Open Thread, 9/23/2018

Curious how many readers recognize the reference on the shirt to the left? You probably know if you’ve read The Double Helix. On the DNAGeeks website now.

Salon is stiffing freelancers of $150. I think this is more a commentary on the market for freelancers than Salon‘s always tenuous finances. The market-clearing price for a lot of web journalism/commentary is pretty low. Salon does this because it knows freelancers will tolerate and accept this behavior more often than not.

This long article from Huffington Post (and boosted on the editor in chief’s Twitter), Everything You Know About Obesity Is Wrong, is being widely shared on Facebook (I haven’t seen it much on my Twitter, but that’s because I follow mostly scientists).

Of course it’s really really light on the science of nutrition. Or should I say “science”? Because the truth is that nutrition science has a lot of problems, so there is space to criticize it. But that being said, this piece is being shared by people who seem to think that there is a conspiracy make it seem like being obese is unhealthy. But most of the article is about how cruel people are to the obese, especially medical professionals. There’s really little evidence presented that being obese doesn’t cause issues with morbidity and mortality. Quotes like this are representative: “But individuals are not averages: Studies have found that anywhere from one-third to three-quarters of people classified as obese are metabolically healthy.” That’s a huge interval. Why?

Ultimately the article should have been titled Everyone Is Cruel to Obese People and That is Wrong and Ineffective.

If you want some real nutrition science, What I learned about weight loss from spending a day inside a metabolic chamber.

I bought Early China: A Social and Cultural History. A lot of archaeology. But that’s what you get! I figure I should know more about Zhou China though. I think next I’ll try to read up on Neo-Confucianism, a topic I’ve been lax in because of my leaning toward “Han learning.”

Highly recommend Viet Nam: A History from Earliest Times to the Present. Most of the book does not deal with the Vietnam War. One curious thing I learned: the Vietnamese identity in the period around 0 AD was strong influenced by the influx of Yue people from southern China, as they imparted their culture and statecraft on the proto-Vietic populace. Of course on top of that came later Chinese migration, which resulted in the emergence of Vietnamese as a tonal language.

Though you’ll probably really want Phở as you read the book….

Also, I knew this, but Viet Nam makes it clear in all the gory details that the Austronesian Cham people of central and southern coastal Vietnam were undergoing the same shift to Islam from Hinduism that was occurring further south in the period after 1500. It seems rather clear that the emergence of a Cham sultanate on the model of Mataram or Johor never occurred because the Vietnamese conquered the Cham kingdom, and then assimilated or exterminated most of the natives. Many Cham fled to Cambodia, where they form the Muslim minority of that nation.

But, a small minority of Cham remain in Vietnam, and amongst these are a substantial Saivite Hindu community. It seems entirely possible that if the Cham had retained their independence as a nationality one would have seen total Islamicization, as occurred among the Malays. As is this, this process was retarded by Vietnamese conquest, and so some Chams still remain Hindu (the same process applies to the Philippines, where the native population was influenced by Hinduism first, and was in the first stages of Islamicization, when the Spaniards conquered the archipelago).

Indonesia: Peoples and Histories is worth a quick read. Not as dense and informative as Viet Nam: A History from Earliest Times to the Present.

Change in sexual signaling traits outruns morphological divergence in a recent avian radiation across an ecological gradient. Not a surprising result I guess.

This AJ+ video about “white feminism” is getting a lot of attention. Mostly because AJ+ is backed and owned by a conservative Salafist regime which runs an oligarchic state on the backs of dark-skinned South Asian indentured labor. I’ve spent a week in Qatar at a really nice hotel. I’ve never encountered service staff as solicitous and courteous in the United States. At some point I may write about how certain organizations and institutions use political movements as instruments…but I always feel this is so obvious.

Digging Into the Genetics of Drug Targets. Derek Lowe, the science blogger who has been blogging for the longest time. This is why it’s worth reading him.

Next week on The Insight we’ll be talking about Indian genetics, again. Partly in anticipation of the ancient DNA paper, which should drop any day now (I have no inside information). Question suggestions welcome.

Quantifying Heterogeneity in the Genetic Architecture of Complex Traits Between Ethnically Diverse Groups using Random Effect Interaction Models

Evolution and Selection of Quantitative Traits has finally been published in book form. It’s a good value on a pound-for-pound basis….

Individual selection leads to collective efficiency through coordination. The last sentence of the abstract is key: “This finding reveals a general principle that could play a role in nature to smoothen the transition to efficient collective behaviors in all games with multiple equilibriums.” You need to figure out ways to get to cooperation.

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. It seems within the Near East farming spread mostly through cultural diffusion. My suspicion is that that is due to the fact that it didn’t provide that huge of a demographic boost in its primitive form. Once the various farmer groups perfect their toolkit, they expanded into areas dominated by hunter-gatherers, not other farmers.

The Austronesian expansion actually makes me consider the possibility that we may never understand why the modern humans in the Near East ~55,000 years ago “broke out” and absorbed all the other hominin groups.

