you have resorted to disrespectful behaviour as I just had to note, and have thereafter tried to improperly reverse the burden of substantiation.

    Worse, in 22 above, I actually provided a link to my always linked substantiation in outline of the sort of configuration space-based calculation that is often presented in an ID related context. (So much for the remark: “As an exercise in humility, you might answer your own questions above…” For, the “exercise” has been long since done, and you as a long time participant here know or should know that.)

    That calculation, anchored in the inherent nature of digital systems, raises serious challenges regarding the reasonableness of the idea that chance + necessity within the gamut of the observed cosmos, could give rise to the sort of discrete state information entities that lie at the heart of cell based life.

    You have provided neither a serious response on the merits nor a link to such. [Onlookers: PG's link to TO is illustrative of just how unserious the response from the evolutionary materialist side too often is. That's why he linked it without further comment.]

    The logical conclusion is that you are diverting from the substantial matter, and are taking up personalities instead. That speaks volumes on your real estimation of the substantial weight of your side’s case on the merits.

    2] The TO assertions:

    TO of course, first, does not wish to acknowledge that anyone other than “creationists” raises serious questions; never mind teh presence of men like Fred Hoyle — a distinguished scientist and a life-long agnostic — in the immediate context:

    Problems with the creationists’ “it’s so improbable” calculations

    1) They calculate the probability of the formation of a “modern” protein, or even a complete bacterium with all “modern” proteins, by random events. This is not the abiogenesis theory at all.

    2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

    3) They calculate the probability of sequential trials, rather than simultaneous trials.

    4) They misunderstand what is meant by a probability calculation.

    5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

    Let’s look a bit closer:

    a –> Events are caused, per massive observation immemorial from the day of Plato, by chance and/or mechanical necessity and/or intelligent action. If we, ex hypothesi, rule out intelligence, that leaves chance [for high contingency situations or aspects -- which side of the die is upppermost] and necessity [for low contingency situations or aspects -- if dropped the die will fall].

    b –> Cell based life, notoriously, rests on macromolecules assembeled from monomers, and cells are thus discrete-state systems, with very high contigency states. For the component DNA and RNA, 4^N, where N for OBSERVED — note TO’s artful, dismissive use of “modern” to dodge this key point — life systems starts at 300 – 500,000. For proteins, 20^N, with 100 – 500 being typical chain lengths. The relevant config spaces therefore START at ~ 10^130, and go up from there, WAAY up from there.

    c –> Biofunctional states of DNA and proteins are highly constrained, the former by a code process and the onward link to proteins, which as GP outlines abiove, are massively functionally constrained. Sensitivity of funcitonality to perturbation of chain structure simply underscores this point.

    d –> Thus, we easily see why the observed functional systems are highly vulnerable to perturbation. (AKA: Why is there no market for deliberate exposure to mutation inducing irradiation? Why is it that most cases of observed microevoltuion are by loss of function?) That immediately means that the probability of gatting to such entities in biofunctional clusters per one variety or another of Darwin’s soup in a prebiotic pond or geothermal vent or a comet, etc, is vanishingly small on ther scale of the observed cosmos. There are many upper bound estimates that show that, very strongly; these are the probability calcs that TO wishes to dismiss.

    e –> So, contrary to assertion no 2, as GP shows above, and taking in the calculations as a class, there is not any imposition of a dubiously arbitrary bound on proteins etc. Instead, there are reasonable estimates of models, with a consistent pattern of results, one that cuts across what TO wishes to sustain. [Much, much more reasonable than say the basis for the GCMs that have so much of the world in a tizzy over climate change.]

    f –> 3 is either a bald lie or reveals grossest incompetence. For, the Dembski type bound is based on the number of quantum states attainable by the observed cosmos as a whole, some 10^80 partticles, sifting through combined states at the rate of one combination of states for 10^80 or so particles, every 10^-43 seconds or so. That is as “simultaneous” AND as “sequential” as it gets. Worse, the very FIRST ID technical level book, TMLO, used an equilibrium state thermodynamic discussion, which is plainly and explicitly based on an overly generous concentration of monomers in a planet-scale prebiotic soup. And the issue is the monomer to biofunctional polymer transition, not hte assembly of a bacterium de novo out of the monomers.

    g –> Furtehr to this, probability calculations, of course are usually based on observed frequencies, or on the Laplacian equal chance of alternatives hypothesis, perhaps biased by some non-uniformity in probability distributions. The equiprobability of microstates is foundaitonal to statistical thermodynamics, a highly successful sceintific discipline. As my point 6 app 1 the always linked therefore shows, this sort of approach is a more or less standard way to look at the relevant probabilities. (In TMLO, which specifically addresses polymerisation [so the simple chemicals to bacteria assertion in TO is a strawman misrepresentation!], polymer expert Bradley actually addresses the Kenyon Biochemical Predestination chemical-bias argument through a statistical study and so convincingly was it overturned that Kenyon took advantage of writing the foreword to publicly recant.) In short, TO’s 4th assertion is little more than a slander.

    h –> Finally, one may assert away all s/he wants that there is a large number of combinations of monomers that are “functional.” The vastly yet larger number that are not, immediately reduces the suggestion to absurdity — the smallest known functional genomes are of order 300 – 500 k.

    i –> That sets up a config space of minimal order 4^300,000 ~ 9.94 *10^180,617. With a generously assumed 10^1,000 islands of biofunctionality, each with 10^1,500 functional configs to choose from, we would be looking at 1 in 10^178,000. Negligibly different from zero probability on the gamut of our observed cosmos, or even for an array of 10^500 such sub-cosmi in some sort of brane sheet or the like.

    j –> “Generous”? Indeed: 10^1,000 or 1,500 is vastly larger than the number of not only bacteria — to a first approximation, every lifeform is a bactrerium! — that could have ever lived in our cosmos, but of the proteins or DNA or RNA strands that could have ever formed. For, the observed cosmos could enfold up to only 10^150 quantum states across its lifespan.

    k –> So, it is safe to conclude that a random walk through such a config space starting at an arbitrary initial point — what a prebiotic soup would do — is maximally unlikely to ever find the shores of any single island of funcitonality, much less get to apply any hill-climbing algorithms such as some vcariety of prebiotic natural selection. [Which itself is a questionable notion.]

    l –> And, if there is an assumed natural law that programs the emergence of life, we should note that the term “natural law” relates to natural regularities, i.e. situations that are of low contingency: if you have heat, fuel and air, you have a fire. But, life systems are just the opposite of low contingency. That would leave only chance or agency as the credible explanations. [Cf the config space taken up by this post's character sequences -- chance or agent or law?]

    m –> Worse yet, the future discovery of such a “life-program law” in the face of such a vast config space and resulting set of oterwise accessible contingencies, would imply pretty directly that the cosmos was programmed at its origin to create life. Programs of course require programmers.

    In short, there is a serious case on the merits to address. And, neither DK nor TO have taken it seriously.

    GEM of TKI

  44. PaV:

    Thanks

    GEM of TKI

  45. PS: I would love to see a case of an observed life-form using small sets of short-length genes, RNA and proteins that in aggregate does not get us into trouble relative to the UPB as I just discussed [and pardon the typos -- ouch!].

    DK, Sparc and CEC09, might you be able to provide us a link?

    Failing such, could you provide us with cogent — non question begging — reason to infer that chance + necessity with no intelligence is a superior explanation to agency for the origin of the functionally specified, complex information in observed life forms?

    Or, just, can you give us an example of FSCI beyond the Dembski type bound i.e. ~ 500 – 1,000 bits of information storage capacity, that — per direct knowledge of the causal process — originated by chance and necessity only? [In short, can you show us that the explanatory filter is an empirical failure, instead of the reliable test for intelligence that we have claimed, per massive observation on the origin of cases of FSCI? (Just as, an observed perpetual motion machine would at once disestablish the laws of thermodynamics.)]

  46. CEC09 (#40):

    You say a lot of correct things which do not change a comma of what I have said. The 100 aminoacid protein is obviously a standard example, just to try a computation. I have to recall that most proteins are much longer, and much more complex.

    It is obvious that the length is not fixed: that makes things even more difficult, and the search space even bigger.

    It is possible that sometimes we can pass from one functional gene to a similar functional gene, with some slight change in function: that’s exactly the rare situation which could in theory occur by random mutation, and the few artificial examples of darwinists (see corticosteroid receptor experiments) are of that kind.

    But are you sayin that all functional genes are similar? Or that all types of proteins (and genes) cluster in the search space? That’s simply absurd. Proteins are extremely different, they fold in completely different ways, they have very different domains and functions. Some proteins have completely no homologues. Even the best known protein families (see myoglobin) exhibit striking variations, often of a compensative nature, so that very different sequences may fold in a similar way.

    So, it is not true, imo, that “we know very little about the topology of the set of functional genes”. We certainly know little, but we definitely know something, and nothing of what we know encourages the strange and fantastic topologies which darwinists like to imagine, like the smooth transitions from one cluster to another in the immense ocean of possibilities.

    It is certainly true that it is difficult to calculate the probabilities exactly, but that does not mean, in any way, that we cannot have a definite idea of their order of magnitude. Frankly, objections like the one you make about the asymmetric nature of the genetic code seem really irrelevant. I made my calculation from aminoacid sequences, and that was just a generous simplification. If you look at DNA sequences, you must add, to all the possibilities of protein sequences, also all the sequences which would never be transcripted and/or translated, and I can’t see how that would help your argument.

    Finally, I see in your reasoning a common misunderstanding: when I use the term “random variation” I refer to any possible variation, and not only to single nucleotide substitutions. You can put in any mechanism which is non directed, be it deletion, duplication, inversion, insertion, and so on. The result does not change. Any of this act is random, and the result is a random sample of the whole search space.

    So, it’s not true, as you say, that ““random search” is highly misleading in suggesting “uniform sampling with replacement.” It does not suggest anything like that. It only suggests that the cause of variation is not directed, and has no informational relationship with the function which is the final result of the variation (is that non teleological enough as a substitute for “search”?).

    It is not even necessary that all results are equally probable. Unless you can demonstrate that there is some law of necessity which determines special probability distributions which favor function, any real probability distribution, having no informational relationship with function, is blind to the result’s functionality. So, the search is still random. In other words, if variation is caused by laws which have no relationship of any kind with a special informational pattern which allows function, the emergence of that pattern is possible only either by chance or by design. If chance is too unlikely, as it definitely is in the case of biological information, then only design is a reasonable answer.

  47. GP

    Well said again.

    GEM of TKI

  48. A thought:

    Here is Wiki on Drosophila, as a little 101-level context will I think be helpful:

    Drosophila is a genus of small flies, belonging to the family Drosophilidae, whose members are often called “fruit flies” or more appropriately vinegar flies, wine flies, pomace flies, grape flies, and picked fruit-flies, a reference to the characteristic of many species to linger around overripe or rotting fruit . . . D. melanogaster, has been heavily used in research in genetics and is a common model organism in developmental biology . . . The entire genus, however, contains about 1,500 species and is very diverse in appearance, behavior, and breeding habitat . . . .

    Drosophila are found all around the world, with more species in the tropical regions. They can be found in deserts, tropical rainforest, cities, swamps, and alpine zones. Some northern species hibernate. Most species breed in various kinds of decaying plant and fungal material, including fruit, bark, slime fluxes, flowers, and mushrooms. A few species have switched to being parasites or predators. Many species can be attracted to baits of fermented bananas or mushrooms, but others are not attracted to any kind of baits. Males may congregate at patches of suitable breeding substrate to compete for the females, or form leks, conducting courtship in an area separate from breeding sites . . . .

    The genus Drosophila as currently defined is paraphyletic (see below) and contains 1450 described species,[3][4] while the estimated total number of species is estimated at thousands.[5] The majority of the species are members of two subgenera: Drosophila (~1,100 species) and Sophophora (including D. (S.) melanogaster; ~330 species). The Hawaiian species of Drosophila (estimated to be more than 500, with ~380 species described) are sometimes recognized as a separate genus or subgenus, Idiomyia,[3] but this is not widely accepted. About 250 species are part of the genus Scaptomyza, which arose from the Hawaiian Drosophila and later re-colonized continental areas . . . .

    Drosophila are extensively used as a model organism in genetics (including population genetics), cell-biology, biochemistry, and especially developmental biology. Therefore, extensive efforts are made to sequence drosphilid genomes . . . . The data will be used for many purposes, including evolutionary genome comparisons. D. simulans and D. sechellia are sister species, and provide viable offspring when crossed, while D. melanogaster and D. simulans produce infertile hybrid offspring. The Drosophila genome is often compared with the genomes of more distantly related species such as the honeybee Apis mellifera or the mosquito Anopheles gambiae.

    In short, the study reported by Zhou et al as linked in the OP, is based on a major focus on this genus, a genus that shows fairly wide diversity and apparently fairly high mutation rates. Doubtless, the projected timelines on the various members and evolutionary divergence are due to the various conventional dating schemes. (BTW, a Q: if “sister species” are interfertile, why are they regarded as separate species?)

    The key inference in Zhou et al, as observed by PaV is: 6) the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.

    That has led to the following calc in the OP:

    Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 [i.e. mid point of the range 5 - 11] new functional genes per million years= 1.75 billion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

    Obviously, the calc is in large part meant to highlight the basic problem: accounting for body-plan level genetic information within the time claimed to be available on the usual reported timeline for life on earth. That problem is of course most notoriously seen in the Cambrian life revolution, where dozens of novel body plans appear in a window reported as being about 10 MY, some 500 – 600 MYA.

    600 or so MY is a lot less than 1.75 BY, i.e. something is wrong with rates and/or dates. Independently of dates issues, we know that the genomes and associated proteins are long-chain discrete state systems, i.e. information-rich, functionally specified polymers. This is already so problematic for the macroevolution and OOL models that we can focus on just this part, taking the usual dates as givens for this discussion.

    The basic information storage capacity of a digital entity such as D/RNA or proteins, is reasonably estimated at 4^N for the former, and 20^M for the latter; and whatever variations in frequencies of component monomers we may bring up, this will not shift the basic order of the calculation. There just is not enough time, mass and material on earth — or in the observed cosmos — to get to the observed patterns and complexity, with reasonable probability relative to chance + necessity without intelligence. But, intelligence easily and routinely produces functionally specified information-rich systems that are of this order of complexity.

    So, Q: why is there such a strong resistance to the idea that intelligence is a reasonable — indeed the best — explanation for the FSCI in life forms?

    Answer: worldview level commitments, often backed up by attempted redefinitions of the nature of science that seek to constrain scientific inference to themes friendly to materialism.

    So, there is a serious issue that needs to be seriously addressed.

    GEM of TKI

  49. PS: I have looked up a relevant timeline, and find one here:

    The Diptera are commonly known as (true) flies and include many familiar insects such as mosquitoes, black flies, midges, fruit flies, blow flies and house flies. Flies are generally common and can be found all over the world except Antarctica. Many species are particularly important as vectors of disease in man, other animals, and plants. In addition, much of our knowledge of animal genetics and development has been acquired using the vinegar fly Drosophila melanogaster (family Drosophilidae) as an experimental subject (Lawrence, 1992).

    The earliest fossil flies are known from the Upper Triassic of the Mesozoic geological period, some 225 million years ago (Evenhuis, 1995). Since that time they have diversified to become one of the largest groups of organisms. There have been about 120,000 species of flies formally described by scientists; thus about 1 in every 10 animals described is a fly. An equal number of species may await description and most of these will be found in environments that remain to be studied intensively, such as tropical forests.

    225 MY or 600 MY, we are looking at significant constraints. And, we have not got to the level of addressing origin of the body plans and the original genomes, underlying codes and algorithms — not to mention the issue of epigenetic information as DS raised in another recent thread — that can diversify by whatever mechanism du jour.

  50. 50

    kairosfocus #43:

    I beg your pardon and that of the administrators for addressing you improperly. I see now that my unwanted expression of familiarity was thoughtless and rude, and I appreciate your forbearance.

  51. DK:

    Appreciated.

    GEM of TKI

  52. 52

    KF, at 49-

    Yes and the body plans are what is really needed. Without an understanding of how we got to “B”, the question of “origins” is not be adressed.

    While everything seems to at some point dissapear into the mysterious voide of first non cause cause- however we can look at formations and determine alot about where they came from- that is where the information, the SC came from. Take a computer- it is dependent on a human for its formation- the computers SC is secondary to the human beings.

    The question is how do we get from simple to complex when the steps are degenerative- that is each step is secondary to the specified complity of the first? What kind of an evolution thinks “ahead”?

  53. CEC09, (31)

    PaV, in the original post, made an estimate for 200 Ma for the calculated human-monkey split, based on new genes and the presumed rate of new gene production in Drosophila. I don’t know if it is safe to assume that he meant the human-chimpanzee split, but if so it would be relevant to your comment. The split from a common ancestor would be 6 million years ago by generally accepted fossil evidence, and thus effectively 12 million years ago. That is still too small by over an order of magnitude.

    Comments by various people on this thread have pointed out that Drosophila multiply some 1200 times faster than humans, and that their numbers vastly outnumber humans, even now when humans are populous, let alone during prehistoric times. This would seem to make the problem worse rather than better. A comment by bFast (34) indicates that 689 new genes are found in humans that are not found in chimpanzees. Those are the data. They indicate a real problem.

    Those who wish to explain away the problem by nibbling around the edges, like pointing out that humans and chimps, according to theory, evolved from a common ancestor rather than humans evolving from chimps, should realize that the problem will not be resolved by one or two such arguments, any more than you will make a million dollars if I give you 5 bucks. Quantity is important.

    I would have more sympathy with the claim (CEC09, 30) that it is dangerous to extrapolate if the person making that claim would also say that it is dangerous to extrapolate from microevolution (variation within species) to megaevolution (differences between classes, orders, and higher taxonomic groups). (BTW, I did not make the term up. See Simpson, G. G. 1944. Tempo and mode in evolution. Columbia Univ. Press, New York.) As it is, without the recognition that the caution goes both ways, this seems like an advocate’s way to shut down the opposition regardless of whether it is fair or not, rather than someone cautiously trying to approximate the truth. Does this person really believe that humans evolving new enzymes some 10,000+ times as fast as fruit flies is not a problem, especially in view of the difference in population size?

    Now, if you want to challenge the numbers, go ahead. But if the numbers are reasonably accurate, it seems to me that we have a major difficulty here.

  54. Good response, Paul. Double standards abound.

  55. Sometimes UD bores me. We spend so much time on the politics of the debate. Periodically we get into a topic about the real data. This has been one of those times. This thread is the reason I spend energy here at UD.

    Paul Giem:

    Now, if you want to challenge the numbers, go ahead. But if the numbers are reasonably accurate, it seems to me that we have a major difficulty here.

    Yes! And if you Darwinists can convince me that the numbers work out, here and in about 15 other places (OOL), you will have converted one to your side.

    ID is in the data. If it were not so, ID would be religion.

  56. Kairosfocus (43) gives a good rundown on the talkorigins site on OOL. However, he omitted the money quote:

    I will try and walk people through these various errors, and show why it is not possible to do a “probability of abiogenesis” calculation in any meaningful way.

    Note that the claim is not that the “creationists” are doing the calculations wrong and that here are the correct ones, or even that we don’t know what the calculations are, but that the calculations can’t be meaningfully done (“it is not possible”). The chutzpah is staggering. This sounds like more lawyerlike (sorry, bFast) argumentation that has no place in science.

    BTW, thanks DaveScot and bFast.

  57. 57

    kairosfocus and Paul Giem,

    Regarding underlying assumptions:

    You assume that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation. This is not only a questionable assumption, it is a fundamental logical error.

    On the contrary, it is a given that the processes that brought about life and its diversification on earth occurred at some time in the past (scientists have evidence that this was somewhere between 3.8 and 3.5 billion years before the present). Events that have occured in the past are historical events. Hypotheses about historical events can only be tested empirically. (Unless you was there, Charlie.)*

    Therefore, a scenario explaining life’s origins is not discoverable solely by speculation. What can be done empirically is to formulate hypotheses based on current understanding of the properties of matter (living and non-living) and its earthly history, and test them for fruitfulness in terms of increasing our understanding. As new data are ascertained, some hypotheses will be rejected, whereas others will lead to further understanding. And on and on.

    Will we ever know exactly what happened? I doubt it, but science frequently surprises us. (Well, it has surprised me. Repeatedly!)
    ————–
    *Should be said with a vaudeville Germanic accent, as by my dear departed grandfather, when I tried to convince him of the reality of heaven: “Vas you dare, Chollie?”

  58. 58

    Sorry, I should have said, “…when I tried to convince him of the reality of an afterlife,” because I knew he wasn’t going to heaven.

  59. Daniel King, (57)

    So speculation cannot “sufficiently and definitively answer “questions about how life arose and diversified” (that would be “a fundamental logical error”), and we need to “formulate hypotheses based on currrent understandings of the properties of matter (living and non-living) and its earthly history, and test them fro fruitfulness in terms of increasing our understanding.”

    Well, let’s see. Is the RNA world “speculation”, or a hypothesis with a lot of evidence behind it, and no major flaws created by the evidence? Or is it one of those “hypotheses” that should be “rejected”? How about the protein world? How about the clay hypothesis?

    Come to think of it, I seem to recall that DNA code is remarkably similar to computer code, and that computer code is usually produced by living matter with the ability to reason and plan ahead. Well, perhaps not entirely matter, but at least where matter interacts with intelligence, and certainly something we know exists. Do you suppose that the code-like quality of DNA could be evidence that it was produced by some intelligence? Maybe we could start a blog about that idea.

    Sorry. That was insulting. But no more so than your comment that kairosfocus and I were assuming “that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation.” There is a lot of experimental evidence to back us up. If you have questions about it, feel free to ask. And the more respectful you are when you ask, the more respectfully you will be answered.

    P.S. Some of us even think that there vas someone who vas dare, but then you don’t believe in old nomadic fairy tales, do you?

  60. Kairosfocus, I can’t put in words how often I will likely end up linking to that comment you made on Ian Musgrave’s article.

    Seems like design critics love to mindlessly cite claims in that article time and time again. I remember one debate I was in on youtube in which a Darwinist evolutionist started to mindlessly vomit point after point on that article. First, they insisted earlier life was much simpler prior to a living cell (while never elaborating on what it could’ve been or explaining how that proto-life changed from there), then went on to say that multiple sequences of amino acids could be functional, etc. And this was after I stated that specificational resources were in play.

    I guess if you can rebut most of the stuff on TO then you can pretty much take on 90% of all design critics.

  61. Regarding the RNA world: A chief problem with it is that for RNA strands to form IN THE FIRST PLACE, you need sufficient amounts of concentrated carbon-5 sugars, phosphates, and also nucleotides bases (adenine, thymine, guanine, and cytosine). The catch is that these three constituents can only be artificially synthesized in completely different circumstances for each of those things listed. A phosphate group cannot develop in the same mix as a carbon sugar, and so on.

    That wouldn’t even begin to explain how the information in the RNA got there in the first place.

  62. F2XL, “a Darwinist evolutionist” Hey! I’m no Darwinist, but I accept common descent, so I am an evolutionist!

    F2XL, another huge problem for the RNA world is that experiments (controlled environments seeded by replicating RNA) have allowed RNA to replicate itself. However, the darn replications simplify rather than becoming complex! See http://en.wikipedia.org/wiki/Spiegelman_Monster

  63. Antibody generation is a perfect example of intelligent engineering

    Wouldn’t that require an engineer? If I understand you correctly you are implying that random variation and selection both are intelligent processes.

    an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen

    Isn’t that true for sequences involved in other protein-protein interactions.

  64. What can be done empirically is to formulate hypotheses based on current understanding of the properties of matter (living and non-living) and its earthly history, and test them for fruitfulness in terms of increasing our understanding. As new data are ascertained, some hypotheses will be rejected, whereas others will lead to further understanding. And on and on.

    Daniel, you have been duped by the Bayesian priesthood! All it takes to transform Bayes into Fisher is a time machine. OK, maybe you logically have to go all the way back to the singularity. That’s an absurdity. But let’s not pick nits. Let’s not be pedantic.

    Paul, if you don’t see the humor, then you might want to look into interpretations of probability. Frequentism does not permit assignment of a probability to the proposition “life on earth originated by abiogenesis.” Bayesianism does. But Bayesian probabilities are subjective, not objective, and don’t give you a basis for making proclamations about Reality. Bummer. Dr. Dembski offered a frequentist workaround, hinging on something like objectification of a subject describing events, but it seems that other frequentists didn’t go for it.

    gpuccio, thanks for differing respectfully. It’s nice when someone recognizes that I’m not just pulling contentious rabbits out of the hat. I apologize to you and others that I’ve got a lot going on, and have to drop out after provoking many responses.

  65. Gentlemen:

    First, thanks for some kind remarks.

    A few follow-up points:

    1] CEC09, 64: Bayesianism-subjectivism?

    I have a little familiarity with the use of Bayes’ work to do probability estimates and revisions, and with how it intersects with the issues at stake relative to the explanatory filter.

    That frame of reference is precisely what is not at work here. indeed, you will see that I am precisely not using Bayesian methods, as was discussed at length online and offline with former commenter here, PO.

    We are, instead, looking at something else: a statistical thermodynamics-tinged look at state spaces, of discrete form, and the issue of “searching out” functional states in the resulting configuration space. In that regard, we also start from the usual scenarios proposed since Darwin [cf my always linked], and ask, what happens in the context of polymerisation chemistry which is not intelligently directed.

    The answer is plain: functional states are vastly isolated in the config space, and even if we envision a very generous provision of islands and archipelagos of functionality, the sea of non-functional states swamps them — recall what we need for OBSERVED life function through the DNA-RNA-enzyme ribosome system and associated issues of protein folding and functionality.

    Indeed, the need for codes and algorithms to make the elements of the cell’s systems work together compounds the problem. have you ever seen a complex code [language] or a similarly complex algorithm originate by chance-driven contingent processes? [And, the isolation issue is what drives any probability estimates. There are only so many search resources in the observed cosmos, and not all things which are logically or physically possible are sufficiently thermodynamically accessible that we can see them arising by chance + mechanical necessity. Indeed, that is the foundation of the statistical form of the 2nd law of thermodynamics.]

    Do you routinely see codes and algors produced by intelligent agents?

    So, which is the better, empirically anchored explanation, then?

    –> The answers are obvious, once you see the issue of search-space, isolation and probabilistic resources to undertake the search.

    –> intelligent agents, of course, use their imagination and insight to cut down the search space dramatically, so we routinely produce entities that are vastly beyond the credible reach of random search; e.g. posts in this thread. [Think about just the space on an ASCII state space search for your last post: 128^1418 ~ 1.06 *10^2988. Which is the better explanation: chance and necessity or agent? Why? (And, if you wish to inject the notion that agents are known to exist now, the point at OOL is that agents are possible absent your ruling them out on solid grounds.]

    –> And, on tone: I do not at all like to see loaded terms such as “duped”; this seems grossly disrespectful and dismissive! (As well as inaccurate.)

    2] Sparc, 63: antibodies stuff

    Kindly reread the wider context of the remark at 38 above:

    Regarding the immune system, the scenario is completely different. Primary antibody diversification is a process which uses random variation very intelligently targeted to generate a repertoire of basic antibody specificities to cover, at a low specificity level, a search space which is very big, but not immense, referring to possible epitopes in nature (an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen). . . . there is nothing in what we know about antibody generation which is inconsistent with my “assumptions”. Antibody generation is a perfect example of intelligent engineering using the realistic resources of probability. It is therefore perfectly natural and reasonable that the immune system of birds or mammals can “produce antibodies against antigens that they or their ancestors never encountered before”.

    In short omission of material context is misleading you.

    3] DK,57: You assume that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation.

    Kindly, first, tell me what is speculative about calculating a configuration space based on a digital element? [This is how memory spaces are routinely calculated, in case you have not done basic digital electronics, for one instance.]

    Last I checked it was uncontroversial that DNA/RNA used a 4-state element, and that there were 20 protein monomers that appear in the vast majority of proteins (a few oddballs notwithstanding). So, to calculate the relevant config spaces is not speculative.

    That DNA/RNA and proteins are sensitive to perturbations from known functional states is a commonplace. Similarly, we could for a first instance look at the proportion of stop codons — UAG, UGA, UAA, i.e three out of 64 — and notice that this high proportion means that most arbitrary DNA/RNA sequences would be non-functional. (Some have observed that the likelihood of getting to a stop codon if one starts to code from an arbitrary initial point on a DNA chain is as sign of the degree of optimisation in the code.)

    So, we first have laid out the config space challenge, onwe that is plainly unmet on the merits.

    on the broader issue of methodology, science works by empirically anchored inference to best explanation. There is a lot of evidence on the above, and so the explanation that a phenomenon such as is observed most credibly traces to agency from the set agency, chance and necessity, is not speculation unlinked to empirical data. Further to this, we have yet to see the proposal of a fourth effective, empirically observed source of cause. Finally, that intelligent agents exist and cause events in our world is a matter of direct experience and observation. So, such agents are plainly possible in our cosmos. (Or, are we here dealing with the evolutionary materialists’ self-referential absurdity of denying the reality of intelligent choice, decision and action, i.e. denial of the reality and credibility of mind?)

    If you desire to deny the reality of cause and of mind as a relevant causal force, you have wandered from the realms of both science and reason.

    4] Events that have occured in the past are historical events. Hypotheses about historical events can only be tested empirically

    And, how is the config space issue non-empirical? How is the incidence of stop codons non-empirical, how is the nature of DNA/RNA as a 4-state code chain non empirical? How is the nature of proteins as based on 20 monomers none empirical?

