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

June 21, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:49 pm

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

An American twist on “joint-family” (?)

Filed under: Culture — Razib Khan @ 9:06 am

June 20, 2019

Of proteins and paleontology

Filed under: Evolution,Genetics,protein,science — Razib Khan @ 9:04 am
Ostrich egg

Ancient DNA has transformed our understanding of the biological past. The sequencing of mammoths, moa, and Neanderthal have opened up a window upon evolution which we had previously only perceived through material remains. Whereas 20 years ago there was only one human genome, today there is an excellent whole genome of a species of human we had not even known existed a generation ago.

Genetic information from the past is so useful because it fills in the gaps of the tree of life. With modern species, scientists have to “infer” the relationships based on assumptions within particular phylogenetic models. Ancient DNA allows them to fill in deeper “nodes” within this tree with a high degree of confidence.

While a skeleton has a great deal of information and allows scientists to make evolutionary inferences, DNA consists of discrete bits which reflect the whole past genealogy of an organism many generations ago.

But there is a downside to DNA: it degrades. Where fossils can be preserved for billions of years, the oldest DNA sequence dates to ~700,000 years ago. There are vast quantities of ancient DNA today in databases, but a very high proportion dates to the last 10,000 years, and an overwhelming number to higher latitude samples.

The decreasing concentration of ancient DNA

In fact, the ~1,000,000 years may be an upper bound for how far back ancient DNA is viable for sequencing analysis. The concentration beyond this point of DNA from the sample itself is just too low to extract it out of bacterial contamination. This does not even consider the reality that in tropical and moist climates the conditions are far less amenable to long-term preservation.

But are fossils the only alternative then for paleontologists? It turns out not. DNA is not the only molecule from ancient remains that is useful for scientists. There are proteins!

Proteins are the product of processes which start with DNA:

DNA is transcribed to RNA which is translated to protein

And, they are far more robust than DNA. Proteins have been extracted from ostrich eggshells in Tanzania dated to 3.8 million years ago. Note that not only does this smash the 1 million year barrier, but it is also from a hot climate where DNA degradation is such that very ancient dates are unlikely in the first place.

That being said, there are limitations to protein analysis. Only about ~1% of the human genome, the exome, is translated into protein. And that proportion of the genome is often less diverse than the other proportions. This is due to the fact that mutations in functional regions of the genome are often strong selected against, as they are more likely to “break” something.

As genetic variation is the raw material for phylogenetic analysis, this means protein sequence will be less informative than DNA sequence.

The second major issue is that protein extracted from bone, dentine, and enamel, to name a few tissues preserved in mammals, is not representative of all the proteins in the body. While DNA is the whole sequence, only a subset of DNA is expressed in particular tissues at particular times. This means that the proteins will differ across the body, and some proteins are going to vary a great deal less than others due to their importance in many species. Collagen is the most abundant protein, so it is not surprising then that the analysis of protein sequence will focus on the collagens.

Because protein offers less information, it will be less useful for generating subtle population genetic statistics than DNA. Rather, ancient protein analysis will shine in taxonomic identification of remains.

In the context of humans, this is relevant, because the hominin lineage dates to considerably earlier than 1 million years ago. The famous discovery, Lucy, dates to 3.2 million years ago.

Over the next few years, ancient protein analysis will become more refined and powerful. It is quite possible that that the “family tree” of our species before 1 million years ago will be rearranged by geneticists again, just as our more recent ancestry and relationship to Neanderthals has been revolutionized. Ancient proteins may aid in resolving who our “first ancestors” actually were….

Of proteins and paleontology was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

June 19, 2019

The Insight Show Notes — Season 2, Episode 32: Tibetan Denisovans!

Filed under: Denisovans,Genetics,paleontology,science — Razib Khan @ 2:50 pm

The Insight Show Notes — Season 2, Episode 32: Tibetan Denisovans!

Denisovan Mandible

This week on The Insight (Apple Podcasts, Spotify, Stitcher, and Google Podcasts) Razib talks to Dr. Frido Welker, a pioneer in the field of ancient protein phylogenetic analysis of human remains. We talked about the recent finding of Denisovans from the highlands of Tibet, work on which he was a researcher.

The paper, A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau, uses protein analysis to find that an ancient sample from Tibet clusters with the Denisova genome. This is important because this is the first confirmed publication which reports on a Denisovan outside of the Altai cave site in Siberia. The authors did not find DNA, so they had to make recourse to protein, which is more robust than DNA.

Using a few positions they inferred that the Xiahe sample was closest to the Denisova cave sample.

Because they had a mandible, the authors confirmed again the robustness of the Denisovans (the teeth of the Denisova cave sample were inordinately large, but that was a single sample). Along with a skull cap reported at a conference in March, this brings confirmed Denisovans to three individuals across Northeast Asia. This, despite the fact that in terms of genomics the most “Denisovan” modern populations are those far to the southeast, in Oceania.

We also discussed how protein analysis will complement ancient DNA analysis. Though proteins have less informative variation than DNA, they are likely to last much, much, longer. The oldest agreed ancient proteins being from nearly 4 million years ago!

