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

May 31, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:44 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

May 30, 2019

Eight-way tie for the bee

Filed under: Culture — Razib Khan @ 9:00 pm

May 29, 2019

The Insight Show Notes — Season 2, Episode 29: Deep Learning and Population Genetics

Filed under: Machine Learning — Razib Khan @ 3:36 pm

The Insight Show Notes — Season 2, Episode 29: Deep Learning and Population Genetics

This week on The Insight (Apple Podcasts, Spotify, Stitcher and Google Podcasts) Razib talks to Andrew Kern, a computational biologist at the University of Oregon who brings together cutting edge genomics and computer science.

The discussion began with a review of the history of population genetics, the discipline in which Kern was trained in the 2000s. One of his mentors was John Gillespie, author of the excellent Population Genetics: A Concise Guide.

We discuss how much the field has changed in the last 20 years. When Kern began graduate school in the year 2000 there was only a single genome published. Today there are thousands.

The biggest change in the last generation has been the influx of data into population genetics, and the development of the field of computational population genomics. In particular, machine and deep learning, which allow researchers to make sense of the patterns within data.

Two of the Kern lab’s publications show the path forward:

We finished the podcast by talking about how science, and biology, in particular, needs to reform itself as a more collaborative, as opposed to competitive, enterprise. Basically, Kern suggests that genomics needs to learn from other big data fields with decades of a head-start: astronomy and astrophysics.


The Insight Show Notes — Season 2, Episode 29: Deep Learning and Population Genetics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

May 27, 2019

I am human, and I think nothing human is alien to me.

Filed under: philosophy — Razib Khan @ 9:45 pm

There was a comment below which I am now reflecting on…that this “This blog pertains to South Asians.” The comment was sincerely made, and I take no deep issue with it.

Rather, I wonder what the purview of pertaining to South Asians is for each of us. Do we all see the same sky above us? Or does where we stand alter the constellations above? Both?

There are so many faces to this question. Some might echo Naipul and suggest that those of us from Muslim backgrounds are shorn from our Indian roots, that we are a people without a spirit. Others might assert a racial component, which in the Western context becomes cloying and exceedingly restrictive. Liminal populations are matters of dispute.

And yet I reflect on my own life, my own orientation, my own upbringing. I spent long enough in Bangladesh as a small child to remember the taste of jackfruit in my mouth…but below are the climatic conditions I grew up with as an elementary and secondary school child and teenager.

I wasn’t born in the cold and ice. But I was raised in it. I was moulded by it. I do not miss the seasons. I do not miss the ice. But the ice is part of who I am.

The cold of winter is deep in my experience, and that is almost one reason that I shudder to think of the cold, and I positively avoid it now that I have a choice as an adult.

And yet this is not typical of the South Asian, Indian, subcontinental, background. It is not part of our deep cultural memory, it is particular to many of us who grew up in the 1970s and 1980s, young children of hopeful immigrants fleeing countries of grinding poverty and deep sclerosis, embedding themselves in frozen landscapes where they traded warmth for hope.

Readers of my other weblog (which as of this current writing is undergoing some maintenance by yours truly) sometimes ask me when I choose to post here, and when I choose to the post there. To be honest that distinction is harder to make for the non-science content.

If there is an election in India. If there are tensions on the border between Pakistan and India. If someone wants to engage in a troll-fest on the Kashmir question. This blog will be a space where those issues are mooted.

But there are more things in heaven and earth, Harjeet, than are dreamt of in your Darśana. 

I think a reasonable position may be “this is a South Asian weblog, this is why we are talking about this.” But, I am very wary of the proposition, “this is a South Asian weblog, this is why we should not be talking about this.”

Seek illumination even if you have to go as far as China, for seeking knowledge is a duty on every human.

Browncast into June….

