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

May 8, 2019

Going beyond the sex “grip strength” binary

Filed under: Sex Difference,Sex Differences — Razib Khan @ 11:20 pm

Jesse Singal brought this piece in Deadspin, She’s Got The Strength, But Who Has The Power?, to my attention.

Some very interesting sections:

When we shove the concept of athletic ability—strength, for instance—into the same black-and-white binary that we try to put gender into, we’re wrong. There is no stark line separating what men can do athletically and what women can. Some women, in fact, are bigger, faster, and stronger than some men. A large data set analyzed for a 2018 study looked at the body composition and endocrine profiles of 689 elite cisgender athletes in various sports. When it came to physical attributes there was complete overlap between the men and women analyzed, McKinnon pointed out. For instance, the shortest person in the data set was male, not female. The lightest male weighed the same as the lightest female. There were men athletes and women athletes who had testosterone levels that hit the top of the chart and the bottom. Simply put, the range of any physical characteristic within a sex, (like, for instance, the six feet of difference between the shortest man in the world and the tallest man) is far greater than the average difference in height between the average man and the average woman (five inches). And elite athletes tend to live at the far ends of these spectra anyway.

USA Powerlifting’s response to transgender athletes is head-spinning. The thing about all this talk equating hormone replacement therapy to doping, and the threat to “biological females,” and the “unfair advantages” of “male puberty,” is that it’s based entirely on social perceptions of gender.

“There’s absolutely no scientific evidence at all that supports their position,” said Rachel McKinnon, an expert on athletes’ rights and a professor of philosophy at the College of Charleston, and a world champion track cyclist to boot.

Recently a very successful person told me that mathematical intelligence is probably overrated in comparison to verbal intelligence. It is true that some women are bigger, faster, and stronger than some men, and therefore a lot of social policy follows from this truth? Well, empirically that seems to be the case today.

Despite the irrefutable sophistication of words, I decided to pull some data from the National Center for Health Statistics. These data are useful because they separate by sex and age (and in some cases race/ethnicity). Rather than focusing on ranges, I was curious about the distributions for two characteristics:

  • Height in males and females of a range of ages and between the sexes
  • Dominant hand grip strength in a range of ages and between the sexes

In some cases, there were age intervals, so I simply took the midpoint (e.g., 25-29 becomes 27). Also, they had an 80 and over category. I just left that as 80.

First, let’s look at the age. The figure below shows the distribution of height for males and females over the years, with intervals along with two standard deviations for each age.

Let’s zoom in on puberty.

None of the results should be surprising. I assume many of you remember age 12 when the girls were taller than the boys?

Now let’s look at the distribution at age 25.

You probably want to know the overlap. The shaded area is 51% of the total area under the union of the two curves.

Not a great surprise. Men are taller than women, on average. But there are many women taller than many men.

But what about grip strength? This is one of those standard metrics that’s used to measure health. People with illnesses tend to weak. So they measure this in many people to get epidemiological data.

Here is the plot by age and sex. Again, two standard deviations. Notice that the two curves are more distinct during adulthood than height. Men have stronger grips than women to a greater extent than their simple size difference.

Let’s zoom in on puberty. Here we can see a very large difference between males and females. The difference is more striking than with height. Between the ages of 12 and 13, males start to zoom away from females in grip strength. There’s basically no difference in grip strength for children of elementary school age, on average.

Now let’s look at the distribution at age 25. Again, it is more striking than that for height.

So finally, what’s the overlap? ~21% of the area under the curves overlaps. This means that are a substantial number of women who could pummel a substantial number of men. But, in these cases, it is the strongest of women and the weakest of men. I would say that that’s not sporting, to be frank.

In media, there is often a depiction of rather petite women taking on larger men in physical fights. Because film and television is fantasy, of course, the women, if they are on the “good” side, will come out victorious (just like the hobbits in Peter Jackson’s films). But reality would not be as pretty.

On the other hand, a large woman and a very small man seem like it would be a reasonably “fair” fight from these data. But I’m certainly glad that Red Sonja was not written and filmed in a more realistic manner, with the towering Brigitte Neilsen avoiding Arnold Schwarzenegger’s Lord Kalidor to only slay smaller fry.

You may have noticed that males are stronger than females when you correct for body size. Why? The average body fat percentage of a male (not overweight or obese, though not fit) is in the low 20s. The average body fat percentage of a similar woman is in the high 20s. In contrast, men have 40% more muscle mass in the upper body, and 33% in the lower body.

I’m just a simple geneticist. I don’t really know much biology. I don’t know what goes on physiologically and structurally beyond what I learned in high school and what I know from being a human being who went through puberty. But something happens that makes males and females quite distinct in their athletic abilities from what I can see in the data.