The Insight Show Notes — Season 2, Episode 32: Tibetan Denisovans! was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

June 18, 2019

Urbanization in the 21st-century

Filed under: Geopolitics,Urbanization — Razib Khan @ 9:58 pm

The world turned upside down

Filed under: Culture — Razib Khan @ 12:43 am

They are told it’s the Kali Yuga, and they rejoice!
The Dharma and the Dao are needful
As they are what not to do!
Striving to virtue is sin,
Abnegation of indulgence the ultimate betrayal of self.
There is no god above to glorify,
Just a sense to glory in….

June 17, 2019

Genetic change, cultural coherency, and social structure

Filed under: History — Razib Khan @ 11:52 pm

A stupid commenter (SC) below keeps opining that the high frequency of R1a across South Asia is due to non-paternity events (NPE). I’m not quite sure SC knows what NPE is. It is, “when someone who is presumed to be an individual’s father is not in fact the biological father.” The hypothesis presented seems to be that outside of the Northwest of the subcontinent, the high frequency of R1a among non-Brahmin populations is a function of cuckoldry.

I think this is a stupid hypothesis for several reasons.

  1. Star phylogenies tend to extend outside of their core sociocultural group (e.g., R1b in Basques)
  2. NPE events outside of ethnicity seem rare given how endogamous South Asian jatis are.
  3. NPE in Eurasian societies seem to be 1-3%.
  4. There isn’t autosomal variation in ancestry within South Asia jatis usually. E.g., autosomally Tamil Brahmins or Chamars don’t vary much. This is in contrast with Mexican Americans or African Americans, who show a great deal of biogeographic variation in ancestry because they are a recently admixed population.

But, in the interests of making lemonade out of SC’s lemon, it’s interesting to observe other cases of disjunction between genome-wide ancestry and Y chromosomes. For example, let’s look at the Hui, Chinese-speaking Muslims.

The most likely origin of these Muslims is during the Yuan dynasty. So about 750 years ago. They were probably originally Central Asian, and so a mix of West and East Eurasian. Around 40% West Eurasian Y chromosomes from the beginning is not totally unreasonable if Islamicized Turks were a substantial proportion of the Muslims. If 5% of their total genome is West Eurasian, it’s probably reasonable to assume that 10% of their total genome derives from Muslims, if the original Muslims about half West Eurasian and half East Eurasian in ancestry.

750 years is 30 generations. My back of the envelope calculations suggests that 7.75% exogamy with Han Chinese per generation would result in a 50% West Eurasian population become a 5% West Eurasian population.  Another way to frame this is about ~90% of the ancestry of the original founding group has been replaced. But what about the Y chromosomes? Even assuming 100% West Eurasian Y chromosomes, the decrease has not been of similar magnitude.

The answer is simple: the dilution could have been mostly female-mediated. China is a patrilineal society, and Central Asian Muslims are also patrilineal. Though there are exceptions (there is a Hui branch of the Kong family due to one of the descendants marrying a Muslim woman and converting to Islam), it seems reasonable to infer most of the gene-flow into the Muslim community was through women. And, women do not have Y chromosomes, and so do not replace that lineage, though they do contribute to the total genome.

This is not an isolated case. There are populations around Lake Chad which carry ~1% Eurasian autosomal ancestry, but with Y chromosomal fractions of R1b, which is Eurasian, on the order of ~20%.

The opposite case can also occur. Because of male-biased European gene-flow to Latin America, populations such as in Argentina can have a very high fraction of indigenous mtDNA, passed from mothers to their offspring, despite the total genome being mostly European.

Which brings us back to South Asia. Though R1a is associated with “upper caste” populations, the reality is that it is widely distributed in South Asia. Including tribal groups such as the Chenchus and Bhils.

The Chenchus are an interesting case. The only groups nearby with high frequencies of R1a would be South Indian Brahmins, who are genetically very distinct. In fact, Brahmins from the four southernmost states of the peninsula are very similar in their proportions of distinct biogeographic components. And, there is not much inter-individual variation. The Chenchus, in contrast, seem to be typical ASI-shifted tribal people from South India.

In an NPE model the ~25% R1a ancestry is due the fathering of sons by Brahmin males, who were raised by their Chenchu mothers as Chenchu (and presumably raised by Chenche males as their own sons). The problem is that then ~12.5% of the ancestry of Chenchu should be Brahmin. This introduces a noticeable steppe shift, and though 12.5% is a small fraction, one should be able to detect it. Additionally, if the R1a entered the population through introgression every generation, there should be variation in ancestry among the Chenchus as a function of biogeography.

I simply don’t see this in the data for the Chenchu. What could explain their high fraction of R1a?

There are two things to consider. First, these marginalized groups often have low effective population sizes due to extreme endogamy. This means the power of drift at a single locus, such as the Y, is strong in these groups. It is not unreasonable to posit some groups, such as the Chenchu, would drift to a higher frequency.

The second dynamic is the one alluded to above: the Chenchu descend from a compound of groups, and a core paternal lineage of R1a bearers was assimilated into a larger population. I see the expansion of R1a across South Asia as greatly synchronous with the development of the ethnolinguistic landscape we see around us. Tribal groups such as the Chenchu are not primal, but part of an ethnolinguistic tapestry which crystallized in the period after the fall of the IVC and the reemergence of India into history in the 6th century BCE.

Note: Will delete dumb comments

Why the Diaspora is not as interesting to me

Filed under: Culture,Diaspora — Razib Khan @ 10:25 am

A friend of the podcast mentioned with a bit of surprise that so much of it was focused on India as opposed to the Indian Diaspora (you can substitute “South Asia(n)” into “India(n)”). When this weblog was started at the end of 2010 it was probably more Diasporic in orientation. That was the era when Sepia Mutiny was winding down, after all.