    We know a lot about such digital systems and the likelihood of accessing desired states by chance, DK. Just, the empirically anchored answers plainly don’t go where you want.

    And, besides, you will note that above and generally, we have pointed out that if you can provide evidence that FSCI can be replicably generated by chance plus necessity, then the EF would collapse as a reliable test of intelligent/non intelligent cause. That is, the EF is subject to empirical test [and if necessary to falsification or corrective refinement in that light. Cf Hyp testing and type 1 and 2 errors thence degree of confidence.]

    We have many observed cases of intelligent action giving us FSCI, but so far over the course of a long time no one has provided a single counter instance of chance plus necessity doing the same.

    Onlookers, what is that telling you about the actual balance of the case on the merits?

    5] As new data are ascertained, some hypotheses will be rejected

    Over the past 50 years, a lot of new data has been coming in. It reveals the intricacy and FSCI-richness of cell based life34. Indeed, it puts such life in the context of information and communication systems and technologies.

    The degree of complexity involved — which is getting higher not lower — is pointing very strongly to the known source of such systems: intelligence and design.

    However, as that does not sit well with the beliefs, worldview commitments and agenda of institutionally powerful forces in our civilisation, that is being stoutly resisted. (BTW, that is why this is not just a scientific issue, bFast.)

    But, plainly, the tide is turning.

    GEM of TKI

  66. PS: Royal Truman, excerpting Gary Parker, gives us an illustrative example in summary here:

    _________

    A cell needs over 75 “helper molecules”, all working together in harmony, to make one protein (R-group series) as instructed by one DNA base series. A few of these molecules are RNA (messenger, transfer, and ribosomal RNA); most are highly specific proteins. ‘When it comes to “translating” DNA’s instructions for making proteins, the real “heroes” are the activating enzymes. Enzymes are proteins with special slots for selecting and holding other molecules for speedy reaction. Each activating enzyme has five slots: two for chemical coupling, one for energy (ATP), and most importantly, two to establish a non-chemical three-base “code name” for each different amino acid R-group. You may find that awe-inspiring, and so do my cell-biology students! [Even more awe-inspiring, since the more recent discovery that some of the activating enzymes have editing machinery to remove errant products, including an ingenious "double sieve" system.[2],[3]] ‘And that’s not the end of the story. The living cell requires at least 20 of these activating enzymes I call “translases,” one for each of the specific R-group/code name (amino acid/tRNA) pairs. Even so, the whole set of translases (100 specific active sites) would be (1) worthless without ribosomes (50 proteins plus rRNA) to break the base-coded message of heredity into three-letter code names; (2) destructive without a continuously renewed supply of ATP energy [as recently shown, this is produced by ATP synthase, an enzyme containing a miniature motor, F1-ATPase.[4],[5],[6],[7]] to keep the translases from tearing up the pairs they are supposed to form; and (3) vanishing if it weren’t for having translases and other specific proteins to re-make the translase proteins that are continuously and rapidly wearing out because of the destructive effects of time and chance on protein structure! [8]

    ___________

    That is the kind of complexity to be accounted for per chance + necessity only, to sustain evolutionary materialist OOL models.

  67. 67

    Yeah KF,

    But you know the issue here that I am concerned with is not the magnitude of the complexity and specificity. Life has always seemed such to me before learning anything thing about the micro world. The issue is that of matter and motion. That is product and destination. I know that the biological matter that makes up identical twins is almost identical but it is obviously not the matter that constructs and validates a person’s existence. The encoding process of the matter- that is the characteristics that make up what we call DNA are the real mystery and the true defining factor of what a living object with becomes. This digital code cannot be accounted for via materialistic mechanisms nor chance and necessity. What then do we appeal to?

    When we talk about design we are usually talking about issues of functionality- and DNA exhibits this in full. It is the form, function and improbability of the arrangement of matter that is needed be accounted for here. Intelligence is the only known cause of FSCI. Intelligence implies design—and, though weaker, a design(er).

    “Intelligent Design is best described as the study of patterns in nature which as best explained as the result of intelligence.”

    -Bill Dembski

  68. GEM:

    , we could for a first instance look at the proportion of stop codons — UAG, UGA, UAA, i.e three out of 64 — and notice that this high proportion means that most arbitrary DNA/RNA sequences would be non-functional.

    So if we induce a start sequence into DNA, then on average we can expect to encounter a stop sequence about 21 triplets later. So the average de novo gene would be 21 aminos long. Assuming the validity of the neo-Darwinian paradyme, as the average gene is about 100 aminos long, either short genes are very unlikely to be effective, or genes must somehow grow in length.

    My math skills are not quite good enought to figure out what percentage of random sequences would produce 100 triplets before a stop, but its got to be rather small.

  69. Paul Giem:

    “Well, let’s see. Is the RNA world “speculation”, or a hypothesis with a lot of evidence behind it, and no major flaws created by the evidence? Or is it one of those “hypotheses” that should be “rejected”? How about the protein world? How about the clay hypothesis?”

    I have no idea. I don’t work in those fields. (I wouldn’t have the courage to attempt something so difficult.) What do those who are actually engaged in the research think?

    “Come to think of it, I seem to recall that DNA code is remarkably similar to computer code…”

    You have stated an analogy. Analogies might suggest hypotheses, and hypotheses might be tested. You have not made an argument.

    “That was insulting. But no more so than your comment that kairosfocus and I were assuming ‘that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation.’ ”

    Insulting? No insult intended, and I am sorry if my honest diagnostic assertion came across that way.

    “There is a lot of experimental evidence to back us up.”

    Is this a case in point?

    “RNA is supposed to polymerize with greater and greater complexity and function as time goes on according to the theory. Yet when RNA and the raw materials for RNA were put into a solution with RNA polymerase, the RNA sequences consistently shortened to the smallest fragments that would be reliably duplicated by the enzyme. That is, instead of evolution, we have devolution. This is actually understandable as survival of the fittest (who says the fittest has to be the biggest? If the only relevant function is reproduction, then smaller reproduces faster). But it doesn’t help the RNA to develop new functions, which it will need if it is to be a steppingstone to life.”

    You did not reference the experiment, so I must guess at its provenance. It resembles something that came out of Sol Spiegelman’s lab many years ago, the purpose of which was to examine the minimum nucleotide sequences required for replication of the RNA. The conditions in that work were set up to select for the “devolution” that was found. Do I have it right? If so, note the power of selection.

    Or this?

    “…so we need 20,000 bases. If we have all the nucleotides we want, a big if, and our minimum requirements are really the minimum and not woefully inadequate, another big if, we are looking at the random production of the long string of RNA that codes all this (with no stop codons and no signals as to where to start or where to cut the resulting RNA) having a probability of 1 in 4^20,000, or 1 in 10^16,666.”

    This is a typical “tornado-in-a-junkyard” formulation. I have highlighted the word “random,” because that is the crucial assumption that anchors this argument, and all such arguments. You are absolutely correct! Given the conditions you outlined, a random process is ludicrously improbable. But what scientist has proposed a scenario for RNA evolution based on random production of a 20,000 base RNA?

    “P.S. Some of us even think that there vas someone who vas dare, but then you don’t believe in old nomadic fairy tales, do you?”

    I suspected you thought as much. Thanks for the chuckle.

  70. gpuccio

    an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen

    The relevant sequences here are the v-genes of heavy and light chain loci. E.g., v-genes of the heavy chain locus are encoded by about 300 nt and you have about 200. As you said:

    The 100 aminoacid protein is obviously a standard example, just to try a computation.

    Even if one takes into account that CDRs are more relevant for antigen binding than FRs you’re still left with a number nucleotides/amino acids that you assume to being beyond the edge of evolution.

    BTW, do other IDists share your opinion that random variation and selection both are intelligent processes?

  71. sparc, “BTW, do other IDists share your opinion that random variation and selection both are intelligent processes?”

    sparc, you are putting words into gpuccio’s mouth. You suggested that his claim that antibody generation is “engineered” is equivelant to saying that random variation is an intelligent process. This is a poor inference. If one can show that engineers use random processes than one can demonstrate that random processes are used by engineers. I would suggest that the random orbital sander is an excellent example of exactly that. As engineers clearly implement randomness as a component of their processes, when we see a “turn on random generator” phenomenon in nature, we can conclude that there is no inconsistency between nature and the metaphore of human-engineered technology.

  72. Re DK:

    Concerning: Speculative OOL models?

    First, though, onlookers, we should note that the PaVian calculation in the original post has yet to be seriously addressed on the merits by the evolutionary materialist advocates.

    The direct implication is that even on the generally accepted timeline, the projected mutation rate for Drosophila, a cluster of species that is part of the Diptera, and is notorious for its high variability, is vastly too low to account for the genome. In short, Darwinian mechanisms might account for micro-evolutionary changes, but not for the body-plan level changes that are the stuff of macroevolution. And, at the heart of that, lies the issue of information origination, another point where we seem to have a diversion from the issue on the merits.

    Getting back to the point raised by DK to PG, perhaps DK is not familiar with the recent exchange between Shapiro [a metabolism first OOL researcher] and the late Orgel [a RNA world OOL thinker], in which the fatal defects in the two main OOL models are painfully exposed:

    ++++++++++

    SHAPIRO, Sci Am:

    The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . . more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

    A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

    To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . .

    The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

    _________

    ORGEL, PLOS:

    If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . Could a nonenzymatic “metabolic cycle” have made such compounds available in sufficient purity to facilitate the appearance of a replicating informational polymer?

    It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield. Each proposed metabolic cycle, therefore, must be evaluated in terms of the efficiencies and specificities that would be required of its hypothetical catalysts in order for the cycle to persist. Then arguments based on experimental evidence or chemical plausibility can be used to assess the likelihood that a family of catalysts that is adequate for maintaining the cycle could have existed on the primitive Earth . . . .

    Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [6]? The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . .

    The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.

    +++++++++

    In short, neither of the major schools of thought rises above the level of highly speculative, empirically challenged models. A similar set of challenges apply to clay world, volcanic vent, cometary iceball, OOL elsewhere and transfer to earth by panspermia, and other proposed OOL models.

    “Speculative” is thus an apt, and perhaps even a charitable term to apply.

    GEM of TKI

  73. Yeah bfast, that would make sense. If simpler strands replicate faster, then that’s all your gonna get. I think I remember Dembski going over this in NFL, glad to see wikipedia actually has an honest article about it.

    Must admit though, I think maybe they should come up with a different term then Spiegelman’s “monster” if all it does is just lose complexity.

    I’ll keep this in mind though for all origins of life discussions I get into from now on, seems like there isn’t enough emphasis put on this.

  74. Frosty:

    When we talk about design we are usually talking about issues of functionality- and DNA exhibits this in full. It is the form, function and improbability of the arrangement of matter that is needed be accounted for here. Intelligence is the only known cause of FSCI. Intelligence implies design—and, though weaker, a design(er).

    Well put.

    GEM of TKI

  75. kairosfocus,

    Thanks for the readings. I bow to your scholarship.

    In short, neither of the major schools of thought rises above the level of highly speculative, empirically challenged models. A similar set of challenges apply to clay world, volcanic vent, cometary iceball, OOL elsewhere and transfer to earth by panspermia, and other proposed OOL models.

    “Speculative” is thus an apt, and perhaps even a charitable term to apply.

    I agree. There are daunting challenges in that field. I’m happy to be merely an occasional student and spectator of those proceedings.

  76. BTW in Biology it’s “transcribed” not “transcripted”. Not as bad as “transcripted proteins” that Jerry introduced at UD but still anoying.

  77. Kairosfocus (#72): “….the projected mutation rate for Drosophila, a cluster of species that is part of the Diptera, and is notorious for its high variability, is vastly too low to account for the genome. In short, Darwinian mechanisms might account for micro-evolutionary changes, but not for the body-plan level changes that are the stuff of macroevolution.”

    Yes, this is PaV’s thesis in the original post, but the limited rate of origination of new genes understates the problem because the genes themselves only code for a fraction of the information to build organisms. To build newly modified organisms a lot more changes are required than new genes (however arrived at) and mutated old genes.

  78. Magnan:

    Correct.

    Epigenetic information is also a key factor, and may actually encode even more information than DNA, through guiding how the embryo develops.

    This simply underscores the force of PaV’s argument.

    GEM of TKI

    PS: DK, I am simply citing Shapiro and Orgel. OOL studies is in utter disorder for those committed to evolutionary materialist models. But, we know a routinely encountered source of FSCI — intelligence. So, worldview agendas aside, why is this so often stoutly resisted as a viable alternative?

  79. Daniel King, (69 and 75)

    It is easier to respond to your most recent posts, as they lay out the reasoning behind your belief. Part of an “honest diagnostic assertiont” is to give the limitations of evidence behind a diagnosis.

    As you noted, your expertise on naturalistic hypotheses on the origin of life is limited. And as kairosfocus noted (72), the experts of the two leading schools find it easier to state why the other guy’s theory is no good than to make a good case for their own theory. The third most popular theory, that of clay first (the origin of Michael Ruse’s attempted explanation of life originating on the backs of crystals in the movie Expelled) has nothing but speculation going for it. That is what the evidence says, as acknowledged by the leading researchers in the field.

    That’s why it just blew me away when you said in (57) that we “assume that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation” and further stated that

    Therefore, a scenario explaining life’s origins is not discoverable solely by speculation. What can be done empirically is to formulate hypotheses based on current understanding of the properties of matter (living and non-living) and its earthly history, and test them for fruitfulness in terms of increasing our understanding.

    It’s the naturalistic OOL researchers that engage in speculation against the evidence.

    You denigrate the observation that DNA code is similar to computer code, calling it an analogy, and saying that it might lead to a hypothesis. I would argue that although by itself it may be weak evidence, it is in fact evidence, and thus to say that we are engaging in speculation without evidence is incorrect. The evidence against other ways of getting life from non-life is also somewhat supportive of our position.

    But what may not always be appreciated is that we now have direct evidence for intelligence causing genetic change. DNA has been deliberately transferred from other flowers to roses, causing a change in their color. DNA has been added to bacteria and yeast by intelligent design; not just DNA for such things as insulin, human growth hormone, and tPA (tissue plasminogen acctivator), but for insulin that has been altered to change its degradation rate in humans. Thus we know that we can get DNA changes by intelligent design. Thus computer code has been proven to be a fruitful analogy and deserves to be taken more seriously than anti-ID websites commonly take it.

    In fact, this raises the question of whether “lateral transfer” should be reconsidered as a mechanism of DNA change. In fact, we have never (AFAIK) observed unassisted lateral transfer beyond about the level of bacteria. If we find bacterial rhodopsin in rice, we may be looking at assisted lateral transfer rather than unassisted lateral transfer.

    Regarding the Spiegelman Monster, it seemed common knowledge enough to me not to have to document precisely where I got it. Obviously, you knew of it too. However, when I first ran into it, disappointment was expressed that the RNA didn’t keep getting bigger and bigger. I am still hunting for that specific reference, but may have found it in Robert Shapiro’s book Origins. I will find out for sure by Monday. Even in the article I read cited by Wikipedia, the researchers stated that they hoped to be able to get longer strings of RNA so that subcellular (positive) evolution could be demonstrated, but I am unaware of any reports of success in that endeavor.

    You apparently agree with me that random formation of enough RNA to code for protein is extremely unlikely. The problem is that there is no known way to get sufficiently specific non-random sequences without intelligent guidance. That isn’t to say that there will never be any known way in the future. But keep in mind that we are looking for “evidence”, not “speculation”. Right now the evidence is against such a non-random pathway.

  80. PG:

    I see your somewhat concessionary excerpt/summary from DK:

    You denigrate the observation that DNA code is similar to computer code, calling it an analogy, and saying that it might lead to a hypothesis.

    This is not really “just an analogy.”

    D/RNA is based on 4-state discrete state — i.e. digital — information storage elements used to implement stepwise control of a process. That — like it or lump it — makes it a digital, algorithm-linked information storage entity.

    So, properly: “instance of,” not “analogous to.”

    That the technology here is based on chemical monomers and shapes of molecules used is simply a matter of how the underlying digital entities are instantiated in a very much analogue physical world. (One of the biggest headaches of digital systems is that we have to implement them physically using very analogue entities . . . sigh!)

    Digital entities can be physically implemented in positions [cams, levers and gears -- cf a Yale lock], voltage or current levels, on/off states of relays and switches [my favourite first teaching system!], magnetic states, and in biosystems, as monomers in specified three-monomer codons in locations on smart polymer chains.

    In each case, chaining of discrete state entities allows for information storage and processing based on symbolic, coded representation and processing elements that respond to input and stored states.

    This is central, and decisive, once we see the resulting config spaces and constraints on functionality. Codes, step-by-step problem solving sequences that use codes and processing machinery and the like are not only routinely observed to be the product of intelligence, but that is the only observed source!

    A glance at the search space issues will show why: absent active information originating in intelligent insight and imagination, the search problem rapidly exhausts the potential search resources of the observed cosmos.

    GEM of TKI

  81. Paul Giem,

    It’s the naturalistic OOL researchers that engage in speculation against the evidence.

    Hardly. Their speculations are grounded in chemistry and geology. The crux of the matter is that their speculations are subject to experimental test. Make a hypothesis and test it.

    You denigrate the observation that DNA code is similar to computer code, calling it an analogy, and saying that it might lead to a hypothesis. I would argue that although by itself it may be weak evidence, it is in fact evidence, and thus to say that we are engaging in speculation without evidence is incorrect.

    Not denigrate. An analogy is not an “observation” or “evidence.” Again, make a hypothesis and test it.

    But what may not always be appreciated is that we now have direct evidence for intelligence causing genetic change.

    Intelligence, yes. Human intelligence.

    Regarding the Spiegelman Monster, it seemed common knowledge enough to me not to have to document precisely where I got it. Obviously, you knew of it too. However, when I first ran into it, disappointment was expressed that the RNA didn’t keep getting bigger and bigger. I am still hunting for that specific reference…

    The reference in question is:
    Kacian, DL, Mills, DR, Kramer, FR, Spiegelman, S
    Proc Natl Acad Sci USA 1972 Oct;69(10):3038-42.
    The abstract is clear enough:

    The aim of the present study is to make available a replicating molecule of known sequence. Accordingly, we sought a molecule that has the following properties: (a) replicates in vitro in a manner similar to phage Qbeta RNA; (b) produces antiparallel complementary strands that can be separated from one another; and (c) is small enough to yield its sequence with reasonable effort.We report here the isolation of a replicating RNA molecule that contains 218 nucleotides and possesses the other features desired for a definitive analysis of the replicating mechanism. Despite its small size, this molecule can mutate to previously determined phenotypes. It will, therefore, permit the precise identification of the base changes required to mutate from one phenotype to another in the course of extracellular Darwinian selection experiments.

    From the discussion of the paper:

    Our goal was to isolate a molecule that replicates in a manner similar to phage Q? RNA and that was small enough to yield the sequences of its complementary strands. This goal has been achieved.

    Do you read disappointment there?

    Right now the evidence is against such a non-random pathway.

    Evidence against. Please provide some.

  82. Paul Giem and kairosfocus,

    I trust that you will take the following in the helpful way that I intend it: Your arguments by means of analogy suffer from a logical problem that I learned about as a stripling. Neither of you would have passed my first year college course in logic if you had tried to defend such arguments.

    Here is a verbatim quote from my textbook, Monroe C Beardsley, Practical Logic, 1950, Prentice Hall, Inc., New York.

    An analogy doesn’t prove anything; it merely calls to mind a possibility that might not have been thought of without the analogy. It’s the experiment that counts in the end. Bohr’s classic model of the atom is only a picture. It has clarified some points about the atom, it has hinted at some good hypotheses; but if you take it as proving anything about the atom, you are misusing the analogy. You can be fooled just as much by it as were those early inventors who tried to construct airplanes that flapped their wings, on the analogy with birds. Analogies illustrate, and they lead to hypotheses, but thinking in terms of analogy becomes fallacious when the analogy is used as a reason for a principle. This fallacy is called the argument from analogy.

    The form of the argument from analogy is pretty clear from this simple example:

    X has certain characteristics a, b, c
    Y has the characteristics a, b, c
    But Y also has other characteristics x, y, z.
    Therefore: X has the characteristics x, y, z.

    This from a professional logician, not a scientist.

    You are both entitled to your own opinions, but you are not entitled to your own logic.

  83. X has certain characteristics a, b, c
    Y has the characteristics a, b, c
    But Y also has other characteristics x, y, z.
    Therefore: X has the characteristics x, y, z.

    Daniel King, how is this bit of reasoning useful in the search for design?

    Because Hamlet does not have characteristic X while War and Peace does, are you saying that is an indication that one may not have been designed?

    Not all variables count, only the relevant ones.

  84. Daniel King, I follow your quote. If phenomenon X has a certain set of characteristics, and analogy Y also has the same set of characteristics, then analogy Y is a good analogy of phenomenon X. However, analogy Y may have some other characteristics which X does not have. Therefore when analysing the analogy rather than the phenomeon, one may be fooled into thinking that all components of analogy Y are part of phenomenon X.

    Now, DNA is a language — it is not “like” a language. When we speak of the “machine language” of a computer’s central processor, it is a language as DNA is a language, as english is a language.

    As a software developer I will often conjur up a new language to allow a user, or another software application to communicate complex material to my program.

    One can therefore deduce that a reaonable definition of language is a syntax that communicates complex details between a sender and a recipient(s). By this definition English is a language. “C” is a language. and DNA is a language because it communicates complex details to the systems that assemble protein, to systems that replicate DNA, and to other systems not yet specified (control systems, etc.) It is a language, calling it a language is not “an analogy.”

    About Spiegelman’s monster’s determination to produce smaller and smaller RNA sequences that replicate. Now, Spiegelman published in ’72. I am reading about Spiegelman in Wikipedia in 2008. My bet is that I am not the first to propose that the next logical question is “does the RNA ever increase in complexity?”

    My simple bet is that if subsequent experiments had produced RNA of increasing complexity, such would be published in Wikipedia under Spiegelman’s monster. However, I am happy to be proved wrong. Please feel free to conjur up for me published evidence that simple RNA replicators will increase in complexity, and will begin to do anything more complex than just making copies of themselves (even making higher resolution copies would likely be useful.)

  85. KF, FSCI (functionally specified, complex information) is not

    stoutly resisted

    here at UD but rather ignored. I am aware that FSCI is regularly mentioned by KF. However, only very few people here took the bait. According to the results of the UD search pages only 14 comments contain replies to FSCI statements (6 by Atom, 2 by Phineas, 2 by Carl Sachs, 2 by aiguy and 2 by Megan.Alavi) while FSCI to my best knowledge has never considered in the posts of Dr. Demski or any other UD contributor. I don’t know if this is the reason but as I understand FSCI it goes beyond Dembskian CSI and is defining some kind of The Edge of Intelligent Design by leaving the realm of ID as defined by the leading heads of the ID movement.

  86. It won’t change much but my FSCI numbers were wrong: I’ve missed 2 comments on KF’s FSCI by Frost122585 and JunkyardTornado. So we now have a total of 16 opinions on FSCI at UD. Actually, I haven’t looked for those entries omitted by the search engine because they are

    very similar to the 55 already displayed.

  87. GEM of TKI, as you know I am another regular on this site, but somehow FSCI has slipped under my rader until now.

    Could you clearly define the difference betwee CSI and FSCI. It would appear that CSI is information that specifies something complex where FSCI is information that specifies something that is both complex and functional. Is that about it?

    As I see it CSI includes some pretty non-functional concepts. For instance, the value of pi seems to be CSI. Certainly the value is complex. It specifies something — the relationship between the radius and the circomference of a circle. As such it would qualify as CSI but not as FSCI, have I got this or am I barking up a different tree?

  88. bfast

    GEM of TKI, as you know I am another regular on this site, but somehow FSCI has slipped under my rader until now.

    If you use the search link on the upper right corner of UD to look for FSCI you will find seven result pages (each with 10 results). Considering the 55 omitted search results FSCI has been mentioned about 120 times at UD only. Thus, it is not surprising that you have missed it.

  89. BFast:

    A quick note — I have used the term Functionally Specified Complex Information, FSCI for short, to identify a subset of Complex, Specified Information that is specified as to function, with biofunction as a particularly relevant instance. [I have usually given the words then the abbreviation in threads where I have used it. BTW, there are at least a few other commenters here who have taken up the concept or the term. Cf here for a discussion of the underlying concepts and terms, including the perhaps surprising point for evolutionary materialists that the concept CSI emerged from the natural development of OOL studies at the turn of the 1980's -- contrary to a lot of ill-informed rhetoric out there, it is not a dubious innovation of ID thinkers such as Dr Dembski et al. Indeed, the first use of the concept I have seen is by ORGEL, in 1973.]

    Thus, we can get around several unproductive definitional debates and zero in on truly substantial matters. A closely related discussion is in Trevors and Abel, 2005, who look at Functional Sequence Complexity, vs Random SC and Ordered SC. (They have a very nice 3D graph, which I use in my app 3 the always linked.)

    BTW, Sparc, in 85, you have taken something utterly out of context when you cited two words only from 78:

    [GEM, 78:] DK, I am simply citing Shapiro and Orgel. OOL studies is in utter disorder for those committed to evolutionary materialist models. But, we know a routinely encountered source of FSCI — intelligence. So, worldview agendas aside, why is this so often stoutly resisted as a viable alternative?

    On basic grammar, “this” speaks to the just past where there is a chain of possible referents; in this case — “intelligence.”

    What is being “stoutly resisted” is not [a] the concept FSCI, but [b] the issue that the only — and routinely — observed source of functionally specific, complex information [and for that matter, after all the debates, CSI in general] is intelligence. And, there is abundant evidence of such stout resistance here at UD and elsewhere.

    Mind you, much of this is on side points and minor, potentially further distractive issues. I therefore observe that the evo mat side are still not seriously addressing the centrally important PaVian challenge at the head of this thread:

    As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

    Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

    GEM of TKI

    PS to DK re 82: The basic fault with your argument about analogies is that you are failing to understand that D/RNA molecules are in fact discrete state informational macromolecules based on chains of 4-state elements and so having up to 4^N configs for a chain of length N, and involved in algorithmic information processing systems within the cell, tha tuse coded information. This is instantiation, not “analogy.” BFast in 84 is quite right. (And I come at this as a “hardy boy” i.e. from the device physics and electronics side of the hard/soft distinction in modern electronics-based systems. “Digital” is not to be confined to electronics based, 2-state systems: our alphabet is a 26 state system, with extensions, and we commonly use 10, 12 and 60 state systems for working with numbers. The ASCII code is thus a 128 state system, which for electronics convenience codes in 2-state chained elements, where 2^7 = 128.)

    PPS, Sparc at 86 etc: Your citation of comments from former threads is quite besides the point (and I am sure that the search results are incorrect, off-point and misleading). As summarised above, I have simply used a subset of CSI where the requisite specification is provided by system functionality constraints. For instance, a random DNA strand has a basic chance of 3/64 that the next 3-letter codon will be a STOP codon. That is sufficiently high that random D/RNA chains are maximally unlikely to code a bio-functional protein. Such a protein has to have a folding sequence, and appropriate key-lock fit to its required environment, with appropriate functional units brought to bear, e.g. cf. the discussion of how enzymes are structured and work at 66 above.

    PPPS: DK at 81, the speculations of OOL researchers are as a matter of fact as excerpted at above, poorly grounded relative to the chemistry and statistical thermodynamics involved, in the case of the Miller-Urey type experiment propose an early earth atmosphere that is unlikely to have been there, and in the case of panspermia, the scenarios are utterly speculative. Quasi-infinite multiverse proposals are similarly a matter of speculation without observation.

  90. H’mm:

    Let me add this from TMLO, ch 8, as cited in my always linked Appendix 3:

    Yockey7 and Wickens5 develop the same distinction, that “order” is a statistical concept referring to regularity such as could might characterize a series of digits in a number, or the ions of an inorganic crystal. On the other hand, “organization” refers to physical systems and the specific set of spatio-temporal and functional relationships among their parts. Yockey and Wickens note that informational macromolecules have a low degree of order but a high degree of specified complexity. In short, the redundant order of crystals cannot give rise to specified complexity of the kind or magnitude found in biological organization; attempts to relate the two have little future.
    __________

    Yockey: J. Theoret Biol, 1977, Vol 67, p. 383

    Wickens: J. Theoret Biol, 1978, Vol 72, p. 191.

    The links to my own descriptive term FSCI should be quite clear from the added emphases in context, and of course the CSI concept actually explicitly appears.

    Here is the 1973 Orgel remark:

    Living organisms are distinguished by their specified complexity. Crystals fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.6 [Source: L.E. Orgel, 1973. The Origins of Life. New York: John Wiley, p. 189.]

    The Specificity in view of course is bio-functional!

    GEM of TKI

  91. I have usually given the words then the abbreviation in threads where I have used it.

    Actually, a google search for
    “Functionally Specified Complex Information” site:uncommondescent.com

    links to 52 pages at UD. If the abbrevation FSCI doesn’t appear in the same threads (which I doubt) this would result in about 170 comments (including KF’s own) in which either the term or its abbrevation occurs.
    I did my best to look through the threads my original UD search linked to but I do admitd that due to the length of KF’s comments which usually run over several screens it is difficult to identify comments by other users that used FSCI. You’ll find comments on FSCI by Atom here, here, here, here, here, and here, comments by Phineas here, and here, comments by Carl Sachs here, and here, comments by aiguy here, and here, comments by Megan.Alavi here, and here, one comment by Frost122585 here, and one comment by JunkyardTornado here. You may add those that I’ve missed.

