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    Jerry Coyne Vs. John Dupré On The Status Of Evolutionary Theory
    By Massimo Pigliucci | October 1st 2012 05:00 PM | 10 comments | Print | E-mail | Track Comments
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    Massimo Pigliucci is Professor of Philosophy at the City University of New York.

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    I read two interesting commentaries on evolutionary theory recently. One was by philosopher John Dupré, the other by evolutionary biologist Jerry Coyne. Actually, the latter was a commentary on the former, and it had a typical Coyne-style title (“Another philosopher proclaims a nonexistent ‘crisis’ in evolutionary biology”). I know both Jerry and John, and I respect them as scholars in their respective fields. As a biology-philosopher crossover myself, I also appreciate (no matter how often I may disagree on the specifics, particularly with Jerry) their respective forays into each other’s field.

    It is this kind of interdisciplinary cross-talk that makes the life of the intellect particularly exciting for me, and which has the potential to generate further understanding, both within academia and the public at large.

    In this case, I have to say that both Jerry and John are (partially) wrong, though for different reasons. Perhaps an analysis of these reasons will shed some light on the actual current status of evolutionary theory, as well as on the always treacherous relationship between philosophy and science.

    Jerry begins his commentary with the usual fiery words I have come to expect from him: “We often see molecular biologists (e.g., James Shapiro) and philosophers (e.g., Thomas Nagel and Jerry Fodor) proclaiming the imminent death of modern evolutionary theory, so someone who wears both hats could be especially muddled — and dangerously misleading. And my suspicions were correct.” I have been critical of Fodor myself, and I dread seeing Nagel’s forthcoming book for similar reasons. Moreover, I do share Jerry’s rejection of Shapiro’s ideas about evolution. But John has always struck me as a reasonable fellow with interesting things to say, so I was a bit weary of Jerry’s quick dismissal of his piece.

    As it turns out, Jerry had a point in chastising John: contra the latter, there is no “crisis” in evolutionary theory. However, most of Dupré’s essay is much more nuanced than it would appear from Jerry’s selective quotations, and it is nowhere near the nonsense that Jerry Fodor and Massimo Piattelli-Palmarini have recently written about evolution.

    Indeed, much of John’s commentary uses rather mild language. While Dupré does mention Thomas Khun’s concept of paradigm change in science, he explicitly says that the new developments in evolutionary biology do not constitute a revolution, but rather a “major, progressive reorganization of existing knowledge, without undermining the fundamental tenets of evolutionary theory.” Dupré ends the article by stating that “Evolutionary theory’s current contretemps — and our inability to predict where the field will be in 50 years — are a cause for celebration,” because they show that science changes through better understanding and new empirical discoveries, a dynamism that he explicitly contrasts with the fossilized attitudes of creationists and intelligent design proponents.

    Seen from Coyne’s perspective, though, Dupré’s essays goes too far and needs to be taken to task. Jerry states that “What bothers me is that, like so many others, [Dupré] casts these new discoveries as things that throw the theory of evolution in crisis. And that plays into the hands of creationists, no matter how strongly Dupré decries creationism.” Ironically, John had foreseen such a move, and had written in his own essay: “Radically rethinking evolutionary theory invariably attracts the attention of creationists, who gleefully announce that if professional advocates of Darwinism cannot agree, the concept must be in retreat. And, evolutionists, confronted with this response, tend to circle the wagons and insist that everyone is in agreement.” The only thing I find objectionable about that excerpt is that the appropriate word is “significantly,” not “radically.”

    So what is going on here? Setting aside John’s a bit overhyped talk of crisis, as well as Jerry’s unnecessarily sharp defense of the purity of evolutionary theory, where is the meat of the disagreement? Dupré lists a number of new discoveries and accompanying conceptual advances that — he claims — are bringing about a rethinking of the Modern Synthesis (often incorrectly labelled “neo-Darwinism”) of the 1930s and ‘40s, which constitutes the equivalent of the Standard Model in evolutionary biology. These include:

    * The rejection of the idea that life’s evolution is best represented as a branching tree, because horizontal gene transfer, especially early on, and particularly among prokaryotes (not to mention frequent speciation by hybridization in plants), is better visualized as yielding a network of genetic relatedness among organisms.

    * The discovery that mutation is not the only generator of heritable variation (to be precise, a second one, recombination, had always been in play as well), again because of exchanges of chunks of genomes between organisms, and occasionally even of full genomes, as in the case of the origin of eukaryotic cells by symbiosis of different types if bacteria.

    * The discovery of a complex layer of epigenetic effects that mediate between genes, environment and development in a way that opens up the possibility of causal loops in which genes produce epigenetic factors (such as methylation patterns, iRNAs, etc.), which in turn respond to environmental stressors by altering the expression of other genes. Note that some of these epigenetic effects act across generations, and some show stability over evolutionarily significant lengths of time (as documented here, here and here).

