A introduction to Chinese philosophy? (thought)

51ryboe8q7L._SY344_BO1,204,203,200_A young friend of mine was asking for recommendations on an introduction to Chinese philosophy. Xunzi: The Complete Text would be hard going for him I suspect, as he has minimal background. My inclination is to suggest A Short History of Chinese Philosophy. My personal experience (yes, I’m still slogging through the medieval section of A New History of Western Philosophy) is that a narrative historical framework makes the abstruse nature of philosophical reflection go down a bit easier.

If you want to get primary sources (translated obviously), Sources of Chinese Tradition would be a good bet, but it’s probably too much without having any reference points. Any thoughts from readers? T. Greer can probably help here….

Open Thread, 2/7/2016

Cultural appropriation must be one of the stupidest concepts to come out of the critical race theory milieu. Back in the day you could just admit that a particular juxtaposition of motifs was dissonant (e.g., I think mixing Arctic and Indian ones might be) or disrespectful (e.g., putting a picture of Jesus on a toilet). Now it requires an NPR think-piece. Despite its jargon, it does strike me that a lot of the long-form discussion veers into the sort of kvetching over intellectual property rights which I find quite annoying and overdone.

pydata_coverA friend of mine was freaking out about Pandas recently. As most of you may know I’m going to be transitioning from Perl to Python, so I was really curious when he mentioned that moving to Pandas also obviated the need for R. So I just got a copy of Python for Data Analysis: Data Wrangling with Pandas, NumPy, and IPython. Figured it would be a good complement to Data Science from Scratch: First Principles with Python.

Since I don’t like to spend time on useless things, I’ve been following the primary race very superficially (sometimes to the extent of asking my labmate every few days what’s going on). But I’d say go long on Rubio. Those following closely freak out too much over debates.

Was talking with a friend recently about the lack of emphasis in biological journals on methods, even though in the long run methods are often more impactful than singular empirical results. Would recommend all readers peruse Ancient Admixture in Human History, with a focus on methods. The paper is now open access.

103296Admixture into and within sub-Saharan Africa, a pre-print worth reading. That being said, I always have a hard time digesting fineSTRUCTURE work. It seems that a lot of stuff is coming out on Africa right now. If so, then it is important to actually know something about the history and geography of the continent. John Reader’s Africa: A Biography of the Continent is the best I’ve run into in that vein. Though The Fortunes of Africa looks interesting, I haven’t read it.

The 13th Bay Area Population Genomics Meeting is going to be held at UC Berkeley on February 13th, next Saturday. As usual, thanks to Dmitri Petrov for starting this, and Fernando Racimo for taking the lead this time around, and the CCB and AncestryDNA for hosting and sponsoring. I plan to be there….

If you live in California, the The California Weather Blog is a must bookmark/subscribe. When I was a wee lad I used to be a weather nerd. I can’t imagine what it would be like growing up today….

Sick and Tired of ‘God Bless America’: ‘The population of nonreligious Americans — including atheists, agnostics and those who call themselves “nothing in particular” — stands at an all-time high this election year.’ This is arguably wrong. During the early American republic with restricted suffrage a large proportion of the eligible electorate may have been freethinkers, at least judging by the fact that the first six presidents would not be considered orthodox Christians by modern evangelical Protestants. The first president who was probably an orthodox Christian while in office, Andrew Jackson, was an ardent church-state separationist:

“I could not do otherwise without transcending the limits prescribed by the Constitution for the President and without feeling that I might in some degree disturb the security which religion nowadays enjoys in this country in its complete separation from the political concerns of the General Government.” — letter to the Synod of the Reformed Church of North America, 12 June 1832, explaining his refusal of their request that he proclaim a “day of fasting, humiliation, and prayer.”

