Archive for January, 2012

How the Amhara breathe differently

By Razib Khan | January 22, 2012 12:23 pm

I have blogged about the genetics of altitude adaptation before. There seem to be three populations in the world which have been subject to very strong natural selection, resulting in physiological differences, in response to the human tendency toward hypoxia. Two of them are relatively well known, the Tibetans and the indigenous people of the Andes. But the highlanders of Ethiopia have been less well studied, nor have they received as much attention. But the capital of Ethiopia, Addis Ababa, is nearly 8,000 feet above sea level!

Another interesting aspect to this phenomenon is that it looks like the three populations respond to adaptive pressures differently. Their physiological response varies. And the more recent work in genomics implies that though there are similarities between the Asian and American populations, there are also differences. This illustrates the evolutionary principle of convergence, where different populations approach the same phenotypic optimum, though by somewhat different means. To my knowledge there has not been as much investigation of the African example. Until now. A new provisional paper in Genome Biology is out, Genetic adaptation to high altitude in the Ethiopian highlands:

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The quest for an Afrikaner genotype

By Razib Khan | January 21, 2012 8:49 pm

Update: If interested, please email me at contactgnxp -at- gmail -dot- com. Also, I am getting some feedback via 23andMe that people with white South African matches noticed Africa segments in many of the ancestry paintings. This has definitely increased by probability that the admixture proportion is ~5 percent. There will probably be a few genotypes coming in shortly, but I am going to see if I can get more people typed (fundraising appeal pending!).

It’s been a while since I’ve gone looking for genotypes of particular ethnic groups. The results were rather good for the Tutsi and Malagasy. So I thought I’d venture out again, despite being a bit busy. Here’s what I want: the genotype of an Afrikaner (or several). A few years ago South African geneticist J. M. Greeff did an analysis of his own pedigree, and estimated that he had ~6 percent non-European ancestry (he did validate this with some genetic markers; e.g., his father’s mtDNA is of the M haplogroup, which is almost always Indian). This is in line with other genealogists who have estimated, about 5 percent non-European heritage. How much should we trust these non-biological studies? The genomic estimates of African American ancestry being ~20 percent European were anticipated by analyses of family histories from text records, so we certainly shouldn’t dismiss them (in fact, it seems possible that these analyses will underestimate non-European ancestry because of cryptic individuals in the pedigrees).

And we have plenty of records of people of non-European ancestry contributing to the Afrikaner population in any case. Greeff found the records for his own pedigree, but the first Governor of the Dutch Cape Colony was himself of mixed-race (his mother was Eurasian). The question is is a matter of degree. Are Afrikaners like American whites, with hardly any non-European ancestry (~1 percent or less), or like Latin American whites, with significant non-European ancestry (~5 to 20 percent)? My own bet is that they’ll be in the middle. The proportion of non-European ancestry is low enough that individuals such as Sandra Laing are very rare indeed. But if the 5 percent estimate is valid, and almost of all these ancestors were women, then a larger proportion of the mtDNA is going to be non-European.

 

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The erectus within?

By Razib Khan | January 21, 2012 4:45 pm

The Pith: More caveman admixture in modern humans, especially Melanesians!

A new paper on archaic adaptive introgression among Melanesians has been discussed elsewhere. But I think it is worth reviewing, because it’s probably a foretaste of what’s to come. Researchers are combing through the human genome, as more and more genomes come on line, in the search of weird and unexpected variation. The paper is in Molecular Biology and Evolution, and is titled Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations (why is it that this journal doesn’t even allow supplemental information to be free to the public?). The two primary figures from this paper do a good job of illustrating the main result.

The first figure is a phylogenetic tree of haplotypes at the OAS1 locus, with pie charts showing the proportion of individuals from a set of populations which contribute to the total number for that haplotye. So you see above that the “deep lineage” is relatively distant from a cluster of other haplotypes (as measured by mutational differences which are proportional to depth of common ancestry), and, that deep linage is exclusively found in Papuans in this set. The second figure shows the frequency of the deep lineage haplotype over a larger set of populations. I cut off the section which shows that Africans are at zero percent. The haplotype is found almost exclusively in Melanesian populations, except for the fact out of over 200 South Asians they sampled, 3 of them carried it (2 Pakistanis, 1 Sri Lankan). There is aspect though not evident in the figures above, but which is clear in the abstract that you need to know:

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The arcologies arise

By Razib Khan | January 21, 2012 2:52 pm

How U.S. Lost Out on iPhone Work:

Apple executives say that going overseas, at this point, is their only option. One former executive described how the company relied upon a Chinese factory to revamp iPhone manufacturing just weeks before the device was due on shelves. Apple had redesigned the iPhone’s screen at the last minute, forcing an assembly line overhaul. New screens began arriving at the plant near midnight.