Cornell Just Found Brian Wansink Guilty Of Scientific Misconduct And He Has Resigned. If Wansink hadn’t become famous through his self-promotion, he could have continued on with his career. What he’s guilty of lots of people are guilty of, and the media and the public are complicit by demanding sexy and practical results.

Detecting archaic introgression using an unadmixed outgroup.

How Connected Is Your Community to Everywhere Else in America? This is incredible data journalism.

Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast.

Large-scale investigation of the reasons why potentially important genes are ignored.

Polygenicity of complex traits is explained by negative selection.

The effects of demography and genetics on the neutral distribution of quantitative traits.

When I’m working sometimes I listen to the Men of the West YouTube channel. It’s run by a Tolkienist who does some serious work in this area.

Tracing the paths of Noah’s sons

 
The above admixture graph is from a new preprint, Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. To be honest, if you read the supplementary text there’s almost no point in reading the main preprint, as it is far more in depth when it comes to the methodology as well as spotlighting a variety of particular results. It’s hard to know where to begin with such a preprint so I want to highlight the “this is a simplified model” portion in the figure above. That’s actually the truth. Remember, no admixture graph is the Truth, it is an attempt by humans to capture concisely and informatively the major features of our species’ population history dynamics. The reality was never as clear and distinct as stylized graphical representations would have you think, and the researchers are aware of this.

In any case, if you want to really get at how they arrived at the conclusions they did, really read the supplementary section SI 2, “An admixture graph model of Upper Paleolithic West Eurasians.” The authors have so many potential combinations of ancestral populations that they can’t simply manually and intuitively posit admixtures. Rather, they have to explore a huge number of combinations (trees/graphs)…at which point they run into computational limits. This section explicitly lays out computationally efficient ways to automatically traverse the possibility space, and arrive at the best fitting set of models, within reason.

The title of the preprint says it all, but let me quote the abstract in full:

The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. Surprisingly, the Dzudzuana population was more closely related to early agriculturalists from western Anatolia ~8 thousand years ago than to the hunter-gatherers of the Caucasus from the same region of western Georgia of ~13-10 thousand years ago. Most of the Dzudzuana population’s ancestry was deeply related to the post-glacial western European hunter-gatherers of the ‘Villabruna cluster’, but it also had ancestry from a lineage that had separated from the great majority of non-African populations before they separated from each other, proving that such ‘Basal Eurasians’ were present in West Eurasia twice as early as previously recorded. We document major population turnover in the Near East after the time of Dzudzuana, showing that the highly differentiated Holocene populations of the region were formed by ‘Ancient North Eurasian’ admixture into the Caucasus and Iran and North African admixture into the Natufians of the Levant. We finally show that the Dzudzuana population contributed the majority of the ancestry of post-Ice Age people in the Near East, North Africa, and even parts of Europe, thereby becoming the largest single contributor of ancestry of all present-day West Eurasians.

Shared drift with Dzudzuana

Longtime readers know that I hate the American racial term “Caucasians.” It’s pretentious when you could just say “white European,” because that’s what people really mean, judging by the fact that the real people from the Caucasus are marginally Caucasian in the eyes of many Americans. The genealogical origin of the term goes back to Johann Friedrich Blumenbach. And yet this paper takes these two samples, and finds that a lot of the ancestry of modern groups can be attributed to them! (also, a religion interpretation of the results is in the title of the post)

To be fair, they caution that these ancient Caucasian samples are representative of a particular thread of human heritage, not that the center of this thread was necessarily in the Caucasus. This does make me wonder about ascertainment bias in the Near East toward samples from mountainous areas which were colder. But, at the granularity they are attempting to understand human population history, it’s probably not that big of a deal. Ultimately, they conclude that this Paleo-Caucasian population contributes “~46-88% of the ancestry” of modern Europeans, Near Easterners, and North Africans. That’s kind of a big deal.

There are so many results in this preprint, so I think we need to back to the “beginning” of the non-African branch. The Paleo-Caucasian sample is of note in part because it is from before the Last Glacial Maximum, and, about halfway back to the massive diversification of most non-African populations around 55,000 years ago.  Using the Paleo-Caucasian samples’ affinities this preprint reinterprets results from last spring on ancient DNA from Northwest Africa. In that paper, the authors conclude that Paleolithic North Africans were a mix between an unspecific Sub-Saharan population and Natufians. Here though the authors suggest that the Natufians and Yoruba both received gene flow from Paleolithic North Africans. And, these Paleolithic North Africans were themselves mixed between something similar to the Paleo-Caucasians (a mix between an ancient West Eurasian ancestry and “Basal Eurasian”), and a “Deep” ancestry which diverged from other non-Sub-Saharan Africans before the Basal Eurasians did.