Today I’m not as interested in Diasporic topics for two reasons. First, the Diasporic identity in the USA is pretty stable and clear. Most Indian Americans are basically Americans with their own particular cultural twist or accent.  This is widely understood. In particular, culturally young Indian Americans have assimilated to the same broad identity as liberal white Americans (with some exceptions). The big questions of who and what brown Americans are going to be seem to have been answered.

The second issue is that India is a bigger deal today than it was in the 2000s. From a purely anthropological perspective, what’s going on with 1.3 billion Indians (+ 400 million other assorted South Asians) is more interesting to me than the concerns of tens of millions of Diasporic browns.

(the exception is something like an interview with an India American going through the modern arranged marriage; in contrast, telling me you only date other South Asians is not too interesting, as it’s basically what everyone else does, but brown)

June 14, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:48 pm

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

What The All-Father Means

Filed under: Genetics,History,R1a1a — Razib Khan @ 4:35 pm

Readers of this weblog may sometimes notice that I break out in pompous and self-important declarations of being a “scion of the All-Father.” This is basically a joke. But, it’s a joke that draws from a legitimate basis of science and mythology. The “All-Father” is another name for Odin. I’m really talking about Indra, who is probably more like Thor. And obviously, Norse paganism is only distantly related to the mythology of the Indo-Aryans. As someone more familiar with the lineaments of Northern European mythology than Indian, of course, it’s easier for me to draw on the motifs of the former to relate to the latter.

R1a distribution

The scientific component has to do with R1a. Specifically, R1a1a, defined by the M17 mutation (discovered by my boss at my day-job 20 years ago). There are two very closely related “clades,” that is, families of pedigrees, of this Y chromosomal lineage, passed from father to son. One of them defines mostly European R1a1a, Eastern Europeans, and to a lesser extent Western Europeans. Another branch is found mostly in Central and South Asia.

When I first saw this distribution around the year 2000 it left me scratching my head. Of course, I knew about the Indo-European languages. But I had always assumed that the demographic impact of the original Indo-Europeans was relatively marginal. And yet this Y chromosome was found at frequencies in the 10-50% range across vast swaths of Eurasia.

Much of the 2000s was spent on arguments as to whether R1a was indigenous to South Asia or to Central Eurasia. Ultimately these arguments were not resolvable due to limitations of the data. To calibrate dates and diversity researchers relied on microsatellites, which are useful due to their high mutation rates, but also erratic for the same reason (not only were confidence intervals wide, some of the assumptions of the model parameters were guesses).

In the early 2010s, whole-genome sequences of Y chromosomes came online. It became very clear that the most common R1a1a lineages exhibited the “star phylogeny.” Demographically, what this means is that men carrying this lineage underwent very rapid population expansion for a short period of time. So rapid that a “father” lineage would give rise to numerous “son” lineages one mutational step away

You can see in the figure that node “A” has given rise to a “star phylogeny.” A large number of individuals are one mutational step away from that genotype. A more normal phylogeny would produce a complex structured tree which accrues mutations across the various branches gradually.

In the South Asian context, a paper from 2004, Independent origins of Indian caste and tribal paternal lineages, introduced a result which prefigured what we now know:

Analyses of molecular variance also suggest that caste groups are more homogeneous for Y chromosome variation than tribal groups, since the variance among caste groups (sampled from all over India) is 3-fold less than that observed among tribal groups and 2-fold less than that observed among all Indian populations grouped together (Table 3). Moreover, if only north caste groups are considered, the variance among populations is not significantly different from zero (Table 3), indicating that spread over the Indian subcontinent although they are located up to ∼1500 km away from each other, these populations have highly homogeneous Y chromosome compositions.

The implications of the lack of structure of R1a on the Indo-Gangetic plain is always something that struck me. It suggested that the paternal lineages only recently expanded since they didn’ have time to build up distinct regional mutations. In contrast, the adivasi populations had a wider distribution of Y chromosomal haplogroups, and they exhibit a lot deeper diverged lineages.

Which brings me to the personal angle. In the spring of 2010, I did my first personal genomic test. I got my Y and mtDNA results back first. It turned out my Y was R1a1a, and my mtDNA was U2b. I was surprised by both. Eastern Bengali has the highest fraction of mtDNA macrohaplogroup M in the world. R1a1a was less surprising. But, it was very strange to have a concrete, personal, connection to this lineage which had been on my mind for a decade or so.

My funny attachment to my haplogroup is probably a function of my upbringing. Growing up as brown in the United States, I wasn’t exposed to Indian culture, nor was I well versed in the details of South Asian communalism. My family is pretty conventional in being upper-middle-class Bengali Muslims, so there is not a jati identity or anything like that I could identify with (and though my parents are Muslim, they are not extremely so, therefore religious identity was a background and not foreground variable). When I looked at my overall genome in 2010 it was clear I didn’t have the “runs of homozygosity” that characterize many people from South Asian backgrounds who come from endogamous communities. I know some of my ancestors were Kayasthas, and my father has some Brahmin ancestry, but the most distinctive thing about me in hindsight is I’m a typical east Bengali with more than a usual dollop of East Asian ancestry (my family is from Comilla).

