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

June 6, 2017

Origin of modern humanity pushed back 260,000 years BP (?)

Filed under: Ancient DNA,Genetics,Khosian,South Africa — Razib Khan @ 12:45 am


The above figure is from a preprint, Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. The title and abstract are pretty clear:

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|’hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) ‘hot spot’ for the evolution of our species.

These results in the outlines were actually presented at a conference. I saw it on Twitter and don’t remember which conference anymore. But this is not entirely surprising.

First, much respect to Mattias Jakobsson’s group for breaking through the Reich-Willerslev duopoly. Hopefully this presages some democratization of the ancient DNA field as expenses are going down.

Second, notice how in most cases ancient DNA shows that modern reference populations turn out to be admixed. This was the problem with much of Eurasia, and why using modern genetic variation to make inferences about the past totally failed.

I am entirely convinced that the genome from Ballito Bay dating to ~2,000 years does not carry the Eurasian inflected East African admixture. The Mota genome implies that Eurasian admixture did not come to eastern Africa much before 4,500 years ago. There needs to be a much deeper big picture analysis of the archaeology of Africa and the genetic information we have to get a sense of what happened back then…but, it seems likely that the Bantu migration has over-written much of the earlier genetic variation.

The fact that ancient genomes always show that our current populations are admixed makes me wonder if the Ballito Bay sample itself is admixed from more ancient populations. That is, if we found a genome from 20,000 years ago, would it be very different from the Ballito Bay samples? The relatively thick time transect from Europe indicates that turnover happens every 10,000 years or so. Australian Aborigines seem to have been resident in their current locations for ~50,000 years, but this seems the exception, not the rule. Do we really think that the ancestors of the Bushmen were living in southern Africa for five times as long as Australian Aborigines?

Another curious aspect of this paper is that it suggests the effective population size of Bushmen is smaller than we might have thought, and they’re somewhat less diverse than we’d thought. That’s because East African (with Eurasian ancestry) gene flow increased heterozygosity, as well as inferred effective population sizes. I’ve mentioned this effect on statistics before. Unless you have a true model of population history (or close to it) your assumptions might distort the numbers you get.

There is another aspect to this preprint mentioned glancingly in the text, and a bit more in the supplements: they seem to only be able to model Yoruba well if you assume that they themselves are a mix of “Basal Humans” (BH) and other African population which gave rise to East Africans and “Out of Africa” populations. Note that the BH seem to diverge from other human populations before the ancestors of Southern Africans like the Ballito Bay sample. That is, BH could push the diversification of the ancestors of modern humans considerably before 260,000 years before the present.

The possibility of deep structure in the Yoruba is pretty notable because they’ve been the gold standard in many human population genetic data sets as a reference population. But this is not result of deep structure is not entirely surprising. For years researchers have been hinting at confusing results in relation to the possibility of Eurasian back-migration. Perhaps the deep structure was confounding inferences?

The authors themselves are quite cautious about their dating of the divergence. It’s sensitive to many assumptions, and in particular the mutation rate being known and constant over time. But I think it’s hard to deny that this is pushing back the emergence of modern humans beyond what we know today. The earliest anatomically modern humans are found in Ethiopia 195,000 years ago from what I know. As I said, I’m convinced that the ancient genome has shown that modern “pristine” populations have some serious admixture. But I’m not as convinced about any specific point estimate, because that’s sensitive to a lot of assumptions which might not hold.

Finally, first a quick shout out to the blogger Dienekes. As early as ten years ago he anticipated the basic outlines of these sorts of results in the generality, if not the details. We really have come a long way from popular science declaring that all humans descend from a small group of East Africans who lived 50,000 to 100,000 years ago. The real picture was much more complex.

Also, I have to admit I considered titling this blogspot “Wolpoff’s revenge.” As in Milford Wolpoff. The reason being that we’re getting quite close to territory familiar to the much maligned multi-regionalist model of modern human origins.

Note: These findings should make us less surprised perhaps by a “modern” human migration before the primary one out of Africa.

St. Augustine knew of the Buddha!

Filed under: Culture,History,St. Augustine — Razib Khan @ 12:04 am

St. Augustine is a very influential figure in Western Christianity. Partly this is surely due to the fact that the Latin Church favored a doctor who was of their own cultural persuasion, schooled in their mores and folkways, as opposed to the ‘logic-choppers’ of the Greek world. In the intellectual Protestant tradition his influence on Martin Luther and John Calvin is well known.

But it was only recently that I realized St. Augustine may have been moderately familiar with the Dharmic tradition. If you recall, he was a Manichaean for some years in his youth. This religion of Persian provenance is relatively well known has having an expansive geographic reach. The last self-conscious Manichaeans probably lived in China in the years around 1500 AD. But in Late Antiquity Manichaeanism apparently had a presence in the Western Roman Empire.

In any case, though notionally a dualistic religion, Manichaeanism acknowledged a strong influence from the Dharmic tradition, in particular Buddhism. Buddha is explicitly mentioned in Manichaean texts, and noted as a one of the prophets. This is not surprising, as the religion emerged in a diverse and pluralistic Late Antique Persian Empire which ruled over many Buddhist and Hindu peoples on its northern and eastern fringes.

I am not claiming that Buddhism had any direct impact on St. Augustine. But simply putting this into the record to remind ourselves that the extent of what we know about the ancients is pretty limited.

June 5, 2017

The issue is how you experience Islam

Filed under: Islam,Religion — Razib Khan @ 12:44 pm

Sadiq Khan: This sickening act has nothing to do with the Islam I know: To murder innocent people, especially during Ramadan, is a rejection of the true values of my religion. Since religion is made up I’ll take Khan’s assertion at face value and not dispute them.

The aspect that people like Khan are not emphasizing when they talk about violence having nothing to do with Islam is that most people are not Muslims, and most people (in the West) do not know Muslims in their personal life. So terrorist acts are quite salient as a representation of the religion when that’s the only time it comes to mind in a visceral sense.

This may not be fair to practitioners, but this is how human cognition works. As an analogy, there is a lot of diversity and range of experience for what it means to be an evangelical white Protestant. But for many young secular liberals the salient aspect of this religious movement is its attitude toward abortion and gays. All the charitable giving, or the incredible personal experience of redemption and reform of white evangelical Protestants, is not relevant in a broader social context to most people because these are two policy positions which are salient and distinctive.

Obviously for most Muslims their religion pervades their life, and most of their associations with the religion have to do with family and community. But non-Muslims are not generally part of this world, so it is not a major element of their perception of the religion in a concrete sense. So one strategy for disassociating Islam and violence would be further integration, so that more and more non-Muslims can experience the whole range of the religion. And yet even here it isn’t as if Muslim experiences are distinctive from other religions.

This does not address the elephant: Islam today as a religious civilization is in ferment and change, and a non-trivial element does engage in violent habitually, against other Muslims as well as non-Muslims.

Consider the lives of Hindus and Christians in Pakistan. The majority of Pakistanis would not condone attacks upon these communities, but a motivated minority of the Muslim majority are clearly targeting this two groups for persecution. From the perspective of non-Muslims in Pakistan it is the actions of the minority who are violent toward them that really matters, because their lives are on the line.

There are so simple answers here. Though in the public realm stylized simplicity dominates. That too is a human cognitive bias….

A reply to a stupid, ignorant, or malicious commenter

Filed under: Comments — Razib Khan @ 11:39 am

A commenter below who probably scores OK on an IQ test left a note which is worth responding to.

First, “If this was a Christian or Muslim emigrant to US who wanted to marry within religion.” In the original post I focused on marrying within subcaste for a reason. It’s generally socially acceptable to marry within religion for ideological reasons in American society. I’m not talking about within-religion marriage because that’s considerably more exogamous than what Ravi Patel was talking about. So the whole thrust of this element of the response either consciously misreads (malicious) what I’m saying, or, does not read in the first place (stupid).

Also, this is Brown Pundits. I think a tendency for Hasidic Jewish sects to in-marry is not optimal for individuals or society…but this is not a blog focused on Judaism.

Next, “Two, you link jati affiliation to hindu-muslim violence.” No I don’t. Please note that I don’t like it when readers engage in “close reading.” Because that’s usually an excuse to impute. I do think that a certain sort of jati-based endogamy is part of a cultural context where communal violence has also emerged. Left-wing Indian American commenters bring up these connections, often obnoxiously in my opinion. But this film was aimed at non-South Asians. So I just wanted to bring up what the obnoxious Indian Lefty would bring up just so that the contrast between Ravi’s liberal West LA lifestyle with a very regressive set of values even in the modern Indian middle class milieu would be more stark (it actually makes the documentary more powerful).

