Reconstructing genetic ripples in time and space

The inimitable Joe Pickrell has dropped his Khoisan-are-part-Italian preprint onto arXiv, Ancient west Eurasian ancestry in southern and eastern Africa. I’m being glib in my characterization of the paper’s core conclusion, but there’s a reason for such a flip response: the inferences that he seems to draw from the genetic data strike me as verging on crazy. But that’s OK, what genetics is telling us is that history was a whole lot crazier than we had imagined.

Let’s back up for a moment here. For several decades now geneticists have assumed that the Bushmen of the Kalahari, the Khoisan-qua-Khoisan, Africa’s last hunter-gatherers who retain their ancestral language along with the Hadza, are the ur-humans. The basal lineage that first diverged from the rest of mankind at the cusp of the Out of Africa event. This is evident in Y chromosomal and mtDNA phylogenies, where the Bushmen and their kin harbor variants which coalesce deeply in time with those of others. And, a few years ago another group revealed the likelihood that Bushmen also are products of an admixture event in the last ~50,000 years with a distinct hominin lineage which diverged ~1 million years before the present from the main line which led up to anatomically modern humanity. Now Pickrell et al. present us with a twist which is perhaps even more astringent than a lime: in their genomes the Bushmen and their Khoisan kin, the Khoe herders, reflect an ancient admixture event with East Africans, who themselves were the outcomes of hybridizations between West Eurasians and indigenous African populations. More relevantly for my concise summation of the conclusion, the West Eurasian component does not necessarily reflect modern Middle Eastern populations, so much as Southern Europeans!

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The intellectual poverty of identity politics & Orientalism

Very interested in Roman & Chinese history
The core focus of this weblog is genetics. Anyone who knows me in “real life” is also aware that this focus is not something that manifests only on the internet, or at the workplace, but suffuses my whole life. Genetics is to me as crack is to Bobby Brown. This is not necessarily always a good thing, as I’ve found my interest in other areas of science diminishing because I lack the marginal time to explore them to the same depth as I can genetical topics. But such is life. Choices are made. Opportunity costs present themselves.

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Who reads this blog

Every now and then Ed Yong has a “de-lurking” post up. That reminds me that it is often useful for long time readers who rarely comment, as they see they are not alone. I won’t put any stipulations on what you have to say (aside from that it has to be about who you are, etc.). So in imitation of Ed I figured that this is as good a time as any to open up the floor (and, I know there’s a large intersection of readership, so you may be practiced).

Addendum: I put the 2011 reader survey raw results online, if anyone wants to process them. I should do something like that again soon….

Circumcision rates: averages which deceive

Update 2: No longer accepting comments on this post. Please stop submitting. Thanks.

Update: Due to the vociferous and emotive nature of many comments, I am not publishing over half submitted on this post. Just so you know your chances…

One thing that I have read repeatedly is that circumcision rates in the United States have fallen over the past generation. For non-Americans in the readership, yes, American males are customarily circumcised even if they are not from a religious or cultural tradition where this is the norm (i.e., they are not Muslim, Jewish, or East or West African). For Americans, yes, circumcision has nothing to do with Christianity (something that would be obvious if more Americans actually read the New Testament, instead of just quoting selective passages from it). But looking more closely at the data it seems that the decline in circumcision is predominantly a function of its collapse as a normative practice in the western states!

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Alexander's soldiers left no mark

It is well known that Alexander the Great invaded the Indus river valley. Coincidentally in the mountains shadowing this region are isolated groups of tribal populations whose physical appearance is at at variance with South Asians. In particular, they are much lighter skinned, and often blonde or blue eyed. Naturally this led to 19th and early 20th century speculation that they were lost white races, perhaps descended from some of the Macedonian soldiers of Alexander. This was partly the basis of the Rudyard Kipling novel The Man Who Would Be King. Naturally over time some of these people themselves have forwarded this idea. In the case of a group such as the Kalash of Pakistan this conjecture is supported by the exotic nature of their religion, which seems to be Indo-European, and similar to Vedic Hinduism, with minimal influence from Islam.