A foreman immediately roused 8,000 workers inside the company’s dormitories, according to the executive. Each employee was given a biscuit and a cup of tea, guided to a workstation and within half an hour started a 12-hour shift fitting glass screens into beveled frames. Within 96 hours, the plant was producing over 10,000 iPhones a day.

“The speed and flexibility is breathtaking,” the executive said. “There’s no American plant that can match that.”

The story emphasizes that labor costs are not the primary issue here. There is the natural discussion of skill levels, and the sheer number of Chinese works coming online. But there simply is no way that Foxconn City could exist in the United States today. There is no way I can deny the massive quality of life improvements in China over the past generation. But, the flip side of this is that a way of life has now emerged organically in places like Shenzen which is rather reminiscent of late 19th and early 20th century dystopian visions of the industrial future.

CATEGORIZED UNDER: Blog, Technology
MORE ABOUT: China

Physical education teachers are not smart

By Razib Khan | January 20, 2012 1:51 am

So there is a website out there, Educational Realist (via Steve Sailer), which made me aware of some statistics from ETS on the intellectual aptitudes of those who passed a teaching certification. This is relevant because those who major in education at university are notoriously rather weak students. The implication here is that teachers are substandard as a whole, a narrative long favored on the American Right, but now spreading in some parts of the Left.

Below are the verbal and mathematical scores by licensing domain. The solid line represents the average SAT score of a college graduate.

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CATEGORIZED UNDER: Education
MORE ABOUT: Education, Teachers

The phylogeography of the trans-Caucasus

By Razib Khan | January 18, 2012 9:52 pm

Randy McDonald points me to this fascinating post, Genetic clues to the Ossetian past. In the post author outlines phylogeographic inferences one can make from uniparental lineages; maternal and paternal lines of descent. Specifically, they are in interested in the origins and relationships of the Ossete people. I assume that one reason Randy pointed me to this post is that the Ossetes are assumed by many to be the descendants or fragments of the Alans. More broadly they’re remnants of a broad array of North Iranian peoples, of whom the Scythians were the most prominent, which have been erased from the pages of history because of the expansion of the Slavs and Turks.

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Barack H. Obama, a liminal black Christian

By Razib Khan | January 18, 2012 8:17 pm

 

It is well known that President Obama has a religion issue. The big looming one has to do with whether he is Muslim or not. My own position that he’s as Muslim as I am. With that out of the way, is Barack H. Obama a Christian? To borrow a turn of phrase from Hillary Clinton, I accept him at his word that he is a Christian. But not everyone does. Some people, such as my friend Eliezer Yudkowsky, Steve Sailer, and Ann Althouse, believe that he is not particularly religious, and his avowal of Christian faith and identification is a matter of political necessity.

Obama has said some things which have raised eyebrows. For example, that evolution is more grounded in his experience than angels. Or his lack of certainty about the afterlife. Finally, there is Obama’s tendency toward universalism, which is a major bone of contention in many quarters.

 

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CATEGORIZED UNDER: Culture, Politics, Religion

The future is here

By Razib Khan | January 17, 2012 12:26 pm

Believe it or not I am probably mildly skeptical about the possibilities for the 21st century as a canvas for human flourishing. That is one reason I like to emphasize the positive, because it is important for me to not get caught up in my own bias. Over the last two human generations (50 years) mean world life expectancy has gone from ~53 to ~69. This is easy for me forget concretely because I come from a relatively long lived family. Though all were born in British India and died in Bangladesh my grandparents lived to ages of 75, 100, 80, and 80. My grandparent who died at the age of 75 still lived 25 years longer than life expectancy in Bangladesh in the year he died.

