Archive for February, 2008

Guest Katz

By Razib Khan | February 29, 2008 10:15 am

Got these pix via a forward. Thought it might be a nice change of pace….

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Rewriting Islam

By Razib Khan | February 29, 2008 5:05 am

Lots of articles on the radical reinterpretation of the Hadith in Turkey. The Hadith serve as the basis for Islamic law, and orthopraxy more generally. I am on the record as saying that texts don’t in the end determine anything, so obviously I’m skeptical. But, I will simply point to a historical analogy; in the 19th century Egypt and Japan attempted to modernize and catch-up with Western nations. Egypt did not truly succeed, Japan did. Where there’s a will there always isn’t a way; Japan had the necessary preconditions in terms of human capital for the task at hand (e.g., high literacy, a preexistent samizdat of “Dutch” learning, etc.), Egypt did not. A revision of the Hadith is a positive sign, and it is a necessary precondition toward modernity in a Western manner (for example, in regards to sexual equality in family law, or a full-throated acceptance of the institutional instruments modern of capitalism1), but I doubt it is sufficient. A genuine reinterpretation of Islam will more likely happen in a place like the United States, where there are endogenous social forces at work at the grassroots. Textual reintrepretation of sacred literature or law is more often concomitant with, or the effect of, change, not the agent of it. Feminist or socialist interpretations of the Bible post-date the emergence of these movements, they did not inspire them.
1 – “Islamic banking” actually goes a long way toward this already by making up excuses and “work-arounds” which violate the spirit but follow the letter of the law. Rather, I think it is in family law where a top-down imposition might be more necessary.


Selection, but for what???

By Razib Khan | February 29, 2008 1:27 am

In my post below about a possible locus to look at to explain the normal variation in hair form we see around us a reader asked:

I was once suckered into giving a course on animal ecophysiology (I was told it was basic ecology until after it was too late to back out) which was a traumatic experience as I’ve only taken one university-level animal physiology course in my life. One of the students asked what the advantage is of kinky hair. I wondered if it might be a better insulator against the heat of the sun but that’s just guessing. I also said that perhaps the question should be the other way round – why do people have straight hair. Perhaps to shed rain more readily? I was hoping this post would answer the question. Are there any suggestions?

Well, I didn’t have one. I’ve read the insulation-from-climate thesis before, and I’m skeptical. I think that these are pretty much the sorts of adaptationist tales which stimulated the counter-reaction in the 1970s. There are many ways to detect natural selection in the genome, or at least identify regions which are possible candidates. There are also more classic techniques derived from ecological genetics. But that doesn’t mean we know exactly why a region of the genome was subject to natural selection, or the exact ultimate cause of an observed fitness differential with a natural population. The lactase persistance story is probably one of the best ones we have. LCT is the region of the genome you want to look at if you want to make sure your test for selection actually works in humans (well, at least if you have sample of European humans). Not only that, we have a good idea about the phenotypic consequences of the genetic variation, we can also relate that phenotype to adaptive value, and hook up the function to cultural and historical correlates. Everything is just lined up there for you, it’s too easy.

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Delegate calculator

By Razib Khan | February 28, 2008 9:44 pm

If you haven’t, check out Slate‘s delegate calculator. It looks hard for HRC….


Science blogs, what are they good for?

By Razib Khan | February 28, 2008 1:25 pm

John Hawks as a long post on the kerfuffle over “good” science blogging. I think John is right to emphasize the importance of search engine traffic for “specialist” posts; there’s a significant long tail effect here.


William F. Buckely was a racist

By Razib Khan | February 28, 2008 4:55 am

Many are quoting this from an editorial by William F. Buckley Jr.:

“The central question that emerges…is whether the White community in the South is entitled to take such measures as are necessary to prevail, politically and culturally, in areas where it does not predominate numerically? The sobering answer is Yes–the White community is so entitled because, for the time being, it is the advanced race.”
–William F. Buckley, National Review, August 24, 1957

I do want to put on the record that he recanted:

Buckley said he had a few regrets, most notably his magazine’s opposition to civil rights legislation in the 1960s. “I think that the impact of that bill should have been welcomed by us,” he said.

