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51WnxzkxMTL._SX312_BO1,204,203,200_The Indo-European Controversy: Facts and Fallacies in Historical Linguistics, by Asya Pereltsvaig and Martin Lewis is a pretty one-sided monograph. The reason, as admitted by the authors, is that they believe a certain sector of academia and the middle-brow reading public are not exhibiting enough skepticism about the application of Bayesian phylogenetics in linguistics. To a great extent The Indo-European Controversy: Facts and Fallacies in Historical Linguistics is a book length rejoinder to a paper published in 2003 to great acclaim, Language-tree divergence times support the Anatolian theory of Indo-European origin. It’s basically a short letter to Nature. When this paper came out I did not have academic access to such things, and there weren’t online resources (like Twitter) to allow one to make an end-around to academic paywalls. So I remember actually going down to the local college library, and getting a paper copy of the edition of Nature, and reading it just like that. In fact that may very well be the last scientific paper I read on paper. And, I went in search of that paper because of an article I saw in The New York Times by Nick Wade, A Biological Dig for the Roots of Language. Pereltsvaig and Lewis correctly peg Nick Wade’s influence in my opinion. My own passing interest in the topic was triggered by coverage in the media. That’s probably true for many people. There are other papers of note which follow in the tradition of the 2003 letter to Nature. In particular, I recommend Mapping the Origins and Expansion of the Indo-European Language Family, in Science. If you don’t know much about Bayesian phylogenetics, read the supplements.

5140FASZyJL._SX330_BO1,204,203,200_The heart of the argument Pereltsvaig and Lewis present seems to be that some key assumptions in the model that Bayesian phylogeneticists are using to make inferences about the emergence and spread of Indo-European languages are wrong. And, those incorrect assumptions lead to empirical results which are also wrong. Though it was difficult for me to follow much of the deep dive into technical linguistics (thanks for that Asya!), some of the problems with inferences are pretty easy to see. They note that in the supplements of the 2012 paper (second one above) the Romani language is placed as an outgroup to the other members of the Indo-Aryan family. This seems wrong to Pereltsvaig and Lewis, and from what I know it is wrong. Linguistic consensus is that Romani dialects are related to those of Northwest India. It turns out that the genetics favors this, as their South Asian ancestry does seem to derive from Northwest Indian populations. We can go on with details in this vein, and the authors do, assembling a list of fallacious inferences, but what’s the root of the problem?

One of the major weaknesses brought up in The Indo-European Controversy: Facts and Fallacies in Historical Linguistics is that these Bayesian phylogenetic models utilize lexical information as data inputs. In particular, a set of a few hundred cognates. There are two elements to the objection. First, the choice of cognates might be biased, or at least bias the output. Second, vocabulary may not be the best foundation on which to generate a phylogeny of language. Rather, something like grammar may be more phylogenetically informative. The authors of the above works under criticism actually state they’re trying to use grammar as an input too. But in any case, the tendency for vocabulary to be exchanged between nearby groups, irrespective of their phylogenetic origin, is presumably the reason that the Romani languages drifted far enough away from the other Indo-Aryan languages to seem like an outgroup. No matter how ingenious your method, if your input data is biased or not informative, your output is not likely to be useful. Pereltsvaig and Lewis allude to the fact that linguistics has not found their “atoms” yet. I’d state it differently: linguistics lacks its DNA sequence. Using a biological analogy, these linguistic applications of Bayesian phylogenetics are attempting to discern evolutionary history from phenotype.

9780631205661_l The second major problem with the papers coming out of the Bayesian phylogenetic tradition in linguistic history is an incorrect model assumption: that populations expand purely through diffusion-like processes. If you read the detailed methods it’s pretty clear that they’re converging on the joint posterior probability of tree given the data as well as the geographic distribution assuming a demic diffusion framework. The Indo-European Controversy tackles extensively the historiography of migrations, or lack thereof. Before World War II archaeologists naively traced migrations through the change in cultural forms, while after World War II the backlash became so strong that the null was always that pots, rather than people, were on the move. And, when people were on the move in pre-state societies, it was envisaged in almost a mechanical fashion, as individuals on the farming frontier had higher fertility, and so endogenous growth simply swamped out other groups like European hunter-gatherers. Part of its appeal isn’t just ideological, it’s an elegant model. Historical detail and contingency isn’t relevant, and inter-group conflict can be sidestepped. It’s all about endogenous growth of a population assuming particular resources, until it hits a Malthusian limit in the locality.

Unfortunately this model is almost certainly wrong for human history. Ancient DNA has revolutionized everything, because it is shown just how punctuated demographic shifts can be. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity highlighted this dynamic a few years back. More recently, Population genomics of Bronze Age Eurasia and Massive migration from the steppe is a source for Indo-European languages in Europe indicate discontinuity. I want to emphasize the term discontinuity, as this is very different from gradual diffusion. Rather than a methodologically individualistic model, where higher fertility in farmsteads or at least villages gradually resulted in the transition from one group to another, a more likely in my opinion is inter-group tension, conflict, and amalgamation. In some cases, near total replacement. It may not have been always violent, rather, agriculturalists on the Malthusian margins may not have been able to withstand the shock of a new culture arriving and sequestering critical resources (an analogy I’m thinking is the massive collapse of Roman culture in the Balkans whenever the imperial limes withdrew toward the coasts; without state support and scaffold the way of like the Latin peasantry just wasn’t feasible, so they quickly migrated or died off).

For example, it looks as if the Uygurs are not descended in large part from the first Indo-Europeans on the fringes of western China. I took the data the Reich lab posted and ran TreeMix on it. After reducing the number of populations, I ran TreeMix on it. Below are 10 plots. The West Eurasian ancestry of the Uygurs is not overwhelmingly Northern European-like. Weirdly the graphs below suggest it is somewhat less Northern European than the West Eurasian ancestry contributing to the Hazara! Though that may be an artifact of some sort. The point is that as suggested by many scholars it seems highly likely that the Indo-European population of the Tarim basin was a composition, and that Tocharians and Indo-Iranians were both present. And, probably did not appear at the same time.

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So a second question that came to has to do with the origin of the Indo-Aryans, and the genetic history of the Indian subcontinent. About five years ago I told John Hawks that I was skeptical of too much European-like contribution to the Indian population because not enough European pigmentation alleles were segregating in the population. My inference was based on a wrong assumption. It turns out that the earliest steppe dwellers were not particularly pale of mien going by their genetic architecture on pigmentation loci. My objection has no basis, because the modern European phenotype is very new, and likely post-dates the arrival of Indo-Europeans to India. Additionally, there is suggestive evidence of a steppe connection, such as the widespread presence of the “European” allele for lactase persistence in Northwest India. This allele is new, and swept up in frequency very recently. Its presence in Northwest India almost certainly indicates non-trivial demographic connections.

The blogger at Eurogenes has illustrated the dynamic, but it’s pretty obvious that Northwest Indian populations have some affinity to the Yamnya population in particular. Below are the results from TreeMix using a narrower set of population than above. Notice how Pathan tends to move toward the Yamnaya…..

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But why the affinity to the Pathan, and not the Iranian samples? Who knows. I’ll pull down the data set from the Willerslev lab soon, but I think ancient DNA from India is going to have to answer the question. But I’m curious how the “Out of India” people spin this, because they will have a ridiculous rationale….

 
• Category: History, Science • Tags: Indo-European

51qciM4cBhL._SX258_BO1,204,203,200_ A friend of mine proudly told me recently that she’d purchased an unabridged edition of The History and Geography of Human Genes. Turns out that there are some affordable used copies floating around (under $50, like the Atari 2600!). Flipping through the old unabridged edition I had to admit: a lot of the assertions derived from classical autosomal markers hold true. It might be that all you really need to get “up to speed” is an annotated version. Also, I’d get rid of the synthetic maps, which no one uses anymore (there are some methodological reasons, as well as the fact that they just didn’t turn out to be a very intelligible visualization).

Of course things have changed between then and now. Thanks to open data you can do much more powerful analysis than you find in The History and Geography of Human Genes on your notebook computer in a few hours. So I had the idea for this post a few hours ago…and thought perhaps I’d accompany it with a few TreeMix plots. Below are the 1000 Genomes data, with 250,000 markers (I pruned by intersecting with HGDP markers as well as those with very low missingness):

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• Category: Science • Tags: Genomics

51WnxzkxMTL._SX312_BO1,204,203,200_ Been reading The Indo-European Controversy: Facts and Fallacies in Historical Linguistics, by Asya Pereltsvaig and Martin Lewis. To a great extent it is a book length response to the research program which made such a big splash with the 2003 Nature paper, Language-tree divergence times support the Anatolian theory of Indo-European origin. I’m over half-way through. Some of it has been hard going, as I’m not very familiar with the details of linguistic science (I get very confused when linguists start using technical terminology for accent changes; anything beyond diphthong). On the other hand, I know a decent amount about the nuts and bolts of Bayesian phylogenetics, and their critiques are cogent so far.

9rj62e To be fair I’m broadly sympathetic to Pereltsvaig and Lewis’ program. There are a decent number of references to genetics in the work, though it looks like they were in final revisions before Massive migration from the steppe is a source for Indo-European languages in Europe. But even without the genetics, I think the case is pretty strong that a simple version of Colin Renfrew’s Anatolian demic diffusion doesn’t work. The contortions necessary to make it plausible in Anatolia during the Bronze Age are too implausible.

If The Indo-European Controversy is a bit too technical, I do recommend everyone check out The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. David Anthony’s work is probably a lot more relevant today because of the findings from genetics. Even if a Steppe-only model can’t explain everything, evidence of massive population replacement in Northern Europe really does overturn any naive idea that Germanic languages somehow derive from the LBK culture….

 
• Category: Miscellaneous • Tags: Open Thread

TaylorSwiftApr09 William Dalrymple in The New Yorker has a reflection up on the 1947 partition of the subcontinent, The Great Divide. It is fine so far as it goes. He reminds us of the scale of the tragedy, millions of deaths, as well as the depravity of the barbarity, as “infants were found literally roasted on spits.” Some day I will have to educate myself about this period, as I only have vague recollections of reading fragments of Freedom at Midnight as a child. I recall stopping at the point where the authors reported how a group of men broke into an obstetrics unit at a hospital and took a newborn who had just breathed their first and smashed its brains out on the walls, while the mother and hospital staff watched in horror. That was enough to get a flavor of the “action.” Fortunately my family did not suffer during this period, Bengal was relatively quiet in comparison to the atrocities washing over Punjab (as many of you are aware, my family experienced more hardship in the 1971 war, though as they were relatively privileged Muslims who were also not very involved in the arts or politics they were not actively targeted).

But there is one section whose assumptions and implications rub me the wrong way. Let me quote:

In the nineteenth century, India was still a place where traditions, languages, and cultures cut across religious groupings, and where people did not define themselves primarily through their religious faith. A Sunni Muslim weaver from Bengal would have had far more in common in his language, his outlook, and his fondness for fish with one of his Hindu colleagues than he would with a Karachi Shia or a Pashtun Sufi from the North-West Frontier.

Many writers persuasively blame the British for the gradual erosion of these shared traditions. As Alex von Tunzelmann observes in her history “Indian Summer,” when “the British started to define ‘communities’ based on religious identity and attach political representation to them, many Indians stopped accepting the diversity of their own thoughts and began to ask themselves in which of the boxes they belonged.” Indeed, the British scholar Yasmin Khan, in her acclaimed history “The Great Partition,” judges that Partition “stands testament to the follies of empire, which ruptures community evolution, distorts historical trajectories and forces violent state formation from societies that would otherwise have taken different—and unknowable—paths.”


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Ten years ago I read Nicholas Dirks’ Castes of Mind. It is a work of history which shows how many caste identities were fashioned de novo under the impetus of British bureaucratic taxonomic impulse (see Census of 1891). Though Dirks is too subtle to assert that the caste system was created by the British, the general thrust of the work is clearly one which emphasizes the role of recent historical contingency in establishing the social order of South Asia as we understand it. The subhead is after all: “Colonialism and the Making of Modern India.” The British are then the agents who operate upon the formless void of the Indian subcontinent’s amorphous peasant culture. They came, they saw, and they created.

