Open Thread, 9/30/2018

A new shirt, Vaccines Cause Adults. I think that’s pretty funny. Since I don’t have that sort of human, it wasn’t my idea. Obviously, Photo 51 t-shirts are still on the  DNAGeeks website.

Patrick Wyman does not recommend The Silk Roads: A New History of the World. The killer observation for me is that whenever Patrick knew a lot about the topic the author was kind of wrong or off. This is an incredibly important sign for me. If you don’t have this still, you probably need to get to a point where you know enough about a topic. Just pick one, any topic. Additionally, he observes that 40% of the book deals with 20th and 21st century history. That’s also a big no-no for me. Contemporary history is well covered in our society. We have a presentism bias.

On the other hand, I would recommend Empires of the Silk Road. Christopher I. Beckwith is kind of cranky, but he’s learned and interesting.

Valerie Hansen’s The Silk Road: A New History is one I’d also recommend. It’s more focused on archaeology and the earlier period before 1000 AD. Hansen also lacks the long narrative ambition of Beckwith’s treatment, but if you want to know how Sogdian merchants rolled during the Tang dynasty, this is for you.

Buddhism and Islam on the Silk Road is also a good book, though its focus is rather narrow.

Lee Jussim asked on Twitter what counts as “white” today since so much social justice discourse (SJD) revolves around the concept. My response is basically “white” is what is necessary for you to win an argument (though another element now is that if you are Muslim you are not white, no matter how white you look, just like if you have a Spanish surname, you are not white either somehow). Here is how it works:

Italians are white: the ancient Romans were white people who oppressed and executed a marginalized person of color, a brown Palestinian named Jesus.

Italians are not white: Until after World War II Italians were actually not viewed as white, and had to “become white” (or, they had to become people who think they are white). They were even lynched!

The takeaway is that sophism is a feature, not a bug. That’s why I’m so good at faking this discourse.

He’s trolling us.

Global alliances and wheels within wheels. Talking about the concern that American Leftists have about Hindu nationalism. Though they seem sanguine about Islamism.

John Horgan interviews Bob Trivers in Jamaica. As usual with Trivers, it’s crazy. Though if you read his autobiography, Wild Life, there’s a lot that’s similar.

Of all Trivers’ books though, I would really recommend Natural Selection and Social Theory: Selected Papers of Robert Trivers. There’s a lot of science and biography in that work. Anecdotes about W. D. Hamilton in particular I enjoyed.

Variation in actual relationship as a consequence of Mendelian sampling and linkage.

What’s China’s new luxury status symbol? A curvy butt. Had a conversation with a friend who is a businessman in China. His female employees have butt-workout apps.

Gen­ome-edit­ing scis­sors will re­volu­tion­ise plant breed­ing, yet a pro­fessor fears EU countries will get side-tracked.

Margins – Save, annotate and share your papers with anyone.

An Empirical Demonstration of Unsupervised Machine Learning in Species Delimitation. The title is kind of weird. STRUCTURE? Also, I don’t really believe in automatic species delimitation. But it’s an effort.

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders.

Reproductive Longevity Predicts Mutation Rates in Primates.

Stronger and higher proportion of beneficial amino acid changing mutations in humans compared to mice and flies. I think I’ll blog this.

Reihan Salam has a new book out, Melting Pot or Civil War?: A Son of Immigrants Makes the Case Against Open Borders. The title is a bit overwrought, but Reihan is not. Obviously we share a lot in terms of our backgrounds and our opinions. And on questions regarding assimilation we’ve been on the same page for a long time.

Sexual selection, environmental robustness and evolutionary demography of maladapted populations: a test using experimental evolution in seed beetles.

The Blank Slateism of the Right. This is really about the Anglo-Right. American conservatives who come out of the liberal tradition are big fans of John Locke. That should tell you all that you need to know.

Robert Plomin’s Blueprint: How DNA Makes Us Who We Are is coming out soon. To be honest it looks like an updated version of Judith Rich Harris’ The Nurture Assumption.

Greg Cochran wrote up a review in Quillette with the expected title, Forget Nature Versus Nurture. Nature Has Won. Nathan Comfort in Nature wrote Genetic determinism rides again.

Stuart Ritchie was not happy with Comfort’s review:

The review is as bad as you’d think. He doesn’t seem to know the science, but that’s a feature, not a bug, for the sort of review he’s going to give. It’s useful for me because I can note who retweets and “likes” the review, as these are people who I will ignore on all things genetics indefinitely.