That doesn’t excuse or negate the past. National Review was a journal of some impact then, and Buckley was a public figure. But I’m a temporal moral relativist, you can’t judge the people of the past by the same standards you judge those of the present. A substantial number of Americans alive today were alive during the 1950s and 1960s; and a substantial number of those Americans were opponents of the civil rights movement. One assumes that the majority of these have changed their minds as well. There is even a former Ku Klux Klan member, Robert Byrd, Democrat of West Virginia, serving in the Senate. Byrd also filibustered the 1964 Civil Rights Act, which he now regrets. The follies of youth are often the follies of one’s age in the more general sense. Perhaps we who are a bit younger will also have cause to feel some shame in our old age when we reflect back, and realize that we too were simply fellow travelers in the spirit of the times.
Note: Speaking of things that might surprise you, Charlton Heston was a civil rights activist. Heston is proud of this obviously because it looks good now; but there was a time when this would have been controversial for a public figure who wanted to maximize his market appeal. To paraphrase Michael Jordan, segregationists bought movie tickets too!
Update: Go here for a more detailed explanation of William F. Buckley Jr’s stances on civil rights, then and relatively recently. As I noted in the comments apologia for segregation was not that abnormal in the 1960s. I pointed out below that J. William Fulbright was also part of the filibuster in 1964 against the Civil Rights Act. But later due to his opposition to Vietnam he became something of an icon, and in the 1970s Fulbright changed his mind (or blacks were enfranchised and so he changed his politics) on the race issues.


Mitty Romney is hyper-typical for a Mormon

By Razib Khan | February 28, 2008 2:00 am

The Audacious Epigone crunches the Pew Religion Survey and comes up with some more insights….


Why is hair kinky?

By Razib Khan | February 27, 2008 2:24 pm

I saw this paper in Nature Genetics, Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair:

The genetic determinants of hair texture in humans are largely unknown. Several human syndromes exist in which woolly hair comprises a part of the phenotype; however, simple autosomal recessive inheritance of isolated woolly hair has only rarely been reported…In all cases, we discovered pathogenic mutations in P2RY5, which encodes a G protein-coupled receptor and is a nested gene residing within intron 17 of the retinoblastoma 1 (RB1) gene. P2RY5 is expressed in both Henle’s and Huxley’s layers of the inner root sheath of the hair follicle. Our findings indicate that disruption of P2RY5 underlies ARWH and, more broadly, uncover a new gene involved in determining hair texture in humans.

Disease loci can tell us a lot about the normal range of human variation; the blue-eye gene was originally implicated in a form of albinism. So I got curious and popped P2RY5 into Haplotter, which detects recent selection events. Here’s what I found….

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Maybe it's agriculture – soft sweep TRPV6

By Razib Khan | February 27, 2008 1:03 pm

Parallel Selection on TRPV6 in Human Populations (Open Access):

…The selective footprints, however, are significantly differentiated between non-African populations and estimated to be younger than an ancestral population of non-Africans. The possibility of a single selection event occurring in an ancestral population of non-Africans was tested by simulations and rejected. The putatively-selected TRPV6 haplotype contains three candidate sites for functional differences, namely derived non-synonymous substitutions C157R, M378V and M681T. Potential functional differences between the ancestral and derived TRPV6 proteins were investigated by cloning the ancestral and derived forms, transfecting cell lines, and carrying out electrophysiology experiments via patch clamp analysis. No statistically-significant differences in biophysical channel function were found, although one property of the protein, namely Ca2+ dependent inactivation, may show functionally relevant differences between the ancestral and derived forms. Although the reason for selection on this locus remains elusive, this is the first demonstration of a widespread parallel selection event acting on standing genetic variation in humans, and highlights the utility of between population EHH statistics.

