Beringians vindicated!

Sometimes science turns out as you’d expect. It’s not revolutionary, but it solidifies what should already be a solid foundation basis for extending knowledge into new territories. The latest ancient genome paper, The genome of a Late Pleistocene human from a Clovis burial site in western Montana, does just that. As the media has correctly pointed out this is probably the end of the Solutrean hypothesis, and a host of other exotic explanations for the ethnogenesis of Native Americans. Rather, the truth is what we’d always assumed. On the order of ~15,000 years ago a small group of Siberians crossed over Berengia into the New World. Their descendants are the various indigenous populations of the Americas which span the expanse from the Canadian Arctic down to Patagonia.

A reader did ask if this had any relevance for the thesis proposed in Reconstructing Native American History, that there was an initial “First American” migration wave, and later a Na-Dene incursion from Siberia (the distinct nature of Eskimo-Aleut populations seems clear). Though they were not particularly explicit about it, it seems that the authors of this paper accede that these results are consistent with the earlier model, insofar as their Clovis sample seems to exhibit a greater affinity with South American populations than nearby Canadian ones. Why? One explanation could be that some admixture occurred in much of North America after the Clovis due to the arrival of the Na-Dene.

The final point of interest, as pointed out by Dienekes, is that there’s still a lacunae of data from the United States. But then that’s a matter of politics. It seems unlike that other nations will fund research on our indigenous people, not to mention laws which put a damper on examination of Native American remains. But in the end it will only put off the inevitable. And what wonders if the authors had found out that the Clovis boy did not match modern Native Americans. They’d be famous, but surely they’d receive flack from many Natives.

Update: Pontus Skoglund corrected me on Twitter, and explained that it looks like the Clovis affinity to South Americans is due not to Na-Dene admixture, but structure among First Americans. That is, by the time of the Clovis period the First Americans had either diverged enough from each other to have discernible structure, or, they had manifested substructure within Beringia or migrated out in a few pulses.

Russia homophobia has little to do with religion

russia-1With the Sochi Olympics there’s a lot of talk about Russia, its values, and its place in the world, right now. Much of the negative attention given to Sochi’s accommodations struck me as rooted in the reality that anti-Russian sentiment isn’t particularly taboo, and draws upon a deep history, and only its recent nominal expiration with the end of the Cold War. As an American I take an American perspective about our interests, and Russian interests. Often they don’t align. Though sometimes, as in the case of Syria, I believe that Russia in the long run probably served our national well being, even if it was not for us that they acted as they did. More frankly I can see where Russian paranoia about Western power and interference is rooted in genuine reason. Both NATO and the EU have seem to be encircling it. Imagine if Russia was a major player in the politics of Mexico or Canada?

But perhaps more interesting that realpolitik is that Russia and the West are now diverging culturally. Or, at least their cultural divergences are just very stark at this moment. The universalist post-materialist globalist wave which began swelling out of the West has crashed up against Russia nationalism and social conservatism. The brouhaha over homosexuality during the Sochi Olympics highlights one of the major fissures. But despite these deep differences Westerners still attempt to understand Russia on Western terms (this is actually a general problem). So, for example, the assumption that contemporary Russian aversion to homosexuality is a function of the real rise in Orthodox religious affiliation over the past generation. This is wrong. Using data from the World Values Survey we can see that Russians have become more, not less, liberal about homosexuality over the past generation. Below are the results. Observe that as Russia has become more nationalistic and Orthodox, the average Russian has exhibited less avowed hostility to homosexuality.

