Razib Khan One-stop-shopping for all of my content

October 21, 2020

Not all societies are identical

Filed under: France,History — Razib Khan @ 10:48 pm

There is some discussion on “Hindu Twitter” and elsewhere about the French response to the murder of Samuel Paty. In short, France is going “medieval” on the asses of a lot of Muslims, even nonviolent but very conservative organizations. To use a German phrase, the French state is entering into a Kulturkampf against militant Islam. Or at least it is signaling that it is.

To all this, some on the Hindu Right are asking why some liberal or Left intellectuals are applauding or tolerating France’s reaction, which is hitting down hard on the Muslim community. Would they be so tolerant of India clamping down on Muslims? My own answer is simple: different nations have different histories, and abstract universal values and standards are often not useful.

Let me illustrate the nature of France, and how it differs from India. When the French emancipation of Jews occurred in the late 18th century, they were quite clear they were liberating Jews as individuals, not as a community. That is, Jews would not have corporate rights as a community. To the Jew as an individual, everything. To the Jews as a community, nothing.

When the modern French nation arose during the Revolution, only a minority of the people of France could speak French as their mother tongue. The creation of the French nation anew, as a bottom-up identity that superseded the monarchy, occurred through the crushing of regional dialects and their absorption into the national language.  The same occurred in the 19th century, as waves of migrants from Poland arrived, assimilating into French identity. In the early 20th century, it was the turn of Italians and Spaniards.

The ideal, which is more a goal than a reality, is that various nationalities, religions, and peoples, could fuse together around a common language, and a common history anchored around the Revolution and the emergence of republican France. This is one reason the French have been cooler to Black Lives Matter than other nations. The idea of racial identity and separatism is offensive to the French self-conception, even if the segregated suburbs of Paris witness to the reality of lack of integration.

There could be much more I say about France, and why there is an arms-length relationship to religion and Catholicism in particular. There’s a history there.

But compare France to India. Whereas France rejects violently the idea of subnational communities, India is organized all around the idea of subnational communities. This is a totally different equation than a society like France, where a hegemonic identity absorbs secondary identities in totality. France and to be French is a unitary ideal.  There’s not unity in diversity.

The situation in India is quite different. Myself, personally, I have long thought something like a “uniform civil code” was necessary and just, and that there was a degree of toleration of illiberalism of Muslims by various political social factions in India that needed to stop. But, as an empirical matter, India is not an individualist WEIRD society, it is a communal society where communities achieve consensus through negotiation.

What does this have to do with France, Islam, and India? The French would have Islam be the religion of some individuals in the French state. Only that. Religion as a political social force in France is consciously marginalized. As such, Islam needs to be modified, or not exist, in the French way of looking at the world. This is obviously not the case in India, where Islam is another community, and communities have rights and integrity that has to be respected from what I can tell.

As an American conservative, I am skeptical of affirmative action and take a dim view of reservations. What does it matter if 90% of doctors are {{{Brahmins}}}?  Do they do their job well? But I am not Indian, and not conscious of the Indian social and political landscape. Even many conservative Indians favor reservations because they are a way to maintain communal harmony, and in India, it’s communities that matter.

Occasionally some of my Indian correspondents message me to apologize for how Hindu Twitter treats me when I get on their bad side. Usually, they see my name and start hurting invective about my Islamic faith and such.

Since I have no Muslim identity I don’t take it very personally, and to be frank, I find it rather amusing.  Most of them, like some of you commenters, are stupid, ignorant, and a large fraction no doubt teenage incels. Though I have never encountered crass vulgarity in the United States, Indians of non-Muslim background have routinely coded me as Muslim even if they see me eating a bacon cheese-burger and drinking beer,  and have a difficult time understanding how I can have no communal affinity or identity.

