Archive for October, 2010

Leigh Van Valen Obit in The New York Times

By Razib Khan | October 31, 2010 4:22 pm

If you haven’t, check out the Leigh Van Valen obituary in The New York Times. I hadn’t been aware of the breadth of his work, and the disciplinary range he showed over his career.

CATEGORIZED UNDER: Biology
MORE ABOUT: Leigh Van Valen

On the "liberal gene"

By Razib Khan | October 31, 2010 2:54 pm

Jim Manzi has already posted on the warranted skepticism of DRD4 being reported in the press as the “liberal gene.” Here’s the original paper. The main issue I have is not with the original research, but the inevitable confusions in the media which always arise. First, we know that complex behavioral phenotypes such as religiosity and personality seem to be heritable. That is, a set of genetic variants within the population seems to track the variation in the trait (just as with I.Q.). But, it’s been a much longer haul to actually connect a specific genetic locus to said variation, though the dopamine related genes are always brought forward as candidates. Additionally, particularly when it comes to politics there’s the norm of reaction looming. One might grant that same genetic variation which predisposes Swedes in Sweden to being on the Left or the Right is operative among ethnic Swedes in Minnesota, but most of the difference is actually between population, and a function of the differing environmental milieus of the Upper Midwest and Scandinavia (though perhaps there were strong selection effects operating upon those who chose to leave Scandinavia for the USA). Finally, as with personality, there’s the problem of characterizing the phenotype in the first place in political orientation. Not insoluble in my opinion, but far less clear than something like height, or even intelligence.

The big picture is that variation on most complex behavioral traits has some upstream genetic correlates. And, we can get some sense of the magnitude (or lack thereof) of the effect in a given environment. But like fMRI the introduction of DNA probably adds more glitz than substance at this point. We’ve long known many traits which we think as purely reflective and environmental have a partial biological basis in disposition. Clearly an area to be continued….

CATEGORIZED UNDER: Behavior Genetics, Genetics
MORE ABOUT: Behavior Genetics

Election 2010 Predictions

By Razib Khan | October 30, 2010 11:20 pm

800px-SarahPalinElonFor Congress, I think that the breakdown will be:

Senate – 50 Republicans, 50 Democrats

House – 240 Republicans, 195 Democrats

My reasoning? I just took FiveThirtyEight‘s numbers and shaded them a bit to the Republican side. There’s no point in making predictions unless you predict something novel and a bit off expectations. Additionally, since the readership here leans a little Left I am inclined to tweak you guys a bit and make the political Götterdämmerung even more terrifying, though I didn’t want to push my luck and give you an implausible value which you’d reject on the face of it.

Image Credit: Therealbs2002, Wikimedia Commons

CATEGORIZED UNDER: Politics
MORE ABOUT: Politics

Have ADMIXTURE run on your genetic data

By Razib Khan | October 30, 2010 10:51 pm

The last 24 hours of the initial sample collection phase of the Dodecad Ancestry Project are upon us. So if you have raw 23andMe data, you got a day to send it in, if you’re of the following groups:

-Greeks (not necessarily from Greece: Cypriots, Pontic Greeks from the former USSR, North Epirotes, Griko speakers from Italy, -Muslim rumca speakers from Turkey, etc. are all accepted)
-People from the Balkans
-People from Anatolia
-People from the Caucasus
-Italians
-Non-Indo-European speakers from Europe (e.g., Finns, Hungarians, Basques)
-Scandinavians and Icelanders
-Iranians
-Armenians
-Jews from Italy, the Balkans, or Anatolia
-Assyrians
-Arabs

The point of the project is to get a better picture of genetic variation in Eurasia, especially in undersampled groups.

CATEGORIZED UNDER: Genetics
MORE ABOUT: Genetics

The global human – II

By Razib Khan | October 30, 2010 10:15 pm

global2A reader pointed me to a second composite image of a “global human.” It is “a composite itself from four composite of Northwest European, South & West Asian, East Asian and African faces….” I was very taken aback by this face, because it was familiar: staring back at me is a younger variant of the faces of my maternal uncles! I asked a friend who has met my family their impression of the photo without a preface, and they immediately wondered if it was a stylized representation of one of my mother’s male relatives.

CATEGORIZED UNDER: Culture
MORE ABOUT: Faces

The possible impossibility of truth and the importance of incorrectness

By Razib Khan | October 30, 2010 12:54 pm

In the post below on the genetic history of India, or earlier when discussing the revisions of European prehistory, one general trend that is cropping up is that the future seems more complex and muddled than we’d presumed. This introduces the real possibility that in the foreseeable future we won’t be able to opine with any credibility about the nature of the pre-literate past, because our tools are good enough to falsify simple models, but not powerful enough to distinguish between the set of more complex models. In contrast, ten years ago when it came to the expansion of farming in Europe on offer we had simple and clear dichotomies; demic diffusion of Anatolian farmers vs. cultural diffusion of farming techniques along trade routes. Ten years ago when it came to India we are mooting the possibilities between elite transmission of Indo-European language, versus demographically significant migrations into South Asia bringing the Indo-Aryan dialects.