Filed under: Podcast — Razib Khan @ 11:37 am

Thanks to everyone who is a patron on the Browncast. I’ll be posting a few more in there today (or very early tomorrow). We won’t be posting anything in public until June 1st. Our podcasts tend to go longer, rather than shorter. Perhaps it’s a brown thing? In any case, regular podcasts of 1+ hours mean that our month quota gets used up regularly.

I won’t be recording too many podcasts for the next month (I may jump on one here and there depending on my availability), but that’s fine because there are already several in the pipeline. Here is a preview:

  • Discussion about the Indian elections. Kushal and Zach almost get into a (friendly) shouting match on this one
  • I talk about Game of Thrones, fantasy, and neuroscience, with Adam Calhoun
  • A discussion with an Israeli American about living in Israel, and perceptions of Israel abroad.
  • A discussion about open science with “data thug” Jordan Anaya
  • A discussion between me and two young millennial tech-bro browns about navigating American society
  • A discussion of Game of Thrones with a historian and a geneticist (this is not recorded yet)

One of the reasons I’ll be taking a break is that I’ve been podcasting pretty intensively recently. I’ve been putting out a podcast every week for my main science one since the end of January, and have gotten about 2 months ahead there (that’s what recording on weekends and two or three times a week sometimes will do).

I will be focusing on other projects for a bit, and not podcasting will make my schedule more flexible.

How Indians invented the universal religion

Filed under: Religion — Razib Khan @ 11:24 am

One of my favorite podcasts is Two for Tea, which tends toward “centrist-edgelordism”. The latest guest is, Armin Navabi, who I have nicknamed the Ayatollah. Armin is literally one of the most logical people I have ever known of, at least in the domain of those who are not visibly already extremely at one end of the spectrum. His views on religion come from this rationalist perspective, and that is where I part ways with him because I don’t see rationality as powerful a force as he does in shaping human behavior.

But in this post, I want to disagree with something Armin said in relation to the history of religion: that universalism and post-tribal religion was invented by Christianity and the Abrahamic tradition. This is clearly false.

From Ashoka’s Edict 13, put down in the 3rd century before Christ:

Now, it is the conquest by the Dharma that the Beloved of the Gods considers as the best conquest. And this one (the conquest by the Dharma) was won here, on the borders, and even 600 yojanas (leagues) from here, where the king Antiochos reigns, and beyond where reign the four kings Ptolemy, Antigonos, Magas and Alexander, likewise in the south, where live the Cholas, the Pandyas, and as far as Tamraparni.

The usual interpretation is that Ashoka was a partisan of the Buddhist school. But whether he or wasn’t (some revisionists claim that the Buddhists coopted him), the fact is that Ashoka was involved in the proselytizing of Indian religious views to non-Indians. This gave rise in the subsequent generations to Indo-Greek kings, such as Menander, who seem to have patronized Buddhism. Again, revisionists might suggest that Menander was not a Buddhist himself, and what did it mean to be Buddhist anyway in the 2nd century B.C.? But, we know that Buddhism arrived in China in the 1st century A.D., almost certainly from Central Asia.

My overall point is that even before the death of Jesus Christ (assuming someone who fit that general description lived, which is the majority consensus), Buddhism was already an international religion. By the time of the birth of Christ, it was probably as important a cultural force in Central Asia, among Iranian-speaking peoples, as it was in India.

This post though is not to engage in “but everything was invented in India!” To be honest, I think the emergence of Buddhism and Christianity as portable universal religions was probably somewhat inevitable in Eurasia during the Iron Age. I don’t discredit the idea that some forms of Buddhism may have had an influence on early Christianity, as the Persian Church was coextensive with a large population of Buddhists in Central Asia, and before the identification of Christianity with the Roman Empire in the 4th century arguably Persia was more congenial to the religion. But the cross-fertilization of religious ideas occurred in many directions.

But, I do wonder at the emergence of universalism within India in particular, because this is a region now renowned for its acceptance of particularism. Buddhism was one of many religious and philosophical movements that rebelled against the traditional religious structures and beliefs of India, which eventually gave rise to Hinduism. The genetic record seems to suggest that jati (caste) and ethno-social segregation has a deep history in South Asia.  Perhaps then a universal religion like Buddhism developed early within India due to a Hegelian dialectical process.

