Eugene Koonin – Evolution Skeptic?

The edifice of the Modern Synthesis has crumbled, apparently, beyond repair.

– Eugene Koonin (2009)

Does this make Eugene Koonin an evolution skeptic?

The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.

I’m still struggling to incorporate Alan Fox’s allegation that I am an evolution skeptic. I still don’t really know what it means to be an evolution skeptic. Eugene Koonin rather obviously rejects the view of evolution held by Alan Fox. Is Eugene Koonin an evolution skeptic?

Or is this just another example of Creationist quote mining. Maybe it’s both.

What say you, “skeptics”?

The Origin at 150: is a new evolutionary synthesis in sight?

115 thoughts on “Eugene Koonin – Evolution Skeptic?

  1. Koonin asks:

    Therefore, this year is perfect to ask some crucial questions: how has evolutionary biology changed in the 50 years since the ‘hardening’ of the Modern Synthesis? Is it still a viable conceptual framework for evolutionary thinking and research? And, if not, is a new (‘postmodern’) synthesis in sight?

    The “skeptical” response? The modern synthesis is as robust and fruitful as ever, there’s no reason to change it?

  2. “Not only the fact of evolution itself but the existence of deep evolutionary connections between different domains of life — to be concrete — evolutionary connections between, let us say, mammals, such as humans, and prokaryotes, bacteria and archaea, have become indisputable. These findings make questioning not only the reality of evolution but the evolutionary unity of all life on earth completely ridiculous and outside of the field of rational discourse.”

    Eugene Koonin, Interview with Suzan Mazur, 2017

    http://m.huffpost.com/us/entry/14597840

  3. Rumraket: Eugene Koonin, Interview with Suzan Mazur, 2017

    I don’t see here any sort of retraction of what he said earlier. Do you?

    all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.

    If the modern synthesis is gone, what replaced it?

  4. Mung: Mung Post authorFebruary 10, 2017 at 6:54 am
    Rumraket: Eugene Koonin, Interview with Suzan Mazur, 2017

    I don’t see here any sort of retraction of what he said earlier. Do you?

    …all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.

    If the modern synthesis is gone, what replaced it?

    Maybe you should actually read the interview?

    Suzan Mazur: In a 2009 paper of yours commenting on the 150th anniversary of the Origin of Species you make the following statement: “So, not to mince words, the Modern Synthesis is gone.”

    Yet in your recent BioMed Central paper you write that it’s time for biologists to start paying attention to population genetics because of advances in functional genomes. But population biology IS part of the Modern Synthesis. So your current position has some in the science community confused. Would you talk about the evolution of your thinking about evolution and begin by how you define “gene” and “genome”?

    Eugene Koonin: Such confusion makes one wish, at least for a moment, they never made such general statements aimed at a mass audience, yet I think such generalizations are necessary. There isn’t really much change in my thinking. There isn’t any dramatic change let alone a turn-around in my thinking. Population genetics is a mathematical framework that is essential for building evolutionary theory but it is not the theory itself. The Modern Synthesis does employ that framework and is a correct theory but only for a narrow range of evolutionary processes in certain groups of organisms. It is quite a typical situation in science, actually.

    Coming back to the evolution of my thinking from 2009 to 2016, which really hasn’t been much. Quite frankly, if I were writing what I wrote back in 2009, I would have been even more cautious and non-combative than I was then. I don’t think I was ever really bombastic. But I would have been even less demonstrative and maybe I would not have written that the Modern Synthesis is gone.

    Suzan Mazur: I think your paper in 2009 does sort of leave the door open for the paper that you just published in BioMed Central.

    Eugene Koonin: Absolutely, all the doors were open. I would not say that it’s [Modern Synthesis] gone just like that. It has to be understood in context. I think now any actively working scientist in evolutionary biology probably realizes that the Modern Synthesis or neo-Darwinism, or whatever the name is, is insufficient in the post-genomic era. This is a set of concepts that is insufficient for understanding the entirety of evolution. It doesn’t mean it’s wrong. It’s only becoming wrong if someone claims that they need nothing past the concepts in the Modern Synthesis.

    Suzan Mazur: Would you like to make a final point?