The reason that the Paleo-Caucasian sample is so important is that it allowed the researchers to see that the early Holocene Near East, where Anatolian and Iranian farmers, as well as Natufians in the Levant, were ancestral to many later groups, was subject to many genetic changes from before the Last Glacial Maximum. The Natufians seem to be well modeled as having ancestry from the Paleolithic North Africans as one of the major ways they are distinctive from the Paleo-Caucasians. This presents us with a reasonable model for the west to east movement of haplogroup E, and, the Afro-Asiatic languages. The gene flow of Paleolithic North African also explains the non-trivial level of Neanderthal admixture which is found in the Yoruba population. This is mediated through the presumed back migration of Paleo-Caucasians from the Near East at some point in the Pleistocene, contributing some Neanderthal ancestry to the genetic background of Paleolithic North Africans.

Additionally, the distinction between western (Anatolian/Levant) and eastern (Iran) farmers during the early Holocene can now be understood as a product of later admixture into eastern proto-farmers of basic Paleo-Caucasian stock. The relative closeness of Anatolian farmers to the Paleo-Caucasian samples is indicative of the fact that there was an “Ancestral North Eurasian” (ANE) admixture cline into the Near East during the Pleistocene, which meant that some populations to the east became rather different from the pre-LGM samples. Probably after the Last Glacial Maximum proto-Siberian ancestry became prominent in the zone between the Caucasus and Iran (additionally, some of the models imply there was eastern Eurasian ancestry). This is in keeping with the fact that ANE ancestry does seem to have been found in places like Khorasan before the expansion south of steppe populations after 2,000 BC.

As noted in the abstract, Paleo-Caucasians had Basal Eurasian ancestry ~30,000 years ago. This increases the likelihood that Basal Eurasians weren’t recent migrants from deep inside Africa. Additionally, for various reasons, the authors are now positing a Deep ancestry which diverged even further into the past. Both Basal Eurasians and Deep populations seem to lack Neanderthal admixture. The authors also repeatedly suggest that Basal Eurasians were part of the Out of Africa bottleneck event. In Who We Are and How We Got Here David Reich presents the model that this bottleneck population had a low effective population size for a long time. This seems plausible because the genetic homogeneity that you see in non-Africans is pretty striking vis-a-vis Sub-Saharan Africans. On the other hand, this work confirms earlier results that imply that Basal Eurasians did not admix with Neanderthals, and also indicates that the divergence has to be greater than 60,000 years before the present from other non-Africans, who diversified more recently.

In contrast, the Deep ancestry group, which nevertheless forms a clade with the new Eurasian lineages (Basal and non-Basal), does not clearly seem to have undergone the bottleneck event according to this preprint. It’s more a matter of what they don’t say, rather than what they say in this case.

The big picture needs to be integrated I think with the new “modern humans emerged through a multi-regional process” within Africa. If you think of modern humans as emerging across an African range which shifted in the Near East based on oscillating climatic conditions, the ancestors of the “non-African” lineages can be thought of as one of the main deeply rooted lineages, probably in the northeast of the continent. During the Pleistocene, the Sahara was even more brutal than today during many periods, so it is not implausible that some of these marginal populations on the edge of Africa were subject to long periods of very small effective population sizes. Most of them presumably went extinct. But one population was probably far enough north and east that it had a little more margin to play with. This population was probably connected along the Mediterranean littoral at some point with the Deep component in North Africa, which had higher effective population sizes because the mountainous terrain of the Atlas region was always going to remain more clement through dry phases.

At some point one a group of the bottlenecked population mixed with some Neanderthals, and began to break out of containment in southwest Asia. If I had to bet money, I suspect there were already other related groups, probably somewhat admixed with local hominin lineages, further east. That is, I believe the archaeological results in Southeast Asia, and think that those in Australia are credible. But these groups were probably small in number, and totally absorbed by the later migration wave.

Also, the timing of the separation of Africans and “non-Africans” is such that I wouldn’t be surprised Qafzeh-Skull people were somehow ancestral to, or closely related to, the ancestors of non-Africans.

Finally, let’s remember that the authors were focusing on North Africa and Western Eurasia in this preprint. Things will get more complicated as East Asia and Africa come “online” in terms of these analyses. Of course, we are going to be helped by the reality that human genetic variation is not arbitrarily and randomly distributed, but reflects real constraints in our evolutionary history and the forces of geography as well as contingency. The non-African story is made simpler in part because of the great bottleneck, and especially the common descent of most peoples from the population that mixed with Neanderthals. The modeling of effective population size changes over time in Sub-Saharan groups does not lead us to believe that it will be so simple in that continent.

Related papers: The genetic history of Ice Age Europe, Tales of Human Migration, Admixture, and Selection in Africa, and Genomic insights into the origin of farming in the ancient Near East.

The great human migrations (coming in waves)


The figure above is from a new paper, Estimating mobility using sparse data: Application to human genetic variation, which uses genomic data from late Pleistocene to the Iron Age in western Eurasia, and then infers migration rate considering both spatial distribution and the variable of time (remember that samples apart in time should also be genetically different, just as those apart in space often are).

The empirical results are shown above, but they validated their method first by running some simulations. Interestingly they modeled the migration as a Gaussian random walk. Which is fine. But I wonder how true this is for a lot of the Eurasian migrations of the last 10,000 years. Perhaps the the distribution of distances from the place of birth would turn out be multi-modal, with a minority of individuals tending to make “long jumps”?

