Thoughts on Science, ID, Evolutionary Continuity, and Eugene Koonin

In 2007, the famous and highly respected evolutionary biologist, Eugene Koonin, published a paper in the peer-reviewed journal Biology Direct. The paper is titled “The Biological Big Bang model for the major transitions in evolution.” In the abstract, he summarizes the problem he aims to address as follows:

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution.

In other words, he is stating the observed fact that there are frequent discontinuous jumps in complexity, with the emergence of entirely new classes of biological entities (including organisms and biochemical molecules).

His model evokes the cosmological concepts of rapid inflation and Big Bang singularity. In the biological case, the inflation is the result of “extremely rapid evolution,” and the biological “Big Bang” emergence of novel complexity “is envisaged as being qualitatively different from tree-pattern cladogenesis.” In other words, not at all Darwinian gradualism.

Koonin is an atheist who despises creationism and Intelligent Design (ID), and he is a fiercely independent and brilliant thinker. One might wonder how the tone and content of this paper was received by reviewers, except that we don’t need to wonder at all. Biology Direct is an open access journal that also uses open review, still fairly rare among scientific journals. The names of the reviewers are published, as are their comments and the author’s replies. I found this fascinating to read.

In one comment, the reviewer (William Martin) writes:

“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.

Koonin responds:

Here I do not really understand the concern… 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…  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… However, I believe that this is totally counter-productive and such a notion is outright false… 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…

(Note: most of what I omitted in that quote are protestations against ID.)

Complaints by some academic scientists about language in scientific papers and presentations that sounds too much like ID or creationism are not uncommon these days. I fully agree with Koonin that such rigid adherence to the dogma of neo-Darwinism is counterproductive in the search for truth. It might, in fact, simply be true that some of the ideas of ID are more consonant with the reality of biological evolution than is generally acknowledged.

In fact, the prediction that ID folks might jump on this and similar ideas has come to pass to some extent. Randy Isaac recently drew my attention to a meeting in Austria where evolutionary biologists presented ideas contesting the standard model of Darwinian gradualism, and even discussed the forbidden word – teleology. Several members of the ID-based Discovery Institute also presented their work at this meeting.

An article about this meeting written by Discovery Institute’s newsletter “Evolution News” claims that some of the speakers from academia expressed fears of possible harassment or worse from their academic departments because of the kind of concern expressed in the reviewer’s quote above. It is certainly the case that hints of Intelligent Design sympathy are not well received in academic biology.

Eugene Koonin has no need to worry about reactions to his thoughts. His position (at the Library of Medicine in the NIH) and his reputation as a brilliant scientist are secure. Like Stephen Jay Gould and the more modern proponents of the extended evolutionary synthesis, Koonin is not afraid (thank God) to move the entire field of evolutionary biology forward with bold new ideas.

Science cannot be stopped by political, religious, or social viewpoints. At least not for long. It is my own belief that just as the original Big Bang theory put astrophysics and Christian cosmology in closer concordance, we will eventually see a similar trend in biology. God willing.


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10 Responses to Thoughts on Science, ID, Evolutionary Continuity, and Eugene Koonin

  1. Fascinating… Returning here when I had time for a more careful read, I decided to refer directly to the source… which has at least resulted in some new vocabulary: cladogenesis, chromalveolate, endosymbiont, Muller’s ratchet…

    That said, I believe that I understand what Koonin is saying. In the same way that Darwin’s “natural selection” has been applied to a multitude of disciplines well beyond its original intent, Koonin has applied a model from physics – although I think it’s actually more accurately associated with information theory – to the process of bio-diversification (and possibly biogenesis). If I’m reading all of this correctly, his assertion is simply that gradual accumulations of biologically-related resource will reach a tipping point where interactions between them allow a sort of quantum jump resulting in a sudden explosion of more complex solutions.

    This sounds to me not unlike the idea of a “singularity” in AI, where some type of thinking-machine will acquire sufficient complexity to solve problems regarding its own ability to think, the result being a sudden explosion of some new type of machine-intelligence. Herein, I would say that I agree with Martin’s early assertion that Koonin’s idea is “evolutionary” as opposed to “cosmological”. Evolution is powered by options to increase efficiency. When enough options become available (ready made?), it seems logical that a point may be reached where entirely new lines of experimentation may become available. In this regard, parsing vocabulary seems rather senseless to me.

    The problem I see with the teleological perspective isn’t that it’s incompatible with the process Koonin describes. In fact, it seems entirely possible. But it’s also like the “many worlds” solution to the consistent resolution of quantum measurement in physics. It’s an untestable approach to a problem more simply resolved through other explanations that are merely unsatisfying to the human aesthetic. Which is correct?

    • Thanks for the comment, Kumi. I agree with everything you wrote, except the last paragraph. I am not so sure that the teleological perspective is not testable. Im hoping that it is, but we will need some new ways of thinking to do it. But I think you are right about the “sudden explosions” probably a good description of emergence, which is still mysterious to me.