Finally:

Finally, on Nicholas Dirks, he like others notices the standard story of jatis classifying into 4 varnas is not correct. He mentions local accounts which are very different. But this was noticed by colonial anthropologists in the 19th century itself. See quote by CF Margath on Page 39 here, https://www.academia.edu/25376339/The_Impossibility_of_Refuting_or_Confirming_the_Arguments_about_the_Caste_System ,

But instead of noticing that the current theory is wrong, and doesnt correspond to the phenomena on the ground, they come with notions like ‘Hinduism’ and ‘caste-system’ where constructed in the colonial era. The fact that many Indians repeat these ideas can be used to support that they were constructed in the 19th century. But mostly, this talk is incoherent. Most people are not able to name 4 varnas and are dimly aware of groups beyond their local region, but would repeat textbook, newspaper accounts which in turn is based on 19th century scholarship.

I read the Dirks’ book about 15 years ago. It is a good and persuasive book, and certainly many aspects are true. But the last 15 years of genetics and genomics has confirmed in fact that broadly speaking varna maps onto real patterns which are at least 2,000 years ago. That is, genetic affinities and relatedness exist on a spectrum that maps very well onto varna spectrum, beyond Brahmins and Dalits.

Priya Moorjani’s paper Genetic Evidence for Recent Population Mixture in India is probably the best single recent summary. Though please see The promise of disease gene discovery in South Asia.

Dirks’ work, and others who emphasize constructionism, capture elements of the truth (e.g., Bengali Kayastha genetic profiles [my maternal grandfather’s family background for what it’s worth] seem a lot like other non-Brahmin Bengalis I’ve seen, so the recent “elevation” of this caste is plausible). But taking it to heart totally misleads people have the depth and nature of caste and jati in the South Asian context.

If you’re not a geneticist you’ll probably not understand the papers above, which is fine. But don’t expect your ignorant comments to be posted on my threads.

Stupidity and ignorance are obviously forgivable sins. The latter is even fixable. But misreadings with the aim of bolstering a rhetorical position are really unforgivable, because they’re a waste of everyone’s time.

Open Thread, 06/05/2017

Filed under: Blog,Open Thread — Razib Khan @ 11:08 am

Just a plug for Elements of Evolutionary Genetics by Charlesworth & Charlesworth. These are two great evolutionary geneticists, and we’re lucky to have a “core dump” from them on hand.

The curious thing is that there is so much science that is tacit and implicit, that the passing of each generation of scholars means that hidden reaches of knowledge are passing away. This is the flip side of the idea of progress being made through the death of older scholars and the acceptance of novel (and more right) paradigms.

Both Charlesworths are authors on a new paper (along with Nick Barton) in The Proceedings of the Royal Society, The sources of adaptive variation. Here’s the abstract:

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today’s understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.

Another riposte to the EES. Entirely unsurprising that these authors and this venue would offer criticism to a reframing of the field of evolutionary biology. But it gets to the heart of the reality that this is going to be an argument that will be resolved through publication of new papers, not books or long popular science articles. The footprint of the EES in evolutionary biology popular science field is heavier than within evolutionary biology itself.

The prominent medical genomicist Dan MacArthur stated yesterday:

Not to be churlish, but let me clarify judging by the numbers of people Dan followed there were conservatives and libertarians he followed, he just didn’t, and doesn’t, know who they are. Also, there were several people he followed with center-right or libertarian views as a point of fact. I know because because I’m open about my right-wing views, and these people feel and felt comfortable telling me that they don’t agree with the vocal Left-liberalism which is pervasive in the political atmosphere on science twitter. Though most science twitter people don’t post much about politics, if they do, a substantial proportion are “social justice” oriented. That’s tolerable for most people because most scientists are on the Left side of the political spectrum.

My tendency to post right-wing political stuff into the feeds of scientists is annoying for many (or as some would say “problematic), but I don’t care. I know I speak for a substantial minority in the aggregate, and in some cases the majority (in terms of the latter, what I mean is that though most scientists are liberal, most are not on that far Left, though they may fear being attacked by the far Left and so are careful not to enter into any public dissent when that contingent starts to get a little out of control).

In a curious inversion with the norm I guess, my Twitter timeline is balanced politically. If anything, it’s more liberal than not. I don’t know what it would be to be in a political silo. I hear it feels good.

Detecting polygenic adaptation in admixture graphs. Educational attainment and unibrows. Yeah. One thing: “An open question in human evolution is the importance of polygenic adaptation.” This is literally true, but I think it is pretty obvious that the latest work is suggesting there has been a lot of it.

Widespread signatures of negative selection in the genetic architecture of human complex traits.

The Genomic Health Of Ancient Hominins.

June 2, 2017

The nadir of genetics in the Soviet Union

Filed under: Genetics,History — Razib Khan @ 8:05 pm

A fascinating excerpt in Slate from How to Tame a Fox (and Build a Dog), :

This skepticism of genetics all started when, in the mid-1920s, the Communist Party leadership elevated a number of uneducated men from the proletariat into positions of authority in the scientific community, as part of a program to glorify the average citizen after centuries of monarchy had perpetuated wide class divisions between the wealthy and the workers and peasants. Lysenko fit the bill perfectly, having been raised by peasant farmer parents in the Ukraine. He hadn’t learned to read until he was 13, and he had no university degree, having studied at what amounted to a gardening school, which awarded him a correspondence degree. The only training he had in crop-breeding was a brief course in cultivating sugar beets. In 1925, he landed a middle-level job at the Gandzha Plant Breeding Laboratory in Azerbaijan, where he worked on sowing peas. Lysenko convinced a Pravda reporter who was writing a puff piece about the wonders of peasant scientists that the yield from his pea crop was far above average and that his technique could help feed his starving country. In the glowing article the reporter claimed, “the barefoot professor Lysenko has followers … and the luminaries of agronomy visit … and gratefully shake his hand.” The article was pure fiction. But it propelled Lysenko to national attention, including that of Josef Stalin.

Sometimes it is easy to believe that the period in the Soviet Union under Stalin or in China under Mao or in Germany under Hitler, to name a few, were aberrations. But I think that’s the wrong way to look at it. The story of how Lysenko became influential hooks into so many historical tropes and psychological instincts of our species that we should be wary of it.

There have been great scholars without requisite qualifications. Ramanujan and Faraday come to mind. But great scholars are exceptional people. They are not average.

What determines the rate of evolution

Filed under: Evolution — Razib Khan @ 7:32 pm


The tweet above from Wiley relates to a paper, Polygamy slows down population divergence in shorebirds. It’s a cool paper. I tweeted it. But does it relate to the “rate of evolution”?

There’s no definitive answer to this question. Different people will have different answers, as it was evident on Twitter. For me my surprise was due to my definition for what evolution is: change is allele frequencies over time. This is far more fundamental than speciation. But then I don’t think much about speciation.

Some people brought up divergence. But divergence for me is not necessary, a population could remain unitary but exhibit large allele frequency changes. Then again, if you study phylogenetics on a macroevolutionary scale, as most people who study phylogenetics do, then you would focus on divergence.

Saving intellectuals from the red guards; it’s a mitzvah

Filed under: Brett Weinstein — David Hume @ 12:35 am

The Left is cannibalizing its own again. Unless you’re under a rock you have probably heard about what’s happened to Brett Weinstein. The Campus Mob Came for Me—and You, Professor, Could Be Next:

I was not expecting to hold my biology class in a public park last week. But then the chief of our college police department told me she could not protect me on campus. Protestors were searching cars for an unspecified individual—likely me—and her officers had been told to stand down, against her judgment, by the college president.

Racially charged, anarchic protests have engulfed Evergreen State College, a small, public liberal-arts institution where I have taught since 2003. In a widely disseminated video of the first recent protest on May 23, an angry mob of about 50 students disrupted my class, called me a racist, and demanded that I resign. My “racist” offense? I had challenged coercive segregation by race. Specifically, I had objected to a planned “Day of Absence” in which white people were asked to leave campus on April 12.

I am not too concerned about the details of what is happening in Olympia. Brett Weinstein is evincing surprise at the insanity of it all, but then he is a self-described progressive who assumes that the the Left is reasonable, and in some way on the “right side of history.” Weinstein is making reasoned arguments, and appealing to facts and evidence, and a general spirit of liberality. This is a recipe for failure.