Homosexuality is….
1990 1995 2006
Never justifiable 88.30% 79.50% 66.40%
2 3.10% 3.70% 4.60%
3 1.60% 3.50% 4.30%
4 1.00% 1.90% 3.30%
5 2.90% 5.90% 9.90%
6 0.90% 0.80% 2.40%
7 0.40% 1.40% 1.90%
8 0.90% 1.40% 1.80%
9 0.30% 0.40% 0.80%
Always justifiable 0.50% 1.40% 4.50%

More importantly though, what’s the relationship between religion and attitudes toward homosexuality? I used the 2005-2008 WVS question, and broke it down by religious self assessment for Swedes, Americans, and Russians. Here are the results:

 

BASE=3876
Weight [with split ups]
Important in life: Religion
Total Very important Rather important Not very important Not at all important
Country United States 1156 (100%) 47.2 % 24.6 % 20.4 % 7.7 %
Justifiable: homosexuality Never justifiable 376 (100%) 71.6 % 15.5 % 9.6 % 3.4 %
2 47 (100%) 66.0 % 22.4 % 10.0 % 1.6 %
3 55 (100%) 50.8 % 28.2 % 18.1 % 2.9 %
4 40 (100%) 62.0 % 16.3 % 21.2 % 0.5 %
5 280 (100%) 35.9 % 31.9 % 27.7 % 4.5 %
6 51 (100%) 39.2 % 31.6 % 14.2 % 15.0 %
7 56 (100%) 37.0 % 30.7 % 26.5 % 5.8 %
8 41 (100%) 29.1 % 34.6 % 18.5 % 17.8 %
9 36 (100%) 31.0 % 18.4 % 42.3 % 8.3 %
Always justifiable 172 (100%) 15.9 % 29.1 % 31.6 % 23.4 %
Sweden 974 (100%) 8.8 % 20.1 % 40.9 % 30.1 %
Justifiable: homosexuality Never justifiable 40 (100%) 29.0 % 36.6 % 17.5 % 16.9 %
2 12 (100%) 7.2 % 22.5 % 52.2 % 18.2 %
3 17 (100%) 17.0 % 32.6 % 29.0 % 21.4 %
4 16 (100%) 12.2 % 14.0 % 53.6 % 20.2 %
5 86 (100%) 14.2 % 17.8 % 48.7 % 19.3 %
6 26 (100%) 7.3 % 30.9 % 40.9 % 20.9 %
7 30 (100%) 10.4 % 43.5 % 22.1 % 23.9 %
8 79 (100%) 11.2 % 16.4 % 42.7 % 29.8 %
9 76 (100%) 2.6 % 23.7 % 45.5 % 28.2 %
Always justifiable 592 (100%) 6.9 % 17.4 % 41.4 % 34.3 %
Russian Federation 1746 (100%) 13.5 % 34.9 % 32.8 % 18.7 %
Justifiable: homosexuality Never justifiable 1162 (100%) 15.6 % 35.1 % 31.6 % 17.7 %
2 78 (100%) 6.4 % 32.5 % 39.1 % 22.0 %
3 72 (100%) 10.5 % 33.2 % 35.0 % 21.3 %
4 58 (100%) 8.0 % 39.3 % 34.0 % 18.7 %
5 178 (100%) 6.2 % 34.5 % 40.7 % 18.7 %
6 43 (100%) 16.1 % 30.4 % 14.9 % 38.5 %
7 33 (100%) 13.3 % 22.2 % 42.9 % 21.6 %
8 33 (100%) 3.0 % 53.6 % 27.8 % 15.6 %
9 14 (100%) 23.2 % 45.1 % 9.2 % 22.6 %
Always justifiable 76 (100%) 14.8 % 31.4 % 36.4 % 17.3 %
Total 3876 (100%) 22.4 % 28.1 % 31.2 % 18.3 %

As you can see there’s not a strong association between religiosity and disapproval of homosexuality in Russia. It is indeed different.

Writing wrong well

This opinion by Norman Finkelstein on writing really spoke to me:

Yeah there’s definitely a place for style and creativity, for good writers it’s definitely an advantage to have. The problem is when – maybe this is going to sound patronizing – but when English majors decide they want to do politics and they have no background in the field of inquiry and that’s quite common. There’s a left-wing tradition of that and they have deep roots but the most obvious prototype was Trotsky who was a revolutionist part of the day and as he famously had done, as he’s under sealed train going to the front waging the civil war in Russia, he’s writing literary criticism. And Trotsky was both a brilliant political analyst and brilliant literary critic. He happened to combine both.

