Razib Khan One-stop-shopping for all of my content

March 31, 2011

My Goodness My Guinea-ness?

Filed under: Genetics,Genomics — Razib Khan @ 11:20 pm

Update: After this post a researcher who is planning on publishing work on the genetic structure of Great Britain and Ireland and who has a very large N forwarded me a PCA which he gave me permission to repost. I’ve uploaded it here.

As you might infer from the post below I’ve started to get interested in African population structure. It’s not just me. Readers regularly query me about the relationship of various groups, such as the Nilotic peoples who reside amongst the Bantu in northeast Africa. Additionally, there is a consistent problem with 23andMe generating weird results for people of African ancestry, usually those with East African ancestry.

But to figure out the nature of African variation in more detail we also need to give some thought to outgroups. My initial assumption was that using Tuscans would be sufficient, but several people pointed out that many Mediterranean groups have trace African admixture. Probably not enough to matter, but why take the risk? So how about looking to Northern Europe? The Utah Whites and Orcadians jump out as plausible alternatives, but there was a third which I thought I’d try out: the Irish.

Last fall my friend Paul bought a bunch ...

Fighting stupid with stupid

Filed under: Culture,Religion — Razib Khan @ 9:16 pm

When I discuss archaeogenetics with people they often automatically bring their preconceptions to the table, and reframe my own position in a way to make it more intelligible to them. For example, the ground-breaking paper Reconstructing Indian Population History shows that modern South Asians can be viewed very confidently as a compound between two parent populations which synthesized at some point in the past. These are termed “Ancestral North Indians” and “Ancestral South Indians.”

Several Indians I’ve discussed this issue with on the internet have expressed anger at the ANI-ASI model, suggesting that I support the “discredited ‘Aryan invasion theory’”. There’s an interesting point: I invariably avoid referring to the ANI as Indo-Aryans because I don’t think they were Indo-Aryans. My own position, held with only moderate confidence, is that the ANI pre-date the intrusion of Indo-European populations to the Indian subcontinent. Granted, I do think that Indo-Europeans are exogenous. That is, their point of origin was probably not in India, but rather in Central Asia. There are various reasons I hold to this position, but the biggest issue I have with Indians is that they behave as if the rest of the world does not exist. All their arguments for the indigenous status of Indo-Europeans to India could apply to the Indo-European Greeks (e.g., the Greeks have no memory of a land before Hellas). But that is neither here nor there.


European Misappropriation of Sanskrit led to the Aryan Race Theory:

In 2007, I played a role in a historic milestone when I was invited to address the first Hindu-Jewish Summit. I spoke on the Aryan myth and the suffering that it had inflicted on both religious communities. Contrary to earlier apprehensions of some Hindus that this was a “risky” topic to bring up, the head of the Jewish delegation, Rabbi Rosen, member of the Chief Rabbinate of Israel’s Commission for Inter-religious Dialogue, was very impressed. The Jewish delegation decided to appoint a team of scholars to study the issue and the references I had supplied. As a result, at the following year’s Summit, a joint declaration was signed, which included the following language from my draft:

“Since there is no conclusive evidence to support the theory of an Aryan invasion/migration into India, and on the contrary, there is compelling evidence to refute it; and since the theory seriously damages the integrity of the Hindu tradition and its connection to India; we call for a serious reconsideration of this theory, and a revision of all educational material on this issue that includes the most recent and reliable scholarship.”

Much of Hindu tradition is a bunch of primitive superstition (and personally I think Vedanta is sophisticated superstition, like almost all of religiously inflected philosophy). Who cares? And before some Hindus bellyache, how about you enjoy this cute reedit:

The forgotten East, part 2

Filed under: Genetics — Razib Khan @ 8:08 pm

A month ago I posted India East and Inward. On a related vein, over at Discover a commenter observes:

It is interesting that four individuals have some African ancestry, no doubt due to the slave trade. The Carribean individual acquired it from the European slave trade and the Sindhi and Balochi individuals from the Islamic slave trade.

