Mutation and evolution

Category: Best of

  • 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…

  • 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…

  • 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…

  • 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 (not one infinitesimal at a time, but a blending flow of infinitesimals).  …

  • 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…

  • 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…

  • 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,…

  • 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…

  • 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?  Can a theory change and, if so, how much?  What is the relationship between mathematical formalisms and other statements of “theory”? Who…

  • 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…