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

February 28, 2011

The residual of the genes & geography correlation

Filed under: Genetics,Genomics — Razib Khan @ 4:14 am

David of the Eurogenes Genetic Ancestry Project has a cautionary post up, When is a genetic map also a geographic map? Always and never. In it, he uses a specific peculiar pattern as a launching point into a broader exploration of the relationship between visualizations of genetic variation, and geography. That pattern is that Russians, the most geographically furthest east of European peoples, are closer to the Slavs of Central Europe than the Balts when plotted on the two largest dimensions of variation. I’ve highlighted this pattern from a PCA David extracted from a paper on northeast European genetics. This disjunction between geography and genetics has a pretty straightforward possible explanation: the current distribution of Russian-speaking peoples is a function of a massive demographic expansion to the east by Slavic farmers within the last 2,000 years. We already know that the borderlands between the steppe and the forest were long dominated by North Iranian people, from the Scythians to the Sarmatians, while further north the Great Russians absorbed a Finnic substrate (clear because some of the absorption is attested down to the early modern period).

With that duly ...

Pre-modern elites were thieves

Filed under: Civilisation,Conquest — Razib Khan @ 2:04 am

Though there were periodic intrusions of South Asia from the west, there seems to have been little flow of people and political power projection from South Asia out to Iran and Turan.* Why? Traditionally I have favored geographically contingent parameters. Populations from warmer climes tend not be well prepared for the winters in northern climes, while those from frigid climes can usually adapt by shedding clothing. The difficulties of the Arabs in pushing their power very far north of the Caucasus was an instance of this, as the records seem to indicate some difficultly in adapting to the reality of the north Eurasian winter (Islam’s penetration of the north came via the conversion of the Turks). In contrast, Turkic peoples have moved south for the past 1,000 years with relative ease.


But I realized another factor which I think is more important in hindsight: pre-modern elites were generally in the business of extracting rents from subjects. The more subjects, the more rents. So, the ruler of India is clearly far wealthier than the ruler of Mongolia, even if the average Mongol has a higher per capita level of wealth and health. On the margin there simply wasn’t much profit in conquering wastelands for autocrats of densely populated regions. This is clear in the historical record, by the time of Claudius it was presumed that his conquest of Britain was more a matter of personal vanity, glory and prestige, than necessity. Though particularly egomaniacal potentates, such as Han Wuti, may have felt that there was a need to send massive armies to conquer lands which were barely inhabited by savages, in general these societies felt it more rational to simply pay off the barbarians outside the gates (the Chinese case is well attested, but the East Roman Empire did this for centuries leading up to, and after, the fall of the West Roman Empire).

It is clear from the early Muslim annals that India was viewed as a land of riches. But, I think we misunderstand the perspective if we view India as the Netherlands or Japan of its era in relation to the Mashriq or Iran. Before the Industrial Revolution the average standard of living in all societies was only marginally above subsistence. Differences of per capita wealth were on the order of 10-20%, or less. Not the multiples, or even orders of magnitude, which we’re familiar with today. So how was India so rich? It was rich in people, so from the perspective of predatory elites it was a place where you could become very rich indeed.

The best analogy for wealth then is how some African pastoralists view their cattle. More cattle = more wealth. More subjects = more wealth. Not because individual subjects were wealthy, but because stealing a small amount from more people sums up into a large pile of rents extracted. Of course such economic-structural arguments have their limits. The Mughals periodically attempted to conquer Samarkand. Why? Because they were Timurids, and Samarkand was the traditional seat of their lineage. In other words, there are emotional reasons to conquer worthless territory which does not redound to one’s bottom line. That certainly explains much of 19th century European colonialism, which was on the balance a transfer of payments from the citizenry to the well-connected aristocrats and plutocrats, who could take advantage of opportunities offered in the colonies.

* I make a distinction here between demographically salient events, such as mass migrations, and culturally influential ones. In the latter case obviously Buddhism, and to a lesser extent Hinduism in Afghanistan, flowed to the northwest.

Around the Web – February 28th, 2011

Filed under: Blog,Daily Data Dump — Razib Khan @ 12:14 am

February always goes by so fast….

