Open Thread, 10/2/2018

Posted on by Razib Khan

I’m reading Ramesh Menon’s The Mahabharata: A Modern Reading before I go to sleep. If you are ignorant, the Mahabharata is about an epic poem that’s an order of magnitude longer than the Iliad or The Odyssey combined. Menon’s prose rendering seems to get some good marks, so I that’s not why I chose it. It’s not the most artful writing, but that’s not what I was looking for, nor would I appreciate it in any case.

My rationale for reading this two-fold. First, as someone who was raised on Bulfinch’s Mythology and has read Genesis in dozens of translations, I thought it was behoove me to become a bit more culturally fluent about brown stuff. Especially in light of the fact that I’m “tagged” on a “Hindu Twitter” thread every few weeks now (12+ hard science disciplines apparently prove the Mahabharata happened 25,000 years ago!).

Second, the age of Indian historical population genetics is coming to an end. Perhaps ten years from now people will be doing temporal transects of eastern Maharashtra, but the bigger framework will be nailed down soon enough. And real intellectual understanding is going to have to synthesize archaeology and mythology with the demographic inferences.

The Urbane Cowboys podcast now has had three Bengali American conservatives on. #representation You should subscribe (I might be on again to talk about CRISPR soon).

Browncast #3. I talk about Indian genetics.

Does DNA Make Us Who We Are? Review of Blueprint: How DNA Makes Us Who We Are. A reader of this weblog shouldn’t find anything new in this book. There are some technical issues in this book you might pick up, as well as airbrushing out of Eric Turkheimer citation. But I left that stuff out of the review since regular people won’t care or understand.

Plomin is definitely an enthusiast on some counts. But most of the book covers his career and views on behavior genetics.

Why There Will Not Be a Beige Future: Skin Color, Genetics, Race and Racism. Written for an audience less familiar with genetics. You shouldn’t need to read this. But some of you still don’t know what the breeder’s equation is.

The New Evolution Deniers. I haven’t read this piece, but people keep asking me about it. Plenty of biologists have these sorts of views from what I can tell, but they’re never going to say a word.

So that’s why this battle is lost in my opinion. I don’t really care. American culture is now a battle between different groups of propagandists who manipulate the levers of power. The rest is commentary, and positivism and critical-rationalism are dead in the broader culture. They only persist in the “inner party” of the elect. Truth is the real conspiracy….

The Harlot by the Side of the Road: Forbidden Tales of the Bible. Good book.

I’ve been defending Marc Lamont Hill’s right to speak and express his views, and retain his professional positions. Mostly because “free speech” really doesn’t matter unless you kind of detest the views you are defending…. So I guess I’ m still delusional and not a realist. I contain multitudes.

Inside the chaos and corruption of Tripoli, where militias rule the streets. We violated the “Pottery Barn rule.”

Mountain lion genomes provide insights into genetic rescue of inbred populations.

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). Last author “Krause.” You’ll be seeing that a lot related to historical genomics from this group in the near future. Ancient DNA is cheap enough that it can be used to resolve historical questions as opposed to shedding light on prehistory.

Simulation of Karyotype Evolution and Biodiversity in Asexual and Sexual Reproduction.

Sex differences in gene expression in the human fetal brain.

The battle for the soul of the Heart of Asia

Posted on by Razib Khan

Kumārajīva was one of the early translators of the Buddhist canon into Chinese. His father’s lineage was reputedly Indian, while his mother was from the elite of the city of Kucha, on the northern edge of the Tarim basin. It was one of the cities where a form of Tocharian was spoken. This enigmatic Indo-European language family is extinct and known from only a few examples in this region of the world (the different forms of Tocharian seem to have been mutually unintelligible, suggesting a long history in this region of the world for these languages). But Tocharian was not the only Indo-European language group that was represented in the Tarmin. Along the southern and western edge of the Taklamakan Iranian dialects were more common, such as in the city of Khotan.

Over the last 1,000 years, the Tarim Basin has undergone major changes. First, the collapse of the ancient Uyghur Turk Empire resulted in their retrenchment to the Tarim Basin. A previously pastoralist people, they became settled city-dwellers. By the time Genghis Khan rose to power, the Uyghurs had become a predominantly Buddhist people, with a focus around Turpan. They seem to have absorbed the predominantly Tocharian city-states of the eastern portion of the Tarim Basin.