With that out of the way, it’s fascinating that migration peaks around the Neolithic transition, the Bronze Age, and then the Iron Age. If you read a book like 1177 BC, you know that there was a major regression in the 13th century BC across the Near East, and for several centuries the region was in a “Dark Age.” In The Human Web William H. McNeill argues that one of the reasons for the length and depth of this Dark Age is that the network of complex societies exhibited less density and so less redundancy to failure.

The authors conclude:

We find that mobility among European Holocene farmers was significantly higher than among European hunter–gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time.

Earlier they say:

We find strong support for a rise in mobility during the Neolithic transition in western Eurasia, likely corresponding to a well-established demic expansion of farmers, originating in the Middle East and resulting in the spread of farming technologies throughout most of Western Eurasia

One of the main findings of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past is that oftentimes change is not gradual. Consider the transition to the Corded-Ware society in Northern Europe.

The “demic diffusion” model is an easy one because it relies on the mass-action of individuals and family-groups as they expand in space through high fertility rates. And yet one thing that I think it misses is the socio-political context of that demic diffusion. For prehistoric periods we don’t have writing, and so no socio-political context. This is why in War Before Civilization the author focused on ethnographies of historical societies which came into contact with literate cultures which recorded their organization and folkways. The short summation is that these societies were often very aggressive and well organized for war. Additionally, hunter-gatherers themselves were keen on expanding farmers, and it seems clear they too could mobilize for violence.

The upshot is we need to think of the rise and expansion of strong states and expansionist polities as the context for an increase in the rate of migration. The reality of low migration rates in Pleistocene Europe was pretty evident even before this formal analysis. The pairwise genetic difference due to drift, and therefore low migration rates, for some nearby populations in the Pleistocene and early Holocene indicates that small-scale societies tend to be quite insulated from each other. In contrast, the Iron Age has witnessed a great deal of admixture, as large states and polities, as well as meta-ethnic identities, have broken down genetic barriers.

A regression around 1000 BC correlates neatly with reduced migration, This was almost certainly due to the fact that without larger states much of West Eurasian society, such as in Greece, had disintegrated into smaller tribal units.

Future historians and geneticists will notice that in the period between 1500 and 2000 the distribution of the Y chromosome lineage R1b1a1a2 expanded far beyond Western Europe. They will also understand the political context for this expansion of the lineage…

The Munda arrived in India 4,000 years ago (probably)

I didn’t plan to talk about the Munda any time soon, in part because I recently wrote a post, The Munda as upland rice cultivators, which outlined my views. But there is a new preprint with new samples which attempts to estimate admixture times using genome-wide data. You can see the results above, and, also note that they found similar estimates using Y chromosome SNP variation around haplogroup O2a1.

The preprint is, The genetic legacy of continental scale admixture in Indian Austroasiatic speakers:

Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000 – 3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.78/0.22 are Lao people from Laos and Dravidian speakers from Kerala in India, while the South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

There is a weird pattern of the affinities in f3 statistics in the IBD in this preprint. I think the explanation that they give, that Vietnamese and Cambodians have been subject to later admixture, probably explains it. In the case of the Vietnamese, it’s southern Chinese ancestry. In the case of the Cambodians…it might be Indian ancestry! This might strike you as strange, but the Indian ancestry in the Cambodians may be more enriched for the West Asian component that’s not found in the Munda specifically: the element brought in by the Indo-Aryans.

The peninsular Malay groups are “proto-Malays,” and these groups tend to be somewhat higher in AASI-like ancestry as well as lower in Austronesian ancestry. High shared drift tendencies with Lao and groups in more isolated areas of Malaysia may be a function of the fact that these are less cosmopolitan populations, with less Indian and Chinese ancestry, than other mainland Southeast Asians and Malays proper.

Click to enlarge

These results are broadly in line with the Narasimhan et al. preprint, which is cited within it. In that preprint the Reich group outlines its general model, where modern South Asians can be thought of as a compound of several different ancestral populations of different affinities. The Munda in particular are enriched for “Ancient Ancestral South Asian” (AASI) vs. any other group, and the hypothesis is given is that the Southeasts Asian mixed first with with an AASI group which lacked the admixture with West Asians, and then mixed again with “Ancestral South Indians”, which had some West Asian (“Iranian Farmer”) ancestry.

Since ALDER based methods, last I checked, tended to pick up the last admixture event, the more recent time for northern Munda groups makes sense. Looking at the Y chromosomes it is pretty clear to me that some of the East Asian ancestry in Bengali-speaking agriculturalists in the lower Gangetic plain is from Munda groups. Conversely, some of the Munda probably admixed populations from in from the west practicing intensive rice agriculture, which apparently did not become a feature of the landscape until after 1000 BC.

One of my points in the post above I wrote on the Munda is that the common words for Austro-Asiatic languages indicates that they were upland rice farmers. This is exactly the modern distribution of the Munda. One hypothesis, which I now am skeptical of, is that the Munda once occupied the bottomlands and were driven into the hills by people from the west and south. I no longer believe this. Rather, the Munda may always have preferred the uplands, and so traversed the flat lands between the Khasi hills and the Chota Nagpur plateau. This preference for uplands may strike us as strange, but it’s not that rare. Yankee farmers in Ohio preferred upland zones, even though these were less agriculturally rich (farmers moving up from the South didn’t have this aversion).