But most people don’t and what you have now is versions of George Packer, Paul Berman. There’s just a large number of people who know nothing about politics, don’t even think it’s important to do the research side. They simply substitute the clever turn of phrase. The main exemplar of that in recent times was Christopher Hitchens, who really hadn’t a clue what he was talking about. But what he would do is come up with three arcane facts, and with these three arcane facts he would weave a long essay. So people say, oh look at that. They would react in wonder at one or the other pieces of arcana and then take him for a person who is knowledgable.

 

People unfortunately don’t care very much about content. They care about cleverness. That’s the basis on which The New York Review of Books recruits its authors, you have to be as they say, a good writer. And the same thing with The New Yorker. Now obviously there’s a great virtue to being a good writer, but not when it’s a substitute for content.

He’s alluding to a general, not specific, problem. It isn’t just brilliant prose stylists who can pull a fast one. Engagement, and the ability to weave a good story, is one of the reasons why someone like Malcolm Gladwell is such a great success. But there’s a flip side: truth need not come in an obscure and awkward package. Great scientists such as Charles Darwin were also great communicators. The unfortunate reality though is that for far too many of the chattering class science as filtered through The New Yorker is science. The same with history, politics, and foreign affairs.

The boring truth about Charles Martel and Tours

51YH1EodlTL._SY300_If you are the type of person to express opinions about major historical turning points, and you haven’t (and probably won’t) read original scholarship such as The Age of Charles Martel, I highly recommend the recent In Our Time episode, The Battle of Tours. The reason that this episode is worth highlighting in a separate blog post (rather than tweeting) is that over the years I’ve run into too many people who seem keen to offer an opinion about this event due to vague recollections of an assessment by Edward Gibbon. In short, Gibbon’s conjecture was if that the Muslims coming up from Spain in the early 8th century had defeated Charles Martel and the Franks on the plains of central France, then the Islamic tide would have swept over all of Europe (perhaps as the Battle of Yarmouk initiated the fall of the Roman Near East, or Qadisiyyah heralded Persia’s doom). But most scholars have not accepted such an importance for Tours in many years, so its persistence in the popular imagination can be frustrating. The reality is that the Muslim presence on the fringes of southern and eastern France, not to mention southern Italy, persisted for decades. It seems likely that the expansion of the Arab Empire had hit its natural limits, just as it had in western India, central Asia, and the trans-Caucasian region. It was left to Martel’s grandson Charlemagne to expunge the Islamic threat to what became France and Italy.

Why does this matter after all these years? Because moderns take lessons from history, and attempt to learn from it. The Battle of Tours has been placed into diverse and disparate early modern and contemporary narratives, rather than standing within its own historical context. In the age of Christendom it was a titanic confrontation between Islam and the True Religion. In the 19th century it became a battle in a long racial-civilization war. Today some reinterpret it in light of the War on Terror (though the 9/11 fever seems to have broken). The problem here, reappropriating history for the ends of the propaganda of the present, is a common one, not limited to one ideology. For example, in the early 2000s a book was published with the title The Ornament of the World: How Muslims, Jews, and Christians Created a Culture of Tolerance in Medieval Spain. The title speaks volumes in terms of intent. In the minds of many liberals Islamic Spain has been recast in a soft-tinted multiculturalist lens. It’s as ludicrous as viewing Charles Martel’s actions at Tours as a blow against Islamo-Fascism. The tolerance of Islamic Spain or the Dutch Republic would have horrified moderns. People in the past were different, and had their own agendas. But through discovering the truth of who and what they were (rather than what we find them convenient to be), perhaps we can gain some skill at seeing our own position in history with greater objectivity.