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CATEGORIZED UNDER: philosophy
MORE ABOUT: Knowledge

Open Thread – October 30th, 2010

By Razib Khan | October 30, 2010 12:27 am

Oren Harman, author of The Price of Altruism is on BHTV. Recommended.
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CATEGORIZED UNDER: Blog

Coon and friends

By Razib Khan | October 29, 2010 12:24 pm

This week’s episode of South Park was OK, but I really loved this take off on a scene from A Clockwork Orange:

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CATEGORIZED UNDER: Blog
MORE ABOUT: Coon, South Park

My Dodecad results

By Razib Khan | October 29, 2010 11:51 am

A few days ago Dienekes opened up the Dodecad project to a wider range of Eurasians. I decided to send my 23andMe sample to Dienekes ASAP, and the results came back today. I’m DOD075. Dienekes also just put up an explanation of the 10 ancestral components he’s generating from ADMIXTURE (along with tree-like representations of their distances). Below I’ve placed myself in the more local context of populations to which I’m close to:

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CATEGORIZED UNDER: Anthroplogy, Genetics

Friday Fluff – October 29th, 2010

By Razib Khan | October 29, 2010 9:25 am

FF3

1. First, a post from the past: Atheism, Heresy and Hesychasm. I used to post about religion a lot more, especially in the fall of 2006. That was back when ScienceBlogs was small enough and tight enough to have a back & forth discussion among the weblogs pretty easily. I also was working a lot of hours at my job at the time and that imposed a sort of tight discipline on me, I remember hustling off posts after work, before sleep, and on Saturday (into schedule queue).

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CATEGORIZED UNDER: Blog
MORE ABOUT: Friday Fluff

Daily Data Dump – October 28th, 2010

By Razib Khan | October 28, 2010 11:57 am

A very special note: I endorse Christie Wilcox for 2010 Blogging Scholarship.

A map of human genome variation from population-scale sequencing. This paper is getting a lot of play. A taste of things to come from the 1000 Genomes Project. It’s OA, so check it out.

Difficulties in Defining Errors in Case Against Harvard Researcher. I think Marc Hauser will be an emeritus professor by the time the case involving his alleged misconduct is resolved.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Daily Data Dump

The global human

By Razib Khan | October 28, 2010 10:55 am

Paul Conroy sent me a link to a Dutch article which purports to illustrate what the average human male’s face looks like. From what I can gather this is a weighted average by population. Click through and tell me what you think. Seems plausible enough to me.

CATEGORIZED UNDER: Culture
MORE ABOUT: Faces

Sons of the conquerors: the story of India?

By Razib Khan | October 28, 2010 2:43 am

munda2

The past ten years has obviously been very active in the area of human genomics, but in the domain of South Asian genetic relationships in a world wide context it has seen veritable revolutions and counter-revolutions. The final outlines are still to be determined. In the mid-1990s the conventional wisdom was that South Asians were a branch of a broader West Eurasian cluster of peoples, albeit more distant from the core Middle Eastern-North-African-European-Caucasian clade. The older physical anthropological literature would have asserted that South Asians were predominantly Caucasoid, but with a Australoid element admixed in at varying proportions as a function of geography and caste. To put it more concretely, and I think accurately, a large degree of South Asian physical variety can be defined along the spectrum between A. R. Rahman and Nawaz Sharif. The regional and caste truisms are only correlations. Subrahmanyan Chandrasekhar was a Tamil Brahmin, but experienced anti-black racism in the United States. I think that is reasonable in light of his appearance.

ResearchBlogging.orgThis rough & ready mainstream understanding, supporting by classical genetic markers, was overturned in the early years of the 21st century. One line of thought argued that South Asians were much more distinctive from the broader Western Eurasian cluster of peoples. Representative of this body of work is a paper like The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. These researchers tended to start with the female lineages, mtDNA, and then supplement that with Y lineages, the paternal descent. A separate line of evidence, generally drawn from Y chromosomal results, indicated that there were deep connections between the people of India and those of Central Eurasia, in particular via the R1a haplogroup. Additionally, one aspect of the first set of results which was very surprising was that it actually placed South Asians closer to East, not West, Eurasians. But by the end of the aughts the uniparental studies had been supplemented by a range of results produced from SNP-chips, which looked at hundreds of thousands of genetic variants. These studies seemed to support the older view of South Asians being closer to West Eurasians than East Eurasians. Finally last year a paper came out which posited that almost all South Asian populations were actually an ancient stabilized hybrid between two groups, a European-like population, “Ancient North Indians” (ANI), and another group which is no longer present in unadmixed form, “Ancient South Indians” (ASI), of whom the Andaman Islanders are distant relatives. Though there was a slight bias toward ANI as a whole, the fraction of ASI increased as one went southeast, and down the caste ladder. The distinctive “South Asian” ancestral group in other words then may actually be conceived of as a compound of these two elements; an admixture of the native substrate against a European-like genetic background.