But what about the E. Asian component? History and geography can explain its presence in Razib’s parents and in Bengali individuals. According to Reich et al. South Asians can be modeled as a linear combination of ANI and ASI or in this model a linear combination of S. Asian and European. The ASI is quite distinct from E. Asian. Why is there some E. Asian in most individuals? Is this real or is it an artifact of the ADMIXTURE analysis?

My response:

first, reich et al. know that there are other minor elements. that’s why they discard outliers which have these minor elements to a great enough extent. second, i assume that it is noise in most of the cases. but some of the south indian samples (tribes) look way too admixed to be noise. the slave trade probably came from southeast asia too. in sri lanka malays have preserved their cultural identity, just as they have to some extent in south africa (less so), but probably this percolated in parts of south india. we aren’t surprised when we see west asian among kerala christians. we should be less surprised if we see some southeast asian in the tamil country.

The Bantu völkerwanderung

Filed under: Africa,Archaeogenetics,Bantu Expansion,Genetics,Genomics — Razib Khan @ 2:34 pm


Image Credit: Mark Dingemanse

I recall years ago someone on the blog of Jonathan Edelstein, a soc.history.what-if alum as well, mentioning offhand that archaeologists had “debunked” the idea of the Bantu demographic expansion. Because, unfortunately, much of archaeology consists of ideologically contingent fashion it was certainly plausible to me that archaeologists had “debunked” the expansion of the Bantu peoples. But how to explain the clear linguistic uniformity of the Bantu dialects, from Xhosa of South Africa, up through Angola and Kenya, to Cameroon? One extreme model could be a sort of rapid cultural diffusion, perhaps mediated by a trivial demographic impact. The spread of English exhibits this hybrid dynamic. In some areas (e.g., Australia) there was a substantial, even dominant, English demographic migration coincident with the rise of Anglo culture. In other areas, such as Jamaica, by and large the crystallization of an Anglophone culture arose atop a different demographic substrate, which synthesized with the Anglo institutions (e.g., English language and Protestant religion). The United States could arguably be held up as a in-between case, with an English founding core population, around which there was an ...

Mapping ADMIXTURE components

Filed under: Genome Bloggers,Genomics,The Jatt Gene — Razib Khan @ 12:05 pm

Over at Harappa Simranjit has been allowing Zack to post his isopleth maps of the frequencies of ADMIXTURE components by region. He now has his own blog, The Jatt Gene. On unrelated note, does anyone know of an easy way to generate isopleth maps which is open source?

March 30, 2011

The New York Times “pay wall”

Filed under: Blog,Media,The New York Times — Razib Khan @ 11:09 pm

So what do readers of this blog think? Pay or no pay? It’s useful, and The New York Times is pretty massive in scope, if sometimes lacking in breadth. I love their data-oriented stuff, but I ignore their columnists and a lot of their “analysis,” which is frankly substandard if I know anything about the topic (which suggests to me if I don’t know about the topic, they barely do too). There are certain areas where blogs have a comparative advantage, and I don’t see why an organization with other strengths would even make an attempt.

Personal genomics gets very personal

Filed under: 23andMe,Personal genomics — Razib Khan @ 10:58 pm

Dan MacArthur points me to this nice post over at Daily Kos, Our Genome Decoded: How Companies Like 23andMe Are Advancing the Field of Personal Genomics:

…However, in the past few years several private biotech companies have started offering a “personal genome service” that involves sequencing the most variable portions of our DNA. The goals are straightforward – to give individuals information about their ancestry and inherited traits. While there are definite limitations – both technically and bioethically – to the amount and type of information that can be obtained from personal genome sequencing, in my case the service answered a lingering question about something important to me, and thus was well worth it.

In this article, I’m going to tell the story about why I chose to purchase a personal genome service, briefly explain how it works, show my interesting results, and finally, provide some commentary on how these services will impact the fields of genomics and medicine.

One step at a time. I also appreciate that Michelle keeps posting on her ADMIXTURE results.

Bravo for Mormons!

Filed under: Joseph Smith,Mormonism,Religion — Razib Khan @ 10:48 pm

Trying to Relish the Big Time, Even When It Brings a Cringe:

The house lights came up and it was intermission at “The Book of Mormon,” the new Broadway musical about a pair of innocent young Mormon missionaries sent to Uganda to spread the faith. John Dehlin, a graduate student who flew in from Utah to see the show with a group of Mormons from around the country, was still riveted to his theater seat, having flashbacks.