Even when I read Castes of Mind I was moderately skeptical of the narrative, as there had been enough genetics done to suggest that South Asian populations were stratified by caste. By this, I mean that caste status as much, or more, than geography predict the genetic structure of Indian society. It was already evident, for example, that South Indian Brahmins were closer to North Indian Brahmins than they were to South Indian Dalits when it came to genetic relatedness. Brahmins and Dalits are two caste groups which are clear and present throughout South Asia (the “middle castes” tend to vary from region to region, and the classical warrior and trader castes do not exist in South India, though there are notionally Sudra groups which occupy their roles). Even those who prioritize the role of the British would accept that the Brahmin and untouchable categories predate the reification of the colonial period. But what the latest genetics is telling us is that caste endogamy has been a feature of Indian life for at least 2,000 years, and perhaps longer. Not only are Brahmins distinct from Dalits, but castes with a less clear position in the classical varna typology, such as the Reddy community of South India, clearly have had long histories as a coherent groups. The British could not have been the dominant causal force in shaping caste as a ubiquitous feature of Indian life if they were already genetically endogamous even before the Muslims arrived.

And so with religion. The contemporary revisionism, which now is approaching mainstream orthodoxy, is that South Asian religious life before the arrival of the British, and the Western outlook more generally, was characterized by a quietist syncretism where communal boundaries were fluid to the point of confessional identity being a flimsy veil which could be shed or shifted dependent upon context. An alternative history then might be proposed of a united subcontinent, where Hindus and Muslims were coexistent, or, perhaps where a Hindu and Muslim identity did not even exist. The cognitive psychologist Pascal Boyer likes to characterize a theory as giving you “information for free.” You don’t really have to know anything, you can simply deduce from your axioms. Though the model of South Asian ethno-religious history I allude to above obviously integrates ethnographic and historical realities, it constructs a post-colonial fantasy-land, where South Asian religiosity was without form or edge before the arrival of Europeans and their gaze collapsed the wave function. Before the instigation of Europeans people of color were tolerant of religious diversity, varied sexual orientations, and practiced gender egalitarianism. In other words, India was like the campus of Oberlin college, except without the microaggressions, and more authentic spirituality!

51J39W7ZRFL._SX306_BO1,204,203,200_ The first problem with this model is empirical and specific to South Asia. Before white Europeans arrived in the Indian subcontinent to roil and upend its social order, to transform its culture, there was already a ruling race of self-consciously white people doing just that. They were the Turks, Persians, and a lesser extent Arabs, who introduced Islam to the subcontinent. As alluded to in Dalyrmple’s piece in some ways Islam was conceived of as a sect of the foreigners by the natives, as well as the Muslims themselves. This is not an entirely strange state of affairs, in the first century or so of Islam the religion was the tribal cult of the Arab ruling caste of the Caliphate. Only with the rise of the Abassids and maturation of Islamic civilization as a pan-ethnic and post-ethnic dispensation did the “converted peoples,” in particular the Persians and Turks, become full members of the Ummah, and turn it into the universal religion that we understand it today (though even today there is an ethnic dimension in Islam, for example, the Islamic State accepts that the Caliph must be an Arab of the Quraysh tribe).

For many centuries Islam in South Asia recapitulated this pattern ancient pattern, whereby those who descended from converts were received as second class citizens (and still called “Hindus,” which simply meant a native of Hindustan). And to this reality must be added the dimension of race, for the Muslims from the west viewed the native peoples as black, and many elite families with origins in Persia and Central Asia maintained their endogamy for generations partly as a matter of racial hygiene. When Muslim elites did intermarry with the descendants of converts, it was invariably with those descended from high caste groups. The Mughal Emperors did wed women from Hindu backgrounds, but these were the daughters of powerful Rajputs, whose values and armies fused with the Muslim invaders to create what we understand as Islamicate civilization.

Yet there are many other stories besides the standard one of the rise and fall of Mughal India. In Crossing the Threshold: Understanding Religious Identities in South Asia, the author shows how the arrival of Islam in the subcontinent often involved a complex process of cultural interaction mediated by esoteric strains of the Ismaili sect. It is not relevant for the purpose of this post to review the nature of Ismaili Islam, but it is important to note that Sunnis view this group as deviant and marginally Muslim. With the arrival of the Mughals there began a long period of persecution of Ismailis in the Indian subcontinent as the new arrivals attempted to enforce conformity on the Muslim population. Both Crossing the Threshold and Mullahs on the Mainframe, an ethnography of a particular Ismaili sect in Gujarat, report that many of the Sunni Muslim communities of the subcontinent may be descended from people who entered Islam via Ismailism. Under the Mughals heterodox Muslim sects like the Ismailis were subject to more persecution than non-Muslims (this echos a similar dynamic in Late Antiquity, where more of the Christian animus was directed toward heretical sects than pagans). In Gujarat this resulted in mass conversions to Sunni Islam. In other regions it might have resulted in a “compromise” state of shifting to a Twelver Shia identity, which though not Sunni, was generally accorded more respectability than Ismailism. These people would be anticipating the life of Muhammad Ali Jinnah, whose recent ancestors (most accounts state his grandfather) converted from Hinduism to Ismailism, but who himself was an entirely irreligious man who avowed a Twelver Shia faith for purposes of formality.

The author of Crossing the Threshold suggests that for many centuries there existed in the subcontinent under the more tenuous and patchwork pre-Mughal Islamic rulers many liminal communities, which straddled the line between Muslim and Hindu. So long as the Muslims of the Indian subcontinent viewed themselves as strangers in a land which offered them opportunities for profit, there was a certain freedom in being viewed as an amorphous black-skinned mass of “Hindus” whose only importance was in the tax that they provided their overlords. The Mughals changed that. Though they were in origin Timurid princes from Central Asia, their long ascendancy in the subcontinent produced a genuine synthesis with the indigenous substrate. By the later years of the dynasty their symbolic and ceremonial roles as Emperors of India became so entrenched that even resurgent Hindu groups such as the Marathas retained the Mughals as figureheads, much as the Zhou dynasty persisted for centuries after its genuine preeminence had faded.

516ZEEEK2XL._SX332_BO1,204,203,200_ Over the 150 years that the Mughals dominated South Asia with their armies they also changed the nature of Islam in the subcontinent thanks to their broader connections. The Naqshbandi Sufi ordered was associated with the dynasty, and objected when rulers such as Akbar bent or rejected what they perceived to be Sunni Islamic orthodoxy. And the Naqshbandi were in a place to judge what was orthodox, as they were an international order with branches across Sunni the Muslim world. The historian S. A. M. Adshead discusses the role of what he calls the “Naqshbandi International” in binding the Islamic world back together after the shattering of the Mongol invasions in Central Asia in World History. It was no coincidence that attempted to root out deviancy and enforce what they saw to be uprightness.

China was another zone of Naqshbandi influence. Unlike India China proper had (and has) never been ruled by Muslims. After period of prominence under the Yuan (Mongols) the Muslim groups became another minority, tolerated by the Han Chinese, but viewed with curiosity and confusion. While the Muslims of what is today called Xinjiang were part of the Turkic world, and even when conquered by the Manchus administered as a separate domain from China, those resident in the east were relatively isolated from the Ummah, and swam in a Han sea. The Dao of Muhammad: A Cultural History of Muslims in Late Imperial China tells the story of the intellectuals among the Muslims of eastern China, who were confronted with accommodating the reality that they existed at the sufferance of non-Muslims, and could only advance to prominence and prosperity playing the game according to the rules of the Han majority. At the popular level in places like Ningxia there emerged Muslim apocalyptic movements which bore a striking resemblance to heterodox variants of Pure Land Buddhism, but among the intellectuals there arose the conundrum of how to render compatible orthodox Islam and Neo-Confucianism. So long as China was reasonably isolated from the rest of the world, this process dynamic proceeded without interference and followed its own logic. What emerged can reasonably be described as a synthesis between Islam and Neo-Confucianism, which resembles in its broad outlines the sort of fusion which occurred in early Christianity after the ruling elites took up the religion and imparted upon it their own philosophical presumptions. Just as some Christians perceived in their religion the completion of the project of the ancient Greek philosophers, so Hui Muslim intellectuals in the cities of eastern China in the 18th century saw in Islam not the overturning of Chinese culture, but its extension and perfection.

Suffice it say this movement among educated Chinese Muslims did not give fruit to a vital modern tradition. Several waves of Islamic reform have blasted into China from the outside world, first from Central Asia, and later from the Middle East proper in the age of modern transport and pilgrimage. The Islamic-Confucian synthesis in its full elaboration was a stillborn sect, pushed aside by the popularity of world normative Islam and the decline in prestige in the 19th and 20th century of Neo-Confucianism. Similarly, the Islamic-Hindu synthesis championed by the Mughal prince Dara Shikoh and prefigured by his great-grandfather Akbar, was forestalled by the emergence of Aurangzeb. Remembered as pious and steadfast by many modern day Muslims, he is reviled by Hindus, and most Western historians, who perceive that the sun set on religious pluralism due to his actions, seem to take a dim view of him. But Aurangzeb was closely associated with the Naqshbandi over much of his life, and he may be less important to the broad social movement of South Asian Muslims being drawn into an international system, with a standard set of beliefs and practices, than we think. Rather, Aurangzeb’s life arc may be consonant with both the indigenization of Islam in the subcontinent, and its need to align itself with external norms.

513yXnWcqDL._SX322_BO1,204,203,200_ Though I use the Indian subcontinent as my primary illustration, the dynamic is likely more general. In The Next Christendom: The Coming of Global Christianity Phillip Jenkins notes that though many claims are made for indigenous African churches, that is, those which have no connection to global denominations and movements and tend to more freely integrate African practices, as African societies become more Christianized they tend to become more mainstream and orthodox in their affiliation. What Jenkins is observing is that with development and modernity indigenous and local practices tend to fade into the background, as African Christians become influenced by the ideas and traditions of Christians from other regions of the world. Individuals who consider themselves part of a religious community start to adhere to the practices and norms of that community’s history.

Despite the homogenization and delineation of identity categories in India there are still liminal communities in the mode envisaged by Crossing the Threshold. The Meo people of Northwest India are Muslims who maintain many Hindu traditions. But the trend among the Meo is to become progressively “more Muslim,” and those Meo who leave their homeland assimilate into the conventional Sunni Muslim milieu and lose their distinctiveness. The Ismaili Khoja community of India is another example of a Muslim group with many Hindu customs and beliefs which has become more “orthodox” within historical memory. In this case the arrival of their spiritual leader, the Aga Khan, from Iran in the 19th century seems to have triggered an Islamic reformation of views and mores. And just as there may have been many groups which moved toward a more standard Muslim identity, there were likely those who became more self-conscious in their Hinduism, as that tradition coalesced as a negation of the exclusive confessionalism of Islam. The Hussaini Brahmins customarily participated in Shia Ashura, and have an origin story which places them at Karbala on the side of the sons of Ali. As noted above it was not unknown for high caste Hindus to enter Islam and intermarry with the Muslim nobility. Over time their Hindu origins may have been obscured, as they constructed wholly Muslim origin narratives. The Hussaini Brahmin community might illustrate a case where the process was halted, and reversed, albeit with a retention of some of their Islamic practices and beliefs. In Crossing the Threshold the argument is made that it the critical aspect for the Sunni Muslim eminences enforcing the new orthodoxy was that Muslim and non-Muslim be clear and distinct categories. Therefore, better a Hindu than a heretic.

51k6n6ma-NL._SY344_BO1,204,203,200_ What have I left out of the story? Note that white Europeans are notably absent from the narrative. To some extent this is an artificiality. European “factories” were present on the margins of Mughal India. Jesuits supplanted Muslims as astronomers in the court of Ming China, and were disputants on religious topics in the court of Akbar the Great. Christianity, Islam, and Buddhism, were all closely associated with each other in Central Asia, to the point where it is difficult to tease apart the arrows of causality. In China it seems likely that some varieties of Christianity with ultimate roots in Persia and Central Asia were subsumed into strands of Pure Land Buddhism. But, the point is that history and peoples are subject to general patterns and dynamics, and European colonialism may be thought of as just one important contingent factor. A critical one, but one factor nonetheless.