Today I see a headline in The New York Times, Majority of Chinese Now Live in Cities. For some reason I was prompted to look up the Wikipedia entry for Shenzhen, a city of 350,000 in 1982, which is now at 10 million. The image below of Shenzhen captures for me the poignant banality of the future present. One the one hand it is nothing special, a typical “world city” skyline. But there is also an aspect redolent of the soft focus depictions of the cities of the future in the children’s books I would read in the 1980s. The photo is proof of nothing. Rather, it is an illustration of fact.

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CATEGORIZED UNDER: Technology
MORE ABOUT: Futurism, Shenzhen

Is Barack H. Obama whiter than Mitt Romney?

By Razib Khan | January 17, 2012 2:09 am

For some reason The New York Times has given the execrable Lee Siegel space to write on its website. Ruminating on Mitt Romney’s candidacy Siegel puts up a post with the title What’s Race Got to Do With It?, and states:

In this way, Mr. Romney’s Mormonism may end up being a critical advantage. Evangelicals might wring their hands over the prospect of a Mormon president, but there is no stronger bastion of pre-civil-rights-America whiteness than the Church of Jesus Christ of Latter-day Saints.

Yes, since 1978 the church has allowed blacks to become priests. But Mormonism is still imagined by its adherents as a religion founded by whites, for whites, rooted in a millenarian vision of an America destined to fulfill a white God’s plans for earth.

There is something to this. The ancient leadership of the present day Mormon church grew up in a very different America, and they sometimes reflect that America in their pronouncements. For example, despite the fact that plenty of Mormons are in interracial marriages (I know this from my Facebook friends), there is still some literature floating around in the Mormon church discouraging the practice. Now, granted most Americans’ revealed preferences indicate that they aren’t too into interracial marriage personally, but the social norm is strongly against expressing disapproval in the abstract against the practice.

All that being said, one needs to be careful about overemphasizing the whiteness of Mormons. First, remember that most Mormon males are missionaries abroad at some point in their life, so it isn’t as if they are unfamiliar with societies where non-whites are the majority. And, it is probable that around half of Mormons in the world today are not white (the claims vary on this issue). But it is also notable that Mormons in the USA today are far less white than they were just a generation ago. To illustrate this point I’ve replicated some religious data from the Pew survey. I’ve highlighted in blue some historical mainline/liberal Protestant denominations, and in red some of their evangelical/conservative counterparts.

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CATEGORIZED UNDER: Anthroplogy, Politics, Religion

Genes and Rex Wandalorum et Alanorum

By Razib Khan | January 17, 2012 12:21 am

The idea of a “folk wandering” was once a well accepted idea in history, in particular for the phase of the Late Roman Empire, and the subsequent fall of the Western Empire. It’s a rather simple concept: the collapse of the Pax Romana occurred simultaneous with a mass ethnic reordering of Europe, primarily via the migration of Germanic peoples across its frontiers and beyond. The most extreme depictions of this can be found in the works of the British cleric Gildas: German hordes literally drove the British into the sea, until they only retained their redoubts around the “Celtic Fringe.”

This was an extreme understanding of the dynamics of post-Roman Europe. It was, and has been, succeeded by another extreme model: that the ethnic change in the post-Roman world was more illusion than substance, a manner of shifting nomenclature, than lineage. For example, I have commonly read in this literature that the Germanic tribes which crystallized as “federates” to the Romans, or on occasion as antagonists (or vassals to hostile powers such as the Huns) were ad hoc collections of mercenaries who created an identity de novo.  In some cases it is posited that masses of Romans simply assimilated to the identity of a small cadre of warriors whose demographic impact was trivial. This is the scenario that is posited for the transformation of Celtic Britain into Germanic England. But let’s shift away from that extreme case, and look at another one: the 5th and early 6th century kingdom of the Vandals in Norh Africa.

 

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Moving Secularism Forward, March 2012

By Razib Khan | January 16, 2012 11:47 am

Because of scheduling conflicts* I can’t make ScienceOnline2012 (I had planned to make it). But I thought I would put in an announcement here that in a month and a half I’ll be at the Moving Secularism Forward conference put on by the Center for Inquiry. I’m going to be on a political panel on Saturday afternoon, the 3rd of March. There are going to be representatives of the progressive, liberal, conservative, and libertarian, positions. I’ll be the conservative, and make a 20 minute presentation. There will be a Q & A. My time in the “spotlight” should be no more than a few hours.

