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

March 19, 2018

The western wolves are back, did you notice?

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

Tensions rise on the range after wolf kills cow in California for the first time in a century:

A wolf has killed a California rancher’s cow for the first time in more than 100 years, raising tensions in the newly reclaimed wolf country in California’s rugged northeastern corner.

California now has two packs in the north. This isn’t world-altering. Perhaps it was inevitable. But sure crept up on me.

Oregon now has nearly 100 wolves. There’s even a pack which wanders the mountains above the town I grew up in!

The gray wolf habitat is forest, so much of California won’t see a swarming of wolves because it is desert or cultivated. But it seems very unlikely that the Shasta pack doesn’t presage an expansion of wolf territory west toward the Pacific, and then down into vast timberlands reaching toward San Francisco. And wolves will surely move south along the western edge of the Sierras.


Denisovans, Neanderthals, Yetis, oh my!

Filed under: denisovan,Human Evolution — Razib Khan @ 12:47 am

An excellent open access paper is out in Cell which explores the distribution of archaic hominin, and in particular Denisovan, ancestry, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture:

Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

Before you get caught up in the results, you should check out the methods. They’re pretty ingenious. Though with novel results like this people also really need to work their way through them as well (the authors present a lot of simulation results to validate the method, so I’m sure that will convince most; it certainly sways me).

The plots at the top of this post show the different distribution of Neanderthal and Denisovan admixture, by matching regions of the genome that they’ve identified as archaically introgressed. The ultimate logic is to look for variants which aren’t found in Africans, and are found in non-Africans, and scan over segments of the genome hoping that you can pick up the haplotypes that would slowly be chopped up over time through recombination that came in from Neanderthals or Denisovans.

At the top-left of the figure, you see “Northwest Europeans.” The segments tend to concentrate at the bottom-right of the panel. That means that they match the Neanderthal reference sequence to a high degree, but not the Denisovan. This makes sense since everything we know from earlier work indicates that Northwest Europeans don’t have Denisovan ancestry.

On the bottom-right you see Papuans. They’re very out of place because they are the only population in the list where Denisovan ancestry is greater than Neanderthal ancestry. This is visible in the match patterns.

South and East Asian populations exhibit a pattern with high (relative) levels of Neanderthal matches, but also a minor amount of Denisovan matching. This aligns with earlier work, which reported low levels of Denisovan admixture among populations with eastern Eurasian ancestry broadly.

The surprise is that the variation in matching to the Denisovan Altai genome exhibited a north-to-south cline. In particular, Northeast Asian populations seem to have a mix of two types of Denisovan. One, which is close to the Denisovan sequence that is normally used as a reference, and one which is diverged from it. The Papuans and South Asians seem to have Denisovan ancestry which is not so much like the Altai sample. This is not very shocking of course.

Finns barely miss the p-value cut-off (Bonferroni-corrected threshold), but they clearly have some Denisovan from East Asian gene flow, and some of it looks to be similar to the Altai Denisovan. Curiously, the Vietnamese (Kinh) don’t show any Altai Denisovan, but the Dai do. The Japanese have a lower proportion of the Altai Denisovan than the two Han Chinese samples. And very strangely the 1K Genomes samples from the New World, a substantial proportion of which have Amerindian admixture, show no Denisovan.

Pontus Skoglund immediately made a very interesting observation:

And Alexander Kim followed up:

In the thread to Skoglund’s original comment Africa Gomez notes that the authors suggest that high linkage disequilibrium in New World populations, due to recent admixture between diverged groups, may reduce the power to detect the Denisovan ancestry. So perhaps that’s that?

But for a moment, let’s set that aside. The best evidence right now is that the Denisovan admixture into Papuans, and therefore South Asians, occurred not too after the Neanderthal admixture event. That mixture is reasonably well dated because of ancient genomes which are closer to the period of admixture. But what about the second event with the Altai Denisovan? If what Skoglund says is true the date for that might be closer to the Last Glacial Maximum, and not when modern humans came to dominate the region. And I say dominate because there’s evidence that anatomically modern humans may have ventured quite far into eastern Eurasia before they finally swept aside more established lineages.

A few years back researchers found that one of the mutations that allow for Tibetan high altitude adaptation seems to have come in from a Denisovan genetic background. Spencer Wells, who knows a thing or two about Central Asia, has always half-seriously suggested that the legends of the Yeti derive from populations of archaic humans who persisted in the uplands of the heart of Eurasia.

But perhaps they weren’t pure Denisovans in any case. Work out of David Reich’s lab has suggested that Denisovans themselves, or at least the Alta Denisovan, harbors a deep ancient lineage diverged from modern humans, Neanderthals, and Denisovans, in low fractions. The “Altai Denisovan” admixture may have come into Northeast Asians via a mixed population, which arose when modern humans came to dominate eastern Eurasia, but only transmitted the Altai Denisovan ancestry later.

March 18, 2018

A preview review of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past

Filed under: History,Who We Are and How We Got Here — Razib Khan @ 4:22 pm

So I read the final version of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. It’s good. You can finally set aside The History and Geography of Human Genes, though with the rate of change in the field of ancient DNA I wouldn’t be surprised if there was a major revision of Who We Are and How We Got Here in two to four years.

I’m writing up a full reaction for National Review Online, so I’m not going to say too much here in specifics. And, since the book is still not out for a bit over a week I think it would be kind of rude of me to spill the beans on anything too juicy (though if you read this blog closely there won’t be any huge reveals).

So let me say something in the generality first. I’ve told the story of my friend Barry* before. Barry is a smart guy. He has a Ph.D. in the physical sciences from an eminent university in the Boston area. Barry works as a senior research engineer at a major semiconductor firm. Barry is interested in many things about the world. In 2011 I mentioned in passing to Barry over dinner that researchers had published in Science last year the fact that most humans alive today carry appreciable Neanderthal DNA. Barry was shocked. This was news to him. When I expressed shock that someone like Barry would be ignorant of this fact, Barry suggested perhaps I needed to expand my horizons as to the nature of things that the typical educated and interested person knows about science at any given time. That’s fair enough.

Someone like Barry is a perfect audience for Who We Are and How We Got Here. Barry hasn’t taken much biology, so the review of concepts such as recombination (even if the author doesn’t use that word) and mutation are useful. But more importantly, Who We Are and How We Got Here catches someone like Barry up to the state-of-the-art knowledge that we have in terms of human history, deep and prehistoric.

But it’s not just Barry. I’ve talked to plenty of people who work in evolutionary genomics who are not totally up-to-speed on the ancient DNA revolution. They too would benefit from reading Who We Are and How We Got Here front to back. I know people who work in the field of cultural evolution, who would also benefit from reading Who We Are and How We Got Here. I know behavior geneticists who would benefit from reading  Who We Are and How We Got Here. And so forth.

If you can’t find it in yourself to read 200-page supplements top to bottom, Who We Are and How We Got Here also is what you need.

Last summer I had the pleasure of having lunch with the author of Who We Are and How We Got Here, David Reich. If you read the prose it’s hard not to hear his precise and careful words echoing in your mind. Who We Are and How We Got Here is not rich with the same stylistic flourish and engagement as one might find in a popularization by Steven Pinker or Richard Dawkins. And I don’t think that was its intent, judging by how much space is given over to the four-population test! This is a serious book that is earnest in focusing on the substance of the science first, second, and last.

David expressed his discomfort with the opportunity cost that writing this book entailed for him when we spoke. While focusing on the book for the past few years he hasn’t had much time to do original analysis himself. His body language indicated the deep discomfort this caused him, and in Who We Are and How We Got Here he admits frankly that devoting himself to the book resulted in him not performing many analyses and publishing many papers.

One reason to write Who We Are and How We Got Here is that a book will reach outside the circle of those consuming and participating in the ancient DNA revolution. And a revolution it is! David Reich is already a highly eminent academic by any measure.  Who We Are and How We Got Here will do nothing to elevate his standing among his peers, because amongst them his stature is measured by the scientific papers published and projects in which he is involved.

So why make the sacrifice and write this book? Let me quote David Reich himself:

…I finally thank several people who repeatedly encouraged me to write this book. I resisted the idea for years because I did not want to distract myself from the science, and because for geneticists papers are the currency, not books. But my mind hanged as my colleagues grew to include archaeologists, anthropologists, historians, linguists, and others eager to come to grips with the ancient DNA revolution.

I would expand the purview here more broadly: all public intellectuals should know about the human past in its fullness. It’s a shadow that hangs over us and frames our arguments about the present. How we came to be where we are matters unless you are the most clinical of logicians. If you are Gilbert Ryle, turn away!

In Who We Are and How We Got Here Reich recounts an encounter with an impudent undergraduate at MIT who wondered at the end of a lecture how it was he got funding for his abstruse projects. He responded with the standard pitch that goes into NIH grant proposals, that to understand human disease, one must also understand human population structure, and to understand human population structure it helps to understand human population history. After recollecting this anecdote Reich observes that he wishes he had responded differently. He concludes:

The study of the human past-as of art, music, literature, or cosmology-is vital because it makes us aware of aspects of our common condition that are profounding important that we heretofore never imagined.