Should you go to an Ivy League School, Part II. I think the value of an Ivy League degree will be more, not less, important in the future. It seems possible that we’re nearing the end of the age when the wage gap between unskilled and skilled workers is relatively modest (roughly, the wage gap decreased between 1800 up to 1970, and has been increasing over the past 40 years). Credentialing and finding juicy rents and sinecures is probably the way to go in the future. As the past was, the future shall be?

Anthropologists Trace Human Origins Back To One Large Goat. “Read the whole thing.”

Advanced Degrees Add Up to Lower Blood Pressure. I’m sure that the paper itself is less irritating in terms of conflating correlation and causation. The problem is that it is the least intelligent people who will think that extra years of education = extra years of life in a magical manner. That being said, peer group effects probably matter, so I suspect that that’s part of what’s going on here after you correct for background variables.

Election Defeat Predicted for Ireland’s Ruling Party. It is rather strange ...

February 27, 2011

My parents, looking east and west

Filed under: Genetics,Genomics,GSS,Personal genomics — Razib Khan @ 5:20 pm

Yesterday Michelle decided to put up a post with her own analysis of her ADMIXTURE results. With that in mind, I thought I’d revisit some results from my parents. After many runs of ADMIXTURE, both by myself and Zack, some consistent differences seem to crop up. To review, one of the big surprises from genotyping my parents is that both of them have about the same “East Asian” element of ancestry which is very distinctive from the conventional South Asian mix. Because both of my parents lack any oral history of recent admixture I posited that this element may be a uniform substrate common among eastern Bengalis, and that it was absorbed during the initial period of settlement and demographic expansion on the frontier in the period between 1000-1500 A.D. By analogy, low levels of Amerindian admixture persist across Brazilians, and African admixture among Mexicans, but because the admixture dates back several hundred years it does not seem to have percolated down to the present in oral history (though some old stock Brazilians of predominantly Portuguese origin have been able to infer Amerindian ancestry by looking at the church marriage records of their ancestors, and ...

India East and Inward

Filed under: Culture,Religion — Razib Khan @ 12:28 am

Vietnamese Hindus (Chams)

One of the peculiar aspects of modern South Asian identity, in particular, that of Hindus, is a sense a of civilizational involution. By this, I mean that Islam and Christendom have an expansive self-conception, which at some point in the future is presumed to reach an equilibrium whereby the whole world is dominated by its particular form of life, while Indians perceive a particular rootedness of their forms in the Indian subcontinent. But this was not always so.

The century or so before Islam has been termed the “Buddhist Age.” Buddhism had taken root in China as an indigenous and vital religion, and began its spread to Korea and Japan. Hindu and Buddhist influences were also evident in Southeast Asia. Men of Indian origin such as Kumārajīva were prominent at the time in China, teaching the tenets of the new religion and translating its scriptures into the local language. Though the figures at the courts of the kings of Angkor and Srivijaya are more vague, it seems implausible that Indian culture could spread without some Indian individuals. In the domain of “hard power,” the peninsular Cholas of the Tamil lands at their peak claimed hegemony over much of maritime Southeast Asia.

What happened? I think without getting into too controversial a territory native Indian cultural traditions clearly took a defensive crouch after the hammer-blow of the Muslim Turk raids, and then later the Islamic hegemony across much of South Asia. Unlike the Zoroastrians of Iran, or the Christians of the Near East, South Asians maintained their indigenous religious traditions by and large. But like Rabbinical Judaism, Indian civilization was transmuted by the thousand year awkward condominium between Islam and the Dharmic traditions. I must admit I find it ironic that some of the most anti-Muslim Indians I’ve met are also the most obviously attached to the involuted and exclusive forms and ways of Hindu civilization as it developed by necessity when faced with a religiously alienated ruling class.

February 26, 2011

Tolerance in Dar-ul-Islam

Filed under: Culture,Islam — Razib Khan @ 1:11 am

I’ll throw this out there as an open question. Which nation in the Dar-ul-Islam is the most tolerant toward non-Muslim faiths? Bonus points for a combination of a substantial non-Muslim minority (so it’s not a moot point) and a devout populace. For example, Albania, Azerbaijan, and Kazakhstan, and probably Bosnia if you could disentangle ethno-nationalism from the equation, would probably come out on top. But these are nations which have experienced secularization, and have a substantial proportion of nominal Muslims among the confessing believers. I think to combine both religious sensibility and tolerance you’d probably have to look to Africa. I nominate Senegal, because it is a relatively stable and democratic Sub-Saharan African nation, which is 90% Muslim, whose first president was a Christian. That’s a large enough non-Muslim minority to make minority rights a live point, but the Islamic dominance in terms of numbers is assured.