My current plan is that I’ll be there Friday, Saturday, and Sunday morning. It’s in Orlando, Florida. I have no idea as to the overlap between the audience for that sort of conference and the readership of this weblog, but I assume that there is some intersection. I don’t really do the reader meetup thing anymore, but if you see me feel free to say hello. I won’t give you a weird look. My only current “social” plans are to meet up with Ron Bailey, who’s going to give the libertarian perspective on the panel, and whose work I’ve been a great admirer of for years.

* Where x = r, E(x) = 0.50, Var(x) = 0.0

CATEGORIZED UNDER: Blog, Culture

The Fulani have an old "Berber" (?) element

By Razib Khan | January 16, 2012 10:26 am


After the second Henn et al. paper I did download the data. Unfortunately there are only 62,000 SNPs intersecting with the HGDP. This is somewhat marginal for fine-grained ADMIXTURE analyses, though sufficient for PCA from what I recall. That being said, the intersection with the HapMap data sets runs from ~190,000 SNPs, to the full 250,000 SNPs (this makes sense since the Henn et al. #2 data set has some HapMap populations in it). So I’ve been experimenting a fair amount in the past few days, and I thought I would post on one issue which was clear in the original paper, but which I have replicated.

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Mendelism is not magic

By Razib Khan | January 16, 2012 1:23 am

Michelle points me to this article in The Lost Angeles Times, The Colors of the Family:

I was holding my 1-year-old, ambling about downtown with some friends. White friends. She must have thought my boy belonged to one of them.

There’s a simple explanation: I’m black but my son, Ashe, is white. At least he looks it.

But things are more complicated than that.

I’m actually half black and half white. It should come as no surprise, though, that even as sophisticated as we’ve become about people of mixed parentage, I’m pigeonholed as black. If someone asks and I don’t have time to go deeper, that’s what I call myself.

Ashe is mixed too. His mother, my wife, Vanashree, is half white and half South Asian, with roots in India. She has olive skin, and Ashe is slightly lighter than she is.

This surprised us. When Ashe was born, one of the first things I said to Vanashree was, “Honey, he’s so light!” We chuckled, poking fun at our assumptions.*

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MORE ABOUT: Genetics, Pigmentation, Race

The milkmen

By Razib Khan | January 16, 2012 12:09 am

Dienekes and Maju have both commented on a new paper which looked at the likelihood of lactase persistence in Neolithic remains from Spain, but I thought I would comment on it as well. The paper is: Low prevalence of lactase persistence in Neolithic South-West Europe. The location is on the fringes of the modern Basque country, while the time frame is ~3000 BC. Table 3 shows the major result:

Lactase persistence is a dominant trait. That means any individual with at least one copy of the T allele is persistent. As Maju noted a peculiarity here is that the genotypes are not in Hardy-Weinberg Equilibrium. Specifically, there are an excess of homozygotes. Using the SJAPL location as a potentially random mating scenario you should expect ~7 T/C genotypes, not 2. Interestingly the persistent individual in the Longar location also a homozygote.

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The extraordinary sex ratio of our age

By Razib Khan | January 14, 2012 9:32 pm

The New Atlantis has a nice piece, The Global War Against Baby Girls. It’s relatively heavy on charts and maps, so I recommend it (yes, it has a particular ideological perspective, but that’s really not consequential, as I assume most readers do not favor skewed sex ratios either). There’s nothing too surprising in it (assuming you won’t be surprised by the finding that in many societies there is a correlation between economic development and higher rates of sex selective abortion). But it’s thorough and highlights the complexities of social dynamics well.

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CATEGORIZED UNDER: Culture, International Affairs
MORE ABOUT: Sex Ratio

Reconstructing a generation unsampled

By Razib Khan | January 14, 2012 3:59 pm

In the near future I will be analyzing the genotype of an individual where all four grandparents have been typed. But this got me thinking about my own situation: is there a way I could “reconstruct” my own grandparents? None of them are living. The easiest way to type them would be to obtain tissue samples from hospitals. This is not totally implausible, though in this case these would be Bangladeshi hospitals, so they might not have saved samples or even have a good record of hem. Another way would be to extract DNA from the burial site. This is not necessarily palatable. But assuming you did this, if you have access to a forensic lab it might be pretty easy (though I think most forensic labs using VNTRs, rather than SNP chips, so I don’t know if they’d touch every chromosome), I’m not sure that the quality would be optimal for more vanilla typing operations, especially for older samples which are likely to be contaminated with a lot of bacteria.

