Open Thread, 11/29/2015

2015-11-29 10.54.09Over Thanksgiving I tried Marie Sharp’s Habanero Pepper Sauce. It is apparently from Belize. Highly recommended. It’s a genuine habanero sauce, in that it actually is spicy. The additives don’t overwhelm the habanero flavor and impact. I would say it is very mildly on the sweet rather than vinegar side, but the other flavors don’t interfere with the impact, nor are they dissonant.

51zlgfgrs2L._UY250_So apparently I forgot that Marcus Aurelius was like Adolf Hitler. More precisely, I read Frank McLynn’s biographies of Genghis Khan and Marcus Aurelius in sequence, and while the exterminationist practices of the Mongols were well covered, I had forgotten that the great philosopher emperor had wanted to blot the Iazyges Sarmatians from the earth during his Danube campaigns. The reason was that unlike the German agro-pastoralists whose mode of life was such that they could have been transferred to the empire and become taxpayers, the Iazgyes were nomadic pastoralists who were likely to be a perpetual thorn in the side of the Roman state who were also not ideal settlers within it. This brings me to a curious historical analogy: that between the Kangxi Emperor and Marcus Aurelius. The two have both been termed philosopher emperors, who wrote down their reflections for posterity. Marcus Aurelius famously in his Meditations, while you can find that of the Kangxi Emperor in Jonathan Spence’s Emperor of China: Self-Portrait of K’ang-Hsi.

And like Marcus Aurelius the Kangxi Emperor also endeavored upon a “final solution” for an ethno-political problem: the destruction of the Dzungar polity which he began, and his successors completed, entailed genocide on a large scale through famine and displacement. More Holodomor than Holocaust. The ethnic character of the northern half of modern day Xinjiang, what was Dzungaria, has been radically reshaped over the past 250 years due to the efforts of the Kangxi Emperor and his heirs (what was once a Oirat Mongol domain passed over to Kazakhs and Uygurs).

UltrasSoc_cover_epubAs promised, Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth, is now available in trade paperback. I’ve started to read it. One thing that I like about Peter’s work is that he’s relatively economical in regards to prose, and like a scientist he balances powerful analytic frameworks which allow for general inferences ,with rich empirical description of specifics. You should probably read his 2013 PNAS paper before you read this book.

ISIS’ Grip on Libyan City Gives It a Fallback Option. Look at the map. The Islamic state has hegemony over a huge swath of the coast between Tripoli and Benghazi. We, the West, and France and the United States in particular, created this situation. This was a war of choice. Liberals who abhorred the Iraq intervention somehow thought that the Libyan one was warranted. The Gaddafi regime was not a good thing. He was a mercurial dictator who sponsored terror against the West and was a source of trouble for his neighbors in the Middle East and Africa. But, he was aging, and beginning to slide into his “bunga bunga” years. Libyans are arguably worse off now than they were before the intervention. The rest of the world most definitely is.

The Heart Disease Conundrum. Here’s the important part:

However, Framingham risk models do not tell the whole story for nonwhite ethnic groups. In 1959, the first study was published showing the increased risk of premature heart disease in Indian immigrant males, who had four times the rate compared with the men in Framingham, despite having lower rates of hypertension, smoking and high cholesterol, and more often following a vegetarian diet.

What is it about South Asian genetics or environments that lead to so much heart disease? We need a Framingham-type study to answer this question.

The problems exhibit themselves among well off South Asians in the West. And, frankly, well off South Asians in South Asia. All four of my grandparents died of issues relating to their cardiac health or the circulatory system (e.g., heart disease, hypertension leading to stroke, etc.). Mind you, they died in their mid-70s, early 80s, and at 100, so one needs to keep in mind that at those ages something was going to happen. Luckily cancer doesn’t seem to run in my family. I’ve got a large pedigree at least to check for these things.

I’ve been running and lifting to various degrees over the past year and a half, going from 155-160 lbs (at 5’8) to 145-150 lbs. Judging from the various body fat percentage meters I’ve used I’ve probably lost ~4%, likely going from ~20% to ~16%. But, I definitely have work to do. South Asians are “fatter” than their weight. This is clearly to a great extent genetic, or a gene-environment interaction relating to activity (or lack thereof), as I don’t eat a South Asian typical diet (“paleo-lite” is probably a good descriptor). That’s just how life is. (though these genetic issues probably don’t preclude a relatively high life expectancy, the Maldives for example has one of 77 years, while Kerala and Sri Lanka are at 74 years).