  2. sallyhawksworth says:

    Thanks, Lightness Traveling, for giving a useful summary of what Koonin was saying. I couldn’t make out from the BoW account what he was actually presenting as new, since it’s at least a generation since Gould & ?Eldridge put forward the idea that major evolutionary change progressed in a sort of “leaping & lingering” fashion, not at a constant rate ( which latter was labelled “Darwinian gradualism” even though I don’t recall Darwin himself ever suggesting that evolution did happen at a constant rate, )

    • Thank you, Sally… and you can call me “Kumi”. (My apologies… I had wondered for awhile if you were someone whom I knew.)

      As neither a biologist nor a biochemist, I’m easily overwhelmed by Sy’s expertise. I think I spent a week getting a grip on something he wrote regarding bio-genesis. My readings of Gould tend to date back to college.

      Reading your comment below reminded me that while considering Koonin’s paper, that it had occurred to me that the “mingling” aspect implied something else. Not only does there need to be an accumulated pool of resources from which to draw for a biological “Big Bang” to take place, but those resources must either be somehow compatible — or there must come to exist some mechanism for making it so. In physics, this would be called “coupling”, which is simply an ability to transfer energy (the information regarding a preceding state) from one frame or field to another. Consequently, two “things” with strong coupling (say a photon and an electron coupling through mutual electromagnetic field interactions) will be highly dynamic. Conversely, two directly non-interacting “things” may only be able to interact intermittently through some mediating interaction (a photon with a Higgs-boson via an electron). I suppose the biological equivalent would be the mediated transfer of some pattern of chemistry, either metabolic or genetic, from one organic frame to another — perhaps through something like the serendipitous replication of beneficial genes through a virus, a fortuitous protein or enzyme, or (as you noted) parasitism that results in symbiosis. In each case, the appearance of a mediating mechanism results in a sudden, non-incremental, and otherwise not possible change.

  3. sallyhawksworth says:

    And now it seems “Darwinian gradualism” is again presented as the target of attack, by proponents of ID mostly. But I note that Koonin, the scientist whose paper was the starting point for this blog, has himself no time for ID, any more than Martin, whose comment you quote. They both are proponents of entirely naturalistic mechanisms for evolution, and anti teleological explanations. Koonin’s Big Bang analogy, and the idea of bio information accumulating till it reaches a tipping point and a new level of complexity is generated, seems to me interesting and quite convincing and enlightening as an explanation of how certain major developments in evolution give the appearance of happening almost overnight, in terms of geological time. (Some actual figures, however approximate, might have been useful at this point, though.) Koonin’s other main contention, that at certain earlyish points in the evolution of life on Earth there does not seem to have been so much a direct line of descent as more of a mingling, is not new either, though the detail and examples he gave in his paper may be. We have known or suspected for some time, haven’t we, that Mitochondrial DNA seems to have hitched a ride with our own, perhaps by a sort of parasitism originally? Genes similarly seem to sometimes have leaped from bacteria to bacteria or bacteria to host. And at the very early biochemical level who knows what strange amalgams occurred! So yes, at these points Darwin’s famous little rough “tree” sketch is not the most appropriate illustration. But the “family tree” is still the best model for the pattern of descent for most complex multicellular animal life forms, surely, which was after all the level that Darwin was looking at. Mid- nineteenth century scientists did not have the technology to enable them to study directly the genome of any organism, or understand reproduction of any sort at the micro cellular level.

  4. sallyhawksworth says:

    At least you DID read Gould at college, Kumi, and studied SOME branches of science to a high level. Whereas I finished my formal education in biology and physics at the O Level stage, and chemistry even earlier, and what more I know of biology is all acquired from reading books designed for the general reader, or from tv and the Net.

    That’s a really interesting idea of yours about the need for either compatibility or some mediating agent to allow “mingling” to occur, and using analogies in physics. In schoolroom chemistry the equivalent might be adding a catalyst to enable two otherwise non-reacting chemicals to react, mightn’t it? it makes sense to me. These are obviously areas which it would pay to investigate further, where we still have a lot to learn and exciting new discoveries and insights to be made.

    What bugs me about IDers is that they are excited for a totally different reason at the thought that there are gaps in our understanding of any stage of evolution. They don’t want to find out naturalistic explanations of these events, which is what scientific investigation is designed to do, but instead immediately proclaim that the gap is evidence for there having been a SUPERnatural agency at work, which they suggest the scientists are obstinately shutting their eyes to. And having once nailed their colours to the mast and committed themselves to the idea of “irreducible complexity”, or “front loading” or whatever other notion it is which (fancy that?) necessitates there being an intelligent agency deliberately engineering some biological feature, because, they say, there is no way it could have arisen naturally, they then not only see no reason to investigate other naturalistic explanations themselves, but they complain of being persecuted or censored when other people persist in doing so, and challenge their assertions on scientific grounds.