None of the above has much sway with the loudest and most assertive elements of the campus activist Left. Mind you, these are not most students on campus, and these are not even most liberal and Left students. But they are loud, and they are frightening.

As expected there is a huge furor on right-leaning Twitter and right-wing publications about what is happening to Weinstein. In general the other side of the political spectrum has been muted in its response. Jerry Coyne has spoken up, but that is to be expected. Coyne has a paleoliberal sensibility out of step with the new order. The New York Times has finally weighed in with some broad liberal platitudes in regards to freedom of speech. Weinstein has been vocal about the fact that none of his colleagues have come to his defense.

But one tendency, including among some academics, is to wonder as to the support Brett Weinstein is getting. In particular, the right-wing is agitating against the students. And Weinstein’s brother, who has been vocal in his defense, is affiliated with Thiel Capital. As one scientist on Twitter said, that’s not a “good look.”

From the perspective of the person being attacked and character assassinated this must seem strange and rather shocking. When you are under attack you take the allies you can get. When people want you fired, and would be happy to drive your family into destitution, you take the help and support you can get. This is human nature. Instead of focusing on the injustice Weinstein claims he is suffering, his erstwhile allies on the political Left seem more worried about the people who are coming to Weinstein’s aid.

What if Brett Weinstein told the right-wing publications and Twitter accounts to stop defending him. Would the currently silent liberals and Leftists spring to take their spots? I doubt it. Basically what they are proposing is that Weinstein stand down with no defenses and if he does not, if he can not, he earns their contempt.

This is an opportunity for conservatism. Weinstein may not identify as a conservative today, but he will remember who showed him charity, who gave him a fair hearing, who came to his defense. Conservatism may gain more traction among intellectuals dealing with nihilist Left activists if it exhibits humanity and compassion, stances which are sometimes lacking in the swarming denunciations of the social justice contingent.

June 1, 2017

Poachers attacking rhinos in the developed world

Filed under: Environmentalism,Poachers — Razib Khan @ 6:44 pm

This is shocking. Poachers Kill Rhino in Brazen Attack at French Zoo:

On Tuesday morning keepers at Thoiry Zoo, in the suburbs west of Paris, found the body of Vince, a four-year-old white rhino, in his enclosure with wounds to his head and one of his horns likely hacked off by a chainsaw, the zoo said in a statement on its Facebook page. His second horn was partially cut off, suggesting that the culprits may have been interrupted or were using defective equipment after they killed the rare animal on Monday night.

The act was carried out “despite the presence of five members of the zoological staff living on site and surveillance cameras,” the zoo said. “The entire staff is extremely shocked.”

Tuesday’s gruesome event follows an attack on rhinos at an orphanage in South Africa, home to 70 percent of the remaining 21,000 white rhinos. Armed poachers broke into the Findimvelo Thula Thula Rhino Orphanage on February 22 and removed the horns of two 18-month-old rhinos, Impu and Gugu, after tying up staff members. One rhino was killed, and the other was later euthanized.

Romanticizing the regressive

Filed under: Film,Media,Meet the Patels,Ravi Patel — Razib Khan @ 4:47 pm

A few months ago I happened to watch the film Meet the Patels. Though you do meet all the “Patels”, the film centers around the love life, or lack thereof, of the actor Ravi PatelM.

Filmed by his sister, the documentary predates Patel’s current modest fame by many years (he has a small recurring role in Aziz Ansari’s Master of None). His life has changed in many ways, and perhaps his views and outlook have too. The comments I’m making in this post are not about Ravi Patel, but rather about the views he expressed many years ago in this documentary at a particular point in his life, and how it reflects a thread of South Asian American nostalgia and romanticism of our cultural roots.

Like many young Indian Americans Patel and his sister grew up between worlds. Their parents arrived in the United States among the very first wave of Indian immigrants, which today makes them somewhat unique, as there has been a huge migration since the 1990s from India due to the H1-B visa program. At one point the matriarch of the small American Patel clan bemoans how Americanized her children are compared to many other Indian Americans, who arrived later, when various South Asian American communities were more mature.

But Ravi and his sister are not entirely Americanized. Or they weren’t. Both avoided the conventional dating rituals of American life deep into their 20s, and as of filming Meet the Patels Ravi had had only one girlfriend, Audrey. Attractive, and depicted as level-headed and kind, on paper Audrey seems to have been the perfect girlfriend. But there was a major problem with her biodata: Audrey is a white American.

Eventually Ravi broke up with Audrey because of his confusions as to what he wanted in his life. Did he want what all his friends had? The American dream of love and marriage. Or, did he want what his parents had? An Indian arranged marriage.

But there is more to the Patels than just an Indian arranged marriage. Ravi Patel’s parents want him to marry someone from the same subcaste of Patels from the region of Gujarat that they come from. This is entirely typical of India culture. But it is rather peculiar in an American context. Though in some ways Ravi finds this all strange, some part of him also moots the idea that his parents have a comfort, a cultural identity, which he envies. At one point he goes back to Gujarat to a celebration of his people, his subcaste of Patels, and he looks around at wonderment at the safety and security of being among his people, his kith and kin.

As far back as Herodotus Indian society seems to have been characterized by caste. Genetically the castes, and more precisely jatis, are very distinct. And their persistence on the Indian scene suggest some level of functional utility.

Realistically Ravi could never recreate what he felt in Gujarat in the United States because such a community does not truly exist. Yes, there is kinship among Patels, as recounted by stories about Ravi and his family on the road, staying at Indian owned motels. But in the United States the Patels are a Diaspora, an archipelago of families scattered across the 50 states.

The romantic notions that Ravi airs in Meet the Patels about group solidarity, and cultural affinity of the sort his parents have, would seem creepy and disturbing if you posited in the context of an upper middle class WASP from New England. But the strong group cohesion evident among the Patels of Gujarat, and many Indian communities, also generates as a byproduct the sort of exclusion illustrated in the 1970 film Love Story.

And the exclusionary tendencies of middle class Gujaratis is reflected in part on the social-political nature of the state of Gujarat. It is in this state that the current prime minister, a tribune of lower middle class Hindu nationalism, grew up, and came to power. In it is in this state in the early 2000s that communal riots occurred, and accusations of organized genocide have been leveled.

The connections between liberal Democratic Indian Americans and right-wing Hindu nationalism in India have been extensively discussed. Meet the Patels is not a political film, it is a personal one. There is no reason that Ravi should address political topics in the documentary, and much of what I am saying here would be implicit to any South Asian watching Meet the Patels. But to many Americans these darker realities would not be visible or implied in the cultural practices which Ravi admires.

The attitudes expressed in Meet the Patels is no different from pining for the “good old days.” The reality is that the old days were often not so good. Or they weren’t how you remembered them. And just as some people pine for the days of yore, others romanticize the “homeland”, where everyone was your uncle and the aunties took care of you when your mother was a way. But this world is in many ways fundamentally regressive and constrained, and the benefits of communal responsibility are often correlated with inter-communal tension and conflict.

Again, there is no reason that Meet the Patels should have gone into this. But I wanted to put into the record what was unsaid so that those who see in it purely a charming inter-cultural story other dilemmas.

Related: Ravi’s AMA.

Beyond cholula, sriracha, and tabasco

Filed under: Hot Pepper,Hot Sauce,Rapture — Razib Khan @ 3:12 pm

In the United States it seems that the restaurant table top hot sauces are dominated by an oligopoly. Cholula, tabasco, and sriracha are ubiquitous. And there’s a reason for this: they are delicious. All of them have their own unique flavor profiles, as you no doubt know. But there is a whole world of hot sauce and spice beyond these three canonical flavorings.

Recently the Trinidad scorpion pepper Rapture was recommended to me by a friend, and I brought it in the office. Almost immediately it became “the” office hot sauce. It’s complex and delicious flavor, and the high spice content fueled by more than 15 peppers per bottle, have fueled an enthusiasm for hot sauces among my co-workers.

The moral of the story is that readers should explore the a bit more of the world of hot sauce taste than they do right now. Don’t limit yourself to the Pepsi, Coke, and Dr. Pepper of hot sauces.

May 30, 2017

The material over the ideological

Filed under: Economic History,Economics,History,Max Weber — Razib Khan @ 11:42 pm

I come not to praise or bury Max Weber. Rather, I come to commend where warranted, and dismiss where necessary.