A point observed and implied in the preprint is that the expansion of Indo-Aryans, Dravidians, and Munda, seems to have happened all rather close in time. Though the northwest region of the subcontinent seems to have developed a settled agricultural society by 3000 BC of long standing, its expansion was limited by climatic restrictions on its crop toolkit. But by 2500 BC it seems pastoralists were already pushing into the Deccan via the dry-zone on the eastern edge of the Thar down from the Punjab. The Toda people of the far south of India are probably representative of the lifestyle of these peoples, who were Dravidian-speaking.

A few centuries after this period is probably when the proto-Munda began pushing out of Southeast Asia. The DNA evidence is pretty strong this was a hugely male-skewed event once it got beyond the Khasi hills. Why? My hypothesis is that these were not quite small-scale peoples. Perhaps the male-mediation of a lot of gene flow in South Asia is due to the emergence of militarized confederacies where elite lineages engaged in conquest of territory from native groups. The Munda have very low frequencies of R1a, and very high frequencies of O2a. The admixture with Dravidian and Indo-Aryan speaking peoples that occurred between 2000 BC and 0 AD was probably overwhelmingly female-mediated.

The narrative above suggests that most of the genetic changes we see in South Asia to result in the landscape of the present occurred in the period between 2500 BC and 500 BC. About 2,000 years. And yet agriculture of some form arrived in Mehegarh in western Pakistan 9,000 to 7,500 years ago, depending on what dates you trust. What took so long? Similarly, millet and rice agriculture in China is 7,000 years old, but only around 4,000 years ago did rice farmers start pushing south (and probably west in the case of the Munda).

I’ll present the hypothesis here that this coincidence wasn’t a coincidence, and that certain things in relation to social complexity have a particular rate of change. In general I agree with economic historians who say that our need to posit an “Industrial Revolution,” or a “Neolithic Revolution,” is somewhat of an imposition because humans don’t want to think quantitatively. It probably takes small-scale societies moving from hunting and gathering to full-brown agriculture a certain amount of time, and then to proceed to greater social complexity that enables migration which is more than due to simple natural increase and Malthusian driven expansion. Mainland India beyond what is today Pakistan and much of Southeast Asia were “filled up” by agricultural peoples around the same time after a long incubation to the west and north because similar social forces were at play.

Indic civilization came to Southeast Asia because Indian people came to Southeast Asia. Lots of them

Reading Indonesia: Peoples and Histories. I selected it because unlike many books it wasn’t incredibly skewed to the early modern and postcolonial period. The author makes the interesting point that the Islamicization of western Indonesia and the rise of the great Javanese Hindu kingdom of Majapahit occurred around the same time. This, in contrast to the skein of Indic civilization which had been layered over maritime Southeast Asia for hundreds of years before the medieval period, starting around 500 AD with polities such as that of Kalingga.

As is usual in these sorts of books, it is emphasized that Indian civilization spread through cultural diffusion (in contrast to the fact that though Chinese trade was evident and present early on, the cultural impact was minimal). Any migrations are dismissed as legends, with the possible exception of a few elite religious functionaries.

I now believe this is wrong. I’ve discussed this extensively in the past, but the Singapore Genome Variation Project (SGVP) data set along with more Southeast Asians allows me to illustrate rather clearly the issues. The short of it is that it is highly likely that substantial South Asian ancestry exists within Southeast Asia, and that that ancestry is not just a function of colonial contact (e.g., as certainly occurred in Malaysia).

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The Chinese eradication of extreme poverty in one generation

There have been write-ups in the media of the decline of extreme poverty due to a World Bank data release in the past few days. This is kind of a pretty big deal, and one of the reasons that books like Enlightenment Now are still worth writing: much of the American public is unaware of the “good news.”

But as made clear in the graphic in The Wall Street Journal, this is to a great extent a regional story. In particular, it is the story of the near eradication of extreme poverty among the ~20% of the world’s population that is Chinese.

As the chart makes visible, the “Third World” or the “Global South” or the “Developing World”, whatever you call it, is very economically diverse. Was very economically diverse. In 1990 most of the world’s extreme poor lived in East Asia. Overwhelmingly in China. Outside of Sub-Saharan Africa and South & East Asia extreme poverty, using this definition, was actually not that common. Latin America, the Middle East & North Africa, and the post-Soviet world suffered by comparison to North America and Western Europe.

People who traveled widely across the “Third World” knew this. In the 1980s and 1990s one of my uncles was an engineer, and later officer, for an Iranian oil tanker, and so traveled across the Middle East. He eventually wrote a peculiar book on poverty in Bangladesh after he retired, and in it he recounted how clear and distinct the differences in acute poverty were when he compared Iran with his homeland.

