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Time has a worthwhile piece up, How to Save a Trillion Dollars. One thing the author brings up in relation to our exorbitant military spending is that in certain sectors the lead of the American armed forces technologically is such that we do not to need to significantly upgrade our matériel for a generation to maintain at least a marginal level of superiority. The F-35 is clearly superior to the F-16, but is it worth it to increase the gap between our air superiority and our nearest competitors at $125 million per unit cost? Not only that, but the American military clearly “sets the curve,” so that the more we invest in our own technological superiority, the more our rivals will have to invest so as to “catch up” and keep the gap relatively constant. The reality is that basically developed nations just need to be advanced enough that they can pummel the leaders of select lesser nations, such as Libya or Ivory Coast, and, have a military beefed up enough to be respectable in the eyes of their peers. An “arms race” between developed nations is not necessary for either of these.

Two years ago Reconstructing Indian Genetic History reframed how we should view South Asian historical genomics. In short, Indians can be viewed as a hybrid between a West Eurasian group, “Ancestral North Indians” (ANI) and a very different group, “Ancestral South Indians” (ASI), which had distant connections to West and East Eurasians. At least to a first approximation. Last fall I posted on a new paper which surveyed the Austro-Asiatic speaking peoples of India, and concluded that they were exogenous to the subcontinent. This is an interesting point. Prehistoric treatments of South Asia often use linguistic terms to denote putative ancient populations. One model is that first it was the Munda, the most ancient Austro-Asiatics. Then the Dravidians. And finally the Indo-Aryans. These genetic data imply that the Munda arrived after the initial ANI-ASI synthesis. The Munda people of India can be thought of as ANI-ASI, with an overlay of East Eurasian ancestry.

Zack Ajmal’s K = 11 ADMIXTURE run has highlighted some further issues. He has a set of Austro-Asiatic samples, as well as a host of Indo-Aryan and Dravidian speaking populations. I now believe we can now further clarify and refine our model of the peopling of India. Here it is:

1) ASI, circa ~10,000 years BP

2) ANI enters the subcontinent from the northwest, synthesis with ASI

3) The ancestors of the Munda enter from the northeast, synthesis with ANI + ASI in their region

4) A subsequent group of West Eurasians, related to the ANI, so I will term them ANI2, enters from the northwest and overlays the ANI + ASI synthesis. In the northeast quadrant of the subcontinent this group marginalizes the Munda people, who are either assimilated or escape to more remote locations. I believe that ANI2 is likely the Indo-Europeans, but it may be Dravidians as well

5) A second group of Austro-Asiatic peoples enters from the northeast, and synthesizes with the AN2 + ANI + ASI. In some regions they are absorbed (Assam), but in other regions they are culturally dominant (Meghalaya)

Below are two plots which illustrate where I’m coming from. The “S Asian” component from K = 11 above seems to overlap, but is not identical to, ANI. The “Onge” component plays a similar role with ASI. The “SW Asian” and “European” elements are pretty straightforward. They’re very closely related to the “S Asian” one, but they do separate from it. Their relationship to distant non-Indian groups as well as a gradient toward the northwest suggests to me a more recent arrival of this element.

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1) First, a post from the past: South Indian Phylogeography.

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No time to blog them now…I’ll get to it. But I really want to point you to two papers of interest in PLoS Genetics (all the good stuff lands on Friday!).

Adaptations to Climate-Mediated Selective Pressures in Humans:

Humans inhabit a remarkably diverse range of environments, and adaptation through natural selection has likely played a central role in the capacity to survive and thrive in extreme climates. Unlike numerous studies that used only population genetic data to search for evidence of selection, here we scan the human genome for selection signals by identifying the SNPs with the strongest correlations between allele frequencies and climate across 61 worldwide populations. We find a striking enrichment of genic and nonsynonymous SNPs relative to non-genic SNPs among those that are strongly correlated with these climate variables. Among the most extreme signals, several overlap with those from GWAS, including SNPs associated with pigmentation and autoimmune diseases. Further, we find an enrichment of strong signals in gene sets related to UV radiation, infection and immunity, and cancer. Our results imply that adaptations to climate shaped the spatial distribution of variation in humans.

Climate would be “Court Jester”, while immune/disease might be “Red Queen” (unless we’re talking relaxation of constraint). Second, The History of African Gene Flow into Southern Europeans, Levantines, and Jews:

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After seeing this post up on how high information levels and education may lead to political polarization, I wanted to revisit the GSS data on political moderation and independence in light of educational attainment and intelligence. For the later I used the proxy of a score on a vocabulary test which has a 0.70 correlation with general intelligence. My question was this: what are the different effects of intelligence and education on ideology and partisanship?

To answer this question I looked at two response variables, POLVIEWS and PARTYID, which measure ideology from very liberal to very conservative and partisanship from strong Democrat to strong Republican. I amalgamated “leaners” so that in the middle I had moderates and independents left. For the vocab test I used WORDSUM. The scores have a value from 0 to 10, out of 10. I combined the 0-4 interval because the sample size there was small. Finally, I limited the sample to non-Hispanic whites after the year 2000 to eliminate some background confounds (e.g., minorities tend to be way more Democratic, all things equal).

I generated some area graphs. First, I looked at proportions of each ideology or party in a particular category. For example, the percentage liberal, moderate, and conservative who get a vocab score of 5, or have high school education. Then, I controlled for education and looked at vocab score. Specifically, I limited the sample to those who had only a high school diploma, and then those who had a university degree and higher. These two classes had large sample sizes. Then I looked at how ideology and party varied by vocab score.

