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

September 20, 2018

The Chinese eradication of extreme poverty in one generation

Filed under: China,Economics — Razib Khan @ 4:45 pm

There have been write-ups in the media of the decline of extreme poverty due to a World Bank data release in the past few days. This is kind of a pretty big deal, and one of the reasons that books like Enlightenment Now are still worth writing: much of the American public is unaware of the “good news.”

But as made clear in the graphic in The Wall Street Journal, this is to a great extent a regional story. In particular, it is the story of the near eradication of extreme poverty among the ~20% of the world’s population that is Chinese.

As the chart makes visible, the “Third World” or the “Global South” OR “Developing World”, whatever you call it, is very economically diverse. Was very economically diverse. In 1990 most of the world’s extreme poor lived in East Asia. Overwhelmingly in China. Outside of Sub-Saharan Africa and South & East Asia extreme poverty, using this definition, was actually not that common. Latin America, the Middle East & North Africa, and the post-Soviet world, suffered by comparison to North America and Western Europe.

People who traveled widely across the “Third World” knew this. In the 1980s and 1990s one of my uncles was an engineer, and later officer, for an Iranian oil tanker, and so traveled across the Middle East. He eventually wrote a peculiar book on poverty in Bangladesh after he retired, and in it he recounted how clear and distinct the differences in acute poverty were when he compared Iran with his homeland.

To give you a different general sense, I pulled the World Bank data and focused on a few large nations of diverse profiles. And, rather than looking at just the % below a very low poverty threshold ($1.90 per day), I increased the threshold ($5.50) and focused on the poverty gap. While the poverty headcount just tells you what % of the population falls below the threshold, the poverty gap is measuring the average distance below the threshold. In other words, it is measuring intensity of poverty.

What you can see above is that China went from having the highest poverty gap to the lowest in 25 years. But the story isn’t just about China. Fifteen years ago Vietnam had just as much extreme poverty as Bangladesh, but today it is in the same range as China. In the 1990s we talked a lot about the “Asian Miracle.” But that was minor leagues. The real miracle has occurred in the 21st century.

But it wasn’t really a miracle at all. Nations such as Vietnam and China (and earlier Japan and Korea) had relatively high literacy rates, and a tradition of meritocratic advancement, long before contact with European colonialism. Before Communism. With high native human capital resources to begin with, they were poised for lift-off before they ever made it down the runway.

My wife happens to know a Chinese man who is now a professor of science at an American Research I University. Because this is someone we know, aspects of his life history have slowly emerged. In short, he grew up in a very poor peasant household in rural China. And not one that had just recently fallen down the class ladder from what we can tell.

Today he is a professor doing rigorous science, who has achieved an upper middle class American lifestyle. My horizons may be narrow, but I have never met a South Asian in the United States who has come from an analogous background of such grinding deprivation. I know they exist. But in general South Asian peasants in deep deprivation, the children of landless laborers and the like, do not seem to have the opportunity or expectation that they could become researcher professors in the United States.

Finally, Communism. It is strange today, though perhaps not, that much of the younger populace of developed nations are beginning to look with eagerness toward some sort of inchoate socialism. And yet here you have more than a billion who sloughed off the dead hand of command socialism, and in the process eradicated extreme poverty.

I understand the qualms about Chinese authoritarianism. I’m well aware that some elements of China’s economic growth are unlikely to be sustainable. Perhaps there will be a correction. Almost certainly there has to be one. But we can’t forget what the very recent past was like. We shouldn’t shrug off the miracle of anti-poverty that has occurred in East Asia.

To Americans, and Mexicans as well, 1990 wasn’t a different land. But in the past generation nations like China and Vietnam have transformed themselves in ways that we can’t even imagine.

Upward nobility in India by geography

Filed under: Economics — Razib Khan @ 12:15 am


The above figure is from Intergenerational Mobility in India: Estimates from New Methods and Administrative Data. Since everyone is talking about the caste results, I wanted to highlight geography.

September 19, 2018

David Burbridge’s 10 questions for A. W. F. Edwards In 2006

Filed under: A. W. F. Edwards,Population genetics — Razib Khan @ 9:30 pm

A few years ago I watched a documentary about the rise of American-influenced rock music in Britain in the 1960s. At some point, one of the Beatles, probably Paul McCartney, or otherwise Eric Clapton, was quoted as saying that they wanted to introduce Americans to “their famous people.” Though patronizing and probably wrong, what they were talking about is that there were particular blues musicians who were very influential in some British circles were lingering in obscurity in the United States of America due to racial prejudice. The bigger picture is that there are brilliant people who for whatever reason are not particularly well known to the general public.

This is why I am now periodically “re-upping” interviews with scientists that we’ve done on this weblog over the past 15 years. These are people who should be more famous. But aren’t necessarily.

In 2006 David Burbridge, a contributor this weblog and a historian of things Galtonian, interviewed the statistical geneticist A. W. F. Edwards. Edwards was one of R. A. Fisher’s last students, so he has a connection to a period if history that is passing us by.

I do want to say that his book, Foundations of Mathematical Genetics, really gave me a lot of insights when I first read it in 2005 and began to be deeply interested in pop gen. It’s dense. But short. Additionally, I have also noticed that there is now a book out which is a collection of Edwards’ papers, with commentaries, Phylogenetic Inference, Selection Theory, and a History of Science. Presumably, it is like W. D. Hamilton’s Narrow Roads of Gene Land series. I wish more eminent researchers would publish these sorts of compilations near the end of their careers.

There have been no edits below (notice the British spelling). But I did add some links!

David’s interview begins after this point:

A. W. F. (Anthony) Edwards is one of Britain’s most distinguished geneticists. He studied genetics at Cambridge as one of the last students of R. A. Fisher, and like Fisher he has contributed actively to both genetics and statistics. In genetics his work includes several influential papers on the reconstruction of phylogenies, and a widely-read recent article on ‘Lewontin’s Fallacy’. In statistics he is known especially for his development and advocacy of the concept of Likelihood as a criterion for scientific inference. He has also made a notable contribution to combinatorial mathematics by finding a method of constructing Venn diagrams for any number of sets. In addition to many scientific papers, he has written four books: Likelihood (1972; expanded edition 1992); Foundations of Mathematical Genetics (1977; 2nd edition 2000); Pascal’s Arithmetical Triangle: the Story of a Mathematical Idea (1987; expanded edition 2002); and Cogwheels of the Mind: the Story of Venn Diagrams (2004). He has written extensively on the history of genetics, mathematics, and statistics, and has co-edited (with H. A. David) Annotated Readings in the History of Statistics (2001), and (with Milo Keynes and Robert Peel) A Century of Mendelism in Human Genetics (2004). He is also a champion glider pilot.

1. You were among the last students of R. A. Fisher. Can you share with us some reminiscences of him?

I first met Fisher in the summer of 1956 and had much contact with him until his death six years later. I saw him last during the Second Human Genetics Conference in Rome in 1961 and subsequently corresponded with him. I have published quite a few of my reminiscences of those times in a number of different places. I have been fortunate in having had a lot of contact with the older generation who knew him better than I did – people like Barnard, Bartlett, Finney, Yates, Race, Ruth Sanger and Bennett – and with members of his family, especially Rose, Harry and Joan (his biographer) amongst his children. Being a fellow of the same Cambridge college (Caius) as Fisher, though not at the same time, has meant daily contact with people who knew him well. But the most important thing is his science, and there everyone can get to know him through his writings, which reveal a mind of extraordinary power and vigour. That is the Fisher whom succeeding generations should learn about and admire.

2. Like Fisher you have worked in both statistics and genetics. How do you see the relationship between them, both in your own work and more generally?

In a sense I have benefitted from being an amateur in both fields so that I see no boundary between them. Though I qualified in genetics the subject almost immediately changed so radically through advances in molecular biology that most geneticists would not now regard me as one of themselves anyway. My generation thought genetics was the study of inheritance; theirs thinks it is the study of genes. As to statistics, I attended eight lectures by Henry Daniels in Cambridge but am otherwise self-taught, being hugely influenced by Fisher’s book Statistical Methods for Research Workers which he told me to buy (and then signed for me). Genetical statistics has changed fundamentally too: our problem was the paucity of data, especially for man, leading to an emphasis on elucidating correct principles of statistical inference. Modern practitioners have too much data and are engaged in a theory-free reduction of it under the neologism ‘bioinformatics’. We had to navigate by the stars; they have GPSs.

3. Much of your early work (some of it in collaboration with L. L. Cavalli-Sforza) was on methods of inferring phylogenies. How do you assess the progress in this field since the 1960s, and how have your own methods stood up to empirical tests?

All my work was in collaboration with Luca Cavalli-Sforza. It was his idea. He hired me to join his group in Pavia in Italy, not specifically to work on phylogenies but to apply the new-fangled computers to human genetics generally. The late delivery of the Olivetti computer was a blessing in disguise because it left us time to talk about what we would do with it when it came. I was initially sceptical because I knew that linkage was statistically difficult and here was Luca proposing what looked like linkage on a tree whose very shape also required estimating!

I think progress on the theoretical side has been incredibly slow, despite the best efforts of Joe Felsenstein, the leading practitioner. In a few months in 1962 and 1963 Luca and I thought up three ways of tackling the problem: least-squares on an additive tree (his), minimum evolution or parsimony (mine) and maximum-likelihood on a stochastic model (very much a joint effort). Forty-odd years on people are still arguing about the relative merits of the descendants of our methods when all along they should have been concentrating on refining the statistical approach through maximum-likelihood, which was our real contribution. Of course, from a practical point of view the computer packages have taken over in a development parallel to that in human genetics, from shakey inferences based on too little data and doubtful logic to computer algorithms trying to digest too much.

4. Your recent article on ‘Lewontin’s Fallacy’ criticises the claim that human geographical races have no biological meaning. As the article itself points out, it could have been written at any time in the last 30 years. So why did it take so long – and have you had any reactions from Lewontin or his supporters?

I can only speak for myself as to why it took me so long. Others closer to the field will have to explain why the penny did not drop earlier, but the principal cause must be the huge gap in communication that exists between anthropology, especially social anthropology, on the one hand, and the humdrum world of population and statistical genetics on the other. When someone like Lewontin bridges the gap, bearing from genetics a message which the other side wants to hear, it spreads fast – on that side. But there was no feedback. Others might have noticed Lewontin’s 1972 paper but I had stopped working in human and population genetics in 1968 on moving to Cambridge because I could not get any support (so I settled down to writing books instead). In the 1990s I began to pick up the message about only 15% of human genetic variation being between, as opposed to within, populations with its non-sequitur that classification was nigh impossible, and started asking my population-genetics colleagues where it came from. Most had not heard of it, and those that had did not know its source. I regret now that in my paper I did not acknowledge the influence of my brother John, Professor of Genetics in Oxford, because he was independently worrying over the question, inventing the phrase ‘the death of phylogeny’ which spurred me on.

Eventually the argument turned up unchallenged in Nature and the New Scientist and I was able to locate its origin. I only started writing about it after lunch one day in Caius during which I had tried to explain the fallacy across the table to a chemist, a physicist, a physiologist and an experimental psychologist – all Fellows of the Royal Society – and found myself faltering. I like to write to clear my mind. Then I met Adam Wilkins, the editor of BioEssays, and he urged me to work my notes up into a paper.

I have had no adverse reaction to it at all, but plenty of plaudits from geneticists, many of whom told me that they too had been perplexed. Perhaps the communication gap is
still too large, or just possibly the point has been taken. After all, Fisher made it in 1925 in Statistical Methods which was written for biologists so it is hardly new.

5. You have written several articles about Fisher’s Fundamental Theorem of Natural Selection. Following a groundbreaking reinterpretation by George Price in the early 1970s, it is now generally accepted that the theorem as intended by Fisher is valid, but some biologists would still question its practical use or importance. Can you explain in non-technical terms the meaning of the theorem, how the correct interpretation differs from earlier misunderstandings of it, and your own view on its biological importance?

Oh, it’s very simple. You must first recall the precise name of Fisher’s book in which it is the centrepiece: The Genetical Theory of Natural Selection. He is studying the mechanisms of natural selection from the point of view of populations regarded as aggregates of genes. Of course he knows, and stresses, that this is not the whole story. But to him selection’s defining effect is to change gene frequencies. He sees that this will only happen if there is variability in the survival rates of different genes.

Animal breeders promote artificial selection by imposing different ‘fitnesses’ on their stock according to desirability, breeding from some and not from others. They thus raise the mean value in the population of the character desired. Fisher saw that this process implicitly relies on a correlation between the character and fitness, so that progress will depend both on the magnitude of this correlation and the extent to which the character is genetically determined. What happens, he then asked, if we designate fitness itself as the character, making the correlation perfect? The answer is that the mean fitness of the genes will increase by an amount that depends on the extent to which fitness is determined by them. This is the fundamental theorem (in a modern paraphrase): ‘The rate of increase in the mean fitness ascribable to natural selection acting through changes in gene frequencies is equal to the additive genetic variance in fitness’.

The theorem does not involve the mean genotypic fitness – that is, the weighted mean of the fitnesses of the genotypes – which is where most interpreters of it went wrong. Fisher’s repeated denials that his theorem referred to the mean genotypic fitness, itself immortalised in Sewall Wright’s ‘adaptive landscapes’, went unheeded. In 1941 Fisher even published an example in which gene frequencies were changed under natural selection but the mean genotypic fitness stayed constant. Nobody noticed.

