Open Thread, 06/05/2017

Just a plug for Elements of Evolutionary Genetics by Charlesworth & Charlesworth. These are two great evolutionary geneticists, and we’re lucky to have a “core dump” from them on hand (for those for whom Elements is too spendy, John Maynard Smith’s Evolutionary Genetics is usually available used more cheaply, though it will be a touch out of date).

The curious thing is that there is so much science that is tacit and implicit, that the passing of each generation of scholars means that hidden reaches of knowledge are passing away. This is the flip side of the idea of progress being made through the death of older scholars and the acceptance of novel (and more right) paradigms.

Both Charlesworths are authors on a new paper (along with Nick Barton) in The Proceedings of the Royal Society, The sources of adaptive variation. Here’s the abstract:

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today’s understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.

Another riposte to the EES. Entirely unsurprising that these authors and this venue would offer criticism to a reframing of the field of evolutionary biology. But it gets to the heart of the reality that this is going to be an argument that will be resolved through publication of new papers, not books or long popular science articles. The footprint of the EES in evolutionary biology popular science is heavier than within evolutionary biology itself.

The prominent medical genomicist Dan MacArthur stated yesterday:

Not to be churlish, but let me clarify judging by the numbers of people Dan followed there were conservatives and libertarians he followed, he just didn’t, and doesn’t, know who they are. Also, there were several people he followed with center-right or libertarian views as a point of fact. I know because because I’m open about my right-wing views, and these people feel and felt comfortable telling me (privately) that they don’t agree with the vocal Left-liberalism which is pervasive in the political atmosphere on science twitter. Though most science twitter people don’t post much about politics, if they do, a substantial proportion are “social justice” oriented. That’s tolerable for most people because most scientists are on the Left side of the political spectrum.

My tendency to post right-wing political stuff into the feeds of scientists is annoying for many (or as some would say “problematic), but I don’t care. I know I speak for a substantial minority in the aggregate, and in some cases the majority (in terms of the latter, what I mean is that though most scientists are liberal, most are not on that far Left, though they may fear being attacked by the far Left and so are careful not to enter into any public dissent when that contingent starts to get a little out of control).

In a curious inversion with the norm I guess, my Twitter timeline is balanced politically. If anything, it’s more liberal than not. I don’t know what it would be to be in a political silo. I hear it feels good. Then again, I enjoy 300,000 scoville unit hot sauces.

Detecting polygenic adaptation in admixture graphs. Educational attainment and unibrows. Yeah. One thing: “An open question in human evolution is the importance of polygenic adaptation.” This is literally true, but I think it is pretty obvious that the latest work is suggesting there has been a lot of it.

Widespread signatures of negative selection in the genetic architecture of human complex traits.

The Genomic Health Of Ancient Hominins.

6 thoughts on “Open Thread, 06/05/2017

  1. “Cumulatively, our data show that the deepest split among modern humans occurred at >260 kya, pushing the emergence of H. sapiens to beyond 260 kya.”

  2. Would be interested to read your thoughts on this Razib –

    My very rough (and badly phrased) interpretation is: Detects time and place of selection in lineages of humans by reconstructing a hierarchical graph (TreeMix style) and then fitting divergences polygenic subsets for a trait to the graph to localize time of selection in a lineage.Not sure what advantages are over PCA methods though (which should find same signals and localise on between population divergences to the same degree?).

    Also: I kind of presume the guys who wrote the paper read your blog, so would comment to them if reading that seems like Uyghurs and Ashkenazi Jewish populations would be useful for them to test on their graph. Seem like pretty model populations for the method, admixture being easy to fit with recent references (no real need of adna), and questions are frequently raised on whether they have their own signatures of selection on polygenic traits.

  3. you should leave comments on the preprint.

    a few of those authors are friends (i went to grad school with middle author!), so i will probably blog in more detail when i have time….

  4. In Applying Intelligence To Genes For Intelligence (5/24/17) you wrote,

    “But Stuart Ritchie’s Intelligence: All That Matters and Richard Haier’s The Neuroscience of Intelligence are both good, and cheaper and shorter.”

    Some feedback.

    I started Ritchie’s book and returned it to the library (big shoutout to interlibrary loan!!!) after reading 70-80 pages (roughly half). Perhaps it was pitched to too low a level for my taste, but it struck me as not only condescending but tendentious.

    I am in the middle of Haier’s book (again roughly half way through) and enjoying it thoroughly. He lays his cards on the table, is intellectually humble and does not make strong claims that he does not support. Reporting on the research chronologically to illustrate the the fog of war or rather research, is, somewhat paradoxically, illuminating. Perhaps the only axe he has to grind concerns the incentive structure of academic research and the structural & political obstacles around funding for research. These have been sufficiently well documented elsewhere that his mildly understated griping makes him seem even more reasonable.

    Thanks for the recommendations (even the Ritchie: I don’t expect a perfect score and I did not lose too much time on it).

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