Open Thread, July 19, 2015

51gYdVvOoQL._SX379_BO1,204,203,200_Occasionally I get emails from students about how they should go about becoming a biologist who studies evolution. As if I would know. But sometimes the blind seek guidance from the blind! The number one thing I tell them though is that you need mathematical and computational skills today. This is true to some extent even if you are going to be mostly a bench biologist. You don’t want to be the person who’s always relying on someone else for basic analysis. With that, let me note that my friend Vince Buffalo’s book, Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools, is finally out, and I’d recommend it to anyone who wishes to bone up in this area. I’ve read a draft, and it’s definitely useful for any undergraduate or aspiring graduate student in getting you ahead of the curve if you haven’t already done work in this area. It will probably save you some time on Stackoverflow once you get there.

hd5C-sZ3_400x400Speaking of friends, it looks like N of Everyone Kick Starter is going to hit its minimum threshold, and will get funded in their campaign. They’ve also now put a demo up of the Reader on their website. Check it out. You can get a flavor of the direction the firm wants to push scientific publishing. This space will get shaken up at some point, so it’s always useful to keep an eye on it.

9780199589883I’m still slowly making my way through A New History of Western Philosophy. I do most of my reading on the Kindle. When I bought the book, and frankly when I started reading it, I did not understand that it was over 1,000 pages. Additionally, the author does not scrimp on detail. He engages in laborious exposition on items such as how Aristotle’s philosophical thoughts on motion were affected by the constraints of expression in the Greek language of particular concepts.

So why do I read this stuff? I’m a scientist (sort of). I come from a scientific background. From the first I assumed that I would pursue science in some way as an adult. Later on I branched out and explored history and geography. In all of these subjects older works are generally superseded or integrated. You don’t need to read Gibbon’s Decline and Fall to know the general outline of Roman history. Michael Grant’s more recent The History of Rome will do. Similarly, you don’t need to read The Origin of Species to understand evolution (though to be fair, I think in hindsight that it is valuable, after reading it a second time as an adult with a better understanding of evolutionary biology). Just get the Doug Futuyma text, Evolutionary Biology, if you want to be technical. Or, What Evolution Is from Ernst Mayr if your taste is more toward something palatable for the generalist audience. That will spare you Charles’ Darwin’s groping attempts at concocting a theory of inheritance.

Philosophy is different. When I encountered philosophy, and I was 20 by the time I seriously engaged the topic, I was shocked by the fact that there was a whole field where the ideas of men who lived over two thousand years ago were still relevant. Let me quote Machiavelli:

“At the threshold, I take off my work-day clothes, filled with dust and mud, and don royal and curial garments. Worthily dressed, I enter into the ancient courts of the men of antiquity, where, warmly received, I feed on that which is my only food and which was meant for me. I am not ashamed to speak with them and ask them the reasons of their actions, and they, because of their humanity, answer me. Four hours can pass, and I feel no weariness; my troubles forgotten, I neither fear poverty nor dread death. I give myself over entirely to them. And since Dante says that there can be no science without retaining what has been understood, I have noted down the chief things in their conversation.”

51K-gkZ7rAL._SX327_BO1,204,203,200_Many, such as Steven Pinker in The Blank Slate, have wondered about our reliance on dead philosophers as authorities on the human condition. In  The Blank Slate Jean-Jacques Rousseau is something of a villain. In agreement with Pinker I believe that most of Rousseau’s conjectures about human nature* have been roundly refuted. Additionally, attempts to construct social arrangements based on Rousseau’s understanding of human nature have failed, sometimes horribly so. More broadly, Pinker has offered that one reason that why the ancients are relevant in philosophy is that the discipline is characterized by the problems which are intractable. They are those domains which remain to philosophy as a discipline after science has carved out huge swaths of its traditional territory. I don’t deny the truth of much of what Pinker says, but when you read Aristotle and Xunzi’s political philosophy, it is hard to deny that their insights are far more relevant and useful than those of Plato or Jean-Jacques Rousseau. And, like good music and art sometimes distance allows us to perceive better the wheat from the chaff. The philosophers who remain relevant and prominent from antiquity were often those of particular genius and creativity. And that is only evident with the passage of historical time.

Obviously I wasn’t anticipating how many comments my post on country rap would generate. I do want to enter into the record that if you use an ethnic slur like “cracker” I’m not going to post the comment. You can just send me an email. I don’t think these slurs are elevating for the conversation.

Finally, on that post, some people seem to think I was casting aspersions on lower class people. That was not my intention at all. Additionally, though I don’t interact with that sort of person much today, I did grow up with a lot of lower and lower middle class rural whites. I even spent time working on a mule farm owned by a friend’s mother. As they say, class isn’t about money. And the poor and working classes have their own folkways in any case. My point is that just because there are particular folkways that are common among a certain class, they don’t have to “own” those tendencies, and can try and transcend them. But we as a culture don’t really engage in this sort of aspiration toward a higher and ennobling state. This actually has its flip case in the flaunted debauchery of the likes of Paris Hilton, who rub in Middle America’s face their exemption from bourgeois norms due to their class status.

* The representation of his conjectures about human nature, for those who note that there is some revisionist work which argues he’s been misrepresented.