My Y chromosomal haplogroup, in contrast, is something clear, distinct, and precise. It is an anchor, something which I use to channel my preoccupations and concerns. I don’t have Omar’s Gujar tribal ancestry, or Zach’s Muhajir/Persian origins. I’m just a brown American whose parents did not instill him a patriotism about the “motherland” (Bangladesh), because they themselves didn’t even live a decade in that nation. Though there is a spectrum, it is clear that many South Asian Americans are less “coconut” than I am, and are attuned to fine differences of status, origin, and background. Growing up around only white people my identity was racialized, not ethnicized.

I have never felt superior or inferior to any community or ethnicity of South Asian because I never belonged to any community, have weak ethnic identity, and don’t believe in any religion. The religious prejudices I do have are probably Anglo-Protestant ones against Catholicism, because of the implicit assumptions and background facts of America’s Whig culture.

What R1a1a symbolizes to me is that I have a concrete connection to a semi-historical phenomenon between the end of prehistory and before the written word, which we have not grasped or understood very well. Though it is true R1a1a is found at higher concentrations in “upper castes,” as well as in the north and west of the subcontinent, and among Indo-Aryan speakers, the reality is it is found in almost every community in South Asia (the main exception being among Tibeto-Burmans and Munda). There are many communities, such as Chenchus, which have very little steppe ancestry but retain a substantial proportion of R1a1a.

For obvious reasons this haplogroup is associated with Indo-Aryans (the earliest find of R1a1a-Z93 is from the Bronze Age Volga Srubna culture), but its reach is far beyond current areas of Indo-Aryan speech. Its ubiquity is a testament to a broader South Asia cultural matrix that emerged in the centuries after 1500 BC, from north to south.

This is of course not a moral judgment. The expansion of this paternal lineage at the expense of others likely occurred through a process of aggression and social exclusion. This is nothing to be proud of…or ashamed of. It’s just a description.

June 12, 2019

The genetics of obesity is about the environment

Filed under: Health,Obesity — Razib Khan @ 11:06 pm
An American classic

In the 1960s the average American man weighed 166 pounds. Today, the average American man weighs 195 pounds. In the 1960s the average American woman weighed 140 pounds. Today, the average American woman weighs 166 pounds. According to the CDC, nearly 40% of Americans age 20 or above are obese. Using the same criteria, less than 5% of Japanese are obese.

Genetically, we know that obesity is more than 50% heritable. That is, within populations, more than 50 percent of the variation of weight is due to the variation of genes. Yet change over a few generations in the distribution of weight implies that genes are not producing a simple outcome here.

Very few genes can explain much of the variation in weight, though on the whole many many genes can explain much of it aggregate.

The FTO gene is one of the major loci implicated in obesity. Those who carry two copies of the “risk” allele are 1.67 times more likely to be obese and are on average 7 pounds heavier than those who carry no copies of the risk allele (those who carry a single copy are 3 pounds heavier, on average). This is not trivial, but neither is it that big of a deal.

Rather, obesity is a highly polygenic trait when it comes to how genetics impacts weight.

There are innumerable genetic factors, some of them implicated in metabolism, while others have to do with satiety and impulse control. This also explains why obesity has varied so much across generations (in the United States) and today varies so much between nations: genes only express themselves in a particular environmental context. There is a “norm of reaction” in a particular environment so that the same genetic profile can result in very different outcomes.

A “Philadelphia Cheesesteak”

Many health professionals argue that the American diet and lifestyle today is very “obesogenic.” Classic 20th-century American foods are often rich in fats, sugars, and processed carbohydrates, which deliver huge servings of calories in massive doses. Calorie density is a feature, not a bug. Extremely palatable processed foods were the end result of an extremely productive agricultural and industrial system.

Meanwhile, whereas 40% of Americans were farmers in 1900, only 2% were in the year 2000. Instead of work that requires physical activity, more and more Americans are office dwellers.

In a world where everyone walked everywhere, daily life was consumed by physical activity, and famine was a constant threat. Latent genetic variation that might result in differences in susceptibility to obesity would not be particularly relevant.

Americans today live in a world where very little of their income goes to food, and calories are in surplus.

Modern agriculture has escaped the “Malthusian trap”

Genetic risk factors in obesity become noticeable in an environment where obesity is common. Historically, the modern period has been an aberration, as humans have escaped the “Malthusian trap,” growing more and more food, while family sizes have decreased. In other words, only in the past century or so in much of the world has the question of the “heritability” of obesity become something that could have been a question in the first place.

Obesity is correlated with many other issues that impact both mortality and morbidity. The past several decades of caloric plentitude and a shift away from manual labor have been beneficial on the whole to human life expectancy and well-being. Famine has become rarer and rarer. But life is often about tradeoffs and as the threat of malnutrition has faded, so the downsides of excess calories have come to the fore.

In this obesogenic environment, genetics can help predict those who are at particular risk for obesity. But genetics is not a solution in any way for the rise of obesity in developed societies, because that rise is due to conditions of the environment.

The genetics of obesity is about the environment was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The Insight Show Notes — Season 2, Episode 31: Obesity & Genetic Prediction

Filed under: cardiology,Genetics,Health,Obesity — Razib Khan @ 3:13 pm

The Insight Show Notes — Season 2, Episode 31: Obesity & Genetic Prediction

This week on The Insight (Apple Podcasts, Spotify, Stitcher, and Google Podcasts) Razib talks to Dr. Amit Khera, a cardiologist, and geneticist. We talk about the relationship of genetics to obesity, and the advance of polygenic risk prediction models.

