Recently Jason Antrosio began a dialogue with readers of this weblog on the “race question.” More specifically, he asked that we peruse a 2009 review of the race question in the American Journal of Physical Anthropology. Additionally, he also pointed me to another 2009 paper in Genome Research, Non-Darwinian estimation: My ancestors, my genes’ ancestors. Normally I don’t react well to interactions anthropologists who are not Henry Harpending or John Hawks. But Dr. Antrosio engaged civilly, so I shall return the favor.

I did read all the papers in the American Journal of Physical Anthropology special issue, as well the Genome Research paper. My real interest here are specific questions of science, not history or social science. But I will address the latter areas rather quickly. I am not someone who comes to this totally naked of the history or social science of the race question. I’ve read many books on the topic. And as a colored person who has moderate experience with racism I get rather bored and irritated with excessively patronizing explanations of how racism afflicts us coloreds from white academics (non-white academics who focus on this subject are usually careerists or activists who don’t have to make much pretense toward scholarly substance and can be duly ignored, at least in my experience). The main point which I think we can all agree upon is that colloquial understanding of race has only a partial correlation with any genetic understanding of race. I myself have ranted against the confusions which have ensued because of the conflation of the two classes, and it is certainly a legitimate area of study, but it is not my primary concern. And importantly, I have no great primary interest in battling racism.

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Greg Cochran pointed out something that I’d been considering about the MacArthur et al. paper: if the average human (OK, non-African human) has ~100 loss-of-function variants, then the standard deviation should be ~10. That’s because the distribution is presumably poisson, and variance = mean, and the square root of the of the variance (~100) is the standard deviation (~10). In plainer English there should be a substantial variation in the number of loss-of-function variants within a population, and across siblings. Though by definition these loss-of-function variants don’t kill you, in general there is the assumption that this class of mutants does exhibit some fitness drag (e.g., the fitness of a heterozygote for a variant which is lethal as a homozygote genotype may be ~0.90). A quick back of the envelope calculation implies to me that there is a 1 out of several hundreds of thousands probability that two siblings may exhibit a range of 60 loss-function-variants. But a 40 unit gap is more like a 1 out of one thousand chance.

This variance in mutational load has been the hobby-horse of intellectuals for a while now. Armand Leroi suggested that it correlated with beauty. Geoffrey Miller with intelligence. In the near future presumably we’ll get to see if there’s anything real in this. And obviously we don’t need to leave it to scientists. We’ll all know the summary statistics about own genomes, and probably be able to intuit rough patterns…if they exist.

From OpenSNP:

At the end of last year we announced that we’ve got some funding from the German WikiMedia foundation to get more people – who are willing to share their results – genotyped. We have now settled on a process that should allow us to perform the project without too many problems.Starting today, you can apply for one of the free genotypings. The deadline for applications is Sunday, 03/25/12 23:59 o’clock, so you still have some time to think about an application. In the two weeks following the deadline, we will select as many participants as we can afford to get genotyped using the 5000 Euros we received from Wikimedia. We’ll get in contact with everybody who has sent an application to let all applicants know whether their application was successful or not.

The genotyping will be done through 23andMe. We will order you a gift kit which will be delivered to your address. These gift kits include prepaid access to the 23andMe website for 12 months, so you can check up on the latest findings about your genetic variation as well. After this 12 month period, those features will expire automatically, you don’t have to cancel any subscriptions.

Our application form contains some standard questions (Where do you live? Does 23andMe deliver to your country? etc.) but also some details about your motivation, why you want to make your dataset available to the public and why your data might be of great interest (For example: Do you have a rare disease where research is lacking?). Additionally, we will also try to get people genotyped who are currently under-represented in publicly available data sets. Most data up to now is from WEIRDs: Western, Educated, Industrialized, Rich and Democratic people (most are probably male, too).

Bastian already contacted me about getting Afrikaners typed this way. I haven’t had time to get back to him, but this might be a viable option if you live in a country where 23andMe ships.

The Fennoscandia Project has now gone through chromosomes 1 to 6 with Chromopainter/fineSTRUCTURE. The conclusion:

If we looker at the bigger picture we see that most of continental Europe is tied to each other more trough mutations than others making them harder to seperate even at this level (6 chromosomes). We see that Lithuanians seem to have stronger affiliation to the large continental European cluster including Scandinavians but this affiliation is weaker for Vologda Russians. This connection is even weaker for Finns and almost non-existing for Saamis. This is in accordance with the MDS plot.

