Thursday, October 09, 2014

Rethinking evolutionary theory

I believe that Gould was correct when he pronounced the death of the Modern Synthesis [Is the "Modern Synthesis" effectively dead?] [Razib Khan doesn't like Gould and doesn't like new-fangled ideas like "neutralism" and "random genetic drift"] [Die, selfish gene, die!] [Gould on Darwinism and Nonadaptive Change] [Extending the Modern Synthesis at the Molecular Level ].

I agree with Arlin Stoltzfus in his description of the Modern Synthesis [Arlin Stoltzfus explains evolutionary theory]. I agree with him, and with Masatoshi Nei, that mutation and mutationism were downplayed in the Modern Synthesis [The Mutationism Myth, VI: Back to the Future] [Mutation-Driven Evolution]. That's one example of why the old-fashioned Modern Synthesis should be abandoned as a description of modern evolutionary theory.

I agree with Gould that hierarchical theory is valid and evolution might well occur at multiple levels—not just populations. I agree with him that microevolution is not sufficient to explain macroevolution even though this was one of the central tenets of the Modern Symthesis [What Is Evolution? ] [Macroevolution].

I agree with Michael J. Lynch that "Nothing in evolution makes sense except in the light of population genetics." In fact, I pretty much agree with everything that Lynch says about evolution [Michael Lynch on Evo-Devo ] [Michael Lynch on Adaptationism ]. I do not think Lynch's view of evolutionary theory (or Koonin's) is compatible with the Modern Synthesis of Ernst Mayr and Julian Huxley. The Modern Synthesis has been substantially changed by modern population genetics and Neutral Theory so that it's no longer useful to describe modern evolutionary theory as the "Modern Synthesis."

So, if the Modern Synthesis of Mayr and Huxley has been superceded by more "recent" (40 years old) concepts that emphasize Neutral Theory and random genetic drift then why is there still a lively debate over evolutionary theory? I think it's because there are people out there who want to incorporate additional concepts into evolutionary theory and also because there are many scientists who don't fully understand (and/or accept) the concepts that were developed in the late 1960s.

What are some of those other concepts that have been discovered in the past two decades or so?

I disagree with the Altenberg 16 (e.g. Pigliucci, Müller et. al "Evolution: The Extended Syntesis") and their view of extending the Modern Synthesis. I have three main reasons for dismissing their arguments [see What do they mean when they say they want to extend the Modern Synthesis?].
  1. None of their claims about evo-devo, facilitated variation, plasticity, epigenetics, etc. have anything to do with evolutionary theory.
  2. All of their claims focus on only a small subset of the history of life—mostly animals. You can't reform evolutionary theory based on what you've learned about animal development because it doesn't apply to most organism and most of evolution.
  3. Their attacks on the Modern Synthesis are based on the hardened version of fifty years ago. They've missed the real revolution [A New View of Evolution].
That brings me to the point of this post. (Thanks for waiting.) Nature has just published a debate between two groups on the topic "Does evolutionary theory need a rethink?" (Laland et al. 2014).

On the "Yes, Urgently" side are: Kevin Laland, Tobias Uller, Marc Feldman, Kim Sterelny, Gerd B. Müller, Armin Moczek, Eva Jablonka, and John Odling-Sme. Only three of them (Müller, Jablonka, and Odling-Sme) were present at Altenberg but they are arguing the same points [Altenberg 16 controversy][The Altenberg 16 Make It into Nature]. These are the same arguments made in Evolution: The Extended Synthesis.

On the "No, All Is Well" side are: Gregory A. Wray, Hopi E. Hoekstra, Douglas J. Futuyma, Richard E. Lenski, Trudy F. C. Mackay, Dolph Schluter, and Joan E. Strassman. They defend evolutionary theory like this ...
A profound shift in evolutionary thinking began during the 1920s, when a handful of statisticians and geneticists began quietly laying the foundations for a dramatic transformation. Their work between 1936 and 1947 culminated in the ‘modern synthesis’, which united Darwin’s concept of natural selection with the nascent field of genetics and, to a lesser extent, palaeontology and systematics. Most importantly, it laid the theoretical foundations for a quantitative and rigorous understanding of adaptation and speciation, two of the most fundamental evolutionary processes.

In the decades since, generations of evolutionary biologists have modified, corrected and extended the framework of the modern synthesis in countless ways. Like Darwin, they have drawn heavily from other fields. When molecular biologists identified DNA as the material basis for heredity and trait variation, for instance, their discoveries catalysed fundamental extensions to evolutionary theory. For example, the realization that many genetic changes have no fitness consequences led to major theoretical advances in population genetics. The discovery of ‘selfish’ DNA prompted discussions about selection at the level of genes rather than traits. Kin selection theory, which describes how traits affecting relatives are selected, represents another extension.
I'm in the strange position of being very uncomfortable with either position.