Universalism as an ideology takes root where it is most needed to counter-act ideologies of particularism?

Population genetics + “deep learning”

Population genetics is many things, but a popular field that gets written up in Wired or the tech-press is usually not one of those things. It emerged out of Mendelian genetics in the early decades of the 20th-century, transforming elegant pedigrees into abstruse algebraic formulae. It was a peculiar hybrid of mathematics and evolutionary biology, both obsessions of late 19th-century Victorian academics. Population genetics was as much a product of a particular history as the topics that it studied.

In the population genetic lens, evolution became simply the “change in allele frequencies over time.” Alleles being the early term for different genetic variants, which were correlated with patterns of inheritance.

Whereas some fields of quantitative science are focused on the analysis of collected data, early population genetics was rather more fixated on logical deduction from theoretical models. These models involved the algebraic inferences that were consequences of assumptions about values of parameters such as mutation or natural selection, in the context of random mating populations. On occasion, these models were supplemented with geometric analogies and illustrations, but by and large, this domain of science was inhabited by thinkers who were comfortable in abstract symbols, rather than the mess and fuss of bench biology.

This was a matter of necessity as much as preference.

There simply was not much data in early genetics on a population-wide scale.

The structure of DNA was not elucidated until 1952. Molecular evolution did not emerge until the next decade, and what we term genomics is the product of the very end of the 20th-century.

But the growth in data since the year 2000 has been exponential. For its first 80 years, population genetics was a field with too little data, fixated on theory. In the last 20 years, as population genomics has bloomed researchers have had to confront the fact that the theoretical edifice built when there was access to genetic variation on dozens of loci within a species is not adequate in a world where one has access to whole genomes from hundreds of individuals.

Population genetics is now as much data science as theoretical science.

Words such as machine learning and deep learning have the characteristic of being both banal and esoteric. Who doesn’t know what a machine is? Or what deep means? And everyone learns! But of course, these terms refer to fields within computer science which have emerged to deal with the mass of data that modern society generates. Machines learning deeply seems to be quite a mysterious feat!

When population genetics was developed in the 1920s and 1930s to model evolutionary processes it was viewed as something of a mystery to most biologists. These theorists focused on the implications of models of the change in frequencies of alleles. They dealt in stylized conceptions of single mutations rising up rapidly in frequency due to strong positive selection, or perhaps a new mutation bouncing up and down in a “random walk” process of genetic drift. Relatively simple mathematical processes described simple evolutionary dynamics, which one could test with the limited data on hand.

Adaptation to malaria in Africa and the emergence of sickle-cell disease is a case in point. This is a situation where the selection pressure for individuals with a single copy of the mutant allele is balanced against the fitness cost to those who carry two copies of the mutant allele, and so exhibit sickle-cell disease. A simple algebraic relationship between the cost of sickle-cell disease and the protection conferred to carriers of the mutation against malaria can allow one to compute the allele frequencies at a single locus within populations.

But it turns out that much of natural selection is not so amenable to classical population genetic models.

A great deal of natural selection in populations is not easily localized to a specific locus. The human genome itself has 19,000 genes, and tens of millions of polymorphisms. Though there are some selected events which fit the model of a classical sweep up from a single mutation, most adaptation may occur through shifting the frequencies of many alleles across the genome in a subtle manner. Population genetic modeling from the early 20th-century was not designed to detect these subtle processes, because they would not have had the data to be able to detect them empirically for decades.

This is where buzzwords step in. Deep learning is a method of extracting features, patterns, out of a mass of raw data which is not digestible by humans. This is why it is applied to online marketing, to learn from the patterns of tens of millions of individuals, as well as their individual preferences, to generate a customized set of choices. This is in contrast to earlier methods of marketing which relies on segmentation by specific demographics defined by analysts. Classical marketing is not useless, but in the context of e-commerce, the newer methods of targeting individuals based on a mass of data are even more effective.

