About Rationally Speaking

Rationally Speaking is a blog maintained by Prof. Massimo Pigliucci, a philosopher at the City University of New York. The blog reflects the Enlightenment figure Marquis de Condorcet's idea of what a public intellectual (yes, we know, that's such a bad word) ought to be: someone who devotes himself to "the tracking down of prejudices in the hiding places where priests, the schools, the government, and all long-established institutions had gathered and protected them." You're welcome. Please notice that the contents of this blog can be reprinted under the standard Creative Commons license.

Tuesday, February 17, 2009

Jerry Coyne and the Extended evolutionary Synthesis

I guess it was only a matter of time before my colleague Jerry Coyne at the University of Chicago lost his patience while reading one of several pieces that appeared in the press about the current and future status of evolutionary theory. After having commented negatively, in both Nature and Science, on a workshop on evolutionary theory that I organized last summer at Altenberg (Austria), Jerry has just published a blog post in which he criticizes highly respected science journalist Carl Zimmer. Zimmer’s sin is to have favorably quoted yours truly about the excitement generated by increasingly common discussions about updating the Modern Synthesis -- the current conceptual structure of evolutionary biology, dating back to the 1940s -- to what some of us have begun calling an Extended Synthesis.

Jerry praises Zimmer’s overall essay on Darwin in Time magazine, but he adds that his enjoyment was spoiled because “Zimmer seems to buy into something he calls the ‘extended evolutionary synthesis.’” I think Coyne is being a bit disingenuous here, writing as if he had never heard before of an extended synthesis and attributing the term to Zimmer. But he goes on to say: “It seems to me that a science journalist should do more than simply tell their readers that something new is in the air: a journalist should EVALUATE these new claims. If all one did was say ‘some evolutionists think ...’ and then describe their thoughts, any old claim could get press.”

Right, and I have amply criticized “journalists” who not only uncritically report competing claims but even make up stuff out of their fertile imaginations, like Suzan Mazur has most outrageously done with her inane “Scoop” series. However, talk of an Extended Synthesis isn’t “any old claim,” it is a serious discussion among credentialed scientists. Coyne, of course, most certainly has the right to disagree with his colleagues, but that doesn’t mean that the topic is not a respectable object of coverage by a professional journalist. (It is true that another skeptic of the necessity of updating the Modern Synthesis, Indiana University’s Michael Lynch, has actually compared -- in print in the prestigious Proceedings of the National Academy of Sciences -- proponents of some new ideas in evolutionary biology to supporters of intelligent design creationism, but I think Jerry Coyne both knows better and has more style in his writings.)

Jerry rightly says that “It just isn’t true to say that every aspect of the Modern Synthesis is fiercely debated,” a claim he attributes to Zimmer in the Time article. Except that Zimmer was clearly writing about the extended synthesis claims, which are, in fact being fiercely debated, as Coyne’s own writings surely attest. At any rate, as Ryan Gregory (over at Genomicron) correctly states in his commentary on Coyne’s piece, “The point is that many people feel that we need to have a conversation about how well the Modern Synthesis covers [a variety of] phenomena, adding that “An extended synthesis would not involve an overthrow of current theory (hence, "extended").”

Coyne then brings up the poor old ghost of Richard Goldschmidt, the geneticist who famously criticized the Modern Synthesis while it was happening, in the 1940s. Goldschmidt, as it turns out, was wrong in his proposed solution to the problem (“hopeful monsters” and such), but he had identified a problem -- the incompleteness of the synthesis in terms of developmental biology and macroevolution -- that has characterized, on and off, evolutionary biology’s discourse ever since.

Jerry’s post continues with a list of issues he thinks are overblown: he says that nobody claimed that natural selection can completely explain species diversity (true, but my original point was that some macroevolutionary patterns are difficult to account for by simple micro-evolutionary extrapolation, as demonstrated in a series of papers by David Jablonski, also at the University of Chicago); he states that gene swapping isn’t important, especially in vertebrates (nobody claimed it is, in that group, but people are seriously reconsidering the whole idea of a “tree of life” as a result of what appears to be extensive gene swapping among today’s non-eukaryotes and early on in the history of life); and he asserts that nobody suggested that gene networks get rewired by any means other than natural selection (actually, Lynch himself has argued that a lot of genomic-level changes are not due to selection, and at any rate my original point was that network-level properties are making simple population genetic models increasingly inadequate as a full description of evolutionary change).

