The positional game and the end of the age

By most material measures we’re doing better as a species than we ever have. That is, in an absolute sense. But a lot of human life is about relative prosperity. I recall hearing once that role playing games which emphasized egalitarianism, with no “winners” or “losers,” often had a difficult time gaining users. We are a cooperative species, but we’re also a competitive species. The idea of a rising tiding lifting all boats is appealing, but so is the idea that one needs to have a larger McMansion than the Jones’. Non-zero sum interactions are splendid, but as social organisms we evolved to a great extent in a world dominated by zero sum games. Our rationality counsels that we trust in reason’s logic, but our emotions drive us toward cognitive biases such as loss aversion.

Three articles in The New York Times prompt me to reflect on the shortsightedness of modern life in the developed and aspiring developed world. First, It Takes a B.A. to Find a Job as a File Clerk. Basically the transformation of college into the new high school. Second, As Families Change, Korea’s Elderly Are Turning to Suicide. The focus of this article is how modern economic and social tumult are tearing apart the fabric of South Korean life. But it also focuses on the mad scramble for the “best” education which drives many to penury: ‘Some parents, the “edu poor,” drained their savings to pay for cram schools that operate after regular school and on weekends.’ Finally, In China, Families Bet It All on College for Their Children. This despite the fact that there is a surfeit of graduates in many areas.

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Genes are not esoteric knowledge

Over at Slate the advice columnist received an email from a man who found out that his wife is really his half-sister. If you don’t want to follow the link, the back story is straightforward, the couples’ parents were lesbians, and used sperm donors. Recently the man sought out the identity of his biological father at the urging of his wife, because they have three children and she thought it would be important to have that information for them. That is how he found out that they shared the same biological father. Here is the part that has me concerned about realism on the part of the advice columnist:

I don’t see how you can keep this information to yourself. She’s bound to sense something off in your behavior and you simply can’t say, “I’m struggling with father issues.” I think you have to sit her down and show you what you’ve discovered. Then you two should likely seek out a counselor who deals with reproductive technology to help you sort through your emotions. I don’t see why your healthy children should ever be informed of this. That Dad didn’t want to find out who his sperm donor was is a sufficient answer when they get old enough to ask about this.

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Is Girls' Generation the outcome of the Pleistocene mind?

There’s an excellent paper up at Cell right now, Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. It synthesizes genomics, computational modeling, as well as the effective execution of mouse models to explore non-pathological phenotypic variation in humans. It was likely due the last element that this paper, which pushes the boundary on human evolutionary genomics, found its way to Cell (and the “impact factor” of course).

The focus here is on EDAR, a locus you may have heard of before. By fiddling with the EDAR locus researchers had earlier created “Asian mice.” More specifically, mice which exhibit a set of phenotypes which are known to distinguish East Asians from other populations, specifically around hair form and skin gland development. More generally EDAR is implicated in development of ectodermal tissues. That’s a very broad purview, so it isn’t surprising that modifying this locus results in a host of phenotypic changes. The figure above illustrates the modern distribution of the mutation which is found in East Asians in HGDP populations.

One thing to note is that the derived East Asian form of EDAR is found in Amerindian populations which certainly diverged from East Asians > 10,000 years before the present (more likely 15-20,000 years before the present). The two populations in West Eurasia where you find the derived East Asian EDAR variant are Hazaras and Uyghurs, both likely the products of recent admixture between East and West Eurasian populations. In Melanesia the EDAR frequency is correlated with Austronesian admixture. Not on the map, but also known, is that the Munda (Austro-Asiatic) tribal populations of South Asia also have low, but non-trivial, frequencies of East Asian EDAR. In this they are exceptional among South Asian groups without recent East Asian admixture. This lends credence to the idea that the Munda are descendants in part of Austro-Asiatic peoples intrusive from Southeast Asia, where most Austro-Asiatic languages are present.

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1 out of 100 benefit from whole genome sequencing

Perhaps. The New York Times has a piece out reviewing the vogue for sequencing the genomes of children who have mysterious diseases. The numbers are what matters here I think:

A few years ago, this sort of test was so difficult and expensive that it was generally only available to participants in research projects like those sponsored by the National Institutes of Health. But the price has plunged in just a few years from tens of thousands of dollars to around $7,000 to $9,000 for a family. Baylor College of Medicine and a handful of companies are now offering it. Insurers usually pay.