Neolithic farmers from Greece and Anatolia. ‘”I think it is time to declare the problem of “Neolithization of Europe” done.’ Basically. Onto the Bronze Age. And Asia.

What It’s Like to Grow Up as a Closeted Gay Extremist Muslim in East London. Unlike my white liberal friends I don’t think Islamophobia is a big issue in most of the West. I say this as someone who “looks Muslim” and has a “Muslim name” who also flies a lot. But what do I know about racism compared to my white liberal friends?

From Indonesia, a Muslim Challenge to the Ideology of the Islamic State. As I pointed out on Twitter, these sorts of articles were common before the 1998 Asian economic flu, though usually they had to do with Mahathir Mohammed and Malaysia at the time. And, as suggested in the article attempts to affect change in the Arab Islamic world from the demographically and economically powerful Asian Muslim periphery probably are not going to work because of ethno-racial chauvinism. Though one might not know this from the vantage point of post-colonial theory dominated academic departments, Arabs identify themselves as white, and have a fair amount of racial prejudice against East Asians, South Asians, and Africans. Though Persians historically had a huge influence on the shaping of Sunni Islam, today Iran is Shia, so they will have a difficult time getting heard. Turkey has its own recent colonial legacy with the Arab world to deal with, as well as Ataturk’s reforms forcing a cultural rupture despite recent attempts to close the gap. Islam’s ethnic valence is somewhere between that of Christianity, which has been re-appropriated multiple times in multiple contexts, and Judaism, which is both a religion and a nationality in its self-conception. I grew up marginally Muslim, insofar as my parents were involved in the Islamic community for the purpose of celebrating religious holidays, and the attitudes of Arabs, and a lesser extent Turks and Persians, in regards to the religion and South and Southeast Asians, as well as African Americans, tended toward condescension. They were happy to accept these groups as legitimately and authentically Muslim, but it was clear that they would never have brooked any lectures on proper practice and belief from these arrivistes.

The Near-Impossibility of Assimilation in Belgium. The headline is misleading. The substance of the article makes it clear that it is totally feasible to assimilate if you are white.

Tibetans Fight to Salvage Fading Culture in China. First, the issue is language. One can imagine that Tibetan identity would persist purely through religion, with the Tibetan language becoming a liturgical vehicle, as Coptic is among Coptic Christians, who all adopted Arabic by about 1800 (there were people speaking Coptic during the European Renaissance, since apparently some Europeans visited Egypt to learn the language during that time). A good model for Tibetans might be the Hui community, who speak Chinese but maintain a distinct Muslim religious identity. Second, there are >100 times more Han Chinese than Tibetans in China. The economic benefit of being able to speak Chinese is pretty clear. As occurred in Lithuania during the period of the Polish-Lithuanian Commonwealth I imagine it’s going to be hard for upper class Tibetans to not be linguistically assimilated by the more numerous Chinese.

Religion_Explained_by_Pascal_Boyer_book_cover‘To hell with their culture’ – Richard Dawkins in extraordinary blast at Muslims. I don’t agree with Dawkins on many things, and think some of his assertions are wrong and/or stupid. But, I do respect him for actually saying what he thinks rather than always testing the wind to stay on the right side of the norms of his “team.” It’s refreshing, rare, and it also adds to his genuine credibility, which is otherwise undermined by his tendency to be emotive and shoot-from-the-hip.

I should also add some specific issue in regards to my relationship to the “New Atheists,” and in particular Dawkins and Sam Harris. As a matter of analysis I disagree with their views of how religion as a phenomenon emerged and how it persists. In general my opinions are reflected most by cognitive anthropologists, such as Scott Atran and Pascal Boyer. But, when it comes to the political and normative debate, I have much more sympathy for Dawkins and Harris, because I think their attitude is a broadly liberal one which is hostile toward multiculturalism in a manner well aligned with a particular Western tradition which goes back to the Enlightenment, with which I have much sympathy (though not without reservations). More plainly, as much as I might disagree with Dawkins and Harris on the nature of religion, I totally reject the idea that they are racist in any way as some of their liberal (and sometimes conservative!) critics suggest. Perhaps some of their comments might have racist implications, or one might argue that the application of some of their policies are necessarily racist, but it is pretty obvious to anyone who knows their biographies that neither of them are racist in their intent or personal views. The accusation is basically just a rhetorical move to silence them. (I might add that I also dissent from some of Harris’ more interventionist foreign policy positions; but reasonable people can disagree on these things)