  92. 92

    kairosfocus,

    I’ve read alot here from you in the last few days about what cannot have been the origin of life.

    I’d be more interested in what you think did happen.

    As best I can tell from your linked website, you consider the origin of life to have been a non-random event.

    Care to comment on what you think was the cause, rather then what was not?

  93. bFast #84:

    One can therefore deduce that a reaonable definition of language is a syntax that communicates complex details between a sender and a recipient(s). By this definition English is a language. “C” is a language. and DNA is a language because it communicates complex details to the systems that assemble protein, to systems that replicate DNA, and to other systems not yet specified (control systems, etc.) It is a language, calling it a language is not “an analogy.”

    Argument by definition.

    Completely convincing!

  94. bFast:

    About Spiegelman’s monster’s determination to produce smaller and smaller RNA sequences that replicate. Now, Spiegelman published in ‘72. I am reading about Spiegelman in Wikipedia in 2008. My bet is that I am not the first to propose that the next logical question is “does the RNA ever increase in complexity?”

    My simple bet is that if subsequent experiments had produced RNA of increasing complexity, such would be published in Wikipedia under Spiegelman’s monster.

    Note that Spiegelman was studying a reaction catalyzed by a bacteriophage (QBeta) RNA polymerase, using the viral RNA as template under highly specified in vitro conditions.

    Irrelevant to your expectations.

    However, I am happy to be proved wrong. Please feel free to conjur up for me published evidence that simple RNA replicators will increase in complexity, and will begin to do anything more complex than just making copies of themselves (even making higher resolution copies would likely be useful.)

    Sorry, don’t know of any, but I’m curious: what do you mean by a “higher resolution copy”?

  95. Argument by definition.

    DK, you are using semantics to avoid the substance.

    Does design exist? Do designed objects have exclusive characteristics? If no, how does one determine whether unfamiliar objects are designed?

  96. DK

    It’s actually an argument by analogy. Bfast accurately described the characteristics of several artificial languages then showed that the language of DNA conforms to those same characteristics. Unless you adhere to some unsupportable dogma that nothing in the universe predating humanity is artificial in nature then the best explanation for a language of unknown origin is that it is, like every other known language, artficial in origin.

    The burden of proof then obviously falls on the person who claims that languages can arise by means devoid of intelligence. Good luck with that.

  97. 97

    One of the features of language is that they can be translated into other languages.

    For example, machine code can be translated into higer level code for us humans. German can be translated into French.

    Hofstader has written an excellent book regarding “information” and where it “is”. By that I mean, what is the thing that is being translated, how can the essence be kept? He translates a single poem mutiple times into different languages and mutiple times (french into german into french again IIRC).

    http://en.wikipedia.org/wiki/Le_Ton_beau_de_Marot

    Can DNA also be translated in a similar way? If so, is anybody doing it? If not, does that indicate an interesting difference from “normal” languages such as English, German etc?

    Tribune7

    If no, how does one determine whether unfamiliar objects are designed?

    How do you determine that? What’s your methodology?

    KairosFocus (from a post you link to above)

    the speculations of OOL researchers are as a matter of fact as excerpted at above, poorly grounded relative to the chemistry and statistical thermodynamics involved

    While I don’t think there is much to get excited about in current OOL research I hold back from belittiling others efforts unless I have something concrete to add to the debate (and even then would hesitate to belittle others, treat others as you wish to be treated etc).

    Care to comment on what you think was the cause, rather then what was not?

  98. The burden of proof then obviously falls on the person who claims that languages can arise by means devoid of intelligence. Good luck with that.

    In linguistics, a language is a set of strings (sentences) over a finite alphabet. Finite state machines, which should be familiar to DaveScot, are language recognizers. The type-3 languages of the Chomsky hierarchy of languages are precisely those recognizable by finite state machines.

    It takes only a two-state machine to recognize the language of all strings over {0, 1} of odd parity (containing an odd number of 1′s). Does anyone REALLY want to argue that a physical system naturally modeled as a parity checker cannot arise by chance?

  99. Me–If no, how does one determine whether unfamiliar objects are designed?

    Rita–How do you determine that?

    Rita, how long have you been lurking on UD? One day? two days?

    What’s your methodology?

    OK, one day.

  100. 100

    tribune7,
    Have you never been told it’s rude to answer a question with a question?

    Rather then start with the passive-aggressive stuff perhaps you could either

    a) Answer the question (links are fine)
    b) Ignore me. This board seems busy and so I don’t see why you would take time out simply to gloat you know more then me. Move onto the substantial debate and ignore my ignorant questions already!

  101. 101

    Tribune7

    Do designed objects have exclusive characteristics?

    Tribune7, if you were transported to alien lands and left to wander round their high technology landscape, perhaps you would encounter a thing the like of why you had never seen. It amazes you, it’s intriciate design, you can’t to work out what it does but it’s obviously doing something, all the lights and liquids moving about.

    When you get a chance, you ask your alien host about it. It turns out it’s simply a natural event, similar in somce ways to Old Yeller, a regular geological event but being on a alien planet surrounded by alien artifacts you were unable to tell. Your “reference” points are missing.

    You say that your list of “exclusive characteristics of designed objects” would save you from making this mistake.

    How?

  102. Rita-Have you never been told it’s rude to answer a question with a question?

    That was one of my points, Rita. Go and look at what I wrote to which you initially responded.

    When you get a chance, you ask your alien host about it. It turns out it’s simply a natural event,

    There is a conception held by many new to ID (or familiar with it via hostile sources) that it is about proving God. It’s not. What it is, though, is showing that design is the best explanation, as of now, for life.

    Basically the method use to do this is taking tested means of determining design, applying them to DNA and having them come back as a yes answer.

    These methods include filters and probability calculations but also much, much more much of which relates to characteristics of information and design.

    Note: to accept ID you have to admit that design exists and has quantifiable characteristics.

    The best place for details is Dembski’s Design Inference website, for which you can find a link at the top of the page.

    Now, with regard to your aliens, there are just three things things that can explain any event: chance, necessity (not nature), and design.

    With standard design searches, chance and necessity are filtered out before design is considered, so you would see this amazing thing and your alien guide would say it is merely a event which, when conditions are right, will happen with a certainty. Hence you would rule out design.

  103. It turns out it’s simply a natural event, similar in somce ways to Old Yeller,

    I’m still traumatized by that movie. :-)

  104. 104

    Basically the method use to do this is taking tested means of determining design, applying them to DNA and having them come back as a yes answer.

    Interesting. Where can I read about this analysis with regard to DNA?

    Now that DNA has been, according to what you say, identified as a designed artifact what next? What follows from that?

  105. 105

    it is merely a event which, when conditions are right, will happen with a certainty. Hence you would rule out design.

    I would say that all events, designed or otherwise fulfill that criteria.

    Can you give me an example of an event that when conditions are right happens with certainty and an example of an event that when conditions are right does not happen with certainty?

  106. Rita start with this from 1998.

    Can you give me an example of an event that when conditions are right happens with certainty and an example of an event that when conditions are right does not happen with certainty?

    You don’t believe in chance? Roll dice. If they are honest you will not know with certainty what the results will be.

  107. GEM of TKI #89:

    What is being “stoutly resisted” is not [a] the concept FSCI, but [b] the issue that the only — and routinely — observed source of functionally specific, complex information [and for that matter, after all the debates, CSI in general] is intelligence. And, there is abundant evidence of such stout resistance here at UD and elsewhere.

    I think that it is an unfair leap to say that FCSI = intelligence. We know that intelligence can cause FCSI, we see it all of the time in our technological world. I also agree with you that biology shows FCSI. However, the question raised by the Darwinian model is whether FCSI is achievable via non-intelligent means. While UDers would agree that FCSI is not possible without intelligence it is not fair argument to use FCSI = intelligence as a premise in this debate. That said, the burden of proof lies squarely in the lap of the Darwinist to demonstrate that FCSI is possible without intelligence.

    Premise, Biology shows FCSI. Premise FCSI is the regular product of intelligence. Premise, no known mechanism other than intelligence has been shown to produce FCSI. Therefore it is reasonable to assume that FCSI is the product of intelligence until another mechanism is demonstrated.

    BTW, I like the term FCSI. It seems that a tighter definition than CSI is more effective in describing that intriguing phenomenon that is going on in life.

    Daniel King, “I’m curious: what do you mean by a “higher resolution copy”?”

    My understanding of RNA replicators is that they have a very high rate of copy errors. If the average copy is 80% like the original, but a new (evolved) RNA replicator was able to produce copies where the average copy was 90% like the original, I would refer to that as “higher resolution”.

  108. 108

    You don’t believe in chance? Roll dice. If they are honest you will not know with certainty what the results will be.

    What does that have to do with it?

    it is merely a event which, when conditions are right, will happen with a certainty.

    You mention nothing about chance? Does chance not affect some events, i.e those that “will happen with a certainty”?

    Can you or can you not give me an example?

    So far the answer appears to be no.

    Which, to me, invalidates a large part of your argument.

    Also I would note that you can still be conned even with honest dice if the thrower is skilled and very much more so when the crooked thrower has control of the envrioment too.
    Fair dice do not mean a fair chance.

    Thanks for the link. Dr Dembski says

    Science faces a crisis of basic concepts. The way out of this crisis is to expand science to include design.

    Tribune7, I would like to know about the analysis with regard to DNA that you mention in comment #102. Please tell me some specifics.

    the method use to do this is taking tested means of determining design, applying them to DNA and having them come back as a yes answer.

    Who, where, when? Where did they publish?

  109. Rita, you asked for an example of an event that when conditions are right does not happen with certainty and I gave you one.

    the method use to do this is taking tested means of determining design, applying them to DNA and having them come back as a yes answer.

    I forgot, you are new to this. Do you know what DNA is and what it does?

  110. 110

    bFast, GEM of TKI

    Biology shows FCSI

    Do different lifeforms have different amounts of FCSI? Or does all living things have the same amount?

    If the amount is different is it possible for you to tell me what amounts various organisms have of FCSI?

    I guess a flagellum is the obvious first one but I suppose the trouble is anything that I might pick other then that likely has not had the analysis done on it.

    So perhaps you two could give me a list of lifeforms and the amount of FCSI in each?

    I would find that very interesting reading!

    If in fact the amount is the same, then does FCSI really tell us anything useful about biology after all?

  111. 111

    I forgot, you are new to this. Do you know what DNA is and what it does?

    I take your condescending attitude to mean that you are not interested in answering my questions.

    Sorry to have bothered you, I should have realised that you simply wanted to talk like a teenage stoner about “design man, DNA IS designed, you test DNA for design and it comes back YES!”.

    It was you who said, quite matter of factly as if it were an everyday occourence

    the method use to do this is taking tested means of determining design, applying them to DNA and having them come back as a yes answer.

    And I simply want more details on how that was done, because between me and you I’ve not heard about that and before I believe it I’ll want more then some anon msg board person telling me it’s so.

    Citations please! :)

  112. 112

    bFast

    That said, the burden of proof lies squarely in the lap of the Darwinist to demonstrate that FCSI is possible without intelligence

    From what little research I’ve had time to do so far on this it seems that most of the web pages talking about FCSI are either this website or Kariosfocus’ website. As such, is it really a worthwhile strategy, a worthwhile way to spend time inventing a concept and then challenging people to knock it over and then claiming victory when it does not happen?

    I’m not saying there is no validity to FCSI, in fact I’m interested in learning more about it and have asked for a few examples already. I’m just saying that it seems like a concept that has yet to meet with widespread acceptance (if a quick google is any guide anyway) and perhaps efforts to promote it outside the small circle that is already using it would be more effective then simply using it as a stick to be darwinists with.

    Just my thoughts!

  113. Rita,

    I am probably wasting my time but do agree that design exists?

  114. Daniel (81 and 82),

    It’s the naturalistic OOL researchers that engage in speculation against the evidence.

    Hardly. Their speculations are grounded in chemistry and geology. The crux of the matter is that their speculations are subject to experimental test.

    I am curious as to how one can transmute “subject to experimental test” into “grounded in chemistry”, without actually passing the experimental test, or more precisely while, as far as we can tell with science, failing the experimental test.

    On the other hand,

    But what may not always be appreciated is that we now have direct evidence for intelligence causing genetic change.

    Intelligence, yes. Human intelligence.

    What is that supposed to mean other than that no other than human intelligence can exist (or at least can have interacted with matter), and that human intelligence cannot have existed at the time of the origin of life? I’ll grant that the latter part of the question should receive an affirmative answer, as if humans exist, then life exists, so the origin of life has to come before humans exist, by definition. But can we be that sure that there is no other intelligence than us humans?

    It appears that any pathway, regardless of how much experimental evidence seems to indicate its practical impossibility, is preferable to postulating an intelligence if that intelligence might lead us in the direction of the supernatural.

    I will say this, though. If that is your sentiment, you have company. Robert Shapiro (I believe the same one whom kairosfocus quoted as a leading OOL researcher), in Origins, A Skeptic’s Guide to the Creation of Life on Earth, states (p. 130),

    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.

    Interpreted, that means, “I will not believe in God regardless of the evidence.” At this point one realizes that one is not discussing science, but rather philosophy. When evidence doesn’t matter, we are no longer in science.

    I read the article by Kacian et al. that you quoted. It is not the one I was looking for. The quotes you gave indicate that the research the article reported was not targeted at finding longer RNA products from shorter initial reactants. Rather it was targeted at getting not just shorter products, which by that time was known to happen, but to get a unique product that could be sequenced.

    But if you read the article, you will note that there were previous articles where the experiments that discovered that RNA would shorten were reported, and those articles are of interest. (Also I need to re-read Shapiro’s Origins.) In fact, even in this article, the eventual goal of a longer RNA molecule is explicit:

    These experiments resolved an interesting dilemma of precellular evolution. THey permit one to see, at least dimly, how selective pressures could have forced replicating nucleic acids to greater length and complexity (11), a necessary prelude to the invention of cells and subcellular components as aids in replication.

    Now ask yourself, have you ever read of experiments that actually resulted in longer RNA strands from shorter initial ones? Why would that be?

    Your argument about analogies is built on a fallacy about science. Science, by and large, is not about logically proving anything. It is about amassing evidence that tends to support, or undermine, theories. Thus arguments that are not logically probative may still have weight. Let me give you two examples, one of which can be properly labeled an argument from analogy.

    First, you should be familiar with statistical tests. The acceptance of the null hypothesis does not disprove the possibility that the real value of a variable is only slightly different from zero. There have been numerous papers that got negative answers when the experiments were simply not sensitive enough to measure the difference that was later actually measured. That is what meta-analysis is all about. On the other hand, the acceptance of positive results at the p=0.05 level is an explicit admission that accepting results like this will wrongly reject the null hypothesis, on the average, one out of every 20 times. Thus science is commonly not about proof, but about evidence.

    The second is more pertinent. In medicine, we commonly study patients, find out how they respond to drugs, procedures, etc., then assume, based on analogy that other patients will respond similarly. We know that this is not always the case (the placebo effect and the study effect being two exceptions), and yet we accept the studies as evidence of how unstudied patients will respond. We presume that the unstudied patients will behave analogously to the studied ones. This is evidence, but not logical proof.

    Likewise, the fact that computer code is similar to DNA code is evidence, but not proof, that they have a similar origin. Your insistence otherwise is mixing up evidence and proof.

    In fact, nobody would be fooled by the argument from analogy if it did not have some basis in fact. If it had no validity whatsoever, people would figure that out and the argument would never be used. Evidence is different from logical proof.

    You quoted me and said, “Evidence against. Please provide some.” The original paragraph that you quoted one sentence from dealt with the formation of RNA and read as follows:

    You apparently agree with me that random formation of enough RNA to code for protein is extremely unlikely. The problem is that there is no known way to get sufficiently specific non-random sequences without intelligent guidance. That isn’t to say that there will never be any known way in the future. But keep in mind that we are looking for “evidence”, not “speculation”. Right now the evidence is against such a non-random pathway

    RNA has been “spontaneously” polymerized in two ways. First, nucleotides have been allowed to join without any guidance whatsoever. WHen they do, they preferentially join in 2′-5′ linkages rather than 3′-5′ linkages. That is, they do not even form RNA. Secondly, they can be joined by RNA polymerase. It is debatable whether this can be considered intelligent guidance, as whether such a complex molecule as RNA polymerase can spontaneously form from amino acids is itself doubtful, and has not been observed in nature. But leaving that aside, what is created is apparently mini-Spiegelman monsters. Remember the goal that I set in the paragraph that you were querying. It was to “get sufficiently specific non-random sequences” to “code for protein”. These mini-monsters apparently only code for some 14-16 amino acids, not counting stop and start codons. That is not enough length to code for protein, let alone enough specificity. Thus it is fair to say that we have evidence (not proof, as I made clear) that is against the idea that there is a non-random pathway to obtain RNA that codes for protein.

    But your question reveals a deeper philosophical bias. which needs to be addressed. In your original comment for this particular discussion (57), you claimed that we “assumed” that “speculation” could answer certain questions, instead of “testing empirically”. In the paragraph I quoted above, I pointed out that in the matter of a non-random pathway for generating RNA that would be specific enough in its sequence to be functional as riblsomes, t-RNA, codes for aminoacyl-t-RNA synthetases, etc., there was no evidence for such a pathway. Thus the pathway remains speculation. In fact, the evidence was against it.

    I have given reasons why, IMO, the evidence is in fact against such a pathway. But what you fail to realize is that even if I were wrong, the evidence would still not point toward such a pathway. Belief in such a pathway in the absence of positive evidence would still be “speculation”. If belief in the polymerization of RNA in ways that are (a) non-random and (b) directed towards useful sequences in creating life from non-life, does not have positive experimental evidence backing it up, then it is not evidence-based but faith-based. Your assumption seems to be, in contrast, that as long as we can’t definitively prove that there isn’t a non-random way of producing useful (for the purpose of producing life) RNA, that this theory should be given preference. That’s only true if one starts out with faith and requires science to definitively prove that faith wrong. But that’s precisely what fundamentalists are accused of doing. Are you a naturalistic fundamentalist?

  115. 115

    Paul Giem,

    The idea that an unsolved problem in science is an argument for the existence of a deity is attractive to many. Given that a deity created life on this planet, would it not be an act of devotion in the tradition of Kepler, Newton, and Einstin to continue efforts to discover how the deity brought that marvel about?

    I read the article by Kacian et al. that you quoted. It is not the one I was looking for.

    Let us know when you find it.

  116. RitaFairclough:

    From what little research I’ve had time to do so far on this it seems that most of the web pages talking about FCSI are either this website or Kariosfocus’ website.

    Maybe you didn’t look hard enough:
    In addition to FSCI you will find Functionally Specified, Irreducible Complexity (FSIC)developed by [name deleted] here in comment 161 which seemingly is similar to FSCI but not identical. It would be interesting if [name deleted] shows up here to discuss the differences between FSCI and FSIC with Kairosfocus.
    In the meantime you may permutate FSCI and google the results.

  117. Rita (sorry to hear you hit moderation, though I’m not surprised.)

    I’m not saying there is no validity to FCSI, in fact I’m interested in learning more about it and have asked for a few examples already. I’m just saying that it seems like a concept that has yet to meet with widespread acceptance.

    FSCI is a term that doesn’t have very wide acceptance. However, the concept has been on the table for a long time. The concept of CSI is a foundational concept of the ID movement. The CSI that is of particular note is the “functional” subset. I think that the term FSCI clarifies the issue, however the issue has been clearly defined for a long time prior to the GEM’s clarifying terminology.

  118. Moderators:

    I have to first bring to your attention Sparc at 116.

    For, for a SECOND time in this thread, my personal name has been used without permission.

    This, in a context where it is notorious that ID thinkers are subject to “expelling” and where on my part there is a definite spamming problem. [I have kept up a link to contact information in my personal site for responsible use.]

    GEM of TKI

  119. Now, on FSCI:

    I find it interesting to observe the various side-debates on the meaning and usage of this fairly obvious sub-set of CSI: FUNCTIONAL specification as a case in relevant point of complex specified information.

    I therefore again draw our attention to the basic, unmet [and often distracted from . . .] challenge put by PaV in the post at the head of this thread:

    As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

    Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

    In short, the evidence is that the search resources available the evolving Drosophila genome across time were inadequate to arrive at the observed variations in the Genus, and indeed, to originate the underlying DNA set itself [which I gather is about 180 mn base prs, or about 360 Mbits of information storage capacity].

    In short, this is a case in point of the issue of FSCI in action.

    In that light, a few remarks on points on FSCI, some [with all due respect to whomever it may concern] corrective:

    a –> There is no subtle distinction between terms to play around with, just the obvious point: specification of complex information is most obvious and objective when the information has to function in a working entity.

    b –> And, anyone who has had to debug a complex software program will attest to just how vulnerable to perturbation or accident such FSCI is.

    c –> In short, we are looking at very limited zones of situationally/contextually required function in the wider configuration space possible for the relevant information storing capacity.

    d –> Indeed, at just 500 – 1,000 bits or so of information storage capacity, we overwhelm the chance-based search resources of the observed cosmos across any credible estimate of its lifetime. (And, mechanical necessity — the third item from the causal factor triad: chance, intelligence, necessity — is associated with low contingency, e.g. as discussed above and in the always linked, heat + fuel + air –> fire. High contingency situations are explained by inference to chance and/or intelligence as a consequence. Cf. classic statistical hypothesis testing for a well-known example, where the null hyp is often a chance hyp and the alternate is deliberate i.e. intelligent action.)

    e –> Intelligent designers, by contrast with chance, use imagination, skill and insight to drastically cut down the zone of search. In turn, that is why the detection of FSCI is a good test for agency: [1] highly contingent, so not a result of mechanical necessity; [2] [functionally] specified beyond the credible reach of available chance-based searches, so not mere chance; [3] i.e., FSCI, so, intelligent design. [4] Thus, FSCI is empirical evidence pointing to design as its best explanation, and if we wish our scientific theories and wider worldviews to be empirically adequate, we should therefore reckon with that fact.

    f –> As I already documented above, when leading OOL researchers were looking at the characteristics of the macromolecules of life across the 1970′s, they came up with the point that such molecules show complex specification, and that the specification is functional. CSI is therefore more generic, FSCI is more specific and is a relevant subset of CSI.

    g –> As to quantification, we easily enough can quantify information storing or transmitting capacity, ever since Shannon and co. Functionality is observable and in principle quantifiable, though that may be situationally specific. Vulnerability to loss of function is equally observable and quantifiable at least on a case by case basis, as software developers know all too painfully well.

    h –> In particular, let us first look at a simple vector quantification: (x, y, z), where x — information storage capacity [bits], y — observed functionality [1/0], z — sensitivity of function to perturbation (we could use a percentage metric relative to observed peak performance). We can then plot FSCI in a 3-D space, highlighting that there is a threshold of 500 – 1,000 bits of information storage capacity.

    i –> And, since FSCI is a strict subset of CSI, the more sophisticated quantification of CSI developed by Dembski et al, e.g. cf here, also applies. Notice that my simplistic 3-d view above is in effect a stage to the fuller quantification. (In short the “how do you measure CSI” argument is too often a strawmannish dismissal in the teeth of the fairly easily accessible facts. But in this field, sadly, there are a lot of very publicly prominent critics who say what they think they can get away with, even though they know or should know better. It is therefore no surprise to see that many are confused by such academic discourtesy or worse.)

    j –> The obvious next point is that we easily enough can know what FSCI is and in fact routinely use it all the time, most familiarly in IT systems, such as even to post in this blog thread.

    k –> So, we further know that routinely, FSCI is produced by intelligence, and we have no case where its cause is known and the source is not intelligence.

    l –> Thus, provisionally — per classic scientific induction, we may see that FSCI is a characteristic of intelligence and/or is sourced in intelligent design and action. That is not to “equate” FSCI and intelligence but rather it is to state its reliably known SOURCE. [Which is exactly what I explicitly stated previously, and linked on!]

    m –> As to irreducible complexity in the context of FSCI, I note that in many situations where FSCI is a relevant inference, the complexity is not just a matter of being beyond so many bits, and the specification is not just a matter of gradual loss of function as we vary across a range. There may often be an irreducible core of components, where the removal of any one causes catastrophic loss of function; as anyone having had to troubleshoot serious electronics systems can fervently testify to. Thus, there is a clear tie-in to Behe’s concept of Irreducible Complexity.

    n –> So, we may, per GP’s suggestion many months ago, imagine a vast pacific ocean, with islands and archipelagos of functionality. Once we are onshore of an island, we may climb up to peak perfoirnmance, but before we can do so we have to arrive on its shores. We may hop from one island to another in an archipelago at random if we have sufficient search resources [cf here the Bahamas], but we have to be IN the archipelago first. And, a random walk search from an arbitrary start-point in the ocean is maximally unlikely to reach to any island or archipelago.

    o –> In short, we can first directly see the OOL problem: getting to first biofunction in a context of vast config space. [This is not just a matter of an as yet unsolved problem [of 150 years standing], it is the sort of issue that is the statistical premise of the second law of thermodynamics: cf my always linked, appendix 1. And, we already know that ther eis a routine and reliably observed source of FSCI — intelligence. So, what is really at work is an imposed worldview level roadblock, in blunt terms: commitment to evolutionary materialism that has hijacked the name, “science.”]

    p –> We can next see the body-plan level macroevolution problem: If the islands of function are sufficiently separate, random walks [or the equivalent] away from an island of functionality will also with absolutely overwhelming probability, exhaust available search resources.

    q –> We also see why significant mutations will be relatively rare, as event eh numbers posed by the researchers cited by PaV point to. This of course also dovetails with the observed sudden appearances, relative stasis and sudden disappearances that are the notorious and longstanding observed characteristic pattern of the fossil record.

    ++++++++

    In short, the issue of FSCI goes to the heart of where the evidence points: design. But, design in the context of OOL and OO body-plan level biodiversity are plainly not very compatible with the institutionally dominant adherence to evolutionary materialism, thus the controversies.

    GEM of TKI

    PS: I repeat, the information in DNA is digitally coded [4 states per element in the informational macromolecule's chain], algorithmically functional information. Here is Wiki on DNA:

    Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information . . .

    This is instantiation, not analogy, and notice how the concept of functionally specified complex information fits in ever so naturally, as the OOL researchers of the ’70′s indicate.

    Next, every time we represent the DNA information as “GCAT” strings, we are translating it into another digital coding system, here, alphanumeric characters. GCAT is of course in turn routinely expressed in binary digital bits, expressed in voltages, light pulses or magnetic states. That is, we see the smooth transfer of information from one language and expression to another. (We could even conceptually at least implement a program that would read and implement GCAT strings by making proteins per specifications — a protein printer if you will. Of course such is a long way off, but a simulation is probably currently feasible.)

  120. GP;

    Re 114: excellent post!

    GEM of TKI

    PS: It is one and the same Robert Shapiro indeed.

  121. Rita:

    I have used a descriptive, clarifying term, and have identified its roots in the natural development of OOL studies, at the turn of the 1980′s. That should be quite enough to show that the term is useful, which makes who does or does not commonly use it or near-enough terms utterly irrelevant.

    And, debating terminology will not resolve the underlying issue.

    That issue is that we can easily enough see that certain information bearing entities are functionally specified [they function and are fairly sensitive to perturbation), and are sufficiently complex [high information storage capacity] that the resulting configuration space isolates the functional islands to a point where chance-based trial and error searches from arbitrary [as opposed to intelligent] start points are maximally unlikely to arrive at first function per available search resources. [Cf my thermodynamics based discussion here (and the onward linked one in TMLO) if you want more details.]

    By contrast, we know that, routinely and reliably, intelligence produces such FSCI-bearing entities. So, we have excellent reason to infer from FSCI to intelligent action as its key causal factor.

    Thus, the mere fact that DNA is an instance of FSCI is good reason to infer that its best explanation is intelligence. That is, DNA is evidence that there was intelligent design involved in the origin [and major diversification] of life.

    That may be unpalatable for those committed to one species or another of evolutionary materialistic thought, but it is what the evidence and inference to best explanation per constraint of said evidence, warrant. Worse, the trend of the discovered evidence is that the degree of complexity involved in DNA etc is much more than we already discern. (Think of what is happening on epigenetics and on so-called junk DNA.)

    So, we are back at what GP has highlighted in 114: the root issue is philosophy and institutional dominance of philosophically linked materialistic worldview agendas, not the verdict of untrammelled science.

    GEM of TKI

  122. PS: Link

  123. 123

    Paul Giem:

    First, nucleotides have been allowed to join without any guidance whatsoever. WHen they do, they preferentially join in 2?-5? linkages rather than 3?-5? linkages. That is, they do not even form RNA.

    Reference, please.

  124. kairosfocus:

    If the islands of function are sufficiently separate, random walks [or the equivalent] away from an island of functionality will also with absolutely overwhelming probability, exhaust available search resources.

    GEM, I like your term FSCI. It seems to more tightly define the characteristic that we see in DNA than the more general CSI term does. I also like the island analogy. I think that it accurately describes the challenge of finding new functionality.

    I think you are right. I think that the fact that DNA is FSCI makes a strong case for it being designed. However, please allow me to play devil’s advocate for a post.

    There remains to be a challenge. That challenge resides in the word “if” in the quote above. The issues are:
    1 – How big are the islands of functionality. Surely DNA has demonstrated an ability to describe a functional component within a vastly larger island of functionality than, say, software languages. (I remember once printing out an error report 6 pages long, caused by a single missing semicolon).

    2 – What is the frequency of islands. Are we talking the thousand islands here, or the middle of the Atlantic?