Ancient Iraqi Christian monastery used as a latrine by the Republican Guard

This issue crossed my mind when listening to the journalist behind the new Frontline documentary, Revolution in Cairo. He was being asked about the role of Islam in the new Egyptian state, and he stated plainly that even today the Egyptian constitution gives particular prominence to the role of Islam in determining the laws of the land, and that special intermingling of religion and state would no doubt continue, and perhaps even wax. And, he asserted that the Copts of Egypt would accept, understand, and have to deal with this fact. This is all absolutely correct as a descriptive matter. But I sat back and reflected that at ~10% of the of the population the Copts form a much larger proportion of Egyptians than Muslims do within the European union. Not only that, but no one doubts that the Copts are authentically Egyptian, with deep cultural roots in the region. And yet they have to accept their role as dhimmi, as they always have. The world dhimmi has negative connotations, but the consistent special place that Muslim majority religions give to the majority religion in their constitutions the world over (even in explicitly secular nations like Bangladesh, which has a Leftist political foundation, not an Islamic one) is simply accepted in a way that would contested be elsewhere. The European Union for example famously omitted mention of the continent’s Christian heritage.

A connection between church and state need not necessarily be frightening. There is intermingling of Buddhism and state in Thailand, and it is relatively anodyne. Similarly, England and Denmark have established or national churches. Perfect neutrality is impossible in any case. Additionally, as Omar likes to note, the “Islamic” nature of states which are explicitly Islamic or give a nod to Islam in their central documents is almost always a substantive illusion. That is, their legal codes and such are generally imitative of those of the West, only modified in particular sections by Islam (often family law). No, the dominance and prominence of Islam has more impact as a identity-group ideology to oppress and culturally cleanse religious minorities. Naive and stupid Westerners are wont to assert that the Islam needs a “Reformation.” What these naive and stupid individuals don’t seem to comprehend is that the Reformation triggered the Wars of Religion and decades of massive sectarian expulsions and migrations of conscience.

I believe that in our age we are seeing the de-Christianization of the Middle East, the extinction of Oriental Orthodoxy. The Coptic Church in Egypt is the most substantial bulwark against the total completion of the process, because 8 million is just too large a number for the rest of the world to accept comfortably. We’ll see what happens in the future.

“Content farms” and the media Precambrian

Filed under: Technology — Razib Khan @ 1:04 am

I’ve only become aware of “content farms” in any significant way over the past few days. Yes, I’m aware of Associated Content and eHow. I use Google! But I’ve always ignored them. But with Google’s turn against these websites I’ve become curious. This Wired piece from October 2009 is a gem. Here’s the part that caught my attention:

Plenty of other companies — About.com, Mahalo, Answers.com — have tried to corner the market in arcane online advice. But none has gone about it as aggressively, scientifically, and single-mindedly as Demand. Pieces are not dreamed up by trained editors nor commissioned based on submitted questions. Instead they are assigned by an algorithm, which mines nearly a terabyte of search data, Internet traffic patterns, and keyword rates to determine what users want to know and how much advertisers will pay to appear next to the answers.

In some ways “mainstream” websites also do this a bit, Nick Denton relies on fine-grained metrics for his Gawker Media properties. But obviously the sort of thing that content farms do, responding so specifically to the interests of the audience, take it to the next level. I started browsing some of the ...

February 25, 2011

The changing face of fame

Filed under: Composites,Culture,Hollywood — Razib Khan @ 2:51 pm

Long time reader Dragon Horse has been generating and collecting (top row images are from Dienekes) composite image of various classes of individuals for a while now. It’s really fun to just skim through and make your own assessments (the “global face” resembles darker skinned versions of Amerasians, whose fathers were white Americans and mothers Southeast Asian, to me).