41JdP75Eu8L._SX321_BO1,204,203,200_ It is hard to deny the influence of European culture and Christianity on Indian national and religious worldviews. Consider Hindutva. Conceived of as a form of Hindu racial nationalism by Vinayak Savarkar, himself an atheist who advocated the dismantling the caste system, it is difficult to understand it without considering the dominant winds of culture in the early 20th century. Those winds invariably blew out of Europe. The colonial imprint, the mirrored reflection of British racial nationalism, is real. Today the intellectual descendants of Savarkar promote bizarre beliefs like the idea that ancient Hindus had flying machines and nuclear weapons, and that astrology is a true science and Ayuvedic medicine is superior to that of the West. It is hard not to see in these beliefs a funhouse distortion of Western movements, such as Christian Science and Creationism. Similarly, the Islamic Creationism of Harun Yahya is explicitly indebted to American evangelical Protestants!

And yet within South Asia the broad trend of confessionalization predates the arrival and dominance of Europeans. It seems entirely likely that a division between Islam and what became Hinduism in the subcontinent was inevitable, as modernity and globalization seem to produce crisper identity groups, which are not diffuse, inchoate, and locally rooted. Yes, illiterate peasant naturally practice syncretistic traditions, but when the illiterate peasant becomes a town dweller a different sort of religious practice takes hold. There is a reason that the city-dwelling Christians of the Late Antique world were contemptuous of the marginally Christianized peasantry, the pagani. The last European people to convert to Christianity were the Lithuanians, in the late 14th century. But the peasantry retained enough of their customary religion that veneration and recollection of sacred groves seem to have persisted down to early modernity.

51W2mxRBC9L._SX326_BO1,204,203,200_ The Reformed Dutch scholar Atonie Wessels wrote a book titled Europe: Was it Ever Really Christian? His thesis is that from an orthodox Protestant perspective which privileges the beliefs and practices of the individual, it can be argued that much of the European peasantry was operationally pagan down to the Catholic and Protestant Reformations of the 16th and 17th century, followed by the secularization of the continent that began after the Peace of Westphalia. In short, during the period after the fall of Rome and Renaissance the elites were steadfastly Christian, but peasants were only nominally so, with their spiritual life dominated by superstitions rooted in local traditions. In contrast, the emergence of Protestant and Catholic identities during the Reformation resulted in a broad based Christian feeling and identity among the populace. So much so that when the Hohenzollerns converted to Calvinism in the early 17th century their subjects remained steadfast in their Lutheranism. But as the populace became more conventionally Christian, the elites began their long slide toward secularism, finally resulting the rise to power of Frederick the Great, who in matters of religion was apathetic at best.

The European example is important, because it shows that even without exogenous European colonialism confessionalism occurs as a society modernizes. The seeds of this confessionalization are clear in South Asia even before the rise to power of the British raj, as Hindu rulers such as Shivaji privileged their own native traditions as against that of the Muslims, while earlier the rulers of Vijayanagar had served as patrons of native religion while the north of the subcontinent was dominated by Muslim polities. It does seem fair to state that Sanatani is not comprehensible without it dialectic with Islam. But, it is important to remember that Buddhism as an organized religion with a missionary impulse predates Christianity by centuries. Obviously institutional religious identity in the subcontinent is not dependent upon the ideas of Europeans and Muslims. What differed with the arrival of Islam is that it was a Weltanschauung which was not digestible to the native cultural traditions.

Though the various Muslim ruling warrior castes held themselves aloof from the people of India, being within the subcontinent, but not of it, it seems inevitable they presumed that their domains were now a permanent part of the Dar-ul-Islam, just as Iran or Central Asia was. Certainly Ibn Battuta could travel in an entirely Muslim India, which operated in parallel with the practices of the vast majority. Over time no doubt the Muslims assumed that the subcontinent would be won over as Iran had. It is hard to remember now, but in the first few centuries of Islamic rule there were periodic anti-Muslim nativist religious eruptions which attempted to overthrow the Muslims, who were perceived as aliens. Prophets arose which told of a time when Islam would fall, and the old religion of the Iranians would come back to the pride of place that it had had. A detailed exploration of this lost world can be found in Patricia Crone’s The Nativist Prophets of Early Islamic Iran, but these movements always make cameos in even traditional works of early Islamic history, such as Hugh Kennedy’s When Baghdad Ruled the Muslim World. But by 1000 A.D. the majority of Persian peasants were Muslim, and Zoroastrianism and its affiliated movements slowly went into their long decline (though still retaining influence through various heterodox Islamic and post-Islamic religious movements).

61H+zZL41QL._SY344_BO1,204,203,200_ In India you have a world where the vision of the Iranian prophets came to be, where Islam which seemed eternal and ever waxing in numbers and influence, lost its hold on power and native dynasties which championed local religious traditions arose. There are many differences between the situation of Iran and India. In no particular order, India is far more populous than Iran, local non-Muslim rulers always managed to retain independence at the far corners even at the height of Islamic power and dominion, and the cultural distance between the Muslims and the natives of India was arguably greater than that between the Arabs and the Persians. Even though the Iranians and northern Indians share Aryan cultural roots and influence, reflected in language and religious ideas, those are distant affinities. In contrast, the Arabs had long been present on the margins of the western Iranian world, and the ecology of much of Iran and Mesopotamia was familiar to them.

One peculiarity of the historiography of India under the Muslims is that many scholars claim that local intellectuals, mostly Brahmins, behaved as if their conquerors did not even exist. This sort of involution though may be less strange than seems on first inspection. Ashkenazi Jews in Central and Eastern Europe are to a great extent a people without a history, as their intellectual class devoted its energies to Talmudic commentary, not recording the history of their people. India was massive, and transformations were pregnant within its cultural matrix in response to the Islamic challenge. The Sikh religion seems an obvious case of synthesis, which while that of Hindu reformist movements such as Arya Samaj seem to sublimate the external variables.

61LXo6U7a4L._SX331_BO1,204,203,200_Though the British may have been a proximate cause for the communal conflicts that tore apart the subcontinent in 1947, they were not the deep cause. As Victor Lieberman observes in Strange Parallels: Europe, Japan, China, South Asia, and the Islands, after 1000 AD there arose several polities dominated by cultural aliens along the edge of Eurasia, such as that of the Muslims in India, the Tai in Southeast Asia and the Manchu in China. But unlike the latter two cases the Islamic elites never sufficiently rooted themselves in the local culture to establish a coherent and unified national identity. While the Manchu racial sense of distinctiveness persisted down to their overthrow, their cultural assimilation to most Han mores was so total that rulers such as Kangxi Emperor arguably became exemplars of Confucian rulers. Though the Tai imposed their language of the Mon and Khmer people whom they conquered, they fostered a genuine cultural synthesis by patronizing the Theravada Buddhism of their subjects and espousing it as their national religion. While the kings of Thailand patronized Brahmins to give their rule a tincture of Hindu legitimacy, the Mughals were styling themselves as Padishahs.

If Dara Shikoh had defeated Aurangzeb and the British had never brought India into their Empire, would history have been different? I would like to hope so, but I doubt so. Akbar had attempted to create a new religion, but it did not last beyond his life. By the 17th century what was becoming Hinduism, and Indian Islam, were already sufficiently developed that they were becoming cultural attractors. Not through cognitive bias, but the weight of inertia of their cultural history and precedent. The transition from Akbar, to Jahangir, to Shah Jahan, and finally Aurangzeb, is one from an individual who brooked the displeasure of Naqsbhandi shiekhs, to one who worked hand in hand with them. An alternative vision is one where the heirs of Akbar turn their back on their dreams of Fergana, and rely upon Rajputs to dominate their lands instead of a mix of Central Asians and native Indians, Hindu and Muslim. Perhaps the Mughals would have become indigenized enough that they would transform into that they would have become fully Indian in their religious identity. Ultimately the answers of history are more complex than can be dreamt of in your post-colonial philosophy, and the white man is neither angel nor the devil, but a subaltern of historical forces.

 
• Category: History • Tags: History, India, Religion

pap

Recently had a discussion with a reporter at a major publication about genetic genealogy, and how genomics and ancient DNA has changed everything about what we know about the human. Though I did put in the caveat that it seems the New World has a mildly simpler history that aligns with what we’d somewhat expected or seen. I was wrong. It turns out that indigenous people of the Amazon have a few percent of ancestry derived from a population with the closest affinities to those of Australasia.

Screenshot from 2015-07-21 10:46:26 The plot to the left roughly shows groups which share haplotypes when comparing the Mixe people of Mexico to other Amerindians. The stronger red shading shows an affinity between pairwise groups due to the putative admixture event. What you can see that various Australasian groups, as diverse as the Andaman Islanders and and Papuans show elevated signals of affinity with particular groups from the Amazon in comparison to the Mixe.

The model is outlined in the figure at the top. What you can see is that a there was admixture into one of the first groups which arrived in the Americas. This group already had ancient Siberian ancestry. It then seems to have absorbed some ancestry from another group with affinities to the peoples of Australia. Because the dominant ancestral component of the hybrid group was similar to the sister American lineage a wide range of ancestral fractions from this group into the peoples of the Amazon are compatible with the statistics yielded by the data. Up to 85 percent, or as low as 2%. The lower the fraction of admixed “First Americans” into the Amazonian groups in question, the higher the Australian element in that group, as that ancestral element only spans a 1-2% range. In other words, if the admixed First American group contributed only 2% to the modern Amazonians, it would be in large part descended from the Andaman-like group.

This detail matters because of what is brought up in the discussion of the paper, and has been mooted elsewhere: a lot of the older skeletons from this region of South America look different. One model, which the authors are skeptical of, is that admixture happened in the New World. That is, and outrider group of First Americans absorbed and older population which arrived earlier to the region. But Kennewick Man tells us that morphology is only a rough guide. The Anzik Clovis result did not yield any evidence of Andaman-like admixture. That means either there was structure coming into the New World. Or, the admixture happened here.

From the patterns in the genome the admixture is old. But the confidence interval is big. It is not detectable by those methods sensitive to recent admixtures. It is older than 4,000 years. But, it is clearly post-Neandertal admixture. So younger than 50,000 years. In fact, the admixture graph at the top of this post suggests that this admixture post-dates that with the ancient Siberians. That means it is highly likely it probably dates to no older than ~20,000 years, since you need some time for the various Eurasian groups to actually diverge from about 40,000 years ago onward.
dstat The authors used a variety of methods to test this affinity that they detected. The ancestry fractions were low, so they wanted to see if the result was robust. It sees to be. I won’t get into the details, but I want to post the D-statistic table from the extended data. It uses a slightly different method the map above. Basically they’re testing explicit trees, and showing deviations from random drift along the independent paths which are compatible with gene flow across the tips of the tree. Admixture.

It strikes me that D-statistics show a lot more affinity with South Asians broadly. Why weren’t the signals as strong as in the Chromopainter analysis above? I have no idea, but perhaps it might have to do with the fact that South and Southeast Asians are themselves admixed between the Andaman-like group, and other populations (West and Northeast Eurasians respectively). This may have made higher to detect the haplotypes in question. Additionally, the Ami, an indigenous people of Taiwan also show up on this list. What this implies is that a broad constellation of eastern peoples who diverged from the ancestors of Northeast Eurasians were widely present in the past. In South and Southeast Asia descendants of these people were probably dominant down deep into the Holocene. The elevated signatures in groups like the Andaman Islanders and Papuans may be due to the fact that these groups are relatively pristine.

gr3 In 2011 the Reich group published a paper which actually suggested that there were multiple waves of old Southeast Eurasians with the Andaman Islanders being remnants of a group which contributed a secondary signal of admixture into the peoples of Oceania. This was published at about the same time as a whole genome analysis which suggested that Oceanians were descended from an earlier migration out of Africa, and not admixed. There are other groups which are supporting multiple out of Africa events now. The plot is getting thick and complicated.