Between the millennia and generations


Iron Age and Anglo-Saxon genomes from East England reveal British migration history
Stephan Schiffels, Wolfgang Haak, Pirita Paajanen, Bastien Llamas, Elizabeth Popescu, Louise Lou, Rachel Clarke, Alice Lyons, Richard Mortimer, Duncan Sayer, Chris Tyler-Smith, Alan Cooper, Richard Durbin

108_322When I first realized of the possible utility of genetics toward anthropology and history I came up against a major problem in addressing extremely fine-grained questions: the tools did not have the power to probe very small genetic distances, constrained in time and space. After reading Norman Davies massive The Isles I was to understand that the Anglo-Saxon transformation of Britain into England was a matter of elite cultural emulation. What did genetics have to say about this? The answer was “not much.” In an earlier era of a few dozen classical autosomal markers or just mtDNA and Y chromosomal fast evolving microsatellites genetics was not powerful enough to distinguish between extremely close European populations. In The History and Geography of Human Genes L. L. Cavalli-Sforza notes that Europe is the most homogeneous of his continental groups where he had many samples. If you remove outliers like the Finns and Sicilians, this is very true today when we have whole genomes. Though conventional whole-genome SNP panels can distinguish Northern European population clusters they are packed very tightly together.

Using the Human Origins Array data set the authors of Iron Age and Anglo-Saxon genomes from East England reveal British migration history projected the genotypes of ancient samples from the Iron Age and the Anglo-Saxon period upon modern groups. As you can see the Northwest European data sets are packed so close it’s hard to discern structure. In the era of pre-genomic phylogeography it was nearly impossible. To answer whether the Anglo-Saxon migration was a mass folk wandering or a tiny mercenary elite one would have to distinguish Germano-Scandinavian heritage from that of the native British, and the reality is that these are all very close groups. We now know that the ethnogenesis, at least in a genetic sense, of Northern Europeans as a whole seems to date to the Bronze Age, on the order of 4,000 years ago. Therefore, to pick up genetic structure you are by and large focusing on only two to three thousand years of drift between these groups! This explains why the older methods were so under-powered. There just wasn’t much raw material for them to work with; not enough time had passed for the populations to diverge.

nedPLOTA few months ago the PoBI project finally published, and revealed local structure across the British Isles. The authors concluded that in England proper a minor, but substantial, proportion of the ancestry derived from the Anglo-Saxons. That is, Germans. The authors used SNP data sets. That is, less than a million markers in the genome (and out of the twenty to thirty million SNPs in the human genome). But, they had a massive sample coverage from which to extract insights from.

51IQSePVDRL._SY344_BO1204203200_This preprint takes a different tack. They take whole genome sequences from ancient subfossils. What they lack in sample size, they make up for in marker set (some of the coverage is high enough that they probably got decent calls), as well as the fact that they are sampling individuals who are from the source cultures in question. Celts, Anglo-Saxons during the invasion period, and also during a some what later epoch. Their results in nearly perfectly in line with those of PoBI. Using their samples as representative they estimate that ~30 percent of the eastern English ancestry is German. A lower proportion is found in Wales and Scotland.

The figure above illustrates this finding. A key point about this paper is to emphasize that since they are using whole genome sequences they can focus on rare alleles. Because the alleles are at low frequency they’re likely to be younger, and if they are younger they are also more likely to yield the power to discern differences between very genetically close groups, such as the Germans and the British. In the plot above you see that the Anglo-Saxon samples are shifted right, while the Iron Age samples are shifted to the left. What this shows is that the Iron Age samples tend to share more rare alleles with the Spanish IBS data set from the thousand genomes, while the Anglo-Saxons share more alleles with the Dutch.  Eastern England and Wales and Scotland occupy positions that you’d expect.

Furthermore, the authors utilized the program rarecoal to explicitly model the population history of Britain using their data. This will be a major feature of future work in this area, as researchers drill-down to a very fine grain and ask precise questions which good quality whole genomes and robust phylogenetic packages can actually tackle.

There is still much that needs to be worked out on this topic. There’s only so much you can say from these handful of individuals. But even with these finite samples much was extracted. The authors observe that one of their Anglo-Saxon era individuals, buried in an Anglo-Saxon fashion, clustered perfectly with the British Iron Age individuals. Additionally, this individual was outfitted in a manner which suggested they were very high status within Anglo-Saxon society. But the authors did not connect this with the fact that all their Anglo-Saxon individuals were female. Hypergamy is entirely typical in human societies, and it is plausible that large numbers of migrating German men arrived on British shores without a wife and family in tow. In the years after the Norman invasion it was not uncommon for noble Saxon houses to give their daughters to an invader. And so the Anglo-Norman aristocracy arose as a synthesis between distinct paternal and maternal lineages. A similar scenario likely played out during the invasions of the Dark Ages.

The cognitive roots of genophobia

Over at Slate Will Saletan has a very long piece Unhealthy Fixation: The war against genetically modified organisms is full of fearmongering, errors, and fraud. Labeling them will not make you safer. The survey is useful if you are unfamiliar with the topic, though it will be sadly familiar to the rest of us. Saletan makes two observations which I think need highlighting. First, he asserts that “the deeper you dig, the more fraud you find in the case against GMOs. It’s full of errors, fallacies, misconceptions, misrepresentations, and lies.” Basically it’s a shell game, and the reason is that those who oppose GMO obfuscate the fundamental roots of their objections (consciously or subconsciously). Saletan notes:

Third, there are valid concerns about some aspects of GE agriculture, such as herbicides, monocultures, and patents. But none of these concerns is fundamentally about genetic engineering. Genetic engineering isn’t a thing. It’s a process that can be used in different ways to create different things. To think clearly about GMOs, you have to distinguish among the applications and focus on the substance of each case. If you’re concerned about pesticides and transparency, you need to know about the toxins to which your food has been exposed. A GMO label won’t tell you that. And it can lull you into buying a non-GMO product even when the GE alternative is safer.