But after 1000 AD a second change began to occur. A group of Turks, who spoke a Karluk dialect, converted to Islam and conquered Kashgar in the west of the Tarim Basin, and began to push eastward, conquering and converting the Buddhist city-states in turn. By 1400 the cultural expansion and military conquest reached the eastern fringe of the Tarim Basin, as Turpan and Hami were absorbed into the Islamic cultural sphere. With this, a new identity unified the city-states of the Tarim Basin. In language they spoke Karluk dialects, and in religion they were Muslim. In the 20th century the Uyghur ethnonym was resurrected in what was known as East Turkestan, but the cultural descendents of the ancient Uyghurs are actually the Yugurs (whose traditional language descends from that of Old Uyghur). Read More

Going beyond WEIRD dichotomies-cultural anthropology with a genetical lens

Posted on by Razib Khan

From my 10 questions for Luigi Luca Cavalli-Sforza I asked him about the reaction of anthropologists to Cultural Evolution and Transmission, a book written in the late 1970s with Marcus Feldman:

I entirely agree that the average quality of anthropological research, especially of the cultural type, is kept extremely low by lack of statistical knowledge and of hypothetical deductive methodology. At the moment there is no indication that the majority of cultural anthropologists accept science – the most vocal of them still choose to deny that anthropology is science. They are certainly correct for what regards most of their work.

He judged that Cultural Evolution and Transmission had little influence. But Peter Richerson and Robert Boyd learned the application of population and quantitative genetic modeling to cultural dynamics from Feldman in the 1980s. In their own turn, they trained researchers such as Joe Henrich.

Henrich in his turn helped train scholars such as Michael Muthukrishna. Here’s a preprint that has me really excited, Beyond WEIRD Psychology – Measuring and Mapping Scales of Cultural and Psychological Distance:

We present a new tool that provides a means to measure the psychological and cultural distance between two societies and create a distance scale with any population as the point of comparison. Since psychological data is dominated by samples drawn from the United States or other WEIRD nations, this tool provides a “WEIRD scale” to assist researchers in systematically extending the existing database of psychological phenomena to more diverse and globally representative samples. As the extreme WEIRDness of the literature begins to dissolve, the tool will become more useful for designing, planning, and justifying a wide range of comparative psychological projects. We have made our code available and developed an online application for creating other scales (including the “Sino scale” also presented in this paper). We discuss regional diversity within nations showing the relative homogeneity of the United States. Finally, we use these scales to predict various psychological outcomes.

For the people who know genetics, they have created a cultural analogy of Fst!!!. From the preprint:

Cultural FST (CFST) is calculated in the same manner as Genetic FST, but instead of a genome, we use a large survey of cultural values as a “culturome”, with questions treated as loci and answers treated as alleles.

Read More

Open Thread, 11/26/2018

Posted on by Razib Khan

So Spencer and I talked to Antonio Regalado today for the podcast (Apple and Stitcher, should be live soon as I just pushed it). We talked way more about Brave New World than I was expecting. The engineering is moved further than I had realized.

Here are the show notes for the episode.

NASA Probe Lands Safely On Martian Surface.

The Siberian unicorn lived at the same time as modern humans.

Robust estimation of recent effective population size from number of independent origins in soft sweeps.

Fire and Fire & Blood: 300 Years Before A Game of Thrones is a quick read.

Historical contingency shapes adaptive radiation in Antarctic fishes.

The Trouble With White Women: An Interview With Kyla Schuller.

Meet Denny, the ancient mixed-heritage mystery girl.

A vast 4,000-year-old spatial pattern of termite mounds.

On the Nature of Patriarchy.

Alice Dreger’s Middle Finger: Sex, Gender and Unhelpful Hair-Splitting.

What the Cult of Ruth Bader Ginsburg Got Wrong. The Right loves Ginsburg.

Woman who inherited fatal illness to sue doctors in groundbreaking case.

I was raised as a Native American. Then a DNA test rocked my identity. Dad “passed” as Native American. He was black American and Chinese American.

Regular Exercise May Keep Your Body 30 Years ‘Younger’.

Worldwide phylogeography and history of wheat genetic diversity.

The human CRISPR revolution will probably be written in Chinese

Posted on by Razib Khan

I am probably biased because of my professional focus, but this may be the biggest story of 2018, Chinese scientists are creating CRISPR babies:

According to Chinese medical documents posted online this month (here and here), a team at the Southern University of Science and Technology, in Shenzhen, has been recruiting couples in an effort to create the first gene-edited babies. They planned to eliminate a gene called CCR5 in order to render the offspring resistant to HIV, smallpox, and cholera.