    • I tend not to worry too much about the differences in the worlds we construct between our ears… so long as the practical decision-making remains rational… or at least, humane. In that regard, Sy has kept my attention.

      Some time back (at a now defunct website), I wrote an article about the statistical relationship between the relative “spins” of two “entangled” particles. It wasn’t especially well-written. But what it tried to show was how these experiments indicate that the universe must necessarily function entirely according to one of two exactly opposing systems — either strong free-will, or super-determinism. However, the science gives no evidence whatsoever as to which case is true:

      John Conway and Simon Kochen, first in 2006, used entanglement to construct a logical argument for a strong version of “free-will” which extends to the functioning of the entire universe. It was a serious mathematical argument, and it appears to be entirely consistent. Moreover, part of their model for decision-making suggested a solution to an entirely unrelated problem regarding quark charges.

      The Nobel physicist, Gerard ’t Hooft, addressed Conway and Kochen’s work in 2007. Somewhat tongue-in-cheek, ’t Hooft observed that any conflict with an otherwise entirely deterministic system is resolved by merely assuming that the experimenter’s actions are also deterministic. He went on to proposes that the “wave function” in physics only appears to be probabilistic because it’s not directly observable.

      I lean toward ’t Hooft. But in all honesty, I can’t say with certainty which is correct. And the debate has continued, with Kochen introducing an entirely new argument for strong free-will just a couple of years back.

      So while I’m not likely ever to become a faithful adherent to an organized religion, I still find a great deal of mystery in what’s behind those curious worlds that exist in our heads. It wouldn’t surprise me too much if there’s a bit of what might seem like “magic” beneath it all. So if Sy can come up with some kind of valid statistical evidence for his teleological assertion, I’d be willing to consider the implication. I keep an open mind – just not enough to let my brain fall out. 😉

      • sallyhawksworth says:

        “I tend not to worry too much about the differences in the worlds we construct between our ears…so long as the practical decision-making remains rational…or at least humane”

        I feel very similarly. It seems like a classic Enlightenment approach. But for me your phraseology highlights a difficulty with our accepting strong determinism (whether argued via physics or, as I have heard it, via brain physiology and philosophy) at anything other than a strictly intellectual and theoretical level. You talk about practical decision-making. And indeed, that is what it feels like to us that we are doing, day in, day out – making decisions, some rational and practical, others much less so. But if determinism is correct, then WE are not actually making decisions at all. We have no autonomy. We could have done no differently than we did. Whatever we do, whatever we think, however harmful or beneficial to ourselves or others, is the inevitable result of a chain of earlier events. In which case, surely, we can bear no personal and moral responsibility for actions over we have no control – which is all our actions, even though we experience them as if we DO have control.

        But can any human society, can any human, function if it really comes to think that this is the way things are (the thoughts over which it has no control) and to base its actions(the actions over which it has no control) on this philosophy? I think not. We have, and have to have, the illusion of autonomy.

        Though of course, according to determinism, I WOULD think that, wouldn’t I? Just as YOU would think whatever you think!

  5. Ha, Sally! I suspect the universe already knew you’d say this.

    Regardless, I sincerely doubt that, “Spinoza’s God made me do it,” would work as much of a defense in court… unless perhaps your attorney is Clarence Darrow (Scopes Monkey Trial)… spared two clients death with the statement that, “There are a lot of myths which make the human race cruel and barbarous and unkind. Good and Evil, Sin and Crime, Free Will and the like delusions made to excuse God for damning men and to excuse men for crucifying each other.”

    Of course, debating free-will is little more than an exercise in academics. Socially, it makes little difference whether it’s real or merely an illusion (and civilized laws waffle on the yopic in the face of humane behavior and convenience). But it illustrates the point that much of what leads to the consistency that manifests itself as the universe we perceive is fundamentally unknowable.

    Science is merely descriptive; it doesn’t reveal a source. In fact, when two descriptions yield the same results, they are said to be the same. So it could be that debating free-will versus determinism is merely a variation on the proverbial blind men describing an elephant. Maybe we’re not even asking the right questions? Nature doesn’t seem to have much concern for the human sense of aesthetic, and consequently appeals to a certain cautious objectivity.

    And my apologies, Sy. It wasn’t my intent to hijack your post… just a good-natured compulsion. 😉

  6. sallyhawksworth says:

    For some reason, Kumi, although I was notified that you liked my last post that does not appear on the site when I visit it, and I don’t seem to have the facility to like posts either. Curious, I have posted in the comment section of another blog using WordPress, and there I can add likes, though admittedly not until I first have posted a comment on that particular day. I gather that the same is true for at least one other poster there. Why this should be is a mystery.

    anyway, you are quite correct that we have drifted away from the blog subject, so we should probably call a halt unless we have any more to say that is relevant to Koonin and his paper.

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