Important papers on recent human evolution

This post is more of a personal note…here are three papers that are really cool must reads:
Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, et al. (2007) Localizing Recent Adaptive Evolution in the Human Genome. PLoS Genet 3(6): e90 doi:10.1371/journal.pgen.0030090
Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biol 4(3): e72 doi:10.1371/journal.pbio.0040072
Tang K, Thornton KR, Stoneking M (2007) A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome. PLoS Biol 5(7): e171 doi:10.1371/journal.pbio.0050171
E.T. Wang, G. Kodama, P. Baldi, R.K. Moyzis, Global landscape of recent inferred Darwinian selection for Homo sapiens, Proc. Natl. Acad. Sci. USA 103, 135-140 (2006). doi:10.1073/pnas.0509691102
All 4 papers are Open Access! The statistical & computational techniques can be hard to follow sometimes, but these HapMap datasets are the tip of the iceberg, so get comfy and start learning if you want to be able to follow the blow-by-blow over the next few years….
P.S.: If you dig flies, read Evolgen.

Fear not the future

What is contingent across the arc of human cultural development? What is inevitable? Interesting, if difficult to answer, questions. Last year I posted No fear of Patrick Henry College – the Borg shall assimilate. My argument was simple: an explicitly Christian institution which attempts to take over “secular” culture will be assimilated. There are long, and tiresome, historical debates about whether this in fact happened to the Christian churches when the Roman state adopted them and turned them into the Universal Church. But more recently, and specifically in the context of universities, there has been a long track record in the United States of Christian institutions being founded to stem the tide, only themselves to be swallowed up by the rising waters.

Harvard was originally a training ground for Calvinist ministers. Over its first century it became progressively more heterodox. Princeton was founded explicitly to serve as a second Harvard, a bastion of Calvinist orthodoxy. It too was suborned. Wheaton college is in many ways the Harvard of contemporary evangelical America; and it reaffirmed its Protestant credentials when it fired a professor who converted to Catholicism. Nevertheless, the act itself was not without controversy on the campus, suggesting that the commitment toward ideological purity has wavered. Additionally, it seems clear to me that Wheaton’s loyalty to one American subculture has resulted in constraining its influence. Patrick Henry College reached out, its aim was to conquer the public space. But last spring while I was busy at something I like to call “life” a shakeup occurred at Patrick Henry, half a dozen faculty members left (there are fewer than two dozen told faculty members). Why? Ideological conformity and theological purity were being compromised. Patrick Henry aimed for the stars, recruited bright students and challenged the faculty. But such an environment naturally leads to intellectual hubris and the pushing of boundaries. Mental meekness and dullness often go together. Like an invasive species unleashed to control a pest any attempt to conquer the mainstream by mastering its toolkit may inevitably be self-defeating.

This is not just true of the evangelical Christian subculture. Books like Bobos in Paradise document the paradoxical stances of the bohemian bourgeois; 60s radicals turned “socially conscious” entrepreneurs & mercenary professionals. American culture is a massive and uncontrollable river. On occasion it changes course or jumps its bed, but it has its own will and logic and can process anything thrown into its maw. The extruded cultural material is often totally transformed, but the the human tendency to self-delude is great enough that those who have been reprogrammed by the river truly believe that they have won. There’s no point in standing athwart history if it will only drown you; ’tis far more productive to make use of the power of the current and outfit your ship appropriately so that your journey is as smooth and pleasant as possible.

Related: The New York Times has an interesting article about a new Christian college, New St. Andrews. I obviously don’t share their presuppositions, but I do respect their passion for learning. As long as books & faith are their focus they will persevere on their island surrounded by the river. If they challenge it then I suspect their fate is predestined.

How the human species kept it together (?)