Machine and deep learning do not mean population genetic theory is irrelevant. On the contrary, classical population genetic theory is invaluable as a guide to the broad sweep of evolutionary change. It generates questions that one can finally test. Data science inference without a firm theoretical basis is directionless. But to test the details of population genetic processes one needs to lean on futuristic computer science.

Modern sequencing machines generate more data in a week than all of 20th-century genetics did over decades.

Only the interpretative tools developed in this century can absorb the scale of 21st-century genomics.

Population genetics + “deep learning” was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Pakistani women, Chinese men, the continuing story….

Filed under: Pakistan — Razib Khan @ 12:38 am

The New York Times has a follow-up story with some nuance, She Thought She’d Married a Rich Chinese Farmer. She Hadn’t.

Now there is coverage of Muslim girls going to China. The model is the same as the Christian girls, rural Chinese men who aren’t as wealthy as the present themselves, go through nominal conversions or affirmations of faith, and take the women back. Here for me is the interesting part:

Then, after a four-hour drive past fields of wheat and corn, they arrived at Dongzhang village in Shandong Province, where she saw her husband’s duck farm. It was not the sprawling operation of a wealthy man that she had envisioned, but a modest family farm where he lived with his parents and two brothers.

The New York Times was unable to independently verify Mr. Zhang’s income. But on a recent visit to the Zhang family home, a Times’ reporter found a newly built housing compound with multiple bedrooms and shiny tile floors.

Outside the family home, Mr. Zhang’s mother, who is in her 60s, recalled being puzzled by Ms. Kanwal’s reactions.

“She is religious, so when she came here I went out of my way not to give her any pork,” she said, as a small guard dog barked nearby. “I stir-fried chicken and made egg omelets for her. But no matter what I served her, she just refused to eat.”

Some of the more sordid stories of prostitution are probably true. And, it seems from the story that some of the girls who moved to China are pregnant, and reasonably happy where they are. But it seems clear from the piece that many of the stories are grayer and not so clear.

The mother-in-law above seems well-meaning, after a fashion, but one can see the perspective of a young Muslim girl from Pakistan, encountering a world filled with pork, dogs, and without the washing facilities she was used to. Additionally, the reporters seem to agree that the farmer was prosperous, if not necessarily wealthy. With no real linguistic common ground, it’s pretty easy to imagine that wires could get crossed her.

Right now these stories are exotic. But if more and more girls stay and settled down in China, that will result in positive word of mouth. The precedent with other Asian countries is tragic and horrible stories will continue. But that may not be the whole, or the main, story.

Pakistani women, Chinese men, the continuing story….

Filed under: Pakistan — Razib Khan @ 12:38 am

The New York Times has a follow-up story with some nuance, She Thought She’d Married a Rich Chinese Farmer. She Hadn’t.

Now there is coverage of Muslim girls going to China. The model is the same as the Christian girls, rural Chinese men who aren’t as wealthy as the present themselves, go through nominal conversions or affirmations of faith, and take the women back. Here for me is the interesting part:

Then, after a four-hour drive past fields of wheat and corn, they arrived at Dongzhang village in Shandong Province, where she saw her husband’s duck farm. It was not the sprawling operation of a wealthy man that she had envisioned, but a modest family farm where he lived with his parents and two brothers.

The New York Times was unable to independently verify Mr. Zhang’s income. But on a recent visit to the Zhang family home, a Times’ reporter found a newly built housing compound with multiple bedrooms and shiny tile floors.

Outside the family home, Mr. Zhang’s mother, who is in her 60s, recalled being puzzled by Ms. Kanwal’s reactions.

“She is religious, so when she came here I went out of my way not to give her any pork,” she said, as a small guard dog barked nearby. “I stir-fried chicken and made egg omelets for her. But no matter what I served her, she just refused to eat.”