We knew this was coming. Soon. But now we can confirm it. It confirms my assumption that gene editing in the human context is going to mostly focus on preventing disease in the near future. In a world of low fertility, every expectant parent prays (literally or metaphorically) for a healthy child. After the child is born they can think about other things like how tall they are going to be or how smart they are. But health, that is always the number one concern.

From what I know the United States still has the largest number of top-flight researchers in the basic and applied sciences. American scientific culture, for all its faults, is second to none. But for various reasons, I can’t see America trying to keep up with the Chinese when it comes to gene editing of humans. CRISPR technology will probably be applied to other things, such as in applied plant and animal sciences, in this country.

The future is here. We’re just along for the ride….

Addendum: As someone who has read S. M. Stirling’s Draka series, I am getting a really weird feeling right now about the trajectory that I see for the next generation….

Update: A computational biologist at Fudan University doesn’t believe in the results:

On the anniversary of the publication of the On The Origin of Species

Posted on by Razib Khan

Today on this date Charles Darwin’s On The Origin of Species was published. If you haven’t, you should read it. I’m not sure if it’s the most influential book of the last few centuries, but it’s definitely up there.

That being said, sometimes people want to read something different that’s more recent. I would highly recommend Evolution: The First Four Billion Years. It’s an anthology of different thinkers from evolutionary biology, from paleontology, to genetics, and even to philosophy.

When ferocity is a feature, not a bug

Posted on by Razib Khan

The sad story of John Allen Chau, the young self-styled missionary who was killed on North Sentinel Island, has some really strange elements that are coming to the surface. The New York Times has published a piece which reports on extracts of a letter he wrote to his parents describing his motivations and observations when it came to proselytizing among the Sentinelese.

The people Mr. Chau chose for his mission are among the most impenetrable communities in the world, known for their intense hostility to outsiders. They have killed or tried to kill many outsiders who attempted to step on their rugged island 700 miles off India’s mainland, where they are one of the last undiluted hunter and gatherer societies.

…

The man yelled, and Mr. Chau tried to respond, singing some worship songs and yelling back something in Xhosa, a language he apparently knew a few words of from when he coached soccer in South Africa a few years ago.

…

In one passage, he asked God if North Sentinel was “Satan’s last stronghold.” In another: “What makes them become this defensive and hostile?”

The article mentions that “Anthropologists say the islanders’ ancestors possibly migrated from Africa more than a thousand years ago.” This really doesn’t make any sense, but it jumped out at me because of the weird fact that Chau tried to speak to them in Xhosa, a Bantu language with influences from Khoesan dialects. Perhaps the reason he did this inexplicable thing is he’s read too much the pap that the people of North Sentinel are some pristine population descended from early Africans?

A more interesting aspect of the article is the questioning of why these last isolated island hunter-gatherers are so hostile. The fact is if they weren’t so hostile, they would almost certainly be extinct by now. The record of hunter-gatherer populations interacting with agriculturalists is one of absorption, assimilation, extermination or subordination.

The hostility of the peoples of the Andaman Islanders to outsiders has long been attested:

Situated in the bay of Bengal, the Andaman islands have been known to outsiders since ancient times. Andaman islanders respond with intense hostility at any attempt of outside contact, hurling arrows and stones at any unlucky visitor approaching their shores.

Early Arab and Persian documents report that Andaman islands were inhabited by cannibals – an exaggeration probably originating from the ferocity of attacks with which these travelers were greeted. Later Indian and European explorers steered clear off these islands to avoid the hostile inhabitants.

And this is why the Andaman Islanders remained relatively distinct ethnographically down to the early modern period. The Negrito people of Malaysia and the Philippines no longer speak their ancestral languages, while the Andamanese did until recently.

This incident reminds me of a dark passage from Jared Diamond’s The Third Chimpanzee. Contrary to the optimism of Carl Sagan, Diamond asserted that if there were aliens out there, we should work very hard not to have them know we exist. His reasoning was that less culturally advanced peoples never had a good interaction more culturally advanced people.