Yesterday I put up a post where I attempted to use a visual analogy for what I believe might be evolutionary forces operative over short periods of time that result in phenotypic diversification across populations with recent common ancestry. But what about the flip side? In the case yesterday the basic genetic substratum, the preponderance of the genome, was not subject to powerful diversifying forces because only drift was presumably operating over short periods of time. It was on selectively salient slices of the genome where differences came into sharp focus quickly. But there is an inverted process which may also occur: divergence on the neutral genome due to low migration which nonetheless is overlain by “species” wide selective sweeps of alleles of large phenotypic effect. In other words, where before the face was different but the flesh fundamentally the same, now we are considering a situation where the flesh is very different but the face remains invariant.

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Cosma on IQ & heritability

Cosma Shalizi has put up a gigantic post on IQ & heritability; he originally titled it “Duet for Leo and Razib,” implying that I, and the audience here @ Gene Expression, are the targets of his eloquence (at least in part). Now, I have to admit something, I’m not really interested in psychometrics that much anymore. It has been a while since I have been, stupid people are obviously stupid and I am not interesting in debating that fact. I take my own opinions in this area as background assumptions, so I’m not going to respond to Cosma. In fact, I won’t read the post right now, there’s some interesting stuff on HLA & heterozygosity that I want to check out! But, I do invite readers to digest what Cosma is saying, because I guarantee you that you’ll see it replicated by lesser minds elsewhere.

How the human races got their stripes

In my post The new races of man I tried to offer a verbal exposition of my current thinking as to how and why human physical variation shows the patterns we see around us. In short, I believe that powerful selective forces have reshaped a subset of the human genome in similar and different ways across a range of populations over the past 10,000 years. Empirically, I would predict that the physical appearance we denote as stereotypically “Chinese” or “Swedish” or “West African” might be rather recent ecotypes, adapted to new circumstances, both environmental and cultural. The types we see are simply a collection of correlations of salient phenotypic featuers (e.g., skin color, nasal form) which are the outcomes of selection driving evolutionary change on a small set of loci in the recent human past. But a great proportion of the genome might be relatively unaffected. And I believe this proportion is what we generally look toward to ascertain the phylogenetic characteristics of a population (generally you examine selectively neutral genes assuming that their evolution has proceeded via a constant molecular clock). Therefore, their may be a discordance between what a small number of recently selected alleles and their salient phenotypic outcomes may imply, and what the total genome content suggests.
Below the fold is my attempt to illustrate all that with a simple schematic representation.

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Blonde Berbers

Sadly, but unsurprisingly, the little blonde girl photographed in Morocco turns out not to be missing British girl Madeleine McCann, but the daughter of a Berber farming family, who are said to have three other blonde children.

Most of us will have been vaguely aware that blonde hair and fair skin are not uncommon among the Berbers, but it has evidently come as a surprise to the general public. It is usually explained by a hypothetical element of European ancestry, whether from Roman slaves (as in this Daily Mail article), the Vandals, or more prosaically from the colonial occupation by French soldiers and government officials (who presumably didn’t just twiddle their thumbs).

I wonder if there is any hard genetic evidence? Y chromosomes might at least show whether the paternal ancestry is recently European. An alternative, and more interesting, explanation would be that the Berbers are the remnants of an older, more ‘Caucasian’, North African population.

The biodiversity of human feet

Native Americans get custom sneaker:

Nike researchers and developers spent two years designing the shoe, traveling to seven locations to look at the feet of 224 Native Americans from 70 different tribes. They created a shoe to fit the average Native American foot, which is wider than the foot the Nike Air Pegasus running shoe is designed to fit. About 164 members of the Confederated Tribes of Warm Springs tested prototypes of the shoe before its release, the company said.

Jeff Piscotta, senior researcher in Nike’s Shoe Research Laboratory, said company researchers have developed a similar custom-fit shoe design for Japanese runners, and as part of the run-up to the 2008 Olympics are researching the feet of Chinese athletes and runners to produce a better-fitting product.

This is fascinating. The reason these shoes were developed was to encourage physical activity, something that comes more naturally when your feet aren’t aching. Assman has noted before that South Asians might be more flexible than the typical human, which likely results in flatter feet, so this foot’s-eye viewpoint might be pretty practical in tailoring shoes toward populations.