The Insight Show Notes — Season 2, Episode 26: The Epigenetics Revolution

Filed under: Epigenetics,Podcast,science,The Insight — Razib Khan @ 3:00 pm

The Insight Show Notes — Season 2, Episode 26: The Epigenetics Revolution

This week on The Insight (Apple Podcasts, Spotify, Stitcher and Google Podcasts) Razib talks about the “Epigenetics Revolution” with John Greally of Albert Einstein School of Medicine. A pediatrician who is interested in diseases with an epigenetic dimension, John also happens to be writing a textbook on the topic!

Conrad Waddington

The term epigenetics goes back to Conrad Waddington’s work in the 1940s. He was interested in developmental biology. At the time this involved descriptions of and mapping out changes over time in the structure of organisms at various scales. Waddington suggested that epigenetics “the task is to discover the causal mechanisms at work…revealed of the mechanics of development.” Developmental biologists of the time were showing the trajectory of change, but not the underlying mechanisms.

In other words, epigenetics in Waddington’s conception was an elucidation of the mapping from genotype to phenotype.

By the end of the 20th-century biologists were living in the DNA era. Ryan Holliday proposed in 1990 that particular molecular mechanisms should be given preeminence:

Epigenetics comprises the study of the mechanisms that impart temporal and spatial control on the activities of all those genes required for the development of a complex organism from the zygote to the adult. Epigenetic changes in gene activity can be studied in relation to DNA methylation in cultured mammalian cells and it is also possible to isolate and characterize mutants with altered DNA methylase activity.

To a great extent for many biologists epigenetics at the end of the 20th-century could be reduced to the examination of methylation of DNA and histone modifications, two molecular mechanisms which are critical in the regulation of genes.

Perhaps the most well-known phenomenon in the public in relation to epigenetics is the intergenerational transmission of negative outcomes due to the Dutch famine of 1944–1945, though this phenomenon is far more well attested in nematode worms.

Today, many researchers are asserting that clarification of terminology is needed to clear up the muddle around epigenetics.

The Insight Show Notes — Season 2, Episode 26: The Epigenetics Revolution was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

China’s demographic disaster impacts Pakistan

Filed under: China — Razib Khan @ 5:32 am

The AP has a long and sad story out, Pakistani Christian girls trafficked to China as brides. One must be careful of sensational stories that hit a lot of our emotional buttons, but it seems deeply reported, and names names.

Because of the surplus of men in China, there has been a recent tendency of “importing” girls and women from poorer East Asian countries. A milder form of this has occurred in South Korea, and earlier Japan. Generally, the men and families who have to make recourse to this are poorer and less attractive on the Chinese marriage market. Some of the same has occurred, to a lesser extent, in South Asia, with Punjabi farmers obtaining wives from eastern India and Bangladesh.

The fact that Chinese men are seeking wives from Pakistan is probably a function of the reality that Vietnam is getting too prosperous, and Laos is not particularly populous (I don’t know the situation in North Korea,  though with the nationalistic nature of that regime I don’t see that as being a sustainable option). And obviously, Pakistan’s alliance with China matters a great deal.

The fact that these are poor Christian women helps as well. To be frank, I suspect that the Pakistani elite does not see their traffic as a matter of honor due to a lack of identification for reasons of class and religion. Additionally, it is far more plausible for a Chinese groom to contend that they are converts to Christianity than they are converts to Islam (there are much stronger cultural conflicts between being Han and Muslim than being Han and Christian).

With 1.4 billion people, it is hard for Chinese matters not to impact its neighbors…

May 7, 2019

The misunderstanding of epigenetics

Filed under: Epigenetics,Genetics,science — Razib Khan @ 11:15 pm
Conrad Waddington’s “epigenetic landscape”

In most graduate programs students must complete a series of oral exams or make a presentation to professors to “qualify” to proceed in their research. The goal here is to make sure that a student goes forward productively, rather than spending years flailing without direction.

Often the examination and review will involve both the research program that the student is specializing within and, general knowledge about the discipline in which they practice. A population geneticist may be asked to derive the coalescent. A molecular geneticist may be asked to sketch out the process of DNA replication.

Usually, all goes well. But sometimes there are unforeseen speed bumps.

One of my acquaintances did research which involved epigenetics for their Ph.D. During their qualifying examination, they were asked to describe some basic epigenetic mechanisms by one of their professors.

But, during the middle of the description, the examiners began to interrupt and it came to be understood that there were some fundamental disagreements as to what epigenetics was within the group of scientists!
A molecular biological view of epigenetics

How could such a thing happen? How can scientists actually disagree about what epigenetics entails? Especially in light of the fact that epigenetics is a scientifically vibrant topic, which has also been of interest to the public!

