Intelligent Design

Eugene Koonin (NCBI) on Biology’s Big Bangs

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Koonin Unresolved Polytomy

Posted without comment. Too busy today: the paper and reviewers’ reports are open access, so check it out. I’ll have more to say tomorrow.

Well, one quick comment. Could Mike Behe or Scott Minnich (to name a couple of my ID friends) have published this paper? — not in the sense of having written and submitted the text, however. Rather, could they have made it through refereeing?

56 Replies to “Eugene Koonin (NCBI) on Biology’s Big Bangs

  1. 1
    idnet.com.au says:

    The original paper contained this line “In each major class of biological objects, the principal types emerge “ready-made”, and intermediate grades cannot be identified.”

    In responding to a reviewer Koonin writes “The position of some ultra-darwinists ,,, that Darwin, “in principle”, solved all the problems of the origin of biological complexity in his eye story, and only minor details remain to be filled in … is outright false … The ID folks are clever in their own perverse way, they see through such false simplicity and seize on it.”

    Eugene Koonin is clever in his own perverse way. He is the SJ Gould of molecular evolution.

  2. 2
    Atom says:

    idnet.com.au beat me to the punch, but here is the extended exchange:

    Abstract [reviewer’s comment]: “In each major class of biological objects, the principal types emerge “ready-made”, and intermediate grades cannot be identified.” Ouch, that will be up on ID websites faster than one can bat an eye.

    Author’s response: Here I do not really understand the concern. I changed “ready-made” to “abruptly”, to avoid any ID allusions and added clarifications but, beyond that, there is little I can do because this is an important sentence that accurately and clearly portrays a crucial and, to the very best of my understanding, real feature of evolutionary transitions. Will this be used by the ID camp? Perhaps – if they read that far into the paper. However, I am afraid that, if our goal as evolutionary biologists is to avoid providing any grist for the ID mill, we should simply claim that Darwin, “in principle”, solved all the problems of the origin of biological complexity in his eye story, and only minor details remain to be filled in. Actually, I think the position of some ultra-darwinists is pretty close to that. However, I believe that this is totally counter-productive and such a notion is outright false. And, the ID folks are clever in their own perverse way, they see through such false simplicity and seize on it. I think we (students of evolution) should openly admit that emergence of new levels of complexity is a complex problem and should try to work out solutions some of which could be distinctly non-orthodox; ID, however, does not happen to be a viable solution to any problem. I think this is my approach here and elsewhere.

  3. 3
    todd says:

    Atom, you beat me to it!

  4. 4
    nullasalus says:

    “ID, however, does not happen to be a viable solution to any problem. I think this is my approach here and elsewhere.”

    Considering “ID” is essentially a relatively new way of looking at things scientifically, and has a fairly large array of proponents and views, isn’t that a bit much? Then again, really, Koonin’s being vastly more fair than most are willing to be. And if an ID proponent gave a mechanism Koonin thought was adequate, I have a feeling he’d bite the bullet and say “This may give weight to a viewpoint I dislike, but it works, so that’s that.”

  5. 5

    If I can paraphrase:

    -this backs ID
    -well, let’s face facts Darwinisms has issues that need new solutions
    -ID isn’t going to get consideration because naturalism is how we do things and/or think.

    Viable solutions are only the ones that fit within the working philosophical model.

  6. 6
    idnet.com.au says:

    It is to the advantage of Truth that even though Koonin does not think ID is a viable idea, he is not afraid to say it like it is.

    Obviously as his reviewers betray, there is a general agreement amongst other science writers to censor their work in cases where it looks like it may undermine NDE or offer support for ID.

  7. 7
    idnet.com.au says:

    A prediction from Nicholas Matzke (August 29th) “this paper will be on every ID/creationist blog on the planet in under 12 hours” http://www.biology-direct.com/.....1/comments

    Wrong Nick. It took us 5 weeks! Perhaps it is because Nick “worked at the National Center for Science Education, where we oppose the ID/creationists and develop a finely-tuned sense of the sorts of things they will pluck from the literature and desperately portray as evidence that they aren’t completely nuts.”

    Maybe we only want the truth to be told without the spin.

  8. 8
    bFast says:

    Atom, I had your exact quote in my clipboard ready to paste into here.

    However, let me highlite the following line, “And, the ID folks are clever in their own perverse way” Let’s make sure we don’t associate with those perverse ID types.

  9. 9
    bornagain77 says:

    Translation,,,Man,, Life sure appears abruptly…Boy is this life we are finding complex and unique with no evidence of transition…We have no clue how it appeared abruptly nor do we know how the complexity got there!!!! But don’t anyone ever, ever, ever, admit that intelligence is needed to explain this complexity and uniqueness we are finding!!!!

    This paper is definitely going in my arsenal!!!

    If they would just throw in the towel, then scientists could get busy trying to figure out how the information was implemented, if that is even possible, and at least figure out the exact parameters needed for “intelligent designing” organism that would be of benefit to man!!!

  10. 10
    bornagain77 says:

    correction:
    “intelligently designing” organisms that would be of benefit to man!

  11. 11
    toc says:

    It is encouraging to see an honest evolutionary biologist who, in spite of criticism, is willing to honestly follow the evidence. Koonin seems unafraid of the consequences, regardless of his own metaphysical presuppostions and apparently believes that Science exists to discover those things that are true. Most likely he will get his flogging in due time, but my, what courage.

  12. 12
    interested says:

    i liked this:

    There seems to be a striking commonality between all major transitions in the evolution of life. In each new class of biological objects, the principal types emerge abruptly, and intermediate grades (e.g., intermediates between the precellular stage of evolution and prokaryotic cells or between prokaryotic and eukaryotic cells), typically, cannot be identified. The events that lead to the emergence of a new level of complexity and, obviously, are crucial in the evolution of life elude representation through a unique tree topology and are notoriously hard to reconstruct. Whatever trees have been constructed for these stages of life’s history, have extremely short, most often, unreliable internal branches, and the tree topology tends to differ for different genes [8] (Fig. 1). Below I list the most conspicuous instances of this pattern of discontinuity in the biological and pre-biological domains, and outline the central aspects of the respective evolutionary transitions.

  13. 13
    Jehu says:

    It is fascinating how he draws the analogy of “Big Bang” and inflation of the universe with the appearance of life and different levels of life. As I read it, it is hard not think about Hugh Ross’ days of creation.

  14. 14
    russ says:

    Most likely he will get his flogging in due time, but my, what courage.

    Do you suppose the producers of “Expelled” should make space in the film for Koonin’s story, or should they wait to see if he ultimately recants?

  15. 15
    tribune7 says:

    ID, however, does not happen to be a viable solution to any problem.

    To what “problem” are they referring?

    If it is true life is designed, it is true that life is designed.