The brilliance of the fundamental theorem is not merely that it expresses the central dogma of natural selection – the connection between genetic variability and selective change – but that it does so exactly. Fisher discovered what the rate of change was proportional to: not to the total variance in fitness of the genotypes but only to that part of it found by fitting a weighted linear regression to the genotypic fitnesses. This is the part accounted for by the regression itself, the so-called additive genetic variance. Animal breeders know it as the variance of the breeding values of the genotypes. The fundamental theorem disregards the way the genes are distributed through the population, which will depend on the amount of heterosis in fitness, the extent of assortative mating, and similar possibly transient effects. What matters to it are the changes to the mean fitness brought about by changing gene frequencies.

This, then, is the theorem whose ‘practical use or importance’ ‘some biologists would still question’. Let them ask the animal breeders if it is any ‘use’, and let them ask themselves whether they think Darwin’s theory of evolution by natural selection is of any ‘importance’. If they do, then the fundamental theorem should help them to a deeper, Mendelian, understanding of it. If, however, they hanker after a theory that can make evolutionary predictions, like Wright’s adaptive landscapes were thought to do at one time, they are crying for the moon. Possession of the fundamental theorem will no more enable you to predict the flow of evolution than possession of Newton’s law of gravitation will enable you to predict the time of high tide at London Bridge.

It should not be forgotten, however, that shorn of its genetical complexities the theorem does have predictive power, just as the law of gravitation does when applied to the celestial movements that underlie the tides. ‘In a subdivided population the rate of change of the overall growth-rate is proportional to the variance in growth rates’. The ‘populations’ could be economic sectors, for example, or even one’s own savings accounts.

6. Your career since the 1950s spans the period in which computers, and off-the-shelf programs, have become widely available. Has this been an unmixed blessing, and do you think the development of statistics or genetics would have been very different if computers had been available in, say, 1900?

A mixed blessing of course, because the existence of programs hinders the development of the underlying theory. This is particularly true in statistics where, despite assertions to the contrary by Bayesians, the underlying theory is still a matter for discussion. The phenomenon can be seen in the field of phylogenetic trees, where programs based on different methods proliferate.

1900 is a peculiarly well-chosen date on which to hang the question. Not only was it the year in which Mendel’s results became widely known but it was also the year of the publication of the second edition of Karl Pearson’s The Grammar of Science, which included chapters on biological science for the first time.The Grammar of Science was hugely influential in its day, proclaiming that the function of science was ‘not to explain, but to describe by conceptual shorthand our perceptual experience’. ‘The man who classifies facts of any kind whatever, who sees their mutual relation and describes their sequences, is applying the scientific method’. The computer implementation of this sterile philosophy would have had a devastating effect, particularly on the development of statistical theory and the acceptance of Mendelism. All Pearson’s formidable energy would have been devoted to amassing vast quantities of information to be sifted for correlations. William Bateson’s 1894 six-hundred-page Materials for the Study of Variation treated with especial regard to Discontinuity in the Origin of Species would have been digitally scanned and computer programmers urged to uncover its secrets. It doesn’t bear thinking about!

7. In statistics you are especially known for developing and advocating the concept of Likelihood and its use in scientific inference. Can you explain how Likelihood differs from probability, and why Likelihood methods are useful in evaluating hypotheses?

Likelihood compares statistical hypotheses; it has nothing to say about a hypothesis on its own, like a test of significance does. Imagine two statistical hypotheses, each of which predicts the probabilities of all the possible outcomes of an experiment – which need be no more complex than tossing a biassed coin a number of times and counting the heads. The experiment is performed, the heads counted. Given this count, was the probability of heads p1 (the first hypothesis) or p2 (the second hypothesis)?

Now imagine doing the experiment lots of times assuming the first, and then the second, hypothesis. Would you not prefer the hypothesis that had the shorter expected waiting time until the exact number of heads observed turned up? If so, you have just chosen the one with the greater likelihood. The likelihood of a hypothesis is proportional to the probability of the data given the hypothesis. Meaningless for a hypothesis by itself because of the undefined constant of proportionality, with two hypotheses to be compared on the same data this constant is irrelevant, and the ratio of their likelihoods (or the difference in their log-likelihoods) becomes a measure of the support for one hypothesis versus the other.

Likelihoods therefore derive from probabilities, but unlike the latter are not additive. Whereas you can sum the probabilities of two possible outcomes of an experiment to form the probability of ‘either one or the other’, you cannot do the same for the likelihood of two hypotheses; ‘either one hypothesis or the other’ is not in itself a hypothesis enabling the probabilities of outcomes to be computed, so no likelihood for it is defined. But you can graph the likelihood as a function of p and pay special attention to its maximum, the maximum-likelihood estimate of the probability of heads.

The concept of the likelihood function is fundamental to all approaches to statistical inference, whether Bayesian, Neyman-Pearson, or Fisherian. Not everyone agrees that it is meaningful standing alone by itself, but I (and others before me) believe it is. Doubters can always fall back on the above ‘how long to wait’ argument, which I think was due to David Sprott.

8. You have written extensively on the history of genetics, statistics, and mathematics. Apart from the intrinsic interest of historical studies, how important do you think a knowledge of the history of science is for practising scientists?

I find it essential, and cannot imagine doing science without it. Much of what counts as science nowadays is rather theory-free. We don’t really have a word for it. Sequencing the human genome, for example, is a marvellous achievement relying on technical advances of great ingenuity but it did not require historical understanding. It differs intellectually from, say, the associated activity of trying to estimate linkage values between gene loci. The history of the latter, on which I have written recently, is an essential part of the study of the problem, and much modern work suffers from its neglect.

Celebrating the centenary of the publication of The Origin of Species in 1959, Fisher said: More attention to the History of Science is needed, as much by scientists as by historians, and especially by biologists, and this should mean a deliberate attempt to understand the thoughts of the great masters of the past, to see in what circumstances or intellectual milieu their ideas were formed, where they took the wrong turning or stopped short on the right track.
I agree.

9. R. A. Fisher was a keen eugenist. What are your own views on the role (if any) of eugenics in the modern world?

Fisher’s world was so different from ours, in three ways in particular. Then (say the period between the wars) nation-states were much more independent of each other so that it was possible to discuss population matters for Britain in relative isolation; secondly, it was a time of concern about the possibility of a declining home population; and thirdly many scientists were in the first flush of enthusiasm for the application of Mendelian principles – so recently elucidated – to man. None of this is true today.

For myself, though I was once a grateful holder of a Darwin Research Fellowship of the Eugenics Society (now the Galton Institute), since boyhood I have been more concerned about the quantity of people on earth rather than their quality. In the early 1960s I was a founder-member of a body called, I think, the Conservation Society, which does not seem to exist today. Its main platform was that too large a population would be unsustainable. At the time there was much discussion about over-population which was seen as one of the greatest dangers facing mankind. Interestingly, the worse the problem gets, the less it is discussed. Yet the mounting dangers we face, such as the possibility of global warming, are all exacerbated by too high a world population, given its enthusiasm for motor-cars, aeroplanes, and environmentally-damaging activity generally. It seems that people fear the charge of racism if they comment on population growth – they intuitively understand Fisher’s fundamental theorem.

10. Like yourself, your brother, J. H. Edwards, is also a distinguished geneticist. Nature, nurture, or sibling rivalry?

Well, certainly not sibling rivalry. It is true that we have been sufficiently alike at some stages of our lives to have been mistaken for each other. At the Rome Conference of Human Genetics in 1961 we were in a lift with the Swedish geneticist Jan Lindsten when he engagingly introduced us to another participant as ‘the two most confused brothers in genetics’.

In fact I am 7 1/2 years younger than John, and due to mother’s illness, father’s war service, and wartime privations generally, I hardly encountered him until the end of the war when I was ten. We developed boyhood enthusiasms for science quite independently, he for biology, me for astronomy. But there was a common factor in our education from thirteen to eighteen. We both attended Uppingham School, though of course not at the same time, and were exceptionally well-taught in science and mathematics, in some cases by the same teachers. I cannot stress this influence too strongly. Since I only went to Uppingham because my elder brother did, is that nature or nurture?

Subsequently John’s main influence was when I was learning about likelihood (see the preface to my book Likelihood). He, being medically qualified, keeps me straight on medical matters and I try to keep him straight on things statistical. I deliberately stayed off linkage theory so as not to get too close to his interests. John was more influenced by Lancelot Hogben and J. B. S. Haldane than I was. There is a wonderful letter from Fisher to R. R. Race in 1960 in which he refers to me as ‘my Edwards from Cambridge’ and to John as ‘only one of Hogben’s [pupils]’, so at least Fisher got us straight.

And John introduced me to gliding. Though not exactly a ‘champion’, to use your word, I have enjoyed fifty years gliding and hope for a few more yet.

The Insight Show Notes — Season 2, Episode 2: The Greatest Human Journey

Filed under: Genetics,hawaii,Podcast,science — Razib Khan @ 8:10 pm

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we touched upon arguably one of the greatest human journeys of humankind, the expansion of the Polynesians across the Pacific.

Bishop Museum

Spencer discussed his visit to the Bishop Museum in Hawaii.

We discussed broadly the interesting confluence of biology, geology, and history one can see in Hawaii. The book The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life discusses the biogeographic characteristics of many islands, including Hawaii.

We discussed the context of Polynesian languages and culture as part of the broader zone of Austronesian language and culture.

The extent of Austronesian languages

Austronesian societies spread over the last 6,000 years from Taiwan to the far west in Madagascar, and far east in Easter Island. The expansion into Polynesia was prefigured by the expansion of the Lapita culture between 1500 BC and 500 BC.

The Lapita culture is defined by its unique pottery. But curiously the usage of pottery disappeared among the Polynesians, the likely later descendants of the Lapita people. Razib mentioned how there is some evidence that cultural bottlenecks and small populations can result in loss of skills such as pottery.

On the other hand, Spencer pointed out that the Polynesians also did not practice rice agriculture, unlike other Austronesian societies. Instead, they expanded with a cultural toolkit of taro, which likely was adopted from the peoples of Near Oceania, New Guinea, and Melanesia.

Sweet Potato

Additionally, Spencer brought up the fact that the cultivation of sweet potatoes in Polynesia likely indicates contact between Polynesians and the peoples of South America. The genomic evidence that Polynesian sweet potatoes derive from South American ones is conflicted. Spencer mentioned that the word for “sweet potato” in Quechua, the language of highland Peru, is kumar. In Hawaiian, it is ku ala.

We mentioned in passing Thor Heyerdahl’s view that there was a South American migration to Polynesia. But the genetic, cultural, and archaeological evidence does not support this.

The Polynesian mtDNA motif was mentioned. With a high frequency in Polynesia, the mtDNA lineage seems to have spread from the west, in line with the idea of a migration to the east. In contrast, the Polynesian Y chromosomes show a mix of Asian and Melanesian heritage.

Much of the arguments hinge on the argument of whether the expansion of Austronesians into the Pacific was via the “slow boat” or “express train” model. The slow boat model suggests widespread cultural and genetic mixture gradually with the Austronesian expansion through Melanesia. The express train model implies a more rapid migration with far less interaction. Culturally the adoption of taro cultivation aligns with the slow boat thesis. As does the existence of Melanesian Y chromosomes across the range of Polynesians. But the overwhelming Asian nature of Polynesian mtDNA lineages fits the express train model.

One way that scholars have reconciled this is that there was a slow expansion of the Lapita people, but that they only assimilated Papuan and Melanesian men into their matrilineal communities. This broad framework was reinforced with the publication of genetic results from native Hawaiians, which showed a minority ancestry from a Papuan-like population.

But wait, there was a twist! Ancient DNA now shows that the Lapita people had almost no admixture with Melanesian people! Follow-up results from Vanuatu and Tonga confirm that the Lapita people had no admixture from Melanesians. Rather, in Vanuatu 2,500 years ago the Lapita people are replaced by an almost entirely Melanesian population, and the Melanesian ancestry begins to show up in Polynesians after this period. The conclusion then is there were multiple migrations into Polynesia!

Spencer and I concluded that the broad sketch is now established, but a lot of complicated details need to be worked out. Instead of express trains or slow boats, some researchers now wonder if Polynesia was more like a subway network.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The Insight Show Notes — Season 2, Episode 2: The Greatest Human Journey was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Hawaii: complicated a journey to paradise

Filed under: anthropology,Genetics,hawaii,science — Razib Khan @ 7:11 pm
The extent of Austronesian Diaspora

Ask any American what they think when you say the word “Hawaii,” and certain words will no doubt reoccur from person to person. That’s because certain images, feelings, come to mind. A gentle breeze, beaches, and volcanoes. The 50th state has been the byword for paradise on the mainland. A certain sense of Hawaii is part of American popular culture.

But Hawaii is a real place with real people. It isn’t a dreamland. Rather, it is one of the most isolated large islands in the world. Over 2,500 miles from the nearest continent, there is only a single terrestrial mammal native to the islands: predictably, a bat!

Obviously, the island is crawling with mammals today. Nearly 1,000 years ago voyagers from the lands of the western Pacific landed on the Society Islands, which includes famed Tahiti, and then sailed northward to the Hawaiian archipelago. When the ancient Polynesians settled Hawaii they did not arrive alone. They brought with them pigs, chickens, and dogs. Naturally, rats tagged along as unwanted passengers.

Humans arrived in Hawaii in catamarans

But the settlement of Hawaii by humans was the end of a long journey which began thousands of years earlier in the mists of prehistory. Six thousand years ago a small group of stone-age seafarers, who we call Austronesians, journeyed south from Taiwan and settled the northern Phillippines.

But they did not stop there. Over a period of thousands of years, these ancient mariners spread out over Southeast Asia, sometimes introducing intensive forms of rice agriculture and their distinctive language. But they did not stop there. For whatever reason, these were a people who wondered what was over the horizon, even if it was the deep blue ocean. They moved on west and east. Over 1,000 years ago their descendants reached the western Indian Ocean, mixing with the Bantu farmers of eastern Africa and occupying the island of Madagascar. In the other direction, Austronesians moved into Oceania, abandoning rice and adopting taro from Melanesians. Less than 1,000 years ago the Pacific expansion finally crested, as Polynesians settled in New Zealand, off the coast of Australia, Easter Island, 2,300 miles west of South America. And of course, they ventured north to Hawaii, an isolated ecologically rich and unique jewel in the midst of the Pacific.