What do you think?


Laland, K., Uller, T., Feldman, M., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G. A., Hoekstra, H. E., Futuyma, D. J., Lenski, R. E., Mackay, T. F. C., Schluter, D. and Strassmann, J. E. (2014) Does evolutionary theory need a rethink? Nature 514, 163-165. [PDF]

24 comments :

  1. All of their claims focus on only a small subset of the history of life—mostly animals. You can't reform evolutionary theory based on what you've learned about animal development because it doesn't apply to most organism and most of evolution.

    Agreed, but that's kind of a problem with the standard Modern Synthesis as well. Standard evolutionary biology is absurdly animal focused -- which is why I'm a bit surprised to see Lenski on the "everything's okay" side -- he must realize that microbial evolution works quite a bit differently than in the diploid, sexual organisms that the standard synthesis deals with.

    ReplyDelete
    Replies
    1. I was a bit surprised at Lenski as well because he's a fan of Lynch.

      Delete
  2. In fairness to Mayr, his book had the strapline "...from the perspective of a zoologist". However, I do agree that this debate seems very animal focussed and if we are to really look for extensions to evolutionary theory, they are likely to come from elsewhere.

    ReplyDelete
  3. I am not a biologist, so let me give a non-biologist perspective. For me, the great challenge of evolution is whether it really can do molecules to man, the rest is details. Genetic drift is interesting to the extent that allows evolution to get around "you can't get there from here" constraints by drifting from "here" to a point where "there" is accessible. But to say that genetic drift means the modern synthesis is "effectively dead" rather than "interestingly modified" strikes me as irresponsible hyperbole.

    If your main interest is the genome for its own sake, then genetic drift is a big deal, since drift seems to make far more changes to the genome than does natural selection for beneficial mutations. For those of us who don't care about genes for their own sake, the fuss made over drift seems rather bizarre.

    One last point. Those biologist who you say don't "understand" drift? I suspect they understand it perfectly well, they just aren't as impressed with it as you think they should be. I apologize for the rather acerbic tone, but I couldn't see how to phrase it more diplomaticly.

    ReplyDelete
  4. I was following the links to refresh my memory and noted the off-hand comment that blood type was probably an example of evolutionary change that was due to random drift. The highly respected Carl Zimmer not so long ago did a big piece on blood types for BBC that didn't explain the possibility. Instead it devoted itself to retailing various adapatationist scenarios. At any rate, it's pretty clear that the main purpose of the posts linked to was to argue that all the radicals are wrong, and they were fools for thinking there was something wrong with evolutionary theory. So, there's nothing strange with being uncomfortable with that side.

    It's true that the other side phrases its case in such a way that it is clear that neither neutral mutation nor random genetic drift make any difference. (And I know of no reason why a layman should think either was ever accepted as truly significant.) So? Gould is dead, Lewontin is a fallacy. Today, Steven Pinker is an authority on evolutionary theory, and evolutionary psychology is the conventional wisdom. The selfish gene is a touchstone of the critical mind. The problem was the Altenburg 16. But Piglucci has feld biology for philosophy. Problem solved! What's strange is being uncomfortable with the results.

    ReplyDelete
  5. Why exactly are you uncomfortable with the "everything's fine" statement? It includes neutral theory, which seems to be your major concern.

    I'm also interested in why you think that microevolution can't account for macroevolution. You may know that I think there are indeed macroevolutionary processes, but I'm not entirely sure we agree on what those processes are and, perhaps, how important they are to evolution.

    ReplyDelete
  6. I need to go back and re-read this carefully, but I suspect I'll share Larry's dissatisfaction with both positions. The "all is well" position seems to be based on the usual bait-and-switch. First, frame the target to be defended very broadly as "evolutionary biology", so that critics can be painted as though they are attacking an entire field, rather than a specific falsifiable theory. Then muddy the waters further by saying "some of us are familiar with phenomenon X and we are studying it, therefore there is no problem." This is not a scientific argument. "We're studying X" does not in any way tell us whether or not X is consistent or inconsistent with a scientific theory. People, including scientists, are capable of incredible feats of double-think, believing two things at the same time.

    Neither side seems to be defining a specific falsifiable theory. This is because, in the past, critics who tried to characterize Darwinism in a way that made it falsifiable were shouted down, and they have given up.

    ReplyDelete
  7. Arlin: Neither side seems to be defining a specific falsifiable theory. This is because, in the past, critics who tried to characterize Darwinism in a way that made it falsifiable were shouted down, and they have given up.

