Your child’s genome before the 2nd trimester?

A long piece in Slate, Will Gattaca come True?:

When Lo licensed his technology to Sequenom, he stipulated that it could not be used for sex selection. Rabinowitz says Natera won’t test for sex at this point, either. But how long such provisions will hold is unclear. Meanwhile, NIPD’s reach is expanding as the technology used to analyze cffDNA improves. In December 2010, Lo published a paper in Science Translational Medicine showing that in principle, at least, scientists can piece together the entire fetal genome from cffDNA. Lo says that exceeded even his own expectations: “If you asked me prior to 2008, I would have probably said that was science fiction.”

At the time his paper was published, the process cost $200,000. Now, with the cost of DNA sequencing dropping faster than that of computing power, he estimates the bill may come to one-tenth of that—still expensive, but no doubt tempting for some parents. Lo wagers complete fetal genome testing might be widely available in a clinical setting within a decade. What fetal genes might one day suggest about a baby’s eye color, appearance, and intellectual ability will be useful to parents, not insurers. But with costs coming down and …

Redefining “impact factor”

In rereading the paper on Pygmy height genetics, I noticed that PLoS had rolled out some nice new metrics. To my shock this paper, which I think is a moderately big deal, had less than 1,000 views, and only ~150 PDF downloands! This is going to change, but it still shocks me. With all due respect to my statistical geneticist friends, but this isn’t an abstruse methods paper debuting a new technique!

I decided to check on an older paper which has been rather influential, A Map of Recent Positive Selection in the Human Genome, from 2006. Here are the metrics:

Good? Bad? What do you think? Did you expect more downloads in the past 6 years?

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Pygmies: “old” populations, and a new “look” (?)

Over the years one issue that crops up repeatedly in human evolutionary genetics and paleoanthropology (or more precisely, the popular exposition of the topics in the media) is the idea that is that “population X are the most ancient Y.” X will always refer to a population within a larger set, Y, which is defined by relative marginalization or retention of older cultural folkways. So, for example, I have seen it said that the Andaman Islanders are the “most ancient Asian population.” Why? The standard model for a while now has been that non-Africans derive from a line of Africans which left the ancestral continent 50 to 100 thousand years ago, and began to diversify. Presumably Andaman Islanders have ancestry which goes back to this original dispersion, just as Europeans and Chinese do (revisions which suggest that Aboriginals may have been part of an earlier wave, still put the Andamanese in the second wave). The reason that the Andaman populations are termed ancient is pretty straightforward: they’re Asia’s last hunter-gatherers, literally chucking spears at outsiders. An ancient lifestyle gets conflated with ancient genetics.

This is a much bigger problem with the …

Comparing American conservative Protestants & Muslims

A few years ago a book came out, American Taliban: How War, Sex, Sin, and Power Bind Jihadists and the Radical Right. The title clearly was aimed to push copies, but the gist of the title has moderately wide circulation. The rough sketch is that conservative American Protestants are roughly equivalent to conservative Muslims. I have always held that this is a qualitatively misleading analogy. The reason is from all I can gather the socially views of mainstream American conservative Protestants are actually in the moderate range of opinion amongst Muslims. But apples-to-apples comparisons are rather difficult in this domain.

But then I realized that the World Values Survey could allow me to do exactly such comparisons. The method is simple. First, you can subsample the data sets, so I could look at Protestants in the United States who identified as political conservatives. I compared these to the view of Muslims in a selection of nations (the WVS doesn’t cover much of the world, and some questions are not asked in some countries).

The results below range from 1, never justifiable, to 10, always justifiable. There is some strangeness in the results below, but they show the general qualitative result: American …

Her identity by descent made flesh

As I have indicated before, my daughter has a family tree where everyone out to 0.25 coefficient of relatedness has been genotyped by 23andMe. This is convenient in many ways. Before, relatedness was a theory. Now relatedness can be ascertained on the genomic level. Sometimes this can lead to peculiar consequences. “On paper” my daughter is 1/8 Scandinavian. Or 12.5%. But truly the expected value is 13.5%! (weighting by contributions from each maternal grandparent). Still, this remains an expected value. I would need a large sample of Scandinavians from that locale to make a truly precise guess as to the genetic contribution. Similarly, though I come in at about ~15 percent East Asian, my daughter looks to be a bit more East Asian than you’d expect based on that value (i.e., closer to 8-8.5 percent; I run her genotype more than a dozen times now). This may be a bias in the methodology, or, more likely it is simply the sampling error from my genome (I contributed more East Asian segments in the chromosomes passed down).