A bigger question that I asked a few liberal academic friends: with all the concern over eugenics where’s the widespread objection among the usual hand wringers about noninvasive prenatal testing and widespread abortion of fetuses that test positive for Down Syndrome? In the Nordic countries nearly 100% of fetuses which test positive are aborted. In France about 75%. In the United states 70%.

My personal suspicion is that academics are much more concerned about future and vague eugenical specters. Not those activities done freely and through the proactive choice of people of their own class and likely liberal politics. Burn a few Robert Plomin’s at the stake, but make sure you don’t jeopardize your colleagues’ dreams of having a “healthy” baby.

Overlooked factors in the analysis of parole decisions. Basically it looks like the old result that judges are harsher before lunch is an artifact of who is seen before lunch (prisoners without attorneys tended to be seen before lunch).

Unless I have looked at the original study, I’m starting to just shy away from retelling results published through peer review. Studies really need to have sample sizes in the title. Small sample sizes are OK in some contexts, but so often they are used to get away with stuff.

The shadow of the Ice Age

As ancient DNA becomes a more standard part of archaeological science it’s going really yield up some doozies. You’ve probably read Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, and how it’s upended old paradigms. But with the human past we probably have a better idea of the range of possibilities. When it comes to other organisms it’s going to be a weirder and wilder ride I predict.

This is why a new preliminary result does not shock me, Ancient Japanese wolf may be rare remnant of ice age wolves:

The wolf’s DNA more closely resembled that of a long-extinct wolf that lived in Siberia more than 35,000 years ago than that of living Eurasian and American wolves, Niemann reported here on Friday at the International Symposium on Biomolecular Archaeology. Most ancient wolves went extinct when the ice sheets that covered the Northern Hemisphere began to melt more than 20,000 years ago and the large mammals the wolves hunted, such as mammoth, died off. But some of their DNA lived on in the Honshū wolf, which could offer a new window on the evolution of wolves as well as dogs, says paleogeneticist Mikkel Sinding of the Greenland Institute of Natural Resources in Nuuk, who extracted the DNA.

Unfortunately the last Honshu wolves were killed more than a century ago. But for the purposes of DNA extract that’s basically yesterday.

From everything I can see the “megafauna” that inhabit the Palearctic ecozone seem to have through a lot of mass extinctions over the last 50,000 years. This extends from Neanderthals, to mammoths, to large canids and felids. Some lineages, such as that of humans and wolves, also underwent expansions from the remaining branches of the phylogenetic tree. But it’s reasonable that various relic groups of earlier diversifications might persist here and there.

China is what you get if your civilization never gets amnesia

The author of Early China: A Social and Cultural History occasionally engages in asides which analogize his own domain of study to other societies and histories. In the process, he illustrates how China is in some ways nonpareil.

When discussing the emergence of philosophical thinking during the Spring and Autumn Period there is a connection made to the same process occurring in India and Greece. It is suggested that during this period the memories of the older Bronze Age world were fading, and in the chaos, new ideas and strictures were arising. The problem is that in fact there is no analogy between the Chinese recollection of their own past, and that of India and Greece.

Homer and Hesiod both lived in the period after the Greek Dark Ages, which lasted from about 1100 to 800 BC. Though the oral history did preserve important fragments of knowledge from the Mycenaean period (e.g., the importance of the Argolid and the distinctive boar’s head helmets), enough was forgotten that the Greeks were not entirely clear that the citadels constructed during the Mycenaean period were in fact constructions of their ancestors. The loss of literacy meant there was no institutional connection to the past, and when Linear B was deciphered most archaeologists were surprised that it was an archaic form of Greek.

For India, the connections are even more tenuous and vague. The Mycenaeans seem to have created a synthetic civilization, repurposing Minoan high culture toward their own ends. But, they were also clearly Greek, with many of their gods being the same gods that we recognize from the Classical era. In Early China the author implies that the people of 6th century India may have had some memory of the Indus Valley Civilization. Though it is likely some elements of culture were passed down from that period, no institutional memory seems to have persisted, in large part because of the likely cultural shock of the arrival of Indo-Aryans around 1500 BC.

The contrast with China here is strong. In Early China the author talks about the Doubting Antiquity School, which was skeptical of the veracity of Chinese historical memory before the Qin period 2,300 years ago. Today, due to archaeology, analysis of inscriptions on bronze vessels, as well as the famous oracle bones, it is clear that historians such as Sima Qian had access to cultural memory that went back at least 1,000 years. The Shang dynasty, once thought to be legend, clearly existed. Names of kings retrieved from the oracle bones matche those provided by classical sources, including their sequence of reigns.

We know that in 1046 the Zhou defeated the Shang. Because of a planetary alignment anomaly the month and date are even remembered.