In Southeast Asia, the Austronesians merged with native populations of farmers which migrated out of southern China earlier. But as they moved west and east they encountered very different populations, whether it be African farmers and pastoralists, on the one hand, or Melanesians in the case of the ancestors of the Polynesians.

Citation: Kim SK, Gignoux CR, Wall JD, Lum-Jones A, Wang H, Haiman CA, et al. (2012) Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study. PLoS ONE 7(11): e47881

And just as the people of Madagascar, despite speaking a language closest to those spoken in Borneo, have a blended with nearby populations. Polynesians carry signatures of interactions with the peoples of Near Oceania, which includes New Guinea, Australia, and Melanesian islands in the western Pacific, such as the Solomon Islands and New Caledonia.

As genomics began to illuminate all the relationships between human populations, in 2012 a paper was published that surveyed the genomes of many native Hawaiians. The results were clear: the indigenous peoples of Hawaii had a dominant signature of ancestry shared with mainland Asian peoples, but also a minority component that had more affinities with the peoples of Near Oceania.

Lapita culture sites

This result was relevant to what traditionally had been termed the “express train vs. slow boat” models of the settlement of Polynesia. The “express train” hypothesis implies that the Austronesian Lapita culture rapidly pushed out of maritime Southeast Asia, with minimal interaction with local Papuans and other Melanesians. In contrast, the “slow boat” model meant that the expanding proto-Polynesians mixed with Papuans and Melanesians as they spread eastward more gradually, creating a fused culture which pushed onward into the far Pacific.

The results above, along with maternal and Y chromosomal lineages seem to support the “slow boat” model. Not only are all Polynesians, including Hawaiians, descended from Southeast Asian farmers, but their ancestors also include the people who first pushed to the edge of the Pacific. These were the ancestors of Oceanians who settled New Guinea, Near Oceania, and Australia more 40,000 years ago with the first “Out of Africa” migration.

Citation: Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., … & Fu, Q. (2016). Genomic insights into the peopling of the Southwest Pacific. Nature, 538(7626), 510.

So case closed? Not exactly. Science and history are often more complex than our elegant human imaginings. Over the past few years, the field of ancient DNA has come upon the scene to disturb hypotheses and provoke the development of new ones. Now researchers can see snapshots of the past with much crisper detail than would have been the case in the past.

Two papers have helped reshape our understanding of the peopling of Polynesia. First, a 2016 paper showed that samples of ancient Lapita people don’t show any admixture from Melanesians. This is in accordance with the “express train” model, which the genetic heritage of modern Polynesians presumably refuted!

An immediate solution to this conundrum is that the old models were too simple. That there wasn’t just a simple migration outward, but rather several, and that Melanesian ancestry arrived later. Within the last 2,000 years.

A paper published in 2018 added more nuance and clarity to what may have been going on. Today the island of Vanuatu is considered to be Melanesian and is settled by people of predominant Oceanian heritage. But ancient DNA from 3,000 years ago yielded individuals of nearly total Asian heritage. But by about 2,000 years ago these people were replaced, by the ancestors of modern Melanesians, as later samples show overwhelming Oceanian heritage.

Poke is a melange of flavors and ingredients from the four corners of the world

Where does this leave us? Appropriately, a paper appeared with the title “Human Genetics: Busy Subway Networks in Remote Oceania?” was penned as a response to all this uncertainty and confusion. The title says it all, doesn’t it?

These findings may actually be consonant with recent archaeological results that eastern Polynesia and New Zealand were subject to a massive demographic expansion and radiation beginning around ~1,000 years ago.

Today modern Hawaii is a melange of peoples, reflected in its cuisines, such as Poke, which has been inflected and modified by new ingredients brought by immigrants from the mainland and Asia. And yet perhaps this was always so, as paradise was never as serene and eternal as we may dream in our imaginings. Rather, Hawaii and the Hawaiians were products of daring voyages generation after generation, and the waxing and waning of peoples and cultures, bringing together diverse and disparate threads of the human expansion out of Africa.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Hawaii: complicated a journey to paradise was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Learning from cultural anthropology as opposed to unlearning from cultural anthropology

Filed under: Cultural Evolution — Razib Khan @ 12:33 am

On my other weblog one of the commenters, who I have nicknamed Syme (others call him Bentwig), proudly boasts about his training anthropology. Those who know me personally are aware that for me this is often a red flag for an individual who is willing to furiously declare that up is down if Edward Said stated that this was so in a footnote somewhere, or that black is the palest color if Michel Foucault averred this offhand in an interview. I exaggerate in the generality, though in the case of Syme/Bentwig there is a common tendency to proudly attempt to forestall arguments with comments of the form “Edward Said said….” or “According to Foucault.”

Of course, arguing from the authority of others isn’t always bad…but with far too many people with undergraduate anthropology backgrounds seem to engage in this sort of argument-by-citation and refutation-by-declaration-of-theory. Perhaps a contrast of interest are people educated in philosophy. There’s not much they know in thick detail, but they often exhibit analytic acuity when presented with startling and novel information. In contrast, many people with anthropological training may express befuddlement and then proceed to fury when confronted with facts which are outside of their domain and foreknowledge.

Enough punching down. Alex Mesoudi, a scholar in the field of cultural evolution, is publishing book chapters as preprints. The author of Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences, Mesoudi’s first submission, The study of culture and evolution across disciplines, should be read by anyone who is interested in the material on this weblog.

Mesoudi reviews the history of the field, from the rise and fall of human sociobiology in the 1970s to the birth of evolutionary psychology in the 1980s, and the gradual but consistent waxing of lesser-known disciplines such as cognitive anthropology and human behavioral ecology (out of which comes cultural evolution). A consistent binding feature of these disciplines is that they attempt to understand human cultural expression as a function of naturalistic processes, in particular, evolutionary ones. This is in contrast to the shift away from analysis to interpretation and description in much of cultural anthropology across the same time period, with the ultimate secession of much of the field from “science.” If you want to read a good primer on the division between scientific and non-scientific anthropology, I recommend Dan Sperber’s Explaining Culture or the anthropological introduction to D. Jason Slone’s Theological Incorrectness. Scott Atran also tackles the issue in In Gods We Trust. The reason this is necessary is that to understand and take in cognitive anthropology, you often need to unlearn to dampened tics obligate in cultural anthropology.

The flight of much of American cultural anthropology from crisp and powerful analytic frameworks, and toward linguistic obscurantism, to me explains the relative poverty of cognition of those students with only an undergraduate training. Without field-work and graduate courses and reading there’s not even the ability to obtain the deep knowledge required to enable feats of “thick description.”

In any case, the genius of the tradition in which Mesoudi operates under is that it allows for powerful analysis and prediction of cultural patterns and dynamics. Using similar formal frameworks, the idea is to do to culture what population genetics has done to biological evolution: produce a formal framework to generate predictions and test them with empirical data.

Here’s a taste of how researchers in this field think of “cultural patterns”:

Boyd and Richerson (1985) developed models showing that transmitted culture is favored when environments change moderately quickly, too fast for genes to track, but not so fast that the culturally transmitted behavior is out of date (see also Aoki et al., 2005). Transmitted culture also evolves when individual learning is costly (Boyd and Richerson,
1985). Under such conditions, however, social learning evolves but does not increase the average fitness of the population. This phenomenon became known as “Rogers’ paradox” after Alan Rogers, the first person to clearly point it out (Rogers, 1988). The fact that social learning does not enhance average population fitness is not inherently paradoxical, but does contradict the common claim that humans are so ecologically and demographically successful because of transmitted culture.

Rogers’ paradox occurs because the success of social learning is frequency-dependent. When rare, social learners do well because they forego the costs borne by individual
learners. But when common, and environments change, social learners will be copying other social learners’ out-dated information. At equilibrium, social and individual learners have equal fitness, which will be equal to the fitness of a population entirely composed of individual learners (which is fixed, because their learning is not dependent on others). Thus, social learning evolves, but does not enhance fitness in a way that could be described as the ‘secret to our success’.

Two small quibbles with the chapter. First:

Bouckaert et al. (2012) reconstructed the cultural evolutionary history of the Indo-European language family, finding that it originally spread along with farming practices from present-day Turkey around 8,000 years ago.

Bouckaert et al. used valid phylogenetic methods, but it seems quite clear that these models have difficulty predicting the protean and punctuated character of many population expansions, which reshape the distribution and relationship of languages. Since 2012 a substantial amount of ancient DNA work has strongly pointed to the likelihood that the distribution of extant Indo-European languages in Europe is due to an expansion out of the Pontic steppe 5,000 years ago (with later secondary migrations into Southern Europe after 4,000 years ago). Though the Anatolian origin may still be preserved if one argues that the Pontic expansion was a secondary one, clearly most of the diversification of the Indo-European languages occurred in the period between 3000 and 1000 BC, in a 2,000-year radiation. The “Indo-European question” ultimately showed to me the limitations of phylogenetic methods because they are sensitive to particular assumptions within the model (e.g., continuous endogenous demographic expansion).

Second:

Note that this is different to Wilson’s (1976) earlier speculations that genetic differences might explain behavioral differences between groups of people. Tooby and Cosmides explicitly disavowed this, instead arguing that people everywhere are genetically far too similar to explain any behavioral variation directly (which concurs with modern genetic data: Feldman, 2014). Genes instead generate a set of universal responses to predictable environmental variation.

Considering the very rapid changes in cultural types across time and between closely related lineages, it seems hard to credit that most behaviorally based cultural variation is due to genetic variation (e.g., walk down a street in Finland and walk down a street in Italy, and see how differently the comportment of the typical passerby is). But, it seems quite possible, probably likely, that there are going to be some behavioral differences due to different distributions in polygenic quantitative traits. The question is more the extent of magnitude. That will depend on the phenotype and between population pair.

Also, there is clearly variation within the cultural evolution community on this issue. I know this from personal communication. Joe Henrich admits the possibility in The Secret of Our Success, without taking a position.

But, with those quibbles out of the way, go and read The study of culture and evolution across disciplines. I think it’s great that Mesoudi is putting out preprints for his book chapters. Makes his research accessible, and this is one field where more publicity would be good (shout out to Paul Smaldino, who apparently inspired Mesoudi on this track).

September 18, 2018

On the whole genomics will not be individually transformative…for now

Filed under: Crispr,Genomics,Personal Genetics,Personal Genome,Personal genomics — Razib Khan @ 4:51 pm

A new piece in The Guardian, ‘Your father’s not your father’: when DNA tests reveal more than you bargained for, is one of the two major genres in writings on personal genomics in the media right now (there are exceptions). First, there is the genre where genetics doesn’t do anything for you. It’s a waste of money! Second, there is the genre where genetics rocks our whole world, and it’s dangerous to one’s own self-identity. And so on. Basically, the two optimum peaks in this field of journalism are between banal and sinister.

In response to this I stated that for most people personal genomics will probably have an impact somewhere in the middle. To be fair, someone reading the headline of the comment I co-authored in Genome Biology, Consumer genomics will change your life, whether you get tested or not, may wonder as the seeming contradiction.

But it’s not really there. On the aggrgate social level genomics is going to have a non-trivial impact on health and lifestyle. This is a large proportion of our GDP. So it’s “kind of a big deal” in that sense. But, for many individuals the outcomes will be quite modest. For a small minority of individuals there will be real and important medical consequences. In these cases the outcomes are a big deal. But for most people genetic dispositions and risks are diffuse, of modest effect, and often backloaded in one’s life. Even though it will impact most of society in the near future, it’s touch will be gentle.

An analogy here can be made with BMI, or body-mass-index. As an individual predictor and statistic it leaves a lot to be desired. But, for public health scientists and officials aggregate BMI distributions are critical to get a sense of the landscape.

Finally, this is focusing on genomics where we read the sequence (or get back genotype results). The next stage that might really be game-changing is the write revolution. CRISPR genetic engineering. In the 2020s I assume that CRISPR applications will mostly be in critical health contexts (e.g., “fixing” Mendelian diseases), or in non-human contexts (e.g., agricultural genetics). Like genomics the ubiquity of genetic engineering will be kind of a big deal economically in the aggregate, but it won’t be a big deal for individuals.

If you are a transhumanist or whatever they call themselves now, one can imagine a scenario where a large portion of the population starts “re-writing” themselves. That would be both a huge aggregate and individual impact. But we’re a long way from that….

The Philippines as a postcolonial exemplar: out of wedlock birthrates

Filed under: Cultural Anthropology,Cultural Differences,Illegitimacy — Razib Khan @ 3:28 pm

Edward Said’s Orientalism was a book I first read in the fall of 2001. I recall not being too impressed and finding simple historical errors in it. But mostly it bore me. I am now rereading it because in 2018 the book is far more relevant to our current American culture, if not the world in a real sense. That’s because Orientalism is one of the most influential and seminal works in the field of postcolonialism (and to be frank, it seems more comprehensible than the stuff written by Gayatri Chakravorty Spivak).

At some point, I may put down into a post my thoughts on Orientalism. But long-time readers are familiar with my position that postcolonialists, and most progressive Westerners, overemphasize the importance of the colonial in most non-Western societies. But this is not the same as saying the colonial is not important, and, that the colonial does not affect different societies in varied ways.

The Philippines is the mostly large majority Christian country in Asia. It is predominantly Roman Catholic, though like many Catholic nations it’s religiosity is declining. The brutal and blunt current president of the country has had some harsh things to say about the Church.