About 30% of Americans are obese, which is defined by a body-mass-index above 30. A further 30% are overweight. Obesity is strongly correlated with a variety of diseases, such as arteriosclerosis and late-onset diabetes. It is also highly heritable, meaning that most of the variation in the American population in the trait is due to variation in the genes. This does not mean that it is a deterministic trait, where certain genes guarantee a particular outcome.

Rather, obesity is the outcome of a host of causes, with the genetic impact being due to many loci.

Only a few genes, such as FTO, actually have a major effect. That means that there are no “fat genes” for most individuals. Rather, there is a wide range of risk factors which lead to obesity. A new paper, with the lead author being Dr. Khera, aims to predict individuals at particularly high risk, Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood.

Though the predictions are modest in consequence for most people, they are highly informative at the extremes. Individuals who are tagged as at high risk for obesity are many times more likely to actually be very obese.

That being said, there is a fair amount of work that polygenic risk scores are highly sensitive to other variables. Though obesity is very heritable, obviously environmental context matters. Americans as a whole have gotten much more obese over the past 50 years despite no change in the underlying genetics.

The Insight Show Notes — Season 2, Episode 31: Obesity & Genetic Prediction was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

June 11, 2019

Between Marx and the mullah

Filed under: History — Razib Khan @ 12:03 am

There is a lot of talk on this weblog about deaths in premodern conflicts. I want to clarify a few points, at least from my perspective.

Both ancient DNA and conventional history and archaeology indicate that massive population turnovers occurred in the past. If you read a book like Genghis Khan: His Conquests, His Empire, His Legacy, you note that there is plenty of record of massacres and killings in targeted fashion during the Mongol expansion. The chaos and demographic collapse induced by the Mongols have been implicated in reforestation across vast swaths of Central Eurasia (which may then have produced climate change!).

We can also look to the deep past, and the more recent past. Latin America is characterized by incredible admixture between people of disparate ancestries. This is due in large part to 1) demographic collapse on the part of native peoples 2) migration of settlers from Iberia 3) transportation of slaves from Africa.

The evidence from Europe and South Asia is also strongly suggestive of massive population replacements. Depending on your model parameters about 50-75% of the ancestors of modern Northern Europeans who were alive 5,000 years ago had descendants who were intrusive to Northern Europe. Another way to say this is that 50-75% of the ancestors of modern Danes did not live in Denmark or nearby regions 5,000 years ago. A similar number for South Asia seems to be in the 10-30% range (again, depends on your model parameters).

This elicits the question: was there genocide?

The evidence from Latin America is clear. Though there was targeted genocide on the part of the Iberian conquerors, on the whole, the deaths were mostly due to the introduction of Eurasian diseases that resulted in a cascade of consequences which resulted in famine (the Black Legend is propaganda which has influenced our modern perceptions). When a human population lives on the Malthusian margin, small perturbations can result in death due to starvation. In the case of Latin America, it is known that incapacitation of a large enough proportion of prime-age adults due to illness resulted in famine, as crops were not planted or harvested in quantities necessary to sustain villages.

In other words, population collapse was a function of reduction in labor inputs into agriculture.

And, the reality is that the Iberian conquerors, who were often younger sons of aristocratic lineages, were not inclined to engage in mass-slaughter due to the reality of their aspiration of becoming rentiers. The importation of African slaves was to a great extent a direct consequence of shortages of exploitable labor (along with the humanitarian concerns of enslaving natives). Contrast this to the situation in the Phillippines or India, where Asian peoples provided resources to support leisure-seeking European elites.

A second fact is that premodern states were not capable of the sort of coordinated genocide that has been seen in the 20th-century. They lacked the weaponry, information technology, and organizational capacity to be particularly efficient. I don’t think it’s a coincidence that the coordinated genocides against Christian groups in the Ottoman and post-Ottoman realm occurred in the modern period (Armenians and Assyrians). The older Ottoman state was neither efficient enough nor did it have the means, to engage in total exterminationism (I also believe that 19th-century European-style nationalism probably made exterminationist feelings more ‘justified’ as well).

Probably the best premodern instance of ethnic cleansing we have on record is the Spanish expulsion of the Moriscos, which occurred on the basis of presumed blood lineage, not belief (e.g., many sincere Christian Moriscos were expelled as well!). But, that effort was incomplete and patchy, effective in some areas, totally ineffective in others, and haphazard in the criteria utilized (e.g., many people with Morisco ancestry were not expelled, while families which had been sincere Christians for generations were expelled).

Which brings me back to the earlier cases. What happened in Europe and India to induce population change?

There are several things going on in my opinion. First, not all late Neolithic/early Bronze Age societies had developed an ideology of elite exploitation to the level that we’d take for granted in the modern world. By this, I mean that the leaders of these agro-pastoralist societies may not have viewed farmers of different ethnicities as potential subjects, and so wealth. In conflicts between hunter-gatherer populations often warfare results in very high mortality rates, with young children and young women of the losers assimilated into the winners. There was no ideology of group assimilation for young men into an alien population, and in societies without specialized professions and economic systems, these men might not be seen as valuable in any sense except as consumption slaves (servants for powerful people, not economic producers).