    3 – Is the neo-Darwinan search truly random. Let me suggest that it is not. Consider for instance the duplicate gene, duplications being one of the common mutational events. The duplicate is now subject to mutation. If it falls off of its island of functionality, no-one cares. However, it is now searching for new shores. But its search is out from where it is. I would think that with functionality, as with oceans, one is much more likely to find an island near another island than one is via randomly sticking a pin in a map.

    4 – Does the sea-level change. If I see a person stuck on an island in the ocean I need not conclude that he got their via a boat. He may have walked there during low tide. Allen MacNeill spoke of a large lake that had never had fish in it. When a small group of fish made it into the lake, they soon split into multiple species. Why? In that land of plenty there were lots of custom niches, and the land was generous to even some level of dysfunction within mutations. Ie, it was like the sea level had dropped, more islands were exposed, and more land bridges were exposed.

    The question remains, could it be that even though DNA is well described as containing FSCI, it is still the product of simple natural processes? I suggest that this can only be determined by carefully analyzing the data, the size and frequency of islands, the proximity of islands to other islands, and the effects of hydrodynamics (tides, sea-level changes etc.)

  125. Sparc,

    You were warned about using KF’s name and even apologized for it so I know you read the warning. And this right after I decided you were trustworthy enough to remove from the moderation list.

    Fool me once, shame on you. Fool me twice, shame on me.

    Adios.

  126. 126

    Kairosfocus:

    Next, every time we represent the DNA information as “GCAT” strings, we are translating it into another digital coding system, here, alphanumeric characters. GCAT is of course in turn routinely expressed in binary digital bits, expressed in voltages, light pulses or magnetic states.

    You have misunderstood my point. I’m saying that one human language can be translated into another imperfectly. DNA (GCAT) is digital and always will be, is it not? Even if expressed in analog languages it can be translated in totality, what you refer to is simply changing the format of representation. A simple cypher if you will. If you know the “code” you can obtain a perfect retranslation even if the data is represented in voltages, light pulses, magnetic states or smoke signals.

    My point (and Hofstaders) is that a poem can be in one language, say French, then translated into German by somebody and then translated into French again by somebody else. Hofstader actually did this, in various ways.

    This cannot be done with DNA

    That is, we see the smooth transfer of information from one language and expression to another.

    And my point is really the opposite can happen with languages. And so this is one way that DNA can be said to differ from language. How many wars are a result of a botched translation?

    And don’t forget that in each language the poem was still a poem, but represented in a different way. Yet it still worked. Does DNA perform the function of DNA when represented in any other way then via deoxyribonucleic acid?

  127. 127

    without being too “strawmanish” could I refer GEM of TKI back to my post at #110?

    So perhaps you two could give me a list of lifeforms and the amount of FCSI in each?

    I would honestly like to know. KF as you have pushed the FSCI button, could you provide such a list?

  128. DaveScot,

    It was Daniel King, not sparc, who used KF’s name on this thread and then later apologized (at 50).

    From sparc’s post (at 116) it appears that he is unaware that the two names have any connection. He cites a blog entry under the offending name only because it pertains to the subject at hand (the definition of FCSI) and mentions the author’s name of that entry. It was KF, and not sparc, who connected the two names via his objections at 118.

  129. 129

    Sorry for the mutiple posts! I wrote:

    My point (and Hofstaders) is that a poem can be in one language, say French, then translated into German by somebody and then translated into French again by somebody else. Hofstader actually did this, in various ways.

    And my point was that the french to german back to french gives a poem (chances are good) that is different to the original poem. It might be about the same thing and have similar language and concepts but chances are it’s expressed in different ways. Very different from the “translation into a different symbolic representation” represented by sequencing DNA and talking about it on a blog, for example. The code has the same values whatever the representation, on the screen or in the testtube.

  130. It appears that sparc knew exactly what he was doing. He said,

    It would be interesting if [name deleted] shows up here to discuss the differences between FSCI and [name omitted by me] with Kairosfocus.

    That would appear to be a deliberate tweak.

    Granted that it was his first time, but he appears to have known better.

    Whoever is doing the editing (DaveScot?) should also remove the link, and possibly the permutation, to make it harder to make the objectionable connection.

  131. Sorry Sparc. You’re back.

    KairosFocus: Stop complaining about people using your real name here. You link to your website constantly and your real name appears on it. Fix it yourself one way or the other but don’t expect us to waste our time on it anymore.

  132. Rita

    DNA is a code structured very much like morse code. Coding DNA performs essentially the same task as computer code in that it consists of abstract instructions which control a machine. Like computer languages it has rigid structure, syntax, and semantics associated with it. We’re very far from being able to “speak” it fluently but it is indeed a machine language. I’m fluent in several machine languages so this is very familiar ground for me.

  133. Rita, I am a bit lost. Why the comparison between translating french to german and back with transcribing DNA?

    BTW, there actually is a very tight parallel to the French-German thing. Consider that a coding gene will translate from DNA to protein. However, it is totally possible to reverse this translation back to DNA. The results, however, will not be identical to the original DNA, the results will produce the identical protein, but will involve different DNA sequence. This because there are multiple DNA sequences that transcribe to the same amino acid in the protein.

  134. Sorry Sparc. You’re back.

    KairosFocus: Stop complaining about people using your real name here. You link to your website constantly and your real name appears on it. Fix it yourself one way or the other but don’t expect us to waste our time on it anymore.

    Thank you Dave.

  135. Daniel King, (115 and 123)

    I found the references. The first is Robert Shapiro, Origins, A Skeptic’s Guide to the Creation of Life on Earth, p. 162. One would have to read most of the book (which I highly recommend) to understand the precise context, but suffice it to say that when, discussing the Spiegelman experiments, when he says, “The RNA did not acquire a new capacity, nor could it do so.” (p. 161), it was a negative remark.

    The reference for RNA naturally forming 2′-5′ rather than 3′-5′ linkages is found in Albert Lehninger, Biochemistry: The Molecular Basis of Cell Structure and Function, 1970, p. 779. I think I actually used the second edition, and it was in that book, but I don’t happen to have a copy of that edition.

    I found out that nucleotides can be joined to yield strings that could theoretically code for a protein up to 81 amino acids long, although the sequence was not, as far as I know, for an actual protein. The size RNA was apparently about that of the Spiegelman monster. Apparently according to Shapiro, there have also been experiments where ribose has been joined to a base, probably adenine, and others where phosphates have been added to nucleosides, although Shapiro did not give references, so I am unable at present to evaluate how important those reactions were. Shapiro didn’t seem too impressed with them, which raises the question of whether they were similar to the very artificial synthesis of pyrimidines. But I though that in fairness I should include this information.

    I am not sure how to interpret one of your comments. “The idea that an unsolved problem in science is an argument for the existence of a deity is attractive to many.” Do you see that as good, or as bad? I am not sure that there is any other way to detect the existence of a deity than otherwise unexplained events in nature or history (which is claimed as a part of nature by believers in naturalism). If there is to be any evidence for the existence of God, it must upset naturalists. Then naturalists will just have to be upset if God really exists and can be detected, as Romans 1 and Hebrews 11 seem to indicate.

    You say, “Given that a deity created life on this planet, would it not be an act of devotion in the tradition of Kepler, Newton, and Einstin to continue efforts to discover how the deity brought that marvel about?” Deuteronomy 29:29

  136. 136

    bFast

    Rita, I am a bit lost. Why the comparison between translating french to german and back with transcribing DNA?

    I’m just making the point that perhaps “language” is the wrong word to use when talking about DNA. Languages, as I have pointed out, have features that DNA does not have and so perhaps a different word would be more accurate when talking about language.

    Earlier you said

    Now, DNA is a language — it is not “like” a language. When we speak of the “machine language” of a computer’s central processor, it is a language as DNA is a language, as english is a language.

    Except one of those things is different to the other.

    If DNA is a language, can it be translated into French?

    If not then it’s not “like” english, at least in that specific way, which can be so translated (and back again if desired).

    DaveScot

    Like computer languages it has rigid structure, syntax, and semantics associated with it.

    And I believe this is another significant difference. New languages can evolve in surprisingly little time, taking their roots from whatever is available. For example, groups of deaf children left to their own devices and neglected have be found to invent their own sign language. Again, this shows that human languages (and indeed comptuer languages) can express rigid structure, syntax, and semantics but none of those things are absolutly required, whereas in DNA they are. So, another way in which DNA needs a better word then “language”. There are too many differences.

  137. 137

    Paul Giem
    The OP says

    14,000 genes/8 new functional genes per million years

    I’m surprised that you have not mentioned some disagreement with that figure. From what I’ve read at the AIG website you appear to believe that the earth is literally less then 100,000 years old, or thereabouts. While your points are interesting I find it more interesting that you don’t make plain your meta-ojection to the whole idea in the first place, I.E that a million years cannot have passed in any case.

    Why?

    Earlier you said

    It is true that standard evolutionary theory assumes that chimpanzees and humans (or monkeys and humans, for that matter) descended from a common ancestor which was not a modern chimpanzee. However, until the ancestor is found, it remains hypothetical, and the ancestor could be essentially a modern chimpanzee, or the ancestor, the modern chimpanzee, and the modern human could be genetically equidistant.

    Yes, the ancestor is yet to be found but I find it, to be perfectly honest, dishonest that your primary objection to the whole thing has not been made clear to all, namely that as you believe the earth is not very many years old none of it could have happened that way in any case.
    Your AIG webpage, presumably written by you says

    It basically forces one into accepting a short chronology for life on earth.

    Thus, if one accepts a designer intelligent enough to produce life, and a short timescale, it becomes very difficult to avoid the claims of the Bible.

    Why do you even pretend to consider things and construct arguments against events that require a long chronology when you already know they are not possible?

  138. Dave and Sparc:

    I must first thank you Dave for being sufficiently concerned to try to stop abusive use of my name in a context where I have specifically requested its non-use, because of the spamming effects.

    [Sparc, your use of my name here cannot get me "expelled," but it can cause me problems and headaches. I ask you to respect that. Also, I think you should be very careful of how you decide to use personal information online, in general; especially in this context. And, above when I noted on a second unauthorised use of my name here in this thread, I had no intent6 that it be taken as by the same person.]

    As I have stated all along, I have left my contact information accessible enough through my personal site for accountability and responsible communication. That is a point where I think I can balance the spamming issue and the need for a measure of accountability and responsible communication.

    As to the issue of irresponsible use, I note that the always linked page lists at its very head:

    A Kairosfocus Briefing Note . . .

    And it states in the note at its foot:

    This briefing note was originally created by GEM of TKI . . . [NB: Because of abuse of my given name in blog commentary threads, I have deleted my given name from this page, and invite serious and responsible interlocutors to use my email contact below to communicate with me.] . . .

    I think that should be clear enough.

    GEM of TKI

  139. Now, on more substantial matters:

    1] Islands and archipelagos of function

    Cf 43 above.

    This will show that it almost does not matter, once we see that functionality is sensitive to perturbation, i.e. the islands are relatively isolated in a vastly larger sea of non-functional configs.

    In particular, we should realise that 500 – 1,000 bits of increment in information capacity is enough to easily exhaust not just planetary scale resources, but those of the observed cosmos. And, that 300 – 500 k bases is actually an underestimate for life functionality, as the organisms with such short genomes are dependent on others to provide key nutrients that they cannot make for themselves.

    1 mn bases is more like the real lower limit. 4^1 mn ~ 6.4 *10^602,059.

    10^1,000 islands of 10^1,500 functional configs each — each of these vastly more than the observed universe can access across its lifetime, would bring that down to searching for 1 in about 10^ 598,500. It here were 10^500 sub-universes of scale similar to ours, that would hardly make a practical difference. In other words, we have excellent reason to see that functionality is truly isolated in the config spaces for DNA of adequate chain length to sustain life.

    2] Translation

    DNA is a digital CODE, with connexion to a defined artificial programming language, and is used in physically executing algorithms through molecular machinery.

    Kindly show a single instance where such FSCI has originated — per directly known cause — through chance + mechanical necessity without intelligent intervention. (By contrast we routinely know that such are produced by intelligent agents.)

    Not only is this a matter of direct observation, but also, the requisite search to produce such a complex, would easily exhaust the search resources of the cosmos. But we know also that intelligent agents use insight, knowledge, imagination and skill to narrow down the search zone to manageable proportions. That is why intelligence outperforms chance-based search.

    Whether or no poems can be translated from French to German and back again is utterly irrelevant to this.

    3] Quantification

    I have given [1] a simple framework in which quantification may be presented as a vector, [2] a link to which the quantification of the wider CSI concept is defined, [3] above, real world discussions on the decisive quantification issue — configuration space and isolation of biofunctional states therein.

    That is more than enough to answer to the real issue: we have a filter for identifying that certain phenomena show objective, empirically identifiable, credibly reliable signs of intelligence as the decisively important causal factor.

    ____________

    That’s all folks.

    GEM of TKI

  140. —–Paul Giem: “It appears that sparc knew exactly what he was doing.”

    I agree. The fiasco with DK would have been hard to miss. While I agree with Dave’s final decision, I note that sparc covered his anatomy very well. That conflict was no accident—it was “designed.” That would explain why he didn’t apologize for the violation.

  141. Rita

    Again, this shows that human languages (and indeed comptuer languages) can express rigid structure, syntax, and semantics but none of those things are absolutly required, whereas in DNA they are.

    They are as required in DNA as in any machine language I’m familiar with and I’ve used a lot of machine languages. I’ll agree that DNA, as far as we know, isn’t a high level structured language like Pascal or English but when we learn more about it we may indeed find out that it is. We only understand a small fraction of it at this point in time. In the nonce, coding DNA, which we understand fairly well, is quite like low-level machine languages (typically called “assembly langauge”) with messages encoded in a serial stream of base-4 digits. Ribosomes read copies of these serial streams sequentially, executing the instructions as they go along, exactly like paper tape going through old computers.

    I’d love someone to describe to me how an abstraction layer like the genetic code can arise without being planned. There is nothing else in nature that utilizes abstraction layers except for living things and manmade machines.

  142. 142

    Paul Giem #135:

    I found the references. The first is Robert Shapiro, Origins, A Skeptic’s Guide to the Creation of Life on Earth, p. 162. One would have to read most of the book (which I highly recommend) to understand the precise context, but suffice it to say that when, discussing the Spiegelman experiments, when he says, “The RNA did not acquire a new capacity, nor could it do so.” (p. 161), it was a negative remark.
    The reference for RNA naturally forming 2?-5? rather than 3?-5? linkages is found in Albert Lehninger, Biochemistry: The Molecular Basis of Cell Structure and Function, 1970, p. 779. I think I actually used the second edition, and it was in that book, but I don’t happen to have a copy of that edition.

    Thanks for your good efforts, but I hope you understand that references to books are not as helpful or as scholarly as references to the primary scientific literature. One reason is accessibility. I don’t have either of these books at hand, but I have good access, mainly through the Internet, to the primary literature. The other is reliability. Book citations are secondary sources, necessarily selective, and possibly inaccurate. For example, the “negative remark” by Shapiro has to be taken in context. I believe I know the reasons for Shapiro’s remark, based on my understanding of the biology underlying the Spiegelman experiments. Do you understand that biology?

    I found out that nucleotides can be joined to yield strings that could theoretically code for a protein up to 81 amino acids long, although the sequence was not, as far as I know, for an actual protein. The size RNA was apparently about that of the Spiegelman monster. Apparently according to Shapiro, there have also been experiments where ribose has been joined to a base, probably adenine, and others where phosphates have been added to nucleosides, although Shapiro did not give references, so I am unable at present to evaluate how important those reactions were. Shapiro didn’t seem too impressed with them…

    And from your #114:

    Now ask yourself, have you ever read of experiments that actually resulted in longer RNA strands from shorter initial ones? Why would that be?

    The synthesis of long strands of RNA under laboratory conditions is a major issue for you. In fact, I believe that I have read of experiments that resulted in longer RNA strands from shorter initial ones. I may even have read of experiments in which RNA strands were synthesized without a primer. Perhaps you could help me narrow down the field, so I can check further.

    Would you like strand elongation catalyzed by an enzyme, or not?

    Elongation on a template (as in the Spiegelman QBeta case) or not?

    Primer, or not?

    I am not sure how to interpret one of your comments. “The idea that an unsolved problem in science is an argument for the existence of a deity is attractive to many.” Do you see that as good, or as bad?

    How I see it is irrelevant. I was simply acknowledging your perspective as a premise for what I said next.

    I am not sure that there is any other way to detect the existence of a deity than otherwise unexplained events in nature or history (which is claimed as a part of nature by believers in naturalism).

    Surely your faith does not rest on such a slender reed.

    If there is to be any evidence for the existence of God, it must upset naturalists. Then naturalists will just have to be upset if God really exists and can be detected, as Romans 1 and Hebrews 11 seem to indicate.

    Apparently the work of naturalists, which does not bear in any way on considerations of the existence of deities, upsets you.

    You say, “Given that a deity created life on this planet, would it not be an act of devotion in the tradition of Kepler, Newton, and Einstin to continue efforts to discover how the deity brought that marvel about?” Deuteronomy 29:29

    That’s it? That’s your entire comment?

    First, let me correct the spelling of Einstein, and then let me add the name of Louis Pasteur to those good theists who understood the scientific method and employed it so effectively, contradicting the notion that there is an inherent incompatibility between science and religious belief.
    Regarding Deuteronomy 29:29. King James version:

    The secret things belong unto the LORD our God: but those things which are revealed belong unto us and to our children for ever, that we may do all the words of this law.

    Does Scripture define the limits of science?

  143. Ritafairclough, (137)

    Your initial “Why?” appears to be based on a common misunderstanding, articulated by Thomas Kuhn, that it is impossible for the same person to work within two different paradigms at will. It also, less excusably, misunderstands the basis for my position.

    Your misunderstanding is made explicit in the following:

    I find it, to be perfectly honest, dishonest that your primary objection to the whole thing has not been made clear to all, namely that as you believe the earth is not very many years old none of it could have happened that way in any case.

    Here, IIUC, you are stating that the young age of the earth is my starting point, and that since a variant of ID is implicit in YEC, ID is simply a freebie. My arguments for ID would therefore be somehow dishonest because I don’t constantly remind people of my opinion on the timescale.

    There are a couple of areas where you have badly misunderstood. If it is an honest mistunderstanding, I suppose an apology will be forthcoming. First, I do not have a webpage at AIG. What AIG did was to reprint my contribution to a book, In Six Days, edited by John Ashton, with an editorial comment interspersed. They did so without asking my permission first, although when I asked them to change their editorial comment and correct a misprint of theirs, they did so. I am not in fact affiliated with AIG, as your comment would imply.

    Secondly, I do not march in lockstep with AIG, and did so even less at the time my contribution was written. I currently am a YEC, although not a YUC (young universe creationist), as is AFAICT their position. At the time I wrote the piece, I was a YLEC (young life on earth creationist) but not a YEC. Note one of the passages you quoted: “It basically forces one into accepting a short chronology for life on earth.” It does not say “for the earth.” And even now, I am not dogmatic either about YUC being wrong or YEC being right. I base my opinions primarily on my perception of the scientific evidence (which can change, and has changed), as I view the Biblical evidence as inconclusive on both those questions.

    But perhaps the most profound misunderstanding is that you apparently think that my primary argument is for short age, and (I am guessing here but your use of the word “know” in your last sentence suggests that I am right), I am really dependent on a literal reading of an “inerrant” Bible for my opinion.

    Let me put it to you bluntly. I don’t believe in an inerrant Bible. The reasons are outlined in chapter 3 of Scientific Theology (a free online copy is available by clicking on my name). (In fact, there are inerrantists who argue that Genesis 1 describes long periods of time, and even TE’s who claim to be inerrantists. Inerrancy turns out to be a plastic concept.) Nor do I start my personal philosophy with the Bible. Other than prejudice, it is inexcusable that you should have read my material on the AIG website and concluded that.

    Rather, I realized early on that the Bible was only one (or perhaps two, or 66, or something) book competing for the title of divine revelation. My number one datum was that the origin of life could not be explained currently, and it appeared unlikely that it would ever be explained, by naturalistic processes. (Actually, that was my number 4 datum, after the facts that science could explain most of the universe, that science was impotent to explain the origin of the universe, and the at mechanism was impotent to explain quantum mechanics. See chapter 2 in my book. But the origin of life was the first and most important area I researched.)

    If one accepts that datum as accurate, then ID becomes a live option as an answer for other questions, and the question of age needs to be revisited without the weight of scientific opinion being essentially determinative, as the substantial majority of scientists have been wrong in one area already. Then it makes sense to look at such areas as carbon-14 dating with a fresh perspective. Then it makes sense to accept the results of carbon-14 dating if they appear to conflict with the standard “scientific” interpretation of age. Then it makes sense to consider afresh the possibility that the Biblical record is substantially correct. Then it makes sense to ask whether the Biblical record might be substantially correct in other ways.

    Given your accusation, it is ironic that I get criticism from YLEC (to use the broadest term) colleagues who want me to start from the Bible. They understand where I am coming from very well. I suspect that you do not because you don’t want to believe that my position can exist.

    As to my not reacting negatively every time I hear long ages being discussed, I think that those who have read this blog for some time are well aware, from my comments, of my belief in a short age for life on earth. I have not tried to hide it. (see the last paragraph of comment 59 above).

    But to refuse time to those who are trying to construct a naturalistic theory for the origin of life, or for that matter, for the diversity of life, would be to force naturalism into a strawman position. Sure, it would be easy to knock down, but it wouldn’t prove that the real theory is wrong. That is, when I discuss naturalistic theories, I try to take them on their own terms. This is partly for argumentative fairness, and partly because, in a sense, I am in this game for keeps also. If someone were to, for example, show that if one just added vanadium, or platinum, or clay, or something else, or all of the above, to a Miller-Urey apparatus, within a year or so some primitive bug would emerge from the soup, my entire inferential chain would essentially collapse. Then I would either have to find a new chain, or give up on YLEC. (I guess that makes my theory falsifiable.)

    In addition, this is not my blog, and I do not have the right, let alone the obligation, to correct every comment to my own way of thinking on age. That is especially true when the majority view of the moderators is long-age. I need to deal respectfully with their views, and one of the ways to do that is to refrain from constantly yapping about short age whenever an age-related question comes up. Paul Nelson doesn’t do that, so why should I?

    If there should be a discussion of age-related issues on this blog, I might say more. But obviously, most of the discussion is on ID, and so that’s where my comments will be directed.

    Hopefully you now understand where I am coming from a little better.

  144. bFast, (68)

    Sorry for the delay in replying. The statistic you are looking for is an exponential distribution, where the probability of any given codon being a stop codon is 3/64 and thus for a non-stop codon being 61/64. The probability of finding a string of at least n codons is 61/64ths to the n power. That calculates out to about 0.3649 at 21 codons, which is fairly close to 1/e (0.3678…).

    At 100 codons, that works out to about 0.00822, which is small, but not astronomically so.

    All this assumes that the genome is random, which, regardless of which side of the ID argument one takes, it is not.

    Daniel, (142)

    I’ll get back to you later.

  145. Paul, thanks for the calculation. As you can see in my discussion #124, point #3, I agree that non-coding DNA is not expected to be truly random withing the neo-Darwinian paradyme.

    I was intrigued by your YLC position. You seem to be able, as many are not, to separate your scientific exploration from your religious perspective. I have met a few others, like yourself, who are not religion-first, yet hold to a belief in young life.

    I have seen evidence that I find irrefutable, that indicates that life is old. My primary source of evidence, other than the commom reading, is my brother, a working geologist. That said, it seems clear to me that your knowlege base in this field is greater than my own.

    Do you have a good single source that presents your evidence for young life? It would be intriguing if you could convince me that life really is young.

  146. Daniel (142),

    Sorry that the references were not all that you had hoped they would be. I agree that references come in a scale of reliability, and that textbooks are not as high on that scale as reports of original research in peer-reviewed journals. However, the latter are not infallible. The fact is that there is nothing infallible in science. And the fact is that nobody has the time to read only journal articles on every point of interest. So some rules of thumb have to be utilized to get through the maze in reasonable time.

    One of the rules of thumb is, the more the primary data are emphasized, and clearly separated from interpretation, the more reliable the source is. A second is, the more experienced and knowledgeable the source is, the more reliable the conclusion is (peer review is simply the concurrence of two or more experts, or at least the view of one expert pre-criticized). A third is, admissions against interest, as the lawyers would say, are more reliable than comments on neutral matters, which are still more reliable than claims that one’s theory is correct, all other things being equal.

    Both the Origins reference and the Biochemistry reference were by knowledgeable experts, and were admissions against interest. Therefore it would seem that they should be accepted as accurate unless and until direct references from original experiments contradicts them.

    Since I took the trouble to find the nearest copy of Origins, and then drive to the library and back (some 30 miles), I find it hard to be too sympathetic to your plea that “I don’t have either of these books at hand”. If you are located in somewhere like Palau, I will be more sympathetic, but otherwise do a little work.

    I find it fascinating that, after stating that you do not have access to Shapiro’s Origins, you go on to state,

    I believe I know the reasons for Shapiro’s remark, based on my understanding of the biology underlying the Spiegelman experiments.

    You then go on to ask,

    Do you understand that biology?

    AFAICT, the Spiegelman experiments were biochemistry, not biology, although I will admit that the lines between biochemistry and molecular biology have become somewhat blurred. But since you think you know why Shapiro said what he did without reading more than the sentence I quoted, perhaps you could state your understanding, then read him and find out whether you were correct. Then perhaps we can discuss “the biology underlying the Spiegelman experiments” and we’ll find out whether I “understand that biology”.

    The synthesis of long strands of RNA under laboratory conditions is a major issue for you.

    It seems to be an important issue for Shapiro, and even for Spiegelman. Is it not important for you?

    Perhaps you could help me narrow down the field, so I can check further.

    Would you like strand elongation catalyzed by an enzyme, or not?

    Elongation on a template (as in the Spiegelman QBeta case) or not?

    Primer, or not?

    I already know that one can get mini-Spiegelman monsters, and even apparently Spiegelman monsters, from enzyme catalysts plus trinucleotides. What I would like to see is systematic elongation of the chain well beyond the Spiegelman monster, either without an enzyme catalyst, or with an enzyme catalyst that could reasonably have been formed in a prebiotic earth. (Plus I’d like to see a reasonable prebiotic synthesis of trinucleotides, and some way of showing that the elongated strings can develop a code and turn into actual living organisms, but first things first.)

    Surely your faith does not rest on such a slender reed

    Why not? Did not the apostle Paul (1 Cor. 15) stake his entire belief system on the historicity of a miracle? Besides, I thought that a religion that was falsifiable would be superior to one that was not. A religion that is not falsifiable cannot, and for that reason, tell us anything about nature. It would seem to be an advantage for a religion to guide us when dealing with nature.

    Apparently the work of naturalists, which does not bear in any way on considerations of the existence of deities, upsets you.

    Right now it doesn’t upset me at all; I’m actually kind of pleased by the way things are going. But if it did, that wouldn’t matter. Just as it doesn’t matter if naturalists become upset because there is evidence in nature for God’s activity. Being upset doesn’t change the truth. The nature of reality is not susceptible to political correctness.

    That’s it? That’s your entire comment?

    Nice catch. I accidentally hit the “Submit Comment” icon before I was quite ready, and ran out of time to correct the comment, so let it stand.

    I agree with “Kepler, Newton,” “Einstein”, and “Pasteur” that there is not “an inherent incompatibility between science and religious belief.” My comments in (143) might be helpful in this regard.

    You ask, “Does Scripture define the limits of science?” I don’t think so. On the other hand, as I read it, this text seems to indicate that some things can be found out by us, and I presume that science can be one way of finding out some of those things, but that others things cannot be found out, and that it is futile to try to do so. I agree with the sentiment of the text. What those secret things are is not clear from Scripture, even assuming that Scripture is accurate on this issue, but we have no right to assume that someday science will find the answer to every question. There may very well be questions to which the answer will always be above the reach of empirical study, and maybe even answers that we cannot grasp at all. It is simply not appropriate to say, for example, that the origin of life must someday yield to scientific inquiry. Maybe, maybe not (even secular OOL researchers acknowledge this possibility).

    If science can’t tell us how life originated, and God doesn’t deign to give us a mechanism, (which is how it looks right now), then we are out of luck. We’ll just have to live with it. But hey, if you want to try, be my guest.

  147. bFast, (145)

    I don’t have a single source that comprehensively presents the evidence for young life. I can tell you of a few sources I would recommend as introductions. Origins: Linking Science and Scripture by Ariel Roth is a good general introduction, as is Faith, Reason, and Earth History by Leonard Brand. For radiometric dating, I recommend Radioisotopes and the Age of the Earth, Vol. II, edited by Larry Vardiman, Andrew Snelling, and Eugene Chaffin. The interpretation of their data is not always completely clear, but the data themselves are fascinating. An earlier version of the carbon-14 data is available at http://www.globalflood.org/papers/2003ICCc14.html

    Finally, there is my own stuff, available by clicking on my name. Chapter 5 of Scientific Theology, my article “Carbon-14 in Fossil Carbon”, and my article “Carbon-14 Dating Models and Experimental Implications”, would all be good reads. There are probably other resources that would be useful that I don’t recall at present.

    I hope that helps.

  148. Paul Giem,

    First, and most important, I wanted to say my appreciation for your refreshingly original thought on several issues, including your structuring of issues on ages and dating of life and cosmos. Well worth a thought or two.

    Having taken a couple of days’ timeout [to allow the personalities games above to cool down], I must note too, sadly, on how the above shows which side is focused on substantial issues and which is reverting to personalities in the noticeable absence of dealing with the material matters substantially.