SciReader is great if you haven’t checked it out. One thing I would really like from these sorts of recommendation engines is the ability to tweak exactly how precise the results should be base on previous preferences. Or perhaps a way to add a “stochastic parameter” into the equation.

b127HB_lgFor example, there are topics I’m interested in which I’m not working on in my current research, and are never showing up on these recommendation engines. E.g., Evolution of the additive genetic variance–covariance matrix under continuous directional selection on a complex behavioural phenotype. It’s open access. I recommend you read it! Check out the G-matrix page.

Donald Prothero has a new book, The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution. I’m not a big fan of the biographies of geologists and paleontologists that get interleaved into the science. I’m a computational biologist, so all I see is digging in dirt, digging in dirt, etc. etc. (obviously I feel differently about biographies about geneticists…but I’m a geneticist!)

But, I really liked Prothero’s previous book, Evolution: What the Fossils Say and Why It Matters. Earlier I said one of the things I like about Peter Turchin’s work is the balance between analytic framework and empirical data. Unfortunately many evolutionary genetics types get a little fixated on their model organism (often it’s Drosophila, let’s keep it real) and forget about the big picture of what evolution is. Sometimes it is useful to actually look at a survey of a lot of the fossils and see how all these evolutionary dynamics play out in terms of morphology.

Finally, I’m not open to debates on my comments policy. Trying to argue with me about it will probably get you banned. I know most of you know this, but some of you don’t, at least judging by the past week. So here I am stating it explicitly.

Building a better Turkey?

Bourbob_red_turkey_Tom-r2Most people know that animal breeding has a long history. At least since the Neolithic revolution, and probably in some fashion earlier if you consider that dog-human interaction/co-evolution dates to the Pleistocene. In some ways this is not always a good thing, when you consider flourishing from the perspective of the animal. It is a well known fact that when you keep selecting on one particular trait of an organism, there tend to be “correlated responses.” That’s because traits are interrelated, sometimes in a direct structural sense, and sometimes due to common genes. In nature these correlated responses often prevent excessive deviation from optimal fitness. E.g., if you make mice too big they can’t breed.

effetmaranelloBut outside of natural circumstances all sorts of things can happen under human tutelage. That’s how we get grotesquely large chickens with breasts so unwieldy that they can’t walk. And, it’s how we get “cute” cats like the Persian breed who are well known to have issues with conventional mastication. The point is that conventional quantitative genetic breeding methods can lead to “monsters,” because there are plenty of mutations floating around in natural populations. There’s nothing exotic, and even before understanding the genetic basis of inheritance humans were engaging in this sort of activity for thousands of years.

41ZhyEU5lGL._SY344_BO1,204,203,200_All this is something you have to keep in mind when reading articles such as this in The New York Times, Open Season Is Seen in Gene Editing of Animals. Basically, probably triggered by the FDA approval of genetically modified salmon, there is now a lot of discussion around genetically modified organisms of the animal kind. The New York Times piece opens with an interesting twist:

Other than the few small luxuries afforded them, like private access to a large patch of grass, there was nothing to mark the two hornless dairy calves born last spring at a breeding facility here as early specimens in a new era of humanity’s dominion over nature.

But unlike a vast majority of their dairy brethren, these calves, both bulls, will never sprout horns. That means they will not need to undergo dehorning, routinely performed by farmers to prevent injuries and a procedure that the American Veterinary Medical Association says is “considered to be quite painful.”

If you read the whole article thought it is clear that what the new techniques are doing is supercharging the aims and methods of conventional breeding. In many cases there isn’t even going to be any transgene that moves between species. Rather, researchers may want to create specialized knock-outs, which lack gene function.