To me, this goes back to the Greek distinction of techne vs. telos. Science as an instrument in expanding the limits of human longevity and health is important, but it is not the only thing that science is capable of. If we turn science into pure instrument, we lose something essential and integral in its purpose.

These are old, ancient, universal disagreements. In ancient China, there were groups of philosophers who outlined a vision that had little use for the fripperies of the past. Legalists who wished to turn the whole society into an instrument of production and power, for whom techne was prominent. The Legalists expressed a cold calculating face of practicality and instrumentality, but the universal altruists who followed Mozi ultimately had some of the same inclinations. How could men make merry with music when there was still suffering in the world? Shouldn’t nonproductive cultural practices be curtailed before we achieve the Utopia of plentitude?

Because the disciplines of Confucius won the ancient culture wars the Legalists and Mohists are remembered as crass caricatures. But the Confucian respect and reverence for accumulated human wisdom, the customs, and folkways of the past, were wise, insofar as a Confucian system persisted in China for over 2,000 years.** They gelled with deep human dispositions.

If we are to view human beings more than production and consumption machines shackled to the modern capitalist hedonic treadmill, then we need to consider the past as part of who we are. It is part of the treasury of human existence, which is more than just feelings of the present, but echoes down through the generations, through family lines, and cultures, and even in our genes. Humans without root float freely, but they are never truly free.

* I’m changing names, though if you know me from college or know me personally, you know who I’m talking about.

** Obviously this is a coarse generalization, one could argue that Legalism was laundered through State Confucianism!

March 14, 2018

Open Thread, 3/14/2018

Filed under: Open Thread — Razib Khan @ 8:46 pm

I finally met my old friend Ramez Naam in the flesh. Ramez’s publisher sent me his book More Than Human: Embracing the Promise of Biological Enhancement in 2005. One thing led to another, and somehow he’s guest blogging on Gene Expression!

CRISPR as we know it did not exist in 2005. Things have really changed since then, and for the better, at least from the perspective of genetic engineering. It’s as if some of the stuff in More Than Human is coming to life.

I also recommend his book The Infinite Resource: The Power of Ideas on a Finite Planet.

Ramez is more optimistic about the future than I am, though cautiously so. I hope he’s right, and I’m wrong. I fear he’s not.

My concern is not with technological innovation. That will happen. It’s with maintaining social stability due to the immiseration of what was the middle class in developed societies. Also, the bourgeois version of the New Class seems to lack empathy toward the future lumpen….

SEC Charges Theranos Founder Elizabeth Holmes With ‘Massive Fraud’. “Fake it ’till you make it” will keep happening if there are no follow-up criminal charges. Holmes may not have gotten away the con, but she was a paper billionaire for a while and funded R & D with the cash that they raised on lies. One moral some are going to take away is that she took a big risk and failed, but it was one that perhaps needed to be taken.

Adaptive landscape of protein variation in human exomes.

Genetic dissection of assortative mating behavior.

Conor Lamb Wins Pennsylvania House Seat, Giving Democrats a Map for Trump Country. I’m pretty bullish on a Democrat takeover of the house. The country will swing back. That being said, I’m also bullish on the idea that the Democrats are their own best enemy, and divisions and lack of coherency in their plan going forward will mean they won’t be able to capitalize on their electoral windfalls over the next few years.

This week’s episode of The Insight is up, 23andMe, the FDA, and Our Genomic Future. We have some potential guests lined up. One of whom is Stuart Ritchie, author of Intelligence: All That Matters.

Please subscribe via iTunes or Stitcher, and leave us 5-star reviews! 

St. Patrick’s Day is coming up. I’ll be avoiding drunk people on the streets of Austin. But I also want to point out that my “side-hustle” DNA Geeks has an M222 t-shirt available. In case you don’t know, that’s the legendary Niall of the Nine Hostages’ possible haplogroup (a sublineage of R1b). About 10% of Irish men are M222.

‘Tomb Raider’: Fans Slam Criticism of Alicia Vikander’s Body. There are two points that I want to make. First, at 5’5 inches, Alicia Vikande is of a very normal height (Angelina Jolie was two inches taller). She’s not physically imposing, and she has a very narrow waist as well. Her figure is “boyish.” Second, since the 1990s there has been a shift in male action stars toward being more shredded/athletic as opposed to jacked-up and exaggerated in their physicality. This is a very different Lara Croft for a very different time.

I decided to check out the new public library today. Saw the book The Invention of Humanity: Equality and Culture Differences in World History. I hate the overuse of the term “invention” in book titles, but when I noted the beginning covered China, I got it. Too often books that are Eurocentric turn out to be more data than narrow/inference, and they rig the data ahead of time to support their thesis (see, Inventing the Individual).

I also got Constructing the World (a David Chalmers book), The Bible and Asia: From the Pre-Christian Era to the Postcolonial Age, Creators, Conquerors, and Citizens: A History of Ancient Greece, The Third Reich: A History of Nazi Germany. That’s ranked in order of likelihood that I’ll get through them.

Also, Philip Jenkins has a new book, Crucible of Faith: The Ancient Revolution That Made Our Modern Religious World. Jenkins is a great scholar, I admire his work a lot. But I think I’m going to take a break from religious history, since I know a fair amount about the topic.

Polygenic scores and tea drinking.

Exposing flaws in S-LDSC; reply to Gazal et al.. Working your way through this literature is often pretty useful, so start at this commentary.

National Geographic has a special on race and what not. One piece being shared is kind of interesting, These Twins, One Black and One White, Will Make You Rethink Race. Here’s an important quote:

In genetic terms, skin color “is not a binary trait” with only two possibilities, Martin notes. “It’s a quantitative trait, and everyone has some gradient on this spectrum.”

Historically, when humans have drawn lines of identity—separating Us from Them—they’ve often relied on skin color as a proxy for race. But the 21st-century understanding of human genetics tells us that the whole idea of race is a human invention.

If you’ve read this blog you know I’ve blogged about “black and white twins” for over ten years. Also, I think a lot of the debunkings of race are pretty facile. But that’s not what I want to talk about. Rather, one of the things that are unmasked unwittingly in pieces such as this is how deeply Eurocentric these conversations are. It’s as if public intellectuals and journalists that write on this topic either don’t know any non-white families or they pretend that they don’t. The “humans” and “Us” implicitly points to white European systems of racial classification (e.g., East Asians relied on skin color somewhat, but since they are not much darker than white Europeans, they also included hair color, to distinguish the Dutch from the Portuguese, and large noses and body hair, to distinguish from themselves).

Twins with different skin tones are striking. But almost any South Asian, black American, or Latino, or Southeast Asian, or even East Asian, can tell you that there is a wide range of pigmentation within many families. Basically, unless you are in a homogeneous European social environment, where most everyone has very light skin on a global scale, you will see the variation of pigmentation within families. Both my parents have large sibling cohorts, and in both of them there are cases where the difference in complexion between siblings is in the same range as the two fraternal twins highlighted in the piece.

Of course, journalists who work for National Geographic or The New York Times know people of varied ethnicities and probably see that there is pigmentation variation within those families. They just pretend as if they don’t for these sorts of pieces which debunk race, and the readers pretend they don’t know this information as well as they take it in in a self-satisfied manner and nod sagely.

I haven’t had much time to read Enlightenment Now: The Case for Reason, Science, Humanism, and Progress. But those who say it’s quite like The Better Angels of Our Nature seem correct from how how far I’ve gotten.

My timeline has been swarming with debunkings of Enlightenment Now from all ideological angles. The best responses to these can usually be found in Saloni’s timeline (from her), who is “Pinker’s bulldog.”

Ex-Muslim TV‘s Twitter account is irritated that some of its stuff is now labeled “sensitive material.” The day before this came up I noted that one of my posts that Jerry Coyne retweeted about Islam and apostasy was also labeled “sensitive material.”

Basically if Muslims find it offensive, it might be subject to scrutiny from Twitter. This may or may not be defensible from Twitter’s perspective in a business sense, or ethically. But it’s just the reality we have to deal with, though I would like to know which school of Islamic jurisprudence Twitter relies on to gauge sensitivity and offense. I suspect it will be the Hanafi fiqh due to its liberal utilization of qiyas, which allow’s Del Harvey’s minions more free play.

The nation-state is dying. What will come out of its ashes? I suspect empire by another name….

The day we saw Stephen Hawking

Filed under: science,Stephen Hawking — Razib Khan @ 6:50 pm

In the spring of 1996, several of my dormmates decided to trek north to the University of Portland, to attend a speech by Stephen Hawking. We were still in that phase where we barely left campus, so intense was our social world. So this was a major undertaking. I don’t recall how we found out about the speech. This is before the internet was a widespread means of distribution of this sort of information (though I think we found out from my dormmate who was a journalism student).

I remember the anticipation and excitement. It was like we were going to a rock concert.

The talk Hawking gave was a typical one about cosmology. He also gave some shout outs to Linus Pauling, who was a native Oregonian.

Like many people, I had read A Brief History of Time. Also, perhaps like most people, I didn’t recall much from that book (I read the book years before going to the talk, in my defense).