Sometimes single steps seem reasonable, but eventually, they lead you down a path into a tangled mess. The definition of epigenetics and its cultural evolution over the past 80 years is an example of that. It has mutated and diversified so that even within science people can mean different things when they say “epigenetics.”

The term was coined originally in 1942, by Conrad Waddington. He used it to define the whole set of processes which mediate how a genotype is translated into a phenotype. Basically, how is it that the information in genes leads to the diverse cells and tissues which define an organism. Waddington was deeply interested in processes of development and how that integrated into an evolutionary context. He was highly influential upon Stephen Jay Gould. But he wrote and was thinking well before the discovery of the structure of DNA.

Today, 70 years into the “DNA age”, many biologists have much more specific ideas, involving particular molecular biological mechanisms, in relation to epigenetics. Even though the cells of each human have the same DNA sequence, genes are expressed differently over time in different tissues. The DNA sequence in the cells of your liver is the same as the DNA sequence in the cells of your muscles, but clearly, the nature of these cells could not be more different. The tissues look different, and the physiological processes are quite different.

Depending on who you talk to (see above), epigenetics today operationally is an exploration of these mechanisms of the expression of DNA code which translate into the structures and processes that go into the creation of an organism. It is on top of the DNA layer of information that guides gene expression and organismal development (don’t be surprised if “histone modifications” get brought up if you talk to a biologist about epigenetics!).

Audrey Hepburn suffered malnutrition during the Dutch famine

Finally, there is the definition of epigenetics that has percolated into sensational popular treatments that it has transformed our understanding of Mendelian inheritance. That it is a scientific revolution. And, that environmental inputs can change one’s DNA, and those changes can be passed down to future generations.

One of the strangest things is the leveraging of this definition for marketing goods and services. Epigenetics is now big business. There are now health spas which claim epigenetic enhancement. There are skin creams which utilize the latest in epigenetics insights. Or so they say.

Much of the hype around epigenetics goes back to a study of the impact of the Dutch famine on the long-term health of those who suffered, and their descendants. The most sensational and impactful result of this study is that environmental stress may leave marks on genomes, which are then inherited by descendants of those who have suffered stress.

The implications from this fact are that “DNA is not destiny”, and that in your environment can impact your descendants through your DNA.

Though the study of the Dutch famine is legitimate science, most geneticists are highly skeptical of inter-generational transmission of epigenetic effects across generations in humans.

Even if this was a real phenomenon, the fact that Mendelian genetics was applicable to humans long before DNA was characterized indicates that very little of inheritance is perturbed by epigenetic effects.

The “epigenetics revolution” is more one of marketing than substance.

The biggest problem with epigenetics from the perspective of science communication is that it is an incredibly fertile and rich field of study, with important consequences in areas such as medicine, but its public perception is defined by a very specific phenomenon which many researchers are skeptical of. The impact of your smoking is going to affect your health. It is not going to have an effect on your descendants’ DNA though.

The misunderstanding of epigenetics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

2019 reader survey

Filed under: Reader Survey 2019,Survey — Razib Khan @ 8:17 pm

I think I’m going to do another reader survey. Whenever I do people complain that I didn’t ask this question or that. To preempt that I’m putting up this post where you can submit your question so you won’t complain later.

Pleistocene rock art in Maharashtra

Filed under: Archaeology,History — Razib Khan @ 12:39 am

Ancient Rock Art in the Plains of India-Two amateur sleuths have uncovered a collection of mysterious rock carvings on the Indian coastal plain south of Mumbai:

In the evening breeze on a stony hilltop a day’s drive south of Mumbai, Sudhir Risbud tramped from one rock carving to another, pointing out the hull of a boat, birds, a shark, human figures and two life-size tigers.

“They’re male,” he said with a smile, noting that the carver had taken pains to make the genitalia too obvious to ignore. He was doing a brief tour of about two dozen figures, a sampling of 100 or so all etched into a hard, pitted rock called laterite that is common on the coastal plain that borders the Arabian Sea.

The carvings are only a sample of 1,200 figures that Mr. Risbud and Dhananjay Marathe, engineers and dedicated naturalists, have uncovered since they set out on a quest in 2012. The two men are part of a long tradition of amateur archaeologists, according to Tejas Garge, the head of the Directorate of Archaeology and Museums for the state of Maharashtra, and the petroglyphs they have uncovered amount to a trove of international significance.

There are no depictions of bulls, so it is pre-agricultural. Additionally, some of the animals depicted disappeared from the area in the later Pleistocene. That means the carvings could date to people who lived in the area between 40,000 and 20,000 years ago, right up to the Last Glacial Maximum.