    Claiming that life is not designed if it should happen to be would actually be a rather serious problem.

  16. 16
    gpuccio says:

    Very good paper. A wonderful summary of ID’s classical arguments, or at least of the minor ones (the fundamental ones, CSI and IC, are obviously not touched, but they seem to inspire, as a constant subtext, the whole article). The attempt to suggest new explanations to what cannot be explained in a traditional context are admirable, but obviously unsuccessful. That reminds me of Robert Shapiro’s recent article “A Simpler Origin for Life”, which was as brilliant in analyzing the failure od all existing models for OOL as unconvincing in suggesting a new one. Well, we probably need these honest scientists who have the courage to admit the holes in current scientific theories, even if they still feel that they have to stay committed to the existing paradigm.

    Besides, Koonin has at least the honesty of admitting (in the correspondence with the reviewer) that his refusal to consider an ID scenario is purely ideological, and not supported by scientific reasons, when he writes:

    “ID, however, does not happen to be a viable solution to any problem”.

    It is interesting that any reference to ID, although negative, can be found only in the correspondence, but obviously not in the paper: in other words, we IDists are really in the heart and mind of our darwinist “friends”, but it is a most secret form of love, one which can only be whispered in dark and solitary places.

    And finally, what a satisfaction! Koonin is kind enough to admit (always in the correspondence, obviously) the existence, if not of an intelligent designer, at least of intelligent IDists:

    “And, the ID folks are clever in their own perverse way”

    I must say I am overwhelmed: “clever”! After years of being only one of a folk of “IDiots”, that’s really a giant leap! My ego is still rejoicing, and with such a new self-esteem, the sky is the limit: I could perhaps even aspire to becoming, in the future, a brilliant darwinist.

    And I think that the idea of being “clever and perverse” is really seductive…

  17. 17
    DaveScot says:

    Paul

    An ID proponent would never have made it through peer review with such an incoherent, disjointed, fantastic yarn. It’s amazing that someone without the taint of ID attached to them could get it through. The reaching and stretching involved in drawing parallels between cosmology and biology smacks of desperation – clutching at straws. I will give credit to the author for at least recognizing that the current biological creation yarn spun out of NDT is untenable and he’s to be congratulated for having the courage to say so and offer an alternative yarn in its stead.

    The striking parallel that evolution story tellers need to recognize is that phylogenesis mirrors ontogenesis. Both processes are ones where unexpressed potentials are expressed in a predetermined sequence with chance playing little if any role in the process and where the environment at most provides cues for when to proceed to the next predetermined stage in the unfolding process. Both processes are self-terminating when the predetermined course of diversification reaches a final stage. A single cell is the beginning of every chicken and an adult chicken is the preprogrammed terminal stage where that cell stops diversifying. Phylogenesis appears to be the same process played out over a much longer span of time. It may or may not have terminated. Certainly many branchings have terminated as evidenced by the extinction of 999 out of 1000 species that ever lived after an average span of about 10 million years of life.

    A big mistake in NDT inspired ideology is that the earth’s changing environment gradually molded life to fit it. That’s bass ackwards. Life molded the environment, paved the way so to speak, for the next predetermined phase of phylogenesis. That’s why the process took billions of years. It isn’t quick or easy laying down foundations that span an entire planetary surface. The atmosphere needed to be oxygenated. The time of great upheavals and catastrophy in a young solar system had to be waited out. Fossil fuel reserves had to be laid down to power an upcoming industrial species. My contention is that industry didn’t arise because a power source was available for it but rather a power source was made available so that industry could arise. The way was prepared in advance. It was planned that way.

    There are two important and basic questions raised by the front-loaded phylogenesis hypothesis.

    First and most amenable to finding a definitive answer is how, when natural selection is unable to conserve unexpressed genomic content, is that content conserved for geologic timespans. That such a mechanism exists seems evident in the result of a knockout experiment where 1.5 million base pairs of DNA highly conserved between mouse and man was deleted from the mouse and the resultant GM mice were indistinguishable in any metric from unmodified mice. *Something* acted to conserve that apparently unexpressed DNA for 180 million years of reproductive isolation between the mouse and man lineages. That much is obvious. What isn’t obvious is what mechanism did the conserving. When we find that mechanism we’ll have our answer, or at least an experimentally demonstrable possibility, to the conservation mechanism required by the front loading hypothesis.

    The second question is less amenable to finding an answer. That question is what was the source of what must have been a hugely complex front loaded genome. How, who, or what generated the original uber-genome? We might never know the answer to that question but that’s just how the cookie crumbles in science. We might never know the origin of the observable universe either. But just because we hit a brick wall where it seems there is no way to find further answers it doesn’t follow that we should ignore the evidence that we can observe as far back as practically possible. *Something* caused the observable universe to come to exist just as *something* caused organic life on earth to come to exist. We can at least follow the story back to the wall beyond which we cannot see. We might not ever discover with any degree of certainty how the universe or organic life first came about but it appears we can at least decipher how it works and how it evolved after it appeared.

    Everything in evolution makes ready sense in light of a front-loaded genome. Little makes sense in the absence of that light.

  18. 18
    bFast says:

    DaveScot, I fully agree with you that this paper is consistent with front-loading. We need to warm MikeGene up to it.

  19. 19
    mike1962 says:

    DaveScot

    Very thought provoking post (#17). Thanks.

  20. 20
    MatthewTan says:

    gpuccio,

    “a folk of “IDiots””

    Return favour to them “the Darwidiots”

  21. 21
    bornagain77 says:

    Dave Scot:
    you stated in support of your “radical front-loading” position which I respect very much:

    Something* acted to conserve that apparently unexpressed DNA for 180 million years of reproductive isolation between the mouse and man lineages. That much is obvious.

    This inference you make to such radical Front Loading is not so obvious for me. So I have to respectfully disagree.

    For one, I severely suspect any information from the DNA sequences that were gathered from the Darwinian perspective and not from an engineering perspective.

    The second is, of course, we have barely touched the surface of the complexity in the Genome itself. i.e. No One really has a clue what is going on in the genome~

    http://www.boston.com/news/sci.....unraveled/

    Specifically: The science of life is undergoing changes so jolting that even its top researchers are feeling something akin to shell-shock. Just four years after scientists finished mapping the human genome – the full sequence of 3 billion DNA “letters” folded within every cell – they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.

    As you well know this revelation from ENCODE sent shock waves through Darwinian camps and powerfully vindicated the ID position! Yet it also highlighted How little we actually know about what is happening in the Genome!

