Wednesday, February 08, 2012

Michael Lynch on Evo-Devo

Michael Lynch had some cogent (and provocative, and true) words on adaptationism in his book The Origins of Genome Architectue [Michael Lynch on Adaptationism].

Here's what he has to say about evo-devo.
Consider the steady stream of recent books by authors striving to define a new field called evolutionary developmental biology (e.g., Arthur 1997; Gerhart and Kirschner 1997; Davidson 2001, 2006; Carrol et al. 2001; West-Eberhard 2003; Carrol 2005a; Kirschner and Gerhart 2005). The plots of all these books are similar: first, it is claimed that observations from developmental biology demonstrate major inadequacies in current evolutionary theory, and then a new view of evolution that eliminates many of the central shortcomings of the field is promised. Developmental biologists are correct in pointing out that evolutionary theory has not yet specifically connected genotype to phenotype's in a molecular/cell biological sense. However, extraordinary claims call for extraordinary evidence, and none of these treatises provide any formal example of the fundamental inability of evolutionary theory to explain patterns of morphological diversity. Those who argue that microevolutionary theory has made no contributions to our understanding of the evolution of form may wish to consult the substantial body of quantitative genetics literature on multivariant evolution. Such work is by no means fully satisfactory, as it is couched in terms of statistics (variances and covariances) rather than the molecular features of individual genes, but a more precise evolutionary framework for linking genes and morphology not be possible until a critical mass of generalities on the matter has emerged at the molecular, cellular and developmental levels.

For the vast majority of biologists, evolution is nothing more than natural selection. This view reduces the study of evolution to the simple documentation of differences between species, proclamation of a belief in Darwin, and concoction of a superficially reasonable tale of adopting the divergence (...). A common stance in cellular and developmental biology is that the elucidation of differences in molecular genetic pathways between two species (usually very distant species) completes the evolutionary story. No need to dig any deeper—because natural selection surely produce the end products, the population genetic details do not matter. In individual cases, this type of informal thinking may do little harm, but in the long-run it undermines the very scientific basis of with the evolutionary biology.

There are two fundamental issues here. First, the notion that interspecific differences at the molecular level reveal the mechanism of evolution ignores the fundamental distinction between the outcome of evolution and the events that lead to such changes. For example, although most animal developmental biologists argue that it was shocking to discover that the development of all animals is based on modifications of the same sets of ancient genes, many evolutionary biologists regard this view with some surprise. It is, of course, easy to criticize based on 20/20 hindsight, but we have known for decades that all eukaryotes share most of the same genes for transcription, translation, replication, nutrient uptake, core metabolism, cytoskeletal structure, and so forth. Why would we expect anything different for development? Although knowing that HOX genes play a central role in the development of all animals provides insights into the genetic scaffold from which body plans are built, it does not advance our knowledge of the evolutionary process much beyond noting that all vertebrates share a heritage of calcified skeletons. It need not even tell us that such genes were involved in the initial stages of differentiation (Alonso and Wilkins 2005). A vast chasm of stepwise (and partially overlapping) changes may separate today's products of evolution, and understanding those steps is what distinguishes evolutionary biology from comparative biology.


  1. Off topic, but I couldn't find your email. Somebody seems to be stealing your stuff:

    1. does it too, especially when I write about atheism. Not so much when I write about evolution. :-)

      Should I sue?

  2. I haven't read Carroll recently enough to be as specific as I'd like in my response. I seem to remember that he does a couple of things that aren't "soft" and may not be strictly adaptationist.

    Not "soft" - I remember at least one paper and sections of his popular books dwelling on what we can tell about the genomes of very, very old LCAs from those of current living things. These did, it seemed to me, try to nail down individual molecular changes to the extent possible.

    Not strictly adaptationist - I recall portions of the popular books discussing the idea of duplications in HOX genes for body segment and limb construction as neutral mutations that created the opportunity for further mutations in the "spare" sets of genes. So there is at least a recognition that not all fixation is driven by adaptation.

  3. Sean B. Carroll knows a lot about population genetics and random genetic drift. When the topics come up in his books, he usually gets them right.

    That's not the point. It's a question of emphasis and perspective. Some adaptationsts are fully capable of understanding non-adaptive evolution and they may even be able to quote some specific examples (e.g. junk DNA). But when it comes to explaining most things about evolution they still have a powerful adaptationist bias and when their guard is down they frequently use "evolution" and "natural selection" as synonyms.

    One of Sean B. Carroll's books is The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. I could never write a book with such a title and neither could Gould, Lewontin, or Lynch.

    Here's a passage from the preface. No pluralist could ever write this.

    Biologists are mining this rich new source [genomes} to investigate and to reveal, in unprecedented detail, how all sorts of traits have evolved in nature. In this book I will tell the story of how the science of genomics—the comprehensive and. most especially, the comparative study of species DNA—is profoundly expanding our knowledge of the evolution of life.

