Merry Christmas!

Because of the nature of modern American ‘work-life balance’ the next week or so is going to be my longest period of being the ‘primary caregiver’ for my daughter in her short life. Needless to say I’m quite excited! Especially because this will be her first Christmas.

I spent most of my childhood in a region on the margins of lake-effect, so I am familiar with a white Christmas in a classical fashion. More recently I’ve been resident on the maritime fringes of the western United States, and snow is rare in the lower elevations of this region. But I persevere!

Over the next week I will likely be blogging a great deal from my daughter’s playroom, where I’ll have a makeshift encampment. But rest assured this will be a great leisure for me. I hope readers of this weblog can find time to relax as well. Hopefully the comments will come back to a civilized state after the New Year….

History as intellectual hydrography

One of the great aspects of owning a Kindle has been that I have been able to load it with cheap copies of “classics.”* As it happens I had physical copies of many of these works, but often it became difficult to keep track of various books in even my modest personal library. Generally scientific references were placed prominently, and I made use of them often, and so always was able to mark exactly where they were. But when it came to Nicomachean Ethics or The Critique of Pure Reason, I would proactively seek them on only rare occasions. Now with a compact and well organized personal digital library I find that I revisit the ancients much more often to engage with them in dialogue. Here I recall what Niccolò Machiavelli once asserted:

When evening comes, I return home and go into my study. On the threshold I strip off my muddy, sweaty, workday clothes, and put on the robes of court and palace, and in this graver dress I enter the antique courts of the ancients and am welcomed by them, and there I taste the food that alone is mine, and for which I was born. And there I make bold to speak to them and ask the motives of their actions, and they, in their humanity, reply to me. And for the space of four hours I forget the world, remember no vexation, fear poverty no more, tremble no more at death: I pass indeed into their world.

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The "Asian quota" and implicit cultural knowledge

The Myth of American Meritocracy, Ron Unz

A recent conversation I had with a friend whose parents are immigrants from Germany made me reconsider and reflect on the power of implicit information in shaping one’s life; that information being culturally mediated. Though my friend was raised in the United States, because of her parents’ immersion in the German expatriate community her upbringing was very bicultural. In fact, she is much more German than I am Bangladeshi. Despite the fact that to anyone who is a Baby Boomer or older she looks American, and I do not, there are many similarities in outlook due to our 1.5 generation background. Both of us are from families where graduate educations in the sciences are the norm. We succeeded in academics and pursued higher education without much effort or obstacles. This is not a story of overcoming the odds in a conventional  sense. In explicit terms we are entirely American, but there are nevertheless implicit aspects of being American of a particular social class which we had to experience after leaving home at 18.

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The causes of evolutionary genetics

A few days ago I was browsing Haldane’s Sieve,when I stumbled upon an amusing discussion which arose on it’s “About” page. This “inside baseball” banter got me to thinking about my own intellectual evolution. Over the past few years I’ve been delving more deeply into phylogenetics and phylogeography, enabled by the rise of genomics, the proliferation of ‘big data,’ and accessible software packages. This entailed an opportunity cost. I did not spend much time focusing so much on classical population and evolutionary genetic questions. Strewn about my room are various textbooks and monographs I’ve collected over the years, and which have fed my intellectual growth. But I must admit that it is a rare day now that I browse Hartl and Clark or The Genetical Theory of Natural Selection without specific aim or mercenary intent.

R. A. Fisher

Like a river inexorably coursing over a floodplain, with the turning of the new year it is now time to take a great bend, and double-back to my roots, such as they are. This is one reason that I am now reading The Founders of Evolutionary Genetics. Fisher, Wright, and Haldane, are like old friends, faded, but not forgotten, while Muller was always but a passing acquaintance. But ideas 100 years old still have power to drive us to explore deep questions which remain unresolved, but where new methods and techniques may shed greater light. A study of the past does not allow us to make wise choices which can determine the future with any certitude, but it may at least increase the luminosity of the tools which we have iluminate the depths of the darkness. The shape of nature may become just a bit less opaque through our various endeavors.

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Holiday reading

Christmas is a time when I accelerate my reading, and catch-up for lost time. Here’s my three books I plan to get through:

The Fall of Rome: And the End of Civilization. I’ve read this twice already. This short book has been one of the most influential works in my own personal thinking. Even if you don’t agree with the thrust of Bryan Ward-Perkins’ thesis, it will clarify your own position.

Through the Eye of a Needle: Wealth, the Fall of Rome, and the Making of Christianity in the West, 350-550 AD. The author, Peter Brown, is the modern day eminence on ‘Late Antiquity’. I’ve read many of his earlier works, and always found his exposition enjoyable. But I’m re-reading The Fall of Rome in part to have a good counterpoint in my head to Brown’s arguments, which are subtle and difficult to box in (for what it’s worth, I think Brown makes a bit too much of Late Antiquity, but to some extent this is a normative judgement).

The Founders of Evolutionary Genetics: A Centenary Reappraisal. This is an exciting time to be interested in evolution and genetics (see Haldane’s Sieve and prepare to be overwhelmed!). But I also think it is useful to have some historical perspective. Science is a human enterprise, and it is critical to step outside of the flowing river, and observe the parameters which shaped its past course and trajectory, and therefore where it may be going.