    Third, it is astonishing to me that after a week and a half, not one truly substantial response has been made in the thread from the evo mat side to PaV’s main point in the original post:

    As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

    Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

    Similarly, once the personalities were out of the way, there was no substantial answer to the implications of want of search resources to achieve genomes by chance + necessity, starting from the origin of life question. [And note, we didn't even touch on the chirality issue!]

    The pattern above, which is all too familiar from all too many cases in point, must be telling astute onlookers something on the true balance of the case on the merits. And, not to the merit of the evo mat advocates.

    Finally, of course 43 above responds to the Ian Musgrave Talk Origins page [linked at "claims" in 20 above from you] which tries to brush aside the force of the issue. I am especially astonished at the strawman argument set up by Mr Musgrave’s third diagram on “creationist” and “real” views of abioogenesis. In fact, not only is it the case that any number of creationist sources [not even counting design theory sources] do make a serious address on OOL issues in light of the typical models used, but it is the OOL researchers who are openly admitting that their frameworks lack empirical warrant! (The cited exchange between Shapiro and Orgel at 72 above, underscores the point.)

    On a further look at the TO page, I find Musgrave’s bland assertion:

    “this [Mycoplasm] is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems”

    –> This is a particularly slick glide-by of the requisite for real-world science that it must rest on observation!

    –> We also have observed life forms, with a genome that has observed minimal fucntional length 300 – 500 k, and that is — with M. g. as the key case in point — for organisms dependent on others for key nutrients; which leads to the inference that the real required DNA length for full independent life function is of order 1 mn.

    –> So, we need to look askance at Musgrave’s dismissal that

    “The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins . . .”

    –> For, in fact M.g. plainly has too few proteins already to be an independent life form!

    –> This is debate tactics, not serious science — as the dismissive and profane title of Mr Musgrave’s piece warns the astute reader.

    –> Indeed, the level of tactics used underscores why so many UD participants view references to To with disdain!

    The want of a serious rebuttal, here or from a Darwinist resource sites such as TO — and let us note how the Musgrave page’s serious problems have not been fixed in ten years! — simply underscores the force of the search resources issue, on OOL and OO body plan level biodiversity.

    Let us take note of this.

    GEM of TKI

  149. 149

    Paul Giem (146),

    You have made a case that RNA synthesis studies have been futile as approaches to understanding abiogenesis. You chose to rest that case on secondary references (books) rather than the primary scientific literature, and you have eloquently defended that choice. I respect your decision, but I offer the following in rebuttal:

    In addition to their other deficiencies, the references you gave are antique. The Shapiro book was published in 1986, twenty-two years ago, and has long been out of print. It was not a scholarly, peer-reviewed publication, but a general-audience work. The Lehninger text dates to 1970. Are we to believe that nothing has been done in this field in the interim?

    Moreover, with respect to Shapiro, you said,

    One would have to read most of the book…to understand the precise context…

    so one is at a disadvantage in evaluating the basis of his “negative remark” about the Spiegelman devolution experiment. Nevertheless, knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issues of abiogenetic RNA syntheses.

    QBeta is a small, icosahedral virus (bacteriophage) that infects E. coli. Its genome is a single-strand of RNA about 4,000 nucleotides in length, encoding three structural proteins and a replicase (RNA-copying enzyme). [see, for example, Klovins, J, Berzins, V and van Duin, J RNA 1998 4: 948-957]

    In earlier work, [Haruna and Spiegelman Proc Natl Acad Sci U S A. 1966 Jun;55(6): 1539-54] had discovered an exquisite specificity of the phage replicase: it only works when provided with its own genomic RNA as a template for copying. This makes sense biologically, for if the replicase recognized and were bound as well as its own genome by the far more abundant messenger RNA molecules in infected cells, replication of the viral genome couldn’t get off the ground to generate new phage genomes. Another biological point: the phage is a highly evolved organism that replicates with maximum efficiency. It contains no genetic sequences that are not essential to its survival. There is no reason (no survival advantage) why its replicase should synthesize any additional information either in vivo or in vitro.
    That’s why I say that Shapiro’s statement, “The RNA did not acquire a new capacity, nor could it do so.” is understandable. Since the Haruna/Spiegelman work on this highly specialized system is irrelevant to abiogenesis, I wonder why Shapiro even considered it. Perhaps he included it because it was a landmark in RNA biochemistry. Since you have Shapiro’s book, perhaps you would kindly shed light on that issue.

    Regarding the Lehninger reference, you have presented nothing for me to work with. Perhaps Lehninger was in a similar position to Shapiro, citing work available up to that time. Neither of those good gentlemen had a crystal ball.

  150. PS: Here is an AiG more or less semitechnical page on OOL issues. It will further underscore just how strawmannish the Musgrave page at TO is.

  151. PPS: It is worth separating out the publication date on the AiG article: CEN Tech. J., vol. 10, no. 3, 1996. That is, BEFORE Musgrave’s hit piece.

  152. Mr King

    Mr Lehninger was a noted expert on biochemistry, whose main textbook was a longstanding classic. Wiki:

    Albert Lester Lehninger (February 17, 1917 – March 4, 1986) was an American biochemist, and is widely regarded as a pioneer in the field of bioenergetics. He made fundamental contributions to the current understanding of metabolism at a molecular level. In 1948, he discovered, with Eugene Kennedy, that mitochondria are the site of oxidative phosphorylation in eukaryotes, which ushered in the modern study of energy transduction. He is the author of a number of classic texts, including: Biochemistry, The Mitochondrion, Bioenergetics and, most notably, his quintessential series Principles of Biochemistry. The latter being a widely used text for introductory biochemistry courses at the college and university levels. As a dedicated educator, it was Lehninger’s argument that a knowledge of biochemistry is useful for all well-informed citizens, no matter their callings–let alone the very real intellectual excitement it can offer

    Now, PG has repeatedly cited — most recently in 135 supra — a statement circa 1970 on the observed tendency of reactions in the monomers for R/DNA. namely that in vitro, they tend to form 2-5 bonds not the 3-5 ones found in life. If that was true in 1970, it is true today, as that is a fact of observation.

    Moreover, as he has said, the statement is by an acknowledged expert [in a context of a standard College textbook; which means his peers would be expected to read it, so there is a further incentive to get the statement right], and it is an admission in the teeth of interests.

    Such statements have a high intrinsic probability of accuracy. That means the burden of proof is on the objector.

    You have not met that burden, but instead have tried to dismiss the claim because it is not from a research document, and now on grounds that it is “old.” Neither of these are likely to be even relevant to the material question of accuracy. For, if a fact claim is true, its age is immaterial. (Indeed, even if subsequently there has been found a way to induce D/RNA in vitro to take up more life-like bonds [through say a suitable catalyst or enzyme], the older tendency is probably indicative of the balance of the thermodynamics. And, in general it is notorious that the molecules and structures of life are inherently energetically unfavourable. That’s why catalysts and especially enzymes play key roles in life. Enzymes, in turn, are characteristically highly complex proteins coded for by D/RNA. This in turn brings us right back to the complexity of observed life systems and the difficulty of accounting for their FSCI per OOL models and empirical evidence.)

    In short, sadly, your arguments appear to be a case of selective hyperskepticism.

    In fact, properly, we have good reason to accept Mr Lehninger’s observation as PG cites, unless you or others can show good reason to reject it.

    GEM of TKI

  153. 153

    kairosfocus,

    Now, PG has repeatedly cited — most recently in 135 supra — a statement circa 1970 on the observed tendency of reactions in the monomers for R/DNA. namely that in vitro, they tend to form 2-5 bonds not the 3-5 ones found in life. If that was true in 1970, it is true today, as that is a fact of observation.

    My respect for Lehninger knows no bounds.

    However, without knowing anything more than Paul Giem’s bald statement, I can’t evaluate its significance. What did Lehninger actually say? What was the context? What were the conditions employed in the experiments? From what source did Lehninger get his information?

    I have tried to find more information by searching The National Library of Medicine’s PubMed data base and Internet search engines, but have not been successful.

    Any help you care to give on the merits? I would be grateful.

  154. DK:

    Cf above. Given the context, it is you as objector who has something to show.

    I have already pointed to the key thermodynamics pattern for the chemistry of life, namely that there is an undelrying reason why life chemistry is so heavily enzyme dependent: life chemistry is largely based on energetically unfavourable reactions, that require the sort of constraints provided by the enzymes. In turn such enzymes are highly complex, rather long-chain proteins coded for in the relevant D/RNA, i.e. we have a circle of cause at work; it works for propagating life forms but not for originating same.

    That is the general context for hte issue of 2-5 and 3-5 bonds, and even if PG is wrong on this point, or if Lehninger is wrong, the basic issue is still unanswered: OOL per the usual models is so vastly thermodynamically improbable that it is for all practical purposes impossible.

    Which brings us back to the underlying point in PaV’s original post.

    And so, we need to come back from the rabbit trail to the main issue, unless you can show us credible evidence that PG and/or Lehninger are wrong on the specific point. Even if you can, that still does not affect the material issue.

    So, if there is just a string of objections without substantive evidence, we know enough to decide the main case on the real merits — and the prudent verdict (provisional though it currently is) is plainly not in your favour.

    GEM of TKI

  155. Kairosfocus,

    Daniel King is arguing in a no concession one concession, maximum objection, you do all the work manner here. If you want to sharpen your arguments against his position, it may be worth arguing with him; otherwise, you are wasting your time.

    That’s a pretty big charge, so here’s the evidence. The one concession I found was in (75), where he said to you,

    Thanks for the readings. I bow to your scholarship.
    * * *
    I agree. There are daunting challenges in that field. I’m happy to be merely an occasional student and spectator of those proceedings.

    Otherwise, if he has no arguing room, he simply drops the subject, as he did with the question of whether DNA code was information (or language), or just an analogy which was therefore not “evidence” (see his comments 81 and 82 and my comment 114, then his further silence on the matter instead of conceding the point, or else contesting it, which he probably knew better than to do).

    If a concession is mandatory, the next step, if possible, is to minimize the point as much as possible. See, for example, when he requested references (115, [with a history], and 123), and then, when I provided them (135), argued against Lehninger because (a.) the reference is not “to the primary scientific literature”, being a textbook (142), (b.) it was not readily accessible to him (142), and (c.) the reference was old (149). Note the complete lack of any sense of responsibility to find any data that contradicts Lehninger, or even any sense that Lehninger carries any weight whatsoever. This is classic advocacy not based in fact.

    Further evidence of this argumentative nature is that. after all his claims that naturalistic OOL scenarios are based on “evidence” and ID is based on “speculation”, and after all the discussion of the shrinkage of RNA strands to the size of the Spiegelman monster, and his attempting to play ‘gotcha” over the fact that Q-beta replicase has produced up to Spiegelman monsters, rather than demonstrating that larger strings of RNA could reasonably be created from Spiegelman monsters, he finally acknowledges what could have ended the discussion early, namely,

    knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issues of abiogenetic RNA syntheses.
    * * *
    Since the Haruna/Spiegelman work on this highly specialized system is irrelevant to abiogenesis, I wonder why Shapiro even considered it. Perhaps he included it because it was a landmark in RNA biochemistry.

    One might think that this is a concession, but actually it is not. He now sees that the evidence is against RNA elongating beyond Spiegelman monsters using nucleotides and Q-beta replicase. But rather than saying so, he chooses to try to take the whole subject off the table by declaring it irrelevant. He probably at least suspects that his postulated reason why Shapiro included it in Origins, that ” it was a landmark in RNA biochemistry”, was incorrect, and that it was there precisely because some had used the Spiegelman experiments to “prove” that the abioltic synthesis of long strings of RNA was reasonably feasible, and that Shapiro was honestly critiquing them. If Daniel really believes what he says, I expect him to criticize anyone who uses the Spiegelman in this way. I’m not holding my breath, but who knows?

    Until such time as he has enough gumption to go to the library (isn’t that how we all did research before the advent of the Internet?), or to explain why he can’t and be willing to abide by the results without further information to the contrary, I see no reason why I should give him exact quotes from Lehninger. It would appear that all he wants to do is to carp and in the meantime send us on ever-widening errands, sucking up our time but never (well, almost never) admitting to being satisfied, even temporarily. Frankly, I am tired of this game.

    As you have commented frequently, most recently in (154), and I pointed out in (53), the main point in this thread has yet to be answered, let alone the vastly more difficult (for believers in naturalism) problem of OOL.

  156. Hi Paul G:

    I hear you loud and clear.

    It does rather look — unless Mr King can show serious progress — like argumentative, closed-minded objectionism, as a manifestation of selective hyperskepticism.

    I have commented latterly above correctively, but with a serious eye to the interested onlooker, who might lack enough context to see that this is a side-track off a side-track.

    It is in that context that I have put the central problem with the OOL models above: they are dealing with the construction of an energetically massively unfavourable system. That is why in the observed cases life chemistry uses enzymes to push reactions that would not occur at appreciable rates in the absence of such constraints. Enzymes, of course, are a principal and highly complex product of the D/RNA coding scheme. (Just think of the ATP synthesis for the required energy flow to keep such energy absorbing reactions going in vivo. Here too, Wiki’s evo mat bias shows: if “ATP is the common “energy currency” of cells,” and is claimed to have evolved from prior functional units, why and how do we get the required “energy currency” before ATP Synthase, and if such existed, why the evolution to a vastly more complex entity, and apparently before life architectures branched out [thus, the info generation challenge and the encoding in D/RNA challenge too . . .]? Currency conversion is of course a major change! And, what has been the in-vivo observed — as opposed to speculative — prior currency regime?)

    RNA world of course, further, was introduced because it was found that sometimes RNA can have a catalytic effect, so there was a hope to cut through the chicken-egg dilemma just noted.

    But, that gets us to RNA synthesis, which falls under the rebuke from Shapiro cited at 72 above. In short, there is a problem with the syntheses, precisely because of unfavourable energetics so that one has to set up rather special circumstances to get to the RNA strands — and note that one of the key issues of chirality [handedness] is that, energetically, L- and R- forms are equivalent; so apart from in life, chemical synthesis gets us racemic, 50-50 products, which would then interfere mutually on polymerisation and shapes. All this, in a context where specific key-lock fit of functional groups of atoms is a crucial part of the chemistry of observed life.

    F2XL summarises the synthesis part of this in 61 [and cf the 1996 creationist summary and critique by Aw Swee-Eng as already linked at 150, and again here; which does address the implications of chirality -- of course two years before the date of final changes in Musgrave's shoddy TO hit piece]:

    Regarding the RNA world: A chief problem with it is that for RNA strands to form IN THE FIRST PLACE, you need sufficient amounts of concentrated carbon-5 sugars, phosphates, and also nucleotides bases (adenine, thymine, guanine, and cytosine). The catch is that these three constituents can only be artificially synthesized in completely different circumstances for each of those things listed. A phosphate group cannot develop in the same mix as a carbon sugar, and so on.

    That wouldn’t even begin to explain how the information in the RNA got there in the first place.

    This is typical of OOL dilemmas, as was summarised in 72.

    Back on the original topic as put by PaV, once we have functioning life forms, evolutionary materialist models have the problem of getting to rather large increments of information required for new body plans and adaptations, without the routinely known source of FSCI — intelligence.

    And, even when such models appeal (circularly!) to inferred evolutionary pathways as Zhou and co do, we then get to implausible rates of evolution even in families of animals notorious for wide variation, here Diptera and Drosophila: 5 – 11 new genes per mn yrs, to account for the variation in the Dibtera in some 225 mn yrs is simply impalusible. So, PaV is right to observe:

    As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

    Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

    Onlookers should note that over the course of two weeks and over 150 comments, this has never been cogently addressed from the evo mat side. The OOL challenge compounds the matter of course, and the observed repeated resort to personalities and rabbit-trail diversions and objectionism underscores that ther eis no solid case on the merits. The TO rebuttal page is amply illustrative of how poor the Evo mat case is on the said merits.

    In turn, that easily explains just why it is that the Darwinista Establishment takes such pains to make sure those who try to challenge in the academy are expelled, and seek to monopolise the education and media environments so that the public and kids coming up are indoctrinated, not educated.

    That is sadly shameful, and deeply revealing.

    Thanks again PG

    GEM of TKI

  157. Paul Giem (155)

    I will try to defend my position further:

    Otherwise, if he has no arguing room, he simply drops the subject, as he did with the question of whether DNA code was information (or language), or just an analogy which was therefore not “evidence” (see his comments 81 and 82 and my comment 114, then his further silence on the matter instead of conceding the point, or else contesting it, which he probably knew better than to do).

    I am satisfied that arguments from analogy are inadequate as proofs, and as an acolyte of Dr Beardsley, whose work I quoted in #82, I await evidence that the analogy in question has been subject to empirical test and has produced new findings of scientific value. What more is there to discuss?

    Note the complete lack of any sense of responsibility to find any data that contradicts Lehninger, or even any sense that Lehninger carries any weight whatsoever.

    How can I find data that contradicts Lehninger, when I don’t know what he said? You haven’t provided a direct quote or any further information beyond your claim. You have only pointed me to an ancient textbook which is out of print and not readily available to me. Bear in mind that you made the claim that this reference is a refutation of the feasibility of exploring abiogenesis scientifically. In scientific circles, it is the responsibility of the person making a claim to support it. It is inappropriate to wave hands and say “refute me!”

    Further evidence of this argumentative nature is that. after all his claims that naturalistic OOL scenarios are based on “evidence” and ID is based on “speculation”, and after all the discussion of the shrinkage of RNA strands to the size of the Spiegelman monster, and his attempting to play ‘gotcha” over the fact that Q-beta replicase has produced up to Spiegelman monsters, rather than demonstrating that larger strings of RNA could reasonably be created from Spiegelman monsters, he finally acknowledges what could have ended the discussion early, namely,
    knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issues of abiogenetic RNA syntheses.
    * * *
    Since the Haruna/Spiegelman work on this highly specialized system is irrelevant to abiogenesis, I wonder why Shapiro even considered it. Perhaps he included it because it was a landmark in RNA biochemistry.

    You made a claim that the Spiegelman devolution work was an example of the futility of studying abiogenesis. I presented evidence from the scientific literature that this work is irrelevant to abiogenesis and that your claim is therefore wrong. You call that playing “gotcha.” But you have not admitted your error.

    One might think that this is a concession, but actually it is not. He now sees that the evidence is against RNA elongating beyond Spiegelman monsters using nucleotides and Q-beta replicase. But rather than saying so, he chooses to try to take the whole subject off the table by declaring it irrelevant…

    I knew all along that there was no extension beyond the viral genomic template in the QBeta case and I don’t recall saying otherwise. In no way did I want to take the whole subject of RNA synthesis and elongation off the table. I claimed only that the QBeta example was irrelevant to abiogenesis. Much relevant work on RNA has been done more recently. I would be pleased to cite some for you.

    …it was there precisely because some had used the Spiegelman experiments to “prove” that the abioltic synthesis of long strings of RNA was reasonably feasible, and that Shapiro was honestly critiquing them.

    That I agree completely with Shapiro’s position on the Spiegelman experiments is evident from the analysis of the QBeta system that I have posted above.

    Until such time as he has enough gumption to go to the library (isn’t that how we all did research before the advent of the Internet?), or to explain why he can’t and be willing to abide by the results without further information to the contrary, I see no reason why I should give him exact quotes from Lehninger.

    You see no reason to give me exact quotes from Lehninger. I had hoped for a more collegial and scholarly attitude.

    You assert that I lack gumption. Do you believe that I am afraid of what I might find in those books? In fact, I have searched every public library in my region and have found no copies of Shapiro or Lehninger 2nd Edition (I hope you had the edition right). I have requested interlibrary loan of both books, and am awaiting the results of those requests.

    While those processes wend their way, I am taking my family to the Finger Lakes region of New York next week. So if you don’t hear from me for a while, it’s because I (hopefully) will have other fish to fry!

  158. Addendum to my #157:

    Contradicting Lehninger is not my aim. Understanding what he wrote in the context of this discussion is my aim.

  159. Daniel King:

    Much relevant work on RNA has been done more recently. I would be pleased to cite some for you.

    Please do.

  160. Mr King:

    Re: “arguments from analogy . . .”

    At this stage, this looks a lot like mere insistent reiteration of an error in the teeth of repeated correction from several commenters who — per professional grade knowledge and experience — understand the nature of digital systems and associated information storage capacity. (Onlookers, cf above . . . )

    So, DK, it is you who now have the burden of showing that D/RNA is not a string-based 4-state discrete state information storage entity that uses a code to control physical implementation of algorithms. (But, in fact this is an otherwise uncontroversial summary description of the state of our understanding of DNA, on say protein coding and expression!)

    In short, the evidence is “you dancin’ wrong but strong . . .”

    So, if you are reduced to that to maintain your position, that tells us all something quite significant about the real balance of the case on the merits . . .

    GEM of TKI

  161. Re DNA:

    To summarise the point that DNA is an informational macromolexcule and that this has long been recognised, I make some excerpts:

    1] Crick in a letter to his son Michael, March 19, 1953:

    “Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)”

    –> in short the nature of DNA as a digital information entity was recogtnised from the outset, by the very discoverers

    2] New Wold Enc, as a general pro-ID reference work:

    The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The main role of DNA is the long-term storage of genetic information. DNA is often compared to a blueprint, since it contains instructions for constructing other components of the cell, such as proteins and RNA molecules. The DNA segments that carry genetic information are called genes, but other DNA sequences have structural purposes or are involved in regulating the expression of genetic information. RNA, also, may serve more than one purpose, but it is most commonly identified as the intermediate between the DNA blueprint and the actual workings of the cell, serving as the template for the synthesis of proteins from the genetic information stored in DNA.

    3] Wiki, as a materialism-leaning similar general reference work:

    Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information [of course the elements used take one of four values, and come in three element codons that code for start, stop and specific protein monomers]. DNA is often compared to a set of blueprints or a recipe, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

    –> Wiki here very plainly served as open source material for the NWE.

    _______________

    That should suffice to show that there is a consensus, with fairly clear implications.

    Those implications of course are not friendly to the anti- design trend of thought, so it is resisted.

    But in the end, facts are pretty stubborn things.

    GEM of TKI

  162. KF

    re; Michael Crick

    As it happens I know Michael Crick well in person, on the phone, and in emails. We worked loosely together over a period of years developing video games. He’s not much older than I am so the letter than his father Francis sent to him in 1953 must have been a letter to a child barely able to read to say nothing of being able to comprehend the molecular structure of DNA.

    Edit: I must correct myself. Michael was born in 1940. He’s 16 years older than me. I would have guessed 10 years older at the most.

  163. DK: Please! Yet again—If [A] and [B] are two EXAMPLES of a general principle, then one is not an ANALOGY drawn from the other. A “little error in the beginning” leads to a big error in the end.

  164. H’mm:

    1] Ouch on grammar above!

    2] Dave S: Wiki, article on Crick: “Children: Michael b. 25 November 1940 [by Doreen Crick] . . .”

    –> The intelligent 12 yo is the classical target of a “good quality” newspaper.

    3] SB: multiple instantiation, indeed, is not analogy.

    GEM of TKI

  165. Daniel King (157),

    I am very pleased to have been, AFAICT, wrong. You have in fact made an attempt to look up Lehninger (and Shapiro), and may yet do so if interlibrary loan works in your area. (I am guessing that you do not have a university library in your area, as I have not yet seen a university library without Lehninger.)

    Given that at least that part is in good faith, I will give you your quote, which, as I previously said, was on page 779 of the first edition, and now I can say is repeated verbatim on page 779 of the second edition, published in 1975. It is chapter 34, entitled The Origin of Life, incidentally the last chapter, under the subheading The Abiotic Origin of Nucleotides and Nucleic acids.
    Here is the quote:

    The next step in the chemical evolution of nucleic acids is the formation of internucleotide linkages between successive mononucleotides. This also has been achieved in simulated primitive-earth experiments in which monomucleotides have been heated at 50-65° in the presence polyphosphoric acid as condensing agent. To date, the internucleotide linkage in abiotically formed oligonucleotides is in most cases the 2′,5′ linkage; the 3′,5′ linkage does not appear to form readily.

    Hopefully, that should be enough to reasonably show that Lehninger believed, on the basis of experiments (note the temperature range), that in fact the wrong linkages were more readily formed than the right linkages when OOL experiments tried to produce RNA abiotically. Would you agree?

    Now, if you have more recent data refuting this idea, I and others would be happy to examine it. For what it is worth, in editions of Lehninger’s Principles of Biochemistry, including up to 2000 (with two new editors, David Nelson and Michael Cox), which was apparently the textbook that succeeded Biochemistry, the chapter on the origin of life, and most of the material in that chapter, disappears. Judging from the index, the origin of life occupies a progressively smaller part of the book. It appears that the authors did not believe it to be a very important part of biochemistry.

    You say,

    You made a claim that the Spiegelman devolution work was an example of the futility of studying abiogenesis. I presented evidence from the scientific literature that this work is irrelevant to abiogenesis and that your claim is therefore wrong. You call that playing “gotcha.” But you have not admitted your error.

    First, I don’t believe that it is futile to study abiogenesis. I am glad it has been studied, because our knowledge of ways life couldn’t have reasonably have arisen comes from just such research. (And if there were such a way, I would want to know). So I would never say that “the Spiegelman devolution work was an example of the futility of studying abiogenesis.” You have mischaracterized my position.

    (This mischaracterization is also found in your statement that I “made the claim that this reference [Lehninger] is a refutation of the feasibility of exploring abiogenesis scientifically.” I don’t mind exploring abiogenesis scientifically. I just think that it is possible that there is no pathway to life without intelligence, and that if so we should not be surprised to not find one, and that if we do not find one we should be honest enough to admit this fact, and that this admission can be, and at present is, an evidence-based statement.)

    Second, I have not seen, from you, any “evidence from the scientific literature that this work is irrelevant to abiogenesis.” I know you have said so. But I haven’t seen you present any actual evidence to that effect. IIRC, the closest thing to “evidence from the scientific literature that this work is irrelevant to abiogenesis” was my citation from Shapiro’s Origins, and until your last post (157) when AFAICT you suddenly changed position you were disputing the validity of that citation. I don’t understand this “I presented” statement.

    Third, it is the claim of others that it is relevant. Remember that Kacian et al. (the al. including Spiegelberg, cited by me in 114) said,

    These experiments resolved an interesting dilemma of precellular evolution. THey permit one to see, at least dimly, how selective pressures could have forced replicating nucleic acids to greater length and complexity (11), a necessary prelude to the invention of cells and subcellular components as aids in replication.

    That would seem to indicate that elongating RNA and making it more complex was seen as a problem, and that the writers believed that these experiments were relevant. So it might be relevant to point out that they do not solve the problem. Your claim that the experiments are not relevant (which I would agree with in the sense that these experiments do not outline a pathway for abiogenesis) would be better directed at Kacian et al. than at me.

    Fourth, your statement about playing “gotcha” is incorrect. The attempt to play “gotcha” came in this quote (i’ll give the full passage from 142):

    And from your #114:

    Now ask yourself, have you ever read of experiments that actually resulted in longer RNA strands from shorter initial ones? Why would that be?

    The synthesis of long strands of RNA under laboratory conditions is a major issue for you. In fact, I believe that I have read of experiments that resulted in longer RNA strands from shorter initial ones. I may even have read of experiments in which RNA strands were synthesized without a primer. Perhaps you could help me narrow down the field, so I can check further.

    Would you like strand elongation catalyzed by an enzyme, or not?

    Elongation on a template (as in the Spiegelman QBeta case) or not?

    Primer, or not?

    That was meant to trap me into saying that RNA couldn’t elongate, or couldn’t elongate without a template or a primer. Then you could use certain experiments with Q-beta replicase to prove that I had my facts wrong. My point was not that Spiegelman monsters could not be made, even from scratch (I knew that they can), but that the way things were set up larger RNA molecules were highly unlikely to be made out of Spiegelman monsters by Q-beta replicase (or by other means). I have not seen any evidence to the contrary. Any evidence you can produce will be welcomed.

    Finally, you say, “But you have not admitted your error.” It is my policy to admit errors when I see them, as I believe those who have followed this blog have seen. Indeed I admitted an error at the beginning of this comment. But in order to do so, I need to understand the error. Perhaps you can specify what I said that you see as an error, other than what has been discussed above, which I don’t see as an error. Or perhaps you can explain why the way I see it is not really the way I should see it.

    You misunderstand me when you say,

    In no way did I want to take the whole subject of RNA synthesis and elongation off the table. I claimed only that the QBeta example was irrelevant to abiogenesis

    When I said, “he chooses to try to take the whole subject off the table by declaring it irrelevant” (155), the whole subject I was talking about was “RNA elongating beyond Spiegelman monsters using nucleotides and Q-beta replicase.” I did not mean to “take the whole subject of RNA synthesis and elongation off the table.” (For one thing, it would take other evidence to take pathways outlined by Lehninger “off the table”.) One thing that is not clear is whether you see the production of Spiegelman monsters themselves from trinucleotides and Q-beta replicase as being relevant to abiogenesis. Perhaps you can clarify.

    Do you remember how disdainful you were about argument by definition (93)? I find your use of analogy worse. Not only do you argue strenuously that DNA code is somehow analogous to computer code rather than an example of a general type called code, and therefore that since it is defined (by you) as an analogy, it doesn’t prove anything, but you completely ignored my point in (114) that analogies are reasonable evidence in everyday science, and that the closer the analogy, the stronger the evidence.

    In that case your statement in (157) that “I am satisfied that arguments from analogy are inadequate as proofs” would be completely irrelevant. We are talking about evidence, not proof. What you need to address is whether arguments from analogy can ever serve as evidence. Before you do so, you may want to look at the rest of science to see whether they are used elsewhere as evidence, and whether this use is justified.