I only bring this up because much of the current work uses copious data to test explicit models. The authors are constraining the sample space of models, and if you select between ten models, it may still be that the best fit is not a really good fit to the “real” model of what actually happened. One reason ancient DNA has been revolutionary is that it has forced researchers to consider models that they would have otherwise thought ludicrous. There were long suggestions for example of common ancestry between Amerindians and Europeans…but these ideas were often discarded as implausible. There are all sorts of details in relation to modeling assumptions which give valid results which are nevertheless inaccurate.

It is turning out that reality is crazier than our imaginations. Hold tight.

Cite: Genetic evidence for two founding populations of the Americas, Skoglund et. al., Nature (2015) doi:10.1038/nature14895

 
• Category: Science • Tags: Genomics

The full documentary from which this clip is extracted is at the Frontline website. I wasn’t really excited about watching this, but I made myself do it. The topic is very disturbing. Most of the film is about the modern day “underground railroad” out of ISIS territory of Yezidi women and children escaping slavery. The scene above is of what looks like a three year old girl who was captured by ISIS along with her mother and one year old brother describing beheadings, which she obviously witnessed. Apparently in disputes with her brother she threatens to cut his head off. The mother of the children tells of her time in one of the slave houses filled with women, and attempting to intervene when one of their ISIS guards started raping a nine year old. Apparently the guard declared that “this was allowed” by his religion. The narrator did not elaborate that the dominant accepted Hadith tradition is that the Prophet Muhammed consumated the marriage to his favorite wife Aisha when she was nine years old.*

Later on in the documentary there is a scene with teenage foreign fighters kicking back and just shooting the shit. The general implication is that they were all raised in Europe. They’re basically horsing around and joking like young men are wont to do. First, they amusedly describe mass killings of Yezidi men. Then later they start making lurid humorous references to Yezidi slave girls.

The truly disturbing aspect is that the body language and the overall mien are so startlingly familiar, but the topics are depraved. I think this goes to the heart of the fact that though we like to dismiss ISIS fighters as sociopaths, they really aren’t. Rather they are motivated by existential and ideological factors. An analogy to Nazi-dominated Germany is probably warranted. Most Germans did not start out as Nazis, but during the early conquest years most seem to have conformed to the new dispensation. There are documented instances, for example, of nurses who were known to toss Jewish children out of the upper stories of hospitals as a way to kill them quickly and free bed up beds for non-Jews, who after World War II went right back to their old profession.

The-Black-Book-of-Communism ISIS seems nihilistic because its aims and means are so alien to the norms of modern civilization, broadly construed. But the same could have been said of the Khmer Rouge regime of the 1970s, or the the Nazi dominion in World War II. And, unlike these two groups international Commmunism for decades managed to appeal to Western intellectuals who believed in its ultimate goals, even if they blanched at the methods of Lenin and then Stalin. They had a dream, and what’s a hundred million broken eggs to make that beautiful omelette?

* No matter if this is true or not, the problem for us in the year 2015 is that many ISIS fighters take this hadith at face value to justify the rape of nine-year-old girls.

 
• Category: Foreign Policy • Tags: ISIS

9780981519425_1Brian Charlesworth, co-author of the magisterial Elements of Evolutionary Genetics, won the Thomas Hunt Morgan Medal from the Genetics Society of America this year. An open access copy of his speech, What Use Population Genetics?, is now online at Genetics. In the speech he makes the case toward a broader audience, which includes people working in molecular and developmental areas far removed from population genetics, as to why his field is important and critical to the broader scholarly enterprise.

First, he argues that without a good intuition for population genetic dynamics, one can not model evolutionary process very well. Of course that intuition only comes over time absorbing population genetics and gnawing on problem sets. But you have to put the work in to talk cogently about evolutionary biology in its broadest scope. Charlesworth suggests that those who don’t know population genetics “run the risk of making mistakes such as asserting that rapid evolutionary change is most likely to occur in small founder populations.” The issue here is that selection is powerful in very large populations. Not so much in smaller ones. I’ve personally encountered this confusion many times from biologists who are not population geneticists. But, I do want to also admit that genetic drift can cause rapid allele frequency changes, so even here I would say that some people might quibble a bit with Charlesworth on the specific details (I am not one to dispute this particular assertion, for the record; I know what he meant).

Second, he addresses the nature of transposable elements (TE) in the genomes of organisms, and why they are so common, and where they are so common, as well as the role of PRDM9 in recombination. Pervasive features of the genome may, or may not, have adaptive origins. That means evolutionary genetics has to step into the fray and address the long term dynamics. Intersecting the frameworks of evolutionary genetics, and the structural constraints of molecular genetics, Charlesworth illustrates how population genetics sheds light on the biophysical character of genomic features, as well as the distribution of those features. If evolutionary biology is the science of why. Population genetics is how. Molecular genetics may be thought of in this schema as the is.

Finally, though Charlesworth alludes to it in passing only at the end of his speech, I think it is critical to remember that the post-genomic era is upon us, and it is incumbent upon us to think in in population terms. The style of analysis which is common in population genetics lends itself easily to big data analyses. I recall a conversation with a young researcher last year at ASHG where he told he was moving from population, to medical, genetics. And yet when his most recent publication came out I had to observe that it was fundamentally a work of medical population genomics. You can take the geneticist out of the population, but you can’t take the population out of the geneticist.

 
• Category: Science • Tags: Population Genetics

FileStack_retouchedAfter my post on GMO and its enemies the usual suspects have been on the attack, accusing me of being a shill for Monsanto. The reality is that I’m a mammalian evolutionary genomicist. I don’t work in applied agricultural genetics, though I have no problem with that discipline. In fact, I’m a big fan. And, because of where I’m based out of I know people who work in and on GMO, and I know their motivations. I can tell you that they sincerely think their research is going to help people. In fact, feed people.

41rxx-UtsWL._SY344_BO1,204,203,200_ Nevertheless, a common refrain is that objections to GMO have to do with objections to capitalist mass agriculture. The issue isn’t the science of GMO, but big ag. As you know, I don’t buy this. But let’s set that aside. This spring one of the panels at the Biotechnology Literacy Project (BLP) Boot Camp had to do with government regulation of GMO. I was shocked by the greatly increased regulatory hurdles that GMO face in comparison to more traditional techniques (it’s analogous to what gene therapy studies have to go through).* This enormous overhead imposed by regulation means that small operations, in particular academic laboratories, can’t do viable research on GMO that can get funded. Though CRISPR technology opens up myriad possibilities of modification of food plants studied by a few labs here and there, no researcher can devote the resources necessary to jump through all the hoops placed in front of this work.

Which type of operations can handle this regulatory straight-jacket? You guessed it: Monsanto. That explains one reason so many mass production crops are GMO. That’s big ag’s bread & butter. So will anti-GMO activists, who are concerned with industrial agriculture, and not the genetic technology, argue for changing the regulations to make academic research more viable and accessible for small and medium sized labs? To my knowledge no one in that community is pushing for this.

* If you engage in some Google punditry you’ll encounter documents which suggest that GMO research approval is easier in the USA than elsewhere. This is true. But, from talking to those who work in the field it’s still a big haul for a normal sized laboratory.

 
• Category: Science • Tags: GMO

51gYdVvOoQL._SX379_BO1,204,203,200_ Occasionally I get emails from students about how they should go about becoming a biologist who studies evolution. As if I would know. But sometimes the blind seek guidance from the blind! The number one thing I tell them though is that you need mathematical and computational skills today. This is true to some extent even if you are going to be mostly a bench biologist. You don’t want to be the person who’s always relying on someone else for basic analysis. With that, let me note that my friend Vince Buffalo’s book, Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools, is finally out, and I’d recommend it to anyone who wishes to bone up in this area. I’ve read a draft, and it’s definitely useful for any undergraduate or aspiring graduate student in getting you ahead of the curve if you haven’t already done work in this area. It will probably save you some time on Stackoverflow once you get there.

hd5C-sZ3_400x400 Speaking of friends, it looks like N of Everyone Kick Starter is going to hit its minimum threshold, and will get funded in their campaign. They’ve also now put a demo up of the Reader on their website. Check it out. You can get a flavor of the direction the firm wants to push scientific publishing. This space will get shaken up at some point, so it’s always useful to keep an eye on it.

9780199589883 I’m still slowly making my way through A New History of Western Philosophy. I do most of my reading on the Kindle. When I bought the book, and frankly when I started reading it, I did not understand that it was over 1,000 pages. Additionally, the author does not scrimp on detail. He engages in laborious exposition on items such as how Aristotle’s philosophical thoughts on motion were affected by the constraints of expression in the Greek language of particular concepts.

So why do I read this stuff? I’m a scientist (sort of). I come from a scientific background. From the first I assumed that I would pursue science in some way as an adult. Later on I branched out and explored history and geography. In all of these subjects older works are generally superseded or integrated. You don’t need to read Gibbon’s Decline and Fall to know the general outline of Roman history. Michael Grant’s more recent The History of Rome will do. Similarly, you don’t need to read The Origin of Species to understand evolution (though to be fair, I think in hindsight that it is valuable, after reading it a second time as an adult with a better understanding of evolutionary biology). Just get the Doug Futuyma text, Evolutionary Biology, if you want to be technical. Or, What Evolution Is from Ernst Mayr if your taste is more toward something palatable for the generalist audience. That will spare you Charles’ Darwin’s groping attempts at concocting a theory of inheritance.

Philosophy is different. When I encountered philosophy, and I was 20 by the time I seriously engaged the topic, I was shocked by the fact that there was a whole field where the ideas of men who lived over two thousand years ago were still relevant. Let me quote Machiavelli:

“At the threshold, I take off my work-day clothes, filled with dust and mud, and don royal and curial garments. Worthily dressed, I enter into the ancient courts of the men of antiquity, where, warmly received, I feed on that which is my only food and which was meant for me. I am not ashamed to speak with them and ask them the reasons of their actions, and they, because of their humanity, answer me. Four hours can pass, and I feel no weariness; my troubles forgotten, I neither fear poverty nor dread death. I give myself over entirely to them. And since Dante says that there can be no science without retaining what has been understood, I have noted down the chief things in their conversation.”

51K-gkZ7rAL._SX327_BO1,204,203,200_ Many, such as Steven Pinker in The Blank Slate, have wondered about our reliance on dead philosophers as authorities on the human condition. In The Blank Slate Jean-Jacques Rousseau is something of a villain. In agreement with Pinker I believe that most of Rousseau’s conjectures about human nature* have been roundly refuted. Additionally, attempts to construct social arrangements based on Rousseau’s understanding of human nature have failed, sometimes horribly so. More broadly, Pinker has offered that one reason that why the ancients are relevant in philosophy is that the discipline is characterized by the problems which are intractable. They are those domains which remain to philosophy as a discipline after science has carved out huge swaths of its traditional territory. I don’t deny the truth of much of what Pinker says, but when you read Aristotle and Xunzi’s political philosophy, it is hard to deny that their insights are far more relevant and useful than those of Plato or Jean-Jacques Rousseau. And, like good music and art sometimes distance allows us to perceive better the wheat from the chaff. The philosophers who remain relevant and prominent from antiquity were often those of particular genius and creativity. And that is only evident with the passage of historical time.

Obviously I wasn’t anticipating how many comments my post on country rap would generate. I do want to enter into the record that if you use an ethnic slur like “cracker” I’m not going to post the comment. You can just send me an email. I don’t think these slurs are elevating for the conversation.

Finally, on that post, some people seem to think I was casting aspersions on lower class people. That was not my intention at all. Additionally, though I don’t interact with that sort of person much today, I did grow up with a lot of lower and lower middle class rural whites. I even spent time working on a mule farm owned by a friend’s mother. As they say, class isn’t about money. And the poor and working classes have their own folkways in any case. My point is that just because there are particular folkways that are common among a certain class, they don’t have to “own” those tendencies, and can try and transcend them. But we as a culture don’t really engage in this sort of aspiration toward a higher and ennobling state. This actually has its flip case in the flaunted debauchery of the likes of Paris Hilton, who rub in Middle America’s face their exemption from bourgeois norms due to their class status.