The problem as I see it is that though a meticulous scholar, Max Weber is the father of erudite sophistry which passes as punditry. Though he was arguably a fox, his genealogy has given rise to many hedgehogs.

Weber is famous for his work on relating the Protestant ethic and capitalism (more precisely, Calvinism). In general I think Weber is less right than he is wrong on this issue. But the bigger problem is that Weber’s style of interpretative historical analysis also has spawned many inferior and positively muddled imitators, whether consciously or not.

To my mind the problems with Weber’s sweeping generalizations, interpretations, and inferences, are clearest on the topic of China. His assertions on the nature of the Chinese mind informed by Confucianism, and how it would relate to (and hinder) modern economic development are very hit or miss.

By the end of the 20th century things had changed in terms of the perception of how Confucianism might relate to capitalism. In the 1990s Paul Krugman famously argued that the East Asian economic miracle did not have to do with a particular model or cultural genius, but simply increases in capital investment and labor force participation (factor inputs). This was too stylized a fact. Though growth has slowed, I think it is undeniable that East Asian economic modernity is here to stay.

And some of that may be attributable to Confucianism in a distant causal sense, because the cultural sensibility does encourage the development of broad-based literacy through self-cultivation. In Strange Parallels Victor Lieberman notes the contrast between Vietnam, with its more Sinic cultural orientation, and the rest of Southeast Asia, with their Indic Theravada Buddhist cultures.

The Vietnamese elites’ orientation toward Confucianism meant that there was stratification in society, as there were constant upward and downward movements across class. The chasm between the Confucian literati and the peasantry was large. In contrast in Cambodia popular religion was relatively unifying due to its accessibility. But it is notable to me that Vietnam in particular is often perceived by those who travel in Southeast Asia to be an industrious and striving nation.

So yes, culture may matter. But simple economic forces, and material conditions, are incredibly important, and our understanding of their origins are more mysterious than we’d like to think.

This is on my mind because of the recent evidence of the power of the slave trade in the Islamic world. Islam gets a bad rap in relation to slavery. This is justified, as Muslim nations have been, and are, the most prominent perpetuators of institutional chattel slavery* in the modern and near-modern world. But it is also correct that in many ways de jure Islamic law gave slaves a degree of dignity and human rights which would not have been called for in Classical antiquity. Though the reality is slaves were often part of the Roman familia in many cases, ultimately they were still human tools, to be abused and disposed as one would domestic animals.

But the genetic data seem clear that African slavery increased greatly during the Islamic period, resulting in a much more human agony, as so many of the slaves died en route (males who were to be eunuchs had a high mortality rate as they had to be castrated before entering Muslim lands). This had nothing to do with the cruelty of Islam per se, but the overall development and advancement of the Eurasian oikoumene, and the role of African slave labor in its post 1000 A.D. economy.

In fact one might argue that the unity of the Islamic world, and its relatively uniform legal and cultural superstructure after the collapse of its political unity, was a factor in fostering the rise of the global slave trade. That is, Islam generated asabiya, social solidarity, within the group, but this ultimately was to the detriment of those who were outside of the group.

A similar story can be told about the New World slave trade. It flourished in the wake of the Reformation and the Renaissance, and just as European society was undergoing a cultural revolution which would usher in modernity. If one looked at the nature of European society in the 17th century, and its increasing moralism, and focus on personal piety, probity, and humanity, would we predict the expansion and scaling up of the European slave trade? No.

That dynamic was driven by economics (in the American case, the triangle trade).

Similarly, the mortality rates of slaves varied greatly by locale and the what they cultivated. The sugar islands were death traps. The rice farmers of coastal South Carolina lived relatively stable lives, even comparable to serfs. Those who grew tobacco were somewhere in the middle. All were under English jurisdiction. The mortality of Brazilian slaves was high, but nominally Roman Catholic jurisdictions were subject to more humanitarian codes. But the primary determinants of mortality, of humanity, were economic. Material, even if ideological variables had an impact on the margin (Rodney Stark has argued that the French legal system was more humanitarian in Louisiana, and one can see this in various vital statistics).

Obviously ideological and material forces interact and influence each other. My point here is to observe that too often public commentary gets caught up on the idea of the great idea driving history. But once we have some distance it is often obvious that on the proximate scale many of the patterns we see are constrained, driven, and conditioned, on material forces and parameters.

And yet ultimately those material forces through gains in productivity relax tight the pressures which constrain ideologically driven change and revolution. Slavery for example was long considered an institution that would always be with us in some form, but over the past few thousand years most societies have frowned upon it. Slave societies, whether ancient Roman or in the antebellum South, develop an unhealthy paranoia. With modern technologically driven economic growth the possibility of a post-slave economy seemed plausible, and opened the window for a practical abolition.

And here we are!

* I said “institutional chattel slavery” specifically to head off annoying nit-picking comments. Please don’t.

Ancient Egyptians: black or white?

Filed under: Egypt,Genetics,Historical Genetics,History — Razib Khan @ 9:20 pm

One of the most fascinating things about ancient Egypt is its continuity, and our granular and detailed knowledge of that continuity. We can thank in part the dry climate, as well as the Egyptian penchant for putting their hieroglyphs on walls and monuments (as well as graffiti!). And we can also thank the fact that both the ancient Greeks and Hebrews, Athens and Jerusalem so to speak, were deeply connected to and perceived themselves to be indebted to Egyptian civilization. Even before the translation of the Rosetta Stone and the deciphering of ancient Egyptian writing the Hebrews’ interactions with Egyptians, in particular in Exodus, mean that their memory would echo down through the millennia (the newly Christianized Irish interpolated Egyptian ancestry into their own genealogy).

The Greek relationship with Egypt was less fraught and at greater remove than the Hebrews. But the Classical period philosophers correctly perceived that Egyptian civilization was ancient, and preceded their own. Aegean-Egyptian connections were actually more longstanding than the Classical scholars knew, in Brotherhood of Kings: How International Relations Shaped the Ancient Near East, the correspondence in state archives which have been retrieved are rather clear that Minoan civilization was part of the orbit of Egypt early on. Though Egyptians never conquered the Aegean polities, mercantile and diplomatic connections were extremely old and persistent. The late Bronze Age eruption of barbarian Sea Peoples who attacked the whole civilized Near East may have been facilitated in part by the broad familiarity engendered by widespread trade networks.

The most recent book devoted to ancient Egypt I have read was Toby Wilkinson’s The Rise and Fall of Ancient Egypt. Synthesizing extensive written material with archaeology, perhaps the most impactful argument in Wikinson’s narrative was the persistence of the temple based institutions from the Old Kingdom down to the Ptolemaic era. Religious institutions carried on even with the shocks of Nubian and Libyan conquest in the post-New Kingdom period, down to Late Antiquity. The temple at Philae in southern Egypt was an active center of the traditional religion, and therefore the culture which dates to the Old Kingdom in continuous form, down to the 6th century A.D. (when it was closed by Justinian in his kulturkampf against ancient heterodoxies).

For various ideological reasons though many people are very curious about the racial characteristics of the ancient Egyptians. There are two basic extreme positions, Afrocentrists and Eurocentrists. Though I have not done a deep dive of the literature of either group, I’ve read a few books from either camp over my lifetime. In fact I believe the last time I read the “primary literature” of Afrocentrist and Eurocentrism was when I was an early teen, and it was rather strange because both groups seem to be recapitulating racial disagreements and viewpoints relevant to the American context, and projecting them back to the ancient world.

In college I stumbled upon Mary Lefkowitz’s Not Out Of Africa, a book length argument against the more sophisticated Afrocentrist views articulated in the wake of Martin Bernal’s Black Athena: The Afroasiatic Roots of Classical Civilization. Lefkowitz was a classicist, so many of her objections were exceedingly scholarly. The reality is that the best refutation of an Afrocentrist view of of ancient Egypt, which reduces to the idea that ancient Egyptians would be recognizably black African today, are the Fayum portraits. It is notable to me how similar these portraits are to modern Copts. In fact the actor Rami Malek, of Coptic background, looks strikingly like someone who stepped out of the Fayum portraits.

I have read no book length refutation of the Eurocentrist, usually Nordicist, perspective. Mostly because this is a view associated with white supremacism, and that ideology is generally attacked on normative, not positive, grounds. But the visible evidence of the Fayum portraits is a strong refutation of the Nordic model. Of course, there is the reality that we now know that the Nordic phenotype, and the genetic components which congealed into that typical of Northern Europe today, was only coming into existence when the Old Kingdom of Egypt was already a mature civilization.