    The second is that Genetic Entropy (information being lost) appears to be a pervasive Phenomena with strong supporting evidence in both Genetics and morphology, that only seems to be violated with the abrupt introduction of parent species in the fossil record.
    Genetic Entropy also seems to explain this puzzling fact that you pointed out, The mysterious extinctions of 999 out of 1000 species that ever lived after an average span of about 10 million years of life, without reference to any natural catastrophe! Genetic Entropy would fit well into why this happens!

    As well

    IDists already agree that life is so complex that information had to be implanted into the Genome…We just disagree as to when…For now until further work comes in from ENCODE, I maintain that introduction of information at the level of parent species would seem to have more supporting evidence, because of the oft overlooked foundational principle of Genetic Entropy!

    Your strongest evidence for your radical front loading scenario seems to be this…

    That such a mechanism exists seems evident in the result of a knockout experiment where 1.5 million base pairs of DNA highly conserved between mouse and man was deleted from the mouse and the resultant GM mice were indistinguishable in any metric from unmodified mice.

    Very suggestive I admit,,yet,,, I could remove major portions of a car and still have a car that performed in its basic functions, but I contend that it would suffer in other areas that may not be noticeable to the test the scientists used to determine robustness!

    I also maintain that the commonly accepted harmful/fatal mutation rates to DNA of + 99.999% are very problematic to your necessity of conserving vast amounts of unscathed DNA through eons of time!

    Plus if it is already agreed, of necessity, that information had to come from an intelligent source at some time,,would not it also be prudent to look to this intelligence to solve these problems of the abruptness of the fossil record and the overriding principle of genetic entropy?

  22. 22
    magnan says:

    I agree with DaveScot that Koonin’s paper has so many flaws from the rigorous scientific standpoint that it is hard to understand how it could get by peer review, except for the obvious bias toward anything no matter how fuzzy minded propping up Darwinism in the face of the evidence.

    He basically is just vaguely speculating that some accelerated unknown mechanism utilizing an expanded repetoire of sources of random genetic change including “various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements” operated in the major innovative transitions in evolution, like the Cambrian explosion.

    His vague speculation becomes expecially egregious and even metaphysical when he makes a big point out of supposed similarities between his “Biological Big Bang” model and the cosmological Big Bang.

    This conveniently ignores the basic problem of how random genetic changes, no matter how spread (and the various mechanisms cited are also random), can create such intricate innovation given the short periods, limited number of generations and actual populations involved. It is mostly speculation without evidence. There is no mechanism to explain the extremely opportune fixing of just the right mutations and other changes in certain organisms that became Gould’s “hopeful monsters”, out of the astronomically greater number of deleterious and neutral changes and transfers. He vaguely refers to this as a “sampling process”.Of course, this speculation acts as a desperate prop to the Darwinian orthodoxy in the face of growing attacks from genetic and other evidence.

    I suppose Koonin is still to be congratulated for at least addressing some of the growing dilemmas of orthodox Darwinian evolution theory.

  23. 23

    DaveScot wrote: “My contention is that industry didn’t arise because a power source was available for it but rather a power source was made available so that industry could arise.”

    Good though. Mirrors some thoughts I’ve had on this front.

    “Certainly many branchings have terminated as evidenced by the extinction of 999 out of 1000 species that ever lived after an average span of about 10 million years of life.”

    I think there is growing evidence that these numbers are probably not accurate. If I recall correctly, the idea that most forms of life that have ever lived on the Earth have become extinct was a proposition initially put forth by proponents of gradualistic evolution in response to the question of how the current complexity and diversity could have come about. Indeed, Darwin himself suggested that there must have been “innumerable” forms that had come and gone to get to the current state of affairs. This helps to maintain the illusion of “slight successive” changes building up to the current state of affairs. However, there has been some recent news and discussion (perhaps also on this website?) about the fact that the number of extinct species is probably significantly less than the numbers/percentages typically thrown around.

    I don’t think this changes Dave’s basic point that branchings have terminated, which is a fair point — I just question the old “99.9% of life has become extinct” idea.

  24. 24
    bornagain77 says:

    Eric Anderson,

    Very,Very interesting point…

    I wonder does anyone reading this have a reference to hard numbers based on actual hard evidence as to the exact extinction percentage and the average time of survival for all species in the fossil record???

  25. 25

    From the PBS Evolution website (as one example among many):

    “An estimated 250,000 fossil species have been recorded to date, which is only about one percent of the 4 billion animal and plant species thought to have existed over the past 600 million years or so. A high percentage of these — perhaps 95 percent — are hard-shelled marine creatures. For all that we have learned about evolution from the fossil record, we know very little, relatively speaking, especially of soft-bodied animals, which generally do not preserve as well.”

    Notice the words “thought to have existed.”

    As near as I can tell from a cursory Internet search, there are several million species currently living (estimates vary widely from 2 million to perhaps 10x or more that number). Given the current species estimate, and given all the time that has past in Earth’s history and all the evolving that must have gone on to get where we are today, the thought is that we must be seeing today only a tiny sliver of all the species that have ever lived on the Earth. Add a few orders of magnitude to the current species count, and viola, we have an estimate for all the species that must have lived on the Earth.

    The fossil record, unfortunately, does not support this story (at least as of yet), so — in keeping with Darwin’s approach a century and a half ago — the fault must again lie with this poor evolutionary whipping boy, those lazy paleontologists, and those evasive soft bodied organisms.

    I’d love to see something more definitive if anyone has it, but on a quick review it looks like we are dealing with (i) a theory that proposes “innumerable” transitional forms as Darwin suggested, (ii) a current species count or estimate, and (iii) an extrapolation of numbers that does two things: (a) emphasizes the vast historical timeframe available for evolution and the ongoing extinction events (keep in mind that RM+NS proponents often confuse extinction as evidence for evolution), and (b) emphasizes the vast number of creatures available for evolutionary trial-and-error (put another way, vastly increases the probabilistic resources).

    It could be that billions of species have inhabited the earth. However, I just haven’t seen anything yet to justify such an estimate.

  26. 26
    Atom says:

    Eric Anderson,

    I was wondering the same thing and also would like to see data.

    The closest thing I have seen approaching a reasonable way of estimation was Michael Denton in “Evolution: A Theory In Crisis.” There he showed that the fossil record was actually *very* close to complete, since almost all extant life forms could be found represented in it. (I don’t remember the exact numbers, someone with access to the text can dig those up.)

    Basically, we have a certain number of species alive today; if we find 99% of those species in the fossil record, we know that the record is pretty near complete. On the other hand, if we only found 1% of all living organisms in the fossil record, we’d then know it is very incomplete, giving the Darwinists more room to breathe.

  27. 27
    idnet.com.au says:

    I looked into this 99.9% extinct figure a number of years ago. As far as I could find, is totally unfounded and based on a theoretical gradualist model.