I bring up the Philippines because in comparison to other Southeast Asia nations it seems clear that it is a creature of colonialism. A hybrid of Western and Asian values that is somewhat out of place. The French influence Vietnam is undeniable, but fundamentally Vietnam remains part of the broader Sinic cultural sphere, as it was before the rise of Europe. This is not so with the Philippines, which was in the early stages of Islamicization when the Spaniards arrived and had only been lightly impacted by Indic civilization in comparison to Java or the Austronesian kingdom of the Chams in mainland Vietnam.

One of the most striking things to me is that more than half of the babies in the Philippines are now born out of wedlock. This is an exception within Asia and even Southeast Asia.

There is one set group of nations which has long had high rates of out of wedlock births: those of Latin America. My reading of the ethnography indicated that this is partly a function of the fact that Iberian males entered into de facto polygynous family relationships early on during the conquest of the New World. And, unlike some other European nations, “natural children” did have some customary rights in Spanish law. Hernan Cortes had two sons with the name Martin. One of them was a mestizo, the product of a relationship with an indigenous woman of New World. The other was the legitimate offspring with Cortes’ aristocratic Spanish wife.

Though Martin Cortes, known as “El Mestizo,” did not have the rights of his brother, he was still provided for. He fought in Central Europe for the Habsburgs, and married and had children.

This pattern of giving some rights and consideration to illegitimate children has been argued as a major reason for the high rates of out of wedlock birth in much of Latin America today. But, the problem with this model is that the number of Spaniards in the islands of the Phillippines was always far lower than in the New World. Demographically they made a marginal impact, and in fact, the Chinese were more numerous.

But it remains the case that Spanish colonial regimes in environs as distinct as the Philippines and the New World left a legacy of high rates out of wedlock births. It could be coincidental, but I doubt that. Scholars genuinely interested in the impact of exogenous colonial shocks should be exploring these cross-cultural patterns theoretically and empirically, not engaging in abstruse linguistic analysis or deploying Theory toward the ends of particular politics.

Open Thread

Filed under: Open Thread — Razib Khan @ 12:26 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

September 17, 2018

Open Thread, 9/17/2018

Filed under: Open Thread — Razib Khan @ 10:13 pm

There are lots of things from Imperial China 900–1800 that I learned, though more often it simply deepened my knowledge. At this point, I am curious about something that is more like economic history (yes, I’ve read The Great Divergence). Recommendations?

Here is a fact I learned from Imperial China 900–1800 that might be of interest: in the late 17th century the expanding Manchu Empire (which had conquered China) and Russia began to jostle for power in Inner Asia, and the Khalkha Mongols, the Mongols proper, were deciding which side to align with. I had long known that the Khalkha Mongols had aligned with the Manchus. What became the Manchu imperial line had a genealogical relationship with the Mongols, as they would often take wives from a particular group of Mongol tribes (Kangxi Emperor’s paternal grandmother was a Mongol). Imperial China makes it clear that Mongol cavalry units were critical elements of the Manchu military machine, and as the Manchu assimilated into the Han culture they became arguably even more important as a population which could provide militarily ready men at a moment’s notice.

But a more interesting aspect of the Manchu alliance with the Mongols are the ethnoreligious implications, and what they wrought across Inner Asia. The Khalkha had become Tibetan Buddhists by the time the Manchus conquered China. According to Imperial China, their religious leaders argued for the furtherance of their alliance as junior partners to the Manchus as opposed to the expanding Russians in part because the Manchus were more respectful of Buddhism. Mind you, the Manchus were not themselves Tibetan Buddhists, though they were always keen to co-opt the various prominent Tibetan lamas. But, they had earlier practiced Chinese and Korean forms of Buddhism (as the Jurchens) and seemed resistant to Tibetan Buddhism in comparison to the Mongols.

The Russian Empire was obviously dominated by an Eastern Orthodox Christian elite. But, eventually, they made accommodations with various minority religions, including Buddhism. But, Buddhism, Islam, Judaism, and non-Orthodox Christianity were all subordinate religions. Historically non-Orthodox ethnic groups invariably suffered erosion due to the social advancement which conversion to Orthodoxy entailed. From the viewpoint of meta-ethnic identity, the Manchus were clearly superior to the Russians, as the Manchus tended toward more neutrality in religion than the Russians.

Dzungaria in red

And yet there are two conditions that need to be highlighted here. The Manchus were responsible for the ethnic cleansing of the Mongol Dzungar tribes in the 18th century. The Dzungars were the last great Inner Asian polity to challenge the gunpowder empires. They were arguably the final flowering of the steppe and its way of war. Unlike the Khalkha Mongols the Dzungar tribes, who were Oirat, were not part of the Mongol expansion under Genghis Khan. Ethnically somewhat distinct, the Dzungar nevertheless were Tibetan Buddhists, just like the Khalkha.

The 18th-century wars to destroy the Dzungar polity and exterminate or scatter its people occurred with the assent and aid of the Khalkha Mongols, who were ethnically close and religiously identical. Some of the Dzungar even fled westward, to joint co-ethnics under Russian rule in the Kalmyk Khanate. The region of Xinjiang that today is labeled “Dzungaria” had very few Mongols after the wars against the Dzungars. Nor did it have many people who we today would call Uygurs. Rather, post-genocide Dzungaria was occupied by nominally Muslim Kazakh and Kirghiz people, while today it has become a magnet for Han and Hui people as Urumqi has become Central Asia’s largest city.

Why am I reviewing all of this? To show how complicated the idea of alliances and affinities based on civilizational identity can be. The reality is that religion and ethnic identity do matter somewhat, but on the medium-scale, they are not as important informatively as on the extremes. Obviously traditionally ethnoreligious groups exhibited ingroup affinity. Buddhist Mongols lived with Buddhist Mongols. Muslim Mongols often assimilated to becoming Turks, while Mongol tribes which had experimented with Islam but eventually became Buddhist lost their Islamic connections. And, on the largest temporal scales and on the margin broader ethnoreligious affiliations matter. Buddhists from as far away as Japan protested to the Taliban when they were mooting the idea of destroying the Bamiyan Buddhas. Christians focus on the persecution of Christians in China. The Mongols, Oirat and Khalkha, became heavily involved in Tibetan politics after their conversion.

Details matter.

A very long post from me, Between the saffron and scimitar, inspired by a lot of the comments we get at Brown Pundits. About six months ago I said something about the Kali Yuga on Twitter in a joking manner, and someone responded: “isn’t that an alt-right meme.” Well, it turns out that some alt-right people are Evola-loving pagans, though I doubt most are. But the idea of the Kali Yuga kind of predates the alt-right in the Hindu tradition, though a lot of people don’t know anything about Hinduism. Similarly, many Indian Hindus (religious or not) have weird perceptions of the origin of any ideas that are also found in Islam…and my name does not help in the way they reflexively respond when I express ideas that might be found in Islam.

But the reality is that it is hard to tease apart Indian culture today from the various influences that domination by Muslims left, even if said Indians are self-consciously anti-Muslim. This is to many people somewhat offensive. I think a good analogy might be some conservative white Americans who don’t want to admit that for many decades white supremacy was considered part and parcel of American patriotism, and constitutive to American nationalism. That arguably has long-term impacts, though unlike many on the Left I do not think that it is an all-pervasive miasma which touches every aspect of American life in 2018.

Pew has a new religious typology out. Not much in the report is surprising.

Here is a surprise to me though: New Age beliefs are more common among the orthodox Christian/religious groups than among the secular subset that is dominated by atheists and agnostics.

There are some interesting distinctions between the “Religion Resisters” and “Solidly Secular.” The latter is 65% male, while the former is majority female. The latter is more educated, wealthier, and more likely to be concentrated in the Northeast and Midwest, while the former is more often in the West. The “Solidly Secular” are the type of people who would be New Atheists. The “Religion Resisters” are actually somewhat more liberal socially and politically issues than the “Solidly Secular.”

Another Pew report suggests that Americans with no religious affiliation have nearly as many Christian beliefs as Europeans who say they are Christian. This is not because those with no religious affiliation in the USA are very Christian. Rather, it’s because European “Christians” are a lot less orthodox than you might expect.

The Next Financial Crisis Lurks Underground Fueled by debt and years of easy credit, America’s energy boom is on shaky footing. Basically, the argument is that the fracking boom, which has driven American fossil fuel supply to the point where we now surpass Saudi Arabia, is an artifact cheap credit pumping money into the system.

Fracking isn’t profitable at current oil prices. I think the author is probably a little too pessimistic, because technology does get better, and increased crude oil prices will probably show up at some point to fuel further investment.

One of the best things about the fracking boom is I don’t have to listen to friends yammer on about “peak oil” in all-knowing tones. That being said, how are books like Confronting Collapse maintaining such high Amazon star rankings? Is it a fraud? Or do these sorts of pessimistic tomes just always sell well?

A thing I’ve noticed since I’ve shifted to mostly reading on Kindle: I read in a more sequential fashion. Obviously, I can still jump chapters, but the reality is that I don’t do it much. Is it just me?

Genomic prediction of cognitive traits in childhood and adolescence. This claim is important: “Polygenic scores for educational attainment and intelligence are the most powerful predictors in the behavioural sciences and exceed predictions that can be made from parental phenotypes such as educational attainment and occupational status.” I’m assuming this is the sort of stuff in Robert Plomin’s new book, Blueprint: How DNA Makes Us Who We Are.

Going to try and get a review copy for National Review.

E-book Sales Fell 10% in 2017:

Adult fiction remained the most popular e-book category–44% of sales in the category were in the digital format–but e-book sales in the segment dropped 14% from 2016, to 108 million units.

E-books have a much smaller share of the adult nonfiction market, 12%, but sales in the segment rose 3% last year, to 38 million units, NPD reported.

The steepest decline in e-book sales last year was in the children’s category, where sales fell 22%. In children’s, the digital format accounted for only 5% of all sales last year. E-book sales were down 8% in the young adult category, falling to 4 million units sold. The format comprised 18% of all young adult unit sales last year.

Makes sense that it would decline in the children’s category. When it comes to reference textbooks, I still go paper. It’s just easier for me to look things up.

Numbers did not add up in the passport revocation story. Unfortunately, this is a pattern in the media. Stuff that happened in the Obama administration was not reported…but when it continues in the Trump administration it becomes teh Nazi!

Genomic history of the Sardinian population. As Spencer and I alluded to on last week’s episode of The Insight, L. L. Cavalli-Sforza and colleagues did a really good job in their sampling. “Low effective migration rates separate these provinces from a broad area that extends to the mountainous Gennargentu massif region, including inland Ogliastra to the west. The Gennargentu region is also where some of the Sardinian individuals in the HGDP originate (A. Piazza, personal communication). We find that the HGDP Sardinian individuals partially overlap with our dataset and include a subset that clusters near the Ogliastra subpopulation.” That is, the HGDP Sardinians are among the more “EEF” Sardinians.

A Game of Thrones: The Graphic Novel is on sale for Kindle. I don’t even know if I’d want to read a novel in graphic form. But then I’m not a very visual person. Some of the original books actually had a few illustrations. But not that many. For the record, Eddard Stark in my head will always look somewhat like the actor Bill Campbell, not Sean Bean.

Eight Decades of Ethnic Dilemmas: Iconic sociologist Nathan Glazer on the problems of group identity, affirmative action and Donald Trump. It’s incredible to me that Nathan Glazer is still around and intellectually active. To a great extent I’m sympathetic to many of the views he expresses in this article. He’s in the same class as Thomas Sowell for me, though to be entirely frank Sowell has gotten a little too predictably partisan with age for my taste.

Inferring Continuous and Discrete Population Genetic Structure Across Space. An important paper.

Gibraltar Neanderthal Genomes on the way….

Bacteria in a Dinosaur Bone Reignite a Heated Debate.

Dating genomic variants and shared ancestry in population-scale sequencing data. When I see Gil McVean on the author list I read.

Two Psychologists Four Beers. Podcast with Alice Dreger. One of the co-hosts seems to have disappeared for most of the podcast. I assume he was just drinking beer. The last third where Dreger talks about journalism is probably the most novel.

Also, Dreger admits that she probably would have defended Bret Weinstein and Heather Heyer with vigor if she had not been so exhausted and drained by her own academic controversy, as she was forced out of her Northwestern position.

I will add on a personal note that I feel some fatigue and exhaustion because many of my friends in academia expect me to “speak up” about topics that are too politically sensitive for them to broach. I’m OK with doing that…but I have my limits, and other peoples’ third rails are not the burning passion of my life.

To be frank, I’m pretty skeptical about the future of the republic of letters and intellectual life in the West. At least in public.

For example, Thousands of scientists publish a paper every five days.

The Many Indian Genomes.

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations.

An Ancient Crosshatch May Be the Earliest Drawing Ever Found. Looks like well-done steak to me.

By the way, the consistently shared drift between Basques and Sardinians, especially highland Sardinians, should make us lean toward the non-Indo-European hypothesis for Paleo-Sardinian.

September 15, 2018

Results of 2018 Reader Survey

Filed under: Reader Survey,Survey — Razib Khan @ 1:34 pm

There was a comment below about who the readers are of this weblog. One thing that is clear is that people who comment are not necessarily representative.

Limiting the sample to those who have American (USA) nationality:

Limited the sample to South Asians:

September 14, 2018

Between the saffron and scimitar

Filed under: India,Islam,Islamicate — Razib Khan @ 10:10 pm

On my other weblog I have a post, On The Instrumental Uses Of Arabic Science, which reflects on the role that the idea of science, the Islamic world, and cultural myopia, play in our deployment of particular historical facts and dynamics. That is, an idea, a concept, does not exist on an island but is embedded in a cultural environment. Several different contexts.