Of course both Afrocentrists and Eurocentrists will reject the evidence of the Fayum portraits became they came from the Roman era, and they would argue that the demographic nature of Egyptians changed quite a bit between that period and the end of the New Kingdom. And they are not incorrect that the period between the arrival of the Romans and the fall of the New Kingdom was characterized by a great deal of change. There were Libyan dynasties, Nubian dynasties, and periods of rule by Assyrians, Persians, and Macedonians. Large colonies of Greeks, Macedonians, and Hebrews-becoming-Jews were also resident in Egypt. Especially, but not limited to, the urban areas.

But now we have ancient DNA! Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods:

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Because modern people care about the Afrocentrist question, the extent of Sub-Saharan African ancestry is highlighted in this paper. I do not think this is actually the most interesting aspect. But I’ll get to that. Since this post will be read by a fair number of people I’ll talk about the relationship of ancient and modern Egyptians to (Northern) Europeans and Sub-Saharan Africans.

The figure to the left is looking at 90 ancient Egyptian mitochondrial genomes (and some modern ones in the two rightmost columns). Since mtDNA is copious it was relatively easy to extract and analyze.  Haplogroup L, the red to orange shades in the bar plots, are associated without dispute with Sub-Saharan Africa. Haplogroup U6, M1 and a few others may be “back to Africa” variants of different periods (they are generally found in Afro-Asiatic groups).

What you can see is that somewhat more than half of Ethiopia’s mtDNA lineages are L, in keeping with the whole genome estimate of Sub-Saharan African ancestry in most Cushitic populations. In Egypt there is a difference over time; haplogroup L goes from low frequencies to much higher frequencies in modern periods. The ~20% fraction in the modern samples is in line with the population wide admixture one sees in modern Egyptians of Sub-Saharan admixture.

I actually recomputed the haplogroups to a finer granularity from the supplements for readers who know this stuff well. Here they are:

 

Haplogroup Count
H 2
H13c1 2
H5 2
H6b 2
HV 3
HV1a’b’c 4
HV1a2a 3
HV1b2 2
HV21 2
I 5
J1d 2
J2a1a1 2
J2a2b 2
J2a2c 4
J2a2e 3
K 16T 2
K1a 2
K1a4 2
L3 2
M1a1 4
M1a1e 2
M1a1i 2
M1a2a 2
N 2
N1’5 2
N1a1a2 2
R 3
R0 2
R0a 2
R0a1 2
R0a1a 3
R0a2 3
R0a2f 2
R2’JT 2
T 3
T1a 3
T1a2 2
T1a5 4
T1a7 7
T1a8a 2
T2 3
T2c1 2
T2c1c 2
T2e 2
U 2
U1a1 2
U1a1a3 2
U3b 3
U5a 2
U6a 2
U6a2 2
U6a3 2
U7 4
U8b1a1 3
U8b1b1 2
W3a1 2
W6 2
W8 2
X 2
X1 2
X1c 2

A quick inspection of mtDNA haplogroup frequencies shows that ancient Egyptians are not typical of modern Europeans. Not that much H, and lots of T, J and K. What that does remind me of are Early European Farmers. These people, who brought agriculture to Europe from Anatolia contributed a large fraction of the ancestry of modern Southern Europeans, and a lesser component to Northern Europeans.

But ultimately what’s great about this paper is that they have ancient autosomal DNA. That is, genome-wide results.

They got three samples of reasonably high quality. More precisely: “Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs.”

You can see the three samples on this bar plot. What is interesting is that they’re all pretty similar.

What you can see here is that to a great extent ancient Egyptians were descended from a population closely related to Natufians, or Natufians themselves. This easily explains the mtDNA affinity to Neolithic farmers: Natufians and Anatolian Neolithic populations were sister populations. The f3 statistic which looks at shared drift shows an affinity of ancient Egyptians with ancient farmer populations with Near Eastern provenance, but also with modern Sardinians. This is a common pattern, as ancient groups do not have later migration waves, with the Sardinians the modern population closest to this.

You see in the bar plot that northern Levantine populations are placed between Anatolian Neolithics and Natufians, as one might expect based on their geographical position and gene flow between these two regions. Additionally, the cyan color is associated with eastern farmers from the Zagros. I’ve already talked about gene flow from this area to the Levant recently. If you compare the Bronze Age Sidon samples I think you’ll see broad affinities with these Late Period Egyptians.

The PCA gives us results consonant with the model-based clustering. If you plot the genetic variation of ancient Egyptians they’re closest to Neolithic eastern Mediterranean populations. No great surprise.

Not the modern Egyptians. Why? It’s pretty clearly because modern Egyptians are shifted toward Sub-Saharan Africans. But there is also another component: modern Egyptians have more of the cyan eastern farmer component. What could this be?

An immediate thought comes to mind. We focus a great deal on Sub-Saharan African slavery. One reason is that it is visible. Black Africans are physically distinct from most Middle Eastern populations. But Egypt was long the center of another slave trade: “white slaves” from the Caucasus. Circassians. For hundreds of years Mamluks were recruited from the Caucasus as military slaves. They eventually became the ruling class of Egypt, until their decimation in the 19th century under Muhammad Ali (who himself was an Albanian Ottoman who never learned to speak Arabic well).

As noted in the paper earlier work looking at patterns in ancestry tracts and LD decay had made it obvious that much of the admixture of Sub-Saharan ancestry in Egypt, as in much of the Middle East, is relatively recent. In particular, it dates to the Islamic period, when trade and conquest took on new dimensions in Africa and north into Central Asia. One way ethnic minorities like Assyrians and Lebanese Christians differ from their Muslim neighbors is that they have much lower fractions of Sub-Saharan African ancestry, and no East Asian component. The latter might surprise, but remember that Central Asian Turkic slaves have been prominent in Muslim armies since at least the 9th century.

But some of the Sub-Saharan ancestry in Egyptians is old. The ancient Egyptian samples have it. To have none of it would seem strange, considering the history of contact between Nubia and Egypt, dating back to the Old Kingdom. Second, there is evidence of low levels of Sub-Saharan African gene flow into Southern Europeans. How did that happen? The highest fractions are in Spain, and can there be attributed to the Moorish period. But that explanation does not hold in much of Italy, where there are a few percent of haplogroup L. This probably is due to south-to-north gene flow across the Mediterranean during the Classical period. Some of the peoples on the south shore of the Mediterranean almost certainly already had some Sub-Saharan African admixture.

Not getting into the details of it, there are ways to explicitly model gene flow into a target population from donors defined by a phylogeny. In this case the authors tested various models of gene flow from Sub-Saharan Africans and Eurasians (non-Africans) to generate allele frequency patterns we see in modern Egyptians and ancient Egyptians.

What they consistently found is that modern Egyptians are about twice as much Sub-Saharan African as ancient Egyptians. The proportions for modern Egyptians ranged from ~10 to ~20 percent Sub-Saharan African against a Eurasian background, with a bias toward the higher values (depending on which populations you put into the phylogeny for non-Africans), and ~0 to ~10 percent for the ancient Egyptians, again with a bias toward the higher values. The pattern is consistent in these tests.

An issue here is that we’re going off three samples. That being said, the authors observe that despite differences in contamination/quality and time period they’re very concordant with each other. If I had to bet I think Old Kingdom samples would have somewhat less Sub-Saharan and eastern farmer ancestry. But the basic pattern persisted down to the Roman period, and was only shifted by admixture due to slavery.

And not to belabor the point, but a paper from a few years ago which had some Copt samples looks familiar in its broad outlines. You see that the Copts have very little Sub-Saharan African ancestry, though it does seem to be evident (the marker set is in the hundreds of thousands of SNPs). Additionally, they are quite distinct from the Qatari Arab sample.

Unfortunately the data for this paper just published is not on the European Nucleotide Archive. I really want to dig a little deeper into it.

What are the takeaways here? Egypt has been the sink for a lot of migration and gene flow over the past several thousand years, and probably earlier. Not surprising considering that it was relatively wealthy in the aggregate. The Natufian population that the Late Period Egyptians resemble the most did not have Sub-Saharan African ancestry according to earlier research. These Late Period Egyptians do have some. This is reasonable in light of the long interaction with Nubia which is historically attested. Similarly, there was clearly gene flow from Southwest Asia. This is again historically attested, especially in the Nile Delta (though foreign garrisons of mercenaries are recorded in Upper Egypt as well).