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A boring man

Immanuel Kant is famous. You’ve probably heard of him. And you know some of his ideas, such as the categorical imperative, or have at some point started the Critique of Pure Reason (if you’re like me, you never finish it). But what do you know about his biography? I may not be able to complete a Critique of Pure Reason, but I did read Manfred Kuehn’s Kant: A Biography in the winter of 2002. From that I learned one surprising fact: Immanuel Kant in his personal beliefs was not an orthodox Christian, if he had religious sentiment at all. This surprised me because I had read elsewhere in passing that Kant was a Pietistic Lutheran. Ultimately whether Kant was religious or not was not a major issue for me, but I did update my personal factual database.

Fast forward six years to 2008. I was at a party kicking back with some philosophers (as in, people completing their doctorates), and it came up that one of them was doing their dissertation on some of Kant’s ideas. This individual happened to be Roman Catholic, and was trying to work in some religious thought. I expressed curiosity, and mentioned offhand how Kant himself was irreligious. My interlocutor expressed surprise and corrected my confusion, explaining that Kant was a devout Lutheran Christian. I shrugged and accepted the correction. I had only read one biography on Kant, and I wasn’t going to make a stand on the views of one scholar (especially when as I said I didn’t really care).

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In my persistent slog beating the drums for open genomics I’ve made the argument that people should have the right to have more information about what their genetic code entails without the necessary and mandatory imprimatur of professional assent. Not only that, but I’d want to know myself. This is not a new found position which I’ve come to of late. I recall 17 years ago having a classroom discussion on this topic in the wake of the tests for Huntington’s disease, and I was certainly pro-knowledge. That being said, there were conditionals. My position was that this sort of information would be the most useful for the young, because they could determine the arc of their life with full knowledge of their probable time window. A friend argued that ultimately you should always live every day as if it is your last day anyhow, so why get tested? This is great as a superficial talking point, but as a concrete matter our decisions are conditioned on the expected number of alloted days we have.

A few years ago I heard about the story of the singer Bobby Darin, and it made me think of those issues. From Wikipedia:

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You don’t need to know Dutch:

Zack Ajmal has been taking his Reference 3 data set for a stroll over at the Harappa Ancestry Project. Or, more accurately, he’s been driving his computer to crunch up ADMIXTURE results ascending up a later of K’s. Because it is the Harappa Ancestry Project Zack’s populations are overloaded a touch on South Asians. He managed to get a hold of the data set from Reconstructing Indian History. If you will recall this paper showed that the South Asian component which falls out of ancestry structure inference algorithms may actually be a stabilized hybrid of two ancient populations, “Ancestral North Indian” (ANI) and “Ancestral South Indian” (ASI). ANI are a population which can be compared pretty easily to other West Eurasians. There are no “pure” groups of ASI, but the indigenous peoples of the Andaman Islands are the closest, having diverged from the mainland ASI populations tens of thousands of years ago.

At K = 11, that is, 11 inferred ancestral populations, Zack seems to have now stumbled onto the patterns which one would expect from this hybrid model of South Asians. Let me quote him:

Now let’s take all the reference populations with an Onge component between 10% to 50% and use the equation above to calculate their ASI percentage. The results are in a spreadsheet. There are several populations with an even higher Ancestral South Indian than any of the Reich et al groups, with Paniya being the highest at 67.4%.

The r-squared between % ASI and % Onge, an Andaman group, is 0.994. That means 99.4% of the variation in the former can be explained by variation of the latter. The % ASI is consistently higher than Onge. Why? The last common ancestors of Andaman Islanders and the ASI diverged on the order of tens of thousands of years ago. Dienekes observed ADMIXTURE needs good reference populations, and the Onge have been so long diverged from the last common ancestor with the mainland ASI populations that it’s not a perfect proxy for this ancient group. But it seems that the underestimate is systematically biased in the same direction, so that explains the good fit between the two trends.

Zack naturally generated a pairwise matrix of Fsts between these inferred ancestral populations. Remember, the value within Fst shows the proportion of the genetic variance in the two populations which can be partitioned across them, but not within them. So it’s a rough measure of genetic distance.

Here’s the matrix. I’ve renamed some populations:

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One of the aspects of fiction is that it serves as a Rorschach test. Over at Slate Nina Shen Rastogi has a post up, Is “Game of Thrones” Racist?:

The Dothraki are dark, with long hair they wear in dreadlocks or in matted braids. They sport very little clothing, bedeck themselves in blue paint, and, as depicted in the premiere episode, their weddings are riotous affairs full of thumping drums, ululations, orgiastic public sex, passionate throat-slitting, and fly-ridden baskets full of delicious, bloody animal hearts. A man in a turban presents the new khaleesi with an inlaid box full of hissing snakes. After their nuptials, the immense Khal Drogo takes Daenerys to a seaside cliff at twilight and then, against her muted pleas, takes her doggie-style.

They are, in short, barbarians of the most stereotypical, un-PC sort. As I watched, I kept thinking, “Are they still allowed to do that?”

I wasn’t the only viewer who found the depiction of the Dothraki uncomfortable, to say the least. Time’s TV critic James Poniewozik, noting that the Dothraki seem to be made up of a “grabbag of exotic/dark/savage signifiers,” wondered if it was “possible to be racist toward a race that does not actually exist.”

First, the author immediately notes that for every swarthy barbarian there is a depiction of another trope, the Evil Blonde Guy. Nina Shen Ragosti’s read the books. She knows that though initially you encounter a story which is framed in black-white Manichean terms that is the norm in the more juvenile sectors of epic fantasy, the development of the characters, and your perception of the world which they inhabit, quickly slouches toward many shades of gray.

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