My father is a professional scientist, and a Muslim who lives in the West. In our house there was always a copy of The Bible, the Qu’ran and Science: The Holy Scriptures Examined in the Light of Modern Knowledge. To those not convinced about the beliefs of Islam, as I never was, it was not a convincing book. But it played a particular role in my father’s life of the mind as both a Muslim and a scientist. Its arguments were less important in their detail than that a French scientist had written a book showing that Islam and science were compatible and that in fact, the Koran had prefigured scientific truths.

The intellectual achievements of medieval Islam, particularly the phase focused around the House of Wisdom, are a real thing in and of themselves. But more often they exist as tools for the implicit or explicit agendas of particular peoples with ends which are separate and distinct from an understanding of the past on its own terms.

For many Muslims, this period defines what Islam could have been. Should have been. More traditionalist Muslims will have a relatively understated take, and perhaps attribute the passing of this period due to external forces (e.g., the collapse of central authority by the end of the 9th century). More progressive Muslims will make a bolder claim, that Islam, that Muslims, made the wrong decisions internally (al-Ghazali often emerges as a villain).

A modernist, perhaps Whiggish, take would be that the 9th century of Islam was a “false dawn.” Illustrative of the acidic power of rationality, but an instance when it receded in the face of faith (the Mutazilites often become heroes in these tales). A more multiculturalist and contemporary progressive Western take would likely emphasize that Islamic cultural production was just as ingenious as that of the West, and its diminishment was due to the suffocating effect of colonialism.

But there are even more exotic takes one could propose. The shift from the Umayyads in Damascus to the Abbasids in Baghdad was a shift of the Islamic world from the west to the east. The prominence of Iranian culture during the latter period was palpable. The Caliph al-Mamun was half Iranian, and almost moved the capital of the Abbasids to Merv in Khorasan. The Barmakid family were ethnically Iranian, but also originally hereditary Buddhists. The historian of Central Asia, Christopher Beckwith, has alluded to an “Indian period” of Islamic civilization when the influence from Dharmic religion and Indian culture was strong. For example, Beckwith and others have argued that the madrassa system derives from that of Central Asian viharas.

But ultimately this post and this blog is not about Classical Islamic civilization and history. Rather, I want to pivot to the discussion of Islam and India.

This blog now gets in the range of the same amount of traffic as my other weblog. But a major difference is the source of traffic. About two times as many visitors to this weblog come from the USA as India. So Americans are dominant. But, on my other weblog, 15 times as many visitors come from the USA as India. Additionally, since this is a group weblog, I’m pretty liberal about comments, and so this weblog receives between 10 to 100 times as many comments as my other weblog. Obviously, since most people in the world are stupid, many of the comments are stupid. I try to ignore that.

Rather, let me focus on the “hot-button” issue of Islam and India, and how it impacts people here. In the comments of this weblog. Let’s divide the comment(ers) into two stylized camps. Or actually, one person and another camp. The person is commenter Kabir, who has taken it upon himself to defend the honor of Indo-Islamic civilization. On the face of it, that’s not a major problem, but he tends to take extreme offense and demand linguistic and topical policing that’s frankly rather obnoxious (this tendency extends beyond Islam, as he is a living personification of Syme). He’s a bully without the whip. Kabir is somewhat annoying, but I can honestly I can always just delete his comments. He’s one person.

In contrast, there are those who Kabir calls “Hindu nationalists.” This is a broad slur on his part, as it basically seems to include any person from a Hindu background who disagrees with any particular social-religious take he has in relation to the Indian subcontinent or Islam. If someone who was a Chinese Catholic lesbian left a common where their identity wasn’t clear, and they disagreed with Kabir’s take, he would no doubt accuse them of being a “Hindu nationalist.”

If you have a hammer, everything is a nail!

But, there are genuine Hindu nationalists who read this weblog of various stripes. I have friends who personally lean toward this direction in their politics, though they are cosmopolitan in their private life. On the other hand, there are others who are more backward and probably as crazy as Kabir depicts them. Honestly, I’ve never met these people in real life…most “Indian” people I meet are either coconuts like me or cosmopolitan blockchain engineers.

At this point, I should step back and reintroduce myself. Unlike many people from an Islamic background who are now rather frankly irreligious, I did not have a traumatic relationship with Islam. Or religion. My parents mostly raised me as a nominal Muslim, so my atheism came about naturally and at a young age. And, unlike some atheists from a Muslim background, I did not grow up in a Muslim community. Neither did I grow up in an immigrant community. I grew up in Ronald Reagan and Bill Clinton’s America as the token brown kid. I have only come to know other brown people of all religions and background as an adult. My stance is one of curiosity, and sometimes perplexment. I have a few memories of distaste when it came to attending masjid as a child because in hindsight it is clear I never believed in what they were saying and saw it as a massive waste of time and totally sterile.

But due to this perspective, I don’t have strong opinions on South Asian politics. I wish atheists and free-thinkers would get a little break in Bangladesh. Pakistan as a nation should go see a good therapist about its identity crisis. And in India, the saffron brigade should chill out on their paranoia on all things “foreign.” The British are gone. And the Muslims are a minority (also, I had a medium-rare hamburger with bacon today!).

Which brings me to the concerns of the Hindu nationalists, and their relationship to Islam. Their hatred of Islam. Their love of Islam. Their inability to quit Islam.

Imagine a beautiful bully. A bully with the social and interpersonal skills to hide their behavior. To get away with it. If Hindu nationalists were to personify the historical rage they feel, that seems to be their attitude toward Islam. What genetics is telling is that though South Asians are diverse, we’re a distinctive and recognizable branch of the human race that emerged out of particular social and historical dynamics that occurred between three and eight thousand year ago.

And yet Hindu nationalists see that one out of three South Asians now identifies as something distinct, part of an alienated (from South Asia) worldwide brotherhood. They used to be called Indians. What used to be called Hindus. But they are alienated from their own ancestral identity now. Their forenames are Ali or Pervez. Their surnames are Islam or Khan. Many of their sartorial choices and customs are dictated by the whims of a 7th century Arab and the norms of his community. Some even have the gall and conceit to claim to be scions of the Arab, Persian, or Turk, when their very faces give the lie to that claim.

As someone emotionally, personally, detached from the Indian subcontinent and its identities this is what I see. What I observe.

As a participant, even at the margins, my perspectives exist as well. Because the social norms in Islam outside of the West look dimly upon irtidāds, my general stance all things equal is to look where the Muslims stand, and take the opposite position. The mainstream view within Islam is that apostasy is punished due to its social and political implications. That is, it is treason. The punishment for treason is death.

Which brings me to reflect on attempting to understanding what Islam is, and why it is the way it is. Most atheists who have never been religious tend to have certain personalities. We’re not really intuitive people. We’re more analytic types. To understand a religion we believe that we should understand its doctrines.

This is easiest with Protestant Christianity, which in the United States of America is defined by a confessional individualistic orientation. That is, religious identity is fluid, and contingent on the freely given profession of faith in the doctrines of a particular sect. More liturgical forms of Christianity, such as Roman Catholicism and Eastern Orthodoxy, are somewhat different, but the overall emphasis on particularities of belief remains.

The landscape changes once one moves to Judaism and Islam, which are both orthopraxic religions. That is, traditional Judaism and Islam have highly developed tradition of religious law which apply to all believers, and not simply religious professionals. At least notionally. Though particular beliefs about the nature of God remain at the heart of customary Judaism and Islam, on the balance formulaic orthodoxy is not given as much overwhelming weight.

Whereas early Christians underwent conflicts over the precise nature of the Trinitarian doctrinal formula, early Muslims divided predominantly along lines of the nature of religious leadership.

When we move to the Dharmic traditions and Chinese and Japanese religion, the landscape alters again. I will forgo exploration of this topic since it is not germane to the post. Suffice to say I am well aware of the diversity and particularity across all these traditions.

Rather, let’s take a step back to Islam. The brutal bully whose life is charmed. The standard narrative is that Islam spread rapidly over a century, from the Indus to the shores of the Atlantic. It is a stupendous feat.

How did this happen? Naturally, Muslims will assert that it was the will of God himself. Islam succeeded in its audacity because it is true. Those of us who are not Muslim do not accept this viewpoint, because to us Islam is obviously not true.

So what explanation can we kaffirs give for this feat? A natural one adhered to by many is that Islam is by its doctrinal nature well suited to obtaining submission, and then in a sort of Stockholm Syndrome those who submit to conquest convert their own identity so they become partners in their own oppression and that of others. This model is one where the sons of pagans, Christians, and Hindus bow before Allah on High and smite the unbeliever in their own turn, in a devilish radius of conquest outward from the center.

And the blueprint is all there in the Koran and the Sunnah. All that one needs to do is to execute the plan was there in the beginning. All the snake had to do was uncoil.

To a great extent, this was my view 15 years ago. Because I was an atheist who had never been religious this made sense to me, because religion was about ideology, and the Islamic ideology was plainly one of submission. After all, Islam means “submission to God.”

Though I have never been a believer in a non-Muslim religion, my impression is that many non-Muslims find this also an easy way to understand Islam. Muslim majoritarianism has traditionally been brutal to non-Muslims, and it isn’t as if Muslims keep their doctrines and practices secret. Their contempt for kaffirs derives naturally from the nature of the religion, not some perverse heritable trait. Muslims are taught to have contempt for non-Muslims. They aren’t born with it.

Of course, there are those who disagree with this position for political and cultural reasons. These are the type of people who claim that Islam is a peaceful religion of tolerance. These people are either lying or deluded. Ultimately they don’t really care about Islam, they care about their own particular positions in culture wars fundamentally having nothing to do with Islam.

Over the years though I have come to revise my views about why Islam is the way it is and how it got to be the way it is. On the whole, I don’t really disagree with my earlier view that Muslims and Islamic societies tend to be characterized by intolerance and exclusion. These are not societies that I would ever want to be a member of. But, I have come to believe that this is less due to the fundamental nature of Islamic doctrine, and more due to historically contingent events. In other words, Islam and Muslim societies are the way they are for reasons that have nothing to do with the doctrines and scriptures of Islam.

This revision in my views has two broad sources. One is the cognitive anthropology of religion. This is a discipline which allows someone like me, who has never been religious, inside the minds of those who believe. Like many sciences, the findings of this field are confusing, startling, and often counter-intuitive. Glossing over the details, I will say though that they have convinced me that the logical consequences from doctrine given by the religious are almost always post facto rationalizations, and not a true inference via propositional logic. This applies to all religions. And it applies to Islam itself.

Consider that 2,000 years ago a poor and pacifistic Jewish preacher triggered a cultural revolution that led to the emergence of a world religion. That world religion eventually became the heart of a civilization that went on to commit the greatest quantity of acts of violent brutality on an aggregate basis in the history of our species. The line between the prince of peace and slaughtering heretics and enslaving Africans is peculiar indeed.

Second, contingent history matters. It will not here recapitulate revisionist scholarship about Islam, but I do not think it unreasonable to contend that much of what we know about Islam developed in the century after the conquest. In other words, the Arabs did not conquer as Muslims, the conquerors became Muslims. The shape of Islam then was defined by the reality that emerged within the context of being an imperial religion, just as the nature of Jews after the failure of the second rebellion against the Romans until the founding of the state of Israel was one of being a pacific and supine religion.

Many Indian commenters on this weblog promote a view of Islam, and the Abrahamic religions to a lesser extent, that is in line with my views from 15 years ago. It’s there right to hold these views, but I will object when individuals assume that these views are self-evidently true. Descriptively I tend to agree with Hindu nationalists that many Muslims of Hindu descent exhibit some level of Stockholm Syndrome, reveling in the brutal conquest of their black ancestors by Muslim Turks. But when it comes to the cause of the symptoms…that is a more complex thing than they are willing to credit in my opinion.

The ideological and missionary impulse of Islam is clearly a real doctrinal thing. And that makes it different from most streams of Hinduism. But there are far more contingent sequences of events than I think we often acknowledge.

Which brings me to the reality that contingent history that has happened cannot be unhappened. The history of Islam within India is a fact. 1,000 years of domination is a fact. Centuries of domination across much of the subcontinent by alien Muslim elites is a fact. It is a fact that the most glamorous ruling dynasty of the last 1,000 years in the Indian subcontinent was that of the Mughals. Though to some extent culturally and genetically assimilated, this ruling dynasty was of Turco-Mongol provenance, and always bowed down to a religion for which India was not holy.

Over the past few centuries, Indians have by and large shucked off Muslim domination. Those areas which are Muslim dominated are no longer India, being distinct nation-states. But the weight of history still hangs over the subcontinent. One could attempt to make the case that the 1,000 years when Muslim ghazis ran roughshod over the subcontinent was an aberration, a fever dream. But the very act of purifying languages of their Arabic and Persian words points to the reality that the serum of the aliens was injected into the veins of Indian civilization.

Pakistanis and Bangladeshis, and many Indian Muslims, especially those of the northern states, have their own deep identity crises. Many of them are raised with a deep and abiding contempt for the traditions and folkways of the non-Muslim peoples of the subcontinent, but on some level most must understand that these non-Muslims are the same people as their own were before the great change. Whereas the vast majority of Persians converted to Islam, and bent the knee to the Arabs for whom they had and still have so much contempt, the majority of South Asians remain non-Muslim. Witness to the cultural identity which Muslims in the subcontinent have turned their backs upon.

And yet many Hindus, envious of the vigor of the Muslims, noticing their international connections, and confused by the bizarre Islamophilic tendencies of the progressive West, may have to admit that the history of Islam is now also part of their history. The Sufi orders which were so instrumental to the spread of Islam served to buttress the great Indo-Islamic polities with their institutional heft, may themselves have been transmuted from Buddhist religious communities early Muslims encountered in eastern Iran and in Turan. If Islam is the snake, then part of the root of the serpent is ultimately Hindu, that is, Indian. It could be no other way, as Islam is the youngest of the great world religions. Constructed from preexistent modules perfected in other traditions. It was a computer assembled at home from commodity parts.