The concrete and coherent objection to GMO which lies just under the surface of the arguments put forward by activist groups like Greenpeace is that the technology is part of the agricultural-industrial complex. But as many have observed, if the problem with GMO is their connection to big agriculture, then why aren’t the arguments simply recycled from those used against industrial agriculture? There are two dynamics at work. First, there is broad popular suspicion of “genetically modified organisms.” Using GMO as a hook, and engaging in FUD, is more effective than arguing against corporate agriculture. Second, as Saletan implies in the piece, even anti-corporate considerations aside there are genuine concerns rooted in the idea that there is something “wrong” with genetically modifying organisms (in fact, with the emergence of cheap CRISPR, we’re potentially at the precipice of a revolution of small scale agricultural innovation, though right now it is unlikely to happen because of regulation).

This sentiment is very broad, and, it is not ideological. Or at least it wasn’t as of 2006, when the EATGM question on for the GSS was put to over 900 respondents. It asks:

Which statement best describes your own view about eating foods that have been genetically modified? 1. I don’t care whether the food I eat has been genetically modified. 2. I am willing to eat genetically modified foods, but would prefer unmodified foods if they are available. 3. I will not eat food that I know has been genetically modified.

The results:

Screenshot from 2015-07-18 16:02:54

As you can see, there’s no ideological difference. The slightly greater skepticism of Democrats can probably be attributed to socioeconomic variables. The less educated, the poorer, and women, are all more skeptical of GMO on the whole. These are groups more well represented among Democrats, and some of these are the most liable to vote and identify Democrat despite not being particularlly socially liberal (e.g., poorer minorities).

gmo1But that’s nearly 10 years ago. I’m not sure that the lack of ideological polarization will be so evident now. As documented by Saletan, and earlier in Slate by my friend Keith Kloor, the really high octane activists and public intellectuals behind the anti-GMO push are on the cultural Left. Last year Oregon had a GMO food labeling ballot measure. It lost narrowly. But as you can see in the scatter plot to the left there is a very tight correlation between a county being Democratic and favoring labeling. Second, there was an earlier attempt to pass such a ballot measure in 2002. It was destroyed at the polls. If trends continue it seems entirely likely that labeling will succeed in Oregon in the next go around. Americans intuitively are biased toward transparency as a good.

Screenshot from 2015-07-18 16:22:39The fact is that the majority of the public remains skeptical of GMO foods. And large majorities support labeling. Which prompts one to ask: why did the labeling measures not pass in Oregon and California? I think the critical aspect here is that attitudes of skepticism toward GMO are wide but shallow beliefs. Only a small minority of the population has very strong views on the topic. Those opposed who have very strong opinions and engage in activism on the topic tend to come from the liberal intelligentsia. Anyone who has been involved in science and policy around this topic (I have friends who work on GMO crops) will vouch for this. Similarly, those enthusiastic about the potential of GMO tend to be a small number of plant scientists (who also, are be politically liberal on the whole, as they are mostly academics). It is true that large agricultural firms are notionally pro-GMO, but here’s the reality: big ag is making money, it doesn’t need GMO. In fact, because of public sentiment and preference big ag naturally sees organic labeling as a profit center! The regulations are such that really only large firms have the resources to overcome the hurdles put in front of research in this area in terms of safety and oversight.

DescartesBabyOnce the issue of GMO become salient, as in the ballot measures here on the West coast, then people become more cautious. Anti-labeling arguments start to be more persuasive, and those with business interests that might intersect with agriculture might come to different opinions, as the precautionary principle starts cutting in other directions. GMO has not become culturally polarizing. Yet. Most peoples’ opinions are inchoate and instinctive. I believe they derive from folk biological intuitions about essences. Ultimately it’s about the fact that people don’t understand genes in any prosaic sense, but they think that they’re somehow magically involved in the nexus of who we are in a deep and fundamental sense. That’s why the translocation of fish genes into tomato is so uncomfortable for people; they imagine that the essence of the fish is somehow being mixed with the essence of the tomato, and that just feels wrong. Genophobia of this sort is comprehensible in a cognitive anthropological framework. Just as we are likely wired for Creationism, I think we’re wired for being very skeptical of the concept of GMO, because of the implicit connotations of muddling categories which we view was fundamental. And, just like Creationism, we can overcome these deep intuitions. Much of natural science in the modern world consists of overcoming and updating of deep intuitions.

410tL5IwqTL._SX329_BO1,204,203,200_But, the deep intuitions can be harnessed toward political movements. In the United States Creationism is not just a sentiment and intuition, but a formalized social-political project which fuses some elite suspicions of scientific naturalism with populist skepticism of common descent. Modern Creationism has a particular intellectual pedigree, but it works with the raw material of gut human feeling. Creationist sentiment is old, as old as our species. But Creationism as a potent political movement is new, and its affiliation with the edges of American conservatism is actually a feature of the past generation. It has a history of how it got from where it was, to how it got to where it is. In American Grace Robert Putnam and David Campbell report data that political and religious affiliation co-vary and influence each other (with the former often effecting the latter!).