Even by the mid-1990s, I was aware that Stephen Hawking was part of a somewhat out of control hype-machine. Though he was an eminent physicist, he was not necessarily the most brilliant physicist since Einstein (one of the claims on one edition of A Brief History of Time I saw at one point). We didn’t have Wikipedia, so I didn’t know about his somewhat messy personal life.

What we did know about Hawking was that he was a man of incredible brilliance who didn’t let his medical condition stop him. We admired him. We admired his achievements. He was heroic. By the time my dormmates and I saw Hawking in the flesh, he was already very frail. The only movement that we could perceive was that you could see he was breathing because of some barely perceptible movement around his neck.

At the end of the talk, people mulled around during the Q & A, trying to get as close as possible. I still have a vivid recollection of seeing Hawking up on the dais, in bright light.

Afterward, on the trip home, we reflected that it seemed unlikely that the great physicist had much time left, seeing as how he was nearly immobile. We felt privileged to be in his presence when he gave a talk. That was enough. Of course, he lived on for more than 20 years.

March 13, 2018

The barbarian invasions, illuminated by genetics

Filed under: Huns,Roman History — Razib Khan @ 1:02 am

My own comprehension or understanding of the fall of Rome and the barbarian invasions probably began when I was about nine years old when I read a book about the various peoples who crashed the gates of civilization. First and foremost in the various descriptions were the Huns, a mysterious and fearsome race who in previous times had almost a talismanic role in the history of this period. Like the Mongols later on, they were more a force of nature that illustrated the hand of an angry God in the world than a people with their own agency.

But their identity was, and is, mysterious. Though contemporary descriptions seem to describe them as alien and repulsive in physiognomy, by the 19th century these antique descriptions were filtered through the racialist framework ascendent in the West of that period to cast them as foreign Asiatics. By the 20th century, a reaction set in and attempts to adduce the Huns’ possible connection to Central Asia seem to have diminished, though no one could deny the proposition either.

The fact that the ethnolinguistic affiliation of the Huns is mysterious to us should give a clue that they weren’t related to the standard Germanic or Iranian groups which operated on the fringes of the European Roman world. If the latter surprises you in the context of the European frontier of the Roman Empire, the Sarmatian tribes which pushed into Hungary and harried Rome defenses were related to groups like the Scythians, and branches eventually gave rise to the Alans (who ended up in the North African kingdom of the Vandals!) and Ossetians.* The German peoples have been observed by the Romans since the time of Cimbri invasions, and the later eruptions were easy to slot into that ethnographic framework.

In contrast, the Huns are mysterious precisely because they were a new cultural force. They seemed to be pure nomads like the Sarmatians, but not out of the Iranian steppe cultural milieu. Though they may have been a linguistic isolate, the most likely probability is that they spoke a Uralic (e.g., Hungarian) or Altaic language (e.g., Turkish). Like later steppe nomad hordes which burst out of Inner Asia into the Eurasian oikumene the genius of the Huns was in part organizational, as they accrued to their confederacy a motley of German and Iranian tribes. One standard narrative of the Gothic migrations is that their peregrinations were triggered by the movement of the Huns and their allies to their east and north.

An extreme social constructionist might assert that the term “Hun” simply brackets a new way to organize mobile barbarians beyond the Roman frontier. That they were not ethnically distinct. Though I don’t know anyone who holds to this extreme view, it’s not entirely impossible.

But now we have some genetic data. Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria:

…we generated genomic data from 41 individuals dating mostly to the late 5th/early 6th century AD from present-day Bavaria in southern Germany, including 11 whole genomes (mean depth 5.56×). In addition we developed a capture array to sequence neutral regions spanning a total of 5 Mb and 486 functional polymorphic sites to high depth (mean 72×) in all individuals. Our data indicate that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from western Europe to East Asia. Particularly striking are women with artificial skull deformations; the analysis of their collective genetic ancestry suggests an origin in southeastern Europe. In addition, functional variants indicate that they also differed in visible characteristics. This example of female-biased migration indicates that complex demographic processes during the Early Medieval period may have contributed in an unexpected way to shape the modern European genetic landscape. Examination of the panel of functional loci also revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ∼1,500 years ago.

The admixture plot is key. They have enough markers that intercontinental genetic differences should be discernible. The male and female symbols should be familiar to you, but they also classified the samples by the cranial deformation (a practice associated with the arrival of the Huns to Europe). Blue ~ no deformation, green ~ intermediate, and red ~ deformation.

You can see that the individuals with cranial deformation, who are females, are genetically very distinct from everyone else. And, in particular, the males who exhibit no deformation are pretty homogeneous. Both PCA and admixture suggest that the males resemble typical North-Central Europeans. That is, Bavarians. The women on the PCA plot are shifted toward Southeastern Europe, where anthropologically the deformations were much more common.

The authors analyzed the features of these women and determined that they were likely darker than the males in eye color. This is entirely reasonable in light of their more Southern European genetic character.

There are a few other random samples too. In the admixture plot, FN_2 is a Roman soldier from ~300 AD from the Munich area. About two centuries before the Bavarian samples. The authors note it is curious this individual seems to exhibit Spanish ancestry (IBS being the Spanish samples). And yet this ancestry did not impact the region. Anyone who reads a history of the Roman Empire and its fall and regression knows that the area of southern Germany, Austria, and Hungary south into the Balkans became highly barbarized. It seems likely that many Roman peasants died or fled back to the safety of the empire.

PR_10 is a Sarmatian from the southern Urals. The individual has more “Finnish” ancestry, but that’s not atypical for Russian samples. The South Asian ancestry is something I’d dismiss normally, but I think this might be shared Yamnaya heritage.

Finally, VIM_2, like AED_1108 (a Bavarian female with cranial deformation), has East Asian ancestry. This individual was sampled in Serbia, dates to the 6th century, and is presumably a Gepid, a relatively obscure German tribe.

The presence of East Asian ancestry in these individuals highlights the likely cosmopolitan character of the barbarian zone stretching from Hungary to Bulgaria. It should definitely increase our likelihood that the Huns spoke a Turkic language of some sort. By the time most Turkic peoples arrive on the scene in Western Eurasia, they’re highly admixed, but they invariably have some East Asian ancestry. I highly doubt that the Huns arrived in Europe with the Southern European ancestry, TSI (Tuscan). So that is probably admixture over the century and a half since they arrived that allows for this individual to be predominantly TSI (though the individual may also have been a later Oghuz migrant). The ancestry of the Huns should have been more like a mix of East Asian and Sarmatia. The latter sorts were the first “West Eurasians” they’d run acros unless they had originally come from further south in the Tarim basin.

In the decades before the Huns turned West, they harried the East Roman Empire, pushed its limes back toward the sea, and extorted tribue out of it. After the collapse of Attila’s Empire, they seem to have retreated back to the territories to the east where they could be self-supporting, as opposed to extorting protection money out of states more powerful than them. Because the Huns become less of a problem for the Roman Empire, we don’t hear much about them by the late 5th century. And yet that does not mean they disappeared. The human and biological ecology of this region seems to have been amenable to the intrusion of Eurasian nomads, by the end of the 6th century the Avar confederacy was dominant in the interior Balkans and toward southeastern Germany.

Though this paper is not exactly revolutionary, it confirms that individuals from a post-Hunnic cultural configuration are mostly indigenous, that some evidence of East Asian ancestry persist, it shows that many of the arguments about Late Antiquity as to the ethnological character of peoples will be resolved. Unlike prehistory, where we have no written records, this period has clear and distinct cultures which we have a grasp of. The empty spots on the map are smaller.

* Some captured Sarmatians were settled in Britain on the frontier looking north. There are conjectures that Sarmatian motifs may have influenced Arthurian legends.

March 11, 2018

Turks are Anatolian under the hood, somewhat more Greek than Armenian

Filed under: Armenians,Greeks,Human Population Genetics,Turks — Razib Khan @ 11:40 pm

My post, Are Turks Armenians Under The Hood?, attracted a little bit of controversy. The main criticism, which was a valid one, is that I did not sample Anatolian Greeks. A reader passed on three Anatolian Greek samples. I also added a Cypriot data set. To my mild surprise, the Anatolian Greeks and Cypriots cluster together, at the end of the Greece cline toward West Asians. Therefore, for further analysis, I pooled the three Greeks with the Cypriots.

Additionally, there are two Balkan Turk samples. Even on the PCA it’s pretty clear that they’re genetically very different from the other Turks (one of them is from what has become Bulgaria), though the shift toward East Asians indicates that Turkification is very rarely a matter purely of religious conversion to Islam and assimilation of the Turkish language (obviously it initially is for many people, but these people then intermarry with those with some East Asian ancestry).

One of the major problems is that the Armenian sample and the Anatolian Greek/Cypriot sample are genetically very close. This is obvious in the Fst distance. This is also totally reasonable since both populations occupy Anatolia, and historically there would have been a lot of gene flow between the two groups through isolation-by-distance dynamics.

The Turk position closer to East Asians is due to their East Asian admixture.

You can see it in the admixture plot too. As we all know there is definitely some northern admixture in the mainland Greeks. I haven’t bothered to check with the Mycenaean paper, but I assume that some of this is due to the migration of Slavs after much of the Balkans was abandoned after the reign of Maurice.

