The Dodecad ancestry project might be of some interest. In particular if you have ancestry from a gold-chain wearing culture.

Dienekes Pontikos, Introducing the Dodecad ancestry project:

1) Project goals

The Dodecad ancestry project has two goals:

– To provide detailed ancestry analysis to individuals who have tested with 23andMe; other testing companies may be included in the future.

– To build samples of individuals for regions of the world (e.g. Greeks, Finns, Albanians, Southern Italians, etc.) currently under-represented in publicly available datasets.

I neither endorse nor am I affiliated with any genetic testing company. I have chosen to base the project on 23andMe results, because (i) I perceive that quite a few people have used the service, (ii) the Illumina genotyping platform it uses has substantial overlap with the publicly available datasets on which my analysis depends.

Basically some of you need to send him your 23andMe raw data files. The potential sample space of this group is going to be in the tens of thousands from what 23andMe representatives have stated about how many of the Complete Edition kits they’ve sold. Naturally due to labor and computational constraints he only wants people from particular populations. I think that’s fine. I’m a little taken aback by how demanding and critical Dienekes’ readers have been about the choice of populations he analyzes. You can install ADMIXTURE yourself, get data sets, and manipulate them in PLINK, etc. I hope many people will participate in this project. I would have given my sample, but I’m not of an appropriate population, and even if he wanted South Asians I’m pretty sure I’m not very representative of South Asians (I have very few runs-of-homozygosity and seem to have recent admixture from other world population groups).

Detailed admixture analysis of West Eurasian populations (+ GenomesUnzipped individuals). Dienekes looks at the Genomes Unzipped guys in the context of Eurasian variation. He explains why he prefers bar plots of inferred ancestral quanta over PCA and MDS charts.

A World Upside Down for Greeks. “In Greece, small businesses — defined as stores or workshops employing fewer than 10 people, though many are one-person operations — account for 96 percent of all enterprises and employ around two million of Greece’s five million-strong work force.” Part of this is presumably familialism. Greeks don’t trust each other, so private sector activity is always on a small scale. And part of it is probably the constricted regulatory framework of the Greek economy which prevents the emergence of corporations with some economies of scale. But either way it seems that this is too strong of a bias to be an efficient allocation of labor.

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In case you don’t know, Dienekes Pontikos has been posting a lot of analyses of available population genetic data sets with the ADMIXTURE program. You can find his myriad posts under the ADMIXTURE-experiments tag. Below is a bar plot he generated today. To follow up a debate which occurred last spring, it does seem from several of his results that there is some evidence of Berber admixture among the Sephardic Jews.

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When I was in college I would sometimes have late night conversations with the guys in my dorm, and the discussion would random-walk in very strange directions. During one of these quasi-salons a friend whose parents were from Korea expressed some surprise and disgust at the idea of wet earwax. It turns out he had not been aware of the fact that the majority of the people in the world have wet, sticky, earwax. I’d stumbled onto that datum in the course of my reading, and had to explain to most of the discussants that East Asians generally have dry earwax, while convincing my Korean American friend that wet earwax was not something that was totally abnormal. Earwax isn’t something we explore in polite conversation, so it makes sense that most people would be ignorant of the fact that there was inter-population variation on this phenotype.

But it doesn’t end there. Over the past five years the genetics of earwax has come back into the spotlight, because of its variation and what it can tell us about the history and evolution of humans since the Out of Africa event. Not only that, it seems the variation in earwax has some other phenotypic correlates. The SNPs in and around ABCC11 are a set where East Asians in particular show signs of being different from other world populations. The variants which are nearly fixed in East Asia around this locus are nearly disjoint in frequency with those in Africa. Here are the frequencies of the alleles of rs17822931 on ABCC11 from ALFRED:

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Whole-genome sequencing is a game-changer for human genetics. It is now possible to deduce every base of an individual’s genome (all 6 billion of them – two copies of 3 billion each) for a couple of thousand euros, and dropping. (Yes, euros). Even Ozzy Osbourne just got his genome sequenced! For researchers searching for the causes of genetic disease (or resistance to vast quantities of drugs and alcohol), this means they no longer have to infer where a mutation is by tracking a sampling of “markers” spaced across the genome – they can directly see all of the genetic information.