    Eugene Koonin: Yes. I would like to come back to this issue of the Modern Synthesis, population genetics theory and the like because it is true that population genetics theory is part of the Modern Synthesis. And that is great. That is part of the power of the concept and why it remains quite relevant in explanations of microevolution but also an important part of the new evolutionary biology. That’s what I wanted to convey in the BMC paper, that population genetics theory (in its modernized form because it too has not remained static over 50 years) has to be systematically applied in evolutionary genomics, which is the new mainstream of evolutionary biology. Indeed, it’s changed dramatically over the last 25 years, and as previously mentioned, has completely transformed the ability to investigate, assess and measure evolutionary processes. The modern version of population genetics theory (it too has not remained static over 50 years) has to be actively, constantly and systematically applied to our understanding of genome evolution. That is too often not the case.

    The whole of Mike Lynch’s work on this, his talks, papers and books are of paramount importance, even if I sometimes disagree with Mike on specific issues. The foundation Mike Lynch laid for modern evolutionary genomics cannot be reasonably disputed and is of huge importance.

    So Koonin was merely saying that the Modern Synthesis is a population genetics theory that does not capture all aspects of biological evolution and as such, alone won’t make you understand all evolutionary change.

  5. So in answer to the OP, which asks “Does this make Eugene Koonin an evolution skeptic?”.

    No, it doesn’t.

  6. Eugene Koonin rather obviously rejects the view of evolution held by Alan Fox

    What view of evolution is held by Alan Fox?

  7. Rumraket: So Koonin was merely saying that the Modern Synthesis is a population genetics theory that does not capture all aspects of biological evolution and as such, alone won’t make you understand all evolutionary change.

    That is pretty much my position as well.
    Does that make me an evolution skeptic?

    peace

  8. Mung,

    Yet another theory of evolution. Or more than one. Who the hell knows.

    Me. I do.

    I don’t know why you go so far out of your way to confuse yourself, or feign confusion.

  9. fifthmonarchyman: That is pretty much my position as well.
    Does that make me an evolution skeptic?

    That is also my position. So no just as for me, and Eugene Koonin, I don’t think it does.

  10. Allan Miller: I don’t know why you go so far out of your way to confuse yourself, or feign confusion.

    Attention whore. It’s always been that way. I bet Mung was pleased as punch when the charts of who replied to who were published.

  11. OMagain: Attention whore. It’s always been that way. I bet Mung was pleased as punch when the charts of who replied to who were published.

    Every group needs an inside joke.

  12. In these statements Eugene Koonin is giving a ringing endorsement to population genetics. And to common ancestry.

    So he doesn’t think that evolution occurred? Hard for me to see that in these statements.

  13. From Amazon.com:

    The Logic of Chance offers a reappraisal and a new synthesis of theories, concepts, and hypotheses on the key aspects of the evolution of life on earth in light of comparative genomics and systems biology. The author presents many specific examples from systems and comparative genomic analysis to begin to build a new, much more detailed, complex, and realistic picture of evolution. The book examines a broad range of topics in evolutionary biology including the inadequacy of natural selection and adaptation as the only or even the main mode of evolution; the key role of horizontal gene transfer in evolution and the consequent overhaul of the Tree of Life concept; the central, underappreciated evolutionary importance of viruses; the origin of eukaryotes as a result of endosymbiosis; the concomitant origin of cells and viruses on the primordial earth; universal dependences between genomic and molecular-phenomic variables; and the evolving landscape of constraints that shape the evolution of genomes and molecular phenomes.

    See, Frankie, I know where to look for the new theory of evolution.

  14. Joe Felsenstein: So he doesn’t think that evolution occurred? Hard for me to see that in these statements.

    I did not say and I would never say that Koonin doesn’t think evolution occurred. I do however think it’s worth noting that someone might think that was the intended point of the OP.

    For the record, again, I think evolution occurred and I accept common ancestry.

  15. Is that the meaning of ‘evolution skeptic”? Someone who denies that evolution occurred? I guess I’m not an evolution skeptic then.

  16. Mung,

    For the record, again, I think evolution occurred and I accept common ancestry.

    I have generally accepted common ancestry too.

    One problem is that cells appear designed to minimize variation both with the DNA repair mechanism and apoptosis.

    It’s not clear to me how speciation occurs based on these mechanisms that are restricting variation. Then we get two species to mate like a donkey and a horse but the mule offspring is sterile.

  17. colewd: I have generally accepted common ancestry too.