Of course, I ran Treemix too. Again, the closeness of the Anatolian Greeks/Cypriots and the Armenians is an issue in making a definitive conclusion.

In terms of drift the Turks seem about as far from Anatolian Greeks as Armenians. There’s the gene flow you’d expect, there are two from East Asians to Turks. I think that’s due to the East Asian source being somewhat heterogeneous, and the Dai outgroup not modeling the source populations perfectly.

Finally, there’s the f3 statistics. They basically show what I’m saying above: Armenians and Anatolian Greeks are both good model sources for Turks. The likely truth is that there is gene flow from all across Anatolia into these Turkish samples.

Group X1 X2 f3 z
Turkey anatolian_cypriot Dai -0.0029 -36.3940
Turkey Armenians Dai -0.0026 -34.2083
Turkey Greece3 Dai -0.0025 -32.7389
Turkey Georgian Dai -0.0026 -30.8836
Turkey Greece2 Dai -0.0024 -29.5462
Turkey GreekCentral Dai -0.0025 -23.6454
Turkey Greece1 Dai -0.0026 -23.0283
Turkey GreekThessaly Dai -0.0024 -20.1595
Turkey Armenians Lithuanians -0.0005 -11.5356
Turkey Lithuanians Dai -0.0012 -10.7473
Turkey Georgian Lithuanians -0.0004 -7.9691
GreekThessaly Armenians Lithuanians -0.0006 -6.6390
GreekThessaly anatolian_cypriot Lithuanians -0.0006 -6.3748
GreekThessaly Greece3 Lithuanians -0.0005 -4.6347
Greece2 anatolian_cypriot Lithuanians -0.0008 -15.7114
Greece2 Armenians Lithuanians -0.0008 -14.4083
Greece2 Greece3 Lithuanians -0.0005 -10.4508
Greece2 Georgian Lithuanians -0.0005 -8.2727
Greece1 anatolian_cypriot Lithuanians -0.0006 -6.5563
Greece1 Armenians Lithuanians -0.0005 -6.3712
Greece1 Greece3 Lithuanians -0.0004 -4.7896
Greece1 Georgian Lithuanians -0.0003 -3.1104
balkan_turk Greece1 Dai -0.0024 -7.1425
balkan_turk GreekThessaly Dai -0.0021 -6.1764
balkan_turk GreekCentral Dai -0.0021 -5.7848
balkan_turk Greece2 Dai -0.0019 -5.6794
balkan_turk anatolian_cypriot Dai -0.0019 -5.5944
balkan_turk Armenians Lithuanians -0.0014 -5.3207
balkan_turk Greece3 Dai -0.0017 -5.0815
balkan_turk Lithuanians Dai -0.0017 -5.0190

The population genomics of South Asia is complicated, and politics doesn’t make it easier

Filed under: India Genetics,India genomics — Razib Khan @ 11:27 am

Many people have been sending me links to this article, By rewriting history, Hindu nationalists aim to assert their dominance over India. Here’s a key section:

The RSS asserts that ancestors of all people of Indian origin – including 172 million Muslims – were Hindu and that they must accept their common ancestry as part of Bharat Mata, or Mother India. Modi has been a member of the RSS since childhood. An official biography of Culture Minister Sharma says he too has been a “dedicated follower” of the RSS for many years.

Sharma told Reuters he expects the conclusions of the committee to find their way into school textbooks and academic research. The panel is referred to in government documents as the committee for “holistic study of origin and evolution of Indian culture since 12,000 years before present and its interface with other cultures of the world.”

Sharma said this “Hindu first” version of Indian history will be added to a school curriculum which has long taught that people from central Asia arrived in India much more recently, some 3,000 to 4,000 years ago, and transformed the population

There are several threads here. First, it is a fact that the ancestors of South Asia’s non-Hindus were Hindu. There are minor exceptions, such as the Parsis, who are ~75% Iranian. One can quibble as to whether many tribal and peasant populations were truly Hindu in a formal and explicit sense. But I think this is a semantic dodge. Muslims would recognize these beliefs and practices as Hindu, no matter if one was a Brahmin monk or a member of a tribe which still sacrificed animals.

I’ve looked at the genotypes of a fair amount of South Asians of Muslim background. The overwhelming (usually exclusive) proportion of their ancestry is South Asian. It’s a fact that the ancestors of non-Hindu South Asians were Hindu.

But, the article and a dominant theme in Hindu nationalism today are that distinctive groups like Indo-Aryans are indigenous to South Asia. This is set against a narrative of invasions and migrations, which is presumed more friendly to a multicultural paradigm (I have a hard time keeping track of the political valence of all these things). To some extent, the reality of invasions and migrations cannot be denied, whether it be Alexander, the Kushans, or the various Muslim groups. But these historical invasions left little genetic imprint.

When 2009’s Reconstructing Indian Population History was published things changed for earlier migrations. By the time the ancient Greeks were noting India in Classical Antiquity, it was already noted as the most populous nation in the world. I was initially skeptical about the result inReconstructing Indian Population History, that there was massive admixture between a West Eurasian and indigenous South Asian group, because that would imply massive migration. Additionally, phenotypically the pigmentation genes didn’t seem to work out if the source population was European-like.

Nearly 10 years on we have a lot more clarity. Ancient DNA has clarified a lot. Massive migrations are common. And, the pigmentation and genetic profile of modern Europeans is recent. The source population(s) for “Ancestral North Indians” may not have been Europeans in the way we’d understand them. In fact, a follow-up paper, Genetic Evidence for Recent Population Mixture in India, hinted at two admixtures. There’s a fair amount of circumstantial evidence now that one component of “Ancestral North Indian” relates to West Asian populations and another component to the more classical steppe Indo-Aryans. The former is more widespread than the latter.

I do understand Indians who want to interpret their own history through the lens of their own cultural priors. The problem is that genetic science has proceeded so fast in the last few years that many propositions which were speculative in the 20th century are testable in the 21st. Some Hindu nationalist friends and acquaintances express embarrassment and worry about the track that Indians are going on this. I don’t know what to say, but Americans have their own delusions and propaganda, so I’m not going to be one pointing fingers. Other Indians have told me via Facebook that they “believe in the results from the 2000s” (when they were more congenial to their viewpoints?). I guess that’s one strategy; just keep up with the science until it starts refuting your model.

That being said, with the ubiquity of datasets one can explore questions oneself. Additionally, the Indian government may suppress analysis of ancient DNA through soft coercion and negative incentives, but I’m sure at some point Pakistan will let people dig things up.

I recently posted my South Asian Genotype Project results. Though the sample size is small, since I have provenance it allowed me to get more clarity on what’s going on in the 1000 Genomes samples for South Asians.

There are several things I can tell you. For example, I have samples for a Sindhi and Gujarati Lohanna. They cluster near each other, and with Sindhis. Similarly, a Gujarati Muslim sample is also in with the Sindhis. A Gujarati Muslim gives the same results.

In contrast, other Gujaratis are placed between Pakistani populations and South Indians. A Vania and Solanki sample helped me label “Gujarati Middle Caste.” The Gujarati Patel samples, in contrast, are even more shifted toward South Indians, and admixture analysis implies less Indo-Aryan in these samples than other Gujaratis.

Gujarat seems to be a state with a lot of connections to Sindh, so you see a wide range of variation in this state on the ANI-ASI cline.

I’ve collected enough Brahmin samples from the four states of Southern India to see that they are very similar genetically (one exception is a Niyogi Brahmin who seemed more ASI-shifted than usual). If they don’t come from the same migration event, they diverged at around the same time.

Brahmins from North India are different from South Indian Brahmins, in being more ANI-shifted. It seems that to a great extent Brahmins from outside the Gangetic heartland can be modeled as North Indian Brahmins with local admixture. Bengali and Maharashtra Brahmins have shifted away from North Indian Brahmins, but not as much as South Indian Brahmins. Bengali Brahmins are also East Asian shifted, confirming the reality of local admixture.

One result that surprises me is how genetically similar Dalits from North and South India are. The Chamar samples from Uttar Pradesh seem to have some levels of Indo-Aryan admixture, but overall they’re not that different from Dalits from Tamil Nadu.

Additionally, non-Brahmin and non-Dalit individuals from places like Bengal and Tamil Nadu/Sri Lanka, and Andhra Pradesh are very distinct from Dalits. In other words, the caste system is not simple the traditional upper castes vs. everyone else, but it’s deeply structured. The implication here is that caste may predate the Indo-Aryans (this is not a new inference). Or at least not be related them.

Finally, there is a curious pattern where gene flow into southern Pakistan (Sindh) is more shifted toward the Middle East than in northern Pakistan (Punjab, the Pathan areas). I suspect this is due to dynamics which date deep into prehistory, rather than more recent events.


March 9, 2018

Yellowbird ghost pepper sauce, 4.5 out of 5 stars

Filed under: Hot Sauce,Yellowbird ghost pepper sauce — Razib Khan @ 12:29 am

Yellowbird is a small-batch artisanal hot sauce brand out of Austin, TX. I’ve talked some smack about their habanero sauce before.