Here is the relevant plot (I have added some labels):

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Over at Genomes Unzipped Dr. Daniel MacArthur has a review up of a paper in Science where he is first author (note for grad students and aspiring post-docs, Dr. MacArthur is starting a new lab, where he posted an ungated version of the paper). He hits all the salient points, so I will cover two issues, a general and a specific.

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Prompted by my posts, Dienekes, A teaser on the Kalash:

I am in the middle of a ChromoPainter/fineSTRUCTURE analysis of a broad dataset designed to explore certain mysteries that have often come up in my previous experiments. Barring the unexpected, the analysis should be completed sometime next week.

Below you can see the normalized number of “chunks” donated by various populations to the Kalash….

Here is the bar plot which Dienekes generated (left to right indicates extent of “donation” to the Kalash):

I highlighted the most significant non-South Asian donor. Dienekes states:

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A recent paper on Turkish genetics has a tree which illustrates a summary of how the Kalash shake out:

I say summary because this tree takes a lot of information and tries to generate the best fit representation. It does hide some information by the nature of its aggregation of patterns. For example, the position of the Burusho, or Turks, has to do with the fact that both of these have low, but noticeable, levels of East Asian admixture on top of a different base. If you removed this eastern element both groups would come much closer to similar groups. The extreme long branches leading to the Kalash and Mozabites are almost certainly a function of endogamy and inbreeding. Their allele frequencies diverged from nearby populations because of isolation.

But notice the nearby populations of the Kalash. They’re northwest South Asian. In many ways if you removed the drift and endogamy from the Kalash I suspect you’d been left with a group very similar to their Pathan neighbors.

Finally, as many of you know I put a substantial number of comments into ‘spam’ on this weblog. Here’s one related to the Kalash which you didn’t see:

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The New York Times and Nature both have favorable reviews of Oxford Nanopore’s showy claims at Advances in Genome Biology and Technology. If you don’t know what I’m talking about, please see the twitter stream, or the post at Genomes Unzipped.

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A “test” post showed up on this website earlier. I’ve been told it was probably an error by IT. I had no idea that it was even up because I was off the internet and not checking my phone for ~18 hours for various reasons. Just thought I’d pass that on….

When Zack ran ChromoPainter/fineStructure on South Asians the results naturally yielded a blueish hue along the diagonal. This is expected because the diagonal represents the population’s own relationship with itself. The bluer the diagonal, the more inbred and isolated the population is likely to be. To the top left you see various Austro-Asiatic tribes, in the middle the “Gujarati A” population from the HapMap (probably Patels), and in the bottom right various Pakistani groups, who presumably have higher rates of consanguinity than the South Asian norm. But one group stands out among the other Pakistani groups: the Kalash. They’re highly endogamous because they’re the last pagan population in Pakistan, isolated in the fastness of the Chitral. It is likely that if their region of Pakistan had been under Afghan, and not British, rule these people would have been forcibly submitted to Islam like their Nuristani cousins across the border 100 years ago. As it is I assume that at some point I may have to update these posts with the note that Pakistani Taliban forcibly converted the few thousand remaining Kalash to Islam. Such is the march of history in the abode of peace.

Religion may be a critical explanation for this isolation, because the similarly isolated Burusho of northern Pakistan are not nearly as inbred. Though the Burusho are speakers of a linguistic isolate, they adopted Islam ~500 years ago, and so are likely to have intermarried more frequently with outsiders. The Kalash isolation means that in some ways they’re relatively useless in comparative genomic analysis. Though they are not an ‘ancestral population’ they routinely jump out as distinctive early on in PCA or ADMIXTURE/Structure/frappe analyses. In short, they are close to one large extended family. Nevertheless, they can be somewhat informative when these particularities are taken into account.

Presumably the Kalash are distant from other populations because of their isolation, but their relationship to other world populations will retain the same general conformation before their endogamous period. With that in mind I ran a narrow South Asian focused ADMIXTURE run. With ~400,000 markers I had: The Kalash, Burusho, Brahui, Pathan, Gujarati Patels, Hazara, Uygur, Russians, Japanese, Bantus of Kenya, Basque, Adygei, and Druze. Below are the results for K = 7 for selection:

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Since my original post on the Afrikaner genotype, I’ve gotten many responses. No genotypes yet though. At some point I need to organize how to pay for typing many individuals. Currently my intent is to pay for those who will allow their identities to be public so that people can confirm their genealogies. Other people have emailed me to say that Afrikaners with whom they have shared genotypes on 23andMe often have African or Asian ancestral segments. But all hearsay so far.