I simply don’t care. I am WEIRD. My children have Germanic names and are assumed to be white. My lineage is destined to fade, it will diminish and pass to the west. I have had to correct Indian American friends who refer to me as an “atheist Muslim.” I don’t care if people call me a Muslim, or Hindu, or Asatru, but I do want people to be clear that I just identify as an atheist, though I’m not a particularly militant type.  As far as religion goes, my personal sympathy probably goes toward the sort of rationalist Confucianism of Xunzi.

In “Guess Who’s Coming To Dinner” Sidney Poitier’s character tells his father that he will always think of himself as a black man, while Poitier’s younger character will think of himself as a man. Indians think, on the whole, in communal terms. If Muslim fisherman in Tamil Nadu acceded to conversion to Hinduism on the condition that their sons and daughters could marry local Hindu communities, would there be enthusiasm for the conversion?

I believe that in India people should marry who they want to marry, irrespective of jati.  But over 90% of people marry within their jati. I believe people should be able to choose their religion, of their own free choice. But 99% of people remain in the religion of their birth. Communal birth should be no privilege or debility. But it is. There is the abstract of what I would prefer as “should be,” and then there is the reality.

Edith Piaf was one of France’s greatest singers. She had Moroccan ancestry on her mother’s side. No one cares. Similarly, the great 19th century French writer, Alexandre Dumas, was 1/4th African. Though of some interest, Dumas is thought of as a French writer, not a black French writer.

Americans in our current moment think our particular history is relevant for everyone. It’s not. Similarly, India is not France, and France is not India. France need not do caste-based reservations, because France has no castes now that the Cagots are gone. Similarly, Indians should probably be cautious about projecting the Charlie Hebdo cartoons on the sides of government buildings.

Tibeto-Burmans, Munda, and Bengalis

Filed under: Genetics — Razib Khan @ 10:58 am


I’m pretty sure I posted this Chaubey lab work as a preprint, but it’s now a published paper. For those who can’t understand the table, it illustrates a big difference between Tibeto-Burmans and Munda. The samples from Bangladesh look to be generic Bangladeshis, the 10% frequency for O2a seems to match the other data I’ve seen for East Bengalis.

This confirms that the East Asian admixture into Bengalis was not Munda. And, the Tibeto-Burmans of the nTibeortheast have no assimilated Munda ancestry. I think it does lend more credence to the idea that the Munda arrived in the Indian subcontinent across the Bay of Bengal, landing in Odisha, rather than from the northeast.

October 20, 2020

The Genetic History of the Middle East: into Arabia

A new massive preprint on the Middle East is out. I’ve edited the first figure to give people a general sense of the broad results and populations sampled. First, you have to know that these are high-quality modern samples. 137 individuals at 30x whole genome coverage.  In other words, basically the best genomic data you can get on sequences. No need to futz around with subsets of the data. This is important and needful because the 1000 Genomes doesn’t have a Middle Eastern population. So when looking to assemble variants there was a deficit in this domain. Even the WGS of the HGDP was not totally sufficient, since the Middle Eastern populations were not Arabian.

The populations here are sampled from both the classical “Fertile Crescent” and various points within the Arabian peninsula. At the end of the preprint, they do some analysis on selection, which I won’t talk about. The most interesting thing is that they confirm that Arabian people have a unique lactase persistence allele that seems to have been selected very recently, just like in Europeans. A lot of the selection analysis seems to be either replicate what you would find elsewhere. Or, they do not have enough power to detect polygenic selection (though they did detect selection on EDU).

The big finding to me is that this work confirms that there is a north-south cline in the Near East defined by a deep population structure. The admixture graph to the right captures the main features using Lebanese and Emiratis as the two extreme populations, but as you can see in the admixture plot above the cline really runs from the Caucasus to southern Arabia. If you analyze these populations one thing you will see is that Fertile Crescent populations, such as Druze, often seem more like Armenians and Georgians, than South Arabians. Why is this? After all, South Arabians and Fertile Crescent populations speak Semitic languages.