Some of the more sordid stories of prostitution are probably true. And, it seems from the story that some of the girls who moved to China are pregnant, and reasonably happy where they are. But it seems clear from the piece that many of the stories are grayer and not so clear.

The mother-in-law above seems well-meaning, after a fashion, but one can see the perspective of a young Muslim girl from Pakistan, encountering a world filled with pork, dogs, and without the washing facilities she was used to. Additionally, the reporters seem to agree that the farmer was prosperous, if not necessarily wealthy. With no real linguistic common ground, it’s pretty easy to imagine that wires could get crossed her.

Right now these stories are exotic. But if more and more girls stay and settled down in China, that will result in positive word of mouth. The precedent with other Asian countries is tragic and horrible stories will continue. But that may not be the whole, or the main, story.

May 26, 2019

Open Thread, 05/26/2019

Filed under: Open Thread — Razib Khan @ 2:39 pm

I’m having issues with the server load on this website in the past week. No idea what’s going on…I suspect that it has to do with WordPress plugins. I’ve tweaked caching and added Cloudflare. We’ll see.

Since this website is kind of intermittent right now, remember to bookmark or note:

* My newsletter.
* My content (RSS).
* Follow me on Twitter.

As you can see I’ve replaced the Twitter widget with pinboard. I still check Twitter for direct messages but have started phasing that out as a way to communicate with people in a reciprocal two-way fashion.

Speaking of Twitter, a friend who is a professor at a major research university told me that first-year graduate students, on the whole, were not interested in joining Twitter. Some of this is probably generational (the youngest of these students are probably “Generation Z”), but some of it might be that Twitter has a reputation for nastiness.

What books are you reading?

Vital stats in South Asia

Filed under: Statistics — Razib Khan @ 12:52 pm

A bunch of vital stats from South Asia from Google Data Explorer. Since Zach and I started looking at these data since the early 2000s Pakistan and Bangladesh have diverged, unfortunately. I don’t understand what’s going on with Bangladesh’s anomalously high adolescent fertility though. This could be a function of variation among women as they age, with those entering the labor force delaying childbirth and the number of children so much that it brings the whole average down.

And of course, the whole comparison between India and the other countries is difficult since the Indian statistics average together many different regions.







Browncast Ep 42: American Arranged Marriage

Filed under: Podcast — Razib Khan @ 12:05 am

Another BP Podcast is up. You can listen on Libsyn, AppleSpotify, and Stitcher. Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe at one of the links above.

You can also support the podcast as a patron (the primary benefit now is that you get the podcasts considerably earlier than everyone else…this podcast was posted a week ago).

Probably the number #1 reason that the “Browncast” is of interest to me is that I can talk to people who are different from me in some deep and important manner. This podcast is a conversation with Amit, an Indian American who is doing a medical residency. Raised on the “best coast” of the USA, after some conventional dating travails, he has decided he will go the route of an “arranged” matched.

If you listen, you will see that the process has been a positive one for Amit, and it includes much more flexibility and volition than most Americans might imagine.

I went into the discussion mildly skeptical and came out of it with an appreciation for how people can make different choices, but those choices are probably the best for them.

I would really appreciate if regular readers/commenters would leave more positive feedback/ratings, especially on Apple and Stitcher.

May 25, 2019

Murray Gell-Mann, R.I.P.

Filed under: Murray Gell-Mann,Physics & Space — Razib Khan @ 10:16 pm

Murray Gell-Mann, Who Peered at Particles and Saw the Universe, Dies at 89:

Murray Gell-Mann, who transformed physics with his preternatural ability to find hidden patterns among the tiny particles that make up the universe, earning a Nobel Prize, died on Friday at his home in Santa Fe. He was 89.

The author of the obit wrote Strange Beauty: Murray Gell-Mann and the Revolution in Twentieth-Century Physics.