  28. 28
    bornagain77 says:

    I found this for extinction rates,,I will I have to dig deeper to confirm if they used actual fossil data:

    Lifespan estimates

    Some species lifespan estimates by taxonomy
    Taxonomy Source of Estimate Species Average Lifespan years (MYA)

    All Invertebrates; Raup (1978) 11
    Marine Inverts;Valentine(1970) 5–10
    Marine Animals Raup (1991) 4
    Marine Animals Sepkoski(1992) 5
    AllFossil Groups:Simpson (1952).5–5
    Mammals Martin (1993) 1
    Cenozoic Mammals Raup (1978) 1–2
    Diatoms Van Valen 8
    Dinoflagelates:Van Valen (1973) 13
    Planktonic ForaminiferaVan Valen (1973) 7
    Cenozoic Bivalves:Raup and Stanley (1978) 10
    Echinoderms Durham (1970) 6
    Silurian Graptolites Rickards (1977) 2

    Adapted from the book “extinction rates”, edited by Lawton, J, and May, R. [7]

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

  29. 29

    Thanks, Adam and idnet.com.au.

    I am familiar with Denton’s approach, although it has been some time since I read his book (I’ll have to reread that section again in light of this discussion).

    Denton’s argument is certainly not watertight. Specifically, finding that most of the existing species are represented in the fossil record does not allow us to say that species not represented in the fossil record did not exist. However, I think his point is well taken that the traditional evolutionary contention that the fossil record is a tiny, poorly-preserved, deceptive fraction of reality is probably not a fair representation. Indeed, if one believes Gould and Eldredge, the fossil record should be taken at face value. The further point is that one should not base one’s position on the absence of evidence (something that both gradualists and Gould and Eldredge are guilty of).

    Finally, a more fundamental point, lest anyone should misunderstand my position:

    I am not sure that a large number of extinct species (in the billions) supports any particular position about the origin and diversity of life on the Earth. Again, this is because extinction says exactly nothing about how species arrive on the scene in the first place.

    The additional probabilistic resources added by a few billion extra species over the course of a few billion years is but a rounding error in the larger cosmic calculation required to produce the specified complexity we witness in the living world today.

  30. 30
    Atom says:

    RE: Eric Anderson #29,

    True enough. Denton’s approach is similar to statistical techniques where you “guess” the size of an enemy army from the serial numbers of captured/destroyed tanks. (A similar technique was used in WWII by the allies.)

    It definitely isn’t water tight, but statistical inferences never are. They are just reasonable estimates.

    And it is Atom, not Adam. 🙂

  31. 31
    bornagain77 says:

    Here’s something interesting

    http://www.dailynexus.com/article.php?a=1216

    The researchers assembled information about the fossil record on a computer database called the Paleobiology Database, and results suggest that the number of species on earth has not been growing as rapidly as previously thought – and possibly, it has not grown at all. John Alroy, a postdoctoral fellow at NCEAS and one of the project’s founders, was one of 25 authors of a paper published May 22, 2001 in The Proceedings of the National Academy of Sciences.

    http://paleodb.org/cgi-bin/bridge.pl

    http://gsa.confex.com/gsa/2004....._75024.htm

  32. 32
    bornagain77 says:

    The average life span of a species in the fossil record is about 4 million years (Raup)

    http://books.google.com/books?.....#PPA108,M1

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

  33. 33
    bFast says:

    bornagain77, re knock-out DNA and front-loading.

    Firstly, though the experiment knocked out 1.5 million base-pairs, most of those base-pairs were not highly conserved. I forget how many were, but only a fraction — just being accurate, not that it affects the argument.

    The possibilities that I can see for this phenomenon include:
    1: The conserved DNA does something important for the mouse, man, and all of the otehr branches that have it, but it was not detected in a laboratory.

    This is an interesting point. There was a heavy discussion on Telic Thoughts suggesting that a 5 year 1000 mouse experiment was called for to falsify this conjecture. However, in light of the challenge that this evidence presents to the darwinian paradyme, such an experiment needs to be done. Its time the scientific community got off its duff and confirmed the theory.

    2: Geological time is all wrong. Mouse and man were created 10,000 years ago. If so, this position would be irrelavent, however point 3 below would also have to be the case.

    3: The similar DNA was implanted into both mice and men by the designer not long ago. This certainly is a possibility, but it doesn’t seem to be supported by occam’s razor.

    4: There is some mechanism other than natural selection, whether that be divine protection or an unknown phenomenon within the organism, that is protecting this DNA. If so, it would surprise me if the DNA was not being protected for some reason. This finding, won’t truly provide positive support for front-loading until some front-loading value is determined for the conserved DNA, but it is very consistent with the front-loading hypothesis.

    Eric Anderson, re serial numbers on tanks — As a software developer producing product for small companies, I always started my serial numbers a bit high, letting the first number be something like 18932, and incremented by 153, just to make the company look big. I wonder if the Germans were as smart as I am?

  34. 34
    Bob O'H says:

    There he showed that the fossil record was actually *very* close to complete, since almost all extant life forms could be found represented in it.

    Fossilised mildew? Fusarium? Amoebae? And that’s before we get to the prokaryotes.

    The argument also doesn’t work because it ignores the “life forms” that went extinct. How do we know (indeed, how can we know) what proportion of these were fossilised.

    Bob

  35. 35

    “And it is Atom, not Adam.”

    Shoot, sorry, I knew that — I’ve even visited your site. Guess I was typing a bit too fast . . .

  36. 36

    “‘There are, arguably, some 2 to 10 million species on earth. The fossil record shows that most species survive somewhere between 3 and 5 million years. In that case, we ought to be seeing small but significant numbers of originations (new species) … every decade.’ Keith Stewart Thomson, Professor of Biology and Dean of the Graduate School, Yale University”

    Excellent quote and very interesting thought.

    Of course this is only persuasive to those who accept the idea that natural processes are largely the same today as they were yesterday. There is a fairly large contingent of evolutionists (including ID evolutionists) who take the view that evolution has run out of steam or has run its course. However, such a position seems more like an ad hoc justification for why we don’t regularly see speciation occurring all around us now, than it is an actual explanation of any biological reality.

  37. 37

    “Eric Anderson, re serial numbers on tanks — As a software developer producing product for small companies, I always started my serial numbers a bit high, letting the first number be something like 18932, and incremented by 153, just to make the company look big. I wonder if the Germans were as smart as I am?”

    I think Atom brought up the tanks comment, but, yes, the idea of estimating the size of something when the source of the data is intent on misrepresenting the size is certainly problematic. I doubt we have that problem with the fossil record! 🙂

  38. 38
    DaveScot says:

    bFast

    Firstly, though the experiment knocked out 1.5 million base-pairs, most of those base-pairs were not highly conserved. I forget how many were, but only a fraction — just being accurate, not that it affects the argument.