* The representation of his conjectures about human nature, for those who note that there is some revisionist work which argues he’s been misrepresented.

 
• Category: Miscellaneous • Tags: Open Thread


Iron Age and Anglo-Saxon genomes from East England reveal British migration history
Stephan Schiffels, Wolfgang Haak, Pirita Paajanen, Bastien Llamas, Elizabeth Popescu, Louise Lou, Rachel Clarke, Alice Lyons, Richard Mortimer, Duncan Sayer, Chris Tyler-Smith, Alan Cooper, Richard Durbin

108_322When I first realized of the possible utility of genetics toward anthropology and history I came up against a major problem in addressing extremely fine-grained questions: the tools did not have the power to probe very small genetic distances, constrained in time and space. After reading Norman Davies massive The Isles I was to understand that the Anglo-Saxon transformation of Britain into England was a matter of elite cultural emulation. What did genetics have to say about this? The answer was “not much.” In an earlier era of a few dozen classical autosomal markers or just mtDNA and Y chromosomal fast evolving microsatellites genetics was not powerful enough to distinguish between extremely close European populations. In The History and Geography of Human Genes L. L. Cavalli-Sforza notes that Europe is the most homogeneous of his continental groups where he had many samples. If you remove outliers like the Finns and Sicilians, this is very true today when we have whole genomes. Though conventional whole-genome SNP panels can distinguish Northern European population clusters they are packed very tightly together.

Using the Human Origins Array data set the authors of Iron Age and Anglo-Saxon genomes from East England reveal British migration history projected the genotypes of ancient samples from the Iron Age and the Anglo-Saxon period upon modern groups. As you can see the Northwest European data sets are packed so close it’s hard to discern structure. In the era of pre-genomic phylogeography it was nearly impossible. To answer whether the Anglo-Saxon migration was a mass folk wandering or a tiny mercenary elite one would have to distinguish Germano-Scandinavian heritage from that of the native British, and the reality is that these are all very close groups. We now know that the ethnogenesis, at least in a genetic sense, of Northern Europeans as a whole seems to date to the Bronze Age, on the order of 4,000 years ago. Therefore, to pick up genetic structure you are by and large focusing on only two to three thousand years of drift between these groups! This explains why the older methods were so under-powered. There just wasn’t much raw material for them to work with; not enough time had passed for the populations to diverge.

nedPLOT A few months ago the PoBI project finally published, and revealed local structure across the British Isles. The authors concluded that in England proper a minor, but substantial, proportion of the ancestry derived from the Anglo-Saxons. That is, Germans. The authors used SNP data sets. That is, less than a million markers in the genome (and out of the twenty to thirty million SNPs in the human genome). But, they had a massive sample coverage from which to extract insights from.

51IQSePVDRL._SY344_BO1204203200_ This preprint takes a different tack. They take whole genome sequences from ancient subfossils. What they lack in sample size, they make up for in marker set (some of the coverage is high enough that they probably got decent calls), as well as the fact that they are sampling individuals who are from the source cultures in question. Celts, Anglo-Saxons during the invasion period, and also during a some what later epoch. Their results in nearly perfectly in line with those of PoBI. Using their samples as representative they estimate that ~30 percent of the eastern English ancestry is German. A lower proportion is found in Wales and Scotland.

The figure above illustrates this finding. A key point about this paper is to emphasize that since they are using whole genome sequences they can focus on rare alleles. Because the alleles are at low frequency they’re likely to be younger, and if they are younger they are also more likely to yield the power to discern differences between very genetically close groups, such as the Germans and the British. In the plot above you see that the Anglo-Saxon samples are shifted right, while the Iron Age samples are shifted to the left. What this shows is that the Iron Age samples tend to share more rare alleles with the Spanish IBS data set from the thousand genomes, while the Anglo-Saxons share more alleles with the Dutch. Eastern England and Wales and Scotland occupy positions that you’d expect.

Furthermore, the authors utilized the program rarecoal to explicitly model the population history of Britain using their data. This will be a major feature of future work in this area, as researchers drill-down to a very fine grain and ask precise questions which good quality whole genomes and robust phylogenetic packages can actually tackle.

There is still much that needs to be worked out on this topic. There’s only so much you can say from these handful of individuals. But even with these finite samples much was extracted. The authors observe that one of their Anglo-Saxon era individuals, buried in an Anglo-Saxon fashion, clustered perfectly with the British Iron Age individuals. Additionally, this individual was outfitted in a manner which suggested they were very high status within Anglo-Saxon society. But the authors did not connect this with the fact that all their Anglo-Saxon individuals were female. Hypergamy is entirely typical in human societies, and it is plausible that large numbers of migrating German men arrived on British shores without a wife and family in tow. In the years after the Norman invasion it was not uncommon for noble Saxon houses to give their daughters to an invader. And so the Anglo-Norman aristocracy arose as a synthesis between distinct paternal and maternal lineages. A similar scenario likely played out during the invasions of the Dark Ages.

 
• Category: Science • Tags: Anglo-Saxons, Genetics

Over at Slate Will Saletan has a very long piece Unhealthy Fixation: The war against genetically modified organisms is full of fearmongering, errors, and fraud. Labeling them will not make you safer. The survey is useful if you are unfamiliar with the topic, though it will be sadly familiar to the rest of us. Saletan makes two observations which I think need highlighting. First, he asserts that “the deeper you dig, the more fraud you find in the case against GMOs. It’s full of errors, fallacies, misconceptions, misrepresentations, and lies.” Basically it’s a shell game, and the reason is that those who oppose GMO obfuscate the fundamental roots of their objections (consciously or subconsciously). Saletan notes:

Third, there are valid concerns about some aspects of GE agriculture, such as herbicides, monocultures, and patents. But none of these concerns is fundamentally about genetic engineering. Genetic engineering isn’t a thing. It’s a process that can be used in different ways to create different things. To think clearly about GMOs, you have to distinguish among the applications and focus on the substance of each case. If you’re concerned about pesticides and transparency, you need to know about the toxins to which your food has been exposed. A GMO label won’t tell you that. And it can lull you into buying a non-GMO product even when the GE alternative is safer.

The concrete and coherent objection to GMO which lies just under the surface of the arguments put forward by activist groups like Greenpeace is that the technology is part of the agricultural-industrial complex. But as many have observed, if the problem with GMO is their connection to big agriculture, then why aren’t the arguments simply recycled from those used against industrial agriculture? There are two dynamics at work. First, there is broad popular suspicion of “genetically modified organisms.” Using GMO as a hook, and engaging in FUD, is more effective than arguing against corporate agriculture. Second, as Saletan implies in the piece, even anti-corporate considerations aside there are genuine concerns rooted in the idea that there is something “wrong” with genetically modifying organisms (in fact, with the emergence of cheap CRISPR, we’re potentially at the precipice of a revolution of small scale agricultural innovation, though right now it is unlikely to happen because of regulation).

This sentiment is very broad, and, it is not ideological. Or at least it wasn’t as of 2006, when the EATGM question on for the GSS was put to over 900 respondents. It asks:

Which statement best describes your own view about eating foods that have been genetically modified? 1. I don’t care whether the food I eat has been genetically modified. 2. I am willing to eat genetically modified foods, but would prefer unmodified foods if they are available. 3. I will not eat food that I know has been genetically modified.

The results:

Screenshot from 2015-07-18 16:02:54

As you can see, there’s no ideological difference. The slightly greater skepticism of Democrats can probably be attributed to socioeconomic variables. The less educated, the poorer, and women, are all more skeptical of GMO on the whole. These are groups more well represented among Democrats, and some of these are the most liable to vote and identify Democrat despite not being particularlly socially liberal (e.g., poorer minorities).

gmo1 But that’s nearly 10 years ago. I’m not sure that the lack of ideological polarization will be so evident now. As documented by Saletan, and earlier in Slate by my friend Keith Kloor, the really high octane activists and public intellectuals behind the anti-GMO push are on the cultural Left. Last year Oregon had a GMO food labeling ballot measure. It lost narrowly. But as you can see in the scatter plot to the left there is a very tight correlation between a county being Democratic and favoring labeling. Second, there was an earlier attempt to pass such a ballot measure in 2002. It was destroyed at the polls. If trends continue it seems entirely likely that labeling will succeed in Oregon in the next go around. Americans intuitively are biased toward transparency as a good.

Screenshot from 2015-07-18 16:22:39 The fact is that the majority of the public remains skeptical of GMO foods. And large majorities support labeling. Which prompts one to ask: why did the labeling measures not pass in Oregon and California? I think the critical aspect here is that attitudes of skepticism toward GMO are wide but shallow beliefs. Only a small minority of the population has very strong views on the topic. Those opposed who have very strong opinions and engage in activism on the topic tend to come from the liberal intelligentsia. Anyone who has been involved in science and policy around this topic (I have friends who work on GMO crops) will vouch for this. Similarly, those enthusiastic about the potential of GMO tend to be a small number of plant scientists (who also, are be politically liberal on the whole, as they are mostly academics). It is true that large agricultural firms are notionally pro-GMO, but here’s the reality: big ag is making money, it doesn’t need GMO. In fact, because of public sentiment and preference big ag naturally sees organic labeling as a profit center! The regulations are such that really only large firms have the resources to overcome the hurdles put in front of research in this area in terms of safety and oversight.

DescartesBaby Once the issue of GMO become salient, as in the ballot measures here on the West coast, then people become more cautious. Anti-labeling arguments start to be more persuasive, and those with business interests that might intersect with agriculture might come to different opinions, as the precautionary principle starts cutting in other directions. GMO has not become culturally polarizing. Yet. Most peoples’ opinions are inchoate and instinctive. I believe they derive from folk biological intuitions about essences. Ultimately it’s about the fact that people don’t understand genes in any prosaic sense, but they think that they’re somehow magically involved in the nexus of who we are in a deep and fundamental sense. That’s why the translocation of fish genes into tomato is so uncomfortable for people; they imagine that the essence of the fish is somehow being mixed with the essence of the tomato, and that just feels wrong. Genophobia of this sort is comprehensible in a cognitive anthropological framework. Just as we are likely wired for Creationism, I think we’re wired for being very skeptical of the concept of GMO, because of the implicit connotations of muddling categories which we view was fundamental. And, just like Creationism, we can overcome these deep intuitions. Much of natural science in the modern world consists of overcoming and updating of deep intuitions.

410tL5IwqTL._SX329_BO1,204,203,200_ But, the deep intuitions can be harnessed toward political movements. In the United States Creationism is not just a sentiment and intuition, but a formalized social-political project which fuses some elite suspicions of scientific naturalism with populist skepticism of common descent. Modern Creationism has a particular intellectual pedigree, but it works with the raw material of gut human feeling. Creationist sentiment is old, as old as our species. But Creationism as a potent political movement is new, and its affiliation with the edges of American conservatism is actually a feature of the past generation. It has a history of how it got from where it was, to how it got to where it is. In American Grace Robert Putnam and David Campbell report data that political and religious affiliation co-vary and influence each other (with the former often effecting the latter!).

I am mildly optimistic that this will not happen with GMO, and that is because scientists are anti-anti-GMO, and, politically liberal. It seems very likely that a GMO food labeling measure will pass in the near future. And I believe that this will galvanize a backlash among scientists on the whole. Something similar happens on the Right with Creationism. Whenever the movement actually scores a victory, elite Republicans, who invariably accept the science of evolutionary biology, become alarmed and roll back gains made by Creationists. Unlike evolution, GMO are not just abstractions in a laboratory. When GMO becomes pervasive enough, or at least the knowledge of how pervasive they are becomes more common, then the public will likely make peace with their reservations, just as they have with in vitro fertilization.

 
• Category: Science • Tags: Genophobia, GMO

51MzSp6UPlL._SY344_BO1,204,203,200_ Probably because I’m reading the perspectives of ancient philosophers such as Plato who had very specific and clear views of human excellence, I’m struck now by the rise of brashly demotic artistic forms, and how they push their way into our public space. Consider the rise of country rap, which is one of the more bizarre cultural syntheses to arise out of the dialectic discourse which permeates American society. Country music has traditionally been dominated by rural white Americans, and reflects a conservative ethos which is notionally aligned with traditional values. Rap, in contrast, emerges out of a hip-hop urban milieu which is oppositional to broader American society, distrusting authority rather than celebrating it.