    What what what now? Who TF are you talking about, "critics who tried to characterize Darwinism in a way that made it falsifiable were shouted down"? WTF!? Who are these critics? Kent Hovind, federal prisoner #06452-017? Ken "I'm cooking the accounting books, Mafia-style" Ham? As Jerry Seinfeld would say, Who are these people? Names please.

    Have you even read The Origin of Species? Whatever that books' flaws, Darwin thought about how to test his theory more than any biologist before him. Compare that to creationist attempts to explain how light from the Andromeda Galaxy can get here in 6,000 years.

    ReplyDelete
  8. Diogenes, I have read the OOS and published peer-reviewed historical work addressing, among other things, what it means relative to subsequent developments in evolutionary theory. See http://link.springer.com/article/10.1007%2Fs10739-014-9383-2#page-1

    ReplyDelete
    Replies
    1. Also, to extend this, Smocovitis's seminal work on the evolutionary synthesis argues that, as a scientific theory, it seemed to become a "moving target" as soon as it was criticized in the 1980s.

      Your superlatives about Darwin are falling on deaf ears. Darwin interested in testing his theory? I think not. Galton, for instance, proposed to test Darwin's theory of heredity by transfusing the blood of rabbits to see if the changeover in gemmules would change their heredity. It didn't work. Darwin responded by saying that the gemmules didn't need to be carried in the blood. So much for testability.

      What on earth are you talking about? How did Darwin, in the OOS or in other works, describe how to test his theory? One thing he said, which has turned out to be profoundly wrong, is that his theory would "utterly break down" if it could be shown that some organ had not evolved by numerous successive slight or infinitesimal increments. We know now that this is not the case.

      Delete
    2. Oh, so as I suspected, you live in fantasy land. If there's one thing Darwin got right, it was that no one would find unevolvable complexity in any biological organism. 155 years later, still true.

      "Darwin interested in testing hid theory?"

      Yes, Darwin obsessed with testing his theory. You've still presented no evidence you've read the book-- it's possible you might have, but insist on misrepresenting it-- at any rate, when you say things so abjectly dishonest or stupid, argument from authority won't work on me. Present evidence, not argument from authority, or piss off.

      How's that DNA 98.7% identical to a chimp's working out for ya?

      Delete
    3. This comment has been removed by the author.

      Delete
  9. Having read this more thoroughly, I'm even more disappointed. Major disappointment #1 is that the "reform" position does not even attempt to focus on substantive theories and to characterize the MS as a falsifiable theory. Instead they are all arguing about "evolutionary biology" vaguely as a discipline. The discussion is essentially about whether the discipline is on the right track, which is a stupid vague way of framing things, impossible to resolve.

    The "shut up and get back to work" position is even worse. They end with a nasty slapdown about how Darwin worked on earthworms for 40 years before publishing, with the clear implication that the EES advocates need to prove their case. At the same time, they are literally arguing that their is no case to be made, no new ideas, because it all goes back to Darwin.

    This is all a sad commentary on the state of evolutionary discourse, IMHO.

    ReplyDelete
  10. And to continue, because this whole thing irks me to no end-- to characterize the MS is very difficult because its expression resides in multiple book-length works (Huxley, Dobey, Mayr, Simpson, Stebbins, ...) that contain many one-off statements but not a consistent obvious expression of what the theory proposes, and what distinguishes it from other theories. To characterize the MS requires a historical research project, based on the conceptual analysis of primary texts.

    Furthermore, that research project *cannot* be based solely on the works of the MS, because the MS architects were ruthless in *mischaracterizing* their scientific rivals. To find out what mutationists, Lamarckians, orthogeneticists, etc. actually advocated, we must read their works, obviously!

    But to return to my point-- one thing we can be sure of, in regard to the MS, is that it is not mutationism. According to history, the MS won a victory over the view of early geneticists. This is sometimes cited as proof that Darwinism is a scientific theory that has survived challenges and defeated rival theories. The story of this victory, from the perspective of population genetics, is told in Provine's seminal history, the Origins of Theoretical Population Genetics. If this victory turns out to be ill-gotten, then the MS is toast.

    Provine himself, in the 2001 reprinting of his work, said that the MS had "come unraveled".

    I have done exactly the research project that is required to address this issue, comparing the mutationist view to the MS based on primary works. The results, in the paper that I cited above, are very damning for the MS.

