One of the pitfalls about talking about genetics, especially human genetics, is that the public wants a specific gene for a specific trait. Ergo, the “God gene” or the “language gene.” In some cases science has been able to pull a rabbit out of the hat, and offer up a gene for a trait. But in most of those instances these are going to be single gene recessive diseases. Not exactly what the doctor ordered. In other cases the association seems trivial. For example, wet or dry earwax?* What people are truly interested in are the genetic basis of complex traits, such as intelligence, personality, and height. Unfortunately complex traits often have a complex genetic basis. A trait such as height, which is highly heritable (i.e., most of the variation in the population is due to variation in genes), turns out to be subject to the control of innumerable genes, each of which has a small impact on the value of the final trait. Then there is the possibility that the heritability is tied up to interaction effects across genes.

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Today I was missing my daughter, so I decided to Skype with her on my phone. The phone has a camera which can record video, so I can talk to her, and if she gets bored I’ll show her something besides my face. I take this for granted, but it is interesting to reflect that my “video phone” is actually just a regular phone on which I installed a third party application to enable two way video calls. It’s a banal and marginal use for the device. Information technology is far more ubiquitous than the occasional video conference.

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I was reviewing some literature for a blog-post-to-come and I noticed a figure in a paper I’ve long been aware of which indicates to me that Afrikaners surely have a non-trivial proportion of non-European ancestry. The paper is Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2. It’s a forensics result. Basically SLC24A5 is useful for differentiating West Eurasians from Africans and East Asians, Amerindians, and Oceanians. But it is not too useful in distinguishing between West Eurasians. The “European” derived variant SNP within this locus is actually present at ~50% frequency as far south and east as India. In contrast, the “European” derived variant of SLC45A2 decreases much more rapidly outside of Europe, so it is a more plausible European-diagnostic-marker.

The figure below illustrates the results from the paper:

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The word “discourse” is used a lot now. I’ve seen it even bleeding out of academic discourse, to general interest news. So I thought I’d look at the comparison between it an a few other terms in Google’s Ngram Viewer, which surveys mentions in books. The results were mildly interesting.

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In Nature Oren Harman has a review up of Nature’s Oracle: The Life and Work of W. D. Hamilton. It seems as if he gives it a B. Not enough science? Too much biography? For those who want more science and depth, Hamilton’s collected papers are where you should start: Narrow Roads of Gene Land: Evolution of Social Behaviour, Narrow Roads of Gene Land: Evolution of Sex, and Narrow Roads of Gene Land: Last Words. These books consist of an alternating series of (auto)biographical sketches and scientific papers. Unfortunately Hamilton died before much work went into the last volume, so we don’t get to hear him in his own voice. This is a shame, because the first two volumes place much of the science in fascinating, if not necessary, social context. The equivalent chapters for the last volume were written by colleagues and collaborators, but the outcome is not surprisingly more pedestrian. The second volume in particular is worth picking up because it is basically unedited Hamilton (his untimely death meant that the normal back and forth which would have slimmed down the verbosity and softened the candor was simply not possible).

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A paper on the genetics of the Roma (“Gypsies”), Reconstructing Roma History from Genome-Wide Data, has finally come out in a journal. It’s been on arXiv for a while, so nothing too surprising. But, reading through the paper I have to note one rather clear aspect for me: there is a crispness and detail to the way they outlined and integrated their methods into the results section. Unfortunately there is an obvious tendency in the pressure to publish for people to use methods and tools (which usually consists of software written by others which you use in a blackbox fashion) in a slapdash manner with an aim toward arriving at a publishable unit. Because of the specialization within science it seems one can entirely make it through peer review by using methods which signal that one does not really know what one is talking about. To give a concrete example, a year ago I was told about a phylogenetic package isin moderate usage which seems to basically be a “random number generator.” The fact that this package is used is a testament to the fact that many researchers who are not phylogeneticists simply reach for the nearest method at hand, and trust the results if they make some intuitive sense (presumably in this case they would simply report the results which were intelligible).

The ultimate future, I’m hoping, is for open data, open code, and open methods. When a shady or sketchy paper makes it through peer review there is now visible public anger which bubbles out of the scientific community, but the process of reproducing the results can still be tedious (see Arsenic life). This is less true in cases where the means are more computational. The only things stopping the process of science from operating more efficiently are human barriers (e.g., cultural norms, institutional barriers toward data release).

Bears are big deal today. I’ve talked about this before, so I won’t belabor the point in this post. Rather, I want to persuade you that there’s a really interesting paper out in PLOS Genetics right now, Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution. I know that seems like a mouthful, and despite the fact that I nodded to the reality that this is highly relevant in part because of policy concerns, the paper itself makes salient the reality that oftentimes we are confronted with the juxtposition between useful abstractions and the empirical shape of the world. In this case the abstraction is that of species, the one taxonomic category which many people find to be a natural kind, so to speak. These sorts of confusions of our expectations are often highly informative. They illustrate the limits of our abstractions, and drive us toward more complex and/or elegant formalisms which are capable of modeling nature as it is, rather than as it we wish it would be.

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I’ve gotten several emails about the Vice interview of Geoffrey Miller on BGI’s Cognitive Genetics Project. It’s a sexy piece, and no surprise given Miller’s fascination with the future of China and science (something I share to a moderate extent). But for the love of God please watch this Steve Hsu video first before reading that.

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Emily Anthes has a new book out, Frankenstein’s Cat. It looks quite interesting, but I’ll be honest and admit I doubt I’ll get to it, mostly because I am relatively sanguine about genetic modification. I don’t think it’s a qualitative difference from what’s been going on for 10,000 years. To me all genuine concerns about this area don’t fundamentally have anything to do with the core idea of genetic modification (e.g., rather, it is about control of the means of production, etc.). If you are wondering if you might like the content of Frankenstein’s Cat, I would recommend this 40 minute interview of Anthes on NPR. It strikes me that she’s presenting a rather “balanced” perspective, acknowledging the concerns of some, while attempting to highlight the genuine benefits of genetic modification.

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Thoughts, for good or ill.