Mutation-biased adaptation reaches the mainstream

The most recent issue of PNAS includes a report by Galen, et al linking enhanced mutation at a CpG site to altitude adaptation in Andean house wrens (Troglodytes aedon), based on clear biogeographic and biochemical evidence of adaptation.  I’ve been waiting for this, both in the narrow sense that I’ve been waiting for this particular study to appear in print, and also in the broader sense that I have been waiting for any paper on mutation-biased adaptation to appear in a prominent venue.  Results like these, one hopes, will overturn the “raw materials” doctrine of neo-Darwinism and stimulate the development of a new understanding of the role of mutation in evolution.

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The buffet and the sushi conveyor

The return of mutationism to mainstream evolutionary biology is evident in the way mainstream articles now describe the role of mutation in evolution, in our reliance on mathematical models that evoke a mutationist view, and in evo-devo research programs that focus on identifying causative major-effect mutations.

This shift has happened in a kind of sub-conscious way, without commentary or reflection.  I’ll comment below on the reasons for that.

My main purpose here is to contrast way that the neo-Darwinian and mutationist views refer implicitly to two different regimes of population genetics evoked in two styles of self-service restaurant: the buffet and the sushi conveyor.

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Some comments on Pachter’s P value prize

In late May, Lior Pachter posted a blog entitled Pachter’s P-value prize, offering a cash prize for providing a probability calculation (P value) based on a “justifiable” null model for the claim of Kellis, Birren and Lander, 2004, hereafter KBL, that some results from an analysis of yeast duplicate genes “strikingly” favored the classic neo-functionalization model of Ohno over the contemporary DDC (duplication-degeneration-complementation) model.

This attracted, not just a huge number of views (for a geeky science blog), but an extensive online discussion among readers that was carried out at a very high intellectual level.  Dozens of scientists commented on the blog, including Manolis Kellis, the first author of KBL, and scientists well known in the field of comparative genome analysis.  Mostly they were discussing what was an appropriate statistical test, but they also discussed the nature of the Ohno and DDC models, the responsibilities of authors, the flaws of the peer-review process, the appropriateness of blogging and tweeting about science, and so on.

Here, I’m going to use graphics and simulated data to illustrate null models in relation to the duplicate gene data from KBL.   I also want to make a comment about the expectations of the DDC model.  All of the plots and calculations are available as embedded R code in the R-Markdown file kbl_stats.Rmd(more…)

Why size matters: Saltationism, creativity, and the reign of the DiNOs

Debates on “gradualism” in evolutionary biology address the size distribution of evolutionary changes.  The classical Darwinian position, better described as “infinitesimalism”, holds that evolutionary change is smooth in the sense of being composed of an abundance of infinitesimals.   The alternative is that evolution sometimes involves “saltations” or jumps, i.e., distinctive and discrete steps.  The dispute between these two positions has been a subject of acrimony at various times in the 20th century, with several minor skirmishes, and a larger battle with at least one genuine casualty (image).

Walter Frank Rafael Weldon (public domain image from wikipedia).  Legend has it that Weldon ignored an advancing illness and worked himself to death trying to disprove the relevance of Mendelism in natural inheritance.

Walter Frank Rafael Weldon (public domain image from wikipedia).  Weldon ignored an advancing illness and worked himself to death (1906) poring over breeding records in an attempt to cast doubt on discrete inheritance.  Along with Pearson and other “biometricians”, Weldon held to Darwin’s non-Mendelian view combining gradual hereditary fluctuations with blending inheritance.

Today, over a decade into the 21st century, we have abundant evidence for saltations, yet the term is virtually unknown, and we still seem to invoke selection under the assumption of gradualism.  Are we saltationists, or not?  I’m going to offer 3 answers below.

But first, we need to review why the issue is important for evolutionary theory.

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The revolt of the clay: an initial progress report

A “chance” encounter

Earlier this month I was contacted by a reporter writing a piece on the role of chance in evolution.   I responded that I didn’t work on that topic, but if he was interested in predictable non-randomness due to biases in variation, then I would be happy to talk.  We had a nice chat last Friday.

I’m only working on the role of “chance” in the sense that, in our field, referring to “chance” is a placemarker for the demise of an approach based implicitly on deterministic thinking— evolution proceeds to equilibrium, and everything turns out for the best, driven by selection.  This justifies the classic view that “the ultimate source of explanation in biology is the principle of natural selection” (Ayala, 1970).  Bruce Levin and colleagues mock this idea hilariously in the following passage from an actual research paper:

To be sure, the ascent and fixation of the earlier-occurring rather than the best-adapted genotypes due to this bottleneck-mutation rate mechanism is a non-equilibrium result. On Equilibrium Day deterministic processes will prevail and the best genotypes will inherit the earth (Levin, Perrot & Walker, 2000)

Wait, I’m still laughing.   (more…)

When “Darwinian adaptation” is neither

Getting stuff right

Early in the evolution of the Sequence Ontology, it was noted (by gadflies like myself) that SO asserts the relationship of mRNA to gene to be the “part of” relationship.  This is obviously wrong.  An RNA molecule is not part of a DNA molecule.   Saying that mRNA is part of a gene is like saying that a CD with some audio chapters from a book is part of that book.