I am mildly optimistic that this will not happen with GMO, and that is because scientists are anti-anti-GMO, and, politically liberal. It seems very likely that a GMO food labeling measure will pass in the near future. And I believe that this will galvanize a backlash among scientists on the whole. Something similar happens on the Right with Creationism. Whenever the movement actually scores a victory, elite Republicans, who invariably accept the science of evolutionary biology, become alarmed and roll back gains made by Creationists. Unlike evolution, GMO are not just abstractions in a laboratory. When GMO becomes pervasive enough, or at least the knowledge of how pervasive they are becomes more common, then the public will likely make peace with their reservations, just as they have with in vitro fertilization.

The domination of demotic chic

51MzSp6UPlL._SY344_BO1,204,203,200_Probably because I’m reading the perspectives of ancient philosophers such as Plato who had very specific and clear views of human excellence, I’m struck now by the rise of brashly demotic artistic forms, and how they push their way into our public space. Consider the rise of country rap, which is one of the more bizarre cultural syntheses to arise out of the dialectic discourse which permeates American society. Country music has traditionally been dominated by rural white Americans, and reflects a conservative ethos which is notionally aligned with traditional values. Rap, in contrast, emerges out of a hip-hop urban milieu which is oppositional to broader American society, distrusting authority rather than celebrating it.

When the Moonshine Bandits “We’re all country” came on my Spotify I was curious about Sarah Ross rapping about how she’s from Jersey, but still country. And, there are explicit shout-outs to blue collar life. They seemed to be owning a denigrated lifestyle and class background. So I looked up the video. The aesthetic was shocking to me. To be entirely frank, it seems to celebrate a gritty slovenliness as the best of all things. Eternal Budweiser, mac & cheese, and poor muscle tone. Many hip-hop and bro country music videos are gauche in their crass superficiality, but at least ultimately there’s often a nod to an aspiration toward excellence, in wealth, in accruing attractive females, in being in shape. You don’t see any of this in the above video. It’s a valorization of the demotic, the pedestrian. Average looking people coalescing together to get inebriated. No symposium, that.

The genetic structure of East Asians

There was a question about East Asian genetic structure. There have been a fair number of papers published on the issue. But over the years I’ve assembled a pretty large personal data set from public sources, as well as stuff people have sent me. I decided to look at the East Asian individuals and how they relate to each.

First, I focused on the major ethno-national groups (or ones of particular interest and relevance, such as Mongols). Second, I LD pruned the data set down to 96,000. Third, I did some outlier removal. For example, I wanted to include some Kalmyk data, but it turns out all the Kalmyk have European admixture at some level. And a subset of individuals from Cambodia and Vietnam are ethnic Chinese. Those were removed.

I ran ADMIXTURE K = 5 unsupervised. Treemix k = 500 and global rearrangements on, and rooted with Cambodians.

Eigenvalues 7.59041, 4.04862, 3.00559, 2.60692 and 2.01554.

Read More

How East Bengalis got East Asian

51KHpfTVbiL._SY344_BO1,204,203,200_Let’s start at the beginning. If you read a book about Indian history in the 1980s it might begin with this sort of stylized narrative: in the beginning were the Mundas. Then there were the Dravidians, then finally the Aryans (and as an afterthought various East Asian groups on the fringes of northern and eastern Aryavarta). The thesis, broadly, was that the Munda people, who speak an Austro-Asiatic language, were the closest that the Indian subcontinent had to genuine aboriginals. The oldest of old. Supporting this contention is the fact that the languages of the Munda people, with distant affinities to Cambodian and Vietnamese, are very alien in comparison to Dravidian and Indo-Aryan (if Dravidian has any connections outside of the subcontinent, they are always posited to the west, in ancient Iran. The Munda languages clearly have eastern connections). The supposition then was that from the Munda arose various peoples of eastern  Eurasia. To cut to the chase this model is probably wrong. The genetic structure of South Asia seems to have arrived at its current outlines relatively recently. In regards to the Munda people their origin is in Southeast Asia. They are not the progenitors of Southeast Asians, they are in part derived from Southeast Asians. Part of the broader expansion of “first farmers” in Southeast Asia from southern China. Their Y chromosomal lineages and autosomal heritage both imply this. Additionally, they carry the Northeast Asian derived variant of EDAR. Though much of their culture is almost certainly exogenous, and of relatively recent vintage, they are clearly highly admixed with the South Asian substrate. In particular, the fusing of an ancient West Eurasian population (“Ancestral North Indians”, or ANI) and a deeply rooted indigenous group with distant affinities further east (“Ancestral South Indians”, or ASI).

Chaubey, Gyaneshwer, et al. "Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture." Molecular biology and evolution 28.2 (2011): 1013-1024.
Chaubey, Gyaneshwer, et al. “Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture.” Molecular biology and evolution 28.2 (2011): 1013-1024.