But even aside from older traditions’ roles in shaping Muslim thought, practice, and institutions, the educated Hindu of 1800 AD surely was influenced and impacted by the arrival and domination by Muslims in comparison to their precursor in 800 AD. Today in the West there are neopagans and other assorted post-Christian types who wish to recapture ancestral pre-Christian spirituality. The problem they always run up against is that that spirituality is passed down only due to the efforts of Christians, often clerics, who in the act of selection and modification likely reframed the old ways in more Christian terms. And, the lived pagan tradition was broken long ago, distributed and diffused through rural folk customs among unlettered peasants who transformed rapidly into modern urban Europeans just as the Romantic pagan awakening was beginning.

Obviously, Hinduism does not have such a great rupture. The tradition of Adi Shankara lives on. Religious reformers and innovators such a Chaitanya Mahaprabhu flourished even under Muslim Afghan rule. There is no need to reconstruct and resurrect Hinduism because it is a lived tradition. But Hinduism, Indian culture, Indian nationality, as it was before the Muslims arrived in large numbers is gone, transmuted and transformed into something new. But even if we can’t move backward, there is no shame in moving forward to better things.

Addendum: Muslim scholars, such as Shadi Hamid (and I believe our own Omar Ali), do sometimes claim that Islam is sui generis. That it may be ideologically, constitutively, resistant to secularism and the normal process of pacification of religion. This is not a crazy position and can be well argued, and to be frank, I am quite open to being convinced again of my old views.

Sequence them all and let God sort it out!

Filed under: Genomics — Razib Khan @ 11:14 am

Researchers reboot ambitious effort to sequence all vertebrate genomes, but challenges loom:

In a bid to garner more visibility and support, researchers eager to sequence the genomes of all vertebrates today officially launched the Vertebrate Genomes Project (VGP), releasing 15 very high quality genomes of 14 species. But the group remains far short of raising the funds it will need to document the genomes of the estimated 66,000 vertebrates living on Earth.

The project, which has been underway for 3 years, is a revamp and renaming of an effort begun in 2009 called the Genome 10K Project (G10K), which aimed to decipher the genomes of 10,000 vertebrates. G10K produced about 100 genomes, but they were not very detailed, in part because of the cost of sequencing. Now, however, the cost of high-quality sequencing has dropped to less than $15,000 per billion DNA bases…

Funding remains an obstacle. To date, the VGP has raised $2.5 million of the $6 million needed to sequence a representative species from each of the 260 major branches of the vertebrate family tree. To reach the goal of all 66,000 vertebrates will require about $600 million, Jarvis says.

Though a lot of the details are different (sequencing vs. genotyping, vertebrates vs. humans), many of the general issues that David Mittelman and I brought up in our Genome Biology comment, Consumer genomics will change your life, whether you get tested or not, apply. That is, to some extent this is an area of science where technology and economics are just as important as science in driving progress.

I remember back in graduate school that people were talking about sequencing hundreds of vertebrates. But even in the few years since then, the landscape has shifted. I’m so little a biologist that I actually didn’t know there were only ~66,000 vertebrate species!

And yet this brings up a reasonable question from many scientists who came up in an era of more data scarcity: what are the questions we’re trying to answer here?

Science involves people. It’s not an abstraction. Throwing a whole lot of data out there does not mean that someone will be there to analyze it, or, that we’ll get interesting insights. To be frank, the original Human Genom Project project should probably tell us that, as its short-term benefits were clearly oversold.

In relation to how cheap data storage is and the declining price point of sequencing, I think my assertion that a genome, a sequence, is not a depreciating asset still holds. There is the initial cost of sequencing and assembling and the long term cost of storage, but these are small potatoes. The bigger considerations are the salaries of scientific labor and the opportunity costs. Sequencing tens of thousands of genomes may not get us anywhere, but really we’re not going to lose that much.

Ultimately I side with those who believe that the existence of the data itself will change the landscape of possible questions being asked, and therefore generate novel science. But it’s pretty incredible to even be debating this issue in 2018 of sequencing all vertebrates. That’s something to reflect on.

September 13, 2018

Avars across a sea of grass

Filed under: Avars,Historical Population Genetics — Razib Khan @ 10:29 pm

That sound you hear is the rumbling of the earth caused by the rippling tsunami that’s coming. The swell of ancient DNA papers focused on historical, rather than prehistorical, time periods. Some historians are cheering. Some are fearful. Others know not what to think. It will be. The illiterate barbarians of yore shall come out of the shadows.

If they had arrived on the edge of Europe two centuries earlier, the Avars would have a reputation as fearsome with the Huns, with whom they are often confused, and rightly so. But the Avars emerged as a force on the European landscape after the end of the West Roman Empire. The post-Roman polities did not have their own Ammianus Marcellinus (sorry Bede, you lived in the middle of nowhere).

And yet for centuries the Avars dominated east-central Europe and held the numerous Slavic tribes in thrall. They smashed past the borders of Byzantium during the reign of the heir of Justinian, and by 600 AD, on the eve of the great battle with Persia Constantinople had lost control of most of its Balkan hinterlands to these barbarians. A Byzantium which still controlled North Africa, much of Italy, southern Spain, Egypt, Anatolia, and the Levant, had been reduced to strongpoints all around the Balkan littoral. During the wars with the Sassanids, the Avars took advantage of the opportunity offered, and even raided the suburbs of Constantinople itself!

So who were these people? The most plausible conjecture is that they were part of the great mass mobilization of Turkic peoples which began in the early centuries of the first millennium after Christ. As Rome and Han China fell, nomadic barbarians rose. A new preprint seems to all but confirms this, Inner Asian maternal genetic origin of the Avar period nomadic elite in the 7th century AD Carpathian Basin:

After 568 AD the nomadic Avars settled in the Carpathian Basin and founded their empire, which was an important force in Central Europe until the beginning of the 9th century AD. The Avar elite was probably of Inner Asian origin; its identification with the Rourans (who ruled the region of today’s Mongolia and North China in the 4th-6th centuries AD) is widely accepted in the historical research. Here, we study the whole mitochondrial genomes of twenty-three 7th century and two 8th century AD individuals from a well-characterised Avar elite group of burials excavated in Hungary. Most of them were buried with high value prestige artefacts and their skulls showed Mongoloid morphological traits. The majority (64%) of the studied samples’ mitochondrial DNA variability belongs to Asian haplogroups (C, D, F, M, R, Y and Z). This Avar elite group shows affinities to several ancient and modern Inner Asian populations. The genetic results verify the historical thesis on the Inner Asian origin of the Avar elite, as not only a military retinue consisting of armed men, but an endogamous group of families migrated. This correlates well with records on historical nomadic societies where maternal lineages were as important as paternal descent.

The samples were from a period about a century after the arrival of the Avars. It is not unreasonable to think that the Avar conquest meant that a continuous stream of Inner Asian pastoralists kept entering into the territory which they occupied for the opportunity, but this sort of genetic distinctiveness indicates that the Avars remained very separate from the people from whom they extracted tribute. Most, though not all, of these people, were or became Slavs.

Around 800 AD the Avars were finally defeated decisively by the Franks, and their elite converted to Christianity. I suspect this was the final step which would result in their assimilation over the next few centuries into the location population until they diminished and disappeared.

The results above support the proposition that the Pannonian Avars of the second half of the 6th century were the descendants of the Rouran Khaganate of the early half 6th century. The kicker is that the Rouran flourished in Mongolia! So like the Mongols six hundred years later, the Avars seem to have swept across the entire length of Eurasia that was accessible to their horses in a generation. To some extent, this is a recapitulation of the pattern we see nearly 3,000 years before the Avar, when the Afanasievo culture established itself in the Altai region, far from its clear point of origin in the forest-steppe of Eastern Europe.

Perhaps the period between 500 BC and 300 AD can be seen as an ephemeral transient between the vast periods before and after when pastoralists had free reign across most of temperate Eurasia?

Gods and wizards in fantasy

Filed under: Fantasy — Razib Khan @ 7:22 pm

A reader in the comments pointed me to Vice and Fire (though I’d already seen it on Twitter), a rumination on 20th century and 21st century fantasy literature by Peter Hitchens in First Things. Hitchens is the religious and politically conservative brother of the late Christopher Hitchens.

The piece is curious because it reflects more about Hitchens than the material which he is describing. First, he begins with perplexity that J. R. R. Tolkien’s secondary world seems to lack a moralistic high religion, as we’d understand it. To Hitchens this is confusing in light of the fact that Tolkien was a very religious Roman Catholic in his own life. But it isn’t as if Tolkien scholars haven’t noticed this juxtaposition, or the contrast with C. S. Lewis’s style, who was extremely heavy on Christian allegory.

I think the most plausible explanation is that Tolkien had something of the same issue as L. Sprague de Camp. An aeronautical engineer by training, Isaac Asimov in his autobiography In Memory Yet Green recounts that de Camp made the shift to explicit fantasy away from hard science fiction because his professional background made it difficult for him to engage in the suspension of disbelief necessary to write plausibly about faster-than-light travel and other such things. In fantasy his own background did not get in the way of his creativity.

Like de Camp, Tolkien was gifted with knowing too much. This was a man whose legendarium was an attempt to create for the English people a mythology similar to what the Scandinavians and Irish took for granted. A philologist who was a scholar of Beowulf, Tolkien knew the whole cultural corpus of the ancient pagan Germanic people well. He mined their mythos in constructing the world in which he set his fiction. As such, he was aware of the violent brutality which characterized pre-Christian, and frankly pre-civilized, Northern Europe, and how its folkways were at variance with Christian morality. If Tolkien applied his scholarly skills to creating religions for the Men of the West, it seems unlikely that he would have been comfortable sanitizing what he knew their practices would be. On the other hand, as an invented secondary world of the imagination, it was not plausible that they would be Christian, and in any case, Tolkien was a sincere and devout believer in the Christian religion and may have been uncomfortable mixing his imaginative fictional world with the metaphysical truths he held sacred.

And yet this does not mean that the ethical monotheism which J. R. R. Tolkien personally adhered to did not bleed into his work. In Return of the King, there is a well-noted reference to “heathen kings” and their practice of burning the dead. The Men of the West may not be Christians, but nor were they pagans.

Which brings me to Hitchen’s diatribe against George R. R. Martin’s attitude toward religion. Unlike Tolkien, Martin seems irreligious. Some fantasists, such a Anne McCAffrey and Ursula K. Le Guin, have created worlds where theism is understated or nonexistent (the Kargads in Earthsea do have something that we’d recognize as a religion grounded in gods…but they are the “bad guys”). Not so with Martin. His world exhibits a great deal of religious complexity and verisimilitude.

Perhaps too much verisimilitude for Peter Hitchen’s taste. Let me quote at length a description of the religions as from the piece above:

Some readers of Martin’s stories see a kind of Christianity in the worship of “the Seven.” This is the most official of several religions in ­Westeros, described in this way: “Worship was a septon [priest] with a censer, the smell of incense, a seven-sided crystal alive with light, voices raised in song.” There are a Father, a Mother, and a Smith. Then there are the Crone, the Maiden, the ­Warrior, and finally the Stranger, who ­represents death. Although the Seven faintly echo the Trinity, there seems to be no equivalent of Christ or the Holy Ghost among them, let alone of the One God. This is not Seven in One and One in Seven but Seven in Seven. I would say that the Seven are much more like classical or Nordic pantheons than like the Trinity…The worship of the Seven is exactly what atheists think Christianity is: an outward vesture.

A rival older faith, officially tolerated, survives in silent groves of ancient trees. There is also a rather nasty Drowned God, who seems to encourage piracy among seafarers (which suits them very well), and a highly intolerant Red God with a touch of the Cathars, but which (unlike the others) manifests itself in acts of violent wizardry and second sight. This is the deity that flourishes in the sweltering, cruel east, and no wonder. So we have on the one hand a vague expression of civic virtue, empty of real force and truth, and on the other a manifestation of supernatural might, quite unconnected with goodness and very ready to ally itself with earthly power if it suits them both. This recalls the way in which, in our time, science and power walk hand in hand, often destructively and dangerously.

This is where it strikes me that the author had a hammer, and everything was a nail. There’s some truth to what he’s saying. The religion of The Seven is never outlined in great detail in comparison to other quasi-medieval aspects of Martin’s world. But there is a backstory to this: apparently the religious institutions were subordinated and suppressed to some extent by the previous Targaryen dynasty (who were clearly only nominal converts in any case). The fact is that the Faith of the Seven is monotheistic, where each god is a manifestation of the single ultimate God. And, it is a religion derived ultimately from revelation to the Andals in Essos. This is not a naive and organic tribal paganism.

As for the religion of the Red God, Martin has admitted that its spread to Westeros is modeled explicitly on the spread of Christianity. It is intolerant, but so was the spread of the religion which Peter Hitchens is a personal devotee of. On the Isle of Wight the last pagans were mostly killed by invading Christians due to their reluctance to adopt the new religion. He claims to have read the books, but he gives no indication that the Red God is a favorite of the Brotherhood Without Banners, who fight to defend the common people against the depredations of warring lords. Though the Red Priest Melisandre commits evil, like those Protestants who burned witches in Northern Europe, she believes that any suffering is ultimately to further the good. The brutality of the followers of the Red God is the other face of the fact that they are zealous and on fire for their faith, and believers who have faith that they walk in the path of virtue. The Cathars who Hitchens allude to were persecuted and then slaughtered by the orthodox Christians.