Reproducible Research Practices and Transparency across the Biomedical Literature:

There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest. In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of 441 biomedical journal articles published in 2000–2014. Only one study provided a full protocol and none made all raw data directly available. Replication studies were rare (n = 4), and only 16 studies had their data included in a subsequent systematic review or meta-analysis. The majority of studies did not mention anything about funding or conflicts of interest. The percentage of articles with no statement of conflict decreased substantially between 2000 and 2014 (94.4% in 2000 to 34.6% in 2014); the percentage of articles reporting statements of conflicts (0% in 2000, 15.4% in 2014) or no conflicts (5.6% in 2000, 50.0% in 2014) increased. Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding. This study provides baseline data to compare future progress in improving these indicators in the scientific literature.

Related: What this scathing exchange between top scientists reveals about what nutritionists actually know.

Silicon Valley has an Asian-people problem

twitterethnicitychart
Twitter workforce breakdown

diversity_brief_fig2The above statistics on the labor force at Twitter compared to the overall labor force indicate that non-Hispanic whites are underrepresented in tech firms in Silicon Valley. This is true overall in prominent tech firms. 51% of Facebook’s employees are non-Hispanic whites.

So how to make sense of these sorts of articles:  Twitter’s White-People Problem? And what about passages such as this which seem to totally defy statistical/demographic reality:

 But while Twitter the platform is bustling with all types of racial diversity, Twitter the company is alarmingly white.

Twitter isn’t alone. Most of the biggest tech companies in Silicon Valley are overwhelmingly white and male. While blacks and Latinos comprise 28 percent of the US workforce, they make up just 6 percent of Twitter’s total US workforce and six percent of Facebook employees.

Of course this is just a lie. Very few people would say a workforce that is 50 to 60 percent white, true of both Google and Microsoft, is “overwhelmingly white.” In fact, it’s less non-Hispanic white than the US labor force as a whole. I’ve linked to statistics in this very piece. They take about 10 seconds of browsing search queries to understand this.

But you don’t need to know statistics. Eat at a Google cafeteria. Or walk around the streets of Cupertino. There is no way that one can characterize Silicon Valley as overwhelmingly white with a straight face. Silicon Valley is quite diverse. The diversity just happens to represent the half of the human race with origins in the swath of territory between India and then east and north up to Korea.

The diversity problem isn’t about lack of diversity. It is about the right kind of diversity for a particular socio-political narrative. That’s fine, but I really wish there wasn’t this tendency to lie about the major obstacle here: people of Asian origin are 5% of the American work force, but north of 30% in much of the Valley. If you want more underrepresented minorities hiring fewer of these people would certainly help. In particular the inflow of numerous international talent coming from India and China could be staunched by changes to immigration law.

But these are international companies. Though they genuflect to diversity in the American sense (blacks and Latinos), ultimately they’ll engage in nominal symbolic tokenism while they continue on with business, with an increasingly ethnically Asian workforce and and increasingly Asian economic focus. Meanwhile, the press will continue to present a false caricature of a white workforce because that’s a lot more of a palatable bogeyman than Asian Americans and international tech migrants, and the liberal reading public seems to prefer the false narrative to engaging with reality.

Addendum: The first article was in The Nation. Take a look at their masthead. Most of the names I recognize are mighty, perhaps even alarmingly, white….

The oldest population structure of all in southern Africa?

safrica

41d3NIUbD8L._SY344_BO1,204,203,200_Southern Africa is kind of a big deal. Not because it is the seat of human origins; I am beginning to think that question is “not even wrong.” Nor because it contains the “oldest human population” in the world; we are all the oldest human population in the world. Rather, the genetic variation one can find across a small region in southern Africa is incredible, and, it is one of the few regions of the world where hunter-gatherers have persisted in a culturally pristine fashion. By this, I mean that there is no evidence that the hunter-gatherers of southern Africa practiced another way of life (i.e., that they are marginalized agriculturalists or nomads), or, that their language was adopted from agriculturalists (as is the case with the Pygmies of central Africa). In other words, the continuity of the peoples of southern Africa is more notable not for their genetics, but their culture. That being said, the cultural conditions under which the KhoeSan peoples existed are of genetic interest, because their high degree of variation may reflect aspects of population dynamics common to hunter-gatherers as a whole.