    Well, I believe evolution has magical powers and so can overcome such difficulties.

    🙂

  18. colewd: I have generally accepted common ancestry too.

    No you haven’t. You have argued against it and have suggested that the preponderance of evidence is against it on several occasions. You may recall that you have demanded evidence of common descent many times, and have rejected or ignored that evidence each time.

    One problem is that cells appear designed to minimize variation both with the DNA repair mechanism and apoptosis.

    It’s not clear to me how speciation occurs based on these mechanisms that are restricting variation. Then we get two species to mate like a donkey and a horse but the mule offspring is sterile.

    Cells are not designed to minimize variation. DNA repair reduces the mutation rate, but that mutation rate is still high enough for the human population (for example) to experience every possible point mutation in every generation. Apoptosis has nothing at all to do with minimizing variation and nothing to do with speciation. And your comment about mules seems a non sequitur too.

    It may be unclear to you how speciation occurs, but that’s just you. Again, I suggest you read Speciation by Coyne & Orr before interpreting your ignorance as everyone’s ignorance. To simplify: mutations happen at a rate sufficient to cause divergence between geographically isolated populations in thousands of generations purely by drift, and more quickly if acted upon by selection, sufficient to result in reproductive incompatibility between those populations.

  19. I guess we need a clearer idea of what’s meant by “evolution skeptic.” Seems clear to me that evolution happens, that common ancestry is by now a slam dunk, and that perhaps most of the mechanisms (considered in isolation) have been identified if not perfectly quantified. If an “evolution skeptic” is anyone who suspects that our understanding of the process of evolution isn’t complete and perfect, then we are all evolution skeptics. No scientific theory CAN ever be complete and perfect, everything is subject to improvement.

    So what, exactly, is the difference between one who accepts (albeit tentatively) our best current understanding, and an “evolution skeptic”? Near as I can tell, in the context of most of these discussions anyway, an “evolution skeptic” is someone who rejects the notion that evolution happens, and has always happened, without any diddling by some supernatural agency. The skeptic, as we know him, is absolutely positive, not skeptical at all that his god is involved in the process somehow. Conversely, the non-skeptic “has no need of that hypothesis.”

  20. Flint: that common ancestry is by now a slam dunk

    Far from it as no one can account for the anatomical and physiological differences between two allegedly related species like chimps and humans. The “science” behind common ancestry is on the level of astrology

  21. Rumraket: Maybe you should actually read the interview?

    Probably. 🙂 Thanks for the link.

    Eugene Koonin: First of all, I think the public may not have much to lose in terms of confidence in the scientific establishment in this case because the public is already extremely skeptical about the value and the scientific nature of evolutionary biology. It’s not quite that way about science in general but I think largely so when it comes to the study of evolution. Much of the public is poorly informed about it, poorly understands it and is highly skeptical for various reasons. So I would frame the discussion a little differently, in the sense that evolutionary science may not be doing the best possible job to convince the public of the true importance of evolutionary biology. That said, I do believe that a coherent understanding of “how it works” is slowly but steadily emerging in evolutionary biology. However, one has to face the facts: first, it is a slow process, and we are still far from the goal; second, the emerging picture is highly complex and, furthermore, makes little sense without mathematical theory. Thus, communicating modern evolutionary biology (as opposed to deceptively simple antiquated ideas) is indeed a daunting task.

    So Frankie, and Bill, and I (and others) come here to get educated and to find out “how it works.” Perhaps we should be more tolerant to those who just take it on faith when they can’t explain it to us, because “communicating modern evolutionary biology (as opposed to deceptively simple antiquated ideas) is indeed a daunting task.”

    But then perhaps those who are “in the know” could be a bit more tolerant of us for pointing out the “antiquated ideas” that continue to riddle discussions about evolution at this site.

  22. Mung: I don’t see here any sort of retraction of what he said earlier. Do you?

    Eugene Koonin: Such confusion makes one wish, at least for a moment, they never made such general statements aimed at a mass audience, yet I think such generalizations are necessary. There isn’t really much change in my thinking. There isn’t any dramatic change let alone a turn-around in my thinking.

    So that ought to settle that.

  23. Koonin thinks the chance hypothesis ought to be the null. Now this is funny, in light of all the crap that creationists have taken through the years for allegedly claiming that evolution is chance-based and random.