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CATEGORIZED UNDER: Genetics, Genomics

The future shall belong to the odorless!

By Razib Khan | October 27, 2010 3:16 pm

My blog post prompted this response:

He notes research hypothesizing a link between high latitudes and the dry earwax gene, and also research that suggests that the dry earwax gene, something that would seem to have little selective impact, may be linked to the same gene that regulates body odor. Low body odor might conceivably confer the 1% per generation selective advantage that would appear to be necessary to account for the current mix of those genes over the 50,000 years the distinction between Asia and the rest of the world is appeared to have evolved.

People can interpret results however they want, it’s a free country. In fact I do so all the time. But I want to enter into the record that I’m skeptical of this particular model of negative selection against stinkiness.

CATEGORIZED UNDER: Genetics
MORE ABOUT: Asians, Body Odor

Daily Data Dump – October 27th, 2010

By Razib Khan | October 27, 2010 1:08 pm

In Mideast House of Cards, U.S. Views Lebanon as Shaky. Some of the problems here are structural demographics. The institutions of Lebanon’s democracy were formed when Maronite Christians were the plural majority, followed by Sunni Muslims, then Shia Muslims, and finally minorities such as the Greek Orthodox and Druze. Today the likely plural majority are the Shia, followed by the Sunnis and Maronites. Add on top of this the fact that the Shia tend to be poorer, and, have an invested international backer in Iran. The connection between the Iranian Shia and the Lebanese Shia has traditionally been closer than between the Iranian Shia and the Iraqi Shia.

Saudi Border With Yemen Is Still Inviting for Al Qaeda. Interesting coincidence that I posted on this issue last week. I think my libertarian friends such as Will Wilkinson and Bryan Caplan will get their wish for relatively open borders in the 21st century as a matter of pure probable prediction (there will be exceptions, I suspect Japan may be one). The future will be something more like the United Arab Emirates, though I hope we’ll be able to effect some humanitarianism on the margins, as well as mitigate the popularity of ugly modernist mega-structures.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Daily Data Dump

Australian Aboriginal people are one?

By Razib Khan | October 27, 2010 1:22 am

ozlang2Richard Broome’s Aboriginal Australians is one of those books which I own which I finally managed to finish recently. It was a quick overview of Australian Aboriginals and their relationship with the settler society, and later in modern Australia. From what I could tell it was a serviceable introduction, though it took a persistent preachy tone whereby one was repeatedly reminded that the Aboriginals were an ever-peaceful people in harmony with nature, notwithstanding their regular burnings of the landscape and inter-tribal brawls. They were in timeless equilibrium with the land that they loved before the white man arrived to destroy their idyll with the shock of modern civilization. The narrative is presented as if the Aboriginals were almost totally static, and perfectly optimized to the environment that was Australia. I personally think this sort of model makes indigenous people less than human, even if it turns them into angels instead of beasts. Of course it’s probably impossible to not have a strong perspective in this sort of material, and I suppose this  type of treatment evens out the ledgers of the past. But one can discern the major themes from the subtle and not-so-subtle polemic easy enough.

One aspect of Aboriginal culture which I have wondered about is its perceived uniformity. The Dreamtime is discussed as if it’s a cultural universal among Australian Aboriginals. Is it? A little poking around indicates that Aboriginals seem to share the idea, though with variations. How’d that come to be? Broome’s model seems to assume that the Dreamtime has deep roots in Aboriginal culture, but we know that the roots likely don’t preexist their arrival in Australia, the people of New Guinea and Melanesia don’t have the concept. It may be that they lost the concept, but I doubt that all of them would. Rather the Dreamtime’s ubiquity in Australia may reflect demographic and cultural change within Australia since the arrival of modern humans ~50,000 years ago.

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CATEGORIZED UNDER: Anthroplogy, Genetics

Daily Data Dump – October 26th, 2010

By Razib Khan | October 26, 2010 12:37 pm

Just a heads up, I might be posting less later in the week and into the weekend. So might skip these at some point.

Are Democrats Overachieving in the Senate? Is Nate Silver is having a downward pressure on other political coverage? I don’t even bother checking the other analytical stuff in The New York Times; they’re just going to basically do souped-up trend stories with cherry-picked quotes from “experts” attempting a bit of man-bites-dog to product-differentiate. The basic outlines of what’s going to happen at the mid-terms is known, as well as the uncertainty. Beyond that most people are guessing and spinning. On the specific issue at hand, I’m not too versed in politics but I had assumed that the Senate was a less volatile institution in election-to-election change in party proportions because only 1/3 of it was up for election in a given year, vs. 100% of the House of Representatives. Silver points out that if the whole Senate was up for reelection we might be looking at filibuster-proof Republican majority, and an outside shot at veto-proof majority.