I’m not as broadly read today as I was when I was younger. Much of my teen years were spent reading popular science books on physics. Murray Gell-Mann regularly made a showing, whether as a principal character, or a cameo. He was one of the great ones of our world, and his passing makes us all poorer.

The decline of the bee

Filed under: Culture,Spelling Bee — Razib Khan @ 3:41 pm


At the Spelling Bee, a New Word Is M-O-N-E-Y – Elite spellers now can pay to get a spot in the national event. For this generation of zealous competitors, it just means another chance to shine:

An extra factor driving the stakes for this generation of spellers is a concerted effort by non-U.S.-born parents, particularly Indian-Americans, to make a mark on the competition. In 1985, Balu Natarajan was the first child of immigrants to win the Scripps bee. Of the 33 contests since then, fellow Indian-Americans have won 17 more, including the last 11 straight.

Indian-Americans, just 1% of the U.S. population, have established their own minor-league spelling bee circuit that adds opportunities to hone on-stage performance. They have led the way in paying for coaching, buying or developing proprietary study software and traveling to participate in more bees. Many spellers’ parents came to the U.S. via the Immigration Act of 1990 that admitted exceptionally skilled immigrants who specialize in STEM topics. It is no mystery that they would value education—and recognition of it—above all else; it is the very thing that gave them access to this country.

Reminds me of the stuff in Jerry Muller’s The Tyranny of Metrics. Now that the national bee is going in this direction it will be impossible to reverse the trend and make it a test of childhood exuberance and passion, as it was until recently. Rather, it will be just another part of the meritocratic conveyer belt, another notch in one’s resume or c.v.

And, unfortunately, it illustrates one of the effects of the rise of Asian American immigrant parents, who come from extremely competitive societies, and so bring the same ethos to the United States. Childhood in the old sense is disappearing, as people begin to prepare their children for adult roles in the economy before they enter elementary school.

The decline of the bee

Filed under: Culture,Spelling Bee — Razib Khan @ 3:41 pm


At the Spelling Bee, a New Word Is M-O-N-E-Y – Elite spellers now can pay to get a spot in the national event. For this generation of zealous competitors, it just means another chance to shine:

An extra factor driving the stakes for this generation of spellers is a concerted effort by non-U.S.-born parents, particularly Indian-Americans, to make a mark on the competition. In 1985, Balu Natarajan was the first child of immigrants to win the Scripps bee. Of the 33 contests since then, fellow Indian-Americans have won 17 more, including the last 11 straight.

Indian-Americans, just 1% of the U.S. population, have established their own minor-league spelling bee circuit that adds opportunities to hone on-stage performance. They have led the way in paying for coaching, buying or developing proprietary study software and traveling to participate in more bees. Many spellers’ parents came to the U.S. via the Immigration Act of 1990 that admitted exceptionally skilled immigrants who specialize in STEM topics. It is no mystery that they would value education—and recognition of it—above all else; it is the very thing that gave them access to this country.

Reminds me of the stuff in Jerry Muller’s The Tyranny of Metrics. Now that the national bee is going in this direction it will be impossible to reverse the trend and make it a test of childhood exuberance and passion, as it was until recently. Rather, it will be just another part of the meritocratic conveyer belt, another notch in one’s resume or c.v.

And, unfortunately, it illustrates one of the effects of the rise of Asian American immigrant parents, who come from extremely competitive societies, and so bring the same ethos to the United States. Childhood in the old sense is disappearing, as people begin to prepare their children for adult roles in the economy before they enter elementary school.

May 23, 2019

Was India ever really “secular”?

Filed under: Election 2019,Politics — Razib Khan @ 6:09 pm

Anton Wessels, a Reformed Christian professor of “missiology”, wrote a book many years ago, Europe: Was It Ever Really Christian? The title reflects on the fact that a secular ‘post-Christian’ Europe may never have been very Christian at all, at least in Wessels’ telling.