The Roman period probably did introduce some gene flow from Southeast Europe and Southwest Asia. But these populations are not that distinct from Egyptians.

Similarly, the Islamic period also brought in different peoples from Arabia and the Caucasus. But the most salient dynamic during the Islamic period was a massive trans-Saharan slave trade (though the Caucasus impact may have been comparable, and I think these results support the proposition that it was).

It seems entirely likely that the Copts are descended from a mix of Roman era Egyptians. Not only do they resemble the people in the Fayum portraits, but the circumstantial genetic data is that they have fewer “exotic” components which increased in frequency during the Islamic era. This would be exactly parallel to ethno-religious minorities in the Levant and Iraq.

One curious element to me is the suggestion gene flow before ~5,000 BCE between Sub-Saharan Africa and the lower Nile valley was low. If it hadn’t been low, it seems unlikely that the fraction of Sub-Saharan ancestry (or shift in that direction in relation to other Eurasians) in Copts would be so small.

So what explains the lack of earlier gene flow? I think the answer is going to be the fact that the human demographic landscape is characterized by lots of local population extinctions. As ancient DNA sampling coverage gets better and better meta-population dynamics are coming into focus, and we see gene flow, and die offs, in several areas. It is fashionable to say that human population variation is characterized by clines. But much of this clinal aspect is an outcome of the period after massive admixture over the last ~10,000 years.

And yet it may not be that the period before the Holocene was not clinal. Rather, it may be that large depopulations of areas of human occupation fragmented clinal ranges, and resulted in new range expansions from “core” zones.

About ~8,000 years ago there was a major desertification period in the Sahara desert. Many trans-Saharan populations may have gone extinct during this time due to rapid climate change. Eventually repopulation may have occurred from outside of the Sahara, so that post-Natufian Levantines and Sub-Saharan Africans from what today call the Sahel pushed up and down the Nile drainage basic respectively, meeting in the zone of Nubia on the boundary of history and prehistory.

Unlike many other areas of the world we have a long attested record of Egyptian history. As we get more mummy samples it seems likely that we’re get a crisper, clearer, picture. And the time transects will not be narrative blind; we already know the general arc of Egyptian history. If, for example, we see a new ancestral component around ~1500 B.C., in Egypt it’s not mysterious what this might be: the Hyksos.

This is just the prologue to a fascinating book that will be written over the next decade.

Related: Blog post analyzing one Copt’s results suggests that Sub-Saharan admixture is more like Dinka than Yoruba (in contrast, Muslim Egyptians have a mix of both, the latter probably coming during the Islamic slave trade, while the former is probably ancient admixture).

Citation: Schuenemann, V. J. et al. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8, 15694 doi: 10.1038/ncomms15694 (2017).

May 29, 2017

Open Thread, 5/29/2017

Filed under: Open Thread — Razib Khan @ 11:45 am


The above talk from David Reich is very good. Highly recommended.

Chris Wickham’s Medieval Europe is pretty good, though it is very similar to his The Inheritance of Rome and Framing the Early Middle Ages.

Rod Dreher finds out it is highly like he has some African ancestry from a slave ancestor. This seems to be detected in 1 out of 10 whites using reasonable thresholds. Probably that that means that genealogically much more than 10% of Louisiana whites have lines of descent from people who were mixed-race slaves (though in French areas it might be mediated often by mixing with “free people of color”).

May 28, 2017

Bitter Libyan Fruit

Filed under: International Affairs,Libya — Razib Khan @ 11:35 am

In Mary Beard’s excellent SPQR: A History of Ancient Rome she describes an “empire of obedience” that emerged in the 2nd and 1st centuries BC. This refers to the often ad hoc arrangements of Roman rule and hegemony which preceded the explicit imperial period, when domination was bureaucratized and formalized.

Sometimes it seems that the United States is an empire of obedience, though we do operate through formal institutions such as NATO and the IMF. There’s an ad hoc schizophrenic aspect to it all.

In Across The Chasm Of Incommensurability many of the commenters seem to be focusing Chinese susceptibility to government propaganda. But my post was in large part pointing to the fact that Americans themselves are often blinkered and biased, though we often exhibit a conceit of all knowing objectivity.

On Twitter I said the following:

People immediately thought I was alluding to the Manchester bomber. Actually I wasn’t. I was thinking about the Copts killed in Egypt (including children) by ISIS-affiliated militants with basis in Libya.

This is not a one off. Since the overthrow of the Gaddafi regime Libya has been an incubator for terrorism. Its current political landscape is anarchic, with rival militias jockeying for power. Libya happens to be right next to the most populous Arab nation. This is not a good recipe for stability in the region.

Some commentators, such as Daniel Larison, have been arguing against the intervention since the get-go. But in general the media seems to have taken a policy of benign neglect toward what’s going on within Libya.

The Western powers take it upon themselves protect the people from their own governments. This is fair enough. But what Iraq showed us is that not all peoples are ready to be Jeffersonian Democrats. This is a fact.

The Roman “empire of obedience” gave way to one of direct rule. That was the only way to keep the chaos in check. Imperialism and colonialism are not fashionable today, but if Western governments keep intervening that seems the only way to keep the chaos at bay.

May 26, 2017

The Canaanites walk among us: ancient DNA edition

Filed under: Ancient DNA,Bronze Age,History — Razib Khan @ 2:09 pm

Ancient DNA from here to there:

Ancient DNA has illuminated many things, but there is a logic as to what topics and questions it tackles. The focus on northern Eurasia is clearly a function of the probability of preservation, though techniques of extraction are getting better and better. I can’t imagine how we’d ever get a sample out of a moist tropical environment, but I won’t be surprised if something is obtained from a cave in southern Africa or high in the Tibesti in the near future.

But another parameter is time since the demographic events in question. Too ancient, and the probability of success is too low(ok, time is a parameter in much of science!). It seems plausible that in idealized circumstances we’re going to push beyond the one million year barrier. And yet too recent is also a problem (or not a problem!). For humans and even non-humans we have lots of corroboration about questions we might ask about the recent past. You could use “ancient DNA” to trace the migration of Mormons across the Intermontane West, but why would you?

So you see the earliest ancient DNA work on humans was biased toward testing models about gene flow and ancestry tens of thousands of years in the past, between modern humans and archaic lineages. Obviously we don’t have oral history or written texts from this period, and archaeology will only get us so far.

More recently the time depth has been getting shallower and shallower. Both David Reich and Eske Willerslev’s work on European prehistory is liminally historical. By this, I mean that what is prehistory in Europe is a historical period in the Near East. We may not have written records from the Corded Ware or Bell Beaker cultures, but we do have plenty of them from contemporaneous Near Eastern groups.

The Cauldron of Peoples:

There are still questions to be asked about European prehistory, but the gaps are getting narrower and narrower. Scholars are finally devoting resources to other regions of the world. Last year Iosif Lazaridis’ The genetic structure of the world’s first farmers finally opened up the box that was the prehistory of the Near East. This was important, because much of prehistory and history began in the Near East. Farmers from this region seem to have moved into Europe, South Asia, Central Eurasia, and Africa. To understand the population histories of these areas one needs to understand the population history of the Near East.

What Lazaridis et al. found this that there were at least two major groups of very genetically distinct Near Eastern farmers at the dawn of agriculture. Once group faced the eastern Mediterranean, while the other seems to have flourished on the slopes of the Zagros. Western and eastern farmers respectively. It is important to note that these two groups were very genetically distinct. If we sampled these two groups of farmers, who faced each other across northern Mesopotamia, in any modern population survey we’d assume that the genetic distance meant that they were sampled from different continents or very distant regions of Eurasia.

This finding suggest that the clinal patterns of variation in much of today’s world may be a consequence of massive population admixture between groups which had heretofore exhibited deep population structure. Why such deep structure existed and persisted is an interesting question, but at this point it is important to note descriptively that the past 10,000 years have seen a massive reduction of this structure due to gene flow between populations.

In the Near East Lazaridis et al. found that there was significant reciprocal gene flow between the western and eastern regions of the Near East after the emergence of farming, down to the historical period. This is one reason that estimates of “farmer” ancestry in modern Europeans always gave very low estimates: the reference populations no longer existed in unmixed form in the Near East. The peoples who brought agriculture to Southern Europe were related exclusively to the western farmers of the Near East, a population which no longer exists in unmixed form in that region of the world (ergo, among modern groups Sardinians are the closest proxies we have).