I think the issues here are multiple. First, there is recent admixture that obscures some of the deeper relationships. This is clear insofar as most Arab Muslim populations have Sub-Saharan African admixture. This is historically attested, and physically visible. The variation and range are quite high, in part due to spatial heterogeneity of slavery (e.g., more African slaves in lowlands than highlands), and the recency of the admixture producing variation due to incomplete mixing (the dates are usually 1000 A.D. and later).

But this is not the only admixture. All of the Fertile Crescent populations, along with groups to the north, have much more steppe drift than those to the south in Arabia. The details of the fractions don’t matter, it’s not much, but it’s not trivial, and it’s always higher than among the Arabians. Additionally, this element is new to the region, in relative terms. You can see the contribution in modern Lebanese in comparison to the Bronze Age Sidon samples, which date to 1800 BC. The source could be continuous gene flow during the Roman and Byzantine period, or even later. Or, it could also be Indo-European migrations.

We know that Indo-Iranian peoples were present in Upper Mesopotamia. The Mitanni Kingdom, which had Indo-Aryan affinities, shows up after 1750 BC. The Hittites, the Nesa, show up to the north in Anatolia a bit earlier.  Interestingly, the Hittites speak an Indo-European language that is often considered basal (the outgroup) to most of the others. Armenian, who emerges later in eastern Anatolia, is also quite distinct, just as Greek to the west is. In contrast, there is a lot of suggestive evidence of either genealogical or geographical connectedness between the ancestors of Indo-Iranian and Slavic language families.

The presence of these two very distinct ancestral components, steppe, and Sub-Saharan African, on top of the ancient Near Eastern base, produce distinctions in the modern populations which obscure some of the deeper strands. In the late 2000s when researchers and bloggers began running admixture analyses on Ethiopians it was clear that this population was a mix between “West Eurasian” and African which wasn’t Bantu. The West Eurasian donor population was often Yemeni, in particular Yemeni Jews. Later on, using more sophisticated methods some models suggested greater affinity in Ethiopian genomes to Levantine populations than Yemenis. What was going on?

We now know. It is quite clear Ethiopian populations lack steppe ancestry. In the earlier Bronze Age, and definitely, the Neolithic, Levantines lacked steppe ancestry. In fact, the Neolithic Levantines usually lacked “Iranian” ancestry. The West Eurasian ancestry in Northeast Africans, on the whole, is enriched for a Levantine ancestry quite similar to Natufian. Modern-day South Arabians are the closest to this population mix, even if they are not descended from ancient Levantines. They lack steppe.

Modern-day South Arabians in fact descend in part from indigenous hunter-gatherers, who were a sister clade to the ancestors of Natufians. The admixture graph makes that clear for the Emiratis with the least African ancestry have half their ancestry from this group. In the book Arabs, the author discusses at length various Yemeni legends of a fusion between distinct peoples on the edge of history. This could be recollections of the merge of indigenous Neolithic Arabians and peoples who expanded from the north.

The analyses of these samples confirm and reiterate what has been found with ancient DNA: at some point late in the Neolithic and early in the Bronze Age a massive admixture event occurred in the Fertile Crescent which brought a considerable amount of “Iranian” ancestry into the region (these ancient people are not like modern Iranians; in particular, they lacked steppe ancestry which is copious in much of Iran, particularly the east). This ancestry pushed south and westward so that ~50% of the ancestry of Arabians seems to be Iranian. That being said, I have some qualms here:

We explored whether this ancestry penetrated both the Levant and Arabia at the same time, and found that admixture dates mostly followed a North to South cline, with the oldest admixture occurring in the Levant region between 3,900 and 5,600 ya (Table S3), followed by admixture in Egypt (2,900-4,700 ya), East Africa (2,200-3,300) and Arabia (2,000-3,800). These times overlap with the dates for the Bronze Age origin and spread of Semitic languages in the Middle East and East Africa estimated from lexical data (Kitchen et al., 2009; Figure S8). This population potentially introduced the Y-chromosome haplogroup J1 into the region (Chiaroni et al., 2010; Lazaridis et al., 2016). The majority of the J1 haplogroup chromosomes in our dataset coalesce around ~5.6 [95% CI, 4.8-6.5] kya, agreeing with a potential Bronze Age expansion; however, we do find rarer earlier diverged lineages coalescing ~17 kya (Figure S9). The haplogroup common in Natufians, E1b1b, is also frequent in our dataset, with most lineages coalescing ~8.3 [7-9.7] kya, though we also find a rare deeply divergent Y-chromosome which coalesces 39 kya (Figure S9).