    Edward Rubin’s team at the Lawrence Berkeley National Laboratory in California deleted two huge regions of junk DNA from mice containing nearly 1000 highly conserved sequences shared between human and mice.

    As I recall the sequences were each at least 100bp in length.

    Edit: I double checked. It was two regions, one 1.5 million bp long and the other 800 thousand bp long. Together they contained almost 1,300 highly conserved (highly = 70% to 95% identity) sequences a minimum of 100 bp in length. If I recall correctly the authors, in a different experiment, tried deleting some ultra-conserved (95% – 100%) sequences and those DID have bad consequences for the GM mouse.

  39. 39
    bornagain77 says:

    A little more information on background extinctions and recovery:

    http://www.enchantedlearning.c.....xtinction/

    Most extinctions (perhaps up to 95 per cent of all extinctions) occur as background extinctions, occurring throughout time. These extinctions are not caused by major catastrophes or horrendous climactic changes, but by small changes in climate or habitat, depleted resources, competition, and other changes that require adaptation and flexibility.\

    http://www.accessscience.com/a.....3dYB010170

    The fossil record of marine animal species reveals that over the last 550 million years the average species lived for only about 4 million years. Thus most species that ever lived on Earth are now extinct. Paleontologists have long recognized that extinction has not been a continuous process. Rather, it has alternated between mass extinction, geologically short intervals of time when substantial proportions of the global biota were eliminated, and background extinction, intervals of lower extinction intensity between mass extinctions.

    http://en.wikipedia.org/wiki/P.....tion_event

    The Earth needs, on average, about 10 million years to recover from a mass extinction of the planet’s species, far longer than most scientists thought, according to a new study by scientists at the University of California, Berkeley, and Duke University.

  40. 40
    bornagain77 says:

    Some quotes on fossil record:

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

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

    “… Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences.” George Gaylord Simpson (evolutionist), The Major Features of Evolution, New York, Columbia University Press, 1953 p. 360.

    “No wonder paleontologists shied away from evolution for so long. It seems never to happen. Assiduous collecting up cliff faces yields zigzags, minor oscillations, and the very occasional slight accumulation of change over millions of years, at a rate too slow to really account for all the prodigious change that has occurred in evolutionary history. When we do see the introduction of evolutionary novelty, it usually shows up with a bang, and often with no firm evidence that the organisms did not evolve elsewhere! Evolution cannot forever be going on someplace else. Yet that’s how the fossil record has struck many a forlorn paleontologist looking to learn something about evolution.” – Niles Eldredge , “Reinventing Darwin: The Great Evolutionary Debate,” 1996, p.95

    “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology.” Stephen Jay Gould, Professor of Geology and Paleontology at Harvard University and the leading spokesman for evolutionary theory in America prior to his recent .

    “If pressed about man’s ancestry, I would have to unequivocally say that all we have is a huge question mark. To date, there has been nothing found to truthfully purport as a transitional species to man, including Lucy, since 1470 was as old and probably older. If further pressed, I would have to state that there is more evidence to suggest an abrupt arrival of man rather than a gradual process of evolving”. Richard Leakey, world’s foremost paleo-anthropologist, in a PBS documentary, 1990.

    A couple of Quotes on Cambrian explosion:
    “Yet, here is the real puzzle of the Cambrian Explosion for the theory of evolution. All the known phyla (large categories of biological classification), except one, first appear in the Cambrian period. There are no ancestors. There are no intermediates. Fossil experts used to think that the Cambrian lasted 75 million years…. Eventually the Cambrian was shortened to only 30 million years. If that wasn’t bad enough, the time frame of the real work of bringing all these different creatures into existence was shortened to the first five to ten million years of the Cambrian. This is extraordinarily fast! Harvard’s Stephen Jay Gould stated, “Fast is now a lot faster than we thought, and that is extraordinarily interesting.” What an understatement! “Extraordinarily impossible” might be a better phrase! …. The differences between the creatures that suddenly appear in the Cambrian are enormous. In fact these differences are so large many of these animals are one of a kind. Nothing like them existed before and nothing like them has ever appeared again.” Evolution’s Big Bang; Dr. Raymond G. Bohlin, University of Illinois (B.S., zoology), North Texas State University (M.S., population genetics), University of Texas at Dallas (M.S., Ph.D., molecular biology).

    “A simple way of putting it is that currently we have about 38 phyla of different groups of animals, but the total number of phyla discovered during the Cambrian explosion (including those in China, Canada, and elsewhere) adds up to over 50 phyla. (Actually the number 50 was first quoted as over 100 for a while, but then the consensus became 50-plus.) That means there are more phyla in the very, very beginning, where we found the first fossils, than exist now.” “Also, the animal explosion caught people’s attention when the Chinese confirmed they found a genus now called Yunnanzoon that was present in the very beginning of the Cambrian explosion. This genus is considered a chordate, and the phylum Chordata includes fish, mammals and man. An evolutionist would say the ancestor of humans was present then. Looked at more objectively, you could say the most complex animal group, the chordates, were represented at the very beginning, and they did not go through a slow gradual evolution to become a chordate.” Dr. Paul Chien PhD., chairman of the biology department at the University of San Francisco, Dr. Chien also possesses the largest collection of Chinese Cambrian fossils in North America.

    this following site has a cool graph that is eye opening:

    http://members.cox.net/wwcw/q-evol4.html

  41. 41
    DaveScot says:

    re extinctions

    I think the more salient bit of evidence isn’t how many modern species can be found represented in the fossil record but rather how many species in the fossil record cannot be found alive today. I understand this is very few with the exception of a few so-called “living fossils” like the coelecanth which has been around virtually unchanged for a hundred million years or more.

    If common descent is true then we would expect to find representatives of all extant species in the more recent fossil record and we should also expect to NOT see them in the more distant fossil record. This is exactly what we see. If gradualism is true we should expect to see a smooth continuum of species with small changes as we go backward in time. This is NOT what we see. As pointed out by the great paleontologist S.Gould what we see in the fossil record is the abrupt emergence of species fully characteristic of their kind, they remain in the record unchanged for an average of 10 million years, then they abruptly disappear. This incontestable and still true picture of the fossil record caused them to come up with the evolutionary theory called “Punctuated Equilibrium”. Their assertion was that the big steps in evolution take place in small isolated populations. The small geographically isolated populations statistically constrains their representation in the fossil record and that is why we don’t see the transitionals. Considerable doubt has been cast on their theory mostly because the very low frequency of beneficial mutations requires a very large population to generate enough of them for natural selection to choose. This in itself is also problematic because as the population size increases it become statistically more difficult for a beneficial mutation to become fixed in the population. The long and the short of it is that NDE is a failed theory. It cannot be shown capable of generating novelty in any size population over any length of time. The fossil record show us saltation, stasis, and extinction. No matter how you contort any evolutionary theory where blind chance (random) mutations are the source of variation it simply doesn’t work out. The best test of NDE I’ve seen to date is described in Behe’s book “Edge of Evolution” where we observed, at the nucleotide level, billions of trillions of generations of single celled eukaryote p.falciparum mutating under intense selection pressure and there was no generation of any novel complexity involving more than a few base pairs at most. NDE was put to the test and it failed miserably. ID was put to the test at the same time and it passed with flying colors. It predicted no significant new complexity would emerge in billions of trillions of replications and that’s exactly what we saw.