In other words, conflicts between primitive societies can be thought of as “animal conflicts,” where two groups fight over resources and don’t view the losers of the other group as resources. In contrast, societies over the past few thousand years have tended to see the defeat of the enemy as a potential for elites to accrue new subjects from which they can extract rents. This was one of the arguments made to Genghis Khan by one of his Khitai advisors as to why he should not clear the land of northern China of people so as to create pastures for horses and sheep. People were more valuable than horses and sheep. He would be richer with more people.

Of course, these are people with spears (and later swords). I don’t think that most of the demographic collapse was due to direct killing. Rather, people living on the Malthusian margin, especially the sort of late Neolithic farming that was likely marginal in Northern Europe, were likely subject to the same famine dynamics as occurred in the New World. The IVC zone in South Asia was clearly more advanced, but it too many have been relatively fragile in comparison to the agricultural regimes of later South Asian societies.

The final issue is looping back to Muslims. Did they commit genocide? Did they exterminate the local populations? Probably. But, 95-99% of the ancestry of South Asian Muslims is the same as that of South Asian Hindus of the same region. Unlike the incursion of Indo-Aryans, the arrival of Muslims, mostly Turks, Afghans, and Persians did not have a major demographic perturbation in a direct sense (indirectly, technology and organizational skills introduced by Muslim elites may have resulted in disparate demographic growth of different regions in South Asia; e.g., Eaton’s argument for the expansion into eastern Bengal).

Additionally, Islam as a dominant ideology developed during the high-tide of rent-seeking elites. Though Muhammad’s status as a merchant meant that the religion was never constitutively anti-mercantile, conquest elites invariably aimed to extract wealth out of conquered populations. Arguably, the development of Islam is a direct consequence of how lightly Christianized Arab conquest elites developing an ideology which justified their extraction of rents (“protection taxes”) from conquered populations,  as well as maintaining their separateness and distinctness.

In the Indian context, many will point out that Islamic chroniclers note the despoilation and slaughter upon the local population. I would suggest that one be cautious about the propagandistic nature of ancient conflict and war (this begins with the Battle of Kadesh). Ancient chroniclers seem to have exaggerated numbers and effectiveness routinely. At least in the early modern period, most casualties due to battlefield injuries were the consequence of infection, not immediate trauma. Similarly, I suspect that the depopulation of an invaded region was more likely a consequence of the disruption of local social fabrics more than direct killing with arrows, swords, and spears (killing people expends a lot of energy and is risky).

Because of the nature of this blog, of course, this post ends with the arrival of Muslims to India. The stupid and the disingenuous (or a mix of both) seem to fix on two extreme positions:

  1. Muslims arrived and ushered in an orgy of slaughter driven primarily by the motive of oppressing the kuffar
  2.  Turks arrived in India, and like earlier invaders aimed to extract resources and dominate the location population

These caricatures serve ideologies but don’t describe reality. Both materialist and non-materialist motives need to be considered. The chroniclers of the arrival of self-conscious Muslim military forces to South Asia clearly wished to present it as an ideological and religious act. These were ghazis, just as far to the west, the Ottomans began as ghazis. But it is also impossible not to notice the family resemblance of Muslim Turks moving into South Asia in the centuries after 1000 A.D. with the invasions and conquest of China by Turkic, Mongolic and Tungusic peoples in the centuries after 1000 A.D.

Not surprisingly, the Khitai, Jurchen, and Mongols, all made some ideological claims for their acts of aggression of conquest, often post facto and tenuously. The Khitai and Jurchen integrated themselves into the Han Chinese worldview and presented themselves more worthy stewards of the Mandate of Heaven than the Song rulers of China. The Mongols also did this, though perhaps even more foregrounded was their own peculiar ideology than their sky god had given the whole world to them to subjugate (the Mongol Yuan dynasty also gave special consideration to Tibetan Buddhism, which alienated their Han subjects).

But of course, we would notice that the major consequence of the Mongol Yuan dynasty was the transfer of resources from Han Chinese elites to arriviste Mongol elites. The overthrow of the Yuan resulted in the expulsion of the killing of many of these hated Mongol landlords. Ideological rationales were given, but the memories of Han elite dispossession were fresh.

And yet despite the fig-leaf that ideology provides, differences may result from such distinctions. The Khitai and the Mongols were more punctilious is differentiating themselves from their Han subjects than the Jurchen. They maintained their separateness due to their reduced respect and veneration of Confucian norms. And, notably, the philo-Sinic Jurchen were assimilated into the Han to a far greater extent than the Khitai and the Mongols.

Similarly, in South Asia, the ideological distinctions between the rentier class of Turks and West Asian Muslims, and native Indians was sufficient for the absorptive process to halt. Synthesis occurred. But amalgamation did not proceed to completion. In David Cannadine’s Ornamentalism the author argues that the religious difference was also the key reason that the Indian elite, Muslim, Sikh, and Hindu, did not intermarry with the British gentry.

The various arcs of history cannot be easily defined by grade-school level Marxism, or internet Hindu level psychoanalysis. In all regions that self-conscious Muslim conquest elites established themselves, their sense of distinctness, superiority, and God-given right to rule are clear. But, all these groups, whether it be the slaving regimes of Arabs in East Africa, the Ottomans in the Balkans, and yes, Muslims in South Asia, exhibited a strong orientation toward pragmatic exploitation of the riches of the regions which they conquered.