Wessels writes from a Reformed Protestant perspective. This tradition has taken a very dim view historically of ‘popular folk religion’ during the medieval period in much of Northern Europe. Wessels’ catalog of non-Christian beliefs and practices before and during the Reformation emphasize that from the perspective of a confessing Reformed Protestant it may actually be a fact that most of the population never truly internalized in the gospel, even if they made outward show of affiliation with the Christian religion. Christendom was nominal, not substantive.

There are many arguments one can bring to bear to critique Wessels’ views. In particular, some historians of religion assert that in fact, late medieval piety resulted in the spread of genuine deeply held Christianity to the peasantry of much of Europe. The argument then is that this sincere Christianity is actually one reason that the Reformation occurred when it did. Additionally, even granting Wessels’ contention about the medieval period, the competition between Protestants and Catholics after 1500 guaranteed attention to popular beliefs and practices for several centuries before secularization. The suppression of pagan practices among Lithuanian peasants occurred during the period when Catholic clerics were fighting off the expansion of Protestants.

And yet I think we need to give the nod to some element of Wessels’ thesis: that popular Christianity was quite distinct and different from the faith promulgated from on high, and officially claimed as the ideological basis of Western societies. Perhaps the rise of modern secularism is in some ways the proletarianization of European culture?

What does this have to do with India? In the comments below, and in the media, some Indians are bemoaning the death of secular India. But was India ever secular truly? Nehru was an agnostic. His great-grandchildren now make a show of attending Hindu temples and asserting their Brahmin lineage.

I grew up in the United States of Ameria with the children of elite Indian Americans, who left in the 1960s and 1970s. These people were all urbane, and most of them were not particularly religious. But, like my own parents, they were all very self-conscious of their “communal” identity. These were people who grew up in a “secular India”, and moved through good universities. Because of the times, and when they left, many still retained socialist sympathies (as my own parents do). But, these were not liberal cosmopolitans. Most of their children were absorbed into American culture, but they were products of something very alien to liberal individualism.

The India that people are mourning was a weird chimera. Traditional, collectivist, and communal on the broad level. But ruled by a small English-speaking elite with cosmopolitan pretentions, Macaulay’s children. Generations of secularism and socialist rule did not erode the ancient foundations of Indian society, with caste and community reigning paramount.

What we are seeing is the death of the chimera and the revolt of the middle class. True change and secularization are going to occur only with broad-based prosperity and urbanization. Secular socialist India couldn’t bring that, and so nothing changed on the fundamental structural level. Its failure laid down the seed-bed for the emergence of the Hindu Right, which draws deeply at the well of communal sentiment which is stitched throughout the fabric of Indian society.

The Jomon contributed little to the Japanese

Filed under: Historical Population Genetics,Japan — Razib Khan @ 5:00 pm

A few months ago there was a preprint with an ancient Japanese genome, Jomon genome sheds light on East Asian population history. I read it but didn’t say anything at the time. I read it again, partly because I’m reading a history of Korea where the Wa, the early Japanese, show up to intervene in mainland affairs. This cameo made me think more deeply about what happened in Japan several thousand years ago.

The above genome comes from Honshu, and dates to 2,500 years before the present. And yet it’s quite different from modern Japanese! Here is the abstract:

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

Let me be frank: the term basal probably is somewhat misleading. Ancient DNA in East Asia is in its infancy. We don’t really know what’s going on, and what went down. But I can offer a guess.

I think in the next few years we will realize that there was a massive demographic expansion out of a few agricultural hearths in the eastern regions of what we now call China during the early Holocene. The Sino-Tibetan peoples, Austro-Asiatic, and Austronesian are derived from this series of expansions. But with hindsight, I think we will see that the peoples to the north and east of China proper, are also downstream of this agricultural revolution.

Within China proper a secondary expansion occurred, dating to the rise of the Chinese civilization. This ‘erased’ a lot of the variation in southern China, and a quasi-panmixia was enforced through the Chinese dynastic cycles, as northerners moved south and vice versa.