When the Moonshine Bandits “We’re all country” came on my Spotify I was curious about Sarah Ross rapping about how she’s from Jersey, but still country. And, there are explicit shout-outs to blue collar life. They seemed to be owning a denigrated lifestyle and class background. So I looked up the video. The aesthetic was shocking to me. To be entirely frank, it seems to celebrate a gritty slovenliness as the best of all things. Eternal Budweiser, mac & cheese, and poor muscle tone. Many hip-hop and bro country music videos are gauche in their crass superficiality, but at least ultimately there’s often a nod to an aspiration toward excellence, in wealth, in accruing attractive females, in being in shape. You don’t see any of this in the above video. It’s a valorization of the demotic, the pedestrian. Average looking people coalescing together to get inebriated. No symposium, that.

 
• Category: Miscellaneous

There was a question about East Asian genetic structure. There have been a fair number of papers published on the issue. But over the years I’ve assembled a pretty large personal data set from public sources, as well as stuff people have sent me. I decided to look at the East Asian individuals and how they relate to each.

First, I focused on the major ethno-national groups (or ones of particular interest and relevance, such as Mongols). Second, I LD pruned the data set down to 96,000. Third, I did some outlier removal. For example, I wanted to include some Kalmyk data, but it turns out all the Kalmyk have European admixture at some level. And a subset of individuals from Cambodia and Vietnam are ethnic Chinese. Those were removed.

I ran ADMIXTURE K = 5 unsupervised. Treemix k = 500 and global rearrangements on, and rooted with Cambodians.

Eigenvalues 7.59041, 4.04862, 3.00559, 2.60692 and 2.01554.

Asian1

Asian2

Asian3

Asian4

AsianTreeix.9

AsianTreeix.8

AsianTreeix.7

AsianTreeix.6

AsianTreeix.5

AsianTreeix.4

AsianTreeix.3

AsianTreeix.2

AsianTreeix.1

Asian_htm_m40027816

First, the evidence of gene flow into the Han ethnicity, or the absorption of the Han of local substrate, is clear in these results. Second, I’m pretty sure that the weird affinity between Yakut (the northernmost Turks) and Cambodians has to do with admixture into both groups from non-East Eurasians that is old. In the case of Cambodians something Indian-like, and for Yakuts something more like “Ancient North Eurasians.”

 
• Category: Race/Ethnicity, Science • Tags: Asian Genetics, Genetics

51KHpfTVbiL._SY344_BO1,204,203,200_ Let’s start at the beginning. If you read a book about Indian history in the 1980s it might begin with this sort of stylized narrative: in the beginning were the Mundas. Then there were the Dravidians, then finally the Aryans (and as an afterthought various East Asian groups on the fringes of northern and eastern Aryavarta). The thesis, broadly, was that the Munda people, who speak an Austro-Asiatic language, were the closest that the Indian subcontinent had to genuine aboriginals. The oldest of old. Supporting this contention is the fact that the languages of the Munda people, with distant affinities to Cambodian and Vietnamese, are very alien in comparison to Dravidian and Indo-Aryan (if Dravidian has any connections outside of the subcontinent, they are always posited to the west, in ancient Iran. The Munda languages clearly have eastern connections). The supposition then was that from the Munda arose various peoples of eastern Eurasia. To cut to the chase this model is probably wrong. The genetic structure of South Asia seems to have arrived at its current outlines relatively recently. In regards to the Munda people their origin is in Southeast Asia. They are not the progenitors of Southeast Asians, they are in part derived from Southeast Asians. Part of the broader expansion of “first farmers” in Southeast Asia from southern China. Their Y chromosomal lineages and autosomal heritage both imply this. Additionally, they carry the Northeast Asian derived variant of EDAR. Though much of their culture is almost certainly exogenous, and of relatively recent vintage, they are clearly highly admixed with the South Asian substrate. In particular, the fusing of an ancient West Eurasian population (“Ancestral North Indians”, or ANI) and a deeply rooted indigenous group with distant affinities further east (“Ancestral South Indians”, or ASI).

Chaubey, Gyaneshwer, et al. "Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture." Molecular biology and evolution 28.2 (2011): 1013-1024.

Chaubey, Gyaneshwer, et al. “Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture.” Molecular biology and evolution 28.2 (2011): 1013-1024.

One of the reasons that the ancient character of Munda residence in South Asia was persuasive is that they are resident in upland zones, which perhaps refuges after being marginalized by later arrivals. Their fragmented distribution is a tell that they occupied wider territories than is the case today. One thesis is that the Gangetic plain was inhabited by Munda people before the Indo-Aryans arrived. Rather than Dravidians, the indigenes in the Vedas may have been Mundas. But I’m interested in a more parochial question: can Munda ancestry explain the high fraction of East Asian ancestry in Bengalis, particular eastern Bengalis?

We can address this question a bit with genetics thanks to the resources we have in terms of population coverage. As readers know I’ve started to work with the 1000 Genomes data set. Luckily it has a large number of Bengalis within it. Meanwhile, the Estonian Biocentre has put its genotype data online, and there are Munda samples in there. I merged the data together, and removed pretty much all missing alleles. At the end of it I had 185,000 SNPs. To explore the questions I had in mind I decided to look at several populations. Bengalis and Telegu speakers (their genetic position would put them as “middle castes”; not Brahmins, but not Dalits or tribals). Georgians (from the Caucasus) as an outgroup. For Southeast Asian groups, Burmese, Cambodians, Filipinos and Dai. Finally, a small number of Munda. I plotted them on a PCA and removed those individuals who were not easily assigned to a cluster. The first PCA: MundaPC1

This isn’t really telling you much you don’t know. Let’s look at PC 3 now: Rplot

As you can see the Munda show a cline toward the Cambodians. This makes sense if the Munda descend from Austro-Asiatic agriculturalists. The Austro-Asiatic expansion in Southeast Asia probably dates to 4,000 years ago or so. Peter Bellwood has stated that archaeologists have excavated villages in northern Vietnam which catch the process of ethnic transition in action at this date (e.g., 75% of the burials are of gracile individuals, whille 25% very robust individuals). Such dates might put a ceiling on how early the Munda arrived inthe Indian subcontinen. In these results the Filipinos are representative of Austronesians, who have their roots in Taiwan and the Fujian coast, while the Dai are the forerunners of the Thai who arrived in Southeast Asia over the last few thousand years, taking over the uplands of Burma (Shan) and Laos (Lao), and swallowing the Khmer civilization which once flourished in the Chao Phraya basin (becoming Thailand). But it’s hard to make out what’s going on with the Bengalis…to me it isn’t clear that they’re shifted as much toward the Cambodians as they should be if the Asian ancestry was due to Munda being absorbed by Indo-Aryan speaking farmers.

So next I ran Admixture. I ran supervised and unsupervised and they showed the same qualitative result. Below is a bar plot of the unsupervised result, K = 5.

plinkAA_htm_mf149510

The Munda ancestry which is Southeast Asian here is overwhelmingly Austro-Asiatic. That is not the case with the Bengalis, who exhibit a range of fractions. There is very little Austronesian ancestry, which is something one might expect. But, there’s a balance of Austro-Asiatic and Daic ancestry in many individuals, though there is inter-individual variation (my mother has one of the strongest Austro-Asiatic skews among the Bengalis, while my father is among the most Daic; previous runs of admixture consistently show that her eastern Eurasian is more Southeast Asian than his, which has suggestions of Northeast Asian). This is not consistent with Munda being the sole source of East Asian ancestry in modern Bengalis.1 Using rolloff based methods researchers have estimated that admixture into Bengalis occurred on the order of 1,000 years ago. There’s nothing here that would contradict that, and the admixture can easily be explained by the Burmese in the data above, or Khasi and Garo people, who live to north and and east of Bengalis.

Finally, I ran TreeMix on the data. I removed the Georgians and Filipinos because they didn’t add much. Additionally, for kicks I broke apart the Bangladeshis into two groups defined by the 25 most Daic, and 25 least Daic. Below are the ten plots from the ten runs.

MTree.9 MTree.10 MTree.1 MTree.2 MTree.3 MTree.4 MTree.5 MTree.6 MTree.7 MTree.8

I don’t think breaking apart the Bengalis did any good. There were runs with the full fused sample, and the results were similar. It is clear that TreeMix also suggests that Munda are not a singular donor to Bengalis of their East Asian heritage. The source of the donor migration arrow is always shifted more toward Southeast Asian groups proper. Breaking apart the Bengalis into Austro-Asiatic and Daic skewed groups did result in the source of the gene flow being somewhat different. But not appreciably. I also ran the f3 and f4 statistics. There’s nothing surprising about who mixes with who…though it is notable in these and the above results that Burmese show nearly as high a gene flow from South Asians as Bengalis show from Southeast Asians. There have long been suggestions of gene flow from India to Cambodia, perhaps associated with the ancient mediation of South Asian cultural forms across Southeast Asia. But the Burmese evidence of gene flow is tragically ironic in light of the fact that modern Burmese are virulently racist toward dark skinned Muslims who clearly have South Asian origins.

51MGYd330tL._SY344_BO1,204,203,200_ So what happened in Bengal? At the top of the post I have an illustration of The Rise of Islam and the Bengal Frontier, 1204-1760. The thesis of this book is that the Islamic nature of eastern Bengal is in large part due to its relatively recent settlement by Indo-Aryan farmers. Though Bengal has always been a marchland, on the fringes of Aryavarta, before the Islamic conquest of the 13th century its center of gravity, culturally and demographically, was in what is today in the Indian state of Bengal, to the west of Bangladesh. The author of The Rise of Islam and the Bengal Frontier, 1204-1760 suggests that Islamic elites were instrumental in opening up the lands to the east of the old core, and the peasant cultivators who came to cultivate the new territory under their leadership identified vaguely with the religious identity of this new elite (though in general practicing on a day to day level their own folk beliefs), as the old organically developed institutions of Hinduism and Buddhism were poorly moored in the virgin lands. To me this is reminiscent of Michelle Salzman’s data in The Making of a Christian Aristocracy, which suggests that Christian elites arose on the frontiers, rather than the old cores, under patronage of the new religious dispensation (these data are predicted by Peter Turchin in War and Peace and War). In contrast the old Roman elite was relatively late to Christianity, as they were attached their own customs and traditions, which had thick and deep roots in the heartlands of the Roman world. Similarly, Hinduism (or what became what we term Hinduism) between the Doab and western Bengal seems to have resisted Islam’s attempt to destabilize local institutions and interpose itself as the dominant religious ethos of the sub-elites. Only on the destabilized fringes of the west and east, where old orders did not exist or were totally torn down, did Islam find purchase as a majority dispensation.

Finally, the high component of East Asian ancestry among the peasants of eastern Bengal is probably a function of the fact that there were groups from the east also pushing into the fertile territory. If the initial population density was low then a modest inflow at the early stages, ~1,000 years ago, could have a major long term impact. The crushing population densities of “Golden Bengal” was centuries into the future. A lack of cultural memory of this admixture is curious, but to a great extent shifting to the new religion meant that the proto-east Bengalis were creating a new identity. Things get lost….

 
• Category: Science • Tags: Bangladesh, History

First Peoples: Europe came and went. I watched it. In case you didn’t see it there was a big reveal: archaeologists in France have uncovered a site where modern humans were producing arrowheads 50,000 years ago. This is strange for two reasons. First, what were modern humans doing with bows and arrows 50,000 years ago? They emerged in the Paleolithic transition to the Mesolithic, spreading from the Old World to the New. That is, they become common over the last 10,000 years. I don’t recall the narrator addressing this issue at all. But let’s set that to the side: if these finds are associated with modern humans then that pushes their arrival to Western Europe 10,000 years further back. Despite all the arguments about dating the presence and disappearance of Neanderthals from Europe, no one presumes that they went extinct 50,000 years ago. That implies that groups of moderns interposed themselves into Neanderthal dominated Europe in some fashion for thousands of years, until finally the Aurignacian culture arrived and replaced Neanderthals in toto.