Well, today I swung by the local hot sauce shop, as I was out. I chatted up the clerk and we were talking Yellowbird, how the serrano sauce tasted so good, and how the habanero one was second-rate. I asked him about the ghost pepper variety, and he told me to try a sample. So I did. And I liked what I tasted!

This is not the spiciest sauce in the world. But very few non-extract hot sauces are killer. And, unlike extract sauces, Yellowbird ghost pepper sauce this doesn’t taste artificial or metallic. Though not as spicy as something like Dave’s Insanity, this will leave most civilians sweating.

But there’s more than spice! This sauce has a rich and complex flavor profile, with a strong sour punch that hits you in the face before you even realize how spicy it is. The savor is pretty flat from the beginning to end, but I tend to get a sweet kick at the end. I’m not a big fan of sweetness in hot sauces, but it isn’t pervasive and overwhelming, and serves as a nice accent before you start to get the sweat on as capsicum binds to your receptors.

Demographic replacement in Southeast Asia during the Holocene

Filed under: Human Population Genetics,Southeast Asia — Razib Khan @ 12:15 am

Well sometimes you feel silly, and it’s not your fault. Yesterday our podcast on Sundaland went live (we talked about Doggerland and Beringia too!). Though I expressed a fair amount of skepticism, I took the argument that Stephen Oppenheimer presented in Eden of the East, that modern Austronesians are long-term residents of Southeast Asia, seriously.

The alternative view, most forcefully put by Peter Bellwood in books such as First Farmers, is that Austro-Asiatic and Austronesian people were agriculturalists issuing out of southern China that transformed the region over the past 4,000 years (the Austronesians from Taiwan specifically, though during the Pleistocene Taiwan was connected to the mainland).

I lean toward Bellwood’s view, and today a preprint came out which basically confirms it in totality, Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia. The abstract:

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

The transition to full-fledged rice agriculture occurred in Vietnam ~4,000 years ago. In First Farmers Bellwood reports on an archaeological site dating to that period where skeletal evidence has been adduced to record the presence of both Northeast Asian and Australo-Melanesian types. These results make clear though that these hunter-gatherers in Southeast Asia are more similar to the Onge of the Andaman Islands, as well as the Negritos of the interior of the Malay peninsula. They’re totally in alignment with the earlier morphological results (also, readers might be curious to know that one site of the Hoabinhian culture is in Yunnan, China). This shouldn’t be surprising, as the Andaman Islands were a peninsula which extended from southern Burma during the Pleistocene.

Already the most accepted model for the introduction of intensive agriculture into Southeast Asia is that it was brought by Austro-Asiatic peoples. These results confirm that. Additionally, it seems clear that Austro-Asiatic ancestry made it to island Southeast Asia, whether directly or through Austronesian admixture before arriving in island Southeast Asia. Java and Bali have some of the higher fractions ancestries most closely associated with Austro-Asiatic groups on the mainland.

Deeper digging into the admixture distributions has long made it pretty evident that some areas had much higher Austronesian fractions in Indonesia than others, and it wasn’t just a function of distance from the Phillippines. Why? My own hunch is that Austronesians brought social and cultural systems which were better adapted to island Southeast Asia, and were more fully able to exploit the local ecology. Meanwhile, aside from a few fringe areas such as the Malay peninsula and coastal Vietnam, they were not successful on the mainland.

The authors also detect migrations into Southeast Asia besides that of the Austro-Asiatics and Austronesians. One element seems correlated with the Tai migrations, and another with Sino-Tibetan peoples, most clearly represented in Southeast Asia by the Burmans. The excellent book, Strange Parallels: Volume 1, Integration on the Mainland: Southeast Asia in Global Context, c.800–1830, recounts the importance of the great migrations of the Tai people into Southeast Asia ~1000 A.D. Modern-day Thailand was once a flourishing center of Mon civilization, an Austro-Asiatic people related to the Khmers of Cambodia. The migrations out of the Tai highlands of southern China reshaped the ethnography of the central regions of mainland Southeast Asia. The Tai also attempted to take over the kingdoms of the Burmans. Though they failed in this, the Shan states of the highlands are the remnants of these attempts (tendrils of the Tai migrations made it to India, the Ahom people of Assam were Tai). Vietnam, shielded by the Annamese Cordillera, came through this period relatively intact. It is also well known that Cambodia’s persistence down to the present has much to do with the shielding it received from France in the 19th century in the wake of Thai expansion.

There are two bigger issues that this paper sheds light on. One is spatial, and the other is temporal.

They detect shared drift between Austro-Asiatic people and tribal populations in northeast India. This is not surprising. A 2011 paper found that Munda speaking peoples, whose variant of Austro-Asiatic is very different from that of Southeast Asia, are predominant carriers of Y chromosome O2a. This is very rare in Indo-European speaking populations, and nearly absent in Dravidian speaking groups. Additionally, their genome-wide patterns indicate some East Asian admixture, albeit a minority, while they carry the derived variant of EDAR, which peaks in Northeast Asia.

One debate in relation to the Munda people is whether they are primal and indigenous, or whether they are intrusive. The genetic data strongly point to the likelihood that they are intrusive. An earlier estimate of coalescence for O2a in South Asia suggested a deep history, but these dates have always been sensitive to assumptions, and more recent analysis of O2a diversity suggests that the locus is mainland Southeast Asia.

Now that archaeology and ancient DNA confirm Austro-Asiatic intrusion into northern Vietnam ~4,000 years ago, I think it also sheds light on when these peoples arrived in India. That is, they arrived < 4,000 years ago. As widespread intensive agriculture came to Burma ~3,500 years ago, I think that makes it likely that Munda peoples arrived in South Asia around this period.

I now believe it is likely that the presence of Austro-Asiatic, Dravidian, and Indo-Aryan languages in India proper was a feature of the period after ~4,000 years ago. None of the languages of the hunter-gatherer populations of the subcontinent remain, with the possible exception of isolates such as Nihali and Kusunda.

The temporal issue has to do with the affinities of these peoples, and how they relate to the settling of Eastern Eurasia. All the Southeast Asian groups after the original Australo-Melanesians share more of an affinity with the Tianyuan individual than Papuans. The implication here is that Tianyuan is closer to the ancestors of various agriculturalists in Southeast Asia than just some random basal Eastern Eurasian. But, since Tianyuan dates to 40,000 years ago, and, is from the Beijing region, it is hard to make strong inferences from comparisons with only it. The heartland of ancient Chinese culture in Henan was to the south of the Tianyuan, after all. More samples are needed before one can truly tease out the pattern of isolation-by-distance vs. admixture that led to the emergence of the proto-farmer populations which settled Southeast Asia.

In the podcast above one thing that came up is that a lot of genetic data indicate decreased diversity as one moves from the south to the north in East Asia. This has long been taken to mean that humans migrated north, and so were subject to bottleneck effects. I pointed out that this may simply be a consequence of admixture between two very different groups of people in Southeast Asia, elevating diversity statistics.

And yet as the map at the end of the preprint suggests it is highly plausible that Pleistocene Asia was marked by a south to north dynamic of migration. The Austro-Asiatic peoples who migrated south during the Holocene may simply have been backtracking the migration of their ancestors. What these results, and ancient DNA more generally, tell us is that humans were often on the move. The Pleistocene world of climate change probably meant that humans had to be on the move.

March 8, 2018

The Nation of Islam has an antisemitism problem, and that’s about it

Filed under: Politics — Razib Khan @ 9:32 pm

Currently, there is a mini-controversy of sorts related to antisemitism, Louis Farrakhan, and some organizers of the 2017 Women’s March. The main problem seems to be that these three co-chairs of the Women’s March, Linda Sarsour, Carmen Perez, and Tamika Mallory, are balking at denouncing their association with and tacit tolerance of Farrakhan. In particular, the focus is on Tamika Mallory.

Personally, histrionic demands of denunciation usually leave me cold.

But in this case, there are strong grounds. Louis Farrakhan and his small splinter sect, the Nation of Islam, have a long history of very extreme perspectives on Jews, and whites more generally. The racism isn’t a minor idiosyncrasy with the Nation of Islam. It’s a constitutive part of their ideology. The Nation of Islam believes that white people are a race of mutants designed by a malevolent black scientist. There are some similarities fundamentally with white nationalist Christian Identity, which dehumanizes non-whites in a literal manner. And, both the Nation of Islam and Christian Identity operationally share very similar and stereotypical views of Jews as evil puppet-masters.

In reaction to this much of the media has taken to writing long analyses. This piece in The Atlantic, The Women’s March Has a Farrakhan Problem, meanders over an enormous amount of territory. Frankly, it seemed a bit much.

First, the co-chairs of the Women’s March are not the marchers themselves. The marchers are to the Left of center, but many of them are quite moderate and mainstream and conventional. I know some personally who aren’t even very liberal and self-identify as centrists. And many are Jewish. The point is that leaders and organizers can have very different politics and associations from the movement they lead. Tamika Mallory has a problem. The Women’s March, not so much.

Second, there was a theme in The Atlantic piece about the fraught and cooperative relationship between blacks and Jews in the United States. Impressionistically there’s something to this, especially considering the Crown Heights riot. But part of me wonders if there really is such that much antisemitism among American blacks that’s out of the ordinary.