In any case, 23andMe has a “family inheritance” feature which is very convenient. …

Elizabeth Warren, Native American


Elizabeth Warren, Native American

It has come to my attention that Elizabeth Warren, who is running for a Senate seat in Massachusetts, claims Native American ancestry. This did not surprise me. Warren is from Oklahoma, where nearly 10% of the population claims some Native American ancestry. The problem, as it is, is that apparently Harvard claimed Warren as a minority faculty member during its periodical head counts. Warren “was told through family lore that her maternal parents were from the Cherokee and Delaware tribes.” This is a moderate problem: family lore often is inaccurate. And it also exhibits biases. Nevertheless, I do think we need to be careful about being too skeptical in this case, because of Warren’s roots in Oklahoma. A friend was told that his maternal grandmother was of part Oklahoma Choctaw background, and he had always dismissed this as romantic distortions made to fit 21st century preconceptions and preferences. But when he got his results back from 23andMe there was a notable “Asian” component, and the Native American relative finder came back positive. He asked me to look at his results more deeply, …

Facing the ocean

Halford Mackinder’s conceptualization of the world

With the recent publication of the paper on the archaeogenetics of Neolithic Sweden I feel like we’re nearing a precipice. That precipice overlooks lands of great richness, filled with hope. It’s nothing to fear. It is in short a total re-ordering of our conception of the recent human past, at minimum. The “pots not people” paradigm arose in archaeology over the past few generations due to both scholarly and ideological factors. The scholarly ones being that intellectuals of the 19th and early 20th century made assumptions of extremely tight correspondence between material and cultural characteristics, and demographic dynamics, which seem to have been false. Therefore, the rise of an Anglo-Saxon England and the marginalization of Celtic Britain to the western fringes was not just a cultural reality, but also a fundamentally racial one, as Germans replaced Celts in totality. The ideological problem is that this particular framework was take as a given by the Nazis during World War II, lending a bad odor to the

hypotheses of migration which were once so ascendant.

No …

Iraq: the model that wasn’t

The magazine Foreign Policy recently had a “sex” issue out. This issue is particularly famous for Mona Eltahaway’s jeremiad against Arab male culture, and their attitudes toward women. Over at bloggingheads.tv Charli Carpenter expresses some concern that the issue seemed so singularly focused on Arabs, as if women’s rights is a problem with particular salience for Arab Muslims. As it is, she admits that as a matter of truth it may be so, but still has qualms about essentialization.

Now, I like to think in terms of distributions, and don’t find essentialization particularly useful on a fundamental level. But, my personal observation is that the term ‘essentialization’ tends to be used when there are phenomena brought to light which make people uncomfortable. For example, I rarely hear essentialization being nearly a great a problem when talking about Republicans or Western Christian conservatives.

But it does make to wonder: how bad are Arab countries when it comes to women’s rights? Let’s look at the World Values Survey. There are two questions in the survey which have a lot of normative baggage:

– If jobs are scarce: men should have more right to a job than women

– It is an …

Handicap breeds excellence?

There’s a wide-ranging story in LA Weekly on the decline of 35mm film. It covers a lot of angles, but this one issue jumped out at me:

No wonder, then, that directors like Christopher Nolan worry that if 35mm film dies, so will the gold standard of how movies are made. Film cameras require reloading every 10 minutes. They teach discipline. Digital cameras can shoot far longer, much to the dismay of actors like Robert Downey Jr. — who, rumor has it, protests by leaving bottles of urine on set.

“Because when you hear the camera whirring, you know that money is going through it,” Wright says. “There’s a respectfulness that comes when you’re burning up film.”

This particular variant of critique of new technologies is very old. It is famously well known that writing and printing both ushered in warnings that these were simply crutches, and might diminish mental acuity. But I’m 99% sure that when bow & arrow become common, some hunters warned that the skills and traditions associated with the atlatl would decay. The piece highlights some genuine advantages of analog over digital. I do not think making filming more difficult is an advantage, to state the obvious.