Eugene Koonin (NCBI) on Biology’s Big Bangs

_{Paul Nelson
October 8, 2007

Intelligent Design

1}_{Categories
Intelligent Design}

Share: Facebook; Twitter/X; LinkedIn; Flipboard; Print; Email

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?

Comments

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.Atom_{October 9, 2007
October
10
Oct
9
09
2007
03:23 PM
3
03
23
PM
PDT}

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.Eric Anderson_{October 9, 2007
October
10
Oct
9
09
2007
02:52 PM
2
02
52
PM
PDT}

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???bornagain77_{October 9, 2007
October
10
Oct
9
09
2007
01:23 PM
1
01
23
PM
PDT}

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.Eric Anderson_{October 9, 2007
October
10
Oct
9
09
2007
01:01 PM
1
01
01
PM
PDT}

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.magnan_{October 9, 2007
October
10
Oct
9
09
2007
12:42 PM
12
12
42
PM
PDT}

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/science/articles/2007/09/24/dna_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?bornagain77_{October 9, 2007
October
10
Oct
9
09
2007
10:56 AM
10
10
56
AM
PDT}

gpuccio, "a folk of “IDiots”" Return favour to them "the Darwidiots"MatthewTan_{October 9, 2007
October
10
Oct
9
09
2007
09:04 AM
9
09
04
AM
PDT}

DaveScot Very thought provoking post (#17). Thanks.mike1962_{October 9, 2007
October
10
Oct
9
09
2007
08:47 AM
8
08
47
AM
PDT}

DaveScot, I fully agree with you that this paper is consistent with front-loading. We need to warm MikeGene up to it.bFast_{October 9, 2007
October
10
Oct
9
09
2007
08:37 AM
8
08
37
AM
PDT}

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.DaveScot_{October 9, 2007
October
10
Oct
9
09
2007
07:40 AM
7
07
40
AM
PDT}

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...gpuccio_{October 9, 2007
October
10
Oct
9
09
2007
06:28 AM
6
06
28
AM
PDT}

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.tribune7_{October 9, 2007
October
10
Oct
9
09
2007
06:16 AM
6
06
16
AM
PDT}

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?russ_{October 9, 2007
October
10
Oct
9
09
2007
04:02 AM
4
04
02
AM
PDT}

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.Jehu_{October 8, 2007
October
10
Oct
8
08
2007
10:24 PM
10
10
24
PM
PDT}

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.interested_{October 8, 2007
October
10
Oct
8
08
2007
05:44 PM
5
05
44
PM
PDT}

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.toc_{October 8, 2007
October
10
Oct
8
08
2007
05:18 PM
5
05
18
PM
PDT}

correction: "intelligently designing" organisms that would be of benefit to man!bornagain77_{October 8, 2007
October
10
Oct
8
08
2007
04:24 PM
4
04
24
PM
PDT}

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!!!bornagain77_{October 8, 2007
October
10
Oct
8
08
2007
04:22 PM
4
04
22
PM
PDT}

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.bFast_{October 8, 2007
October
10
Oct
8
08
2007
03:22 PM
3
03
22
PM
PDT}

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/content/2/1/21/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.idnet.com.au_{October 8, 2007
October
10
Oct
8
08
2007
03:16 PM
3
03
16
PM
PDT}

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.idnet.com.au_{October 8, 2007
October
10
Oct
8
08
2007
02:56 PM
2
02
56
PM
PDT}

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.geoffrobinson_{October 8, 2007
October
10
Oct
8
08
2007
02:19 PM
2
02
19
PM
PDT}

"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."nullasalus_{October 8, 2007
October
10
Oct
8
08
2007
01:55 PM
1
01
55
PM
PDT}

Atom, you beat me to it!todd_{October 8, 2007
October
10
Oct
8
08
2007
01:54 PM
1
01
54
PM
PDT}

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.
Atom_{October 8, 2007
October
10
Oct
8
08
2007
01:45 PM
1
01
45
PM
PDT}

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.idnet.com.au_{October 8, 2007
October
10
Oct
8
08
2007
01:43 PM
1
01
43
PM
PDT}

Prev 1 2

You must be logged in to post a comment.

Leave a Reply