To give you a different general sense, I pulled the World Bank data and focused on a few large nations of diverse profiles. And, rather than looking at just the % below a very low poverty threshold ($1.90 per day), I increased the threshold ($5.50) and focused on the poverty gap. While the poverty headcount just tells you what % of the population falls below the threshold, the poverty gap is measuring the average distance below the threshold. In other words, it is measuring intensity of poverty.

What you can see above is that China went from having the highest poverty gap to the lowest in 25 years. But the story isn’t just about China. Fifteen years ago Vietnam had just as much extreme poverty as Bangladesh, but today it is in the same range as China. In the 1990s we talked a lot about the “Asian Miracle.” But that was minor leagues. The real miracle has occurred in the 21st century.

But it wasn’t really a miracle at all. Nations such as Vietnam and China (and earlier Japan and Korea) had relatively high literacy rates, and a tradition of meritocratic advancement, long before contact with European colonialism. Before Communism. With high native human capital resources to begin with, they were poised for lift-off before they ever made it down the runway.

My wife happens to know a Chinese man who is now a professor of science at an American Research I University. Because this is someone we know, aspects of his life history have slowly emerged. In short, he grew up in a very poor peasant household in rural China. And not one that had just recently fallen down the class ladder from what we can tell.

Today he is a professor doing rigorous science, who has achieved an upper middle class American lifestyle. My horizons may be narrow, but I have never met a South Asian in the United States who has come from an analogous background of such grinding deprivation. I know they exist. But in general South Asian peasants in deep deprivation, the children of landless laborers and the like, do not seem to have the opportunity or expectation that they could become researcher professors in the United States.

Finally, Communism. It is strange today, though perhaps not, that much of the younger populace of developed nations are beginning to look with eagerness toward some sort of inchoate socialism. And yet here you have more than a billion who sloughed off the dead hand of command socialism, and in the process eradicated extreme poverty.

I understand the qualms about Chinese authoritarianism. I’m well aware that some elements of China’s economic growth are unlikely to be sustainable. Perhaps there will be a correction. Almost certainly there has to be one. But we can’t forget what the very recent past was like. We shouldn’t shrug off the miracle of anti-poverty that has occurred in East Asia.

To Americans, and Mexicans as well, 1990 wasn’t a different land. But in the past generation nations like China and Vietnam have transformed themselves in ways that we can’t even imagine.

David Burbridge’s 10 questions for A. W. F. Edwards In 2006

A few years ago I watched a documentary about the rise of American-influenced rock music in Britain in the 1960s. At some point, one of the Beatles, probably Paul McCartney, or otherwise Eric Clapton, was quoted as saying that they wanted to introduce Americans to “their famous people.” Though patronizing and probably wrong, what they were talking about is that there were particular blues musicians who were very influential in some British circles were lingering in obscurity in the United States of America due to racial prejudice. The bigger picture is that there are brilliant people who for whatever reason are not particularly well known to the general public.

This is why I am now periodically “re-upping” interviews with scientists that we’ve done on this weblog over the past 15 years. These are people who should be more famous. But aren’t necessarily.

In 2006 David Burbridge, a contributor this weblog and a historian of things Galtonian, interviewed the statistical geneticist A. W. F. Edwards. Edwards was one of R. A. Fisher’s last students, so he has a connection to a period if history that is passing us by.

I do want to say that his book, Foundations of Mathematical Genetics, really gave me a lot of insights when I first read it in 2005 and began to be deeply interested in pop gen. It’s dense. But short. Additionally, I have also noticed that there is now a book out which is a collection of Edwards’ papers, with commentaries, Phylogenetic Inference, Selection Theory, and a History of Science. Presumably, it is like W. D. Hamilton’s Narrow Roads of Gene Land series. I wish more eminent researchers would publish these sorts of compilations near the end of their careers.

There have been no edits below (notice the British spelling). But I did add some links!

David’s interview begins after this point:

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Learning from cultural anthropology as opposed to unlearning from cultural anthropology

On my other weblog one of the commenters, who I have nicknamed Syme (others call him Bentwig), proudly boasts about his training anthropology. Those who know me personally are aware that for me this is often a red flag for an individual who is willing to furiously declare that up is down if Edward Said stated that this was so in a footnote somewhere, or that black is the palest color if Michel Foucault averred this offhand in an interview. I exaggerate in the generality, though in the case of Syme/Bentwig there is a common tendency to proudly attempt to forestall arguments with comments of the form “Edward Said said….” or “According to Foucault.”

Of course, arguing from the authority of others isn’t always bad…but with far too many people with undergraduate anthropology backgrounds seem to engage in this sort of argument-by-citation and refutation-by-declaration-of-theory. Perhaps a contrast of interest are people educated in philosophy. There’s not much they know in thick detail, but they often exhibit analytic acuity when presented with startling and novel information. In contrast, many people with anthropological training may express befuddlement and then proceed to fury when confronted with facts which are outside of their domain and foreknowledge.

Enough punching down. Alex Mesoudi, a scholar in the field of cultural evolution, is publishing book chapters as preprints. The author of Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences, Mesoudi’s first submission, The study of culture and evolution across disciplines, should be read by anyone who is interested in the material on this weblog.