In light of all this a new preprint on bioarxiv is quite interesting, Fine-scale human population structure in southern Africa reflects ecological boundaries. The title rather says it all, but I’ll admit that it’s hard to keep track of all the populations. It certainly strikes me as plausible, as the genetics suggests that there’s a lot of structure that built up over the years. Of note: “To contrast this with Europeans, the ≠Khomani and the Ju/’hoansi may have diverged over 30,000 ya but live only 1,000 km apart, roughly the equivalent distance between Switzerland and Denmark whose populations have little genetic divergence.” They report trans-Kalahari Fst values on the order of 0.05, which is quite high, on an order of magnitude or so greater than what can be found in Northern Europe. But the latter is more comprehensible when you consider the genetic character of the North European plain only arrived at its current state ~4,000 years ago.

Adam Kok III, last of the Griqua captains
Adam Kok III, last of the Griqua captains

Since the above is a preprint, some critiques are in order. The authors use ancestry tract lengths to assess admixture of Bantu, Asian, and European, elements into the KhoeSan. The implication is that these were separate admixture events. Some of them certainly were. But I’m a little skeptical of the power of these methods to distinguish admixture between the last two non-African components (also, I think it is probably advised for a population genetics paper to dispense with the cultural construct of Asian and make the clear distinction between South and East Asians, since the former are often genetically closer to Europeans, and this previously inflated the European proportion among Cape Coloureds). It’s been many years since I read A History of South Africa, but one of the more interesting aspects that I recall from this book was the cultural distinctiveness of what has now come to be called the Cape Coloured people, and their role as mediators along a fluid cultural frontier with the KhoeSan people. The history of the Griqua in particular shed light on how one might imagine European and Asian (South and East) ancestry arrived into the KhoeSan. Though racially mixed, the Griqua resembled the Dutch in formal and institutional aspects of their culture by the 19th century. But, as a semi-nomadic and pastoralist group they also had affinities with their African neighbors (and often, they played the role of predators with the Africans and their herds), with whom they clearly shared ancestry. It was not an unknown phenomenon to have Griqua scouts “go home to their mother’s people.” Even if their literal mother was also a Griqua, they seem to have had a sense that their maternal ancestors were invariably non-European, and often derived from the KhoeSan (many Griqua still spoke the now extinct Cape Khoi language, though they were shifting toward a Dutch Creole). The probability of assimilation of unadmixed Europeans, South Asians, and East Asians, into KhoeSan groups is not zero, but it strikes me as quite low. On the other hand, Griqua, who were mixed between all the populations of southern Africa, and culturally quite at home in the semi-desert wilderness, seem ideal candidates for the population which could serve as the vectors for transmission of these ancestral elements into the KhoeSan.

A second issue with this preprint is that I’d like to see more methods. E.g., three and four-population tests and TreeMix in particular, since with 320,000 SNPs these should be totally feasible with genotype data. These are not groups that most people have much familiar with, so PCA and ADMIXTURE tend to overwhelm. To develop a decent intuition about what’s going on trees and tables are often helpful (I don’t like tables usually, but often when you are focusing on a finite number of populations per row they can allow for greater focus). Also, there are now interesting ways to analyze spatial genetics beyond Mantel tests.

Ultimately these results confirm what I already held as a prior. It strikes me that the relationship we see between language and genes today is largely a function of the reality that much of the population genetic structure we see around us is a recent phenomenon. That is, massive migrations due to cultural changes (e.g., agriculture) were accompanied by both language and genes, and only a few thousand years are simply not enough time to allow for linguistic differentiation to obscure common origins. In contrast, if, as seems plausible, many of the KhoeSan people were resident in southern Africa for tens of thousands of years, then correlations between language and genes should slowly decouple (in part because deep linguistic affinities may not be discernible). That being said, I would not be surprised if ancient DNA from southern Africa at some point overturns conventional wisdom that these peoples are truly primal….