“It’s way, way too close to home,” he said, recalling his own missionary years in Guatemala: the shock at the poverty and violence, the pressure from the mission president to baptize more natives, the despair when his mission companion ran off with a local girl — and the Mormon mandate, above all, to repress doubt and remain relentlessly cheery.

A friend in the crowded theater aisle, Paul Jones, passed by and gave Mr. Dehlin a high-five and a hug. “It’s right on,” said Dr. Jones, a dentist from Gilbert, Ariz., “but I cringed a little bit, a couple of times.”

The arrival of a Broadway musical that ridicules their religion, produced by the creators of the scathingly satirical television show “South Park,” is proving to be ...

Kala!

Filed under: Colorism,Culture — Razib Khan @ 11:06 am

Indian film stars vs regular Indians:

A couple of points about the article. I disagree that the obsession with fair skin is related to British colonialism to any great degree. Preference for “lightness” does not equate to preference for “whiteness”. It’s far older than British rule and has its basis in the caste system. The conquerors of India have historically come from the north (Indo-Europeans, Muslim Moghuls), and the darker tones of the Southern Indians have acquired a negative association, enshrined by caste. It is probably overlain with an element of the same colour prejudice that occurs in East Asia, which is related to social class and occupation (dark skin = tan from working out in the sun = being a commoner).

Realistically, the likes of Sharma, Gracias and Rajandran are not really dark, when one considers the diversity of phenotypes across India. They are probably in the middle of the skin tone range. The ideal look for Indian celebrities is at the pale end of the spectrum. Male actors can to some extent get away with a degree of swarthiness that females can’t. Still, in a country with significant prejudices against its Muslim minority and hatred towards its Muslim neighbour Pakistan, some of the biggest male stars of Bollywood are Muslims (Aamir Khan, Salman Khan, Shah Rukh Khan), and I wonder how much that is related to their “Aryan”-ness.

Tipu Sultan, a "black" Muslim

It is correct that the preference for light skin predates the British era. Blaming something on colonialism is such a lazy trope. From the Muslim period there’s enough textual evidence to indicate that the Iranian and Turanian ruling caste had contempt for the natives on racial as well as religious grounds. From what I have read there was even some hostility directed at the South Indian Muslim warlord Tipu Sultan because of his clear origins among Hindu converts. The painting to the left makes no effort mask his rich brown pallor.

Whether this attitude toward light skin predates Muslim period is more contested. There is a strong strain of older scholarship which suggests that ancient Hindu texts and traditions do suggest contempt toward the dark-skinned peoples of the subcontinent. Revisionists, often of Indian nationalist bent, have reinterpreted the conflict between the light and the dark in metaphorical terms. For me the recent genetic data indicating partitioning between high and low castes in any given region implies that the view that differences in color were pure metaphor is probably not correct, and there was some genuine racial element even in the antique period. I suspect that the underlying reason is the one given above, that so many military elites in South Asian history have had a northwestern origin. Assam might be an interesting contrast, because the Ahom are Sino-Tibetan, though even in this case the elites would have been lighter skinned.

 

The end of Ayla & The Land of Painted Caves

Filed under: Clan of the Cave Bear,Culture,Jean Auel,Land of Painted Caves — Razib Khan @ 1:03 am

I read  Jean Auel’s Clan of the Cave Bear in elementary school at a friend’s house during a sleep over. It was next to the bedside, and I decided to pick it up. I’d thought it was a human evolution book from the cover. I read  2/3 of the book by dawn, took a few hours to catch up on sleep, and then finished the rest before the afternoon. I read almost no fiction outside of what was assigned in school as a child, but this was the exception (I also read a lot of Greek mythology, though I’m not sure that counts). The three sequels I finished in middle school when I noticed there were sequels! By the time book 5, Shelter of the Stones, came out in the early aughts I’d lost interest. I’ve moved on, but many have not. The last book, The Land of Painted Caves, is now out. The Los Angeles Times has written a retrospective of the series.