Mesoudi reviews the history of the field, from the rise and fall of human sociobiology in the 1970s to the birth of evolutionary psychology in the 1980s, and the gradual but consistent waxing of lesser-known disciplines such as cognitive anthropology and human behavioral ecology (out of which comes cultural evolution). A consistent binding feature of these disciplines is that they attempt to understand human cultural expression as a function of naturalistic processes, in particular, evolutionary ones. This is in contrast to the shift away from analysis to interpretation and description in much of cultural anthropology across the same time period, with the ultimate secession of much of the field from “science.” If you want to read a good primer on the division between scientific and non-scientific anthropology, I recommend Dan Sperber’s Explaining Culture or the anthropological introduction to D. Jason Slone’s Theological Incorrectness. Scott Atran also tackles the issue in In Gods We Trust. The reason this is necessary is that to understand and take in cognitive anthropology, you often need to unlearn or dampened tics obligate in cultural anthropology.

The flight of much of American cultural anthropology from crisp and powerful analytic frameworks, and toward linguistic obscurantism, to me explains the relative poverty of cognition of those students with only an undergraduate training. Without field-work and graduate courses and reading there’s not even the ability to obtain the deep knowledge required to enable feats of “thick description.”

In any case, the genius of the tradition in which Mesoudi operates under is that it allows for powerful analysis and prediction of cultural patterns and dynamics. Using similar formal frameworks, the idea is to do to culture what population genetics has done to biological evolution: produce a machine to generate predictions and test them with empirical data.

Here’s a taste of how researchers in this field think of “cultural patterns”:

Boyd and Richerson (1985) developed models showing that transmitted culture is favored when environments change moderately quickly, too fast for genes to track, but not so fast that the culturally transmitted behavior is out of date (see also Aoki et al., 2005). Transmitted culture also evolves when individual learning is costly (Boyd and Richerson, 1985). Under such conditions, however, social learning evolves but does not increase the average fitness of the population. This phenomenon became known as “Rogers’ paradox” after Alan Rogers, the first person to clearly point it out (Rogers, 1988). The fact that social learning does not enhance average population fitness is not inherently paradoxical, but does contradict the common claim that humans are so ecologically and demographically successful because of transmitted culture.

Rogers’ paradox occurs because the success of social learning is frequency-dependent. When rare, social learners do well because they forego the costs borne by individual learners. But when common, and environments change, social learners will be copying other social learners’ out-dated information. At equilibrium, social and individual learners have equal fitness, which will be equal to the fitness of a population entirely composed of individual learners (which is fixed, because their learning is not dependent on others). Thus, social learning evolves, but does not enhance fitness in a way that could be described as the ‘secret to our success’.

Two small quibbles with the chapter. First:

Bouckaert et al. (2012) reconstructed the cultural evolutionary history of the Indo-European language family, finding that it originally spread along with farming practices from present-day Turkey around 8,000 years ago.

Bouckaert et al. used valid phylogenetic methods, but it seems quite clear that these models have difficulty predicting the protean and punctuated character of many population expansions, which reshape the distribution and relationship of languages. Since 2012 a substantial amount of ancient DNA work has strongly pointed to the likelihood that the distribution of extant Indo-European languages in Europe is due to an expansion out of the Pontic steppe 5,000 years ago (with later secondary migrations into Southern Europe after 4,000 years ago). Though the Anatolian origin may still be preserved if one argues that the Pontic expansion was a secondary one, clearly most of the diversification of the Indo-European languages occurred in the period between 3000 and 1000 BC, in a 2,000-year radiation. The “Indo-European question” ultimately showed to me the limitations of phylogenetic methods because they are sensitive to particular assumptions within the model (e.g., continuous endogenous demographic expansion).

Second:

Note that this is different to Wilson’s (1976) earlier speculations that genetic differences might explain behavioral differences between groups of people. Tooby and Cosmides explicitly disavowed this, instead arguing that people everywhere are genetically far too similar to explain any behavioral variation directly (which concurs with modern genetic data: Feldman, 2014). Genes instead generate a set of universal responses to predictable environmental variation.

Considering the very rapid changes in cultural types across time and between closely related lineages, it seems hard to credit that most behaviorally based cultural variation is due to genetic variation (e.g., walk down a street in Finland and walk down a street in Italy, and see how differently the comportment of the typical passerby is). But, it seems quite possible, probably likely, that there are going to be some behavioral differences due to different distributions in polygenic quantitative traits. The question is more the extent of magnitude. That will depend on the phenotype and between population pair.

Also, there is clearly variation within the cultural evolution community on this issue. I know this from personal communication. Joe Henrich admits the possibility in The Secret of Our Success, without taking a position.

But, with those quibbles out of the way, go and read The study of culture and evolution across disciplines. I think it’s great that Mesoudi is putting out preprints for his book chapters. Makes his research accessible, and this is one field where more publicity would be good (shout out to Paul Smaldino, who apparently inspired Mesoudi on this track).