Demand has soared — at Baylor, for example, scientists analyzed 5 to 10 DNA sequences a month when the program started in November 2011. Now they are doing more than 130 analyses a month. At the National Institutes of Health, which handles about 300 cases a year as part of its research program, demand is so great that the program is expected to ultimately take on 800 to 900 a year.

Experts caution that gene sequencing is no panacea. It finds a genetic aberration in only about 25 to 30 percent of cases. About 3 percent of patients end up with better management of their disorder. About 1 percent get a treatment and a major benefit.

It seems this is a floor in terms of the results outcome for these children, as some of them may receive better or more effective treatments in the future, because the specific nature of their disease is already known. Since most medical treatments today are marginal in effect these outcomes don’t surprise or depress me, and the price point is sure to come down. In the near future I imagine that everyone will have a whole genome sequence, and relevant information about your specific genetic profile in relation to the sea of biomedical literature constantly coming out may be sent to you in a drip, drip, fashion by a phone or web app.

Visualizing European genetic variation: looking at dimensions which aren't so boring

Yesterday I re-ran Plink with a narrower European-biased data set, and generated some MDS plots. I only had a few Asian and African populations, mostly so that I could replicate the standard dimensions 1 and 2, producing the classic “v-shape” which you’ve seen before. But what’s more interesting are lower coordinates. They may not capture as much of the variation in the distance matrix, but illustrate important dynamics. I haven’t used the directlabels package yet, so right now the labels are still imperfect. I’m giving black text as well as colored text. Also, here’s the original data (as in MDS results, not the raw data).

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Two words: Napoleon Chagnon

Just pre-ordered a Kindle Edition of Napoleon Chagnon‘s new book Noble Savages: My Life Among Two Dangerous Tribes — the Yanomamo and the Anthropologists. I didn’t even know this was coming out next week, but The New York Times Magazine has a piece up, The Indiana Jones of Anthropology, which chronicles the controversial the life & times of Chagnon. My previous posts about cultural anthropology were written with no knowledge about the impending publication of this article, or Napoleon Chagnon’s memoir. But the timing is fortuitous. One complaint by rightfully enraged cultural anthropologists (I didn’t deny that I was attacking their profession in the most extreme terms) is that I didn’t really offer an argument. As I said, the reason is that life is short and I’m not interested in convincing anyone.

But here’s a section of the article above which reflects just what I was alluding to:

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Visualizing Europe genetically

This is a follow up to my post from yesterday. In case you care about the technical details (after I clean this stuff up I will put it on GitHub) I’m using R’s adehabitat package to create a 95% distribution curve after smoothing with kernel density. The goal is to give you a better intuition about where the populations are dispersed across two dimensional visualizations of genetic variation.

Thinking about how to plot text, I came up with a quick hack, which just used the initial data and found the median x and y position. That explains why some of the labels are shifted so, in populations with a huge range the label position is going to be sensitive to not being smoothed (if you know how to pull out the centroid out of the kver, tell!). I’ve given them colors and also used black. The latter actually seems to be clearer!

Note: This is not just for fun, as I plan to start rolling out results and methods from some of the data sets I have more regularly in the near future.

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Even the conservative columnist Ezra Klein!

I’ve observed the rise of Ezra Klein out of the corner of my eye for years. Political blogging is not really my thing, but I’ve been “around,” and I’ve brushed up against the “Juicebox” now and then (though I interacted with Matt Yglesias as early as 2003, usually I get on the radar of Washington policy types when my friend Reihan Salam picks up something I say). So I thought I’d point you to a profile in The New Republic, Ezra Klein: The Wise Boy, A tale of striving and success in modern-day Washington.

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Around the net, & of note

As some of you may have noticed, Neuroskeptic has joined Discover. I am rather pleased. There will be others soon enough.

Chris Chabris has a blog. I reviewed his book The Invisible Gorilla a few years back. Here’s one thing I would say about Chabris: I read him very closely, because he is very careful. And I’ve been doing so since the late 1990s, when I first encountered his writing.

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Visualizing genetic variation

I’ve been thinking about how best to visualize PCA/MDS type of results, which allow for the two dimensional representation of genetic variation. Below are a few of my efforts with a data set I have. You can see the individuals in gray, but also ellipses which cover ~95% of the distribution of a given population.

Please click the images for a larger version. They represent coordinate 1 on the y axis and 2 on the z axis derive from a multidimesional scaling representing identity by state across individuals.

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