Some of these dates are hard to credit. For example, I obtain a midpoint estimate of Iranian admixture into Egypt around 1836 BC!

The fraction of Iranian ancestry is substantial. The admixture model in the supplements gives this for Egyptians: 45% Levant_N, 32% Iran_N, 8% EHG (Eastern European Hunter-Gatherer), and 15% Mota (African). The older date is 2700 BC. The oldest Egyptian writing dates to 2700 BC, but proto-hieroglyphs are 500 years older. The authors talk about Semitic languages, and ancient Egyptian is not Semitic. So it could be a minority population mixed into the Egyptians, but this is a massive event that we don’t have records of. In fact, the authors claim that it went into much of Northeast Africa at a relatively late date.

Additionally, the values for the Levant seem recent as well. That being said there was a pre-Sumerian civilization, the Uruk Civilization, which spread broadly from Mesopotamia between 4000 and 3000 BC. This is 6000 to 5000 years ago. The midpoint of this is 5500 years, while the midpoint of the admixture into the Syrians, who were on the edge of the Uruk Civilization is 3800 years ago. Basically, I think the evidence points to various statistical genomic artifacts reducing the age from when the admixture truly occurred (this has long been a problem in this field).

I honestly have no idea how to relate the expansion of Semitic languages to the expansion of Iranian languages. My friend Patrick Wyman believes that Anatolian farmers spoke Afro-Asiatic. These were very different people from the Iranians, who arrived from the east later. Additionally, history teaches us that Mesopotamia during the Bronze Age was very linguistically diverse. The Sumerians were not Semitic, and neither were their Elamite neighbors in Khuzistan. The Akkadians, who were more prevalent in the north of Mesopotamia, but were present from the beginning of Sumerian history, were Semitic.

There is still a mystery around the great admixture between Neolithic Near Easterners of the west and the east. I don’t think we’ve closed that chapter of the book.

That being said, there is a lot that is “solved” in this paper. For example, these authors seem to confirm that there is no evidence of “first wave” modern humans in Arabian populations earlier than the non-African radiation. Arabians, like other non-Africans, underwent a population expansion 50-70,000 years ago. Their separation from Mbuti Pygmies was gradual up until 120,000 years ago. Then there seems to have been a separation. What this is telling us, I believe, is that the ancestors of non-Africans were part of the African meta-population until 120,000 years ago. This is suspiciously close to the Eemian Interglacial, which dates to between 115,000 to 130,000 years ago. The Eemian was characterized by a “Green Sahara”, so it seems that this is when early modern humans ventured in substantial numbers out of the continent and to its peripheries. One issue that seems notable in the data is that proto-non-Africans seem to have been characterized by a period of isolation and small population size. Perhaps

But 50-70,000 years ago a massive expansion of one of these daughter populations occurred. These data confirm that Arabians seem to have the same Neanderthal admixture as everyone else, but, even accounting for Sub-Saharan African ancestry they also have somewhat less. In alignment with earlier research, they argue that this is due to admixture with “Basal Eurasian” populations which did not mix with Neanderthals ~55,000 years ago.  Or, more precisely, did not carry as much Neanderthal ancestry (it seems plausible that the Basal Eurasian populations are themselves a compound of conventional non-African at the base of the broader splits, and a deeper basal group which lacks Neanderthal ancestry).

Going back to the admixture graph, you notice that both western and eastern farmer populations are a compound of Basal Eurasian and various lineages that are broadly “West Eurasian.”  Natufians and Anatolian farmers are descended about half from groups related to European hunter-gatherers, while ancient Neolithic Iranians had ancestry related to these people, but even more to populations distantly related to Ancient North Eurasians (Paleo-Siberians). The events here are distant, but the sample proportion of Basal Eurasian ancestry indicates to me a rapidly expanding population at some point which mixed with a well-structured set of groups in the Near East.