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Ancestry testing as a Rorschach test

Vanessa L. Williams
Credit: Tabercil

The website The Root often has a Q & A with various African Americans, famous and not so famous, about their genealogy in relation to personal genomics. In most cases these tests tell you what you already know, but for African Americans there is often actually value-add in terms of greater specificity and precision, which would otherwise be lacking for obvious historical reasons. Despite its objective scientific patina the processing and interpretation of the resultant information can be rather subject, and illuminating. Recently they sat down with actress, and the first black winner of Miss America, Vanessa L. Williams, to discuss her results. There were two passages which I think were particularly interesting, so I’ll quote them below:

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From the other 95% on the AHA's embargo policy

Update: Also see, Pimpin’ the ghetto:

Pimps who run what little economy exists in the ghetto. They control the humanities ghetto, have old boys patronage networks to fall back on, and have a great deal in a slummy part of town. In other words, folks who get tenure-track PhDs at research universities.

The American Historical Association is run by pimps for pimps — by professors at research universities, for professors at research universities. That their policy does not help the public or most PhD graduates of history programs is besides the point. They are an old boys network protecting themselves.

The AHA isn’t out ot protect disaster tourists, or losers, or escapees. The AHA is by, for, and of pimps.

This isn’t too criticize pimps — if you actually love the ghetto, why not be successful in it? — but to say that not everything they do is in your best interests.

If you are in the AHA, here is your choice: You can like that, or you can get out.

To extend the analogy, do pimps facilitate good healthy sex for society, or do they encourage the spread of unpalatable contagion by perpetuating the ghetto and its conditions? You know where I stand….

End Update

In relation to the AHA’s bizarre embargo policy Patrick Wyman left a long comment which I think is worth promoting up. Observe that some of the same could be applied to the natural sciences (recall the Carl Sagan fiasco). So here you have it….

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A Mongolian genome?

Citation: Xing J, Wuren T, Simonson TS, Watkins WS, Witherspoon DJ, et al. (2013) Genomic Analysis of Natural Selection and Phenotypic Variation in High-Altitude Mongolians. PLoS Genet 9(7): e1003634. doi:10.1371/journal.pgen.1003634

Well, not quite. You have to read the paper, Genomic Analysis of Natural Selection and Phenotypic Variation in High-Altitude Mongolians, to see why I’m skeptical. Frankly it doesn’t seem like they found too much of note in their results, so I’m kind of confused why this paper got into PLOS GENETICS (and to give due credit, this group has published very interesting work in the past which I have smiled upon). So why am I even posting about this paper? Because I was pretty sure they’d release their data, and they have (just page down to the bottom). All researchers who take the trouble to do this should be praised, highlighted, and respected. This improves science. After the AHA fiasco I’m going to redouble the effort to put the spotlight on those who release their data.

Addendum: It must be noted that a “Mongolian” identity is very much an outcome of Genghis Khan’s rise and paramountcy. The Mongols were just one of numerous tribes across what is today Mongolia. With the rise of the Mongol Empire many populations, including Turkic populations who were not part of a dialect continuum in close proximity to the Mongols, were assimilated into that ethnic identity with a few generations. The “Zulu” identity is similar, as it is a function of the rise to prominence of Shaka’s particular clan.

The American Historical Association seems nuts to me

Why the title? Read it for yourself: American Historical Association Statement on Policies Regarding the Embargoing of Completed History PhD Dissertations. Here’s the conclusion:

By endorsing a policy that allows embargos, the AHA seeks to balance two central though at times competing ideals in our profession–on the one hand, the full and timely dissemination of new historical knowledge; and, on the other, the unfettered ability of young historians to revise their dissertations and obtain a publishing contract from a press. We believe that the policy recommended here honors both of these ideals by withholding the dissertation from online public access, but only for a clearly stated, limited amount of time, and by encouraging other, more traditional forms of availability that would insure a hard copy of the dissertation remains accessible to scholars and all other interested parties.

I’m going to try hard not to go “Michael Eisen” on this: did the AHA just compare the dissemination of knowledge with careers? It strikes me that if you do scholarship of any sort the discovery and dissemination of knowledge is all, it is the summum bonum. All else is secondary and marginal. As it is the academic job market is brutally Darwinian in the most extreme sense, and more so for humanities scholars. Can you truly push this thread any further by open access requirements for dissertations? I doubt it. But let’s test this proposition.

Note: I am granting many of the premises of the argument in the statement for the purposes of this post. Even allowing for those premises, when a scholarly discipline goes too far down the careerist rabbit-hole, then it is time for people to start thinking about become actuaries to put bread on the table.