Human population replacement as megafaunal extinction

pleistocene

51pgrGlsM4L._SX327_BO1,204,203,200_About ten years ago a standard model of the understanding of the peopling of the world by modern humans was that ~50,000 years ago a massive demographic swell out of eastern Africa overwhelmed, to elimination, all other human populations. With a few exceptions, such as the New World, these modern Africans quickly settled down, and the extant distributions of genes, generally mtDNA and Y lineages, reflected the long equilibration between then and now (the recent changes in the New World being an exception to that). Human genetic variation then could be understood as having been shaped by a rapid pulse expansion, and then a subsequent stabilization where genetic variation was maintained by geographic barriers across founding populations, and diminished by gene flow governed by isolation-by-distance. To a great extent this is the story you’ll find in Stephen Oppenheimer’s Out of Eden: The Peopling of the World.

To a large extent that story was wrong. Ancient DNA in particular, though not exclusively, has reshaped our understanding of the past (see Toward a new history and geography of human genes informed by ancient DNA). The ubiquity of population discontinuity and admixture suggest that it was naive to assume that modern genetic variation in any way reflects the founding stock which initially arrived in the first wave in many regions of the world. Additionally, the existence of archaic admixture in most modern lineages attests to the fact that the chasm between “them” and “us” was not perhaps quite as great as some might have claimed.

The ubiquity of population replacement is the reason I recent predicted that the first Aurignacian genome would show no relation to modern Europeans. (I was correct for what it’s worth) That is, modern humans in Europe have no special relationship to the first modern humans that settled Europe 45,000 years ago. The work on ancient DNA does suggest that modern Europeans have hunter-gatherer ancestry…but how deep does this go? I hazarded that perhaps the Gravettians are the earliest candidates for being the direct ancestors of the “Western Hunter-Gatherers” (WHG), who contribute a substantial portion of their genes to modern Europeans through Mesolithic hunter-gatherer populations. But, I wouldn’t be surprised if the genomic character of European Mesolithic hunter-gatherers was determined after the Last Glacial Maximum, ~20,000 years ago.

A new paper in Current Biology, seems to tip toward the latter conclusion. Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe. In particular, using a confluence of “best of breed” phylogenoomic methods and archaeological dating the authors contend that there was a major turnover in the mtDNA heritage of Europeans ~14,500 years ago, during the Bølling-Allerød interstadial, a relatively mild and warm period of the Pleistocene before the sharp and harsh regression of the Younger Dryas. The big result is that some very old (pre-LGM, Gravettian) belong to mtDNA haplogroup M. This is one of the two major groups common outside Africa, but it is absent in Europe today (the Roma harbor M because of their South Asian heritage).

u5The lineage that to a great extent has been canonical as that of European hunter-gatherers, U5, seems to have increased in frequency only late in the Pleistocene, during the above warm period.  Because of the nature of random genetic drift we do expect lineage to go extinct over time. These are mtDNA, direct maternal lineages, so only one locus in the genome (though mtDNA is copious, so tends to be low hanging fruit for any new extraction technique). The combination of low long term effective population sizes and meta-population dynamics on the Eurasian fringe might mean that these are not unexpected results. But as suggested in the paper there is also a great possibility that the disruption of the interstadial resulted in some advantage to a particular subset of Pleistocene Europeans, who expanded rapidly, replacing their competitors. Many of the hunter-gatherers of the Mesolithic have relatively low genetic diversity in comparison to modern populations, suggestive of the small population sizes on the European frontier.

The expansion of U5 at the expense of other lineages though around ~14,500 years ago does seem to not be attributable purely to chance according to the models tested within the paper. Then what? One hypothesis is that the climate change resulted in extinction of many populations ill equipped to adapt to climate change, and these were later replaced by newcomers. Another, not exclusive, model is that there was conflict between different groups, and the climate change opened up opportunities for one subculture. There is an allusion to megafaunal extinction in the paper around this period…perhaps we should think of humans as just another megafauna for the super-predator cultures?

One way to look at geological process is that it is uniformitarian, not catastrophic. But it strikes me that with human demography catastrophic pulses are quite common on a geological scale. Why? Likely because cultural evolution is not quite so gradual and continuous, but that innovative revolutions and rapid sweeps of inter-group competition “thin the field,” so to speak.

The main caution I would add is that though we know a lot more than we did, we still no little. What was the ancient population structure in prehistoric Europe? Really we don’t know much, as the sampling is thin at best. That is changing.