Jump to discussion:

A potential selective force that could result in parallel selection in different populations is agriculture. The independent development of agriculture in several different parts of the world within the past 11,000 years…including the Middle East (11,000 ybp), East Asia (9,000 ybp), the Americas (5,000-4000 ybp), and the New Guinea highlands (9,000-6,000 ybp), fits remarkably well with the demonstrated parallel selection on TRPV6 in the ancestors of Europeans and Asians, and potentially in the Americas and New Guinea as well. It may be that dietary changes related to the switch to agriculture underlie the selective event, or that selection on TRPV6 is related to resistance to a particular disease that became important with the increased population densities associated with agriculture.
As a simple test of this hypothesis, we included three hunter-gatherer groups from India in our genotyping of the three tagging SNPs in worldwide populations (Koragas, Mullukurunan, and Mullukurumba…however, all three populations were fixed for the derived, putatively-selected haplotype, suggesting that selection for this haplotype also occurred in the ancestors of these groups. While to the best of our knowledge these populations have always been hunter-gatherers, it is possible that they have reverted from an agricultural to a hunting-gathering lifestyle, as has been documented for other hunting-gathering groups…Genotyping of additional hunter-gatherer groups would therefore be desirable.

I would bet many Old World “hunter-gatherer” populations in close proximity to the Oikumene were driven there, or, gene flow has swamped out any “pure” original signature. In any case, the paper is basically talking about the process whereby extant genetic variation that was always around got selected due to changes in the exogenous pressures. So a switch to a new lifestyle. In contrast, the locus around LCT that’s swept in much of Eurasia seems to be derived from a relatively recent mutant.


Where are brown people short?

By Razib Khan | February 26, 2008 2:18 pm

In the comments to my post, Why brown people are midgets, a reader pointed me to this paper, which tabulates and analyzes some data from the 1960s for males. There isn’t anything too surprising in the data set; Punjabis are tall compared to non-Punjabis, higher castes are taller than lower castes. There is a lot of unaccounted for variation. This was before Indian Shining, and the Green Revolution probably hadn’t sunk in yet (I wouldn’t be surprised if the between-state differences increased, while the between-caste differences decreased, in the past 40 years). So appropriate caveats. The one surprising thing is that being a Muslim was a variable that predicted more height! This is correcting for regional distribution. The reason it’s surprising is that Muslims are genetically no different from non-Muslims (e.g., in Uttar Pradesh the highest proportion of recent West Asian ancestry is 5% across the whole population) and tend to socially disadvantaged in India (i.e., they are a Backward Class). The only explanation I have is that Muslims are less likely to be vegetarian or have dietary taboos which constrain their nutritional choices. Tables below the fold….

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Bee evolutionary genetics

By Razib Khan | February 26, 2008 4:23 am

beerotate.jpgJohn Hawks has commentary on a new paper, A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera. John’s point is that evolutionary dynamics are evolutionary dynamics. I’m sure as a species which spans multiple continents and all the latitudes and longitudes we might be able to learn a bit about ourselves from examining other lineages of great geographic range.


The two streams of American irreligiosity

By Razib Khan | February 26, 2008 1:10 am

Despite the fact that the mainstream media likes to write a lot of stories how religious revival in the United States one of the great unreported facts of the last 15 years is the rise of the proportion of Americans who are not affiliating with any religion. The reason this isn’t reported much is that it won’t sell that much copy; the irreligious by their nature don’t get that excited by irreligion. In contrast religious people want to read about how religion is on the rise. There will always be stories about how religion & science dovetail in the media because that sells magazines; the fact that 9 out of 10 National Academy of Science members are atheists or agnostics won’t sell magazines, and might even make scientists a little worried about the funding pipeline.