    Denialism is rampant amongst NDE proponents.

    There are two reasonable explanations for all this. The first is that some force has tinkered with the course of evolution, intervening constantly with much frequency; injecting complex new genomic information periodically which is expressed immediately into new phenotypic complexity. We have observed no such tinkering in extant life. The second explanation is that genomic complexity has been around since the beginning of life on earth and it was expressed over the course of billions of years into phenotypic complexity. There is much experimental support for this explanation and that support is growing by leaps and bounds as comparative genomics keeps pushing back the dates where genomic complexity is found. Applying Occam’s Razor to these two explanations one comes out a clear winner. We have a choice between frequent injections of complexity into the genomes of innumerable species (which implies a force of some kind that has been around since life on earth first appeared and has stayed around at least until very recent geologic times) and a force which acted one time in the distant past then left the scene. A single instance of the action of an unknown and evidently intelligent agency is the simpler explanation. Francis Crick and Leslie Orgel saw this decades ago and described it in a theory called “directed panspermia” where life was purposely placed upon our planet billions of years ago by some unknown but intelligent agency.

  42. 42
    bornagain77 says:

    DaveScot:

    Your information of:

    they remain in the record unchanged for an average of 10 million years, then they abruptly disappear

    Disagrees with the information I’m finding that says:

    The fossil record shows that most species survive somewhere between 3 and 5 million years.

    Can you give a source for your figure?

  43. 43
    DaveScot says:

    ba77

    I don’t recall where I read it. Do you think it makes any difference to the argument whether the average lifespan of a species is 3 million years or 10 million years? I can’t see how it does but maybe I’m missing something you can point out to me.

    edit: A quick web search found this book Extinction Rates cited as a source for 5 to 10 million years.

  44. 44
    bornagain77 says:

    DaveScot you asked,
    Do you think it makes any difference to the argument whether the average lifespan of a species is 3 million years or 10 million years? I can’t see how it does but maybe I’m missing something you can point out to me.

    I was hoping to correlate a general pattern for Genetic Entropy to the rates of extinction for different types of species (phyla, class or families) in the fossil record ( I was expecting (and still do expect) radically different phyla, or even kingdoms, to have radically different extinction rates)…This seems to be a more difficult task than I had anticipated. All the interrelated possible causes for extinction rates makes a clear inference to genetic entropy in the fossil record hard to properly discern, to put it mildly!

    Although this is not exactly what I would have liked, I still do have hope that the overall fossil record may provide me some solid support for the abrupt “bottleneck” appearance of many parent species with limited gradual radiation from parent species, with no evidence of radical transmutation into radical new parent species! Thus supporting an overall inference to Genetic Entropy!
    This information (abruptness and limited radiation), which seems to be presently available and, might I even say, abundant in current Darwinian “Bottleneck” Literature, will offer some fairly solid supporting evidence for information being implanted at the level of parent species, with “front loaded” conditions of limited radiation that still obey the overall principle of genetic entropy…
    This, of course, is not the crushing knockout blow that I want to establish my case of Genetic Entropy from parent species with, but it will at least support the hard evidence for Genetic Entropy that can be gathered from the genetic data and morphology of species that are observed living today.

    Slightly off topic;
    As well I feel that Darwinists have not been held to strict account for their rapid abandonment of the population genetics (selectable gene) theory once the epistasis (interrelated complexity) of the genome was revealed by ENCODE,,,So if you have any information, which will expose Darwinism’s necessity to strictly adhere to the theory of population genetics could you pas it along”?
    All I have, along these lines right now, is, On page 52 and 53, of Sanford’s “Genetic Entropy”, that says something to the effect,,

    “Haldane’s, Wright’s and Fisher’s work in population genetics saved Darwinists from a early , last century, from the hands of Mendelian Genetics”

    It would be way cool to firmly establish this fact against Darwinists!!!!

  45. 45
    bornagain77 says:

    Dang baby sitter filter ate a word:

    Haldane’s, Wright’s and Fisher’s work in population genetics saved Darwinists from a early de^ath, last century, from the hands of Mendelian Genetics”

  46. 46
    jerry says:

    I have just read the Koonin paper for the second time. Essentially it is about single cell evolution. He speculates a little about the Cambrian Explosion but does not say much.

    How does this paper challenge the Darwinian explanation other than recognizing the Cambrian Explosion as a major problem for gradualism? It is all about single cell hgt which seems a plausible model. I doubt that ID would question this.

    Koonin also got provocative a few months ago by saying the odds of life forming as something of the order of 1 in 10 ^1000 or some other absurdly high number.

  47. 47
    bFast says:

    DaveScot, so the amount of conserved DNA deleted was in excess of 100,000 bp, correct? Sounds right to me. Certainly sounds like a lot to not show up in their battery of fitness tests

    DaveScot:

    If I recall correctly the authors, in a different experiment, tried deleting some ultra-conserved (95% – 100%) sequences and those DID have bad consequences for the GM mouse.

    Over on TelicThoughts this conversation went along for quite a while, mostly between me and I believe it was Mesk. He reported that thought the majority of ultra-conserved non-coding segments that have been deleted caused noticeable degridation, there have been 9 segments found so far that did not.

  48. 48
    bornagain77 says:

    Jerry,

    Here is a little hint at the problem of Darwinian evolution accounting for the complexity for even a simple bacteria:

    The complexity found in the simplest bacterium known to science makes the complexity of any man-made machine look like child’s play. As stated by Geneticist Michael Denton PhD,

    “Although the tiniest living things known to science, bacterial cells, are incredibly small (10-12 grams), each is a veritable micro-miniaturized factory containing thousands of elegantly designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world”.

    So, as you can see, there simply is no simple life on earth as naturalism had presumed – even the well known single celled amoeba has the complexity of the city of London and reproduces that complexity in only 20 minutes.