On the whole genomics will not be individually transformative…for now

A new piece in The Guardian, ‘Your father’s not your father’: when DNA tests reveal more than you bargained for, is one of the two major genres in writings on personal genomics in the media right now (there are exceptions). First, there is the genre where genetics doesn’t do anything for you. It’s a waste of money! Second, there is the genre where genetics rocks our whole world, and it’s dangerous to one’s own self-identity. And so on. Basically, the two optimum peaks in this field of journalism are between banal and sinister.

In response to this, I stated that for most people personal genomics will probably have an impact somewhere in the middle. To be fair, someone reading the headline of the comment I co-authored in Genome Biology, Consumer genomics will change your life, whether you get tested or not, may wonder as the seeming contradiction.

But it’s not really there. On the aggregate social level genomics is going to have a non-trivial impact on health and lifestyle. This is a large proportion of our GDP. So it’s “kind of a big deal” in that sense. But, for many individuals, the outcomes will be quite modest. For a small minority of individuals, there will be real and important medical consequences. In these cases, the outcomes are a big deal. But for most people, genetic dispositions and risks are diffuse, of modest effect, and often backloaded in one’s life. Even though it will impact most of society in the near future, it’s touch will be gentle.

An analogy here can be made with BMI or body-mass-index. As an individual predictor and statistic, it leaves a lot to be desired. But, for public health scientists and officials aggregate BMI distributions are critical to getting a sense of the landscape.

Finally, this is focusing on genomics where we read the sequence (or get back genotype results). The next stage that might really be game-changing is the write revolution. CRISPR genetic engineering. In the 2020s I assume that CRISPR applications will mostly be in critical health contexts (e.g., “fixing” Mendelian diseases), or in non-human contexts (e.g., agricultural genetics). Like genomics, the ubiquity of genetic engineering will be kind of a big deal economically in the aggregate, but it won’t be a big deal for individuals.

If you are a transhumanist or whatever they call themselves now, one can imagine a scenario where a large portion of the population starts “re-writing” themselves. That would be both a huge aggregate and individual impact. But we’re a long way from that….

The Philippines as a postcolonial exemplar: out of wedlock birthrates

Edward Said’s Orientalism was a book I first read in the fall of 2001. I recall not being too impressed and finding simple historical errors in it. But mostly it bore me. I am now rereading it because in 2018 the book is far more relevant to our current American culture, if not the world in a real sense. That’s because Orientalism is one of the most influential and seminal works in the field of postcolonialism (and to be frank, it seems more comprehensible than the stuff written by Gayatri Chakravorty Spivak).

At some point, I may put down into a post my thoughts on Orientalism. But long-time readers are familiar with my position that postcolonialists, and most progressive Westerners, overemphasize the importance of the colonial in most non-Western societies. But this is not the same as saying the colonial is not important, and, that the colonial does not affect different societies in varied ways.

The Philippines is the mostly large majority Christian country in Asia. It is predominantly Roman Catholic, though like many Catholic nations it’s religiosity is declining. The brutal and blunt current president of the country has had some harsh things to say about the Church.

I bring up the Philippines because in comparison to other Southeast Asia nations it seems clear that it is a creature of colonialism. A hybrid of Western and Asian values that is somewhat out of place. The French influence Vietnam is undeniable, but fundamentally Vietnam remains part of the broader Sinic cultural sphere, as it was before the rise of Europe. This is not so with the Philippines, which was in the early stages of Islamicization when the Spaniards arrived and had only been lightly impacted by Indic civilization in comparison to Java or the Austronesian kingdom of the Chams in mainland Vietnam.

One of the most striking things to me is that more than half of the babies in the Philippines are now born out of wedlock. This is an exception within Asia and even Southeast Asia.

There is one set group of nations which has long had high rates of out of wedlock births: those of Latin America. My reading of the ethnography indicated that this is partly a function of the fact that Iberian males entered into de facto polygynous family relationships early on during the conquest of the New World. And, unlike some other European nations, “natural children” did have some customary rights in Spanish law. Hernan Cortes had two sons with the name Martin. One of them was a mestizo, the product of a relationship with an indigenous woman of New World. The other was the legitimate offspring with Cortes’ aristocratic Spanish wife.

Though Martin Cortes, known as “El Mestizo,” did not have the rights of his brother, he was still provided for. He fought in Central Europe for the Habsburgs, and married and had children.

This pattern of giving some rights and consideration to illegitimate children has been argued as a major reason for the high rates of out of wedlock birth in much of Latin America today. But, the problem with this model is that the number of Spaniards in the islands of the Phillippines was always far lower than in the New World. Demographically they made a marginal impact, and in fact, the Chinese were more numerous.

But it remains the case that Spanish colonial regimes in environs as distinct as the Philippines and the New World left a legacy of high rates out of wedlock births. It could be coincidental, but I doubt that. Scholars genuinely interested in the impact of exogenous colonial shocks should be exploring these cross-cultural patterns theoretically and empirically, not engaging in abstruse linguistic analysis or deploying Theory toward the ends of particular politics.