I am free of rare homozygous recessives! (well, perhaps)

I got a notification today from Ian Logan that he set up a page on my genotype using a method which detects rare homozygous SNPs in the ~1 million markers I put up from my 23andMe results. My raw data is online, so anyone can analyze it. Here is the summary of my results:

The program finds about 50 ‘rare/uncommon’ SNPs from the 900,000+ tested by 23andMe.

The are no ‘homozygous-recessive’ results (surprisingly, as 1-2 might be expected).

There are a list other individuals, and sure enough most of them do have a rare recessive homozygous locus or two. I assume that ascertainment bias (the technology finding variation in Europeans better than non-Europeans in most cases) wouldn’t result in my case, because I should have less variation, not more (less variation would presumably result in more homozygous recessives). So I am thinking it may simply be that because I’m from a population with greater genetic variation (South Asians) I am less likely to yield a homozygous recessive.

In most cases population substructure doesn’t yield benefits for South Asians in terms of their genetic variation, because of intra-caste marriage (so the useful scope of ‘population’ is much smaller than the geographic one), …

The moral measure of bad teeth

Recently I was at the dentist and I was told that because I did not have any caries at this age, I would probably not have to worry about that in the future (in contrast, I do have some issues with gingivitis). I wasn’t surprised that I didn’t have caries, I have no great love of sweet confections. I had chalked up my evasion of this dental ailment to my behavior. To make a long story short my dentist disabused me of the notion that dental pathologies are purely a function of dental hygiene and diet. Rather, he explained that many of these ailments exhibit strong family and ethnic patterns, and are substantially heritable. My mother did suffer from periodontal disease a few years back, and that has made me much more proactive of my own dental health.

As someone who is quite conscious of the power of genetics, I was quite taken aback by this blind spot. I realized that not only did I attribute my own rather fortunate dental health (so far) to my personal behaviors, but, I had long suspected those with dental issues of less than optimal habits. Obviously environment (e.g., high sugar diet) does matter. …

Free speech Über Alles!

Will Saletan has has published a piece making a traditionalist American absolutist case for free speech. He points out that in most Western nations there are in fact curbs on speech which is considered offensive, disturbing, and perhaps dangerous. Therefore, Muslims who point to Western hypocrisy have a point. I agree with this argument without reservation. But, I do want to reiterate the putative targets of offense are illustrative of a divergence of values in and of themselves. Though I wouldn’t criticize non-Western Muslims for pointing out the existence of laws banning denial of the Holocaust, I do have issues when Western Muslims bring this point up even innocuously. The reason is simple: the Holocaust concerns the systematic state-sponsored murder of millions of human beings. This is a far more serious issue than the reputation of the prophet Muhammad. Of course that statement reflects my particular values. And, whether you accept the idea of hate speech or not I suspect most Westerners would accept the validity of this proposition.

More generally a major thread running through conflicts about speech is globalization and technology. Today communication and propagation is nearly frictionless, and government curbs on speech either have to be …

The Others, in black and white

New Scientist has a piece up, Europeans did not inherit pale skins from Neanderthals, based on a paper I blogged last month. One thing that I hadn’t though about in detail…how did anatomically modern humans of various shades perceive Neandertals of various shades? For example, it seems highly likely that there were swarthy Neandertals and pale Neandertals. Similarly, there were swarthy modern humans, and soon enough pale ones. Skin color is a very salient trait. Very different populations phylogenetically, Sub-Saharan Africans, Melanesians, and South Asians, have been defined as “black.” Did modern humans perceive Middle Eastern Neandertals, who may have been relatively dark, as much closer to humanlike status because of their similar complexion to anatomically modern Middle Eastern humans? Did they perceive European Neandertals, who may on average have been much lighter, as fundamentally different?

When doing physical reconstructions it seems to me that the gross morphology of Neandertals has been more emphasized. Their brow ridges, large prominent noses, and stocky body plans. But in this manner perhaps they’re like our imaginings of ancient Greek temples as alabaster white. In reality the temples of antiquity and many public buildings were festooned with color. Similarly, Neandertals came in all shades.

Signal of Indo-Aryan admixture in South Indian Brahmins

I’ve mentioned a few times that the Reich lab has been finding suggestive evidence for admixture between indigenous South Asians and a West Eurasian group on the order of ~3,000 years before the present. The modal explanation is probably an Indo-Aryan intrusion. Dienekes used rolloff in ADMIXTOOLS to repeat these general findings. Specifically, he found signal for an admixture event analogous to one between non-Brahmin South Indians and Northern Europeans. I say analogous because I do not mean to imply that the admixture was exactly of this form. Rather, there are general resemblances in the genetic profiles across the four groups (i.e., Orcadian & North Kannadi, and population X and Y which merged to form South Indian Brahmins).

The only thing I would add is that the North Kannadi, representative of non-Brahmin South Indians, are themselves a mixture between West Eurasian and an indigenous South Asian population. And, looking at the patterns of admixture in Harappa, it seems to me that South Indian Brahmins themselves have some admixture which postdates their arrival to South India, which is probably 1 to 2,000 years before the present. In the specific case of South Indian Brahmins my model …

Skewing my winnings

Last spring I made a bet with a friend that Mitt Romney would win. He gave me 5:1 odds, and I assumed a 40% chance that Romney would win. So I expected to lose, but if I won I’d win big. At this point I assume I’m out that money, because I’d put Romney’s chances at less than 40% (though I think people underweight uncertainty, so I believe there’s a lot of variation in this prediction). But now I’m hearing/reading that many Republicans are under the impression that the polls are skewed. If you believe that the polls are skewed would you be willing to bet money that the polls are skewed? Specifically, I want to wager that “unskewed polls” turn out to be further off the mark than the regular polls in reference to the final election results. I’m not 100% sure that the pollsters are correct, and I don’t know more than a superficial amount as to the weighting methodologies, but the track record of skew-skeptics is suspect enough that I think this is a way I can make money off people who I perceive to be suckers. Of course, the people who I perceive to be …

Paleopopulation Genetics

It seems a new field is being born! Jeff Wall & Monty Slatkin have a pretty thorough review out, Paleopopulation Genetics:

Paleopopulation genetics is a new field that focuses on the population genetics of extinct groups and ancestral populations (i.e., populations ancestral to extant groups). With recent advances in DNA sequencing technologies, we now have unprecedented ability to directly assay genetic variation from fossils. This allows us to address issues, such as past population structure, changes in population size, and evolutionary relationships between taxa, at a much greater resolution than can traditional population genetics studies. In this review, we discuss recent developments in this emerging field as well as prospects for the future.

Nothing very new for close readers of this weblog, but the references are useful for later mining.