From admixture to adaptation

ncomms4281-f1
Citation: Nature Communications 5, Article number: 3281 doi:10.1038/ncomms4281
Sherpas, credit
Sherpas, credit

A few years ago there was a paper out on high altitude adaptation in Tibetans which posited a somewhat ludicrous historical demographic scenario: that the population of the Tibetan plateau diverged within the last ~3,000 years from the Han Chinese. Due to the recency of this event the authors argued that high altitude adaptations at these loci were the fastest sweeps on record so far. The problem is that this demographic model didn’t pass the smell test. China is not a region of the world where there is no documentation for that period (Chinese history starts ~1000 BC). To posit a Han migration into the Tibetan plateau, as the media at least was portraying it (though I think this was an easy step from the way the results were presented in terms of the semantics), is difficult to imagine because the ethnogenesis of the Han themselves had not truly occurred in a way that we would recognize today at that period. Today Jeong et al. in Nature Communications, Admixture facilitates genetic adaptations to high altitude in Tibet, may have gone some way to resolving some of the confusions that came out of that paper. The basic conclusion is that the high altitude adaptations have swept up in frequency among Tibetans after the admixture of a Sherpa-like population and a Han-like population on the order of 3,000 years ago.

It seems a plausible model (especially after you take in their qualifications which imply perhaps a somewhat older date for admixture), and might explain why you obtain a test statistic implying a recent divergence between the Tibetans and Han. I suspect that there isn’t a pure Sherpa-like population at this point, and the unsupervised admixture estimates are giving low fractions for Han-like admixture (the “high altitude” fraction showing up in populations as disparate as Gujaratis and Japanese is a tell that it’s an imperfect proxy). If you were a plant geneticist this sort of phenomenon wouldn’t be surprising at all, as one way that you can breed for better cultivars is mix together lineages and allow good phenotypes to introgress across genetic backgrounds. Also, the authors did not find any elevation of archaic admixture in the Sherpa-like element, though I wonder if they might miss a population “X” because they don’t have a reference genome (they looked for Neandertal and Denisovan). Intriguingly the divergence between the Sherpa-like element and the Han-like component is ancient, on the order of ~20-40,000 years ago. Though likely part of the broader family of East Eurasian populations, it seems that this Sherpa-like cluster was well diverged. Not very surprising due to the terrain, but perhaps it illustrates the power of agriculture to demographically and culturally transform societies, and reduce genetic distances over the last 10,000 years. The only reason that the Sherpa-like fraction persists in reasonable fractions is probably the difficulty of farmers and agro-pastoralists invading the terrain.

Citation: Nature Communications 5, Article number: 3281 doi:10.1038/ncomms4281

Note: Sherpa, and Tibetans, speak a language posited to have a distant relationship to Chinese. Ergo, the Sino-Tibetan language family. This implies that the original language of the highlanders was lost, though perhaps a substrate can be excavated.

Open Thread, 2/9/2014

Looking forward to reading Greg Clark’s new book, assuming I can spare the time….

I mentioned on Twitter an idea I had in regards to intellectual property. One of the reasons that intellectual property exists is to foster creativity. But with the proliferation of derivative music through the power of capitalism’s economies of scale, is there really any benefit? (see One Direction today and Backstreet then) Perhaps we should just live off the huge library of music which has been produced and saved across the many decades since storage formats came into existence? Someone pointed out that there really isn’t a need to produce any more porn; everything has probably done, and it is just a matter of familiarity.

The inevitability of sex chromosome degeneration

tonguefish_brenda-bridgettI’m as cynical as anyone about Yet-Another-Genome Syndrome (though it seems to have leveled off in the past few years as sequencing as become accessible enough that people really want to focus on biology earlier on). But a new paper in Nature Genetics, Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle, shows the value of the approach when you’re actually looking at an interesting topic. Though most people might not be fascinated by the flatfish, many are curious about the nature of sex determination. You are likely familiar with the standard XY system of placental mammals, but non-placentals, birds, insects, etc. have different frameworks (and though Drosophila is also XY, it’s not quite the same as the mammalian system).