The most well known composites are of nationalities, but he’s also generated and reposted composites of other classes. For example, the average Bollywood actress is Aishwarya Rai. Not literally, but the resemblance is jaw-dropping (compare to the average Indian woman). But most interesting to me were the comparisons of American film actors, male and female, then and now (“Golden Age” vs. contemporary). I’m pretty sure you can pick out which one is which if you’re American. There seem to be two correlated trends here: 1) more feminine features for both males and females, and 2) more youthful features for both males and females. Correlated, because neoteny and masculinization seemed to generally push in opposite directions of trait value. Projecting in the future I assume that the Global Human Celebrity ...

Friday Fluff – February 25th, 2011

Filed under: Blog,Friday Fluff — Razib Khan @ 12:02 pm

FF3

1) First, a post from the past: “Black” & white twins again.

2) Weird search query of the week: “buff chimpanzee.”

3) Comment of the week, in response to The evolution of man is no cartoon:

I think the confounding notion here is that changes to the DNA which don’t affect a protein’s amino acid sequence are selectively neutral. It’s endemic, and yet there are several very obvious counterexamples.

True. But as a first approximation, it is still a reasonable practice. For every 1000 amino acid changes one will find A LOT more functional effects than for every 1000 silent mutations. Keep in mind that your argument can be taken in reverse, too: there are some obvious examples where amino acid change does not result in a detectable change of properties.

4) And finally, your weekly fluff fix:

Brazilians, more European than not?

Filed under: Brazil,Genetics,Genomics — Razib Khan @ 1:30 am


Credit: Dragon Horse

The Pith: Brazil is often portrayed as the second largest black nation in the world, after Nigeria. But it turns out that the majority of the ancestors for non-white Brazilians are European.

One of the more popular sources of search engine traffic to this website has to do with the population genomics of Latin America. For example, my post showing that Argentina is not quite as European a country as it likes to consider itself is regularly cited in online arguments (people of various “persuasions” are invested in the racial status of the Argentine people). But last week in PLoS ONE a paper looking at the patterns of ancestry in the Brazilian population came to a somewhat inverse conclusion as to the self-conception or perception of the preponderant racial identity of that nation. Let me quote from the conclusion of the paper:

Among the actions of the State in the sphere of race relations are initiatives aimed at strengthening racial identity, especially “Black identity” encompassing the sum of those self-categorized as Brown or Black in the censuses and government surveys. The argument that ...

February 24, 2011

The arrow of history

Filed under: History — Razib Khan @ 7:48 pm

In the comments below there is a debate about the inevitability of progress, the possibility of reversion to past states, etc. I am not going to put a long comment here, but want to enter several points.

- At the end of the day the universe will suffer “heat death,” so eventually all anti-entropic dynamics and phenomena will be reversed

- So we need to constrain the time parameter to something reasonable. The parameter for biological evolution is probably on the order of a billions of years, while for human history we’re talking thousands of years


- For biological evolution I think there has been a general trend toward greater complexity. Some changes seem to be irreversible. Off the top of my head: the emergence of aerobic life and multicellularity. Multiple extifnction events have not been able able to “turn back the clock,” because there’s always a residue of species. The key is that instead of gradual accumulation of complexity, it seems that rather there are “bursts” which reach plateaus. I think it can be argued that we have been at a plateau since the rise of terrestrial tetrapods (the extinction of very large insects is probably a function of the rise of tetrapods, who are “better” at filling the macro-terrestrial niches because of their superior scalability)

- When it comes to history this is much more tendentious, but yes, I do think there has been an arrow of change which has not reversed, and is unlikely to be, excepting in a post-apocalyptic scenario. You can see this cross-culturally, human sacrifice was relatively common across the ecumene during the “Bronze Age,” but disappeared or diminished during the “Classical Age.” This shift has never been reversed, at least so long as institutional frameworks remain robust enough to reconstruct themselves after a collapse.

- The integrative power of polities has improved very definitely over the past 5,000 years. Innumerable punctuated events of “collapse,” political, cultural, and social, allow us to test the proposition that civilization is becoming more robust in maintaining its coherency across the ages. And I believe it has. This is clear in China, where dynastic interregnums progressively have become more attenuated, and also in the West, where national-cores tend to retain integrity once they crystallize (e.g., northern France, central Spain, southwest Iran, etc.).