Bioethicists and animal rights organizations may suggest there are new ethical questions which are confronting us, but there really aren’t. Using traditional breeding techniques humans are already producing animals whose faces barely close in (many flat-faced cats basically have a hair-lip), or which need caesarian section to give birth. We’ve been confronting these questions for a while now, and better genetic modification techniques just amplify them, or, with greater precision allow ways to ameliorate some of the unfortunate side effects by offering more options.

Dubai vs. democracy

151300203I haven’t talked much about the refugee crisis because at this point I’m in a “wait & see” mode. It seems almost fantastical that relatively small northern European countries should allow themselves to be demographically overwhelmed in less than a generation, but that isn’t a totally crazy proposition. But we should be cautious about extrapolations. Cultural norms can change rather fast, because most people are conformists (e.g., Sweden combines a very politically correct mainstream culture with a robust verging-on-volkisch minority party which is far outside of the bounds of anything you would see in the United States)

But an article in The New York Times, Emirates Secretly Sends Colombian Mercenaries to Fight in Yemen, does put into stark relief the sort of choices we’re facing in the modern world. On the one hand technology is advancing apace, but our social structures seem to recycle the same forms. The Gulf petro-state system is in some ways straight out of Dystopian science fiction, combining a modern capitalist economy with the a sort of commoditized attitude toward human life with a neo-feudal tincture. But it also reminds me of another model, that of the ancient Greek city-states. Dubai, Qatar, etc., are basically societies where the majority of individuals engage in production for the capital class, which also subsidizes the citizenry (“liturgies”), which is a minority. Though they are not democracies like Athens, this relationship between a notionally co-equal minority and a majority whose economic productivity allows for the life of the society to flourish isn’t particularly novel.

One thing that set the ancient Roman system apart from the Greek polities was that it was expansive, assimilating local elites. It is well known that many of the emperors were not made in Rome, but some of the patrician clans, such as the Claudii, were themselves of Etruscan or Sabine origin. Roman cosmopolitanism fused with an acknowledgment of the primacy of a core culture was a robust system that persisted for nearly 1,000 years, allowing for political scale. Additionally, it is a notable trend in history that when you reduce other humans purely to commodities, basically units of economic production, they have no loyalty to their contracts beyond self-interest. They’ll often try and take over through violence.

Another system is the Western democratic liberal one. This system presupposes citizens who are co-equal, without large groups of disenfranchised people. Even in the American case with slavery in most of the territory non-free males were a small minority. There is also often a rough cultural homogeneity which is presumed for a nation-state. Ergo, the carving up of the Austro-Hungarian polity after World War I followed ethno-linguistic lines. But these sorts of implicit understandings seem to be falling by the wayside. Not to be conspiratorial, but I think part of what’s happening is that cosmopolitan Western economic elites, the top 0.1% or so, have no real loyalty to the nation-state, and find them impediments to the free flow of their labor and their capital. Though few would explicitly admit this, I think that the Dubai model is quite appealing because it dispenses with the non-economic niceties. The main caution I would offer to this is that the Dubai model is probably a “high reward/high risk” play.

Yes, it is agriculture

000e553e_mediumIn 2007 a friend told me of an encounter at a seminar where L. L. Cavalli-Sforza seem to offer agriculture almost reflexively as a solution to the conundrum of signals of positive selection in the genome of humans. Basically, all paths led to agriculture. I have to say that nearly ten years later Cavalli-Sforza’s deep intuition on these issues seems to be vindicated. Agriculture was an enormously big deal.

Carl Zimmer in The New York Times has a write up of Matheison et al. (it’s in Nature), Agriculture Linked to DNA Changes in Ancient Europe. There aren’t a whole lot of surprises, as the pre-print has been around for a year or so. But, having the work written up in a newspaper allows researchers to engage in some extemporaneous speculation. Ergo, you have:

Why? Scientists have long thought that light skin helped capture more vitamin D in sunlight at high latitudes. But early hunter-gatherers managed well with dark skin. Dr. Reich suggests that they got enough vitamin D in the meat they caught.

He hypothesizes that it was the shift to agriculture, which reduced the intake of vitamin D, that may have triggered a change in skin color.

This was to some extent Cavalli-Sforza’s idea, and I’ve proposed it as well. Then there is the model of sexual selection. These theories aren’t always exclusive, and pigmentation may have multi-causal underpinnings. It is very interesting that the best methods and ancient DNA seem to be suggesting lots of very recent change and likely adaptation. But ultimately, we still have no clear idea.