Addendum: I’m going to delete stupid comments. This means if you leave a 2,000-word comment that’s stupid, it will be for naught.

June 9, 2019

BrownCast Podcast episode 47: Game of Thrones with Jennifer Raff and Patrick Wyman

Filed under: Podcast — Razib Khan @ 8:04 pm

Another BP Podcast is up. You can listen on LibsyniTunes, Spotify,  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…). Would appreciate more positive reviews.

This week Razib talks the end of Game of Thrones with geneticist and anthropologist Jennifer Raff and historian and podcaster Patrick Wyman.

June 8, 2019

To understand Islam one must understand religion

Filed under: Religion — Razib Khan @ 11:09 pm

Over the last few months, the traffic on this website has increased. The proportion of pageviews from India is now approaching parity with the proportion from the USA. To me, this suggests that perhaps it would be useful to outline a few things anyone who has read me in the past would probably know, but new readers will not know. I am in particular aiming this post to moderately above average intelligence readers, such as “Scorpion Eater.” Someone used to being the “smartest person in the room” due to the normal mediocre company of the unread or dull. The sort of person who leaves long comments on other peoples’ posts or articles. There’s a reason they aren’t writing anything original themselves.

In addition to being moderately intelligent, I also want to target the “internet Hindu” segment of the audience. I don’t mean the term pejoratively here, but more as a bracket for a wide range of people of different stances. One of the strangest things about internet Hindus in my experience is that:

1) They, like many Muslims, believe Islam is a religion of preternatural characteristics

2) Despite not being Muslim, and often hostile to Islam, they are convinced they know all about Muslims and Islam, even better than people who might be Muslim or of Muslim origin. They can get themselves inside the minds of Muslims

An analogy might be talking to a white nationalist who is convinced of the unique prowess of black people and seems inordinately confident that they know more about black history than black people themselves.

One thing that both internet Hindus and many atheists have in common is they lack a good intuitive feel for the phenomenology of religion. An internet Hindu or a village atheist will respond to the question of “what is Islam” with “read the Koran!”

I was myself a typical village atheist, or more precisely a philosophical atheist (I had read books like Atheism: a philosophical justification and The Case Against God) in 2003 when I read Scott Atran’s In Gods We Trust: An Evolutionary Landscape of Religion. Atran is a cognitive anthropologist, who treats religion as a natural phenomenon. He is part of the “naturalistic paradigm” within anthropology. A small group of scholars, these intellectuals bring a multi-disciplinary framework to analyzing human cultures, with a strong theoretical basis in cognitive science and evolutionary biology. This is in contrast to the more common “thick description” that is the norm in much of modern anthropology,  which offers few broad generalities (or a Marxist viewpoint, which offers the same generality).

In Gods We Trust is a very dense book. Religion Explained is a similar work but written a bit more accessibly for the lay audience. But you get the picture.

What is the biggest takeaway from cognitive anthropology and religion? That religious phenomenon can best be understood as a manifestation of common psychological intuitions. The reduction of religion to complex theologies is to a great extent a propagandistic narrative promoted by religious professionals, who have written the histories of religion for the past 2,500 years. Those who exhibit mastery of texts, and dispense ritual, will naturally reduce religion to texts and rituals. That’s what they control.

But the underlying psychological impulses remain. This explains why “atheistic” Communist societies so often develop personality cults of charismatic leaders. The religious impulse is simply projected upon a different target.  Strip away the books and the incense, and the human mind still has as the basic fundaments of the religious phenotype.

How does this apply to Islam? In the book Theological Incorrectness, the anthropologist D. Jason Slone reports on his fieldwork in Sri Lanka amongst Theravada Buddhists,  Hindus, and  Muslims. Using psychological experiments, which remove participants from easy to comprehend cues and scripts, he showed that all three religious groups had the same conception of god(s). This is interesting, because, in theory, Hinduism and Islam have different conceptions of gods, while Theravada Buddhism deemphasizes gods.

One reaction to these findings, which tend to be cross-cultural (that is, humans tend to have the same conceptual framework for a god despite theological distinctions), is that believers misunderstand their religion.  I think a better interpretation is that religion can be thought of as two tracks, a conscious verbal track, which is quite superficial, and a deep cognitive track, which is harder to elucidate but primal and universal.

To illustrate, most Christians believe in a Trinitarian God, three persons with one substance. But this is really just a verbal script.  Most Christians don’t even know the technical philosophy of substances and essences which serve as the basis for the Trinity.

All of this brings me back to Islam and the internet Hindu. Muslims are wont to promote a story of a miracle in the Arabian desert 1,400 years ago, and the emergence of the armies of Islam from that desert with Koran in hand. Soon they accomplished a conquest of Persia and much of the Roman Empire.  This incredibly violent and organized religion then smashed against India and raped and assaulted the Hindu civilization. Finally, the assault ended, and India recovered,  though Islam is still a specter haunting South Asia.

I have a revisionist take. I think the most probable model is one where Islam developed organically in the 7th and 8th centuries after the conquest of the Arabs. The Arabs were probably something close to what we’d recognize as heretical Christians but developed Islam to separate and elevate themselves from their subjects. More precisely, Sunni Islam cannot be understood until deep into the 9th century, after the Mu’tazilite period, and the rise of law as the dominant tradition with the Islamic sciences.