    So if evolution is not “a tornado in a junkyard,” what is it, rust in a junk yard?

  24. In the OP, Mung asks:

    I’m still struggling to incorporate Alan Fox’s allegation that I am an evolution skeptic.

    I didn’t and don’t allege you are an evolution skeptic. I don’t know if you are an evolution skeptic. That’s for you to say. I merely mentioned your name when looking for responses in an OP

    I still don’t really know what it means to be an evolution skeptic.

    That, in my view, would be someone not convinced that there is a process, usually summarized as RM + NS, that has resulted in descent with modification producing the diversity of life on Earth that we see.

    Eugene Koonin rather obviously rejects the view of evolution held by Alan Fox. Is Eugene Koonin an evolution skeptic?

    My comprehension of the over-arching theory may be flawed and is certainly not complete. If Mung has any doubts about what Dr Koonin’s current views are, he could always ask him. Here is a link to his email.

  25. Mung: So if evolution is not “a tornado in a junkyard,” what is it, rust in a junk yard?

    Is a tornado the result of intelligent design, or is a tornado the result of a tornado in a junkyard.

    And if the tornado is a result of a tornado in a junkyard, where did the first tornado come from. Or is it turtles tornadoes in junkyards all the way down.

  26. Flint: Near as I can tell, in the context of most of these discussions anyway, an “evolution skeptic” is someone who rejects the notion that evolution happens, and has always happened, without any diddling by some supernatural agency.

    Instead of calling us “evolution skeptics” wouldn’t it be better to call yourselves “supernatural diddling” skeptics ?

    That would seem to be a better way forward. There are lots of ways a supernatural agent can “diddle” that are consistent with evolution

    peace

  27. I would thumbnail an evolution skeptic as someone who has need of that hypothesis.

    A mainstream evilutionist is someone who expects knowledge gaps to be filled by regular processes.

  28. petrushka: A mainstream evilutionist is someone who expects knowledge gaps to be filled by regular processes.

    By regular you mean non-mental, correct?

    peace

  29. Alan Fox,

    My comprehension of the over-arching theory may be flawed and is certainly not complete. If Mung has any doubts about what Dr Koonin’s current views are, he could always ask him. Here is a link to his email.

    6 months ago I was in complete agreement with this position. Evolution was real science and we just had not discovered the mechanism. I read James Shapiro’s evolution of the 21st century and then corresponded with him over some ideas I had come up with i.e. the spliceosome is a mechanism of evolution. Since you could change sequences with alternative splicing it was much easier to get a new animal vs wholesale genome changes. This was not the ultimate mechanism but there were several papers that supported that between reptiles, mammals, primates and man the alternative splicing frequency went up. This paper summarizes the findings.

    The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

    Science
    http://www.sciencemag.org
    Science 21 December 2012:
    Vol. 338 no. 6114 pp. 1587-1593 DOI: 10.1126/science.1230612

    Over the last 6-12 months doing research on the cell cycle for a study on vitamin D levels correlation with colorectal and other cancers I started to become skeptical of the overall theory. Vitamin D was implicated in controlling the cell cycle, DNA repair and apoptosis. So the cell is designed to minimize variation by either repairing DNA or killing itself (apoptosis) when the DNA cannot be repaired.

    These cellular mechanisms fly in the face of evolutionary theory that requires variation.

    The mechanism has to have forward engineering capability as Shapiro has been advocating but is their evidence of this? I am now very skeptical that there is a materialist explanation for how new animal types are formed.

  30. colewd: I am now very skeptical that there is a materialist explanation for how new animal types are formed.

    Is there a non-materialist explanation for how new animal types are formed?

  31. Alan Fox: That, in my view, would be someone not convinced that there is a process, usually summarized as RM + NS, that has resulted in descent with modification producing the diversity of life on Earth that we see.

    Who is convinced by that untestable concept? And seeing that NS includes RM isn’t “RM + NS” unnecessarily redundant? (and yes I know many people do it, just as many people say “PIN number” and “ATM machine”) The point being it should be NS + drift or just blind and mindless processes,

  32. colewd: 6 months ago I was in complete agreement with this position.

    Explain the psychological contortions you go through to give yourself permission to lie in this fashion. I couldn’t do it, so when I see it so obvious I find it perplexing.