    Genomics allows us to peer deeply into the evolutionary process. For more than a century after Darwin, natural selection was observable only at the level of whole organisms such as finches or moths, as differences in their survival or reproduction. Now we can see how the fittest are made. DNA contains an entirely new and different kind of information than what Darwin could have imagined or hoped for, but which decisively confirms his picture of evolution. We can now identify specific changes in DNA that have enabled species to adapt to changing environments and to evolve new lifestyles.

    The contrast between Carroll's book and Lynch's couldn't be more stark. Lynch uses the new genome data to show that evolution by random genetic drift is pervasive. This is the most important discovery about evolution to come out of genomics. I agree with him.

    Lynch points out that the picture we get from studying genomes is entirely different than what Darwin imagined. We now know that the vast majority of evolutionary change has nothing to do with natural selection.

    You can't really say that Carrol is wrong (or Lynch) but the emphasis is very different. The question is, what should we teach students? Should we reinforce their biases by focusing on all the evidence for adaptation or should we challenge their understanding of evolution by teaching them about random genetic drift, Neutral Theory, and population genetics?

  4. I don't think sean carroll said anything about there being a mistake or a flaw in the modern synthesis - but he argued for an extension beyond just population genetics' view of evolution - as much as Gould did. I do think the idea that evolution is a change in developmental pathways is fascinating and worth adding to evolutionary biology textbooks - none that I have seen talk about that. What is odd about this statement: "We can now identify specific changes in DNA that have enabled species to adapt to changing environments and to evolve new lifestyles", is that sean and other biologists know that changes in DNA - mutations - are not THE way to change a trait - but genomic networks is - at least in metazoans. I think this view of evolutionary change - as appose to just allele frequency change - is equally fascinating.

  5. The basic problem is that the genome is not a repository of spatial and morphological information, just that for the synthesis of proteins and RNAs. Until and unless developmental biologists seek explanations other than the genome, they will fail to understand morphogenesis.

  6. Thanks, Larry, that's a very good explanation. Might even be inclined to give Carroll a pass on the title, as folks like to use famous Darwinian phrases in books about evolution for the popular market (in this case a paraphrase of a famous Spencerian/Darwinian usage). But: First, I take the point that Gould, et al., would never use such a title; and second, yes, triggered by your quote I do recall the emphasis in Carroll's writing on a generally adaptationist viewpoint.

  7. The problem I have noticed with evo-devo is that there are several strands of thought within the field, but Carroll's viewpoint seems to dominate the rest. I think Lynch is correct when it comes to Carrollian evo-devo. When it comes to the views articulated by Gerd Müller and Stuart Newman, I fin evo-devo to be far more provocative. A good example of this is their discussion of how Turing reaction-diffusion models and biomechanics influenced the development and evolution of the vertebrate limb. I have no idea if they are right, but it's intriguing nonetheless - more so than "selection on genes did it" anyway.

  8. I agree with Atheistoclast. Evolutionists speak with vague verbosity rather than specific cause-and-effect chains of reasoning. e.g. I read somewhere that the organisms of the Cambrian Explosion "must have invented toolbox genes". QED.

    I was assured by one expert recently that "morphology is controlled by Homeobox genes." QED. But how do Homeobox genes in one cell coordinate their efforts with those in other independent cells to create items such as a vertebra of certain size and shape? Carroll makes vague statements about certain genes "being involved" but avoids the specifics.

    I still cannot understand how Natural Selection caused penis and womb, etc., etc., to evolve in independent male and female organisms, not just man and woman. Dawkins admits he avoids the subject. He just believes it.

    Is history repeating itself? Some Greeks thought matter was infinitely divisible. But then we discovered 92 kinds of atoms. Problem solved. But then came radioactivity . . . and the quest does on.

    Now we have discovered DNA, which, we are assured, explains everything. Problem solved. But then Sheldrake asks a simple question about morphogenesis . . .

    1. The good news is that your ignorance can be cured. The bad news is that you will have to work at it.

    2. You raise some good points, particularly on the subject of coordination. Part of the misconception arises from an over-interpretation of Hox gene functions. These genes are simply transcription factors that bind to DNA (and RNA polymerase) in order to activate other genes. They encode no spatial or positional information. But because their spatiotemporal expression corresponds to the anterior-posterior axes of the body plan, it is assumed that they must be determining this layout.

      The basic fact, however, is that no geometry of anatomy is contained in the genome. Whatever defines this 3-dimensional architecture are not gene products.

      As for sexual organs, you are right to be skeptical considering that men and women possess almost the same DNA, and genes "involved" in the development of both male and female-specific tissue are shared among the sexes.

  9. You say that "no geometry of anatomy is contained in the genome". Is that generally accepted as a fact in the scientific community?