For me the simplest option is to look at relatives. Each of my grandparents happens to have had siblings, so there are many sets of relatives related to just each of those individuals of interest. I also have many cousins, so pooling all the genotypes together and using the information of a pedigree one could ascertain which chromosomal segments are likely to derive from a particular grandparent. To give a concrete example, my mother has a maternal cousin to whom she is quite close. By typing my mother and her cousin one could infer that the segments shared across the two individuals derive from the common maternal grandparents. Of course there’s a problem that cousins have a coefficient of relatedness of only 1/8th, so there is going to be a lot of information missing. But, if you had lots of cousins you could presumably reconstruct the genotypes far better.

 

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The old Amazon

By Razib Khan | January 14, 2012 2:49 pm

Once Hidden by Forest, Carvings in Land Attest to Amazon’s Lost World:

For some scholars of human history in Amazonia, the geoglyphs in the Brazilian state of Acre and other archaeological sites suggest that the forests of the western Amazon, previously considered uninhabitable for sophisticated societies partly because of the quality of their soils, may not have been as “Edenic” as some environmentalists contend.

Instead of being pristine forests, barely inhabited by people, parts of the Amazon may have been home for centuries to large populations numbering well into the thousands and living in dozens of towns connected by road networks, explains the American writer Charles C. Mann. In fact, according to Mr. Mann, the British explorer Percy Fawcett vanished on his 1925 quest to find the lost “City of Z” in the Xingu, one area with such urban settlements.

In addition to parts of the Amazon being “much more thickly populated than previously thought,” Mr. Mann, the author of “1491,” a groundbreaking book about the Americas before the arrival of Columbus, said, “these people purposefully modified their environment in long-lasting ways.”

If one wants to recreate pre-Columbian Amazonia, most of the forest needs to be removed, with many people and a managed, highly productive landscape replacing it,” said William Woods, a geographer at the University of Kansas who is part of a team studying the Acre geoglyphs.

“I know that this will not sit well with ardent environmentalists,” Mr. Woods said, “but what else can one say?”

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CATEGORIZED UNDER: Agriculture, Anthroplogy, Environment
MORE ABOUT: Amazon, Charles C. Mann

The dynasty which created Iran

By Razib Khan | January 13, 2012 12:26 am


Shah Ismail I

The BBC Radio 4 program In Our Time just had an episode on the Safavid dynasty. If you want to understand how Iran as we understand it came to be, and you know nothing about the Safavids, this program is essential. Because of its outsized role in Western antiquity the pre-Christian Achaemenids are well known, while Iranian nationalists may look to the pre-Islamic Sassanians immortalized in the Shahnameh. Obviously these dynasties are important, just as the House of Wessex and the Plantagenets are essential in understanding how Britain came to be. But to truly comprehend England as a Protestant nation with a distinctive identity in relation to the continent the England of the Tudors and Stuarts, who happen to be contemporaneous with the Safavids, are much more important.

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CATEGORIZED UNDER: Culture
MORE ABOUT: Iran, Safavids, Shia

Between the desert and the sea

By Razib Khan | January 13, 2012 12:06 am


Zinedine Zidane, a Kabyle

There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with just one group. The first author on this new paper is Brenna Henn, who was also first author on another paper with a diverse African data set. Importantly the data was posted online. Unfortunately though most of the populations didn’t have too many markers. This isn’t an issue in an of itself, but it becomes a big deal when trying to combine it with other data sets. If you limit the markers to those which intersect across two data sets you start to thin them down a lot, to the point where they’re not useful. Though the the results of the paper are worth talking about, the authors claim that they’ll be putting the data online. This is important because they used a large number of markers, so the intersections will be nice (I can, for example, envisage exploring the relationship between the North Africans and the IBS Iberian sample in the near future).

As for the paper itself, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations:
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More on the "missing heritability" and epistasis

By Razib Khan | January 9, 2012 9:35 am

Please see Luke Jostins’ posts at Genetic Inference and Genomes Unzipped.

Update: Steve Hsu weighs in. He read the supplements! Mad props.

CATEGORIZED UNDER: Genetics, Genomics
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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