At the site in question specifically the researchers have uncovered evidence that moderns and Neanderthals used the same location only a few months apart. But we need to remember modern humans weren’t modern yet, they were just one of the many hominin lineages which have flourished over the past 2 million years. With hindsight we can see that these initial forays were to prefigure what was to come, but at the time the two groups were not quite that different in technology and guaranteed destiny. Modern humans did not have any great advantage, so they may have come and gone depending on the circumstances.

51It8A+EKrL._SY344_BO1,204,203,200_ Perhaps the 50,000 year old moderns in France may be likened to the Norse in Newfoundland. And in fact the analogy to the European settlement of North America, and the replacement of Neanderthals by moderns, is made in First Peoples. But the devil is in the details, as the documentary is somewhat schizophrenic about the specific dynamic until the very end. The two extreme stylized models are “make war” vs. “make love.” With the very clear evidence that modern humans admixed with Neanderthals, the narrative arc of the documentary flips from one where moderns are depicted attacking a Neanderthal camp, to one where a modern human lothario engages in “inappropriate touching” with a Neanderthal female. Though I suppose this was 40,000 years before “affirmative consent” norms, so perhaps we should cut them some slack?

In any case, going back to the analogy with the New World I think we can acknowledge that there were complex scenarios left on the cutting room floor of a one hour documentary. The mestizo population of the New World arose through a variety of means, ranging from love all the way to rape. If modern humans 40,000 years ago were anything like modern humans today, then it seems likely that their interactions would run the gamut from trade and amicable relations, to extermination, with many permutations and positions between these two. We need pick one model as the story.

At the end of it all First Peoples: Europe tells the viewer that Neanderthals were demographically swamped out, rather than killed en masse (there weren’t enough for them to be a mass anyway!). This is an idea that’s been around for a while. With very small populations the idea is that a crest of demographic expansion out of Africa just swallowed up the Eurasian hominins. We literally mated them out of existence. John Hawks elaborates this model at length when he has screen time, which makes sense as he’s been suggesting that large effective population sizes within Africa over the Pleistocene might naturally result in the “out of Africa” pulses we see in the genetic record.

Finally, this episode does now make it crystal clear to me why the original admixture event of Neanderthals with modern humans in the Middle East left its imprint on modern Europeans, and later ones did not. Modern Europeans, whether their ancestry is “hunter-gatherer” or “farmer” descend from a Pleistocene Middle Eastern/Central Asian population in totality, and so only experienced that singular admixture event with Neanderthal Middle Easterners. More concretely, the Mesolithic populations which were overwhelmed and assimilated by farmers during the Neolithic in Europe were themselves descended from peoples who had issued out of the Middle East or Central Asia to replace the first modern Europeans. The Aurignacians (or if later, Solutreans) replaced probably had somewhat higher fractions of Neanderthal ancestry, being further out on the “wave of advance.” But since they left no descendants, to a first approximation there’s no signal of a Neanderthal cline.

The past 50,000 years have been characterized by two phenomena: extinction and admixture. The rest is commentary.

 
• Category: Science • Tags: Paleoanthropology

9780199589883 To give my brain a break after reading Reading in the Brain I am reading A New History of Western Philosophy. I know I should tackle The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies or Warriors of the Cloisters: The Central Asian Origins of Science in the Medieval World, but I feel that that would have taken more mental energy. Histories of Western philosophy are easier hauls since I already know the roadmap and have a conceptual armamentarium. Though if you want to read a history of Western philosophy, I recommend The Truth About Everything: An Irreverent History of Philosophy. It’s written with more humor than most of the books on this topic! The style obviously differs from that in more academic works, but the general structure of The Truth About Everything is pretty much always recapitulated. A yellow-brick road instead of an asphalt one perhaps.

51lW5fpojzL._SY344_BO1,204,203,200_ Reflecting on Western philosophy and its beginnings you always need to go back to Aristotle and Plato. The order in which I listed these two individuals despite their chronology should tell you about my bias. In a A New History of Western Philosophy the author recounts an assertion by Gilbert Ryle, people could be divided into two categories on the basis of four dichotomies: green versus blue, sweet versus savoury, cats versus dogs, Plato versus Aristotle. I suppose three out of four isn’t bad! Like Armand Leroi (see The Lagoon: How Aristotle Invented Science) I have strong sympathies with Aristotle probably because I am a natural scientist, and in particular, a biologist. It is in the domain of biology that Aristotle was mostly wrong, as opposed to not-even-wrong, as in physics. And often he wasn’t even wrong, not too shabby for a man who lived ~2,500 years ago was literally inventing whole fields on the fly. Aristotle’s lack of recourse to mathematical formalism rendered his physics laughable, but his observational acumen lent itself to biology, and his inferences were often quite perspicacious.

But the history of philosophy makes me wonder at contingency and necessity. It strikes me that it is important to observe that Aristotle was a family man. He had a wife and children. Though if you dig into his presonal life it seems to have been conventionally complicated. Plato, in contrast was a lifelong bachelor. Whether he was a homosexual in a physical sense, as a wealthy aristocrat who never married he was somewhat detached from the normal course of affairs in a way the more bourgeois Aristotle never was. Did their life choices affect their philosophy? Or were their philosophies and life choices outcomes of a common cause and personality difference? As the years progress I am less and less convinced by the importance of contingency, in particular reading the ideas of Chinese and Indian thinkers, which in many ways have analogs to the Greeks (even if the emphases might differ). Complex civilization has a Plato-shaped hole, and it has an Aristotle-shaped hole.

This piece in the new TNR, It’s Not Easy Being a Guy in a Country Song, Either, is actually not too bad, as it avoids too much sneering at the subjects. But when implicitly bemoaning the lack of voices in “bro country” which are not white straight, male and culturally* Southern, as well as the topicality of blonde babes, dirt roads, and beer, I’m a little confused as to how the author expects the genre to diversify. If, for example, urban underclass black males were represented in the genre, the topicality would shift. But pretty soon I think it would be hard to differentiate it from hip-hop, because the topics reflect a historical experience. It seems entirely reasonable that the mores and lifestyle of working class Southern white men would be somewhat distasteful to cosmopolitans with a Ph.D.. But if a genre termed “bro country” ever appealed to a feminist whose profession is to be a cultural critic, they’re doing it wrong. If you took Luke Bryan, and just changed his sexual orientation, I doubt that there would be a big audience for songs about his life growing up as a closeted gay man on the dirt roads of Georgia, kicking back with a beer and meeting other guys in the back of his big rig. The cultural landscape is not flat, and some experiences will be more commonly reflected in the arts because they are…more common.

I guess diversity is great, unless it operates outside your narrow ideological purview.

I’ve been busy for the past week. So I’ll answer some of last week’s “open thread” questions here.

First, I’ve been looking for something about ancient+early medieval Arab history. Any suggestions? Here are three: Great Arab Conquests, When Baghdad Ruled the Muslim World, and A History of the Arab Peoples.

9780307819383 Everyone is talking about and asking me about The New York Times piece, The Mixed-Up Brothers of Bogata. Two pairs of identical twins were “switched” at birth in a fashion so that two families raised what they thought were fraternal twins. If the piece fascinated you, you really should read Born that Way. Also, there’s a confusing section in the piece: “On average, the researchers found, any particular trait or disease in an individual is about 50 percent influenced by environment and 50 percent influenced by genes. ” I suspect most readers will take this to mean that the trait in the individual is 50 percent genetic and 50 percent environmental. That is wrong. Rather, 50 percent of the variation in the population is due to variation in genes. There is an obviously implication for individuals, but there is a lot of variation, and for most traits it doesn’t make sense to say that in an individual it is any percent genetic or environmental.

There’s a large section on epigenetics in the article, but they never report results. I assume there’s a publication down the line, and we’ll hear about it. Could epigenetics explain some of the environmental component of variation? Perhaps. But behavior genetics already suggests that non-shared environment is quite large in its effect.

Finally, my wife recommends you watch the documentary (42 minutes) if you have any fluency in Spanish. The article elided a lot of the inter-individual differences which are visible in their manner, speech, and overall physiognomy.

In response to a question about aDNA in China and its utility. The key is sample size. If you are working with Y or mtDNA there is a lot more noise and randomness than intuition would suggest, due to their small effective population sizes.

* Some major figures in the genre, such as Dierks Bentley, were not raised in the South but have assimilated to Southern culture.

 
• Category: Miscellaneous • Tags: Open Thread

Est100_1

I’m currently trying to figure out how best to integrate 1000 Genomes data, along with Estonian Biocentre, and HGDP. First, I converted the VCF files from the 1000 Genomes into pedigree format. I’ll put that up on GitHub in the next few days. Then I filtered the results for SNPs which are found in the HGDP. Finally, I intersected the results with the Estonian Biocentre data sets. I was left with ~250,000 markers after quality control (e.g., removing markers which are missing in more than 0.1% of the 5000+ samples).

In particular I’m curious about the population structure of the South Asian data. When you sample Chinese or Japanese or the English you need to be geographically diverse, but you don’t have to worry about social stratification too much.* Not so with South Asia. You have to be careful who and where you sample, because the variation doesn’t cleanly follow geography. In the Diaspora for example wealthier and higher status groups tend to be represented. In the mid-2000s Noah Rosenberg’s lab published Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India. In the paper itself the authors cautioned their samples were from the United States, so one should be careful about accepting the idea that they might represent the geographic variation in South Asia well. In hindsight it seems likely that their selection bias was too great for them to overcome to make robust conclusions, even with over 700 microsatellites.

Above is a PCA plot I generated for South Asians. I’m not quite sure of the coding of some of the Estonian Biocentre populations, so don’t take that as gospel. I was more curious about the distribution of the 1000 Genomes samples, since they are likely to be widely used in the near future.

First, let’s focus on the Bengalis from Bangladesh:

Parents

I was frankly surprise how genetically homogeneous this group is. The two overlapping black dots are my parents. It seems clear that my family comes from a region of Bangladesh which likely has more East Asian ancestry than is the norm. This makes geographic sense, my family’s roots are in the eastern part of eastern Bengal. Though it is hard to see on this plot a small group of Bengali individuals, specifically six, reside in a tight cluster amidst samples from Tamil Nadu. The fact that they aren’t randomly scattered indicates to me that there’s some genuine structure here. I suspect that there is evidence here of a group which has been assimilated, but retained its separate caste-community identity.

But overall there is a major contrast between the Bengali samples from Bangladesh, and the previous Gujarati samples, now also in the 1000 Genomes (ou can see the Patel cluster on the other side of the Bengalis, as it bulges out). The non-Patel Gujaratis were genetically varied, some very similar to individuals from Pakistan. In contrast there isn’t that sort of cline among the Bengali samples (it doesn’t look like they sampled any Bengali Brahmins in this data set, at least those of full heritage). The Punjabi samples were collected from Lahore, and they range from many individuals who are little different from Pathans to some whose genetic background resembles those from middle castes in Southern India. I don’t know what’s going on here, but there has been some back migration of laborers into the Punjab historically. I believe this is the origin of some low caste groups who are now Christian. Both the Telegu and Tamil samples have a few Brahmins in them. This is clear in the following plot:

SIndia

The two Brahmins are from Tamil Nadu. You notice that several of the 1000 Genomes Tamil and Telegu samples are rather close to them. South Indian Brahmins tend to be genetically very similar, so almost certainly that’s what these individuals are if they are placed here on the PCA. Though the Tamil samples are relatively tightly clustered, the Telegu break out into several groups. One of the major 1000 Genomes groups overlaps perfectly with Velamas, a middle caste from Andhra Pradesh. The individuals who are Telegu speakers between the Velamas and Brahmins may be of mixed heritage. I don’t know.

Ultimately I’d like to do some TreeMix and pairwise comparisons between these populations. But to do that I’m going to have to clean them up a bit so that they make sense as…populations.