The major takeaways

  • Near Easterners are part of the same broad diversification as all other non-Africans
  • The expansion of these non-Africans dates to 50-70,000 years ago
  • Archaeological evidence points to a very intense expansion in the period around ~50,000 years ago, and admixture with Neanderthals somewhat before then
  • At the beginning of the Holocene Near Easterners were deeply structured regionally, and had threaded together disparate ancestral components (Basal Eurasian, related to European hunter-gatherer and Paleo-Siberian)
  • Late in the Neolithic and early Bronze Age much of this structure collapsed, and there was a massive admixture of Iranian ancestry to the south and west (conversely, there is evidence in other work of admixture of western farmer ancestry to the east)
  • Finally, there is evidence for later incursions of steppe people into the northern Arabian fringe and Fertile Crescent
  • On top of this, there is historical admixture from Africans and in the north Turks and other groups

October 18, 2020

Open Thread – 10/18/2020 – Gene Expression

Filed under: Open Thread — Razib Khan @ 9:40 pm

Taking a break from the book club, I’m finishing up books that I never finished though started. So, The Turks in World History. Recommended. Not so deep as to confuse, but not so casual as to be Wikipedia.

In Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past the citation goes to http://www.razib.com/wordpress/. For whatever reason I notice a lot of academics check http://www.razib.com/wordpress/, rather than this weblog. I mention this because http://www.razib.com/wordpress/ is an aggregator that accesses all my RSS, so if I publish something somewhere else, it will be loaded on that website (e.g., if I publish in NRO, City Journal, etc., it automatically gets pushed to the aggregator). I created the website for the total content feed, but just pointing it out for those who like bookmarks rather than RSS feeds. The stylizing isn’t great, but I doubt most readers of this weblog are here for the styling.

The Five Deadly Sins of the Left. The author, Ruy Teixeira, was behind the emerging Democratic majority hypothesis.

Statistics used to infer inter-breeding between humans and Neanderthals are strongly predicted by flanking sequence heterozygosity.

Want to remind readers of Cabellero’s Quantitative Genetics. Excellent book, and pretty affordable and up-to-date.

With Covid-19 Under Control, China’s Economy Surges Ahead. Every time I post something like that someone says (on Twitter): “Actually China’s economy is all fake.” As someone who has been paying attention to China’s economy for 20 years, and frankly been very skeptical of a lot of their numbers, this assertion goes into the true-but-trivial category. There’s a lot of fakery. But that’s irrelevant to the qualitative fact that Chinese prosperity in 2020 is a fact.

The Crypto State? How Bitcoin, Ethereum, and other technologies could point the way to new systems of governance. This is in City Journal. I’ll be having something out in CJ again soon.

New Research (not by me!) on Kids, Babies, Day Care & Schools. It’s hard to navigate between “the sky is falling” and “it’s just the flu bro.” I think Emily Oster has been trying hard to do so. There’s a lot of politicization in public health, so I listen to her since I think she aims to be as free as possible.


He is undoubtedly the most influential intellectual in America today. And, he is also one of the stupidest. I’ve told my eight-year-old daughter some of his ideas, and she looked at me incredulously. Then again, she’s on the order of 2.3 standard deviations or so above Dr. Kendi’s intelligence. In any case, he’s so dull he has no idea when he expresses thoughts which, as Oliver Trialdi pointed out, suggest he’s joining the “Intellectual Dark Web.”

How Mark Zuckerberg Learned Politics. A few years ago Zuck rediscovered spirituality. All this indicates a future public profile much bigger than toady.

Steven Pinker’s obituary for Judith Rich Harris. She was a friend of this blog, and I always enjoyed corresponding with her and her husband.

Not All Identities Are Created Equal.

Introduction to Social Science Genetics.