    You go on to say, “I await evidence that the analogy in question has been subject to empirical test and has produced new findings of scientific value.” In (79) I gave you some undisputed examples of DNA code produced by intelligent design. You later (81) dismissed them as being done by human intelligence. But it is still true that those changes were done by intelligent design. And those changes are in fact DNA code. Would you not say that at least here your argument dismissing the similarities between DNA code and other codes as merely analogies breaks down? For here we are in fact dealing with DNA code itself produced by intelligence. There is direct evidence that meaningful DNA code itself can be produced by intelligence, whatever you think about computer code. Or doesn’t this qualify as evidence?

    There does appear to be one area of agreement. We both appear to agree with Shapiro that the Spiegelman experiments do not help advance a reasonable (at this time) pathway for abiogenesis. Do I understand that correctly?

  166. I am still waiting:
    On June 31 I’ve asked gpuccio for a calculation of the chance that the antibody diversity of mammals isn’t beyond the edge of evolution.
    From my comment (#70):

    gpuccio

    an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen

    The relevant sequences here are the v-genes of heavy and light chain loci. E.g., v-genes of the heavy chain locus are encoded by about 300 nt and you have about 200. As you said:

    The 100 aminoacid protein is obviously a standard example, just to try a computation.

    Even if one takes into account that CDRs are more relevant for antigen binding than FRs you’re still left with a number nucleotides/amino acids that you assume to being beyond the edge of evolution.

  167. BTW, if you include AID you may even calculate the secondary repertoire.

  168. sparc:

    Sorry to have kept you waiting, I have been away and have seen only now your postings. Please, give me time to catch up, and I will try to answer.

  169. sparc:

    let’s begin with what is easiest. In your post #70, you say:

    “BTW, do other IDists share your opinion that random variation and selection both are intelligent processes?”

    Even if bFast has already brilliantly answered that in post #71, let me repeat here that I have never implied what you say. My point was very obviously that both random variation and intelligent selection can absolutely be part of an intelligent process. They are, indeed, in the case of human protein engineering.

    Let’s go now to the more interesting point, which is the generation of the antibody repertoire. You say:

    “The relevant sequences here are the v-genes of heavy and light chain loci. E.g., v-genes of the heavy chain locus are encoded by about 300 nt and you have about 200.”

    1) The first point, and probably the most important, is that here we are dealing with a prearranged functional process which uses random diversification as a step of the intelligent algorithm. In other words, the VDJ recombination which gives rise to the basic repertoire is based on specific, functional genes (the V, D J genes), whose sequence is obviously highly specific for the task they have to accomplish: they are a suitable base for limited random recombination to take place, so that the result may be a suitable covering of a specific conformational space. You cannot get antibodies just by mixing up any random gene of that length! So, I think you are missing the point that most of the intelligent information is already in the structure of the basic genes, before the random recombination takes place. Obviously, that is not in formation about each single antibody conformation, but rather information on the basic set of structures which can easily recombine to build the repertoire.

    2) The random recombination itself, indeed, is in a way controlled. It is a process of variation which is random in its diversification effects, but which is certainly actuated by the biological processes, and is not therefore blind and purposeless. What I mean is that the B cell is programmed to apply specific means of variation (not all of them completely understood) to get a specific purpose: it is not that the genes are there, and some unexpected random variation takes place (which is the model in darwinian evolution). In other words, the cell applies exactly those kinds of random variation which are suitable for the task, starting from the suitable gene base, and applies them exactly to the right target.

    3) Finally, an intelligent selection of the results takes place, as it is always the case in the immune system, which is a tightly controlled network. Obviously, that does not mean that the specific antibodies are selected, but that there is control of what is functional and what is not, and of the general process. That control is very important and complex, involving also the extremely vital acquisition of recognition of the self.

    The meaning of all that is that we are dealing with a highly engineered process. Random variation is only a small part of it, and its role is strictly defined: to create a controlled diversification, which is the best way to cover a specific search space.

    But let’s go to the search space itself. I have stated that in reality the search space is the search space of possible epitopes, and that it is big, but not huge. You say that I should refer to the search space of antibodies, which is much bigger and, in your opinion, well beyond what we in ID consider the “edge” of evolution. I don’t agree.

    Here, we are not dealing with the whole antibody structure, but only with the recognition site. You are obviously well aware of that, and indeed you add:

    “Even if one takes into account that CDRs are more relevant for antigen binding than FRs you’re still left with a number nucleotides/amino acids that you assume to being beyond the edge of evolution.”

    No. The six CDRs (complementarity determining regions) which are the main determinants of antibody specificity are short sequences of few aminoacids, usually about ten, and 5 of them have a rather repetitive structure. It is especially the H3 CDR which gives the highest variability, and it is a matter of a few aminoacids. So, the search space of possible antibody specificities, once the fundamental restraints are intelligently fixed, is probably not so bigger than the search space of epitopes, of which it is a natural complement.

    Does that mean that antibodies are within the range of unguided evolution? Certainly not. It does mean, instead, that the basic antibody repertoire is well in the range of a highly intelligent search process, which uses a random diversification under sever and intelligent restraints to cover the search space in the most economical
    way, which is exactly my point.

    Finally, in your post #167, you say:

    “BTW, if you include AID you may even calculate the secondary repertoire.”

    Frankly, I don’t understand your reference to Activation-Induced Deaminase and to the process of secondary antibody maturation in this context. You seem to miss the point that in the process of antibody maturation, while all the above considerations about the controlled, intelligent use of random diversification remain perfectly valid, the most important feature certainly becomes intelligent selection: indeed, the process is so efficient in yielding high affinity antibodies only because the results of random variation can be immediately and efficiently tested by the immune system against the existing information about the antigen structure. In other words, the system already owns the information about the result, not in the form of the antibody structure, but rather in the form of its complement, the epitope structure, and can therefore exert a perfectly targeted, intelligent selection. That, obviously, infinitely speeds up the search. We are, in other words, in a “Methinks it’s like a weasel” context, and Richard Dawkins could certainly teach us a lot about how easy the search becomes that way! So, no simple random calculation of probabilities applies here.

    I hope I have answered your points. Again, excuse me for keeping you waiting. I am really interested in this debate, and I hope you are willing to go on with it.

  170. bFast # 159:

    Daniel King: Much relevant work on RNA has been done more recently. I would be pleased to cite some for you.

    Please do.

    bFast, if you’re still tuned in to this thread, here you go. (All of the following are available on the Web as free full texts. The Ferris article is a good review of mineral-catalyzed RNA synthesis. The Bartel and Szostak paper is seminal on RNA evolution in vitro.)

    And thank you for your interest.
    ___________________________

    Selection of an improved RNA polymerase ribozyme with superior extension and fidelity.
    H. S. Zaher and P. J. Unrau (2007)
    RNA 13, 1017-1026

    Emergence of a fast-reacting ribozyme that is capable of undergoing continuous evolution.
    S. B. Voytek and G. F. Joyce (2007)
    PNAS 104, 15288-15293

    Improved polymerase ribozyme efficiency on hydrophobic assemblies.
    U. F. Muller and D. P. Bartel (2008)
    RNA 14, 552-562

    Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life
    J. P. Ferris (2006)
    Phil. Trans. R. Soc. B 361, 1777–1786

    New ligase-derived RNA polymerase ribozymes.
    M. S. Lawrence and D. P. Bartel (2005)
    RNA 11, 1173-1180

    Inaugural Article: A self-replicating ligase ribozyme.
    N. Paul and G. F. Joyce (2002)
    PNAS 99, 12733-12740

    RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension.
    W. K. Johnston, P. J. Unrau, M. S. Lawrence, M. E. Glasner, and D. P. Bartel (2001)
    Science 292, 1319-1325

    A complex ligase ribozyme evolved in vitro from a group I ribozyme domain.
    L. Jaeger, M. C. Wright, and G. F. Joyce (1999)
    PNAS 96, 14712-14717

    Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution.
    L. F. Landweber and I. D. Pokrovskaya (1999)
    PNAS 96, 173-178

    Isolation of new ribozymes from a large pool of random sequences
    DP Bartel and JW Szostak (1993)
    Science 261, 1411-1418

  171. StephenB #163:

    DK: Please! Yet again—If [A] and [B] are two EXAMPLES of a general principle, then one is not an ANALOGY drawn from the other. A “little error in the beginning” leads to a big error in the end.

    I agree that examples are not identical to similarities. Yet examples of a generalization would not be examples if they didn’t have some similarities. This situation can lead to equivocation in argument, and in order to avoid assuming a conclusion in such cases, it is important to be specific about what is meant in a given argument, by each of the terms above: [A], [B] and “general principle.” In the context of this discussion, bFast said in #84:

    Now, DNA is a language — it is not “like” a language. When we speak of the “machine language” of a computer’s central processor, it is a language as DNA is a language, as english is a language.

    and I objected in #93:

    Argument by definition.

    In bFast’s case, [A] = DNA, [B] = English, and the “general principle” is… What? A definition of “language”?

    As Professor Beardsley said, in my quote at #82:

    An analogy doesn’t prove anything; it merely calls to mind a possibility that might not have been thought of without the analogy. It’s the experiment that counts in the end. Bohr’s classic model of the atom is only a picture. It has clarified some points about the atom, it has hinted at some good hypotheses; but if you take it as proving anything about the atom, you are misusing the analogy. You can be fooled just as much by it as were those early inventors who tried to construct airplanes that flapped their wings, on the analogy with birds. Analogies illustrate, and they lead to hypotheses, but thinking in terms of analogy becomes fallacious when the analogy is used as a reason for a principle. This fallacy is called the argument from analogy.

    To emphasize:

    It’s the experiment that counts in the end.

    So, as I said in #157:

    …I await evidence that the analogy in question has been subject to empirical test and has produced new findings of scientific value.

    Until you cite such findings in the peer-reviewed scientific literature, I must stand unconvinced by your argument.

  172. Daniel King (171),

    Welcome back from your fishing trip. Now that you have answered StephenB (163), perhaps you can answer (165) which (IMO) makes StephenB’s point in a stronger way. Certainly your arguments against StephenB haven’t answered my points.

  173. Paul Giem #165:

    Thank you for your long and thoughtful post. I will try to respond to it, part by part, as time allows.

    …I will give you your quote, which, as I previously said, was on page 779 of the first edition, and now I can say is repeated verbatim on page 779 of the second edition, published in 1975. It is chapter 34, entitled The Origin of Life, incidentally the last chapter, under the subheading The Abiotic Origin of Nucleotides and Nucleic acids.
    Here is the quote:

    “The next step in the chemical evolution of nucleic acids is the formation of internucleotide linkages between successive mononucleotides. This also has been achieved in simulated primitive-earth experiments in which monomucleotides have been heated at 50-65° in the presence polyphosphoric acid as condensing agent. To date, the internucleotide linkage in abiotically formed oligonucleotides is in most cases the 2?,5? linkage; the 3?,5? linkage does not appear to form readily.”

    Hopefully, that should be enough to reasonably show that Lehninger believed, on the basis of experiments (note the temperature range), that in fact the wrong linkages were more readily formed than the right linkages when OOL experiments tried to produce RNA abiotically. Would you agree?

    Thank you for the quote, and I most wholeheartedly agree that Lehninger believed what he wrote.

    Now, if you have more recent data refuting this idea, I and others would be happy to examine it.

    Refuting what idea? In experiments that had been reported before Lehninger wrote the above, using the stated conditions, the findings were what he said they were. That was then, this is now. Science marches on. See my post #170, especially the Ferris reference, for more recent work on polynucleotide synthesis using different experimental conditions.

    For what it is worth, in editions of Lehninger’s Principles of Biochemistry, including up to 2000 (with two new editors, David Nelson and Michael Cox), which was apparently the textbook that succeeded Biochemistry, the chapter on the origin of life, and most of the material in that chapter, disappears. Judging from the index, the origin of life occupies a progressively smaller part of the book. It appears that the authors did not believe it to be a very important part of biochemistry.

    Anyone who has authored a book or article is faced with choices that are (or should be) influenced by the intended audience. This is especially the case for textbooks. Students who use Principles of Biochemistry have enough on their plates working through those aspects of biochemistry that relate to physiology, molecular biology and medicine.

  174. Daniel King (173),

    Thank you for the reference. You note that “All of the following are available on the Web as free full texts.” Google has not been helpful to me so far in that regard. Do you have a link, or should I head down to the library to read this reference?

    “Refuting what idea?” The idea that “the internucleotide linkage in abiotically formed oligonucleotides is in most cases the 2′,5′ linkage; the 3′,5′ linkage does not appear to form readily”, of course. I will read your reference when I get it.

    I find it fascinating that OOL does not appear to be important to “those aspects of biochemistry that relate to physiology, molecular biology and medicine.” I have been repeatedly told that nothing in biology makes sense except in the light of evolution. Evidently this is not the case for biochemistry regarding OOL. ;)

  175. Paul Giem #174:

    Thank you for the reference. You note that “All of the following are available on the Web as free full texts.” Google has not been helpful to me so far in that regard. Do you have a link, or should I head down to the library to read this reference?

    http://www.ncbi.nlm.nih.gov/sites/entrez

    Is PubMed. Type the author’s name in the search box and scroll down.

    (It works for me.)

  176. Daniel King (175),

    Thanks for the reference. For others who do not wish to search on PubMed, the direct reference is

    http://www.pubmedcentral.nih.g.....d=17008218

    This is, of course, a review article, and thus doesn’t give a lot of data on precisely what results were obtained by actual experiment. But first, note a couple of things. It is sometimes claimed that Miller-Urey apparati can be bypassed as the source of simple organics, as meteorites contain amino acids and could have brought them to earth. As noted in Table 2, the total amino acid content of the Murchison meteorite (presumably including amino acids not used in proteins) was on the order of 10 to 100 parts per million. Considering how slowly meteorites break up, it seems unlikely that meteorites were a major source of amino acids on the early earth.

    Under “3. RIBONUCLEIC ACID WORLD” the second paragraph has this fascinating sentence.

    As will be outlined subsequently, there are no plausible prebiotic syntheses of RNA monomers so that many scientists in this field feel that the spontaneous formation of such complicated structures is very unlikely to have occurred on the primitive Earth.

    But in order to get the results reported, the researchers not only had to have various nucleotides, but had to have them attached, by the phosphate group attached to the 5′ carbon of the nucleotide, to imidazole, 1-methyladenine, and 2-methylimidazole. Still, the resultant dinucleotides, in the presence of montmorillonite, are only about 60% homochiral. While this is relative selectivity, it would not be expected to be good enough to produce long strings of homochiral RNA.

    On the subject of linkages, the entire paragraph says,

    The oligomers produced by montmorillonite catalysis have 2?,5?- and 3?,5?- phosphodiester bonds (figure 8). When the reactions of either purine- or pyrimidine-activated nucleotides occur in the absence of montmorillonite in an aqueous solution, the ratio of 2?,5?- to 3?,5?-linked dimers is about 3:1 (Kanavarioti 1997; Kawamura & Ferris 1999). When the reaction is performed in the presence of montmorillonite, the ratios of ImpA to ImpI are 0.6:1 and 0.2:1 respectively, while those of ImpU to ImpC are 4 and 3, respectively (Ferris & Ertem 1993a; Ding et al. 1996; Ertem & Ferris 1997; Kawamura & Ferris 1999). Clearly, the montmorillonite changes the reaction pathway for the purine nucleotides, while the lowest energy reaction pathway for the pyrimidine nucleotides remains the same as it was in the absence of montmorillonite.

    I’m not sure that this answers the question you were implying that it does. Details of the experiments are mostly absent. One has difficulty deciding what ImpI is, and ImpU and ImpC do not appear to fit with the discussion. Unless you can explain what the discussion means, your reference is not of much help.

    Perhaps even more interesting, the experiments appear not to have used native montmorillonite. In stead they used montmorillonite that had been treated to remove all ions except sodium. This was reportedly “to be sure that the catalytic effect is owing to the clay and not to trace elements bound to it.” However, as some ions do not catalyze RNA formation (e. g. magnesium), and others catalyze 2′,5′ linkages, specifically including uranyl ion, there may be other reasons why sodium montmorillonite is used instead of native montmorillonite.

    All of this makes me wonder whether you actually read the article before you recommended that we read it. Do you just get these references off of a website somewhere and throw them up for us to read and keep busy, or do you read them carefully and think that they somehow answer the questions posed?

    (I note that I get to essentially take back my comments on how Shapiro noted that nucleosides can be made. According to Ferris, “So far, there has been no reported efficient prebiotic conversion of ribose to the corresponding nucleosides by the reaction with purine or pyrimidine bases (Fuller et al. 1972).” Persumably, Ferris is making the best known [to him] case for the RNA world, so he must not know any data to contradict those of Fuller et al.)

    Is there another reference that you think answers the question as to the linkage of RNA precursors to form proper RNA rather than the 2′,5′ isomer?

  177. Paul Giem #176:

    I’m not sure that this answers the question you were implying that it does. Details of the experiments are mostly absent. One has difficulty deciding what ImpI is, and ImpU and ImpC do not appear to fit with the discussion. Unless you can explain what the discussion means, your reference is not of much help.

    Imp = 5′-phosphorimidazolide; I = Inosine, U = Uridine, C = Cytidine.

    The pdf file of Ferris’ review contains some neat hyperlinks. If you click on a reference, it directs you to the reference list. There, most of the references are annotated with a DOI in parenthesis. While connected to the Internet, when you click on the DOI, you will be directed to a relevant Web page, which at a minimum will contain an abstract of the paper or a link to the same.
    What is a DOI?

    A DOI (Digital Object Identifier) is a unique alphanumeric identifier applied to a specific piece of intellectual property, particularly one presented in an online environment — be that object a book, a scientific paper, a song, an image, or something else. Unlike a conventional Web address, or URL, a DOI specifies not the location of an online object, but rather its content; a DOI is thus a “persistent” identifier, and remains associated with the object irrespective of changes in the object’s Web address.

    You asked also:

    Is there another reference that you think answers the question as to the linkage of RNA precursors to form proper RNA rather than the 2?,5? isomer?

    Here is the first part of the abstract from Kawamura and Ferris (1994).
    Kinetic and mechanistic analysis of dinucleotide and oligonucleotide formationfrom the 50-phosphorimidazolide of adenosine on NaC-montmorillonite.
    J. Am. Chem. Soc. 116, 7564–7572.

    The rate constants for the condensation reaction of the 5’-phosphorimidazolide of adenosine (ImpA) to form dinucleotides and oligonucleotides have been measured in the presence of Na+-volclay (a Na+-montmorillonite) in pH 8 aqueous solution at 25 “C. The rates of the reaction of ImpA with an excess of adenosine 5’-monophosphoramidate(NHgA), PI,Pz-diadenosine 5/,5’-pyrophosphate (As’ppA), or adenosine 5’-monophosphate (5/-AMP or PA)in the presence of the montmorillonite to form NHzpA”pA, AS‘ppA3‘pA, and pA3’pA, respectively, were measured. Only 3’,5’-linked products were observed.

    I have highlighted points of special interest that you can compare with your Lehninger quotation.

    Perhaps you will substitute Kawamura and Ferris (1994) or the Ferris review for Lehninger in your future critiques of abiogenesis research.

  178. Response to Paul Giem #165, part 2:

    First, I don’t believe that it is futile to study abiogenesis. I am glad it has been studied, because our knowledge of ways life couldn’t have reasonably have arisen comes from just such research.

    You are glad to learn about ways that life couldn’t have arisen (by natural means). This does not appear to leave room for an interest in learning how life could have arisen by natural means.

    (And if there were such a way, I would want to know).

    Or perhaps this is an expression of such an interest. By what means might that interest be met? By keeping up with the scientific literature?

    So I would never say that “the Spiegelman devolution work was an example of the futility of studying abiogenesis.” You have mischaracterized my position.

    I think I have characterized your position accurately. You made it clear in your second sentence quoted above and repeatedly on this thread and elsewhere (Faith and Reason in the OOL Context , Uncommon Descent, 20 July 2008) that you believe firmly that life came about on this planet not by natural means, but by miraculous invention.

    (This mischaracterization is also found in your statement that I “made the claim that this reference [Lehninger] is a refutation of the feasibility of exploring abiogenesis scientifically.” I don’t mind exploring abiogenesis scientifically. I just think that it is possible that there is no pathway to life without intelligence, and that if so we should not be surprised to not find one, and that if we do not find one we should be honest enough to admit this fact, and that this admission can be, and at present is, an evidence-based statement.)

    More of the same reasoning. You believe that scientific work on abiogenesis can tell us nothing about the real events that brought life about, since those events could not have occurred naturally (“without intelligence”). Moreover, you believe that it is dishonest to keep an open mind about the subject!

    Have you no curiosity about how the Creative Intelligence invented life?

  179. Reply to Paul Giem #165, part 3:

    Second, I have not seen, from you, any “evidence from the scientific literature that this work is irrelevant to abiogenesis.” I know you have said so…

    [......snip.....]

    …Your claim that the experiments are not relevant (which I would agree with in the sense that these experiments do not outline a pathway for abiogenesis) would be better directed at Kacian et al. than at me.

    Then we are agreed. No pathway for abiogenesis.
    And at the very end of your post:

    There does appear to be one area of agreement. We both appear to agree with Shapiro that the Spiegelman experiments do not help advance a reasonable (at this time) pathway for abiogenesis. Do I understand that correctly?

    Yes, you understand correctly. No pathway for abiogenesis.

    (We have shown that it is possible to reach agreement when people discuss things calmly and respectfully.)

    Now will you desist from citing the QBeta work as evidence against abiogenesis research?

  180. Daniel King: “I agree that examples are not identical to similarities. Yet examples of a generalization would not be examples if they didn’t have some similarities. This situation can lead to equivocation in argument, and in order to avoid assuming a conclusion in such cases, it is important to be specific about what is meant in a given argument, by each of the terms above: [A], [B] and “general principle.” In the context of this discussion, bFast said in #84:”

    I think that you are missing the point that DNA says something about the communicator. A communication process contains an encoded message, a medium, a decoded message and a receiver—not to mention noise. In the case of DNA, the message says two things about the communicator: “I was here,” and “Here is why?” The “”why is evident in the functionally specified complex information. There is nothing analogous about this process; it is real communication.

    Now, DNA is a language — it is not “like” a language. When we speak of the “machine language” of a computer’s central processor, it is a language as DNA is a language, as english is a language.

    —–“Argument by definition.”

    Nope. An argument from observation to inference to the best explanation.

    From “Three subsets of sequence complexity and their relevance to biopolymeric information,” by Trevel and Abel.

    “A gene is not analogous to a message; a gene is a message. Genes are literal programs.”

  181. Reply to Paul Giem #165, part 4 (and to StephenB #180):

    Do you remember how disdainful you were about argument by definition (93)? I find your use of analogy worse. Not only do you argue strenuously that DNA code is somehow analogous to computer code rather than an example of a general type called code, and therefore that since it is defined (by you) as an analogy, it doesn’t prove anything, but you completely ignored my point in (114) that analogies are reasonable evidence in everyday science, and that the closer the analogy, the stronger the evidence.

    Let’s take another look at #114:

    Your argument about analogies is built on a fallacy about science. Science, by and large, is not about logically proving anything. It is about amassing evidence that tends to support, or undermine, theories. Thus arguments that are not logically probative may still have weight. Let me give you two examples, one of which can be properly labeled an argument from analogy.

    I agree with your statement that science is not about logically proving anything, although I would subtract the qualifier “by and large.” All of science is empirical, hypothetical, and inductive. Only deductive arguments are capable of providing logical proof. The devil is in the details of evaluating the persuasiveness of the evidence that is brought to bear on an inductive inference (argument).

    I agree with you that analogous reasoning is a form of inductive inference. What one is doing is toting up similarities as evidences. But in the end, one is still faced with a hypothesis that will stand or fall in the face of other data that may have been ignored or are yet to be obtained.
    On the other hand, if you want to claim (deductively) that something is an example of a general principle or type, you have to establish that the example is really an example; and you have to be clear about the properties of the general principle or type. Otherwise, you’re assuming your conclusion: Calling the triplet sequence of nucleic acid chemistry a code can be a convenient semantic shortcut or a useful pedagogic device, but that’s only a grossly simplified way to refer to a rather complicated chemical configuration of atoms. Furthermore, through the good efforts of Nirenberg, Matthaei and Ochoa, we have learned that particular nucleotide triplets specify particular amino acids during protein synthesis at the ribosome. So one chemical configuration (nucleotide sequence) corresponds, through a complicated set of chemical interactions, to another chemical configuration (amino acid sequence). We call that synthetic process, involving these chemical correspondences “translation,” which is another convenient semantic shortcut derived by analogy with translation from one language to another. But, as Alfred Korzybski said, “The map is not the territory.” Figurative language should not mislead us: a metaphorical representation of a concept is not the concept itself.

    What you need to address is whether arguments from analogy can ever serve as evidence. Before you do so, you may want to look at the rest of science to see whether they are used elsewhere as evidence, and whether this use is justified.

    I hope it is clear, from what I said above, that arguments from analogy are hypotheses. Hypotheses are not evidence. We use evidence to support or falsify hypotheses.

    In (79) I gave you some undisputed examples of DNA code produced by intelligent design. You later (81) dismissed them as being done by human intelligence. But it is still true that those changes were done by intelligent design. And those changes are in fact DNA code. Would you not say that at least here your argument dismissing the similarities between DNA code and other codes as merely analogies breaks down? For here we are in fact dealing with DNA code itself produced by intelligence. There is direct evidence that meaningful DNA code itself can be produced by intelligence, whatever you think about computer code. Or doesn’t this qualify as evidence?

    Of course, what you said in #79 qualifies as evidence that human intelligence can manipulate DNA for desired purposes. To reiterate, whether you call this a manipulation of a code is beside the point; it adds nothing other than possible convenience of expression to the fact that the manipulations involve chemical entities with particular configurations.

    To summarize:

    The inductive analogical argument that DNA is a language/code involves making comparisons between features of DNA chemistry and human language/code. The conclusion of this argument is a hypothesis: DNA is a language/code.

    Where one can get into logical difficulty is to employ that hypothetical conclusion as a term in a deductive argument:
    I. All languages/codes are designed.
    II. DNA is a language/code
    Therefore, DNA is designed.

    Note that both premises are questionable hypotheses. So, the argument is formally valid, but the conclusion has not been proven.

  182. I’m having a really hard time following you on how “DNA is a language/code” could be considered a “questionable hypothesis”. For all Darwinists I’ve seen before DNA is not just “like a” language, it IS a language. And, yes, it could be translated into English-based pseudocode if we understood all of this language’s conventions. I find Dawkins to be wrong in many things but at least he has not adopted this awkward position.

    “Flowers and elephants are ‘for’ the same thing as everything else in the living kingdoms, for spreading Duplicate Me programs written in DNA language. Flowers are for spreading copies of instructions for making more flowers. Elephants are for spreading copies of instructions for making more elephants.”
    Richard Dawkins

    He just questions whether Intelligence of any type is required to generate such abstracted information.

  183. Patrick #182:

    I’m having a really hard time following you on how “DNA is a language/code” could be considered a “questionable hypothesis”. For all Darwinists I’ve seen before DNA is not just “like a” language, it IS a language.

    I’m not a Darwininst, but I do have a scientific backqround, and for me, DNA IS NOT a language in the same sense that English is a language. (Incidentally, did you know that English was not designed?
    It evolved!

    Don’t be misled when scientists use figurative language to make pedagogic points. “The map is not the territory.”

    See

    http://en.wikipedia.org/wiki/Reification_(fallacy)

  184. Daniel King:

    DNA IS NOT a language in the same sense that English is a language. (Incidentally, did you know that English was not designed?
    It evolved!

    DNA is not a language in the same sense that English is a language! DNA is a language in the same sense that a computer language — expressly machine language — is a language! It is EXACTLY the same thing!

    BTW, computer languages were all designed, especially machine languages.

  185. bFast #184:

    DNA is a language in the same sense that a computer language — expressly machine language — is a language! It is EXACTLY the same thing!

    You may have me there, because my understanding of computers is likely not as deep as yours, but what the heck, I’ll bite.

    If DNA is EXACTLY the same as machine language, then if I could come up with even a single, solitary difference between the two, no matter how small, you would retract your claim?

  186. Ok, I’ll bite. But remember, each type of computer processor has its own machine language. As such, these processors give a sense of the scope of machine languages. Your difference must be different enough to fall out of that scope.

  187. Thanks, bFast, you’re a gentleman and a scholar.

    Here are what I reckon to be some differences between computer machine language and DNA:

    1. Provenance – computer machine language was designed by human beings :: DNA was not designed by human beings.

    2. Implementation – computer machine language is executed by a central processing unit that contains facilities to fetch, decode, execute, and writeback :: cells do not possess central processing units.

    3. Instruction set – computer machine language contains an instruction set (in a von Neumann implementation), comprising such instructions as arithmetic (add and subtract), logical (and, or and not), data manipulation (move, input, output, load, and store), and flow control (goto, if … goto, call, and return). Recent Intel microprocessors (80486) recognize 142 such instructions :: DNA may be said to contain an instruction set, but it is far more limited and not strictly comparable.

    4. Processing – computer machine language specifies processes that use binary signals :: DNA is not a binary code, but a template, more closely akin to the punched card encoding used in the 19th century for controlling textile looms. DNA is a template for RNA and RNA is a template for protein.