One of the reasons that the ancient character of Munda residence in South Asia was persuasive is that they are resident in upland zones, which perhaps refuges after being marginalized by later arrivals. Their fragmented distribution is a tell that they occupied wider territories than is the case today. One thesis is that the Gangetic plain was inhabited by Munda people before the Indo-Aryans arrived. Rather than Dravidians, the indigenes in the Vedas may have been Mundas. But I’m interested in a more parochial question: can Munda ancestry explain the high fraction of East Asian ancestry in Bengalis, particular eastern Bengalis?

We can address this question a bit with genetics thanks to the resources we have in terms of population coverage. As readers know I’ve started to work with the 1000 Genomes data set. Luckily it has a large number of Bengalis within it. Meanwhile, the Estonian Biocentre has put its genotype data online, and there are Munda samples in there. I merged the data together, and removed pretty much all missing alleles. At the end of it I had 185,000 SNPs. To explore the questions I had in mind I decided to look at several populations. Bengalis and Telegu speakers (their genetic position would put them as “middle castes”; not Brahmins, but not Dalits or tribals). Georgians (from the Caucasus) as an outgroup. For Southeast Asian groups, Burmese, Cambodians, Filipinos and Dai. Finally, a small number of Munda. I plotted them on a PCA and removed those individuals who were not easily assigned to a cluster. The first PCA: MundaPC1

This isn’t really telling you much you don’t know. Let’s look at PC 3 now: Rplot

As you can see the Munda show a cline toward the Cambodians. This makes sense if the Munda descend from Austro-Asiatic agriculturalists. The Austro-Asiatic expansion in Southeast Asia probably dates to 4,000 years ago or so. Peter Bellwood has stated that archaeologists have excavated villages in northern Vietnam which catch the process of ethnic transition in action at this date (e.g., 75% of the burials are of gracile individuals, whille 25% very robust individuals). Such dates might put a ceiling on how early the Munda arrived inthe Indian subcontinen. In these results the Filipinos are representative of Austronesians, who have their roots in Taiwan and the Fujian coast, while the Dai are the forerunners of the Thai who arrived in Southeast Asia over the last few thousand years, taking over the uplands of Burma (Shan) and Laos (Lao), and swallowing the Khmer civilization which once flourished in the Chao Phraya basin (becoming Thailand). But it’s hard to make out what’s going on with the Bengalis…to me it isn’t clear that they’re shifted as much toward the Cambodians as they should be if the Asian ancestry was due to Munda being absorbed by Indo-Aryan speaking farmers.

So next I ran Admixture. I ran supervised and unsupervised and they showed the same qualitative result. Below is a bar plot of the unsupervised result, K = 5. Read More

Modern humans wiped out modern humans from Europe!

First Peoples: Europe came and went. I watched it. In case you didn’t see it there was a big reveal: archaeologists in France have uncovered a site where modern humans were producing arrowheads 50,000 years ago. This is strange for two reasons. First, what were modern humans doing with bows and arrows 50,000 years ago? They emerged in the Paleolithic transition to the Mesolithic, spreading from the Old World to the New. That is, they become common over the last 10,000 years. I don’t recall the narrator addressing this issue at all. But let’s set that to the side: if these finds are associated with modern humans then that pushes their arrival to Western Europe 10,000 years further back. Despite all the arguments about dating the presence and disappearance of Neanderthals from Europe, no one presumes that they went extinct 50,000 years ago. That implies that groups of moderns interposed themselves into Neanderthal dominated Europe in some fashion for thousands of years, until finally the Aurignacian culture arrived and replaced Neanderthals in toto.

At the site in question specifically the researchers have uncovered evidence that moderns and Neanderthals used the same location only a few months apart. But we need to remember modern humans weren’t modern yet, they were just one of the many hominin lineages which have flourished over the past 2 million years. With hindsight we can see that these initial forays were to prefigure what was to come, but at the time the two groups were not quite that different in technology and guaranteed destiny. Modern humans did not have any great advantage, so they may have come and gone depending on the circumstances.

51It8A+EKrL._SY344_BO1,204,203,200_Perhaps the 50,000 year old moderns in France may be likened to the Norse in Newfoundland. And in fact the analogy to the European settlement of North America, and the replacement of Neanderthals by moderns, is made in First Peoples. But the devil is in the details, as the documentary is somewhat schizophrenic about the specific dynamic until the very end. The two extreme stylized models are “make war” vs. “make love.” With the very clear evidence that modern humans admixed with Neanderthals, the narrative arc of the documentary flips from one where moderns are depicted attacking a Neanderthal camp, to one where a modern human lothario engages in “inappropriate touching” with a Neanderthal female. Though I suppose this was 40,000 years before “affirmative consent” norms, so perhaps we should cut them some slack?

In any case, going back to the analogy with the New World I think we can acknowledge that there were complex scenarios left on the cutting room floor of a one hour documentary. The mestizo population of the New World arose through a variety of means, ranging from love all the way to rape. If modern humans 40,000 years ago were anything like modern humans today, then it seems likely that their interactions would run the gamut from trade and amicable relations, to extermination, with many permutations and positions between these two. We need pick one model as the story.

At the end of it all First Peoples: Europe tells the viewer that Neanderthals were demographically swamped out, rather than killed en masse (there weren’t enough for them to be a mass anyway!). This is an idea that’s been around for a while. With very small populations the idea is that a crest of demographic expansion out of Africa just swallowed up the Eurasian hominins. We literally mated them out of existence. John Hawks elaborates this model at length when he has screen time, which makes sense as he’s been suggesting that large effective population sizes within Africa over the Pleistocene might naturally result in the “out of Africa” pulses we see in the genetic record.