The Next China? India Must First Beat Bangladesh. Indians are kind of jumping the shark over this…but, yeah, it’s a bad sign that on a per capita basis Bangladesh will surpass India. But, the real story is India has many regions that lag way behind. Maharashtra, where Mumbai is, has a higher per capita income than Bangladesh and a far larger GDP. But states like Bihar and Uttar Pradesh are huge, and poorer than Bangladesh.

The Age of Confucian Rule: The Song Transformation of China. This is an excellent book. Recommend it to everyone.

Ancient DNA from Guam and the Peopling of the Pacific. Look like the Lapita. I used to play “ratball” with a guy from Guam named Tulio back when I was 15.

Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context.

The rate of whole-genome duplication can be accelerated by hybridization.

Empirical variance component regression for sequence-function relationships.

8 Million Have Slipped Into Poverty Since May as Federal Aid Has Dried Up. I’m against austerity. COVID-19 has been a disaster for the economy, and it’s “no one’s fault.” Not going to lie, I suspect a debt crisis is in our future, but I doubt that this stimulus will be dispositive in either direction.

October 17, 2020

Week 2, Gene Expression book club

Filed under: Book Club,Book reviews — Razib Khan @ 7:39 pm

The second chapter of Not Born Yesterday: The Science of Who We Trust and What We Believe is short. Much of it is re-warmed evolutionary biology, with a focus on ethology. If you’ve read Amotz Zahavi’s The Handicap Principle: A Missing Piece of Darwin’s Puzzle or Dugatkin & Reeve’s Game Theory and Animal Behavior this will be a quick and easy chapter. Basically, the issue being explored here is that social cognition and conformity run up against the fact that there is an incentive to “cheat”, and communication is a two-way street.

Zahavi was the 20th century’s most eloquent expositor of the “handicap principle.” The idea that you need “hard-to-fake” signals to accurately convey information. So, for example, huge antlers are honest signals of robustness and genetic health, even though they are nonfunctional, and reduce individual fitness (it’s easier to find and catch animals with antlers). The idea that people are gullible and credulous in terms of communication and information processing runs afoul of the reality that communicators are incentivized to deceive you to optimize their own fitness (or, just “free rider” off communication altruism of conspecifics).

The strangest part of this chapter is that Mercier threw in a reference to Haig’s theories about mother-offspring genetic conflict due to different life-history incentives. The mother is optimized to not invest too much into the fetus so that resources are left for future offspring, while the fetus is incentivized to extract as much as possible (within reason; the offspring is related to future progeny, though in most mammals that might be 0.25 and not 0.50). All this is true, and it’s a robust area of science, but I thought this chapter would have benefited from more discussion of ethology and behavior, and less on evolutionary genetics.

Basically, the takehome here is that the gullible should be selected against…


Those readers who suggest that Autumn in the Heavenly Kingdom is novelistic surely have the right of it. The second chapter is filled with narrative detail, fixating on the peregrinations of a certain Lord Elgin, and touching up the nascent Franco-British alliance after the Crimean War, the Indian Rebellion, and finally, the arrival of British ships into Chinese territories.

The Taiping rebels make cameo appearances in this chapter, as the real action and viewpoint are that of Europeans and white colonialists more generally. The author does not follow chronology and seems to have jumped deep into the later stages of the rebellion when the Taiping and Manchu regimes were at an impasse. Autumn in the Heavenly Kingdom presents the Europeans as opportunists at this point, taking advantage of the Chinese civil war to extract more concessions out of the Manchu elite through targeted aggression. One of the themes of the chapter is the rise of European and white supremacism as a unifying ideology, which had spread to the Americans, who helped British soldiers against the Manchus when they were ostensibly neutral.

It seems the primary aim of this chapter is to flesh out the dramatis personae of European actors, who are going to play a crucial role in the later portions of the book (I know enough about the course of the rebellion to anticipate that the Europeans will, in the end, help the Manchus against the Taiping).

Note: Here is the page for the book club.

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