The Age of Bronze:

But there is much that occurred after prehistory in the Near East. We know this because we have extensive records going back 4,500 years, and even earlier. And though put into written form in the first millennium before Christ, the Hebrew Bible also records the deeds and names of people who have come and gone well before the Classical Age.

A new preprint on biorxiv sheds some light on a critical transitory period, Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences:

The Canaanites inhabited the Levant region during the Bronze Age and established a culture which became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole-genomes from ~3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalogue modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with massive population movements in the mid-Holocene triggered by aridification ~4,200 years ago. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations such as the Persians and Macedonians.

The period between 1700 and 1800 BCE in the Near East saw many changes and was a sort of nexus. Sumer had fallen, the Hittites had not emerged as a superpower, while Egypt was not heavily involve in the game of kings as of yet. The system of international relationships described in Brotherhood of Kings had not crystallized. That was for the late Bronze Age.

But some of the pieces we were to recognize were already in place. An Amorite Babylon under Hammurabi established the contours of the culture and polity we’d recognize down to the Persian conquest. In Egypt the Middle Kingdom was going into decline, and the Hyksos interregnum would give rise to the New Kingdom, which would become a major player in the Levant (and probably is the model for much of the Egypt we see described in the Bible).

The admixture plot above reflects the five individuals from Sidon dating to about ~1750 BCE. They are about a 50:50 mix of western and eastern farmer. Though they seem to be genetically rather similar to modern Lebanese (the authors sampled Lebanese Christians in particular), there have been some changes between the Bronze Age and the modern period. In particular, a genetic component that seems to be related to the Eurasian steppe is present in modern Lebanese. Explicit admixture estimates give a range of 5-10% mixing into a ~90-95% Bronze Age ancestral background.

This seems to establish basic continuity between the Bronze Age and the modern period. Totally unsurprising. Remember that Italy exhibits deep population structure that dates back to at least 2,000 years ago, and probably earlier. It is likely that much of the same applies to the Near East. Though looking at Muslim populations one can see minor and non-trivial contributions of populations which moved in after Islam (Sub-Saharan and East Asia segments are clear signs of slavery impacting Muslims that would not apply to ethno-religious minorities), most of the ancestry broadly is deeply rooted back to antiquity.

Because of sampling issues one can’t estimate admixture between eastern and western farmers just from looking at ancient DNA transects. We don’t have the density that we have in Europe (yet). So the authors used a more classic inference technique looking at decays of linkage disequilibrium in the genome. In short you can see how many generations that a pulse admixture between two populations occurred by looking at correlations of variants across the genome. The authors arrive at the intervals above, and in particular focus on the period that seems to overlap with the rise and fall of the empire of Sargon of Akkad and correlated with a climatic disruption.

I suspect they are wrong here. First, it seems pretty clear to me that LD based admixtures assuming a pulse event have a bias toward underestimating values. There are theoretical reasons for this. So usually I pad the mid-point value across the interval on these estimates.

One thing that ancient DNA has told us is that often the less complex the society, the more demographic turnover you have. All things equal then we would expect turnover to be an older event, as simple societies are succeeded by complex ones. The succession of complex societies by other complex societies is often less disruptive for the masses because this transformation is more a matter of elite replacement.

By ~2200 BCE the Near East was already quite complex. I believe that the massive western-eastern farmer admixture occurred between 3600 and 3100 BCE, during the Uruk Expansion. The evidence of lower Mesopotamian influence and demographic settlement in places as far afield as Anatolia, the Caucasus, and Syria, are well attested from the archaeology of this period. This was was a time when a very complex and sophisticated civilization emerged almost de novo across much of the Near East. I believe that a prehistoric expansion of Sumerian civilization mediated the merging of eastern and western farmers, though some of the mixing pre-dates and post-dates the Uruk Expansion and collapse (e.g., the movement of western farmer ancestry into Mesopotamia seems certain to have occurred through the arrival of groups like the Amorites).

Additionally, buried in this preprint is evidence of major Y chromosomal turnover. We’ve seen this  before. The prominence of haplogroup J in Bronze Age and modern Levantines seems to be due to eastern farmer migration. In fact, adding haplogroup J and R together we get the inference that more than half the paternal lineages of Lebanese today are not from western farmers native to the area.

Beyond the Bronze Age:

What about the second ancestral component? Drilling down on the Y chromosomes of the Levant, R1b seems to far outnumber R1a, though the R1a clades are all of the Asian/Scythian Z-93 branch which is dominant in Central Asia and the Levant. The R1a may have come with the Persians, but in region of the western Levant for several hundred years after the period of the Bronze Age Sidon samples there was a state, the Mitanni, which clearly had an Indo-Aryan ruling class.

An Aegean influence occurred multiple times. First, at the end of the Bronze Age many of the “Sea Peoples” were clearly of Aegean origin, and so may have brought steppe-like ancestry. Second, there was the long period under Hellenistic and Roman rule, when Greek and non-Greek ethnic identity existed side by side, and movement occurred in both directions. I think only ancient DNA will answer this question, and it may be that there were multiple post-Bronze Age inputs of genes which shaped modern Levantines.

After Babel:

The curious thing that many of these studies are telling us is two-fold:

  1. Most of the population genetic structure we see around us dates to the Bronze Age, on the borderlands between history and prehistory. I think we can start to set this as a strong prior. It holds true for the Near East, Africa, South Asia, Japan and Southeast Asia. We’ll see about core East Asia, but I think probably it is true there too.
  2. Selection has continued, so that alleles for lactose tolerance and lighter skin have changed in frequency even since that period. The derived allele for SLC45A2 is found at about 2/3 frequency in modern Lebanon, but was absent in these five Sidonians. Though the sample size is small, this was somewhat surprising, and suggests that they were a swarthier people than modern Lebanese.

Addendum: I have said little here about Afro-Asiatic languages, as I don’t know enough about this topic.

May 25, 2017

Why many academic departments should be replaced with “think tanks”

Filed under: academia — Razib Khan @ 3:56 pm

Glenn Loury has an important essay up on his website, Self-Censorship in Public Discourse: A Theory of “Political Correctness” and Related Phenomena”. A classic “read the whole thing.” But I want to highlight one section:

Sociologist James Coleman, perhaps the world’s leading scholar of educational policy, recalls that in 1976 the president and a number of prominent memembers of the American Sociological Association (ASA) tried to have him censured for the “crime” of discovering, and announcing, that citywide busing for school desegregation purposes caused White flight. This claim had been denied for years prior to Coleman’s research, and far reaching social policies had been erected on the presumption that it was not true.

40 years later the same attitude is prevalent in much of sociology and has spread to anthropology and other fields. The reality is that the idea of objective scholarship is an illusion. We all know that “think tanks” exist to promote certain ideas and viewpoints, often due to funding strings attached. I know of people who have changed their views, and so have had to change their affiliation (or, simply not published in areas that they knew would not be well received by their institution).

Academia, with the freedom of tenure should be different. But it’s not. The reason it’s not is that it is a social enterprise, and the esteem of one’s colleagues is more important than the abstract idea of freedom to explore what you want. There are strong incentives in many disciplines to toe a particular line, and humans are conformists and they do as they’re expected to.

If all debates come down to politics and power, then putting them in the domain of think tanks makes it more honest and clean.

At an inflection point of archaeology and genetics

Filed under: Genetics,History — Razib Khan @ 1:54 pm

People always ask me what to read in relation to the field of historical population genetics. In the 2000s there were a series of books which focused on the mtDNA and Y results from modern phylogeographic analysis. Journey of Man, Seven Daughters of Eve, The Real Eve, and Mapping Human History. But there hasn’t been much equivalent in the 2010s.

Why? I think part of the issue is that the rate of change has been so fast that scholars and journalists haven’t been able to keep up. And, the change is happening right now, so it would likely mean that any book written over a year would be moderately out of date by publication.

I noticed today that Jean Manco has an updated and revised version of her book, Ancestral Journeys: The Peopling of Europe from the First Venturers to the Vikings. This was needed, because the original book was written before some major recent findings, though after some preliminary ones. As Manco has observed herself it was feasible to replace speculations with facts.

Since it seems likely that George R. R. Martin’s next book will be published before David Reich’s, I think that’s all you got. Any suggestions would be welcome.