Open Thread, 11/22/2015

51DPT3AYDHL._SX321_BO1,204,203,200_People like to quote Martin Luther King Jr., “The arc of the moral universe is long, but it bends towards justice.” This includes the president of the United States of America, arguably the most powerful non-plutocrat in the world. But after reading Frank McLynn’s biographies of Marcus Aurelius and Genghis Khan, I wonder if anyone actually bothers to read history when they say something that is so facile. Now, I agree that the trend does move toward one direction. Over the past 3,000 years the institution of slavery has gone from being a banal practice, to a necessary evil (e.g., as in Islam), to a taboo practice. But the phrase is often bandied about as if moral directionality is fine-grained on the scale of a generation or two, rather than on the scale of centuries or more. For all Marcus Aurelius’ strangeness in comparison to moderns, Genghis Khan was clearly more a figure who would fit in in a pre-Axial world.

In Genghis Khan: His Conquests, His Empire, His Legacy the author mentions legends that the “original” Mongols were a fair skinned and haired, eventually becoming more typically East Asian in appearance through admixture. There are some accounts where Temujin, who became Genghis Khan, had reddish hair. I note that Mongolian people seem to have a small proportion of West Eurasian admixture. My earlier assumption had been that this was recent (from Russians), but now I wonder if this is old. I note that if you look at the phylogeographic literature there is a lot of R1a1a in parts of East Asia. Among the Uyghurs, Altaic people, and to a lesser extent Mongolian groups. The Indo-Iranian modal R1a1a haplotype, Z93, is found among the Altaic people. My supposition at this point is that it may be that Christopher Beckwith’s argument in Empires of the Silk Road that Indo-Europeans were more influential on the eastern fringe of the Eurasian steppe than we may think.

Speaking of East Asia, and specifically China, a question came up on Twitter as to when it joined the rest of the World Island’s oikoumene. Though there were influences from the West at an early period (probably mediated by Indo-Europeans), I believe that the establishment of the Protectorate of the Western Regions around ~0 A.D. probably is a good early date. By the Tang dynasty China was clearly part of the “human web,” but by the first few centuries A.D. Buddhism and Roman merchants had already arrived through Central Asia.

The 2006 paper, Possible Ancestral Structure in Human Populations. Strange that it has only has 149 citations. I recently talked to Mike Hammer about the reception to these ideas in the mid-2000s, and he agrees with my recollection that they were totally marginalized and laugh out of the room back then.

Someone asked last week about a reader poll. I did one about a year ago. You can download and Excel file here of results.

galaxy-s6-edge_gallery_front_blackIn response to this question about writing, I don’t know if there is a most “complicated” writing system. I assume that Chinese is arguably more complicated since it takes longer for children to attain a high level of literacy. I don’t think it changes general fluid intelligence, though it probably has an effect on crystallized intelligence.

Response to this question, start here.

So I got a Samsung Galaxy S6 Edge. My previous phone decided that its sound was going to stop working while I was traveling on business. I don’t make regular phone calls often, but when I do, I like to be able to hear what the person on the other end says! This wasn’t a hardware issue, but a software problem, probably due to an app I downloaded. After wasting a few hours trying to get it working (it worked at one point, but then when I rebooted the problem cropped up again), I ended up just calling my provider to get a new phone for when I was back home.

As I’m a rebel from the hegemonic Apple ecosystem (now that I don’t use an iPod shuffle I don’t use any Apple products), I plunked down for the Edge. I have to say I’m pleased so far, though it does get annoying that some of these phones have so many features that I waste an hour or two just watching “tips & tricks” tutorials.

Recently I encountered the idea that the popularity of the “trans-Atlantic accent” in the 1930s and 1940s might have been due to the utility of this clipped and highly enunciated way of speaking when radio quality was low. Well, voice recognition today on these phones makes me wish I spoke with the trans-Atlantic accent….

Finally, Jerry Z Muller followed me on Twitter! It’s a personal “big deal” for me because his anthology, Conservatism: An Anthology of Social and Political Thought From David Hume to the Present, was very influential in my own thinking back in the late 1990s.

Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth

UltrasSoc_cover_epubA while back I promoted Joe Henrich’s The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. I did finish Frank McLynn’s Genghis Khan book, and am re-reading his Marcus Aurelius biography. There will be a review of the first book coming out soon, but I will tease here that unlike Tyler Cowen I don’t think it would come close to being the best book of the year (in part, because unlike many readers I know a fair amount about the topic). I also have a copy of Mary Beard’s SPQR: A History of Rome, and someday really need to get to Dehaene’s Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts

But here’s another must read, Peter Turchin’s Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth. This seems like an excellent complement to Ian Morris’ War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots, which I have not managed to get to read, in part because I want to hit Foragers, Farmers, and Fossil Fuels: How Human Values Evolve. Yet I’ve read a fair number of Peter’s books (see my 10 questions for him), so I’ll probably be moving this up the stack.

Peter is a serious thinker, and human social complexity and cooperation is an important, and unresolved topic (I am not as sanguine or flip on this David Sloan Wilson). Currently only the Kindle edition is available, but Peter says that the “dead-tree” version should be available in the next few days.

(note, I have to read The Hive Mind!)

Addendum: Here’s Peter’s post on the book….

Children of Eden

chg1

ncomms9912-f2Over the past few years we have seen ancient DNA researchers “carve nature at its joints” when it comes to the paleohistory of Europe after the end of the last Ice Age. In relation to this historical reconstruction we aren’t at the end of the road, but I do think that the terminus is within sight. There are only so many populations one can sample, and so many statistical constructs one can posit, before one is on the plateau of diminishing marginal returns. For example, the model of Holocene Europe being a synthesis of two very distinctive populations which merged after the last Ice Age was too simple. A model with three populations is sufficient for the vast majority of European groups. Though in these sorts of situations more complex models may be consistent with the results, the bias is to go with parsimony, and  attempt some alignment with linguistic and archaeological evidence.

A new paper in Nature Communications, Upper Palaeolithic genomes reveal deep roots of modern Eurasians, fills in some gaps in the broader picture. The figure at the top of this post illustrates the modification that these authors made to the schematic of Lazaridis et al. Iosif Lazaridis himself as weighed in on Twitter:

CHG = Caucasian hunter-gatherers. More specifically, the authors of this paper analyze two subfossils from Georgia dated to ~10 to ~13 thousand years, Kotias and Satsurblia. Kotias, at ~15x coverage (that is, each position is sampled ~15 times, so you have a good sense of variation at any given position), is particularly useful. What they found is as Lazaridis reports above: CHG seem one of the primordial groups to give rise to the extant variation of modern Europeans, and Western Eurasians writ large.

The rough stylized history of the non-African populations is as such: a “basal Eurasian” (bEu) population separates off first, and then west and east Eurasians diverge, and then in the west there is a divergence between the ancestors of western hunter-gatherers (WHG) and ancient north Eurasians (ANE). The early European farmers (EEF) are compounds between WHG and bEu, with a slight bias toward WHG. The Anatolian farmers were also admixed, though biased toward bEu. The eastern hunter-gatherers (EHG) are a balanced mix between WHG and ANE, and this group fused with the CHG to give rise to Yamnaya. This brings up the question: are CHG the basal Eurasians? I doubt it. The paleodemography of the ancient Near East has been barely elucidated. It seems likely that CHG, like the Anatolian farmers, are a compound of some sort. Basal Eurasians may manifest as an allele frequency spectrum across the Middle East during this period, the remnants of a back migration from west Eurasian groups mixing with the ur-Basal Eurasians, who were the first to split off from the Out of Africa migration. In the colder and drier world of the Last Glacial Maximum (LGM) it seems likely that some of the northern hunter-gatherer populations would move into territory occupied by basal Middle Eastern groups. In addition, the Sahara had periods of extreme dryness during the Ice Age, so the ur-basal Eurasians wouldn’t necessarily have been able to withdraw to Africa.