What explains Hitchen’s bile then? I am being pedantic on the points he makes about Tolkien and Martin in part because not all readers of the above essay will have read the source material, and will take his misrepresentation at face value. But it is true George R. R. Martin’s worlds exhibit a high level of brutality and perversion. When I first read Martin’s work I just finished Bernard Cornwell’s Warlord Chronicles, which is a retelling of the Arthurian legend fixedly in post-Roman Dark Age Britain. I decided to email Martin to ask him if he was perhaps influenced by this work, and he did admit that he was a great admirer of the Warlord Chronicles. Martin has said repeatedly that his work attempts to show that just because someone takes a vow of knighthood does not necessarily entail that they are virtuous. As a point of fact many knights in the European Middle Ages were little better than mercenaries and brigands. Codes of conduct and broad ethical frameworks exist in part to tame, constraint, and smooth out the rough edges of military elites who rule by force of arms.

Additionally, like fantasist Robin Hobbs, Martin does not engage in plotting where your precious ones will always come out unscathed. This is a painful feature, not a bug. The idea is to humanize the protagonist, sometimes uncomfortably verging on creating anti-heroes, and to contrast the highs of the payoff with some major lows. The way Martin does this bothers many people, and I think it’s within their rights to be bothered. But for those of us who have read more anodyne and more juvenile fantasy works, encountering Martin’s work was a bracing shock and made us want more precisely because of the rougher texture and sharper edges.

Finally, there is one aspect where George R. R. Martin explicitly attempts to mimic J. R. R. Tolkien, and this is in creating a “low magic” world. More honestly, Martin’s magic is actually magic, rather than a different form of science and engineering. When Martin’s series began to gain prominence, fantasy had fallen into a period where formulaic magical elements resembling Dungeons and Dragons had saturated the genre, to the point where lazier authors often made recourse to magical deus ex machina. If you remember back to Tolkien you observe that there really wasn’t that much magic, and you never saw Gandalf cast spells like a carnival act.

Ultimately George R. R. Martin is attempting to pull off several things at once, and obviously he isn’t always doing it well, nor does he fulfill all the expectations of his readers. The broader framework of the world he is creating does exist in a sort of good vs. evil paradigm with dark magical forces. But Martin enjoys shades of gray, and coming from a background as a Hollywood screenwriter, he worked hard, perhaps too hard, to give his characters moral complexity. They are often both saints and sinners. Finally, though A Song of Ice and Fire is epic high fantasy, he has injected into its veins an element of dark historical fantasy. This does not not always work, and I suspect readers keying in on the high fantasy elements are easily repulsed by the frank brutality and amorality of the historical fantasy. To make an analogy, the flavors clash. Your mileage may vary on whether this is good or bad.

September 12, 2018

The genetics of Afrikaners (again)

Filed under: Afrikaner genetics,Historical Population Genetics — Razib Khan @ 10:18 pm
Click to enlarge

 

I personally get asked about the genetics of Afrikaners, because I’ve written about/analyzed the issue before. The main outlines seem to be established, but I thought I might go and revisit it again. The main reason is that we have ancient South African DNA, and I’ve been adding it to my personal analyses for a while. It might be worthwhile to reanalyze the South Africa samples I do have with some of these added in.

The plot at the top shows the core populations I started with. I did some outlier pruning. I only kept the South African samples that were overwhelmingly white. I picked Malays and a South Indian population because of Cape Coloureds, a mixed-race Afrikaans speaking group which has Asian ancestry that can be attributed to both South and Southeast Asian populations (the Dutch imported many slaves from India and had outposts in Java). I also used Bantu samples from South Africa, Kenya, as well as a Nigeria population. Finally, I also had some Hadza as a different hunter-gatherer population than the San Bushmen. For Europeans, I used white Dutch.

The final marker density as 200,000 SNPs, so not too bad.

As you can see if you click on the image all of the South African whites were shifted away from the Dutch. There were two outlier individuals, one of which was closer to the Dutch cluster, and one further. All the other individuals form a neat cluster. None of these individuals were close relatives.

Click to enlarge

I ran Treemix on the data with multiple migrations until the migrations stopped making sense to me. The African populations’ exhibit migration flows to each other. Much of it is entirely comprehensible. The Esan receive no migration, highlighting that this population did not receive gene flow from any groups in these data. The Kenya Bantus receive gene flow from the direction of Eurasians. This is also certainly Nilotic mediated. The gene flow they receive from the base of the ancient San is more enigmatic, but probably reflects uptake of local ancestry as the Bantus expanded. The southern Bantus receive gene flow from modern San.

The South African whites receive gene flow from a position on the graph between the modern San and other non-San African groups.

Click to enlarge

Next, I ran Admixture in the unsupervised mode with K = 6. The two populations mostly light-blue are South African whites and the Dutch, from the top to the bottom. You can see though that the South African whites clearly have other ancestral components. Most of these individuals have the components modal in the San, Esan Nigerians, Indians, and Malays. The two outlier individuals are also clear. The individual very close to the Dutch, but shifted toward the Asians, in the PCA does not have any African admixture. The individual shifted more toward the non-Europeans in the PCA also has more non-European fractions of ancestral components (that is, those components modal in non-European populations).

Next, I decided to confirm things by running a three population test. If you read this blog you’ve seen this before. Basically this is measuring shared ancestry by looking at deviations from a particular phylogenetic model: (test population(pop 1, pop2)). The relatedness of the test population to either pop1 or pop2 (that is, it’s a mix of the two) is measured by the negative f3 statistic, and I focused on z-scores greater than two.

Here they are:

Outgroup Pop1 Pop2 f3 z
Bantu_NE EsanNigeria Dutch -0.0009 -6.54
Bantu_NE EsanNigeria South_Africa_White -0.0010 -6.54
Bantu_NE EsanNigeria Malay -0.0009 -6.33
Bantu_NE EsanNigeria Telegu -0.0008 -6.00
Bantu_NE Bantu_S South_Africa_White -0.0008 -4.84
Bantu_NE Bantu_S Dutch -0.0008 -4.77
Bantu_NE Bantu_S Malay -0.0007 -4.21
Bantu_NE Bantu_S Telegu -0.0007 -4.05
Bantu_NE Dutch San_Ancient -0.0009 -3.02
Bantu_NE Hadza EsanNigeria -0.0004 -2.97
Bantu_NE Telegu San_Ancient -0.0007 -2.32
Bantu_NE Malay San_Ancient -0.0007 -2.04
Bantu_S EsanNigeria San_Modern -0.0028 -21.62
Bantu_S EsanNigeria San_Ancient -0.0039 -20.78
Bantu_S San_Ancient Bantu_NE -0.0030 -12.91
Bantu_S San_Modern Bantu_NE -0.0019 -12.45
Bantu_S Dutch San_Ancient -0.0031 -10.63
Bantu_S Telegu San_Ancient -0.0030 -10.33
Bantu_S San_Ancient South_Africa_White -0.0027 -9.17
Bantu_S Malay San_Ancient -0.0029 -8.97
San_Modern Dutch San_Ancient -0.0091 -34.96
San_Modern Telegu San_Ancient -0.0087 -33.86
San_Modern San_Ancient South_Africa_White -0.0089 -33.54
San_Modern San_Ancient Bantu_NE -0.0063 -31.93
San_Modern Malay San_Ancient -0.0085 -30.98
San_Modern Bantu_S San_Ancient -0.0052 -28.91
San_Modern Hadza San_Ancient -0.0051 -27.58
South_Africa_White Dutch Bantu_NE -0.0017 -12.96
South_Africa_White EsanNigeria Dutch -0.0017 -12.68
South_Africa_White San_Modern Dutch -0.0018 -12.41
South_Africa_White Bantu_S Dutch -0.0017 -12.36
South_Africa_White Dutch San_Ancient -0.0021 -12.14
South_Africa_White Hadza Dutch -0.0014 -10.41
South_Africa_White Malay Dutch -0.0007 -5.97
South_Africa_White Telegu Dutch -0.0003 -3.64
Telegu Malay Dutch -0.0004 -2.79

 

No surprises so far. One thing that did surprise me though was the extent of the admixture even after PCA outlier removal. So I took the output you saw above and removed individuals that were very mixed, except for the case of the white South Africans. Then, I ran admixture in supervised mode, where the “pure” populations were fixed as references (I merged the moden San without much admixture with the ancient San). You can see the results below:

Click to enlarge

Re-running the three population test with these “pure” populations I only got significant results for the below cases:

Outgroup Pop1 Pop2 f3 z
South_Africa_White Dutch EsanNigeria -0.0017 -13.1937
South_Africa_White San Dutch -0.0020 -12.6910
South_Africa_White Hadza Dutch -0.0014 -9.7246
South_Africa_White Malay Dutch -0.0009 -6.6481
South_Africa_White Telegu Dutch -0.0004 -4.6167

No big surprise.

The average European ancestry I got in my South African white samples, N = 12, is 93.5%. Making a composition individual, note that if someone had great-great-grandparents who were not European, they would be expected to have 6.25% non-European ancestry. That’s 4 generations back. So about 100 years. These individuals are presumably adults. Let’s say they are 25 years old. That goes back 125 years. It’s probably reasonable in a single person admixture people to suggest it was sometime in the mid to late 19th century.

This seems unlikely. The evenness of admixture and balance between different groups indicates that it is older than that, and they are obtaining it from different lineages. Traditional genealogical estimates suggested in the range of 5-7.5% non-European ancestry in Afrikaners, and one study of 185 individuals showed 18% non-European mtDNA.

I will probably some ancestry deconvolution and see if I can get a figure for the time of admixture (though the fractions here are very small, as is the sample size of the admixtured population). But the non-European ancestry of Afrikaners is uncannily similar to the non-European ancestry of the Cape Coloureds. That to me leads us to the conclusion that in the early European settler community a fair number of mixed-race women married in. Those mixed-race women who married mixed-race men helped found the Cape Coloureds.

On the instrumental uses of Arabic science

Filed under: Arabic science,History of Science,Ibn Sina,Islam,Muslim Science — Razib Khan @ 8:41 pm

A new piece in Aeon, Forging Islamic science: Fake miniatures depicting Islamic science have found their way into the most august of libraries and history books. How? is quite rich food for thought. The nuts & bolts of the story are interesting enough, but perhaps the bigger picture is the emergence of (to borrow a phrase) “the idea of Islamic science.”

On the most general level, the spread of these obvious fakes is a matter of the epidemiology of ideas. Basically, the ubiquity of these fakes is like the spread of chain letters or viruses which hack our cognitive biases. By analogy, consider the fondness for Qing China exhibited by some early modern European thinkers, such as Leibniz and Voltaire. With hindsight, it is clear that their affection for Chinese civilization was a reflection more upon their critique and aspiration of their own civilization. For Leibniz, bureaucratic rationalism, and Voltaire, secular humanism.

Centuries on their Sinophilia is of academic interest as a fragment of cultural history which brings into salience particular currents which bubbled up during the period of both European modernization and development vis-a-vis the rest of the world, and the last contact that European civilization made with a powerful and self-assured alien civilization, that of China under the Kangxi Emperor, Yongzheng Emperor, and Qianlong Emperor. If you want to understand China during this period, its culture and politics, then these early modern thinkers are not the ones to consult. Their opinions and views on China shed more light on currents in their own culture than the reality in China.

A similar thing happened to Islam and Islamic civilization after the 18th century.  As Western civilization was secularizing some intellectuals pointed to the world of Islam as evidence that some tolerance of pluralism would be sustainable and preferable. What is being alluded to here is the system of formalized tolerance of the “People of the Book”, dhimmis, within Islam from its earliest period. But the highlighting of the Muslim alternative was less about Muslims and more about the reality of a post-Reformation early modern Europe riven by sectarian pluralism, as well as incipient secularization of a substantial numbers of intellectuals who began to perceive themselves as dissenters from the regnant orthodoxy as a class.

There is a scholarly study that engages in the exploration of the development and crystallization of the Muslim system of tolerance of religious minorities. That scholarship plumbs into the depths of the early formalization of Islam as a distinctive confession and civilization, and its roots (including the tolerance of dhimmis) in Byzantine and Sassanian practice. But when most people speak of the tolerance of early Islam in the West, they are speaking about and engaging issues related to the West, not Islam, which is simply a tool or instrument in an argument particular to factions within the West.

Going back to this specific issue, the fabrication of the depiction of “Islamic science,” there is a particular social and cultural context in the West that needs to be highlighted (as opposed to the Muslim world, which is a somewhat different dynamic, and analogous to the rise of Vedic science). Early modern secular intellectuals who contrasted the intolerance of Christian civilization to the relative tolerance of Islamic civilization were working implicitly within a modernist framework where objective truth would eventually pave the way for a universal civilization which would evolve out of the post-Christian West. This attitude is exemplified by the liberal French nobleman, Stanislas Marie Adélaïde, comte de Clermont-Tonnerre, who when arguing for removing various restrictions on Jews declared “We must refuse everything to the Jews as a nation and accord everything to Jews as individuals.”

These modernist conceits of clear and distinct universal truths and moralities leading to a common human ethos have fallen by the wayside. Rather, today many who espouse multiculturalist viewpoints are careful not to aver that one culture is superior or more advanced than another. This assumption means that today many reject a progressive and Whiggish view of history which implicitly highlights Western exceptionalism between 1700 and the current age.

These people may not be comfortable with the assertion that the form of intellectual inquiry that emerged out of Renaissance natural philosophy that we today call science is sui generis. A particular expression of the genius of Western civilization. Rather, what it is appealing toward many with a multiculturalist viewpoint, where all cultures have notionally similar ethical values, is that all cultures produce their own form of science, just as valuable, exceptional, and illustrative of universal human genius.