* The outcaste group in Japan only crystallized during the Tokugawa period. Not long enough to be genetically that distinct from the broader Japanese population.

 
• Category: Science • Tags: 1000 Genomes, Genetics

416NQwBS-+L._SY344_BO1,204,203,200_ Years ago I walked down the main street of a town I had lived in for years, and noticed some new apartments above the retail shops. When I got back home I told my girlfriend about my discovery, and she rolled her eyes and explained patiently that they’d always been there. The fact is that I’m notorious for not noticing things. I have no attention to visual detail. I’m a tunnel-vision sort of person.

In Stanislas Dehaene’s Reading in the Brain he outlines a neuronal recycling hypothesis, which might explain my strange behavior. The gist is that there are regions of the brain which have been co-opted for reading. In particular, the letterbox region of the brain. It turns out that processing text is localized to a small zone of the left hemisphere, and damage to this area can have consequences for reading comprehension. In many ways the symptoms are similar to aphasia, but a tight analogy would be somewhat perplexing.* Language is a core human competency. Though it needs cultural and social input, it seems clear we have a built in facility toward it. Or at least that is the consensus among cognitive scientists. It has almost certainly been the target of natural selection.

The same can not be said for literacy, which is only 5,000 years old, and, whose widespread penetration among humans is only a feature of the last few hundred years. ~25 percent of the world’s population is still illiterate. In contrast, those who can not speak are considered to have some sort of pathology. How then can there be a region of the brain dedicated to text comprehension? Reading seems to leverage pattern recognition capabilities which have deep evolutionary roots, and those recognition capabilities are localized to particular regions of the brain. This localization occurs early in life, but is not hardwired, so very early damage can result in rerouting to other regions (also, slight differences cross-culturally in positioning can be explained as a function of the nature of letters and length of words).

Dehaene reports that this fact imposes constraints on the nature of symbols utilized in text. For example, letters exhibit a distribution of common to rare patterns which are similar to a sort of stimuli we would experience in nature. That is, particular letter forms are over-represented in all world writing form representations, and those forms correspond to the sort of patterns one sees in the natural environment. The similarities of distributions are curious especially in light of the fact that writing systems evolve over time to become more abstract and less concrete from more elaborate, often pictographic, forms. Convergence in phenomenon rooted in our cognitive architecture implies that there are genuine constraints and biases in the shape of our cultural expression.

51IgD1yKTiL._SY344_BO1,204,203,200_ Many of the reviewers of Reading in the Brain highlight that it is interminably technical across its many chapters. The author admits as much as he nears his conclusion and attempts an apologia for testing the reader’s patience. Certainly the repetitive survey of neuroanatomy, or the deep-dive into the cognitive neuroscience of symmetry, seemed a bit much for me as someone without a neuroscience background. But when he comes up for air it turns out that Dehaene’s ultimate goal is very ambitious: to explain the variation of culture as a function of cognitive neuroscience. To do this he refers to the large body of work produced by Dan Sperber, a cognitive anthropologist who argues that culture is an “epidemiology of representations.” It is basically an elaborated model of viral memes, where the cognitive landscape of our minds canalize cultural expression toward particular aesthetically appealing or functionally effective forms. For Dehaene reading, literacy, is a form of viral culture. It gives us pleasure (novels), and, it is functionally useful (accounting). Developed over the last several thousand years independently at least twice, and likely more than twice, it seems to be at an intersection of our facility for language, memory, and symbolic representation, which is naturally evoked out of the environment of complex societies. If we could create mentats we would. Their non-existence is a testament to the difficulties of such an enterprise. As it is, we’ll have to make do with reading, and the symbolic manipulation which reading allows. Culture then, is a finite set of phenomena which express novel syntheses of our cognitive capacities. Dehaene in particular emphasizes the role of the domain-general neocortex in threading together disparate domain-specific functions into cultural novelties (e.g., the visual recognition and language competencies necessary for reading).

51QrNyN0KzL._SY344_BO1,204,203,200_ Nestled between the abstruse cognitive neuroscience and speculative theorizing about the nature of culture Dehaene has some concrete suggestions on policy. Whole language learning is a travesty, and phonics are the way to go if you want to encourage early literacy. He seems frustrated that some teachers consider phonics “right-wing” and so favor whole language learning. The science says that whole language learning is by and large bunk, even if there are some techniques which are salvageable. Whole language learning shaves years off reading abilities according to Dehaene. Apparently it can take until adulthood for whole language learners to catch up with those who utilized phonics. In an area where policy is probably impotent, English speakers are at a major disadvantage to Italian or Finnish speakers because of irregular spelling (French is between the two groups). Absorption of complex literature is retarded among British and American students because more time in elementary school must be spent mastering the profusion of words (obviously Chinese readers have a similar issue with delayed reading of higher literature due to the cognitive overhead of written Chinese). Finally, though therapy and treatment can mitigate dyslexia, Reading in the Brain left me very happy that my daughter (who is now reading) does not exhibit this problem. It seems a major handicap.

Which brings me back to my anecdote about my personal ability to not “notice” things. I’ve been a big reader my whole life (you can see which books I remember reading at Good Reads). So I was naturally curious about the cognitive neuroscience of this phenomenon. One of the implications of Dehaene’s neuronal recycling hypothesis is that there is an opportunity cost to devoting one’s resources to reading comprehension. The area of the brain which becomes the letterbox region may very well be the area devoted to noticing subtle differences in one’s environment that make trackers among indigenous people seem preternatural in their aptitudes. The way some stems of leaves have become askew, for example, may be the root of many of the letters which we use to represent sounds. Perhaps then my lack of ability to “notice” small things in the world around me is inextricably linked to the fact that my life’s focus has been on text, more or less. It’s a trade-off that I’m happy with.

* Also, damage to the letterbox region can impair recognition of letters, while allowing for number recognition!

 
• Category: Science • Tags: Cognitive Science

Pluto_viewed_by_New_Horizons_1_July_2015 I was offline most of the past day or so with festivities, so I missed that New Horizons went offline yesterday (though they’re back in touch). Very excited about the Pluto mission. It’s not often that new science is immediately so viscerally accessible, but that’s the case with planetary science (obviously the public takes something different from this than the scientists, but same difference).

Does anyone know a good history of the revolutionary movements for independence in Latin America against the Spaniards? I realize I don’t know much about this beyond what I learned in high school. It’s easy to find books specifically about Spain, or portions of South America. But I’m talking about a broader survey.

The Nature paper on the costs of inbreeding is interesting. I’ve read it, and it makes sense. Basically everyone has a load of alleles which have deleterious fitness consequences when they are phenotypically expressed. Most of these are probably recessive in expression, as that way they can “hide” in the population’s gene pool in heterozygotes. When more closely related individuals have offspring, they’re more likely to have alleles which are identical, resulting in a homozygous state in offspring. Ergo, more expression of recessive traits, many of which are going to be bad.

Greece. And Steve Waldman on the culpability of European elites in the Greek situation.

A Planet Money episode, Why People Do Bad Things, reviews research that we are all susceptible to becoming party to fraud in the right context. That being said, I do think it is important to note that the main figure in the story, who was convinced by fraud, had a much older brother who was also convicted of fraud. Personalities are correlated, so it strikes me that there’s no surprise that fraud runs in families (Bernie Madoff’s father was involved in some shady dealings as well).

 
• Category: Miscellaneous • Tags: Open Thread

51VGBO04szL._SY344_BO1,204,203,200_ In the year 2000 I watched the film The Patriot. Some British observers protested that the depiction of frankly Nazi-like behavior by the redcoats in the film was total fiction. There are scenes in the film where slaves are promised freedom in the revolutionary cause. Even those with a cursory knowledge of history during this period know that that was a painfully ahistorical element of the plot (I vaguely recall a few people laughing at this part of the movie in the theater). Finally, the historical individual upon whom the protagonist was based was a nasty fellow.

There is a tendency to compress the past, and turn it all into a blurry equivalent haze. Consider the American Civil War next to the Revolutionary War. Though people of the North were no more angels than those of the South, it eventually came to be that the sectional chasms of the 1850s culminated in the Dred Scott v. Sandford decision, as well as a war in the service of a peculiar institution (do note, I accept the proposition that the upstream causes were structural-economic, even if their cultural manifestations were ideological; see Clash of Extremes: The Economic Origins of the Civil War). As I have noted, as a child who came to consciousness in Greater New England there was never any doubt as to who was on the “right” side in the Civil War. Looking back with hindsight it does seem to me that by and large the armies in blue singing “John Brown’s Body” are more prophetic of a modern outlook than those who fought for the Southern way of life.

OrnamentalismTo be unequivocal about the American Revolution is more difficult for me. Unlike the Lost Cause, Britain did not disappear. Britain is still here. In fact, for a century Britain and the United States of America have been fast friends on the international stage. In the game of “what-if” it is natural that one look to the course of events in the British Empire and consider if that was perhaps a road not taken that might have been a better one at that. Vox offers 3 reasons the American Revolution was a mistake. They are, in order:

- Abolition would have come faster without independence

- Independence was bad for Native Americans

- America would have a better system of government if we’d stuck with Britain

One can agree or disagree with these assertions. The first two do seem more probable than not, though I am not entirely confident. The last is a matter of some complexity which I will set to the side. The key concern that immediately crops up in my mind is that the retention of the thirteen settler colonies would have irrevocably altered the course of British history. History is made up of contingent events, even if there are broad trends, and the addition of the massive dominion of the American colonies, and their likely demographic arc toward parity with the metropole just across the Atlantic, would have changed British culture. As Kevin Philips observed in The Cousins’ Wars the independence of the American colonies and the demographic collapse of Ireland in the wake of the famine resulted in a British population stripped of a large number of dissenting Protestant elements as well as a huge Catholic minority. British national consciousness as an Anglican country was definitely enabled by the independence of the American colonies, which were strongholds for heterodox and dissenter factions.

9780199604548 There is also a line of economic determinism that argues that American secession from union with the metropole was inevitable. That is because of the distinctiveness of the American Northern economy as it progressed in the early 19th century, the conditions of which were already in place by the 18th. While dominions such as Canada and Australia, and the erstwhile Southern colonies and the non-white possessions, were geared toward producing raw inputs for British manufacturing (one reason that the British elite were pro-Southern in their sympathies for much of the Civil War), the North was almost certainly bound to become an industrial rival (this explains the fixation on tariff policy in American politics up until the middle of the 20th century). It is hard to imagine the existence of a Dominion dominated by groups with dissenting Protestant sympathies and economically ascendant in a manner which competes with England not being a major question in the 19th century in lieu of the American Revolution. It may be that many of the things distinctive in British history as opposed to American, and preferred by the sort of people who write at Vox, may not have occurred in the same way if America and Britain remained politically fused, due to greater cultural exchange.

51VLZmyVmRL._SY344_BO1,204,203,200_ Second, there is the likelihood that British elite culture would influence the United States. Within the American experiment there was pregnant a panoply of radicalisms, some of which were resisted by broad swaths of America itself. Britain has a hereditary aristocracy, and class has a particular valence in British culture which it does not in the United States of America. The economic realities of the frontier suggest to me that some of this is structural and not conditional. After all, Canada and Australia are less fixated on class than England. But, it seems that a tighter integration between British and American society could not but help dampen down the populism of American culture in its orientation. Additionally, a quick survey of the population statistics for Canada and Australia show that they are much more British in origin than the white population of the United States. The massive waves of German immigration to the United States may have been much more modest in an America under the Empire, and the Anglo-Saxon demographic character of much of the North would have been more thoroughly preserved (one can imagine knock-on effects, such as a larger wave of German migration to South America and Eastern Europe?)

Reflecting on history is important. And thought experiments, counter-intuitive, even shocking, are to be welcomed. Political correctness should be abhorred in intellectual discussion. But we live in the year 2015, and the past is the past. What has been done can not be undone. So tomorrow I’m going to celebrate the American Independence, because whether the omniscient scales of history judge the arc of utility positive or negative, without it we wouldn’t be who we are, and we can always make the future better no matter the substance of the past.

 
• Category: History, Ideology • Tags: History
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"