The people of the Andaman Islands are not genetic fossils

Posted on by Razib Khan

So this is in the news, Police: American adventurer John Allen Chau killed by isolated Sentinelese tribe on Indian island. There is some talk about whether the guy was a Christian missionary or not, but that’s not really too relevant. Whether he believes in evolution or not (he was a graduate of a very conservative Christian college), he definitely won a Darwin award before he expired.

North Sentinel is totally isolated, and the people who live there, the Sentinelese, are out of contact with the rest of the world. They are hostile to the outside world. And this is probably why the Sentinelese are still around, as the outside world does not have a good track record with hunter-gatherers. The Andamanese as a whole had a reputation for being very hostile to outsiders, as traders knew not to stop too long for water.

Because the Sentinelese are back in the news, lots of stuff is being said about them in terms of their ancestry.

First, they are not that genetically unique. A recent paper on the genetics of Southeast Asia using ancient samples makes their affinities clear.  The Onge, an Andamanese tribe, are positioned close to the two ancient samples from Laos and Malaysia. They emerge out of the same milieu as Paleolithic Southeast Asians (whose  Hoabinhian culture persisted deep into the Holocene).

The Andamanese themselves are probably from mainland Southeast Asia. The gap between the islands and the mainland was smaller ~20,000 years ago when the sea levels were lower. They could have come up from the south or the north.

Second, they are not the most “ancient” people. That doesn’t make any sense. We are all people who are equally ancient. We all descend by and large outside of Africa from a migratory wave that expanded ~60,000 years ago. Andamanese, Chinese, and Europeans. What is “ancient” about them is that they are hunter-gatherers who have continued to practice that mode of production down to the present. But that’s a matter of culture and not genetics.

Third, in alignment with the above two points, they are not uniquely and distinctly isolated from all other human populations. They are not descendants of an early wave out of Africa preserved on these islands. They are not distinct from all other non-Africans. Rather, they seem to be closer to the peoples of Oceania, Papuans, and Australian Aboriginals, than Northeast Asians. And closer to Northeast Asians than they are to West Eurasians. The latest evidence is that the Andamanese were part of a broader diversification of lineages ~40-50,000 years ago to the east of India that gave rise to the peoples of the western Pacific Rim. Within this broader set of groups, some form a distinct clade that is not with Northeast Asians (often these are like “Australasian”).

Finally, the census size for the Sentinelese is in the range of 100 individuals. This seems on the edge of viability over the long term.

The dingo ate our domestication

Posted on by Razib Khan

Below I mentioned the preprint, Genomic analysis of dingoes identifies genomic regions under reversible selection during domestication and feralization. I do think that readers will be quite interested in reading it, and it’s not too technical. As the authors note, the dingo is interesting because of the longest lasting “feral” lineage that is known. Additionally, unlike other feral lineages hybridization with other populations has been pretty minimal until recently (though they detected some in two of their dingo samples).

The phylogenetics isn’t that surprising. Dingos are closest to New Guinea Singing Dogs (NGSD). And this clade is most similar to Indonesian dogs. Basically, as you’d expect dingos are the product of a serial founder event from Southeast Asia into Australia. Their ancestral population is really, really, small.

The authors quote a time of arrival of the dingos to ~3,500 years ago, and their phylogenetic inferences seem to indicate divergence from Indonesian lineages ~5,000 years ago. That divergence is probably sensitive to some parameter estimates. But, it does make me wonder who the domestic dogs came with. Since they seem to be descended from Eurasian wolves, the most likely candidate is the first Austro-Asiatic farmers. From them, dogs could spread rapidly through feralization to neighboring populations of hunter-gatherers.*

But here’s the interesting part from the abstract:

Selection analysis identified 99 positively selected genes enriched in starch and fat metabolism pathways, indicating a diet change during feralization of dingoes. Interestingly, we found that 14 genes have shifted allele frequencies compared to dogs but not compared to wolves. This suggests that the selection affecting these genes during domestication of the wolf was reversed in the feralization process. One of these genes, ARHGEF7, may promote the formation of neural spine and synapses in hippocampal neurons. Functional assays showed that an A to G mutation in ARHGEF7, located in a transcription factor-binding site, decreases the endogenous expression. This suggests that ARHGEF7 may have been under selection for behavioral adaptations related to the transitions in environment both from wild to domestic and from domestic back to wild. Our results indicate that adaptation to domestication and feralization primarily affected different genomic regions, but that some genes, related to neurodevelopment, metabolism and reproduction, may have been reversibly affected in the two processes.

