Dan Vorhaus points me to this Newsweek feature on BGI. My friend Steve Hsu gets some face time in the piece:

…Last year, pharmaceutical giant Merck announced plans for a research collaboration with BGI, as the Chinese company’s revenue hit $150 million—revenue projected to triple this year. “I admire their passion and the willingness to take risks,” says Steven Hsu, a physicist at the University of Oregon, adding that “it permeates the organization.”

…

Satellite research centers have been set up or are underway in the U.S., Europe, Hong Kong, and four other locations in China, and the number of researchers at the main headquarters in Shenzhen has more than doubled during the past year and a half. The institute now employs almost 4,000 scientists and technicians—and is still expanding.

“I’ve seen it happen but sometimes even I can’t believe how fast we are moving,” says Luo Ruibang, a bioinformaticist, who at 23, fits perfectly within the company’s core demographic. The average age of the research staff is 26.

Li Yingrui, 24, directs the bioinformatics department and its 1,500 computer scientists. Having dropped out of college because it didn’t present enough of an intellectual challenge, he firmly believes in motivating young employees with wide-ranging freedom and responsibility. “They grow with the task and develop faster,” he says. One of his researchers is 18-year-old Zhao Bowen. While still in high school, Zhao joined the bioinformatics team for a summer project and blew everyone away with his problem-solving skills. After consulting with his parents, he took a full-time job as a researcher and finished school during his downtime. Fittingly, he now manages a project on the genetic basis of high IQ. His team is sampling 1,000 Chinese adults with an IQ higher than 145, comparing their genomes with those of an equal number of randomly picked control subjects. Zhao acknowledges that such projects linking intelligence with genes may be controversial but “more so elsewhere than in China,” he says, adding that several U.S. research groups have contacted him for collaboration. “Everybody is interested in intelligence,” he says.

Knowledge, information, innovation, these are the only ways that the human race will beat back the Malthusian trap in our age. The world is aging now, and many nations will be moving past peak labor soon. We’ll need to be squeeze more productivity our of fewer at some point.

Zack pointed me to two new ones, Fennoscandia Biographic Project, and Magnus Ducatus Lituaniae Project – BGA analysis project for the territories of former Grand Duchy of Lithuania. So I guess the circum-Baltic region is getting some thick coverage. The latter is also releasing some format conversion tools which seem to work in Windows, if you want to play with the analytic software yourself.

Image credit: Wikimedia

A few years ago I blogged a paper on how inbred the last Spanish Habsburgs had become, leading to all sorts of ill effects. Take a look at Charles II of Spain! He was as inbred as the product of a sibling mating. An extreme case of pedigree collapse in humans if there was one. This came to mind when an amusing feature in The Philadelphia Inquirer popped into my RSS feed, In royal/commoner marriage, a happy mix of genetic diversity. The writer gets a good number of choice quotes from one of the coauthors of the Habsburg paper, who observes that Prince Charles is moderately inbred, but his pairing with the very distantly related Diana (who came from the nobility as well) basically meant that his sons were outbred. Nevertheless, there is the suggestion that extra genetic diversity can’t hurt. I don’t think this is really a major positive worth mentioning. First, there is the possibility of outbreeding depression. Honestly I doubt this will be an issue.  But secondly, I think more relevant is that gains to outbreeding hit massive diminishing marginal returns rather quickly. For example, here’s the coefficient of relationship between pairs of relatives:

0.5 = Full siblings, parent-child
0.25 = Half siblings, Uncle/aunt-niece/nephew
0.125 = First cousins
0.03125 = Second cousins
0.0078125 = Third cousins

As you can see the genetic relevance of relatedness really drops off rapidly in a conventionally outbred population. There isn’t much gain I’d say to Prince William marrying a female who has a greater genetic distance from him. Though the marriage of a common Englishwoman, Kate Middleton, into the British royal family moves it further on from its relatively recent dominant German character.