Which brings us to the Erlitou culture. This archaeological culture flourished in broadly the same region as the Shang dynasty polity, but earlier. The author of Early China contends that this was likely the Xia dynasty. Though we will never be able to validate this in all likelihood, as there are no known forms of writing from this society, we can assume just as with the Shang the legends of the Xia probably have some basis in fact (eventually ancient DNA will accept or reject demographic continuity).

Read More

The sons of Japeth divide the world between them

Most “old hands” in the discipline of historical population genetics remember when grand narratives were constructed out of Y chromosomal haplogroup distributions. One of the most distinctive ones is that of haplogroup R1b, which exhibits very high frequencies in the west of Europe, as high as more than 80% among the Basques. Because the Basques are the only non-Indo-European population which exists today in Western Europe, it was presumed that they are more ancient than other groups. And, their high frequency of R1b (along with other peculiarities such as a high frequency of Rh-), was taken to indicate that they reflected the genetics of Europe’s aboriginal hunter-gatherers when farming arrived.

This turned out to be wrong in a lot of details. Genetically the Basques are quite like the European farmers from Anatolia who replaced the original hunter-gatherers. Less so than the Sardinians, as they have more hunter-gatherer ancestry. But instead of being the language of European hunter-gatherers, it seems plausible that the Basque language descends from that of the Cardial culture.

Read More

Muslims are not a People of the Book

Recently I became a patron of the Secular Jihadists podcast. Ten years ago this wouldn’t be a big deal, but as a “grown-up” with three kids I’m much more careful to where I expend my discretionary income. So take that as a stronger endorsement than usual. I think Secular Jihadists is offering a nonsubstitutable good today. By which I mean a robust, but not cliched or hackneyed, critique of the religion of Islam. For various reasons the modern-day cultural Left has become operationally Islamophilic in public, while the political Right isn’t really too concerned with details of fact and nuance when they level critiques against Islam.

On this week’s episode, the hosts talked about the life of Muhammad, focusing some of the rather unpalatable aspects of his biographies as they’ve been passed down in tradition (in the Hadiths), or as can be found in the Koran. Armin Navabi points out that the prophet of Islam married Safiyya bint Huyeiy Ibn Akhtab on the day her father and husband were killed by his forces. Therefore Navabi’s interpretation, which is entirely in keeping with our modern values, is that Muhammad raped a woman on the day her father and husband were killed.

Of course, this behavior is not shocking in the pre-modern world. In the Illiad Hector’s widow, Andromache, eventually becomes the concubine of Neoptolemus. He is the son of Achilles, who killed Hector. And, in many traditions, Neoptolemus is the one who kills Andromache’s infant son by Hector, Astyanax. Eventually, the son of Neoptolemus by Andromache inherits his kingdom.

Obviously, the Illiad plays things up for drama, but I think it correctly reflects the values of a pre-modern tribal society. One of my favorite books is Jonathan Kirsch’s The Harlot by the Side of the Road: Forbidden Tales of the Bible. Like the Illiad, the Hebrew Bible has within it stories that reflect values of pre-modern societies very different from ours. Moses, like Muhammad, was a military and political leader as well as a religious prophet, and so it is entirely unsurprising that he was a participant in and director of what we would today term war crimes.

The question from the perspective of the hosts of the Secular Jihadists podcast is how Muslims will react to the fact that in the Koran itself, which most Muslims take to be the literal recitation of the words of God through Muhammad, documents the founder of the religion engaging in sex and war crimes. I think the truth though is that most Muslims won’t be very impacted by these revelations, because for most Muslims Islam is not reducible to the revelation within the Koran.

“Higher religions” tend to have scriptures and texts which serve as the scaffold for their intellectual superstructure. But most people who believe in these religions never read these texts. That’s because most people don’t read much, period. The organized institutional and multi-ethnic religions which have emerged over the last 3,000 years have a complex division of labor among the producers of religious “goods and services”, as well as among the consumers and identifiers. A minority are highly intellectualized, and these are the types who will record the history of the religion.

Read More

Do the northern Chinese have Scythian ancestors?

There was some question regarding possible Scythian admixture into the early Zhou below. This is possible because of the Zhou dynasty, arguably the foundational one of Chinese imperial culture (the Shang would have been alien to Han dynasty Chinese, but the Zhou far less so), may have had interactions with Indo-European peoples to their north and west. This has historical precedent as the Tang dynasty emerged from the same milieu 1,500 years later, albeit the Tang were descended from a Turkic tribe, not Indo-Europeans.

I looked at some of my samples and divided the Han into a northern and southern cluster based on their position on a cline (removing the majority in between). I also added Lithuanians, Sardinians, Uyghurs, Mongols, and Yakut. As you can see on the PCA the Mongols are two clusters, so I divided them between Mongol and Mongol2.

Read More

Vietnamese are not that much like the Cambodians

A comment below suggested another book on Vietnamese history, which I am endeavoring to read in the near future. The comment also brought up issues relating to the ethnogenesis of the Vietnamese people, their relationship to the Yue (or lack thereof) and the Khmer, and also the Han Chinese.

Obviously, I can’t speak to the details of linguistics and area studies history. But I can say a bit about genetics because over the years I’ve assembled a reasonable data set of Asians, both public and private. The 1000 Genomes collected Vietnamese from Ho Chi Minh City in the south. I compared them to a variety of populations using ADMIXTURE with 5 populations.

Click to enlarge

You can click to enlarge, but I can tell you that the Vietnamese samples vary less than the Cambodian ones, and resemble Dai more than the other populations. The Dai were sampled from southern Yunnan, in China, and historically were much more common in southern China, before their assimilation into the Han (as well as the migration of others to Southeast Asia).

Curiously, I have four non-Chinese samples from Thailand, and they look to be more like the Cambodians. This aligns well with historical and other genetic evidence the Thai identity emerged from the assimilation of Tai migrants into the Austro-Asiatic (Mon and Khmer) substrate.

Aside from a few Vietnamese who seem Chinese, or a few who are likely Khmer or of related peoples, the Vietnamese do seem to have some Khmer ancestry. Or something like that.

Read More

The lineage of the ancient sage kings

After recording the “India genetics” podcast for The Insight and reading Early China: A Social and Cultural History, I wonder what surprises we’re going to get from China from ancient DNA when it comes online. If there is one thing we are learning by looking closely at DNA, modern and ancient, it’s that at least for humans there are very few ‘primal’ populations from the “Out of Africa” event which haven’t been threaded together from pulse admixtures of continuous gene flow across the landscape.

Early China makes it clear that Erlitou culture which dates from ~1900 to 1500 BC was almost certainly the legendary Xia dynasty. This means that the ethnogenesis of the modern Han Chinese probably dates to the latest ~4,000 years ago. This is centuries before the Indo-Aryans were likely arriving in South Asia, and around the same time that Indo-European groups were pushing into peninsular Southern Europe.

The Y chromosome data does not indicate a Bronze Age ‘star phylogeny’ expansion in East Asia that I know of, so the dynamics were not entirely similar to Western Eurasia. But, it seems quite plausible that the Han themselves are not a chrysalis from the late Pleistocene.

Read More

A clash of civilizations along the lower Mekong

The lower Mekong region is a fascinating zone from the perspective of human geography and ethnography. Divided between Cambodia and Vietnam, until the past few centuries it was, in fact, part of the broader Khmer world, and historically part of successive Cambodian polities. Vietnam, as we know it, emerged in the Red River valley far to the north 1,000 years ago as an independent, usually subordinate, state distinct from Imperial China. Heavily Sinicized culturally, the Vietnamese nevertheless retained their ethnic identity.

Vietnamese, like the language of the Cambodians, is Austro-Asiatic. In fact, the whole zone between South Asia and the modern day Vietnam, and south to maritime Southeast Asia, may have been Austro-Asiatic speaking ~4,000 years ago, as upland rice farmers migrated from the hills of southern China, and assimilated indigenous hunter-gatherers.

But the proto-Vietnamese language was eventually strongly shaped by Chinese influence. This includes the emergence of tonogenesis. Genetically, the Vietnamese are also quite distinct, being more shifted toward southern Han Chinese and ethnic Chinese minorities such as Dai. My personal assumption is that this is due to the repeated waves migration out of southern China over the past few thousand years, first by Yue ethnic minorities, and later by Han Chinese proper. Many of these individuals were culturally assimilated as Vietnamese, but they clearly left both their biological and cultural distinctiveness in what was originally an Austro-Asiatic population likely quite similar to the Khmer.

As I have posted elsewhere it is also clear to me that Cambodians have Indian ancestry. Because unlike Malaysia Cambodia has not had any recent migration of South Asians due to colonialism, the most parsimonious explanation is that the legends and myths of Indian migration during the Funan period are broadly correct. There is no other reason for fractions of R1a1a among Cambodian males north of 5%. Depending on how you estimate it, probably about ~10% of the ancestry of modern Cambodians is South Asian (the Indian fraction is easier to calculate because it is so different from the East Asian base).

Read More

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.