The GSS has a variable, “JEWTEMP”, which measures respond attitudes toward Jews on a scale of 0 to 100 (0 being cooler and 100 being warmer). I binned the results into quartiles. You can see that black Americans are less warm toward Jews than white Americans, but the difference is very marginal.

Louis Farrakhan and the Nation of Islam are clearly antisemitic by any definition. But black Americans are not particularly antisemitic at all. Farrakhan is as representative of black American attitudes toward Jews as those on the “Alt-Right” who obsess over the “JQ”.

In fact, could it simply be that black Americans exhibit a demographic profile that is correlated with somewhat less positive feelings toward Jews, as opposed to something distinctive about black American culture? To check I played around with a multiple regression.

Changing variables around I found three traits that were robustly predictive of warmer feelings toward Jews:

1) The biggest effect was vocabulary score, which is correlated with general intelligence (r=0.7). If you don’t put this variable in, education matters. But once WORDSUM is in the equation the effect of education disappears.

2) Being a woman.

3) Being younger.

Being black as opposed to white is associated with being somewhat more antisemitic in many regressions, but it’s very weak as an association, and, it’s not statistically significant (this is probably due to sample size).

What’s the point of this post? Not to sound too much like Steven Pinker, but there isn’t a looming threat of antisemitism in the United States from any large demographic. Rather, there are small old groups like the Nation of Islam and white nationalists, which remain resolutely antisemitic. And, the Israel-Palestine issue does loom over campus politics in a way that blurs the line between being anti-Zionist and antisemitic. A small number of campus radicals and students from Muslim backgrounds do step pretty clearly from anti-Zionism to antisemitism in my opinion. In the latter case, it’s from personal knowledge, as when I was a graduate student a few kids approached me during controversies related to BDS from Islamic backgrounds expressing their strong reservations about Jews and taking courses from Jewish professors. These conversations were not welcome by me, but because of my physical appearance and name, they assumed I’d be sympathetic.

The problem here is simple, and it’s the indulgence that the black intelligentsia (that includes you President Obama) and some of the radical non-black Left, have given the Nation of Islam and Louis Farrakhan for decades. Remember, he was on Arsenio Hall‘s show in 1995. The issue isn’t the Women’s March (whose politics I somewhat disagree with), nor is it antisemitism in the black community. And most of the public doesn’t even know what BDS stands for.

Slack killed IRC? (sort of)

Filed under: Technology — Razib Khan @ 1:28 am

Interesting piece channeling some early internet nostalgia, Picking Up The Slack:
Internet Relay Chat beat Slack to real-time chat by decades and helped define much of our early online culture, yet way more people use Slack. Why is that?
. The article caught my attention because I use Slack at work, and have for a couple of years. In contrast, I probably check in to IRC once every few years now (I actually just installed an IRC client on my computer, it’s been so long).

And yet back during the summers between school years in college, I’d spend a fair amount of time haunting several IRC channels, mostly on UNDERNET. You met some weird people, some nice people, and some unpleasant people. Generally, my utilization of IRC was heavily cyclical, just like my reading and posting in USENET groups. If I had better thing to do, I’d go do them.

Perhaps one of the strangest things about IRC and USENET is a few people from those days actually ended up finding me on the web, with the rise of the paleoblogosphere. At least one long-time commenter knows me from a USENET group back in the late 1990s, while the RSS aggregator that pushes my total content feed was written by an anarcho-libertarian programmer and philosopher who I actually met first when he was a teen nerd in the Deep South.

That old internet culture is disappearing and becoming legend, just like the “homebrew computer” era of the 1970s was for my generation.

March 6, 2018

On the semiotics of “Judeo-Christian” as a misdirection

Filed under: Jews,Judeo-Christian,world history — Razib Khan @ 11:21 pm

Recently on Twitter there emerged another flare-up of the debate as to whether the term “Judeo-Christian” was coherent, useful, and defensible. In general, I take a very skeptical view of the term, because I think it misleads the public as to the nature of some important facts and dynamics in the history of the West.

Perhaps intellectuals can agree amongst themselves that the term has utility for manipulating the masses, but oftentimes it seems even intellectuals don’t have enough of a grasp of religious history to understand why the usage is literally problematic (I’m not using problematic in a euphemistic catchall manner, I think it’s semantically confusing, not offensive).

First, traditionally Jews and Muslims have been much clearer in recognizing each other as non-idolatrous monotheists, as against Christians. The dominant non-Unitarian nature of Christianity, and the importance of divine representation in both medieval Eastern and Western traditions (with statuary in the latter1), were the key issues for Muslims and Jews. This point is not dispositive, but it’s not irrelevant.

In the Western context, it seems American Christians in particular are attached to the term Judeo-Christian. I believe this is the outcome of a specific American history, where different European immigration streams were forged into a common people in the 20th century, especially in the post-World War II era. The general model is the one outlined by Will Herberg in Protestant, Catholic, Jew, the emergence of a white America united by shared values, with establishment mainline Protestantism at the center, and Roman Catholicism and Judaism as helpmates. Though the title of the book points to the real religious particularism still prevalent in that period, it was an early form of what Rod Dreher and his fellow travelers would term “morally therapeutic Deism.” The idea that it didn’t matter as to the details of the confession and practice of your faith, so long as you believed in God and were a good person.

Of course not all people who assert the utility of Judeo-Christian as a category are so religiously naive. But most Christians who adhere to the category seem to have a hard time not understanding Judaism as anything other an earlier form of their religion. In other words, Judaism as Christianity without the Christ.

I think this is very misleading. Rather, Judaism as it evolved after the rise of Christianity, and then Islam, was a distinct religion from the Judaism which Christians are familiar with from their Old Testament. Jewish religion in the first millennium A.D. became the religion of the Pharisees. That is, Talmudic Judaism, or Rabbinical Judaism. What we in the West often term Orthodox Judaism. Though there were schismatic sects, such as the Karaites, developments such as Hasidism, and isolated groups such as the Bene Israel of western India who seem to have practiced a more archaic form of the religion, over time Judaism qua Judaism became the religion which evolved out of the same milieu of Roman antiquity as Christianity. Though Christianity evolved out of the religion of the Hebrews, the Jews, the religion of the Jews evolved at the same time as well. It was not static, in chrysalis.

A whole Jewish Diaspora, what became the Ashkenazim, Sephardim, and Mizrahim (and Yemenite Jews and other assorted groups), developed a parallel cultural world to that of Western and Eastern Christianity, as well Islam.* Though Jews interacted with gentiles in a professional capacity, whether as physicians, merchants, or money-lenders, the intellectual exchange was relatively limited (Al-Andalus being an exception).

This may surprise many people, because Jews are extremely prominent intellectually in the West today. But this is a feature of the last few centuries, as they became absorbed by Western culture during the Jewish Enlightenment. Even a Jew who predates this period and influenced the course of early modern Western philosophy, Baruch Spinoza, did so after being expelled from the Jewish community, and occupying a sort of gray land of Deism. Neither Christian nor Jew.

What this gets to is that even if Judeo-Christian has some abstract ideal reality, there was no Judeo-Christian civilization before large numbers of Jews abandoned the civilization of Judaism as it had developed organically over the centuries. The civilization only became labeled Judeo-Christian in rhetoric after most Western Jews had abandoned their customary and traditional religion, whether for a congregational faith more recognizable to Christians in the form of the Reform movement, out and out secularism, and in a large number of cases, conversion to Christianity (to name three individuals of Jewish familial origin who were raised Christian no matter their adult faith, Ludwig Wittgenstein, Karl Popper, and Karl Marx).

The civilizational tension among Jews is evident today in the world’s only Jewish state, Israel. Many secular Jews are for all practical purposes members of Western civilization who happen to have a Jewish ethnic and nominal religious identity. In contrast, Haredi Jews are fully steeped in the mores and orientation of the classical Jewish civilization that matured in early modern Europe. The conflict between the Haredim and secular Jews is not just one of religious observance but of civilizational identity and affinity (with Masortim occupying the middle ground).

Western civilization as a project after Late Antiquity and before the modern period was never a partnership between the Jews and Western Christians. It was the project of Western Christian societies, which eventually fractured during the Reformation, and repaired themselves back into some sort of whole in the wake of the Peace of Westphalia. The transformations of the 18th century ushered in the revolutionary changes which allowed for Jews to become participants in Western civilization as something besides Christians.

In general, though I understand that for the public history is often a useful fiction, I prefer attempting to model the past with the greatest fidelity to the reality we can reconstruct among those with the will and ability to understand. The emergence of Western civilization as we understand it, post-Christian civilization, the nymph stage of the universal liberal democratic civilization which was to conquer the 21st century (but hasn’t, and may never!), is historically contingent on particular peoples, places, and cultural threads. Those threads properly constituted simply make the term Judeo-Christian seem peculiar and inappropriate. Therefore, amongst those who aim to know, the proper appellations must be applied so as to illuminate rather than obscure and obfuscate.**

* Some Jews also existed outside of the world of Christianity and Islam, such as the Cochin Jews of southern India, or the Jews of Kaifeng, who were probably originally an extension of Central Asian Jewry. These groups were part of the Diaspora intellectual and culturally, at least initially (the Jews of Kaifeng eventually lost their last rabbi, probably in the 19th century, and assimilated into the Han majority or converted to Islam).