The US Religious Landscape Survey by Pew doesn’t come burdened by the need to satisfy the consumer market. From chapter 2:

The biggest gains due to changes in religious affiliation have been among those who say they are not affiliated with any particular religious group or tradition. Overall, 7.3% of the adult population says they were unaffiliated with any particular religion as a child. Today, however, 16.1% of adults say they are unaffiliated, a net increase of 8.8 percentage points. Sizeable numbers of those raised in all religions – from Catholicism to Protestantism to Judaism – are currently unaffiliated with any particular religion.

The unaffiliated group provides a good example of the high degree of religious movement that has taken place in the U.S. Overall, 3.9% of the adult population reports being raised without any particular religious affiliation but later affiliating with a religious group. However, more than three times as many people (12.7% of the adult population overall) were raised in a particular faith but have since become unaffiliated with any religious group.

Here are some breakdowns:

Percentage of Adults Entering and Leaving Each Group
  Childhood Religion Entering Group Leaving Group Current Group
Atheist 0.5 +1.4 -0.3 1.6
Agnostic <0.3 +2.3 -<0.3 2.4
Nothing in particular 6.6 +9.6 -4.1 12.1

But do note that not all unaffiliated people are atheists are agnostics, in fact, the majority are not. The Pew study notes that this unaffiliated group is divided between those who are secular (religious sentiments are not important) and those who are believers of some sort, if not affiliated (one could term these the “spiritual” segment). Below are some tables of interest from the Pew study.

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F*cking Ben Affleck

By Razib Khan | February 25, 2008 11:33 pm

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Biology determines what language you speak….

By Razib Khan | February 25, 2008 1:20 am

Well, sort of. I’m reading Henry Kamen’s Empire: How Spain Became a World Power. Kamen is no Charles C. Mann, his story isn’t 1491. For him the conquest of the Aztecs and Incas were haphazard affairs driven more by entrepreneurial intent than religious zeal or Spanish patriotism; his lens is that of social and economic history. Kamen’s goal is to debunk those who would attempt to assert that the colonization of the New World was part of some grand imperial plan. It obviously wasn’t, the personal correspondence of Charles V, the titular sovereign under whom the original New World conquests occurred, show a far greater attention and focus upon the geopolitical circumstances of Central Europe.1 Nevertheless, Kamen can not ignore the large role that the immunological parameter played in aiding the Spanish conquest. More accurately, Spain did not conquer the New World, the societies of the New World collapsed and the Spaniards took over in the vacuum. I couldn’t but help note that Kamen points out that the Inca redoubt at Vilcabamba, which remained an independent locus of indigenous political power for decades after the initial Spanish victories, was being wracked by pestilence as the final defeat loomed. Obviously if you are going to engage in a guerilla rearguard action it is tough going when your demographic base is being wiped out from under you. It seems that a good conservative rule of thumb is that 9/10th of the indigenous American population in any given region was struck down within a generation of contact.2 Luckily for the peoples of the Andes, they have their own biological adaptations to high altitudes which the Spaniards did not. This meant they were better suited to eventually bounce back as outsiders had a harder time settling their lands.

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Why brown people are midgets

By Razib Khan | February 24, 2008 2:59 am

midgetbrown.jpgI’m 5 feet 8 inches tall. 1.73 meters. In the United States that’s somewhat on the short side, most of the charts suggest I’m around the 30th percentile for white men. Of course, I’m not white. In any case, though I’m on the short side for the typical American male, I’m a giant in my family. My father is 5 feet 4 inches. My mother is around 5 feet now. They’re possibly shorter than they were due to age, but they would have been short in the United States no matter what. As I was growing up, and surpassed my parents in my mid-teens, I assumed that their relative lack of height was a function of childhood nutritional deprivation. After all, they were born in Bangladesh!
If I had thought it through that was probably a pretty stupid reason for assuming they were short; my parents were from affluent families. Affluent enough that older family members were comfortably plump. Additionally, as Muslims they had no food taboos aside from pork, and milk and meat were widely consumed (though fish was of course a primary protein source). Though a significant proportion of the population in Bangladesh, what was East Bengal, is malnourished, no one in my family fell into that category. But this is all post facto, there’s a very specific reason I rejected my prior assumptions. I have three siblings and their heights are basically in the range of my parents (correct for sex, etc.). I’m the odd one out, not my parents. I have some “tall” uncles on both sides of my family, which in Bangladesh means around my height. My paternal grandfather was also relatively tall, reputedly above 5 feet 10 inches, while my maternal grandmother was tall for a woman in her youth. When I visited my family in 2004 one of my cousins was taller than me, around 5 feet 10 inches or so. He was the only one, there were a few who were around my height, but most were shorter. No one in my family is on the edge in terms of nutrition, though not approaching American obesity levels plumpness is not unknown even among young adults. Though we’re not plutocrats on the whole, many of my cousins have professional jobs, accountants at NGOs or systems administrators at universities and what not. Nevertheless, among them I am a giant, and my brother at 5 feet 4 inches is typical.