    What the fuck is wrong with you?

    Trying to save souls from hell, is that it?

  33. Rumraket: Explain the psychological contortions you go through to give yourself permission to lie in this fashion. I couldn’t do it, so when I see it so obvious I find it perplexing.

    What the fuck is wrong with you?

    Trying to save souls from hell, is that it?

    He doesn’t even know when he “gave up” evolutionary theory. Here he is almost a year ago:

    I think you are missing the point. If evolutionary biology abandons the scientific method as a standard and uses inference as a standard then ID as it is currently described as evidence that more likely infers an intelligent cause is fair game. Who the designer is does not need to be described. The debating trick has been to ask about the designer but the inference standard does not require this and therefor asking who is the designer amounts to creating a straw man. The inference standard makes ID as it stands scientific. Methodological naturalism no longer matters. I personally prefer sticking to the scientific method but evolutionary biologists do not want this because evolution is not a legitimate theory under this standard. It becomes an untested hypothesis.

    Feb. 20, 2016, UD

    Aside from the mindless prattle written there, apparently he can’t keep track of time.

    Needless to say, I don’t really buy into his “I once was an evolutionist” shtik. If he were, clearly he didn’t understand it or how science operates (look at the BS about inference in that comment), and at most assented to it. But I don’t know if that’s true, either, as he’s so entrenched in the usual inability to understand science seen in creationists that it’s hard to believe that he’s ever not been creationist. Certainly one who never grasped science, anyhow.

    Glen Davidson

  34. OMagain: Is there a non-materialist explanation for how new animal types are formed?

    Yes, the mechanism of poofing. And we now know enough about evolution to know that this is how evolution works and we also now know that materialists are fine with it.

  35. Rumraket: Trying to save souls from hell, is that it?

    🙂

    I think TSZ is hell. If I can get someone to leave then I have saved them from hell.

  36. Neil Rickert: You are free to leave at any time.

    Haven’t you heard that Jesus went and preached to the souls in hell? Just carrying on the tradition Neil. 🙂

  37. The genomic revolution did more than simply allow credible reconstruction of the gene sets of ancestral life forms. Much more dramatically, it effectively overturned the central metaphor of evolutionary biology (and, arguably, of all biology), the Tree of Life (TOL), by showing that evolutionary trajectories of individual genes are irreconcilably different. Whether the TOL can or should be salvaged – and, if so, in what form – remains a matter of intense debate that is one of the important themes of this book.

    – Eugene V. Koonin. The Logic of Chance. p. viii

    Alan Fox: If Mung has any doubts about what Dr Koonin’s current views are, he could always ask him. Here is a link to his email.

    I should bother the man because some “skeptics” on an internet blog question whether he actually meant what he said in some book or paper? I’m trying to imagine what my initial email to him might look like.

  38. Koonin:

    Uprooting the TOL is part of what I consider to be a “meta-revolution,” a major change in the entire conceptual framework of biology.

    And:

    Our unfaltering admiration for Darwin notwithstanding, we must relegate the Victorian worldview (including its refurbished versions that flourished in the twentieth century) to the venerable museum halls where it belongs, and explore the consequences of the paradigm shift.

    Koonin also writes of “…the overhaul of evolutionary biology…”

    Now to me it seems that IDists are leading the way in trying to bring attention to this “paradigm shift” while the old school Darwinists and their materialist friends are trying desperately to keep it all a secret or denying that it even exists.

    If the evolutionists here don’t want to be relegated to the venerable museum halls along with the dinosaurs, they should join with us in exploring this exciting new science.

  39. …our understanding of evolution – and, with it, the very nature of biology – have forever departed from the prevailing views of the twentieth century that today look both rather naive and somewhat dogmatic.

    – p. x

    Now please don’t blame me for pointing out when people here cling to the naive dogmatism of the past. That doesn’t make me an evolution skeptic or anti-science.

  40. colewd, to John Harshman:

    Do you understand the concept of variation?

    Oh, the frikkin’ irony.

  41. Mung citing Koonin:

    Mung:…evolutionary trajectories of individual genes are irreconcilably different.

    This comes up in Nick Lane’s book that I’m currently reading. Horizontal gene transfer would be expected to show different paths for different genes. This is what the evidence shows. We’re off out for a walk now but I’ll look up the reference when I have more time.

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