    5. Versatility – computer machine language can be manipulated in ways that are limited only by human imagination and engineering skill :: DNA is limited to operations that can be performed upon it in living cells.

    6. Stability – computer machine language is not subject to random mutational change :: DNA is highly mutable.

    The above are off the top of my head. I’m sure smarter and better informed people can come up with more examples.

    The bottom line remains: what further fruitful hypotheses follow from the hypothesis that DNA is a language?

  188. Lets see how I do with this:

    1 – Provenance. This is a bit of a stretch, isn’t it.

    2 – Implementation. “Computer machine language is executed by a central processing unit.” Not necessarily. The feature that set microcomputers apart from mainframes was the creation of the CPU. Prior to that the processing was done by an assemblage of electronic systems. DNA is processed by an assemblage of proteins that unwinds it, runs along it, produces an RNA copy, sends the RNA copy to be translated into a protein sequence which then folds it. As comuters have been known to work with an assemblage rather than a nice packet called a CPU, I fail to see the difference. You may point out that an organism is not limited to a single processing system running against the DNA. Well, modern computers have, effectively, four separate CPUs executing the memory at four separate locations. I have seen computers running up to 50 CPUs on the same chunk of code simultaneously.

    About “fetch, decode, execute, and writeback”, DNA has fetch (DNA to RNA conversion) DNA has decode (RNA to Protein). Computers don’t have execute, they just execute. Not all computers have writeback, especially small dedicated computers like the one in your microwave — though I understand that retroviruses actually use a writeback system.

    3 Instruction set. The size of the instruction sets in the range of modern computers is huge. The computer in your microwave likely has a very small instruction set. However, DNA does have an instruction set. Especially once you examine start and stop sequences, you must conclude that this is more than just a punch card — but an instruction set. I don’t know enough of how DNA is translated to know if scientists even understand the instruction set yet, but the discovery of intronic data would indicate that the instruction set is more complex than first thought. However, DNA translates the same way when the conditions are the same (translating differently when specific commands to translate differently such as “make a skin cell” is warranted). The fact that DNA follows such a tight discipline establishes that it follows a disciplined instruction set.

    4 Computers use binary code. Well, not all. The IBM System 32, for instance, used BCD code. I inderstand that some computers have at least been experimented with which use a tri-state system based on if a magnetic donut was positively charged, negitively charged or not charged. Furthermore, the punch-card systems used in looms are often seen as simple computers.

    5 – Versatility. To suggest that DNA lacks verstaility is ludicrous. While DNA is limited to act on living cells, computers are limited to act on their own memory, and some simple boolean I/O ports. Both systems are extremely versatile. They work in separate environments, but in both environments they offer incredible flexibility.

    6 Stability, “computer machine language is not subject to random mutational change” The computer techs are howling now! The reality is that periodically, too often, RAM slips a bit. Periodically, all to often, a program writes data into the wrong place. I remember once writing a bug that was detectable becaues, though it wasn’t supposed to do screen work, it twiddled with the characters on the screen.

    Now, computers under normal operation twiddle with the memory in a very controlled fashion. Even there, however, computers will intentionally initialize memory to a random sequence. Certainly computer A will share executable segments with computer B, aka horizontal gene transfer.

    However, the software types on this board are unconvinced that the productive work of DNA development is done by random twiddling and selection. We seem to think that computers can’t be programmed that way. Random twiddling happens in computers and DNA, but in computers random twiddling is invariably either destructive, or in a place that is currently not used. Could it be that random twiddling is pretty much either distructive or ignored in DNA also? Could it be that all of the real code of DNA was developed by an intelligent agent? This is the ID hypothesis.

    You haven’t convinced me that I have lost this one. Ultimately you presented little that I had not considered before I chose to “bite”. DNA is computer memory, the proteins that act on the DNA, the RNA intermediate, are the central processing system.

  189. Daniel King,

    In (177) you apparently missed my point. I could perhaps guess that ImpI had to do with inosine, although the article itself did not make this clear (it is also not clear from the article why ImpI was used instead of ImpG). But I was not implying that ImpU or ImpC were ambiguous so much as that they did not seem to have much to do with the question of 2′,5′ linkages versus 3′,5′ linkages. That was what I referred to when I said, “Unless you can explain what the discussion means, your reference is not of much help.”

    Regarding Kawamura and Ferris, the abstract you gave looks interesting. I am curious as to why you did not refer me to it first instead of to the Ferris review. I will reserve further comment until I have read the actual article.

    In (178) you state,

    You believe that scientific work on abiogenesis can tell us nothing about the real events that brought life about, since those events could not have occurred naturally (”without intelligence”). Moreover, you believe that it is dishonest to keep an open mind about the subject!

    This is either ignorant (which I prefer to believe) or dishonest. Assuming that it is in fact ignorant, let me help make it less so.

    I do not believe that it is dishonest to keep an open mind about OOL, and in fact believe that it is preferable to do so. I have indicated this on a number of occasions. One example is at
    http://www.uncommondescent.com.....ent-292935
    where after others label my obstacles as dealbreakers, I say,

    I don’t look at these obstacles so much as dealbreakers as they are obstacles that must be dealt with if one is to have a good theory. I am prepared to be completely openminded about the origin of life. I’m not locking and barring the door if someone wants to go there. But if that person expects me to follow him/her, he/she needs to deal with the obstacles. If the obstacles are not dealt with, I see no reason why I should exercise faith that they will disappear. I have been told for decades that science has no room for faith. I could buy skepticism. What I can’t buy is selective skepticism.

    Thus at least the last sentence in your quoted paragraph is incorrect, and I view the other two sentences as at least in theory overstatements.

    You ask, “Have you no curiosity about how the Creative Intelligence invented life?” Well, yeah, but that doesn’t mean that I have the right to demand an answer compatible with naturalism. One has to be open to the possibility that such an answer will not be forthcoming, either because the events were unique enough that we never do find the right (or even a possible) combination, or because it didn’t happen without intelligence, or even naturalistically. (Remember, we’re supposed to be open here.)

    On (179), it looks like we may have a deal. I would only ask for three more conditions. You say,

    Now will you desist from citing the QBeta work as evidence against abiogenesis research?

    1. I would like the right to cite the relevant Qbeta work as evidence against abiogenesis if someone else (as Kacian et al. did) cites it as evidence for abiogenesis.
    2. I would like your agreement that you will without prompting point out that the Qbeta work does not in fact indicate a pathway for abiogenesis if you run into someone who claims it does so (absent further evidence, of course).
    3. I would like an explicit acknowledgment that in this specific area, my claim (79) that

    It’s the naturalistic OOL researchers that engage in speculation against the evidence.

    has not been falsified.

    In that case, we have a deal.

  190. Daniel King (187),

    I have to agree with bFast (188); your differences fail. The first and the last fail worst.

    The last one is the worst; it is a true FAIL. ROFL! Do you have any idea how many programs get corrupted every year? The problem isn’t that computer programs never change and DNA changes; the problem is that when computer programs change, the results are almost invariably either silent or deleterious. Come to think of it, the same is true for DNA. You have just outlined a similarity. Try again.

    1. Provenance – computer machine language was designed by human beings :: DNA was not designed by human beings.

    That is quite simply begging the question. The whole point of looking at the other similarities is to suggest that an intelligence somewhat similar to (although probably more intelligent than) human intelligence created DNA. You can’t list that as a significant difference unless you want to win the argument by fiat.

    But probably more important, you appear to make two concessions that support my original thesis. You concede (181) that “I agree with you that analogous reasoning is a form of inductive inference. What one is doing is toting up similarities as evidences.” You later try to take it back by saying, “I hope it is clear, from what I said above, that arguments from analogy are hypotheses. Hypotheses are not evidence.” But if analogous reasoning is inductive inference, then the evidence behind that inductive reasoning is in fact evidence. That would mean that the similarities between DNA code and say, computer code, are in fact evidence which can be reasonably construed as supporting a hypothesis of intelligent design.

    In addition, you concede that “Of course, what you said in #79 qualifies as evidence that human intelligence can manipulate DNA for desired purposes.” That means that we know with moral certainty that DNA code can be caused by intelligent agents. That is evidence that can be reasonably construed as supporting a hypothesis that an intelligent agent or agent caused some of the DNA code in living organisms.

    Thus it is fair to say that my claim (79) that “to say that we are engaging in speculation without evidence is incorrect” is in fact correct.

    You try to blunt the force of these observations by arguing that “the argument is formally valid, but the conclusion has not been proven.” Nobody ever made that claim. The claim was about evidence, not proof.

    In fact, this is not the first time you have made that claim about proof, and I have pointed out that the dispute was not about proof. Please stick to the subject. Your point about proof is granted, but irrelevant to the subject. The question is about evidence. Is there any reason to believe, on the basis of evidence, that ID is the correct explanation for OOL? The answer, judging from your own posts, is yes. You may call the evidence weak (although others will differ), but there is in fact evidence.

  191. While DNA is limited to act on living cells,

    Eh? Last I heard people were working on using DNA for high density data storage with a MUCH longer shelf life than CDs/DVDs.

    Daniel King,

    Anyway, I’ve got to ask…if DNA is not a language, then what is it?

  192. bFast #188:

    1 – Provenance. This is a bit of a stretch, isn’t it.

    A stretch? How so? What I said in #187 was:

    1. Provenance – computer machine language was designed by human beings :: DNA was not designed by human beings.

    Is that statement incorrect? Does it not point to a difference between DNA and computer machine code? A rather fundamental difference, I think.
    Remember, you said in #184:

    DNA is a language in the same sense that a computer language — expressly machine language — is a language! It is EXACTLY the same thing!

    It looks like there’s some “stretch” to the meaning of EXACT in your mind. Here are some typical dictionary definitions:

    Exact: 1 : exhibiting or marked by strict, particular, and complete accordance with fact or a standard
    Exact: 2 : marked by thorough consideration or minute measurement of small factual details.

    There also seems to be some “stretch” to your concept of implementation:

    2 – Implementation. “Computer machine language is executed by a central processing unit.” Not necessarily. The feature that set microcomputers apart from mainframes was the creation of the CPU. Prior to that the processing was done by an assemblage of electronic systems. DNA is processed by an assemblage of proteins that unwinds it, runs along it, produces an RNA copy, sends the RNA copy to be translated into a protein sequence which then folds it. As comuters have been known to work with an assemblage rather than a nice packet called a CPU, I fail to see the difference. You may point out that an organism is not limited to a single processing system running against the DNA. Well, modern computers have, effectively, four separate CPUs executing the memory at four separate locations. I have seen computers running up to 50 CPUs on the same chunk of code simultaneously.

    Looks to me like you are defining the sequence of operations that lead from DNA through its transcription into RNA to its translation into protein as EXACTLY the same as “an assemblage of electronic systems.”

    Not all computers have writeback, especially small dedicated computers like the one in your microwave — though I understand that retroviruses actually use a writeback system.

    So DNA is EXACTLY like the firmware in my microwave oven.

    3 Instruction set. The size of the instruction sets in the range of modern computers is huge. The computer in your microwave likely has a very small instruction set. However, DNA does have an instruction set. Especially once you examine start and stop sequences, you must conclude that this is more than just a punch card — but an instruction set.

    The start of translation is signaled by a particular codon; similarly, there are special termination codons. These are not “sequences.” (A sequence is a series of codons.) Your analogy is comparable to saying that the use of a capital letter to start a sentence and the use of a period to end it are “instructions”. Possibly useful pedagogically. But a deep insight?

    I don’t know enough of how DNA is translated to know if scientists even understand the instruction set yet, but the discovery of intronic data would indicate that the instruction set is more complex than first thought. However, DNA translates the same way when the conditions are the same (translating differently when specific commands to translate differently such as “make a skin cell” is warranted). The fact that DNA follows such a tight discipline establishes that it follows a disciplined instruction set.

    You don’t know any more than “start” and “stop” about the hypothetical DNA instruction set, but you do know that it is EXACTLY like a computer machine language, because “DNA follows such a tight discipline”.

    4 Computers use binary code. Well, not all. The IBM System 32, for instance, used BCD code. I inderstand that some computers have at least been experimented with which use a tri-state system based on if a magnetic donut was positively charged, negitively charged or not charged. Furthermore, the punch-card systems used in looms are often seen as simple computers.

    So, DNA is EXACTLY like the machine language used in microprocessors, microwave ovens, IBM System 32, and punch-card systems. The analogical possibilities seem to be unlimited.

    5 – Versatility. To suggest that DNA lacks verstaility is ludicrous. While DNA is limited to act on living cells, computers are limited to act on their own memory, and some simple boolean I/O ports. Both systems are extremely versatile. They work in separate environments, but in both environments they offer incredible flexibility.

    Please cite examples of DNA code versatility and flexibility for my edification.

    6 Stability, “computer machine language is not subject to random mutational change” The computer techs are howling now! The reality is that periodically, too often, RAM slips a bit.

    There’s a heritable change in the machine code?

    Now, computers under normal operation twiddle with the memory in a very controlled fashion. Even there, however, computers will intentionally initialize memory to a random sequence. Certainly computer A will share executable segments with computer B, aka horizontal gene transfer.

    Since you’ve brought my microwave oven into the big tent of computer machine language, please explain how the firmware is subject to random mutational change. Ditto for my CD player, dishwasher, cell phone, iPod, etc., etc.

    DNA is computer memory, the proteins that act on the DNA, the RNA intermediate, are the central processing system.

    More precisely:
    DNA may be likened to computer memory, the proteins that act on the DNA, the RNA intermediate, may be likened to the central processing system.

    Other than possible employment in pedagogy, of what heuristic value is the analogy?

  193. Paul Giem #189:

    Regarding Kawamura and Ferris, the abstract you gave looks interesting. I am curious as to why you did not refer me to it first instead of to the Ferris review. I will reserve further comment until I have read the actual article.

    I assumed that you would find the Ferris review helpful as an overview.

    In (178) you state,
    You believe that scientific work on abiogenesis can tell us nothing about the real events that brought life about, since those events could not have occurred naturally (”without intelligence”). Moreover, you believe that it is dishonest to keep an open mind about the subject!
    This is either ignorant (which I prefer to believe) or dishonest.

    I was referring to your statement that I quoted just above my comment:

    I just think that it is possible that there is no pathway to life without intelligence, and that if so we should not be surprised to not find one, and that if we do not find one we should be honest enough to admit this fact, and that this admission can be, and at present is, an evidence-based statement.

    “We should be honest enough to admit this fact…,” in reference to not being surprised about not finding a “pathway to life without intelligence…” I take this to mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest.

    You ask, “Have you no curiosity about how the Creative Intelligence invented life?” Well, yeah, but that doesn’t mean that I have the right to demand an answer compatible with naturalism. One has to be open to the possibility that such an answer will not be forthcoming, either because the events were unique enough that we never do find the right (or even a possible) combination, or because it didn’t happen without intelligence, or even naturalistically. (Remember, we’re supposed to be open here.)

    My question was directed at HOW, not WHETHER. If a Creative Intelligence invented life, HOW did it do it?

    On (179), it looks like we may have a deal. I would only ask for three more conditions. You say,
    Now will you desist from citing the QBeta work as evidence against abiogenesis research?
    1. I would like the right to cite the relevant Qbeta work as evidence against abiogenesis if someone else (as Kacian et al. did) cites it as evidence for abiogenesis.
    2. I would like your agreement that you will without prompting point out that the Qbeta work does not in fact indicate a pathway for abiogenesis if you run into someone who claims it does so (absent further evidence, of course).
    3. I would like an explicit acknowledgment that in this specific area, my claim (79) that
    It’s the naturalistic OOL researchers that engage in speculation against the evidence.
    has not been falsified.

    1. If you would like to continue to cite the QBeta work, please do so.
    2. I agree without prompting and without reservation that if any person makes such a claim, I will laugh that person to scorn.
    3. If your blanket claim has been supported by anything other than quotations from Shapiro and Kacian et al., please advise. In any case, speculation against the evidence is a matter of opinion. From what I’ve seen from serious OOL researchers are good faith efforts to speculate in light of the evidence.

  194. Paul Giem #190:

    I have to agree with bFast (188); your differences fail. The first and the last fail worst.
    The last one is the worst; it is a true FAIL. ROFL! Do you have any idea how many programs get corrupted every year? The problem isn’t that computer programs never change and DNA changes; the problem is that when computer programs change, the results are almost invariably either silent or deleterious. Come to think of it, the same is true for DNA. You have just outlined a similarity. Try again.

    See my response above to bFast on this point.

    1. Provenance – computer machine language was designed by human beings :: DNA was not designed by human beings.
    That is quite simply begging the question. The whole point of looking at the other similarities is to suggest that an intelligence somewhat similar to (although probably more intelligent than) human intelligence created DNA. You can’t list that as a significant difference unless you want to win the argument by fiat.

    My statement (1) was not an argument. It was a datum. An iota of evidence. Just as “hypotheses are not evidence,” so “evidence is not an hypothesis.” No hypothesis = no argument = no possibility of question-begging. I was addressing bFast’s claim of equivalence. You are free to deal with that datum as you wish and as you have done.
    I have agreed that your speculations have evidence to support them. Those speculations have led you to hypothesize:

    Is there any reason to believe, on the basis of evidence, that ID is the correct explanation for OOL? The answer, judging from your own posts, is yes. You may call the evidence weak (although others will differ), but there is in fact evidence.

    Well put, and agreed to.

  195. Patrick #191:

    Last I heard people were working on using DNA for high density data storage with a MUCH longer shelf life than CDs/DVDs.

    Yes, human beings are capable of manipulating DNA (among other entities) in imaginative ways for computing or other purposes. But in the context of my remarks to bFast, I was comparing DNA, as it functions in natural biological systems, to computer machine language.

    Anyway, I’ve got to ask…if DNA is not a language, then what is it?

    It’s a RECIPE!

    See this:

    A language is considered to be a system of communicating with other people using sounds, symbols and words in expressing a meaning, idea or thought. This language can be used in many forms, primarily through oral and written communications as well as using expressions through body language.

    I assert that all other usages of the word “language” as employed by you and other worthy persons (including computer scientists) are figurative and therefore not probative.

    Are those figurative employments profitable for scientific purposes (except pedagogically)? Once again: What matters is the bottom line, which awaits a response from you and your colleagues:

    What Further Fruitful hypotheses Follow from the hypothesis that DNA is a language?

  196. Would you also assert that the bacterial flagellum is not a machine?

  197. Daniel King, (193)
    Thank you for your responses (193 and 194). It looks like we almost have a deal, and the only sticking point is 3.

    My original statement was,

    3. I would like an explicit acknowledgment that in this specific area, my claim (79) that

    It’s the naturalistic OOL researchers that engage in speculation against the evidence.

    has not been falsified.

    Your response was,

    3. If your blanket claim has been supported by anything other than quotations from Shapiro and Kacian et al., please advise. In any case, speculation against the evidence is a matter of opinion. From what I’ve seen from serious OOL researchers are good faith efforts to speculate in light of the evidence.

    Your reply addresses the larger picture, not the very limited point I was making and trying to get agreement on. I specifically was not saying, and not trying to get your assent to, the proposition that my quoted statement from (79) had been proved, or was correct, or even had evidence for it. We can discuss that later.

    Rather, my point was the narrow one that the Qbeta experiments were not evidence against the statement that

    It’s the naturalistic OOL researchers that engage in speculation against the evidence.

    My understanding is that you would not regard it as evidence either for or against that proposition, and so it cannot serve as evidence against it. Do I understand correctly? If so, we have a deal, and in future lists of obstacles to evolution, at least until the other side brings it up, I would plan not to mention the subject.

    You said,

    I assumed that you would find the Ferris review helpful as an overview.

    As you can see, the overview had several significant defects, especially as regards the question of 2′,5′ versus 3′.5′ linkages. It also has the inherent defect of being secondary versus the primary reporting of experiments. But I can appreciate your reasoning.

    You say,

    “We should be honest enough to admit this fact…,” in reference to not being surprised about not finding a “pathway to life without intelligence…” I take this to mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest.

    You have misinterpreted me. Let me make it clearer. My original statement was,

    I just think that it is possible that there is no pathway to life without intelligence, and that if so we should not be surprised to not find one, and that if we do not find one we should be honest enough to admit this fact, and that this admission can be, and at present is, an evidence-based statement.

    The pronoun “this” could be taken ambiguously. My intention was to take it in the following way:

    “. . . and that if we do not find one [a pathway to life without intelligence] we should be honest enough to admit this fact [the fact that we have not found a pathway to life without intelligence]”

    Note that what I said was not that the quest was futile, not that it could not achieve its goal, but rather the more limited claim that it had not achieved its goal.

    And there are some OOL researchers that recognize this. See the extensive quotes by kairosfocus in (72), and read Shapiro’s Origins (which hopefully you will get soon through interlibrary loan). So I do not “mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest.” I was not talking about futility. I was talking about honesty about where the evidence is at present, and at least some of them are in fact honest about that fact.

    You say,

    My question was directed at HOW, not WHETHER. If a Creative Intelligence invented life, HOW did it do it?

    But the same answer still applies. If it was done by an intelligence (or Intelligence), thousands, let alone billions, of years ago, do we have the right to demand that we can reconstruct the mechanism without asking any eyewitnesses? And if we can’t do so, and there are no earthly eyewitnesses, we’re kind of out of luck, aren’t we? That is, unless the one (or One) who did it tells us how, but let’s not go there right now.

  198. Daniel King,

    I have finally been able to get a copy of Kawamura and Ferris (1994) [J. Am. Chem. Soc. 116, 7564–7572], and I have some comments.

    First, judging from the products’ reaction with RNase T2, the linkages of some parts of the experiment were nearly pure 3′,5′-linked. So at first glance it would appear that 3′,5′ linkages can be made using natural materials. So the experiments seem to suggest one possible way that RNA can be made without 2′,5′ linkages. That would be a way around one of my obstacles.

    It is also interesting to note that the authors of the paper see this as related to OOL. The last 4 sentences of the paper (excluding the acknowledgment) were:

    Structure analysis of the reaction products revealed that only the 3′,5′-linked dinucleotide was formed in each reaction. The observation of the regiospecific formation of the corresponding 3′,5′-linked dinucleotide was unexpected. This observation suggests that it will be possible to synthesize 3′,5′-linked oligonucleotides on montmorillonite if the activated monomer, in this case ImpA, is the limiting reagent. This is also a plausible prebiotic scenario for regiospecific oligonucleotide synthesis since it is likely that the concentrations of activated mononucleotides were quite low on the primitive earth.

    However, on second glance, things aren’t quite what they seem. The montmorillonite (clay from weathered volcanic rock) isn’t just dumped in. Only certain clays, ones from American Colloid Compound (unstated provenance), Japan, and Wyoming, would significantly cause the reaction. Clays from the San Diego, CA area (Otay), Arizona, and Texas “exhibit little or no catalytic ability”. There is some evidence suggestion that iron may have something to do with the catalytic activity.

    But not only must we carefully choose the clay; we must also pretreat it with hydrochloric acid, then neutralize it with sodium hydroxide. This is a bit more difficult to visualize on the primitive earth. Then we must add magnesium chloride (calcium chloride is not nearly as effective). By this point we are starting to reach.

    We start to overbalance in our reach when we realize that HEPES (N-(2-hydroxyethyl)piperazine-N’-2-ethanesulfonic acid) is added to the reaction. Where HEPES came from on the primitive earth is not clear.

    The starting compound, IMO, pushes us over the edge. It is the 5′-phosphorimidazolide of adenosine. Adenosine itself is hard enough to make. Now we must add a phosphate group, then remove an oxygen from that phosphate and add an imidazole group. The authors’ laconic comment that “it is likely that the concentrations of activated mononucleotides were quite low on the primitive earth” is a breathtaking understatement.

    Of interest in this regard is that, judging from figure 5, the major reaction catalyzed by montmorillonite, consuming roughly 3/4 of the reagent (estimated from the graph) is simply hydrolysis of ImpA. That makes the reaction even less likely. And even in ideal circumstances, oligomers of 10 parts seems to be the practical maximum.

    The authors note that “The exclusive formation of 3′,5′-linked dinucleotides under the condtions used for the kinetic studies was an unexpected finding.” Presumably, most other experiments had found a significant number of 2′,5′ linkages.

    Given this paper, IMO, my obstacle 8 should be rewritten to read:
    8. Except in highly unusual and somewhat artificial situations, when nucleotides polymerize naturally into RNA, they commonly form 2′,5′ linkages rather than the 3′,5′ linkages normally found in RNA.

    Would you dispute that obstacle using evidence from the literature?

    Finally, how would you classify this paper? Is it evidence for a “plausible prebiotic scenario”, as the authors seem to think? Is it not relevant to OOL research, as you have stated about the Qbeta research? Or is it net evidence against abiogenesis? Compare and contrast this work with the Qbeta work. I would be quite interested in your analysis.

  199. Daniel King, (194)

    You refer me to your response to bFast defending your claim that “computer machine language is not subject to random mutational change”. You ask, innocently I presume,

    There’s a heritable change in the machine code?

    I hate to tell you this, but if a program you are using develops a bug, and you copy it to another computer, the new copy will still have the bug.

    You go on to ask bFast, “Other than possible employment in pedagogy, of what heuristic value is the analogy?” Which leads me to ask, have you ever programmed a computer? Because, to someone who has, your question sounds uninformed, to put it politely.

    You stated,

    My statement (1) was not an argument. It was a datum. An iota of evidence. Just as “hypotheses are not evidence,” so “evidence is not an hypothesis.” No hypothesis = no argument = no possibility of question-begging.

    But it is not a datum. Part of what I pointed out is that in fact, humans have designed DNA. Perhaps small pieces of DNA, but they have done so. Furthermore, without further evidence, one cannot say that humans did not create the DNA needed to start life, or to create the Cambrian explosion, or whales, or other humans. For all we know from science, the whole mess could have been created by a very intelligent graduate student )or series of graduate students) with a supersupercomputer.

    Now, that’s not what I think most likely happened. But I do think that it was some kind of intelligence. Your argument starts to sound like “we know it wasn’t aliens, and God either doesn’t exist or doesn’t muddy his hands with nature.” That is effectively an antitheist position. Don’t be too surprised if some of us find it unconvincing as the starting point for an argument.

    I will finish on a note of agreement. As you quoted me and commented,

    Is there any reason to believe, on the basis of evidence, that ID is the correct explanation for OOL? The answer, judging from your own posts, is yes. You may call the evidence weak (although others will differ), but there is in fact evidence.

    Well put, and agreed to.

    This means that an ID approach to OOL issues is not simply a matter of “speculation”, as you indicated in (57). I claimed in (59) that “There is a lot of experimental evidence to back us up.” One may dispute how much “a lot” is, but is it good to see that we can at least agree that there is evidence for the proposition that ID is the correct explanation for OOL.

    You may not argue this way, but I have run into multiple people who will argue that there is no evidence for ID, and a lot of evidence for “evolution”. This us usually related to the claim that ID is not science (because there is no evidence for it), and therefore must be religion, since it refers to God (DaveScot notwithstanding), whereas OOL research is scientific. This sets up a Science versus Religion debate, and the “religious” side is presumed to automatically lose, without even a need to consider the evidence. With your agreement that there is evidence for ID, at least in the case of OOL, one can dispense with this line of reasoning. :)

  200. Paul Giem

    I hate to tell you this, but if a program you are using develops a bug, and you copy it to another computer, the new copy will still have the bug.

    I don’t mind telling you that you’re quite wrong. If the program develops a bug while being used the bug won’t be on the write-protected copy that software is distributed upon. Generally when software is copied onto a computer it will be from a write protected diskette or CD-ROM onto a hard drive. When the software is copied onto another computer it is generally from the original diskette or CD-ROM not the local copy on a hard drive.

  201. DaveScot (201),

    You are quite right that a professional program will be write-protected and that therefore if you copy the backup copy onto another computer, the bug in the first computer’s copy will not affect either the backup copy or the other computer.

    However, if you copy the first computer’s copy to another computer, the bug will be replicated. And if the backup copy develops a bug, say, through a scratch, the bug will be replicated as well. If you lose the backup copy, or forgot to make one when you programmed (I know, I know, how stupid can one get? Pretty stupid!), you have only two choices; fix the bug (and make a backup copy), or live with a defective program.

    The point I was making, which is still valid, is that mistakes in computer code are heritable, just like DNA changes.

    It is interesting that DNA comes with a built-in backup copy. What a neat idea! It’s almost like someone designed it that way!

  202. Whoops! That was DaveScot (200)

  203. Patrick #196:

    Would you also assert that the bacterial flagellum is not a machine?

    Of course I would. The bacterial flagellum can be likened to a machine, such as an outboard motor – a device designed and built by human beings. Similarly, my exercise trainer used to tell me that he was going to transform me into a “Lean, mean, fighting machine.” (He failed.) But I didn’t take him literally, because I know that I am not a device that was designed and built by human beings.

    Giving a name to something does not make it into that thing. As a notorious ex-president of the US once said, “It depends on what the meaning of the word is is.”

  204. Paul Giem #197:

    Rather, my point was the narrow one that the Qbeta experiments were not evidence against the statement that
    “It’s the naturalistic OOL researchers that engage in speculation against the evidence.”

    My understanding is that you would not regard it as evidence either for or against that proposition, and so it cannot serve as evidence against it. Do I understand correctly? If so, we have a deal, and in future lists of obstacles to evolution, at least until the other side brings it up, I would plan not to mention the subject.

    As long as you understand that I do not accept your quoted statement, I agree that you understand my thinking about the QBeta work. As I believe I said above, I consider it to be irrelevant to abiogenesis.