    Here are a couple of quotes for the complexity found in any biological system, including simple bacteria, by two experts in biology:

    “Most biological reactions are chain reactions. To interact in a chain, these precisely built molecules must fit together most precisely, as the cog wheels of a Swiss watch do. But if this is so, then how can such a system develop at all? For if any one of the specific cog wheels in these chains is changed, then the whole system must simply become inoperative. Saying it can be improved by random mutation of one link, is like saying you could improve a Swiss watch by dropping it and thus bending one of its wheels or axis. To get a better watch, all the wheels must be changed simultaneously to make a good fit again.” Albert Szent-Györgyi von Nagyrapolt (Nobel prize for Medicine in 1937). “Drive in Living Matter to Perfect Itself,” Synthesis I, Vol. 1, No. 1, p. 18 (1977)

    “Each cell with genetic information, from bacteria to man, consists of artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction and a capacity not equaled in any of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours” Geneticist Michael Denton PhD.

    To give an idea how impossible “simple” bacterial life is for naturalistic blind chance, Sir Fred Hoyle calculated the chance of obtaining the required set of enzymes for just one of any of the numerous types of “simple” bacterial life found on the early earth to be one in 10^40,000 (that is a one with 40 thousand zeros to the right). He compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Sir Fred Hoyle also compared the chance of obtaining just one single functioning protein (out of the over one million protein molecules needed for that simplest cell), by chance combinations of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously.

    The simplest bacteria ever found on earth is constructed with over a million protein molecules. Protein molecules are made from one dimensional sequences of the 20 different L-amino acids that can be used as building blocks for proteins. These one dimensional sequences of amino acids fold into complex three-dimensional structures. The proteins vary in length of sequences of amino acids. The average sequence of a typical protein is about 300 to 400 amino acids long. Yet many crucial proteins are thousands of amino acids long. Proteins do their work on the atomic scale. Therefore, proteins must be able to identify and precisely manipulate and interrelate with the many differently, and specifically, shaped atoms, atomic molecules and protein molecules at the same time to accomplish the construction, metabolism, structure and maintenance of the cell. Proteins are required to have the precisely correct shape to accomplish their specific function or functions in the cell. More than a slight variation in the precisely correct shape of the protein molecule type will be for the life of the cell. It turns out there is some tolerance for error in the sequence of L-amino acids that make up some the less crucial protein molecule types. These errors can occur without adversely affecting the precisely required shape of the protein molecule type. This would seem to give some wiggle room to the naturalists, but as the following quote indicates this wiggle room is an illusion.

    “A common rebuttal is that not all amino acids in organic molecules must be strictly sequenced. One can destroy or randomly replace about 1 amino acid out of 100 without doing damage to the function or shape of the molecule. This is vital since life necessarily exists in a “sequence—disrupting” radiation environment. However, this is equivalent to writing a computer program that will tolerate the destruction of 1 statement of code out of 1001. In other words, this error-handling ability of organic molecules constitutes a far more unlikely occurrence than strictly sequenced molecules.” Dr. Hugh Ross PhD.

    It is easily demonstrated mathematically that the entire universe does not even begin to come close to being old enough, nor large enough, to ally generate just one small but precisely sequenced 100 amino acid protein (out of the over one million interdependent protein molecules of longer sequences that would be required to match the sequences of their particular protein types) in that very first living bacteria. If any combinations of the 20 L-amino acids that are used in constructing proteins are equally possible, then there are (20^100) =1.3 x 10^130 possible amino acid sequences in proteins being composed of 100 amino acids. This impossibility, of finding even one “required” specifically sequenced protein, would still be true even if amino acids had a tendency to chemically bond with each other, which they don’t despite over fifty years of experimentation trying to get amino acids to bond naturally (The odds of a single 100 amino acid protein overcoming the impossibilities of chemical bonding and forming spontaneously have been calculated at less than 1 in 10^125 (Meyer, Evidence for Design, pg. 75)). The staggering impossibility found for the universe ever generating a “required” specifically sequenced 100 amino acid protein by would still be true even if we allowed that the entire universe, all 10^80 sub-atomic particles of it, were nothing but groups of 100 freely bonding amino acids, and we then tried a trillion unique combinations per second for all those 100 amino acid groups for 100 billion years! Even after 100 billion years of trying a trillion unique combinations per second, we still would have made only one billion, trillionth of the entire total combinations possible for a 100 amino acid protein during that 100 billion years of trying! Even a child knows you cannot put any piece of a puzzle anywhere in a puzzle. You must have the required piece in the required place! The simplest forms of life ever found on earth are exceedingly far more complicated jigsaw puzzles than any of the puzzles man has ever made. Yet to believe a naturalistic theory we would have to believe that this tremendously complex puzzle of millions of precisely shaped, and placed, protein molecules “just happened” to overcome the impossible hurdles of chemical bonding and probability and put itself together into the sheer wonder of immense complexity that we find in the cell.

    Instead of us just looking at the probability of a single protein molecule occurring (a solar system full of blind men solving the Rubik’s Cube simultaneously), let’s also look at the complexity that goes into crafting the shape of just one protein molecule. Complexity will give us a better indication if a protein molecule is, indeed, the handi-work of an infinitely powerful Creator (Super-Intelligent Designer).
    In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, that is 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it is estimated it will take one entire year for it to analyze the mechanism by which JUST ONE “simple” protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape. In real life, the protein folds into its final shape in a fraction of a second! The computer would have to operate at least 33 million times faster to accomplish what the protein does in a fraction of a second. That is the complexity found for JUST ONE “simple” protein. It is estimated, on the total number of known life forms on earth, that there are some 50 billion different types of unique proteins today. It is very possible the domain of the protein world may hold many trillions more completely distinct and different types of proteins. The simplest bacterium known to man has millions of protein molecules divided into, at bare minimum, several hundred distinct proteins types. These millions of precisely shaped protein molecules are interwoven into the final structure of the bacterium. Numerous times specific proteins in a distinct protein type will have very specific modifications to a few of the amino acids, in their sequence, in order for them to more precisely accomplish their specific function or functions in the overall parent structure of their protein type. To think naturalists can account for such complexity by saying it “happened by chance” should be the very definition of “absurd” we find in dictionaries. Naturalists have absolutely no answers for how this complexity arose in the first living cell unless, of course, you can take their imagination as hard evidence. Yet the “real” evidence scientists have found overwhelmingly supports the anthropic hypothesis once again. It should be remembered that naturalism postulated a very simple “first cell”. Yet the simplest cell scientists have been able to find, or to even realistically theorize about, is vastly more complex than any machine man has ever made through concerted effort !! What makes matters much worse for naturalists is that naturalists try to assert that proteins of one function can easily mutate into other proteins of completely different functions by pure chance. Yet once again the empirical evidence we now have betrays the naturalists. Individual proteins have been experimentally proven to quickly lose their function in the cell with random point mutations. What are the odds of any functional protein in a cell mutating into any other functional folded protein, of very questionable value, by pure chance?

