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