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85% of genetic variation is within groups…

By Razib Khan | February 23, 2008 2:56 pm

…yes, true. On a typical single locus (on some loci, such as SLC24A5, most of the variation is between groups). But that doesn’t mean that you can’t use genetics to differentiate population clusters. Here are 938 individuals (the points) from 51 world populations (the color of the points) displayed on a figure with the two largest principle components of the variation.
From Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. Also see Lewontin’s Fallacy.


Shadows of the past in genes

By Razib Khan | February 23, 2008 2:35 pm

A new paper came out in Science this week, Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation, that’s getting some media play. The second-to-last author is L. L. Cavalli-Sforza, and the general combination of means and ends on display in The History and Geography of Human Genes, is all over it. From the introduction:

We first studied genetic ancestry of each individual without using his/her population identity. This analysis considers each person’s genome as having originated from K ancestral but unobserved populations whose contributions are described by K coefficients that sum to 1 foreach individual. To increase computational efficiency, we developed new software, frappe, thatimplements a maximum likelihood method (13)to analyze all 642,690 autosomal SNPs in 938 unrelated and successfully genotyped HGDPCEPH individuals…Figure 1A shows theresults for K= 7; those for K= 2 through 6 are in fig. S1. At K= 5, the 938 individuals segregate into five continental groups, similar to those reported in a microsatellite-based study of the same panel…At K= 6, the new component accountsfor a major portion of ancestry for individuals from South/Central Asia, separating this regionfrom the Middle East and Europe…K= 7, the new component occurs at highest proportions inthe Middle Eastern populations, separating them from European populations. In many populations, ancestry is derived predominantly from one of the inferred components, whereas in others, especially those in the Middle East and South/Central Asia, there are multiple sources of ancestry….

All good. Do note that the South Asian populations in the HGDP set are all from the northwest edge of the subcontinent, so the separation between the South Asians as an outgroup to the Middle Eastern & European branches of the broad West Eurasian cluster is going to be understated in these studies. In any case, I was interested in some details of the the first figure, so I reedited it a bit for clarity:

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Christians in East Asia are smarter than non-Christians

By Razib Khan | February 23, 2008 5:25 am

In my post below, Pentecostals are stupid? Unitarians are smart?, I derived some conclusions from data which suggests that different religious groups in the United States have different IQs and/or academic aptitudes. The data are not particularly surprising, as some noted the class biases of American Protestantism have long been observed, and class usually has some correlation with education and performance on intelligence tests. That being said, one must be careful about extrapolating from one nation to others. Darwin Catholic stated:

For comparison, I seem to recall reading that Christianity correlates highly with educational and professional success in some Asian countries (Japan was the one I was reading about). In that case, as with Unitarians in the US, it would again be a case of a self selected group: only people who had actively searched out a religion different from that they were born into.

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בנות יהודיות לוהטות

By Razib Khan | February 22, 2008 3:58 pm

(if you don’t see Hebrew in the title please change “Character Encoding” to “Unicode”).

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By Razib Khan | February 22, 2008 5:29 am

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