    “From actual experimental results it can easily be calculated that the odds of finding a folded protein (by random point mutations to an existing protein) are about 1 in 10 to the 65 power (Sauer, MIT). To put this fantastic number in perspective imagine that someone hid a grain of sand, marked with a tiny ‘X’, somewhere in the Sahara Desert. After wandering blindfolded for several years in the desert you reach down, pick up a grain of sand, take off your blindfold, and find it has a tiny ‘X’. Suspicious, you give the grain of sand to someone to hide again, again you wander blindfolded into the desert, bend down, and the grain you pick up again has an ‘X’. A third time you repeat this action and a third time you find the marked grain. The odds of finding that marked grain of sand in the Sahara Desert three times in a row are about the same as finding one new functional protein structure (from chance transmutation of an existing functional protein structure). Rather than accept the result as a lucky coincidence, most people would be certain that the game had been fixed.” Michael J. Behe, The Weekly Standard, June 7, 1999, Experimental Support for Regarding Functional Classes of Proteins to be Highly Isolated from Each Other

    “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed – along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

    Even if evolution somehow managed to overcome the impossible hurdles for generating novel proteins by totally natural means, Evolution would still face the monumental hurdles of generating complimentary protein/protein binding sites in which the novel proteins could actually interface with each other in order to accomplish specific tasks in the cell (it is estimated in Behe’s “EOE” that there are least 10,000 different types of protein-protein binding sites in a “simple” cell). What does the recent hard evidence say about novel protein-protein binding site generation from what is actually observed to be occurring on the protein level of malaria and HIV since they have infected humans?

    Once again the naturalists are brutally betrayed by the hard evidence that science has recently uncovered!

    The likelihood of developing two binding sites in a protein complex would be the square of of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by ) in the (entire) history of life. It is biologically unreasonable. Dr. Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

  49. 49
    bornagain77 says:

    Jerry you asked;
    How does this paper challenge the Darwinian explanation other than recognizing the Cambrian Explosion as a major problem for gradualism?

    What is surprising about the paper Jerry is that it is like pulling teeth to get evolutionists to even admit the fossil record is overwhelming characterized by abrupt appearance of exceedingly complex novelty,,as well as stability afterwards.

    It is quite refreshing for IDers to have such a candid admission of the true state of evidence from a Darwinist, when we are use to such blatant distortions of evidence from them!

  50. 50
    bFast says:

    BornAgain77, post #48.

    Excellent encapsulation of delicious quotes about the state of the challenge of life, especially of abiogenesis.

  51. 51
    jerry says:

    bornagain77,

    I think you missed the point. First, you are preaching to the choir. I am aware of lot of your arguments and have never disputed them. I was not aware of the IBM computer. The OOL is the biggest of all problems for the materialist because it obviates multiple universes. Even if there were multiple universes, if there no way that life could form then they are still up a creek in terms of a naturalistic explanation.

    As I said, I am not questioning the complexity of individual cell organisms. Koonin is primarilyy making the point that a lot of the diversity in individual cell organisms is probably due to hgt which I believe is a similar position that Woese makes.

    He also subscribes to Margulis’s Endosymbiotic theory which is highly speculative. However, I believe there is evidence for hgt so this is not a speculative process. What is speculative is that different cell types could have formed this way especially if there are specific processes that are unique to the different cell organisms.

    What I am disputing is that this is a major attack on Darwinism. James Valentine makes a similar point and he is considered one of the top paleontologist in the world. He hypothesizes some unique mechanism that is responsible for the Cambrian Explosion and that it in no way can be explained by Darwin’s ideas. However, Valentine believes that neo-Darwinism explains everything after the Cambrian Explosion. This is essentially what Koonin is saying. So it is not necessarily ture that is hard to get an anti Darwin comment out of the scientific community when it applies to the pre Cambrian era. It is after the Cambrian Explosion that they seem to be in lock step.

  52. 52
    bornagain77 says:

    Sorry Jerry,
    I’m so use to debating Darwinists, that I ally mistook your sincere questioning, of the merits of the paper, for a defense of Darwinism.

  53. 53

    DaveScot wrote:

    “The fossil record show us saltation, stasis, and extinction.”

    Well said.

    bornagain77 wrote:

    “Sir Fred Hoyle also compared the chance of obtaining just one single functioning protein (out of the over one million protein molecules needed for that simplest cell), by chance combinations of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously.”

    With all due respect to Sir Hoyle, we need to tighten up his example. There are several people in the world today who can solve the cube blindfolded, having studied it for a few minutes. Further, a blind man is still an intelligent being with the capacity to understand that there is a goal and to direct his efforts toward that goal. To tighten Sir Hoyle’s analogy, we would have to say that we are dealing with a solar system full of blind men who have been tasked with turning faces of the cube with (i) no knowledge of what is on the faces of the cube, (ii) no knowledge of the algorithms required, (iii) no awareness of the goal, (iv) no inclination to try to figure out if there is a goal, and (v) even if there is a goal, no inclination to direct their efforts towards that goal.

  54. 54
    bFast says:

    Responding to Eric Anderson,

    Though people can solve the cube blindfolded after carefully observing it, to date I have never heard of anyone solving a rubics cube with no chance of seeing it. (I’m sure a “blind man’s cube” is possible with braille on it, but hey.) Hence Hoyle, who specifically stated that the solvers were “blind” made no error of logic.

  55. 55

    Thanks, bFast. You and I are in complete agreement that he didn’t make an error of logic. I didn’t suggest that he made a formal error of logic – I simply said that his example needs to be tightened.

    It is indeed unlikely that someone who had no chance of seeing a cube first would be able to solve it blind. However, even without seeing it first, a blind man with a grasp of the task at hand, a knowledge of the algorithms involved, and a desire to accomplish the goal is still a very far cry from a process with no comprehension of the task at hand, no intelligent input, and no goal.

    Look, the point of his example is that it is very unlikely. Definitely the case — I accept his point. I just think his example could be better both quantatively (the odds are probably worse than his example suggests — and yes, that’s just my gut feeling) and qualitatively (an intelligent agent — albeit with a significant physical limitation — trying to accomplish a goal).

  56. 56
    bornagain77 says:

    Just re-read the paper and will probably re-read it many times for it is a wealth of knowledge!

    It just blows me away that so much intellectual talent is wasted on trying to prove a theory that is clearly proven false from basic mathematical precepts!

    I just wonder what breakthroughs would happen in science if this talent was directed to productively finding proper solutions to the origins questions,,,, instead of fruitlessly wasting away in a scientific de^ad end!

    It truly makes me sad,,Not only for the wasted brain power,,but also from what I feel is a threat to their eternal spiritual weel being,,,Maybe, in all truth, I should be a lot sadder than what I am for the wasted lives I see!

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