Using G-PhoCS they inferred separation dates between the various populations. I have two issues with this. First, their mutation rate seems likely, but there is still some debate about the exact value and whether it is constant across a lineage (for this level of phylogenetic distance the assumption of constancy seems valid). Second, the confidence intervals from these results are huge. The authors report the results, and tentatively attempt to relate separation to the LGM ~20 thousand years before the present, but know that they can’t assert anything robustly. It strikes me that we know the sequence of separations between the groups better than the period of separations.

ncomms9912-f4But one definite result is the pattern of ancestry (or shared drift) which is derived from CHG. It is high in the Caucasus, as one would expect, but also in South Asia. This is not surprising. Several papers have suggested that the West Eurasian admixture into South Asians seems to have an affinity with northern West Asians. Agriculture in South Asia began at Mehrgarh with a traditional West Asian cultural toolkit, and likely the character of the ANI-ASI admixture took root here. In Europe many researchers believe that the replacement of the hunter-gather populations in most areas was rather complete after the initial admixture event that occurred when farmers initially entered the continent, and it seems possible that the same is true in South Asia as well. There are no “Ancestral South Indians” in pure form left, and the variation in ancestry between tribes and caste groups in many areas is not very large.

dstatWhen you into the supplements though it all becomes much clearer. To the left you see a table of D-statistics, where the left column are Indian populations, and in the right column are the top hits, X, for these groups in terms of inferred gene flow with the tree form (Yoruba, X; Onge, Indian population). The key thing to note is that while some Indian groups have the strongest hit from the Kotias CHG sample, others, and of note the North Indian Brahmin Tiwari community, the signal from the Afanasevo is strongest. The Afanasevo are genetically basically the eastern extension of the Yamnaya. In other words, the D-statistics are showing evidence of a migration from the steppe, and a migration from West Asia. This also makes sense of supplementary figure 3, which shows non-trivial shared drift among some South Asian groups with the Swiss Bichon WHG sample. The Afanasevo would have brought this via their EHG ancestry, which was about half similar to WGH.

The evidence from uniparental (Y and mtDNA) and functional genes is also interesting. CHG carry mtDNA haplogroups H13 and K3, and Y chromosomal groups J and J2. It seems likely that the prevalence of haplogroup in H is due to post-Neolithic population replacements. The CHG contribute about half the ancestry to Yamnaya, but these two did not have haplogroup R1a or R1b. Haplogroup J2 is particularly common among caste groups in South India. All this points to the likelihood that the Dravidian languages are probably derived from agriculturalists with West Asian roots, and gives a touch more plausibility to the idea that ancient Elamite in Khuzistan may have been a distant relative of Dravidian.

Additionally, the derived light-skin variant of SLC24A5 is found among the CHG, as it is among the Anatolian farmers. The haplotype is the common one found in West and South Eurasian populations. The variant for SLC45A2 in Kotias is definitely homozygous for the ancestral variant. On the whole most South Asians do not share European light-skin variants except for SLC24A5. The exceptions tend to be groups in the Northwest, and upper castes. Exactly the same groups which likely have the strongest Afanasevo stamp.

One thing the authors note is that the Caucasus themselves have been subject to great change. It is clear that a farmer group related to EEF has mixed with the CHG descended groups. And, today the Caucasus has very high fractions of ANE ancestry in some groups, but these samples did not at all. At ASHG a few years ago a prominent population geneticist offered to me that he thought ANE might not have been the best term, as there was no strong evidence that this group wasn’t more common elsewhere. But CHG did not have ANE ancestry, despite that being very salient in modern trans-Caucasian groups. This suggests a later expansion and mixing event. From what I know ANE drift is not evident in many Indian populations, pegging the arrival of ANE-bearing groups to a later period after agriculture. Gene flow into Amerindian groups, and high ANE fractions in Central Siberia and the Altai, do point to their locus of habitation in Northern Eurasia.

Finally, let’s remember that we’re constructing the past from the slim remains which we have on hand. Ten years ago we were using extant genetic variation, because that’s all we had, and that led us astray. In the broadest sketches the inferences were right, but in many details they were misleading. Similarly, we shouldn’t think that the ancient DNA yielding populations are necessarily the direct ancestors of any modern groups. We know, for example, that Ma’lta is actually not ancestral to the ANE population which contributed to both Europeans via the EHG and Native Americans. The ANE drift of these two groups has more in common than with Ma’lta. Like the ancient Ethiopian genome there are many interesting conclusions one can derive from novel results, but to the first carving of nature’s joints is not always the best.