Finally, this episode does now make it crystal clear to me why the original admixture event of Neanderthals with modern humans in the Middle East left its imprint on modern Europeans, and later ones did not. Modern Europeans, whether their ancestry is “hunter-gatherer” or “farmer” descend from a Pleistocene Middle Eastern/Central Asian population in totality, and so only experienced that singular admixture event with Neanderthal Middle Easterners. More concretely, the Mesolithic populations which were overwhelmed and assimilated by farmers during the Neolithic in Europe were themselves descended from peoples who had issued out of the Middle East or Central Asia to replace the first modern Europeans. The Aurignacians (or if later, Solutreans) replaced probably had somewhat higher fractions of Neanderthal ancestry, being further out on the “wave of advance.” But since they left no descendants, to a first approximation there’s no signal of a Neanderthal cline.

The past 50,000 years have been characterized by two phenomena: extinction and admixture.  The rest is commentary.

Open Thread, 7/12/2015

9780199589883To give my brain a break after reading Reading in the Brain I am reading A New History of Western Philosophy. I know I should tackle The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies or Warriors of the Cloisters: The Central Asian Origins of Science in the Medieval World, but I feel that that would have taken more mental energy. Histories of Western philosophy are easier hauls since I already know the roadmap and have a conceptual armamentarium. Though if you want to read a history of Western philosophy, I recommend The Truth About Everything: An Irreverent History of Philosophy. It’s written with more humor than most of the books on this topic! The style obviously differs from that in more academic works, but the general structure of The Truth About Everything is pretty much always recapitulated. A yellow-brick road instead of an asphalt one perhaps.

51lW5fpojzL._SY344_BO1,204,203,200_Reflecting on Western philosophy and its beginnings you always need to go back to Aristotle and Plato. The order in which I listed these two individuals despite their chronology should tell you about my bias. In a A New History of Western Philosophy the author recounts an assertion by Gilbert Ryle, people could be divided into two categories on the basis of four dichotomies: green versus blue, sweet versus savoury, cats versus dogs, Plato versus Aristotle. I suppose three out of four isn’t bad! Like Armand Leroi (see The Lagoon: How Aristotle Invented Science) I have strong sympathies with Aristotle probably because I am a natural scientist, and in particular, a biologist. It is in the domain of biology that Aristotle was mostly wrong, as opposed to not-even-wrong, as in physics. And often he wasn’t even wrong, not too shabby for a man who lived ~2,500 years ago was literally inventing whole fields on the fly. Aristotle’s lack of recourse to mathematical formalism rendered his physics laughable, but his observational acumen lent itself to biology, and his inferences were often quite perspicacious.

But the history of philosophy makes me wonder at contingency and necessity. It strikes me that it is important to observe that Aristotle was a family man. He had a wife and children. Though if you dig into his presonal life it seems to have been conventionally complicated. Plato, in contrast was a lifelong bachelor. Whether he was a homosexual in a physical sense, as a wealthy aristocrat who never married he was somewhat detached from the normal course of affairs in a way the more bourgeois Aristotle never was. Did their life choices affect their philosophy? Or were their philosophies and life choices outcomes of a common cause and personality difference? As the years progress I am less and less convinced by the importance of contingency, in particular reading the ideas of Chinese and Indian thinkers, which in many ways have analogs to the Greeks (even if the emphases might differ). Complex civilization has a Plato-shaped hole, and it has an Aristotle-shaped hole.

This piece in the new TNR, It’s Not Easy Being a Guy in a Country Song, Either, is actually not too bad, as it avoids too much sneering at the subjects. But when implicitly bemoaning the lack of voices in “bro country” which are not white straight, male and culturally* Southern, as well as the topicality of blonde babes, dirt roads, and beer, I’m a little confused as to how the author expects the genre to diversify. If, for example, urban underclass black males were represented in the genre, the topicality would shift. But pretty soon I think it would be hard to differentiate it from hip-hop, because the topics reflect a historical experience. It seems entirely reasonable that the mores and lifestyle of working class Southern white men would be somewhat distasteful to cosmopolitans with a Ph.D.. But if a genre termed “bro country” ever appealed to a feminist whose profession is to be a cultural critic, they’re doing it wrong. If you took Luke Bryan, and just changed his sexual orientation, I doubt that there would be a big audience for songs about his life growing up as a closeted gay man on the dirt roads of Georgia, kicking back with a beer and meeting other guys in the back of his big rig. The cultural landscape is not flat, and some experiences will be more commonly reflected in the arts because they are…more common.

I guess diversity is great, unless it operates outside your narrow ideological purview.

I’ve been busy for the past week. So I’ll answer some of last week’s “open thread” questions here.

First, I’ve been looking for something about ancient+early medieval Arab history. Any suggestions? Here are three: Great Arab Conquests, When Baghdad Ruled the Muslim World, and A History of the Arab Peoples.