In the first figure, the Treemix panel shows that only ~3% of the modern Japanese ancestry needs to be accounted for by an edge from this Jomon genome. This implies that there was massive population replacement of the Jomon by the Yayoi people, from southern proto-Korea. I say “proto-Korea,” because the origins of the ancestors of the modern Korean culture seem to be located much further north, in what is the border region of Manchuria and North Korea today. The Yayoi is quite possibly derived from one of the indigenous peoples of the southern Korean peninsula, who were assimilated by the expanding Koreans as they moved southward around 0 A.D.

Within the preprint, the authors seem to converge on two facts. First, the Ancestral North Eurasian (ANE) admixture into much of East and Southeast Asia was minimal but much more substantial in Siberia. This is entirely plausible, though I think there needs to be more ancient East Asians besides Tianyun to conclude there isn’t some basal fraction The authors suggest that shared drift between Hoabinhian hunter-gatherers in ancient Southeast Asia and the Jomon individual confirm the likely southward origin of modern-day East Asians. I suspect the inference is correct, though I don’t know the shared drift tells us that much without more samples.

In the preprint, the authors observe that this is a much stronger affinity among coastal East Asians to the Jomon sample than from interior peoples. I don’t know what to say about this, except that it seems likely to me that coastal pre-agricultural populations would have greater numbers than interior peoples.

The steel and the star

Filed under: Agriculture — Razib Khan @ 2:26 pm

I recently recorded a podcast with Anders Bergstrom discussing his paper from a few years back, A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea. This got me to thinking a bit about the patterns over the last ~5,000 years within the island, and more broadly. The island of New Guinea is about the size of Texas. That means it’s a bit larger than France. Much of the population is concentrated regionally in the highlands, where a productive system of gardening agriculture dates back 7,000 years.

One of the main results from Anders’ paper is that though New Guinea seems to undergone demographic expansion with the rise of agriculture, there is no evidence of star-phylogenies on the Y chromosome that you see elsewhere in the world, and genetic distances between populations seem to be rather high at a local scale. You’ll have to listen to the podcast (I think it will probably go live in August, so just subscribe) to get the precise way Anders said this, but one thing I got from the conversation is that the cultural and genetic diversity of the highlands is a function of evolution after a Neolithic expansion of a more homogeneous population. That is, I had assumed that the “Papuan” language family was an artificial construct where a bunch of different unrelated dialects was thrown together, but it seems perhaps they have a common genetic origin in an ancestral population that took up taro farming.

This has huge implications for the rate of linguistic evolution of human societies. Like genetic diversity linguistic diversity emerges in the context of cultural parameters. For example, without literacy and widespread trade, one can imagine oral dialects diverging rapidly. Similarly, without gene flow between neighboring populations, they can rapidly differentiate with small effective populations.

One thing I wonder about is how similar this was the spread of swidden agriculture in Europe. Where the Cardial and LBK cultures originally homogeneous, but eventually fractured into small paramountcies? And why and how did the steppe-derived populations roll over these populations so quickly, and give rise to the ‘star-phylogeny’ Y chromosomes we see today?

Bergstrom makes some general allusion to the emergence of metal. But at this point, geneticists usually pass the buck to prehistorians, archaeologists, and economists. What about the rise of metals resulted in the explosion of paternal lineages, and cranked up gene flow between neighboring populations?

The easy way to explain this is that spears and swords of metal impose the rule of the few upon the many. But I think we need to consider the economic consequence of widespread metal (especially iron) in agriculture, where clearing virgin and the second-growth forest became much easier for peasants, and the social and manufacturing systems needed to produce metal weapons and tools at scale. Combined with the mobility of the horse, the shift into the Bronze and Iron Age across Eurasia resulted in the rise of an almost totalitarian and globalist social order in comparison to the localized and decentralized village societies of the Neolithic.

May 22, 2019

Indian Elections 2019 Thread

Filed under: Open Thread — Razib Khan @ 8:24 pm

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:42 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

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