Jerry is “irritated” by what he calls “BIS–the Big Idea Syndrome,” where any new idea that comes about, be it modularity, evolvability, evolutionary capacitors, epigenetic inheritance, phenotypic plasticity, genetic accommodation, species selection, cis-regulatory evolution, and so on and so forth, “becomes the centerpiece of a claim that modern evolutionary theory is ripe for a revolution.” Again, nobody I know is calling for a revolution, but the above mentioned ideas and empirical evidence cannot simply be filed away as “more of the same.” Gregory’s post referred to above lists 16 new, broad empirical findings that occurred after the formulation of the Modern Synthesis, a very partial list indeed. Are these all simply variations on a theme established at the onset of the 20th century? At some point Coyne, Lynch and others need to do a bit more than just shak their heads and play armchair curmudgeon (Jerry’s word). They need to address the hundreds of papers and dozen or more books, written by a good number of respected colleagues, that have detailed why the Modern Synthesis needs updating and what this update is beginning to look like.

None of this, of course should give any comfort to creationists and their ilk (though I can’t wait to see the inane posts that will surely result from this exchange between Jerry and me!), because incompleteness and tentativeness are inherent features of scientific theories in all branches of science. Physicists have been discussing how to reconcile relativity and quantum mechanics for decades, and they still don’t know what their next standard model will look like. This doesn’t mean that physics is dead; on the contrary, it is a tribute to the vitality of the scientific enterprise and to the people who passionately devote themselves to it. Jerry and I are probably wrong on some of the details of what we are saying. Time will probably show that he is much too conservative and I am much too liberal about what is needed in evolutionary theory and where it’s going to come from. But it is precisely this continuous dialectic within the scientific community that makes for eventual progress. Welcome to the excitement of science!

A brief (and certainly incomplete) guide to the literature advocating an extended evolutionary synthesis and/or making specific proposals for it:

Carroll SB (2008) EvoDevo and an Expanding Evolutionary Synthesis: a genetic theory of morphological evolution. Cell 134: 25-36.

Colegrave N and Collins S (2008) Experimental evolution and evolvability. Heredity 100: 464-470.

Gould SJ (2002) The Structure of Evolutionary Theory. Cambridge MA, Harvard University Press.

Hansen TF (2006) The evolution of genetic architecture. Annual Review of Ecology and Systematics 37: 123-157.

Hendrikse JLT, Parsons E and Hallgrimsson B (2007). Evolvability as the proper focus of evolutionary developmental biology. Evolution & Development 9(4): 393-401.

Jablonka E, Lamb MJ (1995) Epigenetic Inheritance and Evolution. Oxford: Oxford University Press.

Kirschner M, Gerhart J (2005) The plausibility of life: resolving Darwin's dilemma. New Haven: Yale University Press.

Kutschera U, Niklas KJ (2004) The modern theory of biological evolution: an expanded synthesis. Naturwissenschaften 91:255 – 276.

Love AC (2006) Evolutionary morphology and EvoDevo: hierarchy and novelty. Theory in Biosciences 124: 317-333.

Müller GB (2007) EvoDevo: extending the evolutionary synthesis. Nature Reviews Genetics 8: 943-949.

Müller GB, Newman SA eds. (2003) Origination of Organismal Form. Cambridge MA: MIT Press.

Odling-Smee FJ, Laland KN and Feldman MW (2003) Comments on Niche Construction: The Neglected Process in Evolution. Princeton, Princeton University Press.

Pigliucci M (2007) Do we need an extended evolutionary synthesis? Evolution 61(12): 2743-2749.

Pigliucci M (2008) Is evolvability evolvable? Nature Reviews Genetics 9: 75-82.

Robert JS (2004) Embryology, Epigenesis, and Evolution: Taking Development Seriously. Cambridge, England, Cambridge University Press.