- The key seems to be that civilizations do not seem to regress in a stepwise fashion, and reverse, but rather collapse and lose total coherency. Once that process happens, and societies revert to tribal scale entities, then slavery, human sacrifice, organized animism, etc., pop back to the foreground. In other words, a total reversion back to a state of extreme savagery is plausible contingent upon a nearly absolute destruction of the institutions of civilization in toto and universally. It’s the extremity of the collapse which I think we should be skeptical of, at least within reasonable time scales (e.g., a few thousand years in the future).

Run as fast as you can!

Filed under: Genetics,Genomics,Personal genomics — Razib Khan @ 5:31 pm

Since his move to Wired I swear that Dr. Daniel MacArthur has gotten a bit more pugnacious. In any case, today he has a post up which smacks-down the A.M.A.’s attempt to expand the long arm of its regulatory capture:

The American Medical Association has written a letter to the US Food and Drug Administration as part of the lead-up to the FDA’s meeting on direct-to-consumer (DTC) genetic testing next month. The tone is predictable: the medical establishment is outraged by the idea of people having access to their own genetic information without the supervision of its members, and they want the FDA to stop it….

Over the past six months I’ve gotten really into analyzing genotypes of friends & family. Sometimes I talk about this excitedly, and people worry about the “risks.” When I ask what  risks they’re worried about, usually people offer the vague and content-free fear of “what you could find out.” First, if you have family information, that’s usually much more powerful than the “disease risk” estimates that these firms are giving you. In 99% of the cases, if that’s your primary concern it’s not worth the money. Second, if you’re terrified about what ancestry inference ...

A mental map of the world

Filed under: Climate,geography,science — Razib Khan @ 3:58 pm

One of the major issues in our world today is that we’re a people of specialties. This means that we don’t have basic interpretative frameworks in which to place novel facts. Because of the abstruse and formal nature of the discipline, this is probably starkest in the domain of science, but it is not restricted to only science. Consider geography. In many ways this is “low hanging” cognitive fruit in the shallow part of the learning curve which mostly consists of assembly of facts, but because of the shifts in emphases in American education geography has tended to get short shrift. This means that whenever there’s a foreign policy crisis middle-brow journals of record such as The New York Times have to commission pieces about nations such as Libya which read like a “first book” for six year olds on that nation (and on political weblogs commenters proudly brandish their “first book” level of knowledge).

But a bigger general issue seems to be in relation to climate. “Climate Change” is in the news constantly, but the average person on the street seems to have zero historical perspective on events such as the Medieval Warm Period, the Little Ice Age, ...

The community doesn’t speak with one voice

Filed under: Culture,Multiculturalism,Religion — Razib Khan @ 2:24 pm

Who speaks for the Semitic Sky God?

One of the problems with being an atheist and not a member of an organized religion is that life’s not a “package deal.” My materialist metaphysic, or perhaps more precisely my skepticism of metaphysics, doesn’t entail anything except what it entails. I am, for example, a political conservative, which goes against expectations. In contrast, religious folk have huge elaborated systems of thought. Since most people are stupid they’re generally garbled and inchoate as to what they should believe, but they have off the shelf ideas which they can marshal.

All fine and well. But, there’s a serious problem with adherents of organized barbaric superstitions presenting an authoritative Christian/Muslim/Jewish/Hindu/Buddhist point of view. What they’re doing more accurately is present the view of a Christian/Muslim/Jewish/Hindu/Buddhist. Even stipulating the existence of a Truth undergirding organized superstition, humans by their nature look through the glass darkly, and can not speak authoritatively as if there is a singular clear and distinct Truth which they can comprehend (as an atheist, I think the reality of the matter is that complex religio-philosophical systems are incoherent gibberish without systematic logical integrity).

I thought of that we I stumbled upon this article, Evolution, from Hinduism’s point of view: LifePoints. The author is Dr. Narayana P. Bhat, secretary of the Board of Trustees of the Hindu Cultural Center of North Alabama. He’s writing in The Huntsville Times, so no doubt this is one of the few exposures to Hinduism which the benighted residents of northern Alabama will have, and Dr. Bhat is putting his best foot forward. But he really doesn’t speak for Hinduism, anymore than any crazy bug-eyed mullah speaks for the True Islam.