** I have no written much about Islam in this post, but the term Judeo-Christian also misleads many people into thinking that traditional Christianity and traditional Judaism have more similarities of belief and practice than either do with Islam. In fact Islam and Judaism are arguably more similar than either is to Christianity due to the emphasis on prescribed ritual and law incumbent upon the laity guided by a non-priestly scholarly class, whether it be rabbis or the ulema.

The 23andMe BRCA test

In case you were sleeping under a rock, 23andMe got FDA approval for DTC testing of markers related to BRCA risk. Obviously, this is a pretty big step, in principle.

But the short-term implications are not that earth-shaking.

From the FDA release:

The three BRCA1/BRCA2 hereditary mutations detected by the test are present in about 2 percent of Ashkenazi Jewish women, according to a National Cancer Institute study, but rarely occur (0 percent to 0.1 percent) in other ethnic populations. All individuals, whether they are of Ashkenazi Jewish descent or not, may have other mutations in BRCA1 or BRCA2 genes, or other cancer-related gene mutations that are not detected by this test. For this reason, a negative test result could still mean that a person has an increased risk of cancer due to gene mutations….

Apparently, women with one of these variants have a 45-85% chance of developing breast cancer by age 70. So the penetrance is high.

It seems that you’ll know if this sort of test is going to have utility for you based on family history.

The big thing is the transition to DTC. This will increase availability and drive the price down. That’s probably going to mean more work for those engaged in interpretation and education. False positives are going to start being a major thing….

Open Thread, 4/6/2018

Filed under: Open Thread — Razib Khan @ 1:03 am

Eden in the East is a weird book. Written in the late 1990s before modern-day genomics, its central thesis about the origin of Southeast Asian people in Pleistocene Sundaland seems likely to be wrong (at least most of their ancestry). But the author, a polymath medical doctor, marshals an enormous amount of archaeological and textual data supporting old ideas of cultural diffusionism, much of it plausible.

Despite my skepticism of the general theses promoted, reading Eden in the East is useful insofar as you need data and interpretive sieve for the swell of ancient DNA.

The University of Wisconsin-Stevens Point is eliminating many majors and adding new ones. This is eliciting a lot of outrage on Twitter.

Public universities are funded by the public. If they aren’t fulfilling the public role then things will have to change. Unlike many people, I don’t shed too many tears about the elimination of some of these majors because most graduates of them are stupid and uninformed (some of them actually have a less accurate view of the world coming out than before they arrived at university).

Here’s the breakdown:

Expanding programs Change into majors Discontinuing the programs
Chemical Engineering Aquaculture/Aquaponics American Studies
Computer Information Systems Captive Wildlife Art – Graphic Design will continue as a distinct major
Conservation Law Enforcement Ecosystem Design and Remediation English – English for teacher certification will continue
Finance Environmental Engineering French
Fire Science Geographic Information Science Geography
Graphic Design Master of Business Administration Geoscience
Management Master of Natural Resources German
Marketing Doctor of Physical Therapy History – Social Science for teacher certification will continue
    Music Literature
    Political Science
    Sociology — Social Work major will continue


Let’s set aside the fact that some of these programs, such as sociology and American Studies, are often de facto political action outfits. As someone who has talked to people who have history degrees from universities of various prestige and stringency, institutions of higher learning are doing a really shitty job inculcating knowledge into these kids. Or love of the topic. Also, their critical faculties aren’t the best. Too much critical theory, not enough critical thinking. Recitation doesn’t cut it.

Aquaculture and aquaponics is a vocational program of study which isn’t sexy, but at least it aims to impart skills. That’s what a lot of these kids need.

So my buddies at DNA Geeks unveiled a new t-shirt, Pipe(tte) Dream.

I kind of thought it was funny, but it turns out there’s some demand for stuff like this. Is bench biology still a thing? I guess so…. Anyway, if you are interested, click on through!

Evolutionary inferences about quantitative traits are affected by underlying genealogical discordance. This is an important preprint. Read it.

The Silicon Valley elite’s latest status symbol: Chickens. Some of the people caught up in this are quite self-aware: Citroen’s 19-year-old son, Luca, who grew up around the family business, puts it this way: “Being able to say you have chickens says, ‘I have a back yard,’ and having a back yard says, ‘I have space.’ And having space means you have money, especially when it comes to Silicon Valley real estate.” Chickens are a “hard to fake” signal of wealth. Yeah (the Romans had sacred chickens).

My main hope is that some of these rich Silicon Valley hobby-farmers pick up a copy of Introduction to Quantitative Genetics. It would do them some good (and perhaps the world?).

Do any readers have a review copy of She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity? It’s Carl Zimmer’s new book and the publisher is out of galleys.

Speaking of reviews, I’ll be writing one up for Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past for a publication most of you have heard of. Have to put the “writer hat” back on for a bit. Between my job, my intellectual interests, and family, I haven’t put much effort into that.

You probably know that Antifa went after Christina Sommers:

To be honest these forays by centrists (Sommers is a registered Democrat with libertarian leanings, similar to Steven Pinker) into the academy are starting to remind me of those ridiculous “debates” that Jews had to have with professional anti-Jews (mostly apostates) in the courts of medieval European monarchs. There were the outward forms of debate, but everyone knew what it was about (since Sommers and Pinker are from Jewish backgrounds perhaps that’s apposite).

Similarly, when the campus Left is against some speaker many people roll their eyes, and the administration makes the usual noises, but you know that the protestors are going to get a slap on the hands no matter how obnoxious or aggressive they are. For most academics, for various reasons, there are no enemies on the Left. Communists and Communist sympathizers like Angela Davis can be fulsomely praised with no worries about reputation, but those academics who think Sommers or Pinker are making reasonable points have to furtively communicate on secret direct message groups.

That’s where we are.

I now understand why Benedict Anderson’s Imagined Communities has been assigned to so many undergraduates: it’s a short and simple book. It’s depressing but unsurprising that it could be so influential. More on that later.

The criticisms that Enlightenment Now doesn’t really delve into the intellectual archaeology of the Enlightenment are spot on. But this seems a case where the title is a bit off, but the text itself is solid. I have seen on Twitter quotes about how Pinker has apologia for the Tuskegee experiment. My prior at this point about these sorts of invidious accusations is that they’re lies. For a variety of reasons, people lie about Steven Pinker. That’s sad, but we live in a world where liars prosper, so it shouldn’t be surprising.

My podcast with Spencer, The Insight, has been pretty successful so far. I just submitted it to a bunch of podcast directories this weekend to cover bases. Our goal is to get highlighted by iTunes, so if you haven’t, subscribe and leave a good review! (also, there are only three reviews on Stitcher so far)

We interviewed Chris Stringer a few weeks ago. This week we’re trying to get Milford Wolpoff recorded (to be posted next week). We have some ideas about guests we might have on. Currently, we want to mix personal genomics/biotech, genetics, and paleoanthropology. I think I want to mix in some straight history at some point, since so much ancient DNA is starting to percolate into that field.

Retweets Are Trash. Basically, the argument is that if you get rid of RTs some of the toxic effects of Twitter are dampened. Skeptical, but hopeful.

How Twitter Lost The Internet War. The most important part is the assertion that Twitter has a lot of tech-debt that it hasn’t retired or discharged, and that’s why it hasn’t been able to solve its troll problem in a non-manual manner. I have a hard time crediting this. But perhaps that’s how it is?

Turkey Is Turning Into the Next Pakistan. Being totally honest, it’s hard for me to believe that the media hasn’t been underplaying this story. Back when ISIS was a thing, Turkey was turning a blind eye to thousands of foreign fighters that were streaming into Syria. Even if Turkey isn’t pro-Islamist (and it kind of is), they are clearly backing Sunni Islamists who will impose a nasty majoritarianism if they ever win. Not that the anarcho-communist Kurds we’re backing would be any better in the long run.

Ultimately in Syria, I can’t begrudge ethnoreligious minorities for siding with the Assad regime against the rebels. And, I can’t begrudge the Sunni population their reliance on militants who are more fierce and principled in defending them and their interests against the government. But we’ve been through Iraq twice. Our Saudi ally has birthed monsters over the past generation. We turned a blind eye when our ally of convenience in the 1980s, Iraq, engaged in gas attacks against Iran and the Kurds.

We need to learn, and just stop. Stop!

On the lookout for Kindle deals in books. Here’s what I got recently:

* The Rise and Fall of Communism.
* Carthage Must Be Destroyed: The Rise and Fall of an Ancient Civilization
* The Sleepwalkers: How Europe Went to War in 1914.

I have a lot of books on Communism that I need to read!

Interesting paper, Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome.

The 500 errors on this site are due to a plugin and some of the issues with porting this blog over a few months ago. I need to allocate a day to figure this out, but I’ll do it. The same issues with the South Asian Genotype Project. I will update it. But I need to have four or five uninterrupted hours, and that’s just hard to come by.

SXSW should be interesting this week. As per usual I’ll avoid most of the festivities.