9780307819383Everyone is talking about and asking me about The New York Times piece, The Mixed-Up Brothers of Bogata. Two pairs of identical twins were “switched” at birth in a fashion so that two families raised what they thought were fraternal twins. If the piece fascinated you, you really should read Born that Way. Also, there’s a confusing section in the piece: “On average, the researchers found, any particular trait or disease in an individual is about 50 percent influenced by environment and 50 percent influenced by genes. ” I suspect most readers will take this to mean that the trait in the individual is 50 percent genetic and 50 percent environmental. That is wrong. Rather, 50 percent of the variation in the population is due to variation in genes. There is an obviously implication for individuals, but there is a lot of variation, and for most traits it doesn’t make sense to say that in an individual it is any percent genetic or environmental.

There’s a large section on epigenetics in the article, but they never report results. I assume there’s a publication down the line, and we’ll hear about it. Could epigenetics explain some of the environmental component of variation? Perhaps. But behavior genetics already suggests that non-shared environment is quite large in its effect.

Finally, my wife recommends you watch the documentary (42 minutes) if you have any fluency in Spanish. The article elided a lot of the inter-individual differences which are visible in their manner, speech, and overall physiognomy.

In response to a question about aDNA in China and its utility. The key is sample size. If you are working with Y or mtDNA there is a lot more noise and randomness than intuition would suggest, due to their small effective population sizes.

* Some major figures in the genre, such as Dierks Bentley, were not raised in the South but have assimilated to Southern culture.

Structure in 1000 Genomes South Asian data

Est100_1

I’m currently trying to figure out how best to integrate 1000 Genomes data, along with Estonian Biocentre, and HGDP. First, I converted the VCF files from the 1000 Genomes into pedigree format. I’ll put that up on GitHub in the next few days. Then I filtered the results for SNPs which are found in the HGDP. Finally, I intersected the results with the Estonian Biocentre data sets. I was left with ~250,000 markers after quality control (e.g., removing markers which are missing in more than 0.1% of the 5000+ samples).

In particular I’m curious about the population structure of the South Asian data. When you sample Chinese or Japanese or the English you need to be geographically diverse, but you don’t have to worry about social stratification too much.* Not so with South Asia. You have to be careful who and where you sample, because the variation doesn’t cleanly follow geography. In the Diaspora for example wealthier and higher status groups tend to be represented. In the mid-2000s Noah Rosenberg’s lab published Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India. In the paper itself the authors cautioned their samples were from the United States, so one should be careful about accepting the idea that they might represent the geographic variation in South Asia well. In hindsight it seems likely that their selection bias was too great for them to overcome to make robust conclusions, even with over 700 microsatellites.

Above is a PCA plot I generated for South Asians. I’m not quite sure of the coding of some of the Estonian Biocentre populations, so don’t take that as gospel. I was more curious about the distribution of the 1000 Genomes samples, since they are likely to be widely used in the near future.

First, let’s focus on the Bengalis from Bangladesh:

Parents

I was frankly surprise how genetically homogeneous this group is. The two overlapping black dots are my parents. It seems clear that my family comes from a region of Bangladesh which likely has more East Asian ancestry than is the norm. This makes geographic sense, my family’s roots are in the eastern part of eastern Bengal. Though it is hard to see on this plot a small group of Bengali individuals, specifically six, reside in a tight cluster amidst samples from Tamil Nadu. The fact that they aren’t randomly scattered indicates to me that there’s some genuine structure here. I suspect that there is evidence here of a group which has been assimilated, but retained its separate caste-community identity.

But overall there is a major contrast between the Bengali samples from Bangladesh, and the previous Gujarati samples, now also in the 1000 Genomes (ou can see the Patel cluster on the other side of the Bengalis, as it bulges out). The non-Patel Gujaratis were genetically varied, some very similar to individuals from Pakistan. In contrast there isn’t that sort of cline among the Bengali samples (it doesn’t look like they sampled any Bengali Brahmins in this data set, at least those of full heritage). The Punjabi samples were collected from Lahore, and they range from many individuals who are little different from Pathans to some whose genetic background resembles those from middle castes in Southern India. I don’t know what’s going on here, but there has been some back migration of laborers into the Punjab historically. I believe this is the origin of some low caste groups who are now Christian. Both the Telegu and Tamil samples have a few Brahmins in them. This is clear in the following plot:

SIndia

The two Brahmins are from Tamil Nadu. You notice that several of the 1000 Genomes Tamil and Telegu samples are rather close to them. South Indian Brahmins tend to be genetically very similar, so almost certainly that’s what these individuals are if they are placed here on the PCA. Though the Tamil samples are relatively tightly clustered, the Telegu break out into several groups. One of the major 1000 Genomes groups overlaps perfectly with Velamas, a middle caste from Andhra Pradesh. The individuals who are Telegu speakers between the Velamas and Brahmins may be of mixed heritage. I don’t know.

Ultimately I’d like to do some TreeMix and pairwise comparisons between these populations. But to do that I’m going to have to clean them up a bit so that they make sense as…populations.

* The outcaste group in Japan only crystallized during the Tokugawa period. Not long enough to be genetically that distinct from the broader Japanese population.

How the mind reads

416NQwBS-+L._SY344_BO1,204,203,200_Years ago I walked down the main street of a town I had lived in for years, and noticed some new apartments above the retail shops. When I got back home I told my girlfriend about my discovery, and she rolled her eyes and explained patiently that they’d always been there. The fact is that I’m notorious for not noticing things. I have no attention to visual detail. I’m a tunnel-vision sort of person.