Harappa Ancestry Project update

Filed under: Genetic,Genetics,Genomics,Harappa Ancestry Project — Razib Khan @ 11:23 am

If you haven’t, please check in with what Zack Ajmal is doing. There is still a great deal more to be done in terms of population coverage, but I think we’re getting some sense of the overall picture, even if the error bars are kind of large at this point…

February 23, 2011

Better comprehension through visualization

Filed under: Genetics,Genomics,Harappa Ancestry Project — Razib Khan @ 11:56 pm

Zack has started to improve on static R plots with Google powered charts. Check it out. Alas, I can’t inject script tags into the body of my posts, so that’s not feasible for me. Notice on Zack’s plot that I’m more East Asian than either of my parents. The tendency first cropped up with 23andMe’s ancestry painting, and I have seen it in my own ADMIXTURE runs, so I don’t dismiss it as V2 vs. V3 chip anymore. Though I’ve ordered an upgrade myself, so we’ll see for sure. Also, though both my parents are about the same East Asian, they exhibit a different balance of East Asian subcomponents. I’ve seen this in my own ADMIXTURE runs, and I’m going to check for more fine-grained matches with the HGDP East Asian populations soon to ascertain whether their eastern ancestral mix is different. Good times.

Sweeping through a fly’s genome


Credit: Karl Magnacca

The Pith: In this post I review some findings of patterns of natural selection within the Drosophila fruit fly genome. I relate them to very similar findings, though in the opposite direction, in human genomics. Different forms of natural selection and their impact on the structure of the genome are also spotlighted on the course of the review. In particular how specific methods to detect adaptation on the genomic level may be biased by assumptions of classical evolutionary genetic models are explored. Finally, I try and place these details in the broader framework of how best to understand evolutionary process in the “big picture.”

A few days ago I titled a post “The evolution of man is no cartoon”. The reason I titled it such is that as the methods become more refined and our data sets more robust it seems that previously held models of how humans evolved, and evolution’s impact on our genomes, are being refined. Evolutionary genetics at its most elegantly spare can be reduced down to several general parameters. Drift, selection, migration, etc. Exogenous phenomena such as the flux in census size, or ...

The Invisible Gorilla: And Other Ways Our Intuitions Deceive Us

Link to review: The illusions of intuition.

Visualizing “typical” Eurasians

Filed under: Genetics,Genomics — Razib Khan @ 4:50 am

A few weeks ago I started looking at the 23andMe raw files of some of my friends and integrating them into HGDP and HapMap population data sets. One of the first things I did is remove the African populations from my total data. The reasons is as you can see to the left, Africans occupy the largest principal component of variation, which sets them apart from Eurasians. Without this dimension of variation the non-Africans are squeezed into one dimension, and groups like Oceanians and Amerindians show up in the strangest places. But that’s because these groups are non-African, and do not differ as much along the primary west-east axis of genetic variance which shakes out out of any such analysis. Africans aren’t the only issue though. As I’ve noted before I’ve been running ADMIXTURE, and isolated groups such as the Kalash can “monopolize” one particular color. This may be due to the Kalash being some distilled essence of an ancestral population, but I suspect that it’s more genetic drift due to isolation which has made these sorts of groups distinctive. So I removed these outliers…though do note that other “outliers” ...

February 22, 2011

The evolution of man is no cartoon

ResearchBlogging.orgI was semi-offline for much of last week, so I only randomly heard from someone about the “Science paper” on which Molly Przeworski is an author. Finally having a chance to read it front to back it seems rather a complement to other papers, addressed to both man and beast. The major “value add” seems to be the extra juice they squeezed out of the data because they looked at the full genomes, instead of just genotypes. As I occasionally note the chips are marvels of technology, but the markers which they are geared to detect are tuned to the polymorphisms of Europeans.

Classic Selective Sweeps Were Rare in Recent Human Evolution:

Efforts to identify the genetic basis of human adaptations from polymorphism data have sought footprints of “classic selective sweeps” (in which a beneficial mutation arises and rapidly fixes in the population). Yet it remains unknown whether this form of natural selection was common in our evolution. We examined the evidence for classic sweeps in resequencing data from 179 human genomes. As expected under a recurrent-sweep model, we found that diversity levels decrease near exons and conserved noncoding regions. In contrast ...

Older Posts »

Powered by WordPress