Since Amazon has a 1 to 5 star rating system, I thought I’d plot the results for the first five books. On the y-axis you have the number who gave ...

March 29, 2011

The day of the farmer

Filed under: Agriculture,Anthroplogy,Farmers,Genetics,Genomics,Neolithic Revolution — Razib Khan @ 10:01 pm

About five months ago I read Peter Bellwood’s First Farmers: The Origins of Agricultural Societies. Bellwood’s thesis is simple: that the first adopters of farming entered into a period of rapid demographic expansion and by and large replaced non-farming groups. The populations which dominate the world today in this model are then the descendants of the very small set of cultures which ~10,000 years ago triggered the Neolithic Revolution. When Bellwood presented his thesis in the mid-2000s many would have dismissed it out of hand. Today I believe we have to take this model seriously.

There are two primary reasons from my perspective why I am now thinking about Bellwood’s thesis a great deal. First, the archaeogenetic inferences based on distributions of modern allele frequencies which suggested that the Neolithic Revolution in Europe was a matter of cultural diffusion seem far shakier. With such genetic models no longer taken for granted the recent historical, semi-historical, and ethnographic evidence, on farming transitions must be given much more weight. The case of the Bantu expansion in Africa seems to be semi-historical. The Bantu farmers themselves were not literate but their wave of advance was in historical time. Tellingly, the Bantu speaking populations ...

The excitement of clothed porn stars

Filed under: Pleasure,Porn,Psychology — Razib Khan @ 12:59 pm

Porn Stars, Clad? They Seem to Appeal to Indonesian Filmgoers:

Ms. Aoi, and others like her, are the secret of a winning formula stumbled upon by Maxima Pictures, the production house where Mr. Hidayat is an executive producer. For two years, Maxima has made some of Indonesia’s most popular domestic films based on a simple premise: that many in Muslim-majority Indonesia will pay to see foreign porn stars perform — clothed — in local films. Just don’t expect Indonesians to own up to it.

“We’re hypocrites,” said Mr. Hidayat, who is a Muslim. “People know who they are, but they won’t admit it. It’s a love-hate thing.”

This sort of “counter-intuitive” behavior makes total sense in light of the work reported in Paul Bloom’s How Pleasure Works: The New Science of Why We Like What We Like. People consume in a particular context. The hedonic experience can’t be isolated from its history and the prior facts (and expectations) you bring into it. This sort of insight is essential when we start talking about utilitarianism as if it’s a simple calculus.

The limits of computational power – shades of 1982

Filed under: Genetics,Genomics,Harappa Ancestry Project,Personal genomics — Razib Khan @ 12:44 pm

Two Steps Forward, Two Steps Back:

I got my daughter a netbook, so now my computer is doing Harappa Prohect work 24×7.

Also, Simranjit was nice enough to offer me the use of a server. For privacy reasons, I am not going to upload any of the participants’ data there but it is much faster than my machine and hence very useful for running Admixture on the reference data (especially with crossvalidation).

As for steps back, I downloaded the current 1000genomes data (1,212 samples, 2.4 million SNPs). It’s in vcf format. Using vcftools to convert it to ped format will take about 3 weeks. Yes you heard that right. BTW, the good stuff from a South Asian point of view will come later this year with a 100 Assamese AhomF, 100 Kayadtha from Calcutta, 100 Reddys from Hyderabad, 100 Maratha from Bombay and 100 Lahori Punjabis.

Also, I spent most of Sunday evening and night in the ER and got a diagnosis of ureterolithiasis for my efforts. All I can say is: Three cheers for Percocet!!

First, wish Zack well. Second, he has over 70 individuals in the Harappa Ancestry Project data base (in addition to the public data sets). If ...

Genetic paternalists are very patronizing

Filed under: FDA,Genetics,Genomics,Paternalism — Razib Khan @ 10:17 am

An comment below on my post Genetic paternalism & the F.D.A.:

I came across your inflamed post from March 9th and the more I read the more disappointed I became, especially when I read your comment “following twitter, it seems there may be a distinction between raw sequence and interpretation. it may be the latter where there are “gatekeepers.” probably for reasons of liability, public safety, etc. (ergo, FDA). i see the logic, but from a perspective of utility i don’t think that the regs will improve human well being. though that’s probably not the implicit rationale behind “interested parties.””
The distinction there is ABSOLUTELY CRUCIAL. There is a huge difference between providing your raw genomic information, and providing diagnostic interpretation.