There are lots of arguments about how the dog got domesticated. One thing to remember is there is a distinction between population divergence of the ancestors of dogs from the ancestors of Eurasian wolves and the domestication of the dog in various steps and stages. One can imagine, for example, a close association between some groups of wolves and humans, with the former existing in a symbiotic relationship with nomadic bands. This state could persist for thousands of years (in fact, I have heard that this may resemble the relationship of the dingo to Aboriginal people, whose landscaping through fires may have been helpful to dingo predation).

Eventually, though humans settled down into sedentary villages. It is hard not to imagine that the village garbage pile dogs didn’t evolve to be even more human accommodating at this stage, with some of them being helpmates to human populations as work dogs (watch-dogs, hunting-dogs, and even war-dogs).

The dingo may illustrate a shift back toward more detachment from humans. The Aboriginal people never lived in large agricultural villages, so the opportunities for extremely close coexistence did not present themselves. But it is interesting that the dingo did not revert to becoming an Australian wolf, but remained distinctively dog-like. This may be a function of loss of genetic diversity through the bottleneck, a different ecological niche than the wolves of Eurasia, or, irreversible evolutionary genetic changes in the morphology and physiology of the canid lineage.

* Australians on the north coast have a legend of a dog arriving in a boat. Most likely they arrived from Sulawesi in Indonesia.

Open Thread, 11/19/2018

Posted on by Razib Khan

I figure I should post the “Open Thread” sooner than later since people are using last week’s “Open Thread” to post stuff.

So I’m getting a copy of Fire & Blood: 300 Years Before A Game of Thrones tomorrow according to Amazon. But I have a legitimate reason to get this book: we’ll be talking about the “genetics of Game of Thrones” soon on The Insight, my podcast with Spencer Wells.

Finally recorded a second episode of the Brown Pundits podcast, where we talk about the woman imprisoned for blasphemy in Pakistan and colorism. Mostly it’s Zach talking to be honest since he has a lot more passion about these topics, especially the former one.

This guy is a legitimate University of Chicago biologist. What have you done with your life?


Demographic histories and genetic diversity acrosspinnipeds are shaped by human exploitation,ecology and life-history. Pinnipeds.

Genomic analysis of dingoes identifies genomic regions under reversible selection during domestication and feralization. An interesting thing is that dogs almost certainly descend from a wolf/wolf-like population, but when they go feral they don’t quite become wolves. Perhaps it would be different if they went feral in northern Eurasia. But the ones in tropical/mid-latitude zones that “de-domesticate” don’t become Eurasian wolves. Perhaps something to do with genetic variation lost, but I think some of it is different selection pressures.

Sigrid Johnson Was Black. A DNA Test Said She Wasn’t. The title comes from an early forensic test that probably used hundreds of ancestrally informative markers. If you read the whole thing you see that the results kept getting closer and closer to reality.

Psychology’s Replication Crisis Is Running Out of Excuses.

Middle Palaeolithic occupations in central Saudi Arabia during MIS 5 and MIS 7: new insights on the origins of the peopling of Arabia and Late Middle Pleistocene Levallois stone-tool technology in southwest China. The spread of non-Africans around ~60,000 was responsible for most of the non-African ancestry. But there were probably some “false dawns.”

In relation to Robert Plomin’s Blueprint: How DNA Makes Us Who We Are probably worth it if you haven’t ever read behavior genetics. But really a lot of it is reemphasizing/reintroducing results from the field over the past generation. Hopefully will write review soon.

Super-smart designer babies could be on offer soon. But is that ethical? I suspect that the vast majority of the customers for many years will be focused on diseases. The best way to have tall and smart children is to select a tall and smart spouse. We might be talking about something different in the 2030s. I’m struck by how little discussion there is from bioethicists and geneticists about NIPT tests for stuff like Down Syndrome. They’re ubiquitous, but talk is limited generally to pro-life circles.

A friend told me that Conquerors: How Portugal Forged The First Global Empire is pretty good. I might quibble with the subtitle, but he confirms that the Portuguese were indeed huge dicks. The Iberians as a whole were brutal and nasty. Though not as nasty as the Anglo-Protestant “Black Legend” would imply. Mostly they didn’t follow the norms and rules which were present in parts of Asia and the New World between states and peoples.

Is anyone still getting 500 errors very often?

Happy Thanksgiving to Americans.