Though  I suspect our big-picture understanding of the origin and diversification of sex chromosomes is going to be enabled far more by the work on Drosophila, the authors make some good arguments for why this organism might give us insights. With a small genome, presumably it was technically easier to assemble. Additionally, teleost fish have young sex chromosomes, so whatever general forces reshape this region of the genome is going to be incipient. Like birds, the flatfish have a ZW sex-determination system. This means that females, not males, are the heterogametic sex. So in flatfish, like birds, females would express sex-linked diseases. Or at least that’s the expectation.

It turns out that the 30 million year old W chromosome hasn’t lost nearly as many of the functional gene copies as the bird W (or the mammal Y). There has been some gene loss, but it isn’t nearly as degenerated as the chromosomes of lineages where the system of sex-determination has an older origin. The authors claim that the mammalian system for example is hundreds of millions of years old. This puts into stark relief how ludicrous it was when Bryan Sykes began to assert that the mammalian Y chromosome was on its last legs, and that mammals were well nigh on the verge of going extinct (due to the disappearance of males). These results show that sex chromosomes can persist in a gene-poor state for a very long while. Though gene loss isn’t nearly as total on the bird W or mammalian Y, it has been significant even in these flatfish, indicating that much of the degeneration occurred early on in many lineages.

The reason that understanding of the evolution of sex-determination is important is that the phenomenon illustrates the constraints imposed by the nature of our genomic architecture. The rise and fall and rise of sex chromosomes can perhaps tell us about the borders of the canvas upon with evolution must work. Evolutionary genetic change is not just about possibilities, but also the rules of the game.

Citation: Nature Genetics (2014) doi:10.1038/ng.2890

My Big Five personality profile

The Big Five personality traits are apparently much more scientifically accepted than the Myers-Briggs categories (to be more precise, the latter have no scientific support, while the former have some). So I just took a Big Five test which matches you up with a particular president. I have no idea how it does this, but I guessed ahead of time correctly which president would be my match. I think long time readers of this blog will not be surprised by the fact that it suggests I have high extroversion and low agreeableness.

teddypersonality

The fading of the most basal of basal

ncomms4163-f1
Citation: Nature Communications 5, Article number: 3163 doi:10.1038/ncomms4163
Mbuti
Mbuti

Etienne Patin has another paper out on the genomics of Central Africa, and the relationship of the Pygmies to their agriculturalist neighbors, The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists. It is to a great extent expanding upon earlier work with denser marker sets, larger sample sizes, and of course ~2014 statistical genomic techniques (e.g., ALDER). As background you have to remember what Patin established before: the western and eastern Pygmy populations of the Congo rainforest seem to have diverged tens of thousands of years ago, tens of thousands of years after their divergence from the ancestors of their agriculturalist neighbors. By and large these neighbors speak Bantu languages, which have swept out of the eastern fringe of what is today Nigeria only within the last 3,000 years. The numbers alluded to the paper are separations on the order of ~20,000 years before the present for the Pygmy groups (west vs east), and then ~50,000 years for the ancestors of the agriculturalists vs. the proto-Pygmies. Think about this: diversification within Africa occurred at about the same time that the most distant of the non-African groups were starting to become isolated from each other. The Pygmies are not just interesting from an ethnological perspective, along with the Khoisan they preserve to a high degree an ancient and diverged group of populations which have largely been marginalized due to the demographic expansions of peoples speaking Niger-Congo and Nilo-Saharan languages (the Pygmy speak the languages of their agricultural neighbors, but this seems a recent development).

An interesting twist revealed in this paper is that admixtures seem to be relatively recent (on the order of 1,000 years), and, those levels are quite high indeed in many Pygmy populations. This is not the case with agriculturalists. In other words, the genes of agriculturalists seeped into the Pygmies, but far less moved in the reverse direction. As analogy, consider that the average Native American is far more European than the average European American is Native. But, as with the case of the Pygmies and their neighbors it may be that there is more Pygmy ancestry in the aggregate in their numerous neighbors, than among the relatively rare Pygmies!