The AMA letter http://www.ama-assn.org/resources/doc/washington/consumer-genetic-testing-letter.pdf clearly stated that it was directed to ” direct to consumer (DTC) genetic tests that make medical claims” and it is “the making of medical claims” that puts certain offerings of DTC genetic testing squarely in the FDA’s domain; uninterpreted DTC genetic test results – the raw sequence – are NOT in the FDA’s domain under current regulations. Medical claims are. And I have not heard the FDA claim that they would even try to ...

The flat and the fit

Filed under: Evolution,Evolutionary Genetics,Genetics — Razib Khan @ 1:10 am

ResearchBlogging.orgThe Pith: In evolution if you want to win in the long run you don’t want all your eggs in one basket, even if that’s the choicest basket. Sh*t happens, and you better have some back up strategies.

Diversity is a major question in evolutionary biology. In particular, why is there so much diversity, so that the tree of life manifests a multitude of morphs? Might there not be some supreme replicator which emerges from the maelstrom to conquer all before it? This is actually the scenario which unfolds in much of science fiction, with monomorphic grey goo eating everything in its path (a more aesthetically differentiated variant of the super-species emerges in Brian W. Aldiss’  Helliconia Winter). As it is, life on earth does not seem to be converging upon an optimum phenotype for all individuals. In contrast, it seems to be going in the opposite direction broadly speaking (thinking on billion year scales), with the shift from the monotony of communal cyanobacteria to the riotous diversity of tropical forest biomes and coral reefs.

There are many ways you might be able to explain this diversity. Temporal and spatial heterogeneity ...

March 28, 2011

India as an idea

Filed under: civilization,Culture — Razib Khan @ 2:07 pm

Overselling India?:

I am familiar with some of the India-merchants that Chaudhuri mentions but not all; I should therefore withhold judgment on the quality of the entire literary output. However, I can see the dangerous pitfalls (and the inevitable pratfall) facing anyone who undertakes to convey the “idea” of India, an ancient, vast and immensely populous nation with a dizzying diversity of ethnicities, languages, religions (subdivided into castes) and cultures. A few times in passing, some of us here have complained about the unnecessary “exoticization” of India which unfortunately is often a two way traffic. Non-Indian seekers of ”India as an experience“ go there to validate a preconceived notion of the place and certain sellers of India enthusiastically and cynically provide reinforcement. The trade often results in hypocrisy and disillusionment. The most disappointing (and disappointed) reporting usually comes from those who expect a limited foray into India as a spiritual retreat to resolve all or most of their existential conflicts. I will paraphrase here what I once wrote as a comment in response to an article of discontent written by a traveler to India who did not find there what he had sought.

I think one has to make recourse to analogies here. Imagine the idea of Europe. Or the idea of Latin America. The idea of Europe is not trotted out very often because Europe is well known to all, and we live in many ways a Eurocentric world imaginatively. No one would presume that Sweden and Spain are interchangeable. Rather, each are special, distinctive, and must be taken on their own terms. In contrast, people do distill Latin America into one amorphous whole. But if you ask Latin Americans, an Argentine, a Mexican, and a Panamanian would protest their distinctiveness. If you they have spent time in America they will also tell you how often people assume something about them because of a mistaken generalization about “Latinos” as a whole.

Who thinks the sun goes around the earth?

Filed under: Data Analysis,Geocentrism,GSS — Razib Khan @ 2:00 pm

My post earlier today prompted a few emails about the bizarre result that a substantial minority of Americans accept that the sun goes around the earth. The General Social Science variable is EARTHSUN, and it asks:

Now, does the Earth go around the Sun, or does the Sun go around the Earth?