With Islam and science anyone with superficial interest in the topic can be easily convinced of the genius of individuals such as Ibn Sina. If the the great Bukharan polymath had been born today it would not be surprising if perhaps he became a scholar of some renown. But the reality is that most of the people who will tell you that Islam once had great scientists could not name a single scientist of pre-modern Islam. Just as with Voltaire and the Chinese, modern Western intellectuals who have moved beyond Whiggishness and naive modernism see in other cultures something that serves to critique and comment on their own. The legend of Islamic science is an instrument, a tool, in a particular deconstruction of the “myth” of Western science.

A curious aspect of this viewpoint, which is in some ways highly relativistic in relation to epistemology (“other ways of knowing”), is that it is also highly universalistic in ethics. Other cultures are shoehorned into frameworks and paradigms of Western making, particular mirrors through which all are seen darkly.

This is the same observation that could be made of early modern Whiggishness, where all cultures are seen as ascending slowly up a ladder of complexity and progress, with Northwest Europe in particular leading the way. Whigs viewed history in a linear fashion, and all societies could be placed along the sequence.

So what’s the multiculturalist/progressive/post-modern analog? It is common today in progressive Western circles to strive toward radical gender, sexual, and ethnoreligious egalitarianism. Justice. Many a time I have seen that patriarchy or sexual traditionalism are presumed to be colonial (white, Western) impositions on other societies. Western Muslims of a progressive bent may even assert that Islam is fundamentally and originally feminist and egalitarian. Hindu progressives likewise may highlight the depictions of sex acts Khajuraho temple complex as indicative of a liberal and tolerant attitude toward these matters before the arrival of the British, who introduced conservative bourgeois morals (note that often the terminology itself points to the operation of these individuals in a very Western tradition).

Nearly two hundred years ago the British Whigh politician Thomas Macaulay declared:

“We must at present do our best to form a class who may be interpreters between us and the millions whom we govern; a class of persons, Indian in blood and colour, but English in taste, in opinions, in morals, and in intellect. To that class we may leave it to refine the vernacular dialects of the country, to enrich those dialects with terms of science borrowed from the Western nomenclature, and to render them by degrees fit vehicles for conveying knowledge to the great mass of the population.”

Today progressive Westerners would never say such a thing. In part, because they would never assert that the West, and its culture, was in any way superior to that of the non-West. On the contrary, the tacit assumption might be that it was the West which manufactured and perfected the modes of oppression which spread across the world and caused human misery. With decolonization and the recession of Western imperialism, one would then see a diminishment of oppression and presumably human misery.

The difference between a 19th century liberal such as Thomas Macaulay is that whereas he perceived that the Indians would have to change their morals and develop their intellects to ever be equal to the English, today his progressive counterpart fundamentally assumes that the natural state of humanity was one of moral and intellectual equivalence. That is, oppression, the subjugation of women and minorities, the “marginalized”, was invented by Western Europeans, and imposed on non-Europeans. It is Western colonialists who brought the sin of oppression into the garden. They were responsible for the fall from ethical perfection, the stage of original grace.

Non-Europeans do differ from Europeans, but only in matters of detail, outward dress, food, and architecture. Accidents. But in matters of essence, there is no difference at all.

This conceit leads to all sorts of confusions.

After purchasing his papers, John Maynard Keynes declared Isaac Newton “was the last of the magicians, the last of the Babylonians and Sumerians.” One can not deny that Isaac Newton was a genius, invariant of the age. Nor can one deny his scientific contributions, which modern undergraduates doing any scientific course of study must master to some extent. But the world of Isaac Newton was a different world, where witches were still burned, and men and women the British Isles could still be executed for atheism. People did science, but not quite in the modern way. People were religious, but not quite in the modern way. There is a gap between 1700 and 2000.

Similarly, the ancient Greeks did science. But it was different from modern science, which is contingent on a sequence of events which are rooted in the latter Rennaissance. Did the Muslims of the “Islamic Golden Age” do science? I would say so. But like the Greeks, it was different from what came later (one could say the same of the “Aristotelian Renaissance”).

One must take the history of different cultures on their own terms, and understand them in the broad scope of human history. Theories are useful, but only in concert with a genuine engagement of the empirical record. Whigs and Marxists had theories, which grasped at essential fragments of reality but often obscured critical detail. There is a particular type of fashionable intellectual today who claims to eschew theory and focus on “thick description,” who nevertheless sneaks a particular theory of history through the back door, a variant of the “Noble Savage.”

In particular relation to “Islamic science,” there is some interesting detail in the texture of reality that is exposed when we attempt to understand it on its own terms. One thing which jumps out at you is that since most people are not particularly interested in the details, the terminology you use matters a great deal. Usually, we are focusing on the period between 750 A.D. and sometime around 1000 A.D. Now, when you use the term “Islamic Golden Age” or “Islamic science,” you obscure the reality that many prominent intellectuals during this period were not Muslim.

For example, Thabit ibn Qurra was a Sabian, which referred to the pre-Islamic and pre-Christian inhabitants of the city of Harran. The natives of Harran seem to have preserved religious traditions from Mesopotamian antiquity, in particular, astral cults. Additionally, they were also preservers and connoisseurs of Greek philosophical thought.

Though Sabians were exotic, Christians were dominant features of the scene during the early years of Islam and were instrumental in translation and preservation. In the Aeon piece, the author suggests that it should be called “Arab science” as opposed to “Islamic science.” But among the Muslims, most of the great thinkers were Iranians. That is Persians, or from related peoples. It is true that they wrote in Arabic, but Arabs were only a minority of the subjects of the Arab Caliphates before 1000 A.D. One reason Al-Kindi is exceptional is he was an Arab of the Arabs. A scion of an Arab tribe, with a lineage rooted in that ethnicity before Islam.

Matthew Cobb, an evolutionary biologist, uses the term “Arabic science” in his work to avoid these confusions. This reflects the fact that Arabic was the medium of communication between these scholars, irrespective of religion and ethnicity. In this way, it’s analogous to “Latin science,” which is probably a good term for the intellectual tradition which flourished in Western European during the Aristotelian Renaissance, and later on into the early modern period.

The universal moral of the story is that understanding history, and intellectual history, in particular, is hard. One must balance between commensurable universality and startlingly different local particularity. What is easy is co-opting and hijacking the shape of reality for one’s own ideological preferences. Humans are natural system-builders, theoretical thinkers. The reason being that systems allow one to come to conclusions without doing much research. Logical inference from presuppositions takes more mental effort than an intuitive reflex. But, it takes far less effort that researching the abyss of data from which one can make robust and genuine inferences, and test one’s theoretical reflexes.

But that journey is rewarding. Because it leads to understanding other peoples as ends unto themselves, rather than instruments.

Season 2, Episode 1: The Legacy of L. L. Cavalli-Sforza

Filed under: anthropology,Evolution,Genetics,History — Razib Khan @ 1:15 pm
L. L. Cavalli-Sforza, 1922–2018

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we discussed the life and legacy of L. L. Cavalli-Sforza, who died on August 31st, 2018. See the Stanford obit. From John Hawks, The man who tried to catalog humanity on Medium is probably the most thorough review of his life and works.

Cavalli-Sforza’s magnum opus

We discussed the popularization of PCA and phylogenetic trees by Cavalli-Sforza and his colleagues, outlined in his magnum opus The History and Geography of Humans. The methods of analysis developed in the 20th century prepared us for the avalanche of data we confront into the 21st century.

Also, Cavalli-Sforza’s collaboration with Marcus Feldman that laid the seed for the field of cultural evolution. See the book Cultural Transmission and Evolution. Today the field of cultural evolution is being pushed by researchers such as Joe Henrich.

Cavalli-Sforza was also instrumental in synthesizing the application of formal demographic models to archaeology. See The Neolithic Transition and the Genetics of Populations in Europe.

L. L. Cavalli-Sforza remained active into the 21st century. See this interview from 2012.

After his retirement, several labs have carried on the project of exploring population genetic history. David Reich’s lab’s publications. Also, see Eske Willerslev’s work.

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. A 2008 study that uses the HGDP sample on a SNP-array, bringing The History and Geography of Humans into the 21st century!

Finally, the cultural anthropologist wrote a full-length biography of L. L. Cavalli-Sforza’s life, with a focus on his scientific contributions, A Genetic and Cultural Odyssey.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Season 2, Episode 1: The Legacy of L. L. Cavalli-Sforza was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

September 11, 2018

The Munda as upland rice cultivators

Filed under: Genetics,Munda — Razib Khan @ 7:32 pm


I’m reading Ben Keirnan’s Viet Nam: A History from Earliest Times to the Present. I picked it up mostly because over half the book does not consist of the history of the Vietnam War (a major failing I’ve noticed with books which are histories of Vietnam, as opposed to histories of Vietnamese-American relations).

The section on Austro-Asiatic languages (Vietnamese is one) has something of relevance to the “Munda question”. But before that, let me review a few things.

Until very recently many historians and prehistorians of India have suggested that the Munda people, who speak very distinctive dialects related to the Austro-Asiatic languages of Southeast Asia, are the primal people. That is, they are the aboriginals. The original adivasis.

I do not believe that this case is tenable. Because I am a geneticist, I make this judgment on genetic grounds. Chaubey et al., Population Genetic Structure in Indian Austroasiatic Speakers: The Role of Landscape Barriers and Sex-Specific Admixture, reveals what we know about the genome-wide patterns in the Munda.

1) They are highly enriched for East Asian ancestry compared to other South Asians.

2) Many Munda males carry a haplogroup, O-K18 (once O2a), that is very common in Southeast Asia, especially Austro-Asiatic groups. Additionally, it is more diverse in Southeast Asia. The Munda O-K18 branch seems to be a side shoot from the broader Southeast Asian tree.

3) The Munda mtDNA, defining the maternal line, is uniformly South Asian. This is in contrast to the situation with Bengalis, who have East Asia Y and mtDNA. This indicates that the Munda migration was heavily male-mediated.

4) The Munda carry mutations in genes that are associated with recent selective sweeps in East Asians (e.g., on the EDAR locus). Though this may be a parallelism, it’s unlikely. Rather, it is through shared common descent that this occurs.

The Genomic Formation of South and Central Asia has a graph which shows population relationships and gene flow that illustrates important aspects of the Munda ethnogenesis (Juang below):

AASI in this model = Ancient Ancestral South Indians. These are very distantly related to Andaman Islanders, Australo-Melanesian Southeast Asians, and more distantly to eastern Eurasians generally. They are likely aboriginal people to South Asia, with no West Eurasian ancestry.

The model above indicates that an East Asian (Austro-Asiatic) population encountered an AASI population and produced a daughter population. Then, that daughter population mixed with an ASI population, ASI being an old and stable mix of West Eurasian Iranian farmer (~25%) and AASI (75%).

This means two things for the Munda. First, they are very AASI enriched. This is obvious in any analysis. And, their West Eurasian ancestry is almost all Iranian farmer and not steppe. This is totally not surprising either. Using more naive model-based clustering Munda samples always seem to lack the components which are most easily adduced to be Indo-Aryan. They have very low frequencies of Y haplogroup R1a1a-Z93.

Let’s take a step back now. The fact that the Austro-Asiatic males arrived when there were unmixed AASI indicates that this was somewhat early. There are no unmixed AASI on the Indian subcontinent today. When we reach the Iron Age, by 500 BCE it is clear that Indo-Aryan society had pushed at least to Bihar. This component would bring steppe ancestry, as well as mixing into any remnant AASI.

So when could the Austro-Asiatics have arrived at the earliest? Two papers with extensive ancient DNA, Ancient genomes document multiple
waves of migratin in Southeast Asian prehistory
and The prehistoric peopling of Southeast Asia give us a good sense. It seems that the expansion of Austro-Asiatic farmers dates to about 4,000 years ago. That is when the transition seems to occur in northern Vietnam.

One thing that is also evident: the East Asian gene flow into the Munda seems to come from northern Austro-Asiatic groups in Thailand, not the southern branch which resulted in the people of the Nicobar Islands and was eventually submerged by Austronesians. On a final note, a site in northern Burma yielded an individual who was clearly Tibeto-Burman, and not Austro-Asiatic, 3,000 years ago. So even at that date mainland Southeast Asia was heterogeneous.

But, considering that there is no evidence of Tibeto-Burman ancestry Munda, whose Austro-Asiatic ancestry seems to have come through Burma through a mainland route (as opposed to up from maritime Southeast Asia), I think one should push the date of their arrival before 1000 BCE. With the expansion of farming in mainland Southeast Asia at around ~4,000 years ago, that puts the arrival of a distinctive Munda culture in South Asia to between 2000BCE and 1000 BCE. It is entirely reasonable that during this period there were unmixed AASI in eastern South Asia, though the admixture graph may also be picking up assimilation Austro-Melanesian ancestry in southern China/Southeast Asia.

This is where Viet Nam: A History from Earliest Times to the Present comes in: the author suggests that the early Austro-Asiatic farmers were dry-land rice farmers who occupied uplands. The reason being that reconstructed Austro-Asiatic common words for rice culture is indicative of dry-land practices, with later wet-rice terminology often being borrowings from Tai and Austronesians.

I don’t know enough Indian archaeology and agricultural history to comment further, but, a visual inspection of where Munda are concentrated does suggest upland farming….

September 10, 2018

This is a trial run (I hope!)

Filed under: ancient protein,phylogenetics — Razib Khan @ 10:14 pm

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny:

Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa. Outside the permafrost, however, irreversible aDNA post-mortem degradation has so far limited aDNA recovery within the ~0.5 million years (Ma) time range. Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides direct access to older genetic information, though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae using ~1.77 million years (Ma) old dental enamel proteome sequences of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus). Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference, and also provides additional information about the sex and the taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

Dmanisi. If that doesn’t mean something, look it up!

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