    Nonsense, responds Coyne, deploying two well worn strategies of conservative scientists (I don’t mean the term politically here, of course): minimization and absorption of novelty. For instance:

    “Yes, we’ve known for a while that microbes can have ‘wide gene exchange‘ — movement of chunks of DNA between distantly related species of bacteria. ... This hasn’t really changed the theory of evolution one iota, though it’s changed our view of where organisms can acquire new genes.” (Well, it depends on what Jerry means by “the theory of evolution,” and on just how much change would count — in his view — for more than “one iota.”)

    [Concerning the role of horizontal gene transfer and symbiosis] “This is true, but what Dupré doesn’t mention — and I hope he knows better, because he should if he’s learned anything about evolution — is that these big events of symbiosis that produced mitochondria, chloroplasts, and perhaps flagella, are extremely rare, and we’ve known that for a few decades.” (Besides the unnecessarily patronizing tone toward Dupré, is Coyne saying that rare events are unimportant? It is likely because of the very long term effects of a rare event — an asteroid impact — that a primate rather than a dinosaur is writing this blog, and “extremely rare” endosymbiosis has created cells with nuclei, which have made multicellularity possible, which in turn has changed the course of evolution in countless and dramatic ways. Jerry here is confusing infrequent with unimportant. Imagine a physicist telling his readers that the Big Bang wasn’t a crucial part of physics’ view of the cosmos, because after all it only happened once!)

    “Other kinds of epigenetic change that are produced solely by the environment and not by the genome itself, such as changes in weight or flower color, are not stable because the DNA reverts to earlier forms. Hence such changes do not last more than a few generations, and so cannot be the basis of permanent evolutionary change.” (This is incorrect, as we do have examples of long term heritability of epigenetic changes — see links above — and besides, I thought evolution took place generation by generation, which means that any heritable change, no matter how short lived, has the potential to alter the evolutionary trajectory of a population, however indirectly.)

    And of course Jerry just has to include a veiled ad hominem in his attack on Dupré: “Dupré doesn’t seem to be a goddie, but he still seems susceptible to the nebulous woo of ‘top down causation.’” No, Dupré isn’t a “goddie,” whatever that may be, and his causal talk is perfectly understandable: all he means is that the arrows of causality in evolution, genetics and development go in all sorts of directions, not just from the genes upward: genes produce proteins which help building cells, but environmental signals often cause genes to be transcribed or silenced, development is the result of epigenetically mediated interactions between genes and environments, and of course — as Jerry himself states, natural selection is the mother of top down causal processes in biology.

    As it turns out, Dupré has — I think — not gone far enough, leaving out a number of other crucial points that would have strengthened his case and undermined Coyne’s response. The decades since the Modern Synthesis (MS) have seen also the rise to prominence in evolutionary biology of phenotypic plasticity, a ubiquitous phenomenon that helps understand how gene-environment interactions affect population dynamics and that was dismissed as noise by early supporters of the MS. Moreover, contra the received wisdom, multi-level selection (including group and even species selection or sorting) are here to stay, greatly enriching the theoretical arsenal of evolutionary biologists beyond the one provided by the MS (which, of course, in turn had greatly enhanced the original Darwinism, which had indeed undergone an actual crisis at the turn of the 20th century). Want more? How about the now well documented phenomenon of “facilitated variation,” which shows how natural selection has apparently to do much less work than previously thought, because a good number of biological structures develop by taking advantage of the physico-chemical properties of cells rather than by direct genetic encoding of countless details? Or the fact that paleontologists have now convincingly shown that macroevolutionary dynamics are not simply reducible to the sort of microevolutionary ones that are the only conceptual arsenal of the MS? Or perhaps Jerry should consider the fantastic empirical and theoretical work on evolvability, robustness and modularity, ideas that are entirely alien to the MS?

    Jerry concludes his critique of John’s essay thusly: “As an evolutionary biologist — which Dupré is not — I think I’d know if my field was in crisis.” No Jerry, plenty of us have been telling you that a change is in the cards (though, again, not a crisis!), you just haven’t been listening.

    First appeared on Rationally Speaking, September 11, 2012 

    Comments

    Hank
    Seen from Coyne’s perspective, though, Dupré’s essays goes too far and needs to be taken to task. Jerry states that “What bothers me is that, like so many others, [Dupré] casts these new discoveries as things that throw the theory of evolution in crisis. And that plays into the hands of creationists, no matter how strongly Dupré decries creationism.” 
    This sort of thinking is always going to be a negative in a science discussion.  We have seen the hijacking of science academia by militants because they declare some science topics, no matter how legitimate, off limits. And then scientists don't discuss them because they don't want the cultural drama. That is not better for anyone and it has bled over into other fields too.

    Saying that you can't talk about evolution or the creationists win is silly.  Evolution is a lot more firmly regarded than string theory but you never hear physicists say 'you can't criticize string theory or X wins'. Biology doesn't need a string theory because evolution works.  Embrace it, love it.
    Gerhard Adam
    I don't think the problem has ever actually been about evolution, but rather the mechanisms of it.  As a result, it is only proper that the more we learn, the more we understand that it is more complex than originally envisioned.  Part of the problem in biology has [and continues to be] physics envy, which is simply the desire to reduce everything down to simple mathematical laws.  Unfortunately this doesn't work particularly well when examining the wide range of organisms one actually has to contend with.