The Myth of Charter Schools. It’s basically a review of the problems with Waiting for “Superman”. I think this current educational enthusiasm is at a bubble-point, I noticed a few weeks back The New York Times published a downbeat assessment of Geoffrey Canada’s results with the Harlem Children’s Zone.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Daily Data Dump

'dem bones tell strange tales

By Razib Khan | October 26, 2010 1:16 am

There is a new paper in PNAS on remains from China which re-order and muddle our understanding of the emergence of anatomical and behavioral modernity in Eurasia. Human remains from Zhirendong, South China, and modern human emergence in East Asia:

The 2007 discovery of fragmentary human remains (two molars and an anterior mandible) at Zhirendong (Zhiren Cave) in South China provides insight in the processes involved in the establishment of modern humans in eastern Eurasia. The human remains are securely dated by U-series on overlying flowstones and a rich associated faunal sample to the initial Late Pleistocene, >100 kya. As such, they are the oldest modern human fossils in East Asia and predate by >60,000 y the oldest previously known modern human remains in the region. The Zhiren 3 mandible in particular presents derived modern human anterior symphyseal morphology, with a projecting tuber symphyseos, distinct mental fossae, modest lateral tubercles, and a vertical symphysis; it is separate from any known late archaic human mandible. However, it also exhibits a lingual symphyseal morphology and corpus robustness that place it close to later Pleistocene archaic humans. The age and morphology of the Zhiren Cave human remains support a modern human emergence scenario for East Asia involving dispersal with assimilation or populational continuity with gene flow. It also places the Late Pleistocene Asian emergence of modern humans in a pre-Upper Paleolithic context and raises issues concerning the long-term Late Pleistocene coexistence of late archaic and early modern humans across Eurasia.

I read the paper, and I really didn’t understand anything between the introduction and discussion. Mostly because it was a detailed exploration of anatomical details, and I’ve never taken an anatomy class. I basically rely on people like John Hawks to tell me what’s going on in that domain. He hasn’t blogged the paper (well, as of this writing), but he did give an assessment to National Geographic:

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CATEGORIZED UNDER: Evolution, Human Evolution

The Dodecad ancestry project

By Razib Khan | October 25, 2010 3:47 pm

Dienekes Pontikos, Introducing the Dodecad ancestry project:

1) Project goals

The Dodecad ancestry project has two goals:

– To provide detailed ancestry analysis to individuals who have tested with 23andMe; other testing companies may be included in the future.

– To build samples of individuals for regions of the world (e.g. Greeks, Finns, Albanians, Southern Italians, etc.) currently under-represented in publicly available datasets.

I neither endorse nor am I affiliated with any genetic testing company. I have chosen to base the project on 23andMe results, because (i) I perceive that quite a few people have used the service, (ii) the Illumina genotyping platform it uses has substantial overlap with the publicly available datasets on which my analysis depends.

Basically some of you need to send him your 23andMe raw data files. The potential sample space of this group is going to be in the tens of thousands from what 23andMe representatives have stated about how many of the Complete Edition kits they’ve sold. Naturally due to labor and computational constraints he only wants people from particular populations. I think that’s fine. I’m a little taken aback by how demanding and critical Dienekes’ readers have been about the choice of populations he analyzes. You can install ADMIXTURE yourself, get data sets, and manipulate them in PLINK, etc. I hope many people will participate in this project. I would have given my sample, but I’m not of an appropriate population, and even if he wanted South Asians I’m pretty sure I’m not very representative of South Asians (I have very few runs-of-homozygosity and seem to have recent admixture from other world population groups).

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: 23andMe, Dodecad

Daily Data Dump – October 25th, 2010

By Razib Khan | October 25, 2010 11:55 am

Detailed admixture analysis of West Eurasian populations (+ GenomesUnzipped individuals). Dienekes looks at the Genomes Unzipped guys in the context of Eurasian variation. He explains why he prefers bar plots of inferred ancestral quanta over PCA and MDS charts.

A World Upside Down for Greeks. “In Greece, small businesses — defined as stores or workshops employing fewer than 10 people, though many are one-person operations — account for 96 percent of all enterprises and employ around two million of Greece’s five million-strong work force.” Part of this is presumably familialism. Greeks don’t trust each other, so private sector activity is always on a small scale. And part of it is probably the constricted regulatory framework of the Greek economy which prevents the emergence of corporations with some economies of scale. But either way it seems that this is too strong of a bias to be an efficient allocation of labor.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Daily Data Dump
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