    Note that what I said was not that the quest was futile, not that it could not achieve its goal, but rather the more limited claim that it had not achieved its goal.
    And there are some OOL researchers that recognize this. See the extensive quotes by kairosfocus in (72), and read Shapiro’s Origins (which hopefully you will get soon through interlibrary loan). So I do not “mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest.” I was not talking about futility. I was talking about honesty about where the evidence is at present, and at least some of them are in fact honest about that fact.

    Thanks very much for the clarification. I would, however, object to the aspersion of dishonesty among “some” abiogenesis researchers. Such ad hominems are bad form in scientific discourse. If you really want to make that kind of case, name names and back up your assertions with evidence.

    My question was directed at HOW, not WHETHER. If a Creative Intelligence invented life, HOW did it do it?
    But the same answer still applies. If it was done by an intelligence (or Intelligence), thousands, let alone billions, of years ago, do we have the right to demand that we can reconstruct the mechanism without asking any eyewitnesses? And if we can’t do so, and there are no earthly eyewitnesses, we’re kind of out of luck, aren’t we? That is, unless the one (or One) who did it tells us how, but let’s not go there right now.

    On the contrary, we not only have the right to ask questions and to think about the past (no matter how far past), we have the obligation as thinking beings to do so. That’s what God gave us brains for. Eyewitnesses are not essential to a number of sciences, including history, astronomy, archeology, paleontology, geology, etc.

    Life was invented out of chemicals. Somehow.

  205. Paul Giem #198:

    I have finally been able to get a copy of Kawamura and Ferris (1994) [J. Am. Chem. Soc. 116, 7564–7572], and I have some comments.

    [...SNIP...]

    Given this paper, IMO, my obstacle 8 should be rewritten to read:

    8. Except in highly unusual and somewhat artificial situations, when nucleotides polymerize naturally into RNA, they commonly form 2?,5? linkages rather than the 3?,5? linkages normally found in RNA.
    Would you dispute that obstacle using evidence from the literature?

    A nice critique. In the current state of our ignorance, all experimental conditions may be judged artificial, so you may make as much of that as you like. The work “commonly” is too vague, I think. Based on the Ferris work, “more commonly under some conditions” would be more accurate.

    Finally, how would you classify this paper? Is it evidence for a “plausible prebiotic scenario”, as the authors seem to think?

    Yes, it is evidence for. Possibly. A teeny weeny bit. We’re taking baby steps at this stage of development in the field.

    Is it not relevant to OOL research, as you have stated about the Qbeta research?

    Yes, it’s relevant, as the QBeta work was not.

    Or is it net evidence against abiogenesis?

    How can it be evidence against? You have argued that it’s not evidence for. Your opinion doesn’t constitute evidence against.

    Compare and contrast this work with the Qbeta work. I would be quite interested in your analysis.

    The contrast is that the QBeta work was not directed at abiogenesis from its inception, and yielded no data relevant to the subject.

  206. Paul Giem #199:

    You stated,

    My statement (1) was not an argument. It was a datum. An iota of evidence. Just as “hypotheses are not evidence,” so “evidence is not an hypothesis.” No hypothesis = no argument = no possibility of question-begging.

    But it is not a datum. Part of what I pointed out is that in fact, humans have designed DNA. Perhaps small pieces of DNA, but they have done so. Furthermore, without further evidence, one cannot say that humans did not create the DNA needed to start life, or to create the Cambrian explosion, or whales, or other humans. For all we know from science, the whole mess could have been created by a very intelligent graduate student )or series of graduate students) with a supersupercomputer.

    Now, that’s not what I think most likely happened. But I do think that it was some kind of intelligence. Your argument starts to sound like “we know it wasn’t aliens, and God either doesn’t exist or doesn’t muddy his hands with nature.” That is effectively an antitheist position. Don’t be too surprised if some of us find it unconvincing as the starting point for an argument.

    Don’t be surprised if I find your equivocations about current capabilities of human genetic engineers and the historic origin of DNA unconvincing.

    Here is my statement again:

    computer machine language was designed by human beings :: DNA was not designed by human beings

    Looks like a datum to me.

    With your agreement that there is evidence for ID, at least in the case of OOL, one can dispense with this line of reasoning.

    I have much sympathy for the ID position. I wouldn’t have engaged in this discussion if I didn’t think there were issues worth analyzing. And I have enjoyed and profited from this engagement. I thank you especially for calling my attention to Shapiro’s Origins, which I now have in hand and am reading with pleasure. It is a beautiful example of scientific writing for non-scientists.

  207. Daniel King,

    You said, (204)

    As long as you understand that I do not accept your quoted statement, I agree that you understand my thinking about the QBeta work.

    I agree that our agreement about the Qbeta work is not adequate to prove, or even reasonably prove, my quoted statement. That means that I wouldn’t expect you to accept that statement without something else as evidence. All I wanted to point out is that the Qbeta work does not falsify the statement. It looks like we have agreement here.

    You said, (204)

    Thanks very much for the clarification. I would, however, object to the aspersion of dishonesty among “some” abiogenesis researchers.

    You are overreading. I said

    And there are some OOL researchers that recognize this. . . . I was talking about honesty about where the evidence is at present, and at least some of them are in fact honest about that fact.

    I was only stating what I could prove. It is possible that all OOL reserchers recognize explicitly that they have not reached the goal of showing how life developed from non-life, or could have developed. If so, I haven’t read it. Notice the “at least some”, which leaves open the possibility that “all” could fit the statement. I suppose it might have made it easier for you if I had said “there are some OOL researchers that explicitly recognize this.” But as you wish me to read them more charitably, I wish that you would read me more charitably.

    (I have run into people defending naturalism who insist that naturalism has solved the OOL problem. None of them, to my knowledge, are OOL researchers. I can name at least one name, if you wish. Otherwise, we can just move on.)

    To the question of how life came to be, you quote me (204, accurately) as saying,

    But the same answer still applies. If it was done by an intelligence (or Intelligence), thousands, let alone billions, of years ago, do we have the right to demand that we can reconstruct the mechanism without asking any eyewitnesses? And if we can’t do so, and there are no earthly eyewitnesses, we’re kind of out of luck, aren’t we? That is, unless the one (or One) who did it tells us how, but let’s not go there right now.

    You then reply,

    On the contrary, we not only have the right to ask questions and to think about the past (no matter how far past), we have the obligation as thinking beings to do so. That’s what God gave us brains for. Eyewitnesses are not essential to a number of sciences, including history, astronomy, archeology, paleontology, geology, etc.

    I never said that we do not have the right to ask questions. I merely said that we don’t have the right to demand answers. There is a difference. There are some questions I’d like to ask about the first three flights on 9-11 that I’d like to know. Did any of the passengers think that they ought to take control of the airplane, and perhaps even try to do so but in a disorganized way? But I know of no way, either now or in the future, that we will ever know, or even have good evidence for a hypothesis regarding the question. Some things are just beyond our ability to discover. That doesn’t mean that we can’t ask the question. It just means that we can’t demand an answer.

    Life was invented out of chemicals. Somehow.

    Well, yeah. Science may or may not find out how. If science eliminates a whole category of causes, and the real answer lies within that category, then science will not find the answer. That much is guaranteed.

    Commenting on your (205),

    A nice critique.

    Thank you.

    The work “commonly” is too vague, I think. Based on the Ferris work, “more commonly under some conditions” would be more accurate.

    Let me try again.

    8. Except in highly unusual and somewhat artificial situations, when nucleotides polymerize naturally into RNA, a significant number of linkages are 2′,5′ linkages rather than the 3′,5 linkages normally found in RNA.

    Keep in mind that this is a fallible obstacle. If we discover that a montmorillonite from Antarctica can be simply added to ATP without pretreatment (or perhaps pretreatment with dilute seawater), and without HEPES, with the specificity noted by Kawamura and Ferris, then the obstacle will essentially fail. These obstacles are scientific, and therefore cannot be absolute. That’s why I preferred to refer to them as obstacles rather than dealbreakers.

    But the possibility that they may be wrong is not evidence that in fact they are wrong. Currently, the assertion that they are wrong is a faith statement, and the evidence we have now argues that in fact they are right.

    I believe that faith has a place in our trying to sort out reality. I even believe on occasion without evidence, and occasionally against the evidence. Without that belief, I would never do research into a controversial subject that most scientists would consider closed. But I wouldn’t dream of telling those who differ with me on the basis of evidence that they should just take it from me, in spite of the evidence, that they are wrong, let alone stupid for their belief.

    Yes, it is evidence for. Possibly. A teeny weeny bit. We’re taking baby steps at this stage of development in the field.

    he contrast is that the QBeta work was not directed at abiogenesis from its inception, and yielded no data relevant to the subject.

    Your evaluation of the difference, in my book, doesn’t fly. What a given experiment was aimed at does not determine its relevance. Let me give two relatively uncontroversial examples. The research that discovered the first antibiotic, penicillin, was in fact initially aimed at studying bacterial growth, not chemicals that are toxic to bacteria. It was nevertheless highly significant in the latter field. And the research that discovered the primary effect of Viagra was originally aimed at controlling angina, and Viagra was a failure in that regard. However, it has been extremely helpful in treating erectile dysfunction.

    Perhaps you can find another difference between the Qbeta research and the montmorillonite reseearch.

    Regarding (206), on your statement (1), perhaps we should just agree to differ, as we seem to differ on the definition of the word “datum”. Should I take your silence regarding your statement

    6. Stability – computer machine language is not subject to random mutational change :: DNA is highly mutable.

    that you no longer would maintain this argument?

    I have much sympathy for the ID position. I wouldn’t have engaged in this discussion if I didn’t think there were issues worth analyzing. And I have enjoyed and profited from this engagement. I thank you especially for calling my attention to Shapiro’s Origins, which I now have in hand and am reading with pleasure. It is a beautiful example of scientific writing for non-scientists.

    Thank you. And even though the conversation has had some rough edges at times, I think we’ve all learned from it. I know I have, and I have appreciated the opportunity to learn.

    You’re certainly welcome regarding Shapiro. I agree wholeheartedly with your assessment of his writing. I’m glad I could introduce you to him.

  208. Daniel King, thanks for the sited studies in post #179, I had missed this post. It’ll take me a while to absorb them, but I will.

    Anyway, I’ve got to ask…if DNA is not a language, then what is it?

    It’s a RECIPE!

    One thing is clear, DNA seems to use a fundimentally different coding technique than we programmers use, a technique that may need to find its way into computer programming. This technique is well described as a recipe.

    Computer software has gone through a number of fundimental changes, from sequential, to block structured, to object oriented. Custom languages have used even different structures, like lisp and its list structure. In each case, the CPU needed to make no changes to adapt to the different coding styles. To describe the coding style in DNA as “recipe” style makes lots of sense. However, it does not change the fact that the underlying technology is a pretty straightforward computer.

    Note the wiki in 119 states: “it contains the instructions”. This statement clearly defines DNA as computer code — it is a bunch of instructions!

    As to your wiki definition of language, please note that computer languages do not meet the definition any better than DNA does.

  209. Oops, the studies are in #170.

  210. bFast #208:

    Daniel King, thanks for the sited studies in post #179, I had missed this post. It’ll take me a while to absorb them, but I will.

    Again, bFast, thanks for your interest. The people who seem (to me) to be doing the most interesting work on the RNA world are Jack Szostak, Gerald Joyce, and David Bartel. A good way to get free full text of many of their papers is to Google Szostak lab, or Joyce lab or Bartel lab and go to their bibliographies. Take a look at Szostak’s more recent work on artificial cells for some imaginative approaches to inventing life in the lab.

    As to your wiki definition of language, please note that computer languages do not meet the definition any better than DNA does.

    Exactly my point! “Computer languages” and “DNA as a language” are both figurative uses of the word “language.” And one of my objects here has been to criticize such figurative uses as sloppy talk that leads to faulty thinking.

    I’m enjoying all of the agreement we’re reaching on this thread.

  211. Reply to Paul Giem #207, part 1:

    All I wanted to point out is that the Qbeta work does not falsify the statement. It looks like we have agreement here.

    The relationship, if any, of the QBeta work to your statement, “It’s the naturalistic OOL researchers that engage in speculation against the evidence,” is so remote that I am delighted to certify agreement here.

    You are overreading. I said
    “And there are some OOL researchers that recognize this. . . . I was talking about honesty about where the evidence is at present, and at least some of them are in fact honest about that fact.”
    I was only stating what I could prove. It is possible that all OOL reserchers recognize explicitly that they have not reached the goal of showing how life developed from non-life, or could have developed. If so, I haven’t read it. Notice the “at least some”, which leaves open the possibility that “all” could fit the statement.

    The only way to find out what all OOL researchers recognize explicitly would be to poll them.
    But you have already noted with satisfaction that some of them criticize the work of others, which is an exemplary corrective.

    But as you wish me to read them more charitably, I wish that you would read me more charitably.

    I am doing the best I can to understand what you are saying.

    I never said that we do not have the right to ask questions. I merely said that we don’t have the right to demand answers. There is a difference. There are some questions I’d like to ask about the first three flights on 9-11 that I’d like to know. Did any of the passengers think that they ought to take control of the airplane, and perhaps even try to do so but in a disorganized way? But I know of no way, either now or in the future, that we will ever know, or even have good evidence for a hypothesis regarding the question. Some things are just beyond our ability to discover. That doesn’t mean that we can’t ask the question. It just means that we can’t demand an answer.

    (Emphasis added)

    How does one determine those limits? Have we already reached those limits with respect to abiogenesis? From what you have written, it appears that you think so. And your view has a theological basis. For example:
    You said in #114:

    I am not sure that there is any other way to detect the existence of a deity than otherwise unexplained events in nature or
    history (which is claimed as a part of nature by believers in naturalism).

    To which I replied in #142:

    Surely your faith does not rest on such a slender reed.

    To which you responded in #146:

    Why not? Did not the apostle Paul (1 Cor. 15) stake his entire belief system on the historicity of a miracle? Besides, I thought that a religion that was falsifiable would be superior to one that was not. A religion that is not falsifiable cannot, and for that reason, tell us anything about nature. It would seem to be an advantage for a religion to guide us when dealing with nature.

    And let’s not forget your reference to Deuteronomy (#135)

    It seems to me that you feel a need to protect the miraculous, so you oppose science that calls the miraculous into question. You are absolutely entitled to your view, of course. But for many other religious people, belief in the miraculous is not such a big issue; other consideratons sustain their faith. Such persons seem to be more comfortable with letting science go wherever curiosity leads it.

    I was brought up a Catholic, and you may know that my Church has learned a lot from its conflict with Galileo and Copernicus. As I see it, the politics of the Counter-Reformation were a major factor in that blunder. St Roberto Bellarmino should have been more cognizant of what St. Augustine wrote in The Literal Meaning of Genesis:

    Usually, even a non-Christian knows something about the earth, the heavens, and the other elements of this world, about the motion and orbit of the stars and even their size and relative positions, about the predictable eclipses of the sun and moon, the cycles of the years and the seasons, about the kinds of animals, shrubs, stones, and so forth, and this knowledge he hold to as being certain from reason and experience. Now, it is a disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. The shame is not so much that an ignorant individual is derided, but that people outside the household of faith think our sacred writers held such opinions, and, to the great loss of those for whose salvation we toil, the writers of our Scripture are criticized and rejected as unlearned men. If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods and on facts which they themselves have learnt from experience and the light of reason? Reckless and incompetent expounders of Holy Scripture bring untold trouble and sorrow on their wiser brethren when they are caught in one of their mischievous false opinions and are taken to task by those who are not bound by the authority of our sacred books.

    You also wrote (first quoting me):

    “Life was invented out of chemicals. Somehow.”
    Well, yeah. Science may or may not find out how. If science eliminates a whole category of causes, and the real answer lies within that category, then science will not find the answer. That much is guaranteed.

    Science can only grasp what it can reach. The miraculous is out of its reach. And therefore safe from science.

  212. Reply to Paul Giem #207, part 2:

    “The contrast is that the QBeta work was not directed at abiogenesis from its inception, and yielded no data relevant to the subject.”

    Your evaluation of the difference, in my book, doesn’t fly. What a given experiment was aimed at does not determine its relevance. Let me give two relatively uncontroversial examples. The research that discovered the first antibiotic, penicillin, was in fact initially aimed at studying bacterial growth, not chemicals that are toxic to bacteria. It was nevertheless highly significant in the latter field. And the research that discovered the primary effect of Viagra was originally aimed at controlling angina, and Viagra was a failure in that regard. However, it has been extremely helpful in treating erectile dysfunction.
    Perhaps you can find another difference between the Qbeta research and the montmorillonite reseearch.

    My statement quoted above was in response to your request in #198:

    Compare and contrast this work with the Qbeta work. I would be quite interested in your analysis.

    My statement had two clauses. The first was “…the QBeta work was not directed at abiogenesis from its inception…” That is a truth, a datum, that distinguishes the QBeta work from the Ferris work. So it was responsive to your request. The second clause was “…yielded no data relevant to the subject.” It’s in the second clause that I addressed relevance.

    I have already given you reasons for my opinion about the QBeta work (#149):

    …knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issuesof abiogenetic RNA syntheses.

    QBeta is a small, icosahedral virus (bacteriophage) that infects E. coli. Its genome is a single-strand of RNA about 4,000 nucleotides in length, encoding three structural proteins and a replicase (RNA-copying enzyme). [see, for example, Klovins, J, Berzins, V and van Duin, J RNA 1998 4: 948-957]

    In earlier work, [Haruna and Spiegelman Proc Natl Acad Sci U S A. 1966 Jun;55(6): 1539-54] had discovered an exquisite specificity of the phage replicase: it only works when provided with its own genomic RNA as a template for copying. This makes sense biologically, for if the replicase recognized and were bound as well as its own genome by the far more abundant messenger RNA molecules in infected cells, replication of the viral genome couldn’t get off the ground to generate new phage genomes. Another biological point: the phage is a highly evolved organism that replicates with maximum efficiency. It contains no genetic sequences that are not essential to its survival. There is no reason (no survival advantage) why its replicase should synthesize any additional information either in vivo or in vitro.

    But if you want to consider the QBeta relevant to abiogenesis, that is your privilege.

    Regarding (206), on your statement (1), perhaps we should just agree to differ, as we seem to differ on the definition of the word “datum”.

    Call it a datum, call it an hypothesis, it still constitutes a difference between computer machine code and DNA. To the best of my knowledge, computer code was invented by human beings, whereas, to the best of my knowledge, DNA was not invented by human beings.

    But if you want to argue that human beings invented DNA 3.5 billion years ago, that is your privilege.

    Should I take your silence regarding your statement
    “6. Stability – computer machine language is not subject to random mutational change :: DNA is highly mutable.”
    that you no longer would maintain this argument?

    See again #192, my response to bFast:

    bFast: 6 Stability, “computer machine language is not subject to random mutational change” The computer techs are howling now! The reality is that periodically, too often, RAM slips a bit.

    Daniel King: There’s a heritable change in the machine code?

    bFast: Now, computers under normal operation twiddle with the memory in a very controlled fashion. Even there, however, computers will intentionally initialize memory to a random sequence. Certainly computer A will share executable segments with computer B, aka horizontal gene transfer.

    Daniel King: Since you’ve brought my microwave oven into the big tent of computer machine language, please explain how the firmware is subject to random mutational change. Ditto for my CD player, dishwasher, cell phone, iPod, etc., etc.

    I don’t think it should be up to me to clarify your analogies for you, but surely you are not equating the information in DNA (read-only memory) with occasional glitches in RAM electronics. If I couldn’t count on my BIOS to boot my machine, and if I couldn’t count on my hard drive to maintain the integrity of my operating system and programs, my computer wouldn’t be of much use.

    But, if you want to equate DNA to RAM, that is your privilege.

    (Note how conciliatory and agreeable I have become.)

  213. Modern hard drives (2008 models) have an average non-recoverable read/write error rate of 1 in 10^15 per hard drive. This is quite an improvement because I believe the error rate was around 1 in 10^13 just a few years ago and far worse 10+ years ago. And I just fixed a laptop where key OS files had been degraded. The machine was less than one year old.

    DNA viruses have error rates between 10^6 to 10^8 mutations per base per generation, while the human genomic error rate is at ~2.5×10^8 per base per generation. Despite these estimated error rates people can still “count on” reproducing successfully.

    Also, these error rates are estimates and under contention:

    http://www.uncommondescent.com.....ent-177561

    Now I could understand if you were asserting that “language” is too vague or not specific enough. But I find even “recipe” too vague. Now “code” would be better, but even that’s a subset of “language”, and you reject that because in your mind “code” signifies “human intelligence”…which does not explain SETI. Finally, no one can argue against it being a form of abstracted information. Or do you?

  214. Hi, Patrick,

    Thanks for adding more support for my point: DNA error rates are higher than computer hard drive reading rates. My guess is that reading error rates for solid state ROM are even lower than for hard drives. Do you have any info on that?

    Finally, no one can argue against it being a form of abstracted information. Or do you?

    If you mean by “it” that DNA is a form of abstracted information, then I can only ask WHO is doing the abstracting?

  215. Daniel King,

    I am happy to see you being so conciliatory and agreeable. Areas where we have substantial agreement will not be commented on, but they are still appreciated.

    You continue to insist, speaking about my scientific view regarding the origin of life, that “your view has a theological basis.” You seem incapable of understanding that it is precisely the reverse; that my theology has a scientific basis.

    Look at what you quoted in (211), your statement from (142),

    Surely your faith does not rest on such a slender reed.

    To this I replied (146), “WHy not? . . .”

    Is it not obvious that my faith “rests on” science rather than vice versa?

    You go on to recite an old, and in my case tired, canard:

    Such persons [presumably persons who do not use miracles to sustain their faith] seem to be more comfortable with letting science go wherever curiosity leads it.

    Do they really? Why the resistance to simply saying that, regarding OOL, “we don’t know how it happened without intelligence, we may never know, and it may not even be true”? Did you read the quote from Robert Shapiro in (114)? Let me quote it again:

    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.

    Does that sound “more comfortable with letting science go wherever curiosity leads it”?

    Look at what I wrote in (143) to Ritafairclough. I made it clear that my theology was based on science, rather than the reverse. I agree that the Catholic Church made a mistake regarding Copernicus and Galileo. I agree that it was part of a series of mistakes. But it is at least possible that by the time of Lyell and Darwin the pendulum had swung the other way.

    And as far as the mistake went, it could even be argued that the church thought too much of traditional “science”, and that is why they made the mistake they did. After all, ask yourself which side the majority of the academics was on at the time. So much for consensus.

    In fact, even in the case of Augustine and The Literal Meaning of Genesis this mistake was made; Augustine was arguing for instantaneous creation, rather than in 7 days, because a slow creation implied the lack of perfection in the incipient stages, and according to the dominant philosophy, God couldn’t create anything that wasn’t absolutely perfect. Besides, according to Ecclesiasticus, God made all things “simul” (a bad Latin translation), and why should light go around a round earth in 24 hours? It was easy for the sun to do it, but why disembodied light? Of course, now we don’t need light to go around the earth. The earth turns. Augustine just blew it, because he had too much respect for “facts which [infidels] have learnt from experience and the light of reason”. (These are my conclusions from my own reading of Augustine.)

    Thank you for allowing me to be “absolutely entitled to [my] views”. I will be even more happy if you try to understand and accurately state them, rather than criticize views which I do not hold as if I held them.

    You say,

    Science can only grasp what it can reach. The miraculous is out of its reach. And therefore safe from science.

    Are you saying that potentially there are some areas of physical reality that are out of the reach of science? Or that miracles aren’t physically real?

    You (212) are right that your response to the Qbeta-montmorillonite comparison question had two parts. I addressed the first part in (207), and you did not respond. Once we settle that part, we can discuss the second.

    Let me illustrate the problem with your difference another way. Supposing that some researchers were trying to create oil from methane using montmorillonite. They added ammonia, water, and calcium phosphate, and heated the mixture. When they examined the mixture, they discovered that it contained 0.01% ATP. Would you instantly denigrate that information on the basis that it wasn’t aimed at OOL research? Would you denigrate any further research in this area (say, trying to see if GTP or CTP could be created in this way) because the original research was not aimed at OOL?

    On the question of whether there is a difference between computer code and DNA code regarding mutability, I read your response in (192) and responded to it in (199), and you didn’t respond to that. That is why I asked in (207), “Should I take your silence regarding your statement

    6. Stability – computer machine language is not subject to random mutational change :: DNA is highly mutable.

    that you no longer would maintain this argument?”

    I am not arguing that there are no differences between DNA code and computer code. That is one reason why, in contrast to bFast, I have not argued against your calling the two groups of systems analogous rather than members of one group.

    But your hard drive will eventually fail. If you want to keep you data pristine, you will eventually need a backup. I know from personal experience. Ram can introduce glitches, as you acknowledged. Even ROM can fail. I have had that happen too. And I just had to discard a disc because part of the data had been corrupted.

    Look, make it easy on yourself. Without having to surrender your main point, that DNA code and computer code have significant differences, just admit that mutability is not one of those differences. That’s the “conciliatory and agreeable” thing to do.

  216. Thanks for adding more support for my point:

    I would not say that…

    DNA error rates are higher than computer hard drive reading rates. My guess is that reading error rates for solid state ROM are even lower than for hard drives.

    The higher unrecoverable error rate in DNA is an engineering tradeoff based upon density/compactness and transfer rate. For example, increasing the transfer rate with a DVD burner increases the error rate. That’s a designed tradeoff. Besides, we are comparing machines that are as big as my hand to something that is sub-cellular. I’d LOVE to see if humans can produce a data storage at that scale that maintains better data integrity at similar transfer rates.

    Never mind, the real question is, “how badly do I want to maintain data integrity”? As in, you can have many layers of error correction. Biology even has a backup system for error correction. Damage to the DNA can completely block the high-fidelity polymerases so a different DNA polymerase, termed zeta, copies over many types of DNA damage. Unfortunately, it is not very good at matching the right DNA base when there is no damage. But tests where zeta was removed resulted in dead cells and dead mice since without zeta there are breaks in the chromosome. It’s possible that genetic entropy has caused additional but not “necessary” error correction mechanisms to become deleted or scrambled over time. It is possible that zeta used to be more effective.

    (On a side note that highlights the difference in how a Darwinist and an ID proponent would look at evidence. Let’s say we find a creature where zeta “functions better”. A Darwinist would say it’s “more highly evolved” while an ID proponent would see it as a conserved element that had managed to survive the damages of time.)

    ROMs? Every single CD/DVD has errors on it. It’s been found by engineers that allowing errors to occur and then correcting during replication/reading actually allows for higher copying performance. The reading of compact discs have a huge number of read/write errors (call them mutations if you will) designed into the system which are then corrected via Reed-Solomon coding. One would be inclined to ask why not make more reliable read/write processes so error correction is not needed, and why deliberate design a system with a high error rate? The answer is that if one’s teleological goal are for compactness of storage, according to Shannon’s theorem, this is the optimal way to store data: “allow numerous errors and then correct afterward”.

    The uninitiated however, upon looking at this method of information storage would be inclined to criticize the designers as incompetent. Biologists will say exactly that, “a competent designer would not have made DNA copy mechanisms which require error correction, he would have made a copy process which got it right on the first pass.” That is why they are biologists, not engineers.

    Finally, the CD/DVD medium degrades fairly quickly within a decade, while apparently DNA can maintain data integrity in an inert state for quite a while.

    Besides, biology NEEDS its error correction.

    If you mean by “it” that DNA is a form of abstracted information, then I can only ask WHO is doing the abstracting?

    I would say that is the wrong question to begin with. “WHAT is doing the abstracting” can be answered readily: it’s the physical mechanisms that know the conventions of the abstracted information and converts from one state to another. Unfortunately, we do not fully comprehend these conventions at this time since we cannot look at the information and say, “look, this information here is what makes a horse a horse and a fly a fly”.

    As for the WHO, can you tell WHO designed a hard drive by analyzing the conventions and mechanisms? Yes, you could go to the patent office but unfortunately we don’t have that link-in-the-identification-chain for DNA. But you seem to be under the impression that ID proponents must identify the Designer(s) in order for core ID to be valid…but that assertion has been answered in book-form many times and I won’t reiterate it here.

  217. Paul Giem and Patrick:

    Your last two posts are so elegantly responsive and persuasive that I have concluded that I can add nothing more to this thread.

    My thanks to you and bFast, and all the rest who have been so kind to engage with me here.

    This will be my last post on Uncommon Descent. There are two reasons for this: Jack Krebs and Ted Davis. Perhaps we will meet again in other venues.

    Best wishes,

    Daniel

  218. I realized I never responded to Daniel at #203 regarding the status of biological objects as machines.

    This brought it to mind

    I have two quotes from two references referring to the bacteria flagellum as a “nanomachine” and with parts such as a “drive shaft, bushings, mounting plate, and a switch complex.”

    One from Current Biology Vol 18 No 16, by Howard C. Berg:

    “The flagellar motor is a remarkably small rotary electric motor that includes a stator, drive shaft, bushings, mounting plate, and a switch complex. The motors are powered by protons or sodium ions, that flow through channels from the outside to the inside of the cell. Depending upon the configuration, the rod, hook, and filament are driven clock wise or counter clock wise. Other components include a rod cap, discarded upon rod completion, hook cap, discarded upon hook completion, hook-length control protein, and a factor that blocks late-gene expression.”

    and another from Nature Reviews Microbiology volume 6 June 2008 p 455:

    “The bacterial flagellum, one of the most remarkable structures in nature: a complex self-assembling nanomachine” where “dozens of proteins, many of which have intrinsic self-assembly properties, need to come together in an ordered assembly process to complete these molecular nanomachines.”

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