With that, an “open thread” for what you are reading, and why.

Note: The comments systems should be improved in the near future. Or so I’m told.

Buddy, can you spare some ascertainment?

The above map shows the population coverage for the Geno 2.0 SNP-chip, put out by the Genographic Project. Their paper outlining the utility and rationale by the chip is now out on arXiv. I saw this map last summer, when Spencer Wells hosted a webinar on the launch of Geno 2.0, and it was the aspect which really jumped out at me. The number of markers that they have on this chip is modest, only >100,000 on the autosome, with a few tens of thousands more on the X, Y, and mtDNA. In contrast, the Axiom® Genome-Wide Human Origins 1 Array Plate being used by Patterson et al. has ~600,000 SNPs. But as is clear by the map above Geno 2.0 is ascertained in many more populations that the other comparable chips (Human Origins 1 Array uses 12 populations). It’s obvious that if you are only catching variation on a few populations, all the extra million markers may not give you much bang for the buck (not to mention the biases that that may introduce in your population genetic and phylogenetic inferences).

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Gene surfing with David Dobbs

Over at National Geographic David Dobbs of Neuron Culture has an eminently readable and engrossing piece up, Restless Genes. I have never really read about ‘allele surfing’ on the wave of demographic expansion in the way that Dobbs’ rendered it. I certainly wouldn’t have been able to produce that sort of spare but informative prose.

On Twitter there was some concern about the focus on DRD4. The issue is a general one in much of behavioral genomics, and I’m not too interested in rehashing the point. But the broader question of heritability of behavior remains. It seems to me that we have some ‘natural experiments’ now. For the past 50 years there have been a series of cross-cultural adoptions from Asia to North America and Europe. If human behavior variation across and within populations is substantially heritable than this might be a good place to start. Rather than focusing on genes, we need to focus on heritability first.

Unveiling the genealogical lattice

To understand nature in all its complexity we have to cut down the riotous variety down to size. For ease of comprehension we formalize with math, verbalize with analogies, and visualize with representations. These approximations of reality are not reality, but when we look through the glass darkly they give us filaments of essential insight. Dalton’s model of the atom is false in important details (e.g., fundamental particles turn out to be divisible into quarks), but it still has conceptual utility.

Likewise, the phylogenetic trees popularized by L. L. Cavalli-Sforza in The History and Geography of Human Genes are still useful in understanding the shape of the human demographic past. But it seems that the bifurcating model of the tree must now be strongly tinted by the shades of reticulation. In a stylized sense inter-specific phylogenies, which assume the approximate truth of the biological species concept (i.e., little gene flow across lineages), mislead us when we think of the phylogeny of species on the microevolutionary scale of population genetics. On an intra-specific scale gene flow is not just a nuisance parameter in the model, it is an essential phenomenon which must be accommodated into the framework.

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Conservative atheists not rare in South Korea?

In a few days South Korea will have a new president, and this is very important because of how large North Korea looms in geopolitics. An interesting aspect of this race for Americans is that the candidate of the conservative party, Park Geun-Hye, may be an atheist, running against a Roman Catholic liberal. I say may be because there are some confusions over Park Geun-Hye’s religious identity. Her parents were Buddhist, she was baptized as a young woman as a Roman Catholic, and seems to have drawn without much discrimination from a variety of religious teachings to inform her world-view. It wouldn’t be shocking if Park Geun-Hye was an atheist. According to the World Values Survey ~25% of South Koreans are convinced atheists.

I was curious if atheists in South Korea leaned to the Left or the Right, and from what I can tell there’s no strong correlation. This may surprise Americans, but the historical experience of the two nations is very different. Until recently South Korea has had weak institutional religions, and a substantial portion of what we might term “progressives” were Christians, in particular Roman Catholics. Below are the results for the USA, Great Britain, Sweden, and South Korea for the World Values Survey using religious identification and political self positioning. Percentages and sample sizes are included.

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Buyer beware in ancestry testing!

Over at Genomes Unzipped Vincent Plagnol has put up a post, Exaggerations and errors in the promotion of genetic ancestry testing, which to my mind is an understated and soft-touch old-fashioned “fisking” of the pronouncements of a spokesperson for an outfit termed Britain’s DNA. The whole post is worth reading, but this is a very grave aspect of the response of the company:

…The main reason is that listening to this radio interview prompted my UCL colleagues David Balding and Mark Thomas to ask questions to the Britain’s DNA scientific team; the questions have not been satisfactorily answered. Instead, a threat of legal action was issued by solicitors for Mr Moffat. Any type of legal threat is an ominous sign for an academic debate. This motivated me to point out some of the incorrect, or at the very least exaggerated, statements made in this interview. Importantly, while I received comments from several people for this post, the opinion presented here is entirely mine and does not involve any of my colleagues at Genomes Unzipped.

From what I can gather this firm is charging two to three times more than 23andMe for state-of-the-art scientific genealogy, circa 2002. So if you can’t be bothered to read the piece, it looks like Britain’s DNA is threatening litigation for researchers having the temerity to point out that the firm is providing substandard services at above-market costs. Plagnol’s critique lays out point-by-point refutation of assertions, but the interpretation services on offer seem to resemble nothing more than genetically rooted epic fantasy. A triumph of marketing over science.

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