What is known and unknown

https://www.youtube.com/watch?v=1bi1iMPVIY0

51jFjmwJ3SL._SX317_BO1,204,203,200_Several weeks ago I found out that the historian Lisa Jardine had died. This saddened me, as I have appreciated Jardine’s works. In particular two works stand out in my mind. Worldly Goods, which I read when I was 18, and which helped me to understand that there was a different sort of history from the standard one written by diplomats and taught in elementary schools, and Going Dutch: How England Plundered Holland’s Glory.

The subtitle for the second work is in my opinion somewhat misrepresentative of what the tone of the book is, from what I recall. That being said, Going Dutch does impart to one a sense of the menace which was threaded through the symbiotic and antagonistic relationship between these two similar Protestant North Sea nations. And, while the 17th century is recalled as the period when England rose and Holland fell as great imperial mercantile polities, Lisa Jardine’s narrative does highlight that the so called Glorious Revolution was implemented with more of a Dutch fist than is commonly recalled.

One American’s freedom fighter is another person’s terrorist

300px-Abdullah_Öcalan
Abdullah Öcalan

The Middle East is complex. I tried to get at that with my post The Islamic State Is Right About Some Things. Of late I have noticed the peculiar tendency toward soft-tinted reportage of the PKK-affiliated YPG and the nature of life in Rojava. Typical of what you see in the American media is this piece, On the Road in Syria, Struggle All Around (here is a more gritty take, Fried Chicken and Skulls of ISIS Fighters in The Daily Beast). Scott Atran, author of one of my favorite books, was actually in northern Iraq in Kurdish areas last year during an offensive against ISIS, and he reported (on his Facebook) first-hand the gratitude that the Yezidis in refugee camps felt toward the YPG militias, who saved them at great risk to their own lives when the Iraqi peshmerga fled and left them for dead. It’s not just propaganda, the YPG does care about Kurds and minorities to further their goals. They have Asabiyyah. So does ISIS. So does Hezbollah. The Alawites with their backs against the wall supporting the Assad regime probably have it as a matter of survival at this point. Most of our “allies” on the ground in Syria and Iraq, not so much.

Today we are reading that the coordinated push to retake the road supplying Mosul that goes through Sinjar seems to be a success, at least for now. But even this glowing report can’t suppress the reality that there are tensions between the various Kurdish factions. This will likely cause issues in the future, but it is also important to look back to the past. The PKK is basically an extension of the ideas of the imprisoned Kurdish nationalist, Abdullah Öcalan. In the context of the Middle East Öcalan is a genuinely heterodox figure. He began as a Marxist-Leninist, and to this day remains an atheist. But today his movement seems to promote some sort of Left-wing anarchism. The PKK has a long history in Turkey, and has been labelled as a terrorist group, not without some reason, though one can admit these designations are to a great extent political acts.

Though the YPG units are clearly on the side of justice, it is important to remind ourselves that the point of comparison here is ISIS. Even conservative Arab villagers with no sympathy toward Kurdish nationalism and suspicious of the aggressive secularism and gender-egalitarianism of the YPG units and seem to be welcoming them as liberators. For now. There is a history of Left-wing anarchist Utopian movements, and it does not terminate in an “end of history”, where all is sugar plums and good-fairies.

The Obama administration is catching a lot of flack for its handling of the crisis in the Middle East. There are liberal internationalists offering their critiques, and of course the whole American conservative establishment is chronicling every misstep. Some Europeans are even trying to point the finger at the American lack of intervention in the Syria war as the reason for their refugee crisis. Many of these criticisms have some validity. But they always seem to presuppose that their alternative solutions would be like magic fairy dust, and render the whole morass soluble. The fact is that this may be one of those scenarios where the world is going to muddle on for years, and there is no obvious solution. Fifteen years ago the George W. Bush administration decided to take an “all-in” approach, and go big. How did that exactly work out? I for one am not happy with the American policy in the Middle East. But I’m also terrified about the negative consequences for our nation, and the world, of too aggressive a stance which overplays our hand and explodes in our faces.

As a practical matter the Kurds in Syria and Iraq are our allies. The government of Turkey will never abide by that. I support Kurdish self-determination, but the idea that the YPG will enact a regime of of non-sectarian anarchistic amity when it is ascendant is a total fantasy. There are no good choices, and there are no angels. We are united by the devil before us, ISIS. That is all that is clear to me.