In other news, I’ve got a Dinka gentoype I’ll be analyzing soon (some minor technical issues with merging datasets has delayed this some).

Most of you know that Stephen Jay Gould proposed ‘non-overlapping magisteria’ for science and religion. I don’t care much for the framing myself, though neither am I on the same page as Sam Harris and company. But I thought of this model when reading this comment below:

Kind of a tangent, but I think it gets slippery considering which construction is more “real.” We tend to come at it as the “reality” being genetic ancestry upon which a socially constructed (“not real”) conception of race is sloppily mapped. However, I get the social science perspective that the socially constructed race is the category that is often much more “real” — it is the lived experience of everyone in that group. If you are visibly black (or white) and part of that community, then you “really” are black (or white) in many, many ways that matters, whether you’re 90% African or 0%.

In the context of the topics we mainly discuss here — population genetics, medical genetics, etc — genetic ancestry is “real” and social race categories matter less. This is why I’m mostly in favor of letting social science have the word “race” and would really push for biologists to use better-defined terms (like ancestry).

It’s a mistake to say that human artifice is “less real” than genetics, it’s context dependent. I recognize that the social construction of race is a sort of unrefereed crowd-sourced attempt at deriving ancestry, but as we start to divide causal factors into social / biological aspects of race, this mapping is more of a hindrance than a help. A first step is to stop using shared language to discuss them.

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Uyghur girls

A few people have pointed me to the paper, Implications for health and disease in the genetic signature of the Ashkenazi Jewish population. You should check it out if you don’t have academic access to papers, it’s not gated. Rather, I want to focus on a methodological issue.

In the genetics reader survey only 20 percent of you agreed that you understood how to read an ADMIXTURE plot. After looking at some of the results in this paper I have a lot of sympathy. Understanding what’s going on requires more prior information than is often present in the legends of the figures.

It is known that to a first approximation Ashkenazi Jews, that is, the Jews of Europe, can be understood as an admixture between a European population and a Middle Eastern one. But Ashkenazi Jews also exhibit their own genetic distinctiveness, probably due to long term endogamy. This shows up in various genetic statistics. In this paper the authors show that Ashkenazi form their own cluster in both PCA and ADMIXTURE, two ways in which to ascertain population structure. Below I’ve reedited and highlighted some populations of note in one of their ADMIXTURE plots. It’s rather informative of the bigger problem with interpreting these sorts of results in the absence of context.

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I just attended a presentation where a researcher outlined how epigenomics could help patients with various grave illnesses. Normally I don’t focus on human medical genetics too much because it always depresses me. I don’t understand how medical geneticists don’t start wondering what hidden disease everyone around them has. In any case the researcher outlined how epigenomic information allowed for better treatment, so as to extend the lives of patients. All well and good. But then one individual in the audience began asking pointed questions as to the medical ethics of the enterprise, and whether the researcher had cleared some legally sanctioned hurdles. More specifically, there was a question whether exploring someone’s epigenomic profile might expose private information of their relatives! (because relatives share epigenomic and genomic profiles to some extent)

Frankly I began to get enraged at this point. People are suffering from terminal illnesses, and considerations of the genetic privacy of their near relatives are looming large? Seriously? The reality is that manifestation of a disease itself gives one information about the risks of their relatives. In any case, the researcher admitted that further progress in this area is probably going to be due to the investments of wealthy individuals (e.g., people like Steve Jobs who have illnesses) as well as outside of the United States. You’re #1 America!

Rod Dreher at The American Conservative, White Working-Class ‘Seculars’:

What’s interesting to think about is that these working-class non-churchgoers are probably not secular in the same way white intellectual elites are secular. I bet if you polled them, 999 out of 1,000 would say they believed in God and considered themselves to be Christians. It’s just that they don’t go to church. Where I live, during deer hunting season, to be a white male is to be seasonally “secular” in this way.

One way to answer this question is look at the GSS. I used the ATTEND (attend church that is) variable to ascertain secularity. Those who never attended church or did so less than once a year (in other words, some years they did attend, in other years they did not), are “secular.” Those who attend nearly weekly, or more, are “religious.” To assess class I simply divided the non-Hispanic white population into those who had a college degree or higher (middle class), and those who did not (working class).

Below are some responses to a selection of questions.

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