    This is no different that the "controversy" about nature vs nurture.  Anyone that was actually paying attention couldn't possibly believe that the two were separate, and yet somehow there was still the perception of a controversy regarding this.
    Mundus vult decipi
    If you criticize string theory, the terrorists win.

    There, I said it.

    Steve Davis
    "Saying that you can't talk about evolution or the creationists win is silly."
    Exactly, Hank.
    Jerry's problem is that he's stuck in a time warp.
    Or prefers to be.
    He thinks the last word on evolution was written with the publication of The Selfish Gene, and is afraid, albeit unconsciously, that wide discussion will blow that nonsense out of the water.
    Hank
    I don't think Coyne stopped learning in the 1970s.  He wrote a good - maybe great - book on evolution three years ago. I just think evo/devo people are seeing too much through a prism of 'how will it help creationists?', which I think has been a trite concern since 2004, and Coyne does not much like when people with lay knowledge of biology claim to know how wrong things are. 
    Scientific theories are not carved into stone and they may be modified over time as new data comes in.
    News at 11-

    @Steve Davis... are you serious?... that last comment sounds pretty darned ridiculous.

    Steve Davis
    Anonymous bravely said "Steve Davis...are you serious?...that last comment sounds pretty darned ridiculous."
    What's actually ridiculous is Jerry coyne, as late as 2011, defending The Selfish Gene on his blog, from a critique that was considered, insightful and relevant. 
    Now, if you wish to enter that discussion, feel free, I look forward to that.
    "Saying that you can't talk about evolution or the creationists win is silly. "

    That really is the perfect response. Whether something is a "crisis" or just a "challenge" is pure semantics. This absurd fear of creationists has got to stop. The danger of dogmatism is far worse that the danger of "losing" to dogmatists.

    Richard Lewontin has pointed out problems with the gene-centric view of evolution for decades. And the fact that the Human Genome Project yielded zero (to a first approximation) practical medical knowledge could well be designated a crisis, especially if you were a gullible member of the public, or a government grant agency putting money of the line in the hope of genetic wonder-treatments.

    In any case what's the problem with a radical reorganization of biological knowledge? "When the facts change I change my mind."

    Given that biology has virtually no predictive value, some humility is warranted. Or perhaps, the lack of predictive value is precisely why public scientism-supporting intellectuals fight criticism so voiferously -- beneath the rhetoric there is very little to "prove" their ideas beyond nonmathematical restrospective argument.

    Perhaps it's because I studied physics, but wo things always amaze me when I read discussions about evolution theory.

    1) Everybody always seems to want Evolution Theory to be true. Why? In modern physics, after a while - and certainly after 50 yrs - everybody secretly (or openly) hopes a fundamental theory is wrong. The HEP community would love to see observations by the LHC that suggest the Standard Model is wrong. Some people think that it would be a disaster if the SM turned out to be the last word. I can't remember an evolution theorist declaring that it would be a disaster if ET were the last word. Why?

    2) In physics, fundamental theories have an odd way of announcing their own fundamental problems. What is exactly that "action at a distance" in Newton's theory of gravity? Classical mechanics and electromagnetism are superb theories, but they are incompatible. When you combine classical physics with statistical mechanics you get the ultraviolet catastrophe. Why are there so many parameters in the SM? Why U(1) x SU(2) x SU(3), etc. etc. These are more than merely unsolved problems, quite apart from observations they point to fundamental problems with the theories.

    If you would explain the SM to a Martian, he (it?) would probably point out that the theory has an awful lot of undefined parameters, for a fundamental theory, even if he didn't know if the SM fitted the facts or not. If the same Martian would learn about ET, what would he point out?

    Physicists can't stop talking about the problems that are announced by their best theories. But where in the structure of Evolution Theory is that pointer to a fundamental, structural problem that's larger than a merely unsolved question?

    I find these comments here very encouraging. I have felt for over a decade that too many knowlegable scientist have been unduly influenced by the debate with creationists. Evolutionary theory is in flux. Some previous ideas that we all accepted are no longer valid. It does not hurt the scientific enterprise to accept those changes. Unfortunately, some who have debated creationist have painted themselves into a corner insisting that what seemed like reasonable theoretical constructs ten or thirty years ago are less viable today. "Nested hiarchies" is just one. As has been suggested above this moves scientific theory into the realm of orthodoxy.

    For those intersted in seeing a very recent summary of the "Evolutionary implications of Horizontal Gene Transfer" let me refer you to a recent compilation on this topic. If you want to read the paper there is a link at:
    http://www.vme.net/hgt/ and paper 15 provides a path to the paper that avoids the Ann Rev pay wall.

    Full disclosure, this is my review of the subject but I do believe it is a reasonable summary of recent information on this topic.

    This subject does not in any way challenge these major tenents of evolutionary theory. Natural selection remains quite robust. Descent with modification is unchallenged. Common ancestry of homologous genes is not challenged. What does change are the molecular mechanisms evolutionary change. Common ancestors take a big hit (eg LUCA is an illusion). Finally the beloved evolutionary tree to describe organismal descent needs to be completely re-evaluated.

    This might not be a Kuhnian revolution but it has to be considered a major shake up.