Rose MR, Oakley TH (2007) The new biology: Beyond the Modern Synthesis. Biol Direct 2:30.

Sansom R, Brandon RN eds. (2007) Integrating Evolution and Development: From theory to practice. Cambridge: MIT Press.

Wagner A (2005) Robustness and Evolvability in Living Systems. Princeton, NJ, Princeton University Press.

Wagner GP and Altenberg L (1996) Complex adaptations and the evolution of evolvability. Evolution 50: 967-976.

West-Eberhard MJ (2003) Developmental Plasticity and Evolution. Oxford, England, Oxford University Press.


  1. A couple more:

    Carroll, R. L. 2000 Towards a new evolutionary synthesis. Trends in Ecology and Evolution 15, 27-32.

    Gregory, T. R. 2005 Macroevolution and the genome. In The Evolution of the Genome (ed. T. R. Gregory), pp. 679-729. San Diego: Elsevier.

    Johnson, N. A. & Porter, A. H. 2001 Toward a new synthesis: population genetics and evolutionary developmental biology. Genetica 112, 45-58.

  2. Having read about a quarter of Plausibility of Life, the main idea is that the source of variation of phenotype is an under explored area. This type of stuff can definitely be ADDED to the Modern Synthesis.

  3. Having read one quarter of one book on a list of 20 sources, I can conclude...

    Sorry, that struck me as rather humourous.

  4. I really like this blog. It is full of resources with links to them, and some really nice people comment on here.

    I am a theist and I believe the Bible is God's Word. So I don't believe in evolution. But it is good for me to see what people have to say about it instead of staying in my corner with my christian buddies, you follow me?

    I am not a learned guy and I do not follow a lot of what you wrote on here but there is a link below that talks about our DNA determining our behavior. It proves that the evolutionary theory is wrong even logically speaking.


  5. As a scientist working a fair fraction of those
    phenomena you group into an extended evolutionary synthesis, I often feel we have quite enough reviews and philosophical pieces published on the subject already, and your list is heavy on those. The ratio with primary research articles is all wrong. We need to buckle down to the job of answering these questions, not simply wringing our hands about how important it all is. It's not enough to need an extended evolutionary synthesis, but the quest for one has to inspire good primary research. Those reviews we need most should focus on techniques, tools, methodologies, model systems etc that point the way to productive research progrems. After the science is in place, any trends will be perfectly obviously retrospectively.

    I would love to see another list that is restricted to primary research that is most relevant to the extended evolutionary synthesis.

  6. Joanna, that is pretty funny coming from someone who has been working on pretty conceptual pieces of research, such as simulation models of the evolution of capacitors. Or did I get the wrong Joanna Masel?

    At any rate, if you look at that list of "philosophical pieces" they are in fact full of references to empirical research pertinent to an Extended Synthesis. By the way, do you consider the books that made the Modern Synthesis just "philosophical" too (which I take to be a dismissive in this context)?

  7. I'm not dismissive of philosophy, I just think the current ratio is way out of balance. And some of the empirical research cited can be analyzed in other ways too: I'm asking for core empirical work with clear results either whose motivation relied in an essential way on these ideas, or whose results had clear and nonobvious implications for these ideas. And as you know, books played a rather different role in science in the first half of the 20th century than they do now, so that is not a fair comparison.

    In fact, we could break down the analysis further

    - speculation about where the field will go in the future
    - reviews of where we stand now, possible containing some philosophical analysis of our current state
    - analytical or theory work (including mine), also conceptually driven but trying to pin down data-driven constraints of specific systems in the models too, and hopefully refining hypotheses in the process
    - empirically testing hypotheses

    I think the current ratio at all levels is wrong, tilted towards too much at the top at every comparison in the list above. I have published only one paper in the bottom category so far (although I have more in preparation), and so am guilty too, but I am at least attempting to move towards more balance in this list. And I do believe that historically, the second last category was more important than the two above it in formulating the original evolutionary synthesis, so I offer that in partial defense.