March 2, 2018

Do the Amerindians descend from Southeast Asians?

Filed under: Archaeology,Native Americans — Razib Khan @ 12:03 am

Many people have recommended I read Johanna Nichols’ Linguistic Diversity in Space and Time over the years. I checked out the book in grad school once but didn’t get around to reading it. But today I see it being referenced in Stephen Oppenheimer’s very strange book about Lemuria-I mean Southeast Asia, Eden in the East.

Both of these books were written in the late 1990s, before the current swell of genome-wide and ancient DNA analysis. Oppenheimer reports Nichols’ comparative analysis of linguistics implies that the ancestors of the Amerindians were not interior Siberians, but coastal people who came up from Southeast Asia.

Today we know this is somewhat wrong. About 30 to 40 percent of the ancestry of modern Native Americans derives from Ancient North Eurasians, who seem to be most commonly found in the great Eurasian heartland, probably to the east of what we think of today as Europe, but west of the Pacific.

But there’s more. Most of the ancestry of Native American peoples seems to be more like that of East Asians. Today this component extends rather far north, into Korea, Japan, and such. But these are consequences of recent demographic movements. Nichols’ Southeast Asian hypothesis may actually not be off-base, in particular in light of other evidence suggesting admixture with an Australo-Melanesian population.

One of the major issues with the field of ancient DNA and the historical inferences people make is that the theories and models are often quite ad hoc, and emerge in response to the data. But these earlier ideas, informed by linguistics and archaeology, are actually a pretty good source of possible ideas. They may not be constrained by genetics, because we didn’t have that information (aside from mtDNA), but are richly informed by other disciplines.


February 28, 2018

Who We Are and How We Got Here, a book worth reading

Filed under: Human Evolution,Human Genetics — Razib Khan @ 7:18 am

Yesterday I talked to a friend who has a review copy of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. They gave me a preview (their overall assessment was positive).

I haven’t personally asked to get a copy because, to be honest, I thought there wouldn’t be anything new in it. If you “read the supplements” what more could there be in 368 pages? So I was waiting until the end of the month to buy the book and read it in my own sweet time as due diligence.

Well, this morning I asked a publicist to send me a copy. I will be getting it next week. The reason is that I’m told the latter portions of the book are quite challenging and candid as to what genetics may tell us in the 21st century. Who We Are and How We Got Here is a 21st-century revision and update of The History and Geography of Human Genes. But it’s apparently a lot more.

Also, I make a small cameo in the book, as does Eurogenes and Dienekes. I have always appreciated how the David Reich and Nick Patterson and their whole lab has taken people outside of the halls of the academy seriously. They didn’t need to as a matter of professional necessity but often engage as a matter of decency and seriousness.

Idle theories are the devil’s workshop

Filed under: Evolutionary Genetics,Evolutionary Genomics — Razib Khan @ 12:35 am

In the 1970s Richard C. Lewontin wrote about how the allozyme era finally allowed for the testing of theories which had long been perfected and refined but lay unused like elegant machines without a task. Almost immediately the empirical revolution that Lewontin began in the 1960s kickstarted debates about the nature of selection and neutrality on the molecular level, now that molecular variation was something they could actually explore.

This led to further debates between “neutralists” and “selectionists.” Sometimes the debates were quite acrimonious and personal. The most prominent neutralist, Motoo Kimura, took deep offense to the scientific criticisms of the theoretical population geneticist John Gillespie. The arguments around neutral theory in the 1970s eventually spilled over into other areas of evolutionary biology, and prominent public scientists such as Richard Dawkins and Stephen Jay Gould got pulled into it (neither of these two were population geneticists or molecular evolutionists, so one wonders what they truly added besides bluster and publicity).

Today we do not have these sorts of arguments from what I can tell. Why? I think it is the same reason that is the central thesis of Benjamin Friedman’s The Moral Consequences of Economic Growth. In it, the author argues that liberalism, broadly construed, flourishes in an environment of economic growth and prosperity. As the pie gets bigger zero-sum conflicts are attenuated.

What’s happened in empirical studies of evolutionary biology over the last decade or so is that in genetics a surfeit of genomic data has swamped the field. Some scholars have even suggested that in evolutionary genomics we have way more data than can be analyzed or understood (in contrast to medical genomics, where more data is still useful and necessary). Scientists still have disagreements, but instead of bickering or posturing, they’ve been trying to dig out from the under the mountain of data.

It’s easy to be gracious to your peers when you’re rich in data….

February 27, 2018

The tall and long tales that elephants tell (also, ancient DNA never forgets)

Filed under: Speciation — Razib Khan @ 1:01 am

The new paper on ancient DNA from elephants, mammoths and mastodons, A comprehensive genomic history of extinct and living elephants, is pretty cool. It leverages next-generation sequencing and ancient DNA, to reconstruct the demographic history of several species of elephants, extant and extinct.

The major core finding is that ancient DNA along with better data from extant species suggests that straight-tusked elephant of Europe (P. antiquus), which went extinct 50,000 years ago, seems to have been an evolutionary synthesis of sorts. A substantial portion of its ancestry as from a deeply diverged lineage of elephant. But another fraction seems to derive from a branch of the African forest elephants, in particular, the West African variety. Finally, earlier on there was also admixture with an Asian pachyderm related to the woolly mammoth.

You can see from the figure at the top that the divergence between these lineages is on the order of hundreds of thousands to millions of years.

This section from the conclusion is a huge takeaway:

Our genomic analyses of present-day and extinct elephantids revealed a history of multiple major interspecies admixture events. Evidence for gene flow among closely related mammalian species is not unprecedented. Examples include cases of unidirectional gene flow [e.g., from polar bears into brown bears (47), similar to the Columbian mammoth gene flow into woolly mammoths observed in our study]; emergence of admixed species [e.g., North American wolves with ancestry from coyotes and gray wolves (48), similar to the straight-tusked elephants in our study]; different extents of gene flow [e.g., between gray wolves and Eurasian/African golden jackals (49), and between bonobos and central/eastern chimpanzees (50), as in the case of straight-tusked elephants and west African forest elephants/woolly mammoths in our study]; extended periods of gene flow during the initial diversification of species [e.g., between eastern and western gorillas (39), Sumatran and Bornean orangutans (39), and the ancestors of humans and chimpanzees (39, 51), like those inferred from most pairwise species comparisons in our study]; and adaptive introgression [e.g., in the great cats of the genus Panthera (52)], which could have played an important role in the evolution of elephantids as well. Our results in elephantids thus add to the growing weight of evidence in favor of the view that capacity for hybridization is the norm rather than the exception in many mammalian species over a time scale of millions of years.

Big speciose mammal lineages seem to have hybridzed a lot. Should this surprise us? Probably not.

Placental Invasiveness Mediates the Evolution of Hybrid Inviability in Mammals:

A central question in evolutionary biology is why animal lineages differ strikingly in rates and patterns of the evolution of reproductive isolation. Here, we show that the maximum genetic distance at which interspecific mammalian pregnancies yield viable neonates is significantly greater in clades with invasive (hemochorial) placentation than in clades with noninvasive (epitheliochorial or endotheliochorial) placentation. Moreover, sister species with invasive placentation exhibit higher allopatry in their geographic ranges, suggesting that formerly separated populations in mammals with this placental type fuse more readily on recontact. These differences are apparently driven by the stronger downregulation of maternal immune responses under invasive placentation, where fetal antigens directly contact the maternal bloodstream. Our results suggest that placental invasiveness mediates a major component of reproductive isolation in mammals.

Monkeys and apes (including humans), have very invasive placentas. Afrotheria, somewhat less so. Placental invasiveness isn’t the only criteria to predict or gauge the viability of hybridization, but it’s a major one.

I’ve stated before that genomics didn’t really change our understanding in a qualitative way in relation to evolutionary biology. Yes, stupid arguments about selectionism vs. neutralism really don’t happen anymore because there’s a mad scramble for data, as opposed to rhetorical tactics. But, perhaps in the area of understanding speciation with regards to mammals genomics has really changed things. That is, it’s a lot more about reticulation and a lot less about bifurcation.

To a great extent the “biological species concept” (BSC), which to the general public is the scientific species concept, is mammal focused. If plant geneticists had the catbird seat I think we’d have a different view of what species were. As it is, that’s not what happened. Species are human constructs and reify a certain Platonic sense of categories and kinds. What genomics is showing us here is even in the “best case” circumstances of the BSC, in mammalian lineages, when evaluated over reasonable time spans species barriers are highly porous.

February 26, 2018

Roman Empire and Indian Ocean Trade

Filed under: geography,Indian Ocean,Roman Empire — Razib Khan @ 7:04 pm

I periodically check up on Amazon’s monthly deals. Though the science section is usually pretty thin, the history deals are more numerous. A lot of them are not too good, or are reprints of very old books. But now and then you get a scholarly and dense work which is magically priced at below $2.00.

So I bought a copy of The Roman Empire and the Indian Ocean: Rome’s Dealings with the Ancient Kingdoms of India, Africa and Arabia, and skimming over it it’s definitely not the most scintillating prose, but there’s a lot of interesting material in the book. If you are looking for a good book, I would recommend it, especially at that price.

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