As for the flip side for history that might be useful to understanding the genetics results, J. M. Roberts The History of the World is the best cliff notes I can think of. It’s obviously a high level survey, but frankly that would improve the interpretation I see in some papers. The fact that much of the history has no contemporary relevance is pretty unimportant, since you want to focus on the older stuff, which is where ancient DNA really shows its metal.

At some point ancient DNA will start to exhibit diminishing returns. Then the long hard slog of interpretation and synthesis will have to begin in earnest.

May 24, 2017

Across the chasm of Incommensurability

Filed under: China,Epistemology,India — Razib Khan @ 11:23 am

The Washington Post has a piece typical of its genre, A Chinese student praised the ‘fresh air of free speech’ at a U.S. college. Then came the backlash. It’s the standard story; a student from China with somewhat heterodox thoughts and sympathies with some Western ideologies and mores expresses those views freely in the West, and social media backlash makes them walk it back. We all know that the walk back is insincere and coerced, but that’s the point: to maintain the norm of not criticizing the motherland abroad. The truth of the matter of how you really feel is secondary.

Tacit in these stories is that of course freedom of speech and democracy are good. And, there is a bit of confusion that even government manipulation aside, some of the backlash from mainland Chinese seems to be sincere. After all, how could “the people” not defend freedom of speech and democracy?

Reading this story now I remember what an academic and friend (well, ex-friend, we’re out of touch) explained years ago in relation to what you say and public speech: one can’t judge speech by what you intend and what you say in a descriptive sense, but you also have to consider how others take what you say and how it impacts them. In other words, intersubjectivity is paramount, and the object or phenomenon “out there” is often besides the point.

At the time I dismissed this viewpoint and moved on.

Though in general I do not talk to people from China about politics (let’s keep in real, it’s all about the food, and possible business opportunities), it was almost amusing to hear them offer their opinions about Tibet and democracy, because so often very educated and competent people would trot out obvious government talking points. In this domain there was little critical rationalism. One could have a legitimate debate about the value of economic liberalization vs. political liberalization. But it was ridiculous to engage with the thesis that China was always unitary between the Former Han and today. That is just a falsehood. Though the specific detail was often lacking in their arguments, it was clearly implied that they knew the final answer. I would laugh at this attitude, because I thought ultimately facts were the true weapon. The world as it is is where we start and where we end.

Or is it? From the article:

Another popular comment expressed disappointment in U.S. universities, suggesting without any apparent irony that Yang should not have been allowed to make the remarks.

“Are speeches made there not examined for evaluation of their potential impact before being given to the public?” the commentator wrote.

“Our motherland has done so much to make us stand up among Western countries, but what have you done? We have been working so hard to eliminate the stereotypes the West has put on us, but what are you doing? Don’t let me meet you in the United States; I am afraid I could not stop myself from going up and smacking you in the face.”

Others were critical not of Yang’s comments but of the venue in which she chose to make them.

“This kid is too naive. How can you forget the Chinese rule about how to talk once you get to the United States? Just lie or make empty talk instead of telling the truth. Only this will be beneficial for you in China. Now you cannot come back to China,” @Labixiaoxin said.

There is a lot of texture even within this passage. I do wonder if the writers and editors at The Washington Post knew the exegetical treasures they were offering up.

To me, there is irony in the irony. Among the vanguard of the intelligensia in these United States there is plenty of agreement with the thesis that some remarks should not be made, some remarks should not be thought. Especially in public. The issue is not on the principle, but specifically what remarks should not be made, and what remarks should not be public. That is, the important and substantive debates are not about a positive description of the world, but the values through which you view the world. The disagreements with the Chinese here are not about matters of fact, but matters of values. Facts are piddling things next to values.

So let’s take this at face value. Discussions about Tibetan autonomy and Chinese human rights violations cause emotional distress for many Chinese. I’ve seen this a little bit personally, when confronting Chinese graduate students with historical facts. It’s not that they were ignorant, but their views of history were massaged and framed in a particular manner, and it was shocking to be presented with alternative viewpoints when much of one’s national self-identity hinged on a particular narrative. Responses weren’t cogent and passionate, they were stuttering and reflexive.

Now imagine the psychic impact on hundreds of millions of educated Chinese. They’ve been sold a particular view of the world, and these students get exposed to new ideas and viewpoints and relay it back, and it causes emotional distress. Similarly, for hundreds of millions of Muslims expressing atheism is an ipso facto assault on their being, their self-identity. This is why I say that the existence of someone like me, an atheist from a Muslim background, is by definition an affront to many. My existence is blasphemy and hurtful.

And the Chinese view of themselves and their hurt at insults to their nationhood do not come purely from government fiction. There’s a factual reality that needs to be acknowledged. China was for thousands of years was one of the most significant political and cultural units in the world. But the period from 1850 to 1980 were dark decades. The long century of eclipse. China was humiliated, dismembered, and rendered prostrate before the world. It collapsed into factious civil war and warlordism. Tens of millions died in famines due to political instability.

In the late 1950s and early 1960s between 20 to 50 million citizens of the Peoples’ Republic of China starved due to Mao’s crazy ambitions. This is out of a population of ~650 million or so. Clearly many Chinese remember this period, and have relatives who survived through this period. A nation brought low, unable to feed its own children, is not an abstraction for the Chinese.

On many aspects of fact there are details where I shrug and laugh at the average citizen of China’s inability to look beyond the propaganda being fed to it. And I am not sure that the future of the Chinese state and society is particularly as rosy as we might hope for, as its labor force already hit a peak a few years ago. But the achievement of the Chinese state and society over the past generation in lifting hundreds of millions out of grinding poverty have been a wonder to behold. A human achievement greater than the construction of the Great Wall, not just a Chinese achievement.

But it is descriptively just a fact that nations which have been on the margins and find themselves at center stage want their “time in the sun.” The outcomes of these instances in history are often not ones which redound to the glory of our species, but it is likely that group self-glorification and hubris come out of a specific evolutionary context.

There are on the order of ~300 million citizens of the United States. There are 1.3 billion Chinese. If offense and hurt are the ultimate measures of the acceptance of speech than an objective rendering might suggest that we lose and they win. There are more of them to get hurt than us.

But perhaps the point is that there is no objectivity. There is no standard “out there.” Once the measuring stick of reality falls always, and all arguments are reduced to rhetoric, it is sophistry against sophistry. Power against power. Your teams and views are picked for you, or, through self-interest, or, your preferences derived from some aesthetic bias. Sometimes the team with the small numbers wins, though usually not.

Discourse is like a season of baseball. At the end there is a winner. But there is no final season. Just another round of argument.

Ten years ago I read Alister McGrath’s The Twilight of Atheism. I literally laughed at the time when I closed that book, because the numbers did not seem to support him in his grand confidence about atheism’s decline. And since the publication of that book the proportion of people in the United States who are irreligious has increased. Contrary to perceptions there has been no great swell of religion across the world.

But on a deep level McGrath was correct about something. Much of the book was aimed at the “New Atheism” specifically. A bold and offensive movement which prioritized the idea of facts first (in the ideal if not always the achievement), McGrath argued that this was a last gasp of an old modernist and realist view of the world, which would be swallowed by the post-modern age. He, a traditional Christian, had a response to the death of reason and empiricism uber alleles, his God of Abraham, God of Isaac, and the God of Jacob. Primordial identities of religion, race, and nationality would emerge from the chaos and dark as reason receded from the world.

With the rise of social constructionism McGrath saw that the New Atheists would lose the cultural commanding heights, their best and only weapons, the glittering steel of singular facts over social feelings. On the other hand, if facts derive from social cognition, than theistic views have much more purchase, because on the whole the numbers are with God, and not his detractors.

And going back to numbers. The Washington Post is owned by Jeff Bezos. And China is a massive economic shadow over us all. Anyone who works in the private sector dreams of business in China. Currently Amazon is nothing in China. What if the Chinese oligarchs made an offer Bezos couldn’t refuse? Do you think The Washington Post wouldn’t change its tune?

When objectivity and being right is no defense, then all that remains is self-interest. Ironically, cold hard realism may foster more universal empathy by allowing us to be grounded in something beyond our social unit. In the near future if the size of social units determines who is, and isn’t, right, than those who built a great bonfire on top of positivism’s death may die first at the hands of the hungry cannibal hordes. Many of us will shed no tears. We were not the ones in need of empathy, because we were among the broad bourgeois masses.

In the end the truth only wins out despite our human natures, not because of it.

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