  8. Joanna,

    again, those dozens of review papers and books do review something, and that something isn't just each other, it's primary literature. Take, just as an example, Jablonka and Raz's forthcoming review on epigenetic inheritance in the Quarterly Review of Biology (mentioned in the NYT: http://www.nytimes.com/2008/11/11/science/11gene.html?pagewanted=all). At my request as the managing editor for the manuscript, it includes a table listing a whopping 101 empirical papers addressing the topic.

    Or consider the history of research on phenotypic plasticity: the explosion of empirical papers in the 90s happened after the publication of several influential reviews that pointed out the conceptual importance of the phenomenon, as well as the scarcity of empirical papers then available. If people don't think it's important, they won't do it.

    Finally, I doubt that scientists don't read books anymore. I know the climate is different from the 1940s, but I keep having to turn down publishers who ask me to write new books, and journals who ask me to review them. Who the hell is reading all this stuff?

  9. OK, I accept that both epigenetic inheritance and phenotypic plasticity are phenomena that now have an adequate primary empirical literature.

    My comments on an unbalanced ratio refer primarily to genetic assimilation/accommodation and evolvability.

    As for the books, publishers don't care who reads them, as long as they buy them...I think there are a lot of unopened books sitting on shelves. Book reviews, on the other hand, still get read, and may even get people to buy (if not read) the books. Or to feel better about not reading them.

  10. One of my profs used to ask if I was "familiar" with a book.

    His translation of familiar: read the introduction and conclusion, skim the rest.

    Well, at least he didn't say Get your students to read it.

  11. I surely can't say anything about many of the subjects approached by the list of references (thanks a lot for that, I'll try to read it).

    But I felt exactly like Joanna describes after I finished reading "The Plausibility of Life". I have to read it again sometime to try and see if I missed something. I liked the book, for sure, everything makes good sense, great ideas and all that. But I was disappointed that they did not give any "real hard results" of the wonderful new paradigm that (some) people so ardently say is the only way to go, while "wringing our hands about how important it all is" (as Joanna puts it) was mostly what it was. I understand it is supposed to be a "review" type of book, and not primary research, but some detail would be nice anyway. If Sean Carroll can do it very well in his incredibly layperson-accessible books, why not? As I said before, I'll read it again to see if there is something hidden there that I missed the first time, maybe I wasn't paying too much attention.

    Would this (the subject of "Plausibility...") be biology's string theory? I myself actually feel we are still waiting for the techniques and analytical methods that will allow us to really see into the systems biology data and do the wonderful things Kirshner and Gerhart describe. Which is a very hard thing to do. We are still fighting with microarray data...

  12. I would like to read more widely. Of the references you've listed above, which one would should I read first? What is the best compendium of examples and concepts that should be in an EES? Thanks!

  13. Emily,

    hmm, tough question. My Evolution paper is a brief account that has most of the elements in place, and is accessible: Pigliucci M (2007) Do we need an extended evolutionary synthesis? Evolution 61(12): 2743-2749.

    The book on the plausibility of life (Kirschner M, Gerhart J (2005) The plausibility of life: resolving Darwin's dilemma. New Haven: Yale University Press) deals with one aspect of it, but manages to paint a broad picture. A more technical version of that is in Müller GB, Newman SA eds. (2003) Origination of Organismal Form. Cambridge MA: MIT Press.

    Finally, next year MIT Press will publish the proceedings of the Altenberg meeting, which I think will then be the most comprehensive (though still partial) presentation of the Extended Synthesis yet.

  14. Hi Massimo,
    I have read most of the papers in the recommended reading list advocating an EES but I am having trouble finding philosophical papers arguing directly against an EES. What papers would you recommend on that front?

  15. Rachel,

    good question. I don't know of philosophical papers arguing against an ES, though there is a range of opinions about the role and meaning of population genetic theory among philosophers (see, for instance, the works by Roberta Millstein vs the stuff that Jonathan Kaplan and I have written).

  16. Thanks Massimo,

    I also found today a nice dialogue between Dawkins and Laland and Jablonka on the extended phenotype in B&P Volume 19, Number 3 / June, 2004 in which Dawkins directly addresses some of the motivations for an EES.


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