Finally, I think we need to now broach the topic of genomic value for posterity. It is well known that in the Congo region today Pygmies have been the target of conscious genocide, as well as suffering from the consequences of the great wars of the past few decades (I recommend Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa to anyone with a modicum of interest in this topic). But the results in this paper indicate that the Pygmies are under clear threat of being demographically absorbed by their neighbors before the passing of this century. In particular this paper reinforces what has been clear in other results: the Mbuti of the eastern regions of Congo in particular harbor unadmixed genetic variation. While the Khoisan of southern Africa reside in a quiescent zone of the continent, the Mbuti are not so fortunate. I hope that we get at least hundreds of whole-genome sequences from this population within the next decade, for the sake of all of humanity. Ancient DNA seems unlikely from most of Africa, so massive surveys of the contemporary genomic landscape of this continent is going to be essential to understanding our species’ collective past.

We have the technology to avoid suffering

CRISPR associated protein
CRISPR associated protein

When I first started writing on the internet in the early aughts times were different. Preimplantation genetic diagnosis (PGD) was more science fiction than  a topic which touched the realm of reality. Yes, there was screening for a handful of classic recessive diseases, and somewhere Leon Kass was reflecting upon human dignity being undermined by the very idea of PGD with all the clarity of Martin Heidegger ruminating upon Being. But really this was a speculative period, when we were test driving arguments, positions, and talking points. I believe most of us understood that we were rehearsing for the true battles which would erupt at the center of modern civilization with the rise of biological engineering.

The era of test-driving arguments is over when you see articles by Gina Kolata about real people in The New York Times. Ethics Questions Arise as Genetic Testing of Embryos Increases:

On the spot, Ms. Baxley, 26, declared she would not let the disease take another life in her family line, even if that meant forgoing childbirth. “I want it stopped,” she said. The next day, her boyfriend, Bradley Kalinsky, asked her to marry him.

But the Kalinskys’ wedded life has taken a completely unexpected turn, one briefly described on Monday in The Journal of the American Medical Association Neurology. Like a growing number of couples who know a disease runs in the family, they chose in vitro fertilization, and had cells from the embryos, created in a petri dish with her eggs and his sperm, tested first for the disease-causing gene. Only embryos without the gene were implanted. The Kalinskys are now parents of three children who will be free of the fear of GSS.

The subject of the story is still likely to die at some point during or before her 50s. And, that process of death may span as much as two decades. So the disease, and the couple’s choice to have children, is not without consequences which are less than optimal. But the bottom-line for me is that the decision made here was fundamentally a noncontroversial pro-life act. In the face of the darkness of a potential terminal diagnosis this woman and her husband have brought forth life, and as a new father I truly know in my bones the joy of that as I never would have before. But this isn’t a human interest piece, much of the article is given over to the vague and to be expected platitudes from ethicists. There is “trouble.” The implications are “unsettling.” To me these sorts of talking points have all the power of “think of the children” as an argument against interracial marriage. You can see where they’re coming from, and it’s nowhere substantive.

I assume that professional ethicists not constantly being interviewed by high profile journalists have opinions which aren’t easily condensed into one sentence triteness. Or perhaps more fairly that’s just what gets distilled from a long interview. But I’m rather sick and tired of ethicists being “troubled,” and also fed up with reductio ad absurdum arguments. At one point Kolata paraphrases one of her sources as saying: “Eliminating embryos with such genes is essentially saying someone like Ms. Kalinsky should never have been born.” What does that even mean?

To truly get to the heart of these questions we have to ask deep philosophical questions about the nature of one’s own existence, being, and identity. Obviously that’s not appropriate fare for The New York Times, which seems to be cautious about treading beyond its core milquetoast mildly liberal reading audience. The sorts who are self-satisfied in their unexamined enlightenment received from on-middlebrow. But PGD and the assorted technologies of the mass applied biology of the first few decades of this century will force us as a society to elucidate once more what we truly believe the good life is. What is the life worth living? Is it truly just the lives which parents deign worth living? Society? Gods on high? These are the real questions which strike at the heart of the matter, and the sooner we get to them, the sooner we’ll achieve our unsatisfying resolutions.