You can read about the details here. Interestingly, Christopher Mims has been tweeting the “secret” early history of ScienceBlogs under the #SBhistory hashtag. I was one of the original 14 in January of 2006, so I saw a lot of things go down between then and the spring of 2010, when I moved here to my comfy new digs at Discover. I’d been blogging for over 3.5 years when Chris Mims contacted me out of the blue in the fall of 2005 about some “secret project.” It was weird timing, because Hylton Jolliffe of Corante had also contacted me 1.5 months earlier, though he never got back to me after I responded to his initial email. Blogging was a fun hobby, but I wasn’t a journalist, so I was pretty skeptical about it all. Chris and I had a back & forth before we finally agreed to terms. My main reason for joining was obviously not money, but perhaps the possibility of greater access to interesting people (e.g., I met Dr. Daniel MacArthur as a commenter on my blog in the spring of 2006, before meeting him in real life years later and striking up a lasting internet friendship). I thought this tweet was very amusing because I’m pretty confident that I was the subject:

I’m not an ideologue, but any Left-liberal worth his or her salt would certainly term me a “kooky conservative” (and which blogger do you think would have had a look at the list of others invited to the network beforehand? Not too hard to guess!) After the fact I did ask Chris and a few other Seed Magazine staffers how the hell I was included on the list. Yes, I was a prominent blogger, but I was certainly on the fringe in terms of my norms in relation to the whole network. But this explains it:

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Aside from transient memes such as Jesusland sectional sentiment tends to be implicit and remain below the surface, especially outside of “Dixie”, in the United States today. In a nation the size of a continent and populated by over 300 million we first start with an aggregation, as if we’re just another nation-state. This is evident when we compare how the United States is doing compared to…France, or the United Kingdom, or Denmark. Except the Russian Federation the proper point of comparison for all the large European nations is probably California. If we do disaggregate the United States first we generally start with race, and then perhaps move on to politics. But many of these variables are rooted in deeper sectional identities, which were much more salient in the early republic. Many of the arguments about the nature of the Civil War in terms of whether it was “about” slavery or economics or states rights misses the bigger picture that all of these issues contributed to, and emerged out of, an organic historical process where the new republic crystallized as a divergent set of regional interests which predate the founding.

Here is an fascinating section from the New England polemicist and minister Theodore Parker from The great battle between slavery and freedom:

In 1850…Arkansas had 97,402 white persons under twenty, and only 11,050 attending school; while of 210,831 whites of that age in Michigan, 112,175 were at school or college. Last year, Michigan had 132,234 scholars in her public common schools. In 1850, Arkansas contained 64,787 whites over twenty, – but 16,935 of these were unable to read and white; while, out of 184,240 of that age in Michigan, only 8,281 were thus ignorant, – of these, 3009 were foreigns; while, of the 16,935 illiterate persons of Arkansas, only 37 were born out of that State. The Slave State had only 47,852 persons over twenty who could read a word; while the free State had 175,959. Michigan had 107,943 volumes in “libraries other than private,” and Arkansas 420 volumes….

Arkansas and Michigan were of particular interest because these were old frontier states which were settled primarily (at least initially in the case of Michigan, before 20th century industrialization) by whites from particular regions of the United States; the Old South in the case of Arkansas, and New England and upstate New York in the case of Michigan. A new paper, Black and White Fertility, Differential Baby Booms: The Value of Civil Rights, has some old Census data which I thought would be of interest. In particular, they report fertility and years of education for a given Census region. Here’s a map which shows the divisions:

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One of the things that happens if you read ethnographically thick books like Nicholas Dirks’ Castes of Mind: Colonialism and the Making of Modern India is that you start to wonder if most castes were simply created by the British and for the British. Granted, even Dirks would not deny the existence of Brahmins prior to the British period, but those who work within his general paradigm might argue that a group like Kayasthas were the product of very recent developments (e.g., the uplift of a non-Brahmin literate group willing to serve Muslim and British rulers). The emergence of genomics complicates this sort narrative, because you can examine relationships and see how plausible they would be given a particular social model.