The answers are “Earth around the Sun,” “Sun around the Earth,” and “Don’t Know.” A substantial minority of Americans answer #2. What’s going on here? This isn’t something limited to America. The same question has been asked internationally. I’ve underlined the geocentrism/heliocentrism question below:

I apologize for the small font. What you’re seeing though is that substantial minorities, on the order of 1/7th to 2/5th of people in the regions above give the wrong answer on whether the earth goes around the sun, or vice versa. Is geocentrism rampant? No, I don’t think so. My explanation is that many people don’t think scientifically habitually, so scientific facts aren’t background priors which pop up reflexively. On surveys which require a rapid first-blush reaction you may give the “intuitive” result, and only later realize that your answer ...

Genetics as the myth buster: Indian edition

Filed under: Genetics,Genomics,India Genetics,India genomics,Vishwakarma — Razib Khan @ 12:17 pm

Whenever Zack Ajmal posts a new update to the Harappa Ancestry Project he appends some data to his ethnic database. This sends me to Wikipedia, because how many people are supposed to know what a “Muslim Rawther” means? Well, if you are a Muslim Rawther, and perhaps from Southern India, you would. But South Asian ethno-linguistic categories and hierarchies are notoriously Byzantine, and I have difficulty making sense of them. This isn’t too surprising in my case, as my family’s background is relatively mixed in the very recent past (e.g., Hindus and Muslims, and people of various caste backgrounds), so we’re not the sort who can go at length about our pure ancestry and all that stuff. Unfortunately, Wikipedia isn’t always useful, because the people editing the entries on particular South Asian ethnic groups are often people from those ethnic groups, so you get a lot of extraneous information, and a particular slant on how awesome and high achieving the group (also, sometimes there’s funny stuff about how notoriously good looking that particular caste!). On occasion there are other sources which are informative. For example, Zack has several individuals from the Tamil Nadar caste. I know ...

March 27, 2011

The Republican fluency with science

Filed under: Data Analysis,GSS — Razib Khan @ 11:44 pm

The Audacious Epigone has a post up, Republicans are more scientifically literate than Democrats or independents are, where he reviews pro vs. anti-science attitude by party in the General Social Survey. He concludes that in fact Republicans are more scientifically literate across the issues than Democrats. Jason Malloy saw this trend four years ago in the GSS, and to some extent so have I. One point to keep in mind is that a few specific politicized scientific issues are very much the outliers in exhibiting tight partisan valences in opinion.

So another question: are conservatives more scientifically literate than liberals? If scientific literacy correlates with being Republican, and being Republican correlates with being conservative, shouldn’t scientific literacy correlate with being conservative? Not necessarily. Such correlations are not transitive. Generally what I’ve seen in the survey data is that Republicans tend to be more pro-science than conservatives. I think part of it is the voting by economic position which has become less stark in our culture, but still remains a force. In any case, my table to accompany AE’s is below. I used his variables:

ASTROSCI, SCIBNFTS, EXPDESGN, ODDS1, HOTCORE, RADIOACT, BOYORGRL, LASERS, ELECTRON, VIRUSES, CONDRIFT, EVOLVED, EARTHSUN, ...

It’s about heritability….

Filed under: Behavior Genetics,Behavior Genomics,Genetics,Genomics,Heritability — Razib Khan @ 1:25 pm

I’m going to promote a comment:

…would knowing the root biological cause for differences which are already apparent to us change anything?

It’s obvious to you that there’s a contradiction here, but to the average educated person this makes total sense.

The proximal reason seems to be that in thinking about “genetic” and “environmental” factors, the average educated person still fundamentally views “genetics” as equivalent to genetic determinism and “environmental” factors as equivalent to social norms or parenting tactics. In this black-and-white view of human development, quantitative distinctions and complex causal models have no place. Genetic causes are irremediable and ever-lasting, whereas environmental causes are a generation-away from disappearing with the right appropriations to social programs. That’s why an environmental cause for phenotypic differences doesn’t “count” but a genetic one is game changing.

It seems as if the nature-nurture world view painted in the 1970s by the anti-heredity crowd has remained largely intact with only minor modifications in the mind of the average educated person. Since the 1970s, they now know to respond to questions about nature-vs-nurture by saying “both”, but their understanding goes no deeper than that. As best as I can ...

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