The problem is, they directly see all of the genetic information. If each of us carries thousands of mutations – changes that are very rare or may even have never been seen before in any other person – then telling which one of those changes is actually causing the condition is a tough task. Researchers in psychiatric genetics are currently grappling with how to handle this glut of information.

The problem is particularly acute in this field, where there is a (very slowly) growing realisation that many so-called common disorders, such as schizophrenia and autism – are really umbrella terms for collections of very rare disorders. Each of these conditions can be caused by mutations in single genes. The reason they are so common is that there are so many genes required to wire the brain properly – mutations in any of probably hundreds of genes can lead to the kinds of neurodevelopmental defects that ultimately result in psychopathology. (At least, that is the working hypothesis – see review below for a discussion of the evidence supporting it).

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In my post earlier in the week I mentioned the possible relationship between attitudes toward evolution and the causes and likelihood of Global Warming. I haven’t seen any survey data myself relating the two, so naturally I wanted to poke into the General Social Survey. Two variables of interest showed up, both from 2006:

1) GWSCI, “Understanding of causes of Global Warming by environmental scientists.” A five-point scale, from understanding “Very well” (1) to “Not at all” (5).

2) SCIAGRGW, “Extent of agreement among environmental scientists.” A five-point scale, from “Near complete agreement” (1) to “No agreement at all” (5).

I paired these up against EVOLVED, which is a simple True vs. False answer in relation the question as to whether “Human beings developed from animals.”

Tables below.

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Stephen Hsu on developments at the Beijing Genomics Institute:

I was floored today when the director of BGI told me they would soon reach a sequencing rate of 1000 (human) genomes per day (so, 10^5 to 10^6 genomes per year is right on the horizon). According to him, they can be profitable at a price of $5k per genome! [Clarification: I later learned this might mean at 10x coverage … not exactly sure, although I tried to get a more precise statement.]

Five years ago I asked Armand Leroi:

[Q] 10) If in 10 years you could purchase your own full genome sequence for a month of your salary, would you do it? (assume privacy concerns are obviated)

[A] Yes.

It looks like I didn’t anticipate the rate of change in this area, as 10 years was also certainly too conservative or pessimistic. Dan MacArthur has given a plausible estimate of ~2 years for the realization of a $1,000 genome, but it looks like we’ll hit a genome at the cost of a month’s salary for a professional person on the order of months and not years.

Autumn is here. And winter is coming.

The fresco to the left is the cover jacket illustration for Why we’re all Romans, a new cultural history which attempts to argue for the unique debts of Western civilization to Rome (in particular as a mediator of the wisdom of the Greeks and Hebrews). If you’re on the culturally conservative side it might be of some interest, it sports endorsements from a Fellow at the Hoover Institute and E. Christian Kopff. The fresco is from Pompeii, explaining its good state of preservation and present day fame and ubiquity. The man’s name is Terentius Neo, a wealthy merchant or magistrate apparently. The woman is presumed to be his wife. A strange question to throw out: am the only one who thinks that he resembles Laurence Fishburne? The fresco is used a lot because of its quality and prior fame, but I always start thinking of something ludicrous like The Matrix when I see it.

If you have some time to kill, the Paleo-Future weblog is really awesome. It shows what people thought the future was going to be like (often around the year 2000) from the 1870s through every decade of the 20th century. As usual with this sort of thing it tells you more about the salient aspects of a given time period, as people have a tendency of projecting contemporary fashions, technologies, and trends, rather than being able to anticipate innovation and changes of kind. Here’s a depiction of flying machines which dates to between 1900 and 1910: