Open Thread, 02/02/2020

Spider biologist denies suspicions of widespread data fraud in his animal personality research. There is a lot more talk on backchannels than you see in this piece, partly because until the full investigation is complete people don’t feel comfortable airing suspicions and rumors. But, it is likely to get worse before it gets better from everything I hear.

Last week a friend in psychology asked whether this was similar to Diederik Stapel. I said at the time that it wasn’t that bad, but I’m really not sure anymore.

Is It Fair to Award Scholarships Based on the SAT? Being WSJ the piece at least mentions Asians. “Worcester Polytechnic Institute in Massachusetts stopped using the test for merit scholarships last year, said Andrew Palumbo, dean of admission. Instead, the school is weighing grades, community service and leadership.” Biased against Asians, since it is known Asians lack “leadership.” Also, grades will basically disappear as a useful measure since all mostly pre-college prep high schools will be under pressure to give good grades. As for community service, which economic class has the most time for this?

Not Born Yesterday: The Science of Who We Trust and What We Believe. I quite enjoyed the last Mercier book, The Enigma of Reason.

I would appreciate more positive reviews for The Insight on Apple Podcasts. This week we’ll be posting an episode I recorded with Anders Bergstrom on the genetics of New Guinea.

Her Uighur Parents Were Model Chinese Citizens. It Didn’t Matter.

Family History Assessment Significantly Enhances Delivery of Precision Medicine in the Genomics Era.

Phylogenetic signal is associated with the degree of variation in root-to-tip distances.

Integration of polygenic risk scores with modifiable risk factors improves risk prediction: results from a pan-cancer analysis.

Global reference mapping and dynamics of human transcription factor footprints.

I got Coalescent Theory about five years ago. Finally starting to go through it.

Genomic novelty versus convergence in the basis of adaptation to whole genome duplication.

Chiefs Defeat 49ers in Stunning Super Bowl Comeback. Twenty years ago I would have cared because the Steelers still have more wins than the 49ers.

I haven’t been tracking the impeachment or coronavirus since I don’t think they’ll seem too consequential in a few years.

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The details of Eurasian back-migration into Africa

Carl Zimmer has an interesting write-up on the new method to detect Neanderthal ancestry in Africa, Neanderthal Genes Hint at Much Earlier Human Migration From Africa. There are two quotes from researchers that are of note.

First, from David Reich:

Despite his hesitation over the analysis of African DNA, Dr. Reich said the new findings do make a strong case that modern humans departed Africa much earlier than thought.

“I was on the fence about that, but this paper makes me think it’s right,” he said.

It’s possible that humans and Neanderthals interbred at other times, and not just 200,000 years ago and again 60,000 years ago. But Dr. Akey said that these two migrations accounted for the vast majority of mixed DNA in the genomes of living humans and Neanderthal fossils.

Over the years I have had several discussions with members of the Reich lab about whether there was a major migration of the antecedent lineage of modern humans before the one that we detect 60,000 years ago. Many were quite skeptical because of the lack of clear genetic signal of anything before 60,000 years ago, as well as its correlation with a strong archaeological record. But, it seems now that David Reich at least is convinced that the evidence of admixture into Neanderthals means that there were descendants of the same lineage that led to the major “Out of Africa” expansion 60,000 years ago who had spread earlier (though the footprint was small, and their impact on later humans difficult to detect).

Second, Sarah Tishkoff says something that I forgot to mention in my earlier post:

Sarah Tishkoff, a geneticist at the University of Pennsylvania, is doing just that, using the new methods to look for Neanderthal DNA in more Africans to test Dr. Akey’s hypothesis.

Still, she wonders how Neanderthal DNA could have spread between populations scattered across the entire continent.

The second part isn’t that inexplicable. In the paper, they mention that they don’t have the power to analyze small sample numbers. So they focused on the 1000 Genomes samples, which are from West and East Africa. From agriculturalist and agro-pastoralist populations. If you listen to this week’s episode of The Insight Spencer and I talk extensively about the recent agriculturally mediated expansions within Africa. Much of the genetic landscape of the continent is novel, new, and of short historical time-depth. The Africa of Old Kingdom Egypt, 4,500 years ago, was very different.

As hinted by Tishkoff the key is going to be when we get samples from hunter-gatherers. Some of these have much lower Eurasian affinities, and likely they’ll carry less Neanderthal ancestry.

On a final note, this paper and the first author, Joshua Akey, hints at some resolution in the interminable disagreement about continuous gene flow vs. pulse admixture. Some of the methods to infer and detect admixture assume pulse admixture, and so our conception of the past has been skewed. On the other hand, I think it is plausible that in a patchy low population density Paleolithic landscape continuous gene flow may have been quite attenuated over long distances. Admixture then would occur when there were cultural revolutions and long-distance contact for short periods of time, before an equilibration. Basically, it’s some of both.

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Neanderthal ancestry in Africa and West Eurasian gene flow


A new (open access) paper in Cell, Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals, is making a big splash in the media. Whether you believe this paper on its own is conditional on how deeply you can grok the methods. Honestly I don’t know if I trust myself to render any judgment until I’ve replicated the whole analysis pipeline. Intuition doesn’t come from a priori.

That being said, in light of other factors and our general understanding of hominin gene flow this is a highly plausible result. They conclude that “A model that combines both of these events, elevated back migration and human-to-Neanderthal gene flow, matches the empirical data best across all features.” Gene flow from neo-African modern humans into Neanderthals seems very likely. Similarly, it is quite possible that there was widespread Eurasian back migration into Africa. But, that back migration was West Eurasian.

The “problem” with the older models is that it simply assumed that groups such as the Yoruba had no Neanderthal ancestry, presupposing a particular model of paleoanthropological gene flow where Africa is purely a source, rather than also a sink. Assume nothing!

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Liberal democracy as a balance between deontology and consequentialism

Not often I comment on politics as such, but this piece, The Joe Rogan controversy revealed something important about the American left, is more interesting than its title. The author basically suggests that the conflict is due to the fact that individuals switch between operating in a deontological or consequentialist framework, depending on the context.

As you surely know, deontology is the idea that you always have a duty to do the right thing, whether that right thing is convenient for you, or even for the world. To me, this is most evident once you become a parent. You can make a contrived utilitarian explanation for why you behave selflessly in relation to your children in a proximate sense (as opposed to ultimate evolutionary one), but really it’s that in their bones most people feel they have a duty to their children. As far as consequentialism, for Americans, I think we’re often told that the bombings of Nagasaki and Hiroshima hastened the end of the Pacific War.* The needs of the many outweigh the needs of the few.

Though the author doesn’t frame it this way, I think the deontological and consequentialism framework map onto the liberal and democratic strains of our republic. Liberalism is about rights, liberties. Humans as ends in and of themselves. Democracy is about the body politic, the aggregate will as opposed to individual preference. If you emphasize deontology too much in a democratic contest, I predict you’re likely to lose more often than not. If you emphasize consequentialism to the total exclusion of deontology, you lose the human dignity which democracy is supposed to safeguard.

The piece above brings up the cases of Colin Powell and Henry Kissinger, both of whom could be argued to have been party to and/or directed war crimes. Both these individuals have been associated with or had connections to contemporary members of the liberal-Left (Barack Obama and Hillary Clinton). Of more timely relevance, it is curious to me how neoconservative hawks such as Max Boot and William Kristol are now accorded some (often grudging) acceptance on the moderate Left. Not only did Boot and Kristol support the Iraq War, but they went along without too much objection to the economic positions of the Right up until recently. The question we have to face then is why is Joe Rogan such a problem, while these reformed conservatives are not?

It seems to me that the key here is that liberalism, the deontological impulse, has limits and scopes. Parents may act in a way that is governed by deontology in relation to their children, but the same people can be coldly utilitarian when it comes to strangers. American foreign policy is nasty and brutish. But the policies which Powell acceded to, Kissinger architected, and Kristol and Boot cheered, resulted in the death or misery of foreigners. Obviously even people on the center-Left object to the killing of foreigners, but operationally their empathy and identity are with people in their own nation-state (even if they espouse the rhetoric of no borders). Similarly, many of the loudest voices in “cancel culture” are from the middle-class and above. Though these people favor redistributionist policies, they may not concretely be familiar with people who have dealt with inter-generational poverty (as opposed to a stint as a ‘starving artist’ in one’s 20s). Offensive comments by a famous influencer are more impactful for such individuals than the removal of social services which few of their intimates use in any case.

One final thing in relation to deontology and consequentialism is that many on the moderate Left who are behaving in a deontological manner in relation to Joe Rogan’s endorsement of Bernie Sanders also assert that Donald Trump’s reelection in 2020 is an existential threat to the republic. If that is true, then I am curious about their deontological tendencies here, where they make the case that one shouldn’t give on some principles to gain votes. Perhaps the revealed preferences show that they don’t actually believe Trump to be an existential threat?

* I am aware people dispute this.

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Open Thread, 01/26/2020

I’ve been posting a fair amount about Southeast Asia. This an important part of the world. As outlined in Victor Lieberman’s Strange Parallels, there are similarities to Europe in terms of the ‘naturalness’ of nation-states. Especially in mainland Southeast Asia. Burma is dominated by Burmans. Thailand is dominated by Thais. Laos, but the lowland Lao. Cambodia by the Khmers. And Vietnam by the Kinh. Liberman’s hypothesis is generally geographical. He contends that the ‘protected’ geographic character of mainland Southeast Asia has analogs to Western Europe, which also was relatively sheltered by the impact of the Eurasian steppe.

One of the primary similarities between Europe and mainland Southeast Asia is that there is a combination of deep indigenous ethnocultural traditions as well as important external influences. Burma, Thailand, and Cambodia leverage Indian religious and political theory to maintain coherence. In contrast, Vietnam replicates much of the character of China. The “standard model” has been Indian influence is a function of “cultural diffusion.” But looking more deeply at the genetic data, it seems that 5-20% of the ancestry might be Indian. This is a minority element. But it is not trivial, especially in light of the likely dilutive effects of the Tai migration, as well as the Chinese in Thailand.

In Coronavirus, a ‘Battle’ That Could Humble China’s Strongman. One thing I will say is that public health professionals are focused on the tail risk. The risks are real. But please note that the worst-case scenario may not be the most likely scenario.

A Glittering Crossroads: In Damascus’s Umayyad Mosque, Roman paganism, Christianity, and Shiite and Sunni Islam all intersect. The Umayyad’s are Islam’s “first dynasty.” But they have a bad reputation among Muslims. The Shia hate them because their founder was an enemy of Ali, and eventually killed his grandsons. The Sunnis dislike them because they are perceived as impious Arab warlords, rather than Muslims. The latter view is colored by the commentaries of intellectuals who were patronized by the Abbassids, the successors of the Umayyads. But the piece above illustrates the reality that the Umayyads likely weren’t Muslims as we’d understand it for much of their history.

San Francisco Mayor London Breed endorses Mike Bloomberg for president. Weird.

The Saudi Connection: Inside the 9/11 Case That Divided the F.B.I. Money corrupts.

Medical data and machine learning improve power of stroke genome-wide association studies.

After Culinary and Literary Acclaim, She’s Moving to the Woods. ‘…every weekend from May to October, 10 people will each pay $750 to nearly $1,000 to relax in the woods and immerse themselves in what some chefs and writers have started calling “new gatherer” or “deep nature” cooking.’

Insight into the genomic history of the Near East from whole-genome sequences and genotypes of Yemenis.

Unrelated males in colonies of facultatively social bee.

Dynamic evolution of great ape Y chromosomes.

On the origin and evolution of RNA editing in metazoans.

Singer-songwriter David Olney dies on stage during performance at Florida festival.

Roger Scruton, a Provocative Public Intellectual, Dies at 75.

3000 years in the Levant, with Marc Haber. The Insight is cranking along.

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Indian ancestry maritime Southeast Asia

In the comments, people keep asking about Indonesia, and Java in particular. The reason is pretty simple: before wholesale conversion to Islam maritime Southeast Asia was dominated at the elite level by Indic social and religious forms. I say “Indic” because unlike mainland Southeast Asia Theravada Buddhism did not supplant other Indian religions, and in fact, while indigenous Buddhism that led to the Borobudur temple complex in the 9th-century went extinct, Hinduism persisted for quite a bit longer and persists to this day. Not only are there long-standing Hindu traditions in Bali, but far eastern Java remained a Hindu kingdom until 1770, and there remain Javanese Hindus (some of them are recent converts).

As several mainland Southeast Asian groups seem to have Indian admixture, what is the evidence for Indonesia? (the Singapore genome data offers up some Malays, and though some show recent Indian admixture, all of them have some Indian admixture). Luckily, there is a paper and data, Complex Patterns of Admixture across the Indonesian Archipelago. It uses the GLOBETROTTER framework, so I decided to reanalyze the data in a simpler manner, adding the Cambodians as a check (since from my previous posts you know a fair amount about that as a baseline).

Three points.

1) Definitely gene flow. But on the whole less than mainland Southeast Asia?

2) Lots of heterogeneity. Not surprising. The Sumatra samples seem to be taken from Aceh. This may matter a great deal.

3) In mainland Southeast Asia east of Burma there hasn’t been lots of colonial migration of Indians, nor a great deal of trade. The opportunities within maritime Southeast Asia for contact with outsiders are far greater. The inspection of results from Malaysia indicates continuous gene flow over a long period of time. In contrast, the results from Thailand and Cambodia indicate an early pulse.

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The Indian admixture into Southeast Asia is not just a function of distance

In the comments to the post below about Indian ancestry in Thailand, some observed that this should not be surprising due to reciprocal gene flow and proximity. Implicitly, I think what is being suggested here is that there is isolation by distance and continuous gene flow. Obviously some of this is true, but there details here which suggest that it is simply not just geography at work.

The reason I was curious about the Dusun people in coastal Borneo is that while Malays all seem to have Indian ancestry, many tribal Austronesian groups in maritime Southeast Asia do not. The Indian admixture into the Malays is not just recent. Some of it seems quite a bit older than the colonial period.

In the context of Southeast Asia, it seems that some of the more ancient Austro-Asiatic people, in particular, the Mon and Khmer, have Indian ancestry, and groups which mixed with Austro-Asiatic substrates, such as Burmans and Thai, also have this.

Additionally, some groups in the northeastern states of India have less “Indian” admixture than the Thai and Khmer. To show this, see this PCA:

Read More

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Thais may have more Indian ancestry than Cambodians and less than Burmese

Click to enlarge

There were some questions about the Indian ancestry of the Thai. The dataset released by the Reich lab has some Thai. I pulled that data, and some other Southeast Asian groups, and Tamils and Tajiks. The merging only left 62,000 SNPs, but that’s probably enough to answer this question. The PCA above shows the West Eurasian shift of some groups. The Thai definitely seem pulled to the Tamils, and are similar to the Cambodians, but with a bit more Indian ancestry and less “southern” Southeast Asian.

Below the fold are admixture and TreeMix plots. Basically you see what I’m talking about but in more detail. The Indian-like ancestry in the Luzon samples is really Spanish. The Ami and Atyal are Taiwanese aborigines. You see that they have the least West Eurasian ancestry. Even southern mainland Chinese seem to have some of that, indicating long-distance gene flow. But groups like Miao, Vietnamese/Kinh, and Dusun (Austronesians from Borneo) don’t the Indian ancestry that Thai/Lao/Cambodians/Malay have.

Read More

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A different time comes

When I was younger I read many of Frank Herbert’s Dune series of books. Though there was a notable decline after the first installment (or at least diminishing returns), I read the whole original series (and follow-ups), so I must have enjoyed it to some extent. I’m not really a completist, as such.

But an aspect of the world-building always bothered me.  The societies just seemed highly regressive, and that truly bothered me. My problem is best illustrated by the title of God Emperor of Dune. It struck me as almost sacrilegious that in the bright and shining future humans would still have emperors, whom they worshipped as gods. That they would organize themselves in such a hierarchical manner. The whole idea struck me as…Bronze Age!

“Everyone” knew, after all, that liberal democracy, and in particular the American flavor, was going to be the future. There would be changes on the margin, but the general structure which would allow humans to flourish had been established. We were at the end of history. We had figured out how best to be human.

As a young person, I simply did not reflect on the fact that every age, and every place, takes its own values and preoccupations for granted. And, people of every age and every place cannot imagine a different scenario. We are always at the center of the universe’s story, no matter who we are and where we are. But the reality is that no one truly has a privileged place. At some point, the eternal equilibrium will arrive. But not this day.

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All the commotion within Africa

Unless you’ve been asleep, you probably know by now that the Reich lab has come out with a paper that analyzes the remains of 4 individuals from western Cameroon, dating to 8,000 and 3,000 years ago (2 of each, with one of the older individuals yielding 18.5x coverage DNA!). The location and timing both matter.

This area of Cameroon is hypothesized to be the point of expansion for the Bantu migration. This expansion began about 3,000 years ago and swept east and south until the agricultural streams met back up in southern Africa.

Perhaps then the authors then “caught history in action” with a change between 8,000 and 3,000 years ago? No such luck actually. Here is the abstract, Ancient West African foragers in the context of African population history:

… One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region…However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

Basically, just like elsewhere in Africa where the Bantu expanded, you see massive discontinuity in this region of Cameroon (the modern agriculturalists in the area are Bantu-speaking). If you have ever analyzed African genetic data, the lack of high magnitude structure of the Bantu over wide areas is pretty shocking. The reason there’s little structure seems to be two-fold

  1. Rapid population expansion, so not much time to accumulate distinct variants (you see this in Northern Europe too)
  2. Minimal admixture with local populations, at least until you get to modern-day South Africa (then there is an admixture cline with Khoisan)

Meanwhile, you have these zones of relic hunter-gatherers here and there. These samples seem to be one of those cases. I think it’s analogous to the fact that hunter-gatherers persisted in pockets for thousands of years after the initial arrival of Neolithic farmers in Europe.

There are two types of things you can take away from a paper like this. General insights. And specific details. The plot at the top of this post illustrates a model that they generated with these data. It seems quite clear that the details are not crisp, and subject to a further specific revision. But the general insights seem robust and extend what we already knew.

First, there were several human lineages that diverged 500,000 to 1 million years ago. In Eurasia, these became Neanderthals and Denisovans. In Africa, one of the branches led to what we call “modern” humans. But a variety of lines of evidence indicate that within Africa there were also highly diverged human groups, analogous to Neanderthals and Denisovans. One could call them “African Neanderthal” analogs. But within the context of this paper, they are “ghost archaics.” But those aren’t the only “ghosts.”

Extant human populations sample only a fraction of the “modern” family tree, which seems to have diversified from one of the African human groups 300,000 years ago or so.

There is now a fair amount of circumstantial evidence that Neanderthals mixed with an African lineage that is an outgroup to most other Africans and descended-from-Africans. Because of its size and warm climate, I believe that Africa was quite a good habitat for humans, and there were a variety of them across the continent. Though I don’t discount deep-time back migration of Neanderthal/Denisovan groups into Africa, I think due to the different population sizes it is probably more the case that Africans went into western Eurasia than vice versa. Additionally, Southeast Asia seems to be a good target habit for any African species due to similarities of biome (e.g., Sundaland).

Finally, there is the fact that it seems non-African ancestry is closest to the Mota sample, dated to 4,500 years ago in Ethiopia. This makes geographic sense, though I do wonder if this is an artifact of continuous gene flow back from Eurasia, as much as the likelihood that this is near the exit path of African humans.

What about the details of this paper? Look a the supplements and notice all the admixture graphs. There are lots of potential fits to the data, and more data will come in. The paper is clear to not put too much faith in one set of weights for gene flows, and different graphs might explain the patterns in the data. Additionally, a highly dense African landscape of hominins might exhibit lots of continuous gene flow and isolation by distance. There’s a lot more to learn. Nothing is being closed in this case.

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