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 insurers interested in other aspects of the fetal genome, a Gattaca-like two-tiered society, in which parents with good access to health care produce flawless, carefully selected offspring and the rest of us spawn naturals, seems increasingly plausible.

First, it’s rather crazy that as we live and breathe it is on the order of $20,000 to get a genome of your unborn children! I say on the order because no one knows, and I assume that they’re being optimistic here for media consumption. We plan to get screening for karyotype scale issues for our next child, so I keep track of this area with some interest.

All that being said, without pre-implantation genetic diagnosis it’s going to be very unlikely that you will get the “perfect child,” barring gene therapy. I may be unimaginative, but I can’t see the actionable use of a relatively dense genotype, let alone a full genome, at this stage once you eliminate the risks of very problematic diseases. I suppose at this point I can divulge that I tried to get my daughter’s genetic material from a c.v.s., so she could get typed while she was in utero, but that was mostly for the “wow!” factor (for what it’s worth, it’s really hard to get genetic material back from large biomedical firms).

Finally, I don’t find the beating-around-the-bush about “trick ethical questions” that is par for the course of these sorts of pieces useful. The reality is that most of the public finds this aspect of personal genomics “scary.” You don’t need to genuflect to it, just accept it as a given. Rather, lay out the issues in explicit detail, and let the people make their own judgement.

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?

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 hunter-gatherers of Africa, the Pygmies, Hadza, and Bushmen. The reason is that these populations are of particular interest because they seem to have diverged from the rest of humanity rather early on. Both Y chromosomes and mtDNA confirmed this, and now autosomal analyses looking across the whole genome are confirming it. In other words, they’re basal to the rest of humanity. I believe this is moderately misleading. With the Bantu Expansion much of African genetic diversity disappeared. The hunter-gatherers seem exceptional long and bare branches on the phylogenetic tree because all their relatives are gone!

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Rise and fall of celebutantes

Kim Kardashian was at the White House Correspondents Association Dinner. Wow. But it made me wonder whatever happened to Paris Hilton? Did she drop off the face of the earth? Here’s Google Trends:

The bottom panel is news, the top panel public searches. The media seems to exhibit some latency in relation to the public, but at this point they both agree: Paris is near a nobody.

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 conservative Protestants are in the main to the center or social liberal end of Muslim public opinion. They are not comparable at all to Muslim reactionaries.

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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. It illustrates visually chromosome by chromosome the extent to which two individuals match genomic segments. Presumably this is useful for those who are distant cousins, who may match on a segment here and there. Instead of just focusing on one base pair, A/C/G/T, the method looks at the correlations of bases across a sequence of the chromosome. Below are the visualizations for matches of each individual with my daughter, in sequence: father, mother, paternal grandfather, paternal grandmother, maternal grandfather, maternal grandmother, paternal uncle, paternal uncle, paternal aunt, and maternal uncle. And no, I don’t know why it has an XY in the plots. For those of you without a biological background I hope that this can help in getting across how Mendelism manifests in a concrete manner. And if you do have a biological background, you can infer from these matches other interesting information about the meiotic process.

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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, and it was pretty obvious that yes, he was part Native American, in actually the proportions that you would have expected.

But this doesn’t always work out. It seems the majority of white Americans who suspect Native American ancestry find none from what I can tell. Recently I received a copy of DNA USA: A Genetic Portrait of America. Here’s a section on Cherokee genetic results:

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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

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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 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 essential characteristic of democracy that women have the same rights as men

As a matter of pedantic accuracy obviously it is not an essential characteristic of democracy that women and men have the same rights. Ancient Athens and America before the 1920s are generally considered democracies. But, the question is a rough gauge of attitudes toward male and female legal equality. I relabeled these questions as “economic” and “legal” equality. They are given as percentages, so I converted the categories into numbers, and then took the weighted average. These two indices measure the two dimensions of equality, with higher values favoring more equality. Below I generated a scatterplot showing the relationship between the two (naturally positively correlated). I’ve also attached table data after the figure.

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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.