Ontologies are supposed to support formal reasoning: errors in representation will lead inevitably to erroneous results.  For instance, if we are reasoning about the chemical composition of a cell using mRNA part_of gene as a constraint, we would conclude falsely that the mass of DNA must always be at least as much as the mass of mRNA, because the mass of a thing is always at least as great as the mass of some specified parts.

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The Great Non-Debate on Evolutionary Theory (Nature, Oct 2014)

Some of you may have noticed a recent exchange in Nature on the question of whether evolutionary biology needs a re-think. The online article does not make clear the alignments of the listed authors, but those arguing in favor of a re-think are:

  • Kevin Laland, Tobias Uller, Marc Feldman, Kim Sterelny, Gerd B. Müller, Armin Moczek, Eva Jablonka, and John Odling-Smee

and those arguing against are:

  • Gregory A. Wray, Hopi E. Hoekstra, Douglas J. Futuyma, Richard E. Lenski, Trudy F. C. Mackay, Dolph Schluter and Joan E. Strassmann

I was a bit surprised that they didn’t get people who actually disagree about science, like Mike Lynch and Sean Carroll.  Instead, the debate takes place between participants who disagree on the meta-scientific question of whether the field needs a re-think.  What is each side saying?
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Evolution: A View from the 21st Century (book review)

Last year I read James Shapiro’s Evolution: A View from the 21st Century (2013, FT Press) along with 2 other recent books, Nei’s Mutation-Driven Evolution and Koonin’s The Logic of Chance.  All 3 fall into the category of recent books by seasoned researchers whose primary focus is molecular, and who argue that we ought to rethink evolution based on findings of molecular biology or molecular evolution.   The 5-word summaries of these books are:

  • Engineering, not accident, provides innovation (Shapiro)
  • Mutation, not selection, drives evolution (Nei)
  • After Darwinism, things get complicated (Koonin)

In the case of Koonin, you have to read the whole book to understand what he means. If you are not familiar with the past 10 to 20 years of findings from comparative genomics, then it will be educational, and regardless of your familiarity with genomics, it will be entertaining and thought-provoking.  In the case of Nei, you can read the whole book and still not understand his thesis because he never defines terms and never actually compares mutation and selection to determine which one drives evolution (the wikipedia “mutationism” page has links to a handful of reviews of Nei’s book, including my review in Ev & Dev).

In Shapiro’s case, the book explains precisely what is meant by the idea that innovation is the result of engineering, not accident, though he leaves open the question of what are the general implications of this for evolutionary theory. (more…)

Theory vs. Theory

What does it mean to invoke “evolutionary theory”? Is “neo-Darwinism” (or “Darwinism”) a theory, a school of thought, or something else? What gives a theory structure and meaning (e.g., axioms, themes, formulae)? What is the relationship between mathematical formalisms and other statements of “theory” (e.g., what does it mean for a lecturer to show a key equation of quantitative evolutionary genetics and assert “this is neo-Darwinism” 1)? Who decides how a theory is defined, or redefined (e.g., is Ohta’s “nearly neutral” theory an alternative to, or a variant of, Kimura’s Neutral Theory of Molecular Evolution)?

In this post, we’ll begin the process of developing a shared framework for productively discussing “theory” and “theories”. We will begin by addressing an ambiguity in the use of the word “theory”, partly because this particular ambiguity is important, and partly as an exercise in addressing semantics. 2
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The Mutationism Myth (3): Foundations of evolutionary genetics

This is the third in a series of 2010 blogs entitled “The Mutationism Myth” (a more scholarly version of this material ended being published in J. Hist. Biol. by Stoltzfus and Cable, 2014)

In this oft-told story (see part 1), the discovery of genetics in 1900 leads to rejection of Darwin’s theory and the rise of “mutationism”, a laughable1 theory that imagines evolution by mutation alone, without selection. “Mutationism” prevails for a generation, until Fisher, Haldane and Wright show that genetics is the missing key to Darwinism. In the conclusion to the story, the world is set right again when the “Modern Synthesis”, combining selection with Mendelian genetics, shoulders aside the mutationist heresy, which ends up in the dustbin of history with the other “doomed rivals” of Darwin’s great theory.2

Thats the story, at least. In reality— as we found out in part 2—, the Mendelians rejected Darwin’s errant principles of heredity, not his principle of selection. What kind of view did the Mendelians develop? Addressing this question is our next challenge.  Today, in part 3, we’ll consider aspects of the Mendelian view that became the foundations of mainstream 20th-century thinking. In part 4, we’ll delve into some “non-Darwinian” or “anti-Darwinian” aspects that were rejected, or merely ignored. (more…)