In Stanislas Dehaene’s Reading in the Brain he outlines a neuronal recycling hypothesis, which might explain my strange behavior. The gist is that there are regions of the brain which have been co-opted for reading. In particular, the letterbox region of the brain. It turns out that processing text is localized to a small zone of the left hemisphere, and damage to this area can have consequences for reading comprehension. In many ways the symptoms are similar to aphasia, but a tight analogy would be somewhat perplexing.* Language is a core human competency. Though it needs cultural and social input, it seems clear we have a built in facility toward it. Or at least that is the consensus among cognitive scientists. It has almost certainly been the target of natural selection.

The same can not be said for literacy, which is only 5,000 years old, and, whose widespread penetration among humans is only a feature of the last few hundred years. ~25 percent of the world’s population is still illiterate. In contrast, those who can not speak are considered to have some sort of pathology. How then can there be a region of the brain dedicated to text comprehension? Reading seems to leverage pattern recognition capabilities which have deep evolutionary roots, and those recognition capabilities are localized to particular regions of the brain. This localization occurs early in life, but is not hardwired, so very early damage can result in rerouting to other regions (also, slight differences cross-culturally in positioning can be explained as a function of the nature of letters and length of words).

Dehaene reports that this fact imposes constraints on the nature of symbols utilized in text. For example, letters exhibit a distribution of common to rare patterns which are similar to a sort of stimuli we would experience in nature. That is, particular letter forms are over-represented in all world writing form representations, and those forms correspond to the sort of patterns one sees in the natural environment. The similarities of distributions are curious especially in light of the fact that writing systems evolve over time to become more abstract and less concrete from more elaborate, often pictographic, forms. Convergence in phenomenon rooted in our cognitive architecture implies that there are genuine constraints and biases in the shape of our cultural expression.

51IgD1yKTiL._SY344_BO1,204,203,200_Many of the reviewers of Reading in the Brain highlight that it is interminably technical across its many chapters. The author admits as much as he nears his conclusion and attempts an apologia for testing the reader’s patience. Certainly the repetitive survey of neuroanatomy, or the deep-dive into the cognitive neuroscience of symmetry, seemed a bit much for me as someone without a neuroscience background. But when he comes up for air it turns out that Dehaene’s ultimate goal is very ambitious: to explain the variation of culture as a function of cognitive neuroscience. To do this he refers to the large body of work produced by Dan Sperber, a cognitive anthropologist who argues that culture is an “epidemiology of representations.” It is basically an elaborated model of viral memes, where the cognitive landscape of our minds canalize cultural expression toward particular aesthetically appealing or functionally effective forms. For Dehaene reading, literacy, is a form of viral culture. It gives us pleasure (novels), and, it is functionally useful (accounting). Developed over the last several thousand years independently at least twice, and likely more than twice, it seems to be at an intersection of our facility for language, memory, and symbolic representation, which is naturally evoked out of the environment of complex societies. If we could create mentats we would. Their non-existence is a testament to the difficulties of such an enterprise. As it is, we’ll have to make do with reading, and the symbolic manipulation which reading allows. Culture then, is a finite set of phenomena which express novel syntheses of our cognitive capacities. Dehaene in particular emphasizes the role of the domain-general neocortex in threading together disparate domain-specific functions into cultural novelties (e.g., the visual recognition and language competencies necessary for reading).

51QrNyN0KzL._SY344_BO1,204,203,200_Nestled between the abstruse cognitive neuroscience and speculative theorizing about the nature of culture Dehaene has some concrete suggestions on policy. Whole language learning is a travesty, and phonics are the way to go if you want to encourage early literacy. He seems frustrated that some teachers consider phonics “right-wing” and so favor whole language learning. The science says that whole language learning is by and large bunk, even if there are some techniques which are salvageable. Whole language learning shaves years off reading abilities according to Dehaene. Apparently it can take until adulthood for whole language learners to catch up with those who utilized phonics. In an area where policy is probably impotent, English speakers are at a major disadvantage to Italian or Finnish speakers because of irregular spelling (French is between the two groups). Absorption of complex literature is retarded among British and American students because more time in elementary school must be spent mastering the profusion of words (obviously Chinese readers have a similar issue with delayed reading of higher literature due to the cognitive overhead of written Chinese). Finally, though therapy and treatment can mitigate dyslexia, Reading in the Brain left me very happy that my daughter (who is now reading) does not exhibit this problem. It seems a major handicap.

Which brings me back to my anecdote about my personal ability to not “notice” things. I’ve been a big reader my whole life (you can see which books I remember reading at Good Reads). So I was naturally curious about the cognitive neuroscience of this phenomenon. One of the implications of Dehaene’s neuronal recycling hypothesis is that there is an opportunity cost to devoting one’s resources to reading comprehension. The area of the brain which becomes the letterbox region may very well be the area devoted to noticing subtle differences in one’s environment that make trackers among indigenous people seem preternatural in their aptitudes. The way some stems of leaves have become askew, for example, may be the root of many of the letters which we use to represent sounds. Perhaps then my lack of ability to “notice” small things in the world around me is inextricably linked to the fact that my life’s focus has been on text, more or less. It’s a trade-off that I’m happy with.

* Also, damage to the letterbox region can impair recognition of letters, while allowing for number recognition!