The Koran cannot explain Islam because most Muslims were and are illiterate in the Arabic of the Koran, and Islam itself did not develop in its full form until well after various elements of the Koran had already come into being. The weakness of scripture in predicting religion can be illustrated by the fact that the Hebrew Bible is more violent than the Koran,  but Jews have been relatively pacific since the 2nd century A.D. (the reality of two failed rebellions left its mark on Jewish memory).

Of course, Muslim fundamentalists will tell you this is nonsense. That their religion is all about the Koran. That it’s a special religion.   And the internet Hindu agrees.  It is special (though in their case not a “good” way).

I am skeptical of that. I agree with Samuel Huntington’s empirical observation that “Islam has bloody borders.” At least today. But I would offer caution on chalking it up to something primal. In 1900 we might be wondering about in Jesus Christ’s message made it so that Christianity was an imperial religion of world domination and hegemony. Today we would laugh at that.

Note: I’m usually pretty lax about moderation on this blog, but if you are stupid, and you probably are, I will like trash your comment.  This post exists mostly to familiarize people with books.

Gene Expression status update

Filed under: Admin,Gene Expression — Razib Khan @ 1:45 pm

Since people keep asking, I will post here (it will post to my total feed). Gene Expression the website kept maxing the shared hosting plan’s CPU a few weeks ago. I took it down because I didn’t want our host to blacklist it. When I have some time to spare that’s continuous I will get it back up, alone with archives. The issue has been time (I used Cloudflare for what’s it worth). The host looked at the logs and suggested it might have been targeted by DoS attack.

The downside of me hosting the blog is that I have to do all the tech stuff. On the other hand, I have total control of the platform. In this day and age I am not going to give up the control, so just be patient. Honestly, I obviously don’t have as much spare time as I did when I started the blog as a 20something 17 years ago. But I’m not ditching it either.

June 7, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:47 pm

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

June 6, 2019

Since 1989

Filed under: China — Razib Khan @ 2:17 pm

China is an authoritarian, in some ways totalitarian, nation-state. But we need to keep the larger perspective in mind as well.

Judge a society by how the odds are for the least of them.

June 5, 2019

Evolution and human family

Filed under: 1950s,Evolution,Family — Razib Khan @ 10:08 pm
1950s nuclear family in the USA

For many people who grew up in the United States in the years after World War II, it was a time of stability and a return to old verities and values. In those decades one saw the flourishing of the “nuclear family.” Mother, father, and children, living in a single-family home in a sanitized suburb. The television show Leave It To Beaver exemplified this lifestyle, reflecting back to the audience its aspirations.

In the 1960s many young people who had grown up in the 1950s rebelled against this “traditional” lifestyle. They perceived it to be artificial, constraining, and conservative.

But what if it wasn’t conservative at all? A revisionist understanding of the nuclear family, as outlined in books such as Marriage, a History, is that the nuclear family was a relatively recent cultural innovation of the 19th century, even in the West.

Two individuals, married, would raise a family, separate from their relatives. Their evenings would be occupied with “family time,” with friends and civic organizations being ancillary. The rest of the world faded away, as the family came into the focus, singular and insular.

Meanwhile, anthropologists studying non-Western societies were noticing that the “traditional” nuclear family was not common in most cultures. In South Asia, the “joint-family” extends the nuclear family across the generations. In many tribal societies in the Middle East, patrilineages dominate social relationships. Other cultures idealize various sorts of polygamous marriages.

But perhaps a key issue that many human behavioral ecologists have noted is that the nuclear family is exceptional in diminishing the importance of alloparenting.

The nuclear family as conceived of in the West over the past two centuries has deemphasized the caretaking of children by individuals besides the parents. Most of the responsibilities are placed upon the mother. The close relationship between mother and child in most societies is accentuated during the period of breastfeeding. But after weaning supervision usually becomes more distributed, as older siblings, aunts, and uncles, may engage in extensive caretaking of young children.

This is far less true in the world of Leave It To Beaver. Rather than being complements to Beaver’s mother and father, the neighbors in 1950s suburban sitcoms were to be avoided, as they might get angry that you were messing around on their lawns. The nuclear family was situated in a world of separateness, and clean rational division between homes, families, and social worlds.

In the 20th-century anthropologists and evolutionary theorists argued about the nature of human relationships in the context of the nuclear family. Are humans monogamous? Are they polygamous? Are extended families more natural?

What the flexibility and variation in familial arrangements, albeit around some core commonalities (e.g., alloparenting), tells us is that asking what the ancestral evolutionary family type was might not be the right question. Humans are culturally flexible, and social learning is critical to our adaptation to local environments. Second, the nuclear family, in particular, seen by modern Westerners as the family qua family, may actually be an outlier in many ways, in particular, due to its atomized and socially disembodied character.

The truly innovative modern family is that of Leave It To Beaver!

Evolution and human family was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Browncast Ep 45: Jordan Anaya on “data thuggery”

Filed under: Podcast — Razib Khan @ 3:24 pm

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).

If there is one person who combines keen attention to scientific methodology and toxic masculinity, it’s Jordan Anaya, a “data thug.”

A brutal realist who helped destroy the career of Brian Wansink, Anaya revels in is status as a one-man Occam’s Razor.

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