    The MS, contrary to what the "all is well" view suggests, is *not* a generic framework that merely follows the implications of genetics wherever they lead. Instead, it was the early geneticists (Mendelians, mutationists) who were inclined to follow genetics wherever it may lead. The advocates of neo-Darwinism, by contrast, were committed to Darwinian doctrines of gradualism and externalism. Driven by these ideological commitments, they constructed a picture of evolutionary genetics that produces behavior consistent with Darwin's original non-Mendelian theory, argued that this was sufficient to account for evolution, and then claimed that all rivals had been defeated. It is Fisher's 1918 paper, in particular, that seems to fulfill this Darwinian vision, which is why it is given so much attention. But does anyone today really believe that the idealized version of quantitative genetics is the foundation of evolutionary theory? I think not. That is precisely why Provine says that the MS became unraveled.

    As a specific example, read my recent review with David McCandlish about origin-fixation models (http://www.ncbi.nlm.nih.gov/pubmed/25195318). Origin-fixation models depict a mutationist view of evolution by mutation and fixation-- the "lucky mutant" view that Mayr and Dobzhansky derided as simplistic and unrealistic. In their view, evolution was "shifting gene frequencies", which meant shifting from one multi-locus distribution of allele frequencies via recombination and selection, without new mutations (see Provine). In origin-fixation models, the power of mutation to determine the dynamics and direction of evolution is particularly strong, contrary to DArwinian thinking. Origin-fixation models are widely used today, because evolutionary biologists have abandoned the MS view and reverted to mutationism.

    ReplyDelete
    Replies
    1. I read the piece and I was completely confused regarding who is attacking/defending what (because it was never defined). So your clarifications are definitely very helpful, but the fog has still not cleared.

      If the EES folks are attacking the MS, then that's a strawman and probably there isn't much point discussing it in depth. But I have this inescapable feeling that while they are attacking MS they are actually being understood by many as attacking the current state of the art molecular/population genetics understanding of the process. In which case there is a problem.

      Delete
    2. This comment has been removed by the author.

      Delete
  11. Yes, there is utter confusion about what is the object of dispute. Is it a research program, or a theory, or something else?

    But attacking the MS is not a strawman. The MS can be construed as a specific, falsifiable theory that has been falsified.

    That depends on treating the MS as a falsifiable theory. But very frustratingly, the debate in _Nature_ is not about theories, but about research programs, it seems.

    ReplyDelete
    Replies
    1. I didn't phrase that properly - the MS is the strawman if one is out there talking about the need for an extended evolutionary synthesis, because the MS is not what the current theory is.

      Delete
    2. What effect might this have on evolutionary theory?

      "Non-coding half of human genome unlocked with novel sequencing technique"

      http://www.sciencedaily.com/releases/2014/10/141007091753.htm

      Delete
    3. @The whole truth,

      Be patient. I'll get to it.

      Delete
    4. Larry,

      When you read that press release, watch your blood pressure. And any other potentially head-exploding factors.

      Delete
  12. 'Does evolutionary theory need a rethink" the article asked. YES
    A creationist can say here AHA. A rethink is public admittance the thinking is not done and someone is wrong about something important.
    Within this crack of a opening creationism can say evolution is not proven in its mechanisms since its proponents don't even agree.

    I was , a little , surprised at the rejection that micro equals macro in making the case for evolution.
    Creationists always get hit on this micro equals proof or macro or as a reasonable option.

    ReplyDelete
    Replies
    1. Byers: "Within this crack of a opening creationism can say evolution is not proven in its mechanisms since its proponents don't even agree."

      No Byers. Creation of all species by magic 6,000 years ago is not proven in its mechanisms (evolution is), and proponents of creationism do not agree amongst themselves. E.g. is that ape-man fossil transitional or not? Half of all creationists say it's "obviously" all man and 0% ape, the other half say it's all ape and 0% man.

      Please explain the mechanism by which God turned dirt into the human genome 6,000 years ago.

      Delete
  13. This is just a great example (the Nature commentary) of how absurd a debate is when the terms are not defined from the beginning. If there is no delimitation and agreement among all the authors about what the Modern Synthesis is, then the debate gets extremely confused.

    Furthermore, I doubt the Modern synthesis can be easily and clearly defined. It was a movement in evolutionary biology that spanned at least two decades, probably four, that included numerous authors with somewhat heterogeneous views, of course with agreements on main unifying principles, but allowing some flexibility. Gould has carefully analyzed it in 'The Structure of Evolutionary Theory' in order to make his case. He describes an initial period of consistency with Mendelian genetics, followed by a hardening. He argues that theories have histories, being dynamic entities that change through time, but also have essences that help define them.

    We all have to agree on these essences, and how much flexibility we are going to concede them given their dynamic history (and changing views of participants) before we can have a proper dialogue. Here I see the real challenge.

    ReplyDelete