Zack Ajmal is now at 90 participants in the Harappa Ancestry Project. He’s still undersampling people from the Indo-Gangetic plain between Punjab and Bengal, but that’s not his fault. Hopefully that will change. He posted K = 4 recently for the last 10 participants, but I notice K = 12 in his spreadsheets. So this is what I did:

1) I aligned the ethnic identification information with the K = 12 results.

2) I removed relatives and those who were not 100% South Asian.

3) I added some reference populations in. These are all upper case below. All other rows are individuals (HRP numbers provided).

4) I removed five ancestral groups. The three Africans, Papuans, and Siberians.

Then I arranged the rows alphabetically by ethnic identification. Helpfully many people provided their caste information as well. I’ve uploaded a csv with the information. But skim the plots & table below. Those of you who are brown can probably make more sense of them than I can. But I think some of the patterns are pretty interesting already. For me the big thing that jumps out is how uniform some of these caste groups are. Remember that HRP22 and HRP23 are my parents.  If the British made these groups up, they were very punctilious about their ancestral make up in constituting them!

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Season premier this Wednesday. Three days and counting….

Sometimes in the comments of this weblog people get into heated disagreements about one figure and its proper interpretation. I don’t get much involved most of the time because different visualization techniques often differ on the margin, so getting obsessed with minor details is a fool’s errand. For example, in the paper I reviewed below there was a neighbor-joining phylogenetic tree. Take a look. The length of the branches are proportional to genetic distance.

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Last week I reviewed ideas about the effect of “exogenous shocks” to an ecosystem of creatures, and how it might reshape their evolutionary trajectory. These sorts of issues are well known in their generality. They have implications from the broadest macroscale systematics to microevolutionary process. The shocks point to changes over time which have a general effect, but what about exogenous parameters which shift spatially and regularly? I’m talking latitudes here. The further you get from the equator the more the climate varies over the season, and the lower the mean temperature, and, the less the aggregate radiation the biosphere catches. Allen’s rule and Bergmann’s rule are two observational trends which biologists have long observed in relation to many organisms. The equatorial variants are slimmer in their physique, while the polar ones are stockier. Additionally, there tends to be an increase in mean mass as one moves away from the equator.

But these rules are just general observations. What process underlies these observations? The likely culprit would be natural selection of course. But the specific manner in which this process shakes out, on both the organismic and genetic level, still needs to be elucidated in further detail. A new paper in PLoS Genetics attempts to do this more rigorously and deeply than has been done before for one particular world wide mammalian species, H. sapiens sapiens. We have spanned the latitudes and longitudes, and so we’re a perfect test case for an exploration of the broader microevolutionary forces which shape variation.

The paper is Adaptations to Climate-Mediated Selective Pressures in Humans. Its technical guts can be intimidating, but its initial questions and final answers are less daunting. So let’s jump straight to the last paragraph of the discussion:

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Matt Ridley has a predictable op-ed in the WSJ (based on our knowledge of his prior normative frame), Your Genes in an Envelope? More, Please. But the last section is interesting:

If freedom does not appeal, the clinching argument for allowing consumers unfiltered access to their own genes is a scientific one. The only way slight genetic influences on health are going to emerge is if thousands of people submit their genomes for testing, and the only way that is going to happen is voluntarily. Academic research projects cannot promise to create the huge databases that an enthusiastic populace applying to an entrepreneurial testing industry can spawn. Genetic knowledge, whether the high priests like it or not, is going to be a crowd-sourced phenomenon.

I think “crowd-sourcing” has limits, but in many areas it will probably be the way of the future because there is a constraint on the labor hours of scholars. This was implicit in Joseph Pickrell’s argument in Why DTC genetic testing is good for research. My post Resolutions in the Indian genetic layer cake was based on Zack Ajmal’s particular interest in Indian genetics which prompted him to ask for both the Reich et al. and Chauby et al. data sets. Bringing the two data sets into one ADMIXTURE run easily allowed for the resolution of a major question about the prehistory of South Asia. There’s was nothing preventing scholars from doing this first, but they are busy people and have a finite number of labor hours that they can devote to the sea of questions which are begging to be answered.