May 6, 2019

War before civilization in Late Neolithic Europe

Filed under: Corded Ware Culture,Globular Amphora culture,Neolithic — Razib Khan @ 11:19 pm

A new ancient DNA paper, Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave:

We sequenced the genomes of 15 skeletons from a 5,000-y-old mass grave in Poland associated with the Globular Amphora culture. All individuals had been brutally killed by blows to the head, but buried with great care. Genome-wide analyses demonstrate that this was a large extended family and that the people who buried them knew them well: mothers are buried with their children, and siblings next to each other. From a population genetic viewpoint, the individuals are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in violent conflict.

The context is that these individuals were from the Globular Amphora culture (GAC), which preceded the Corded Ware culture (CWC), which itself was descended from the broad complex of Yamna and Yamna-related cultures of the steppe. The genetics here are not new findings. The GAC culture seemed to be dominated by individuals descended mostly from “Early European Farmers” (EEF), and on a genome-wide level, their broad genetic patterns were almost exactly the same as the Neolithic people of Ireland, thousands of miles to the west.

Genetically, and judging by the pigmentation loci, physically, the GAC’s closest analogs today are probably the people of Sardinia, who have the largest fraction of EEF ancestry among modern Europeans. Because EEF fractions are still rather high in Southern Europe, the late Neolithic people of much of Northern Europe are genetically more similar to modern Southern Europeans than they are to later Northern Europeans who succeeded them.

These later Northern Europeans, the predominant ancestors of modern Northern Europeans, had an ancestral component which comes out of the steppe and forest-steppe zones. In the context of the North European plain the massive replacement of Neolithic European societies by these post-steppe societies in the centuries after 2800 BC happened so quickly and substantially that the genetic differentiation between modern Northern European groups remains very modest (and is due to a combination of substrate admixture, accrued genetic drift, and in some cases later admixture from the east).

Rather than the broader human geographic context, the most fascinating thing about this paper is the granularity they bring to what was clearly some sort of directed violence that may have been genocidal in intent. I will quote extensively from the paper:

Overall, we identified four nuclear families in the grave, which are for the most part represented by mothers and their children (Fig. 3). Closely related kin were buried next to each other: a mother was buried cradling her child, and siblings were placed side by side. Evidently, these individuals were buried by people who knew them well and who carefully placed them in the grave according to familial relationships. For example, individual 14, the oldest individual in the grave, was buried close to her two sons (individuals 5 and 15), whereas individual 8, a 30–35-y-old woman, was buried with her teenage daughter (individual 9) and 5-y-old son (individual 13). Using genome-wide patterns of IBS, we were also able to reconstruct more complex relationships: individuals 5, 10, 11, and 15 all appear to be brothers, and yet they do not have the same mother (individual 14 is the mother of individuals 5 and 15, but not 10 and 11), suggesting that they might be half-brothers. However, all four of them share the same mitochondrial DNA haplotype, suggesting that their mothers might also have been related.

Interestingly, the older males/fathers are mostly missing from the grave, suggesting that it might have been them who buried their kin. The only father present in the grave is individual 10, whose partner and son are placed together opposite him in the grave. In addition, there is a young boy (individual 7), aged 2–2.5 y, whose parents are not in the grave, but he is placed next to other individuals to whom he is closely related through various second-degree relationships. Finally, there is individual 3, an adult female, who does not seem to be genetically related to anyone in the group. However, her position in the grave close to individual 4, a young man, suggests that she may have been as close to him in life as she was in death. These biological data and burial arrangements show that the social relationships held to be most significant in these societies were identical with genetic and reproductive relationships. However, they also demonstrate that nuclear families were nested in larger, extended family groups, either permanently or for parts of the year.

These prehistoric people lived in a sometimes brutal world. But they were just like us in deep and fundamental ways. This was a patrilineal kinship group, sharing the same Y chromosomes. The women too may have been distantly related.

Details of kinship relationships and how they were placed next to each other in death flesh out the world of these people in an almost novelistic manner. And, it asks us to consider the motivations of the people who killed them (the authors speculative CWC, though obviously, they can’t be sure). In many premodern societies, women and children of the enemy are viewed as goods which can be captured and appropriated. “Male-mediated gene flow” is a word that describes what happens genetically, but in terms of history and anthropology we are pointing to the phenomenon of men moving across a landscape rapidly without women and children, and eventually obtaining families by hook or crook. There is some suggestion that agricultural words in Germanic languages come from a pre-Indo-European substrate. Not all of these people were killed.

So why kill these women and children in this case? If these people were the same as us, with the same capacity for horror, then imagine the feelings of the men and women who arrived back in the village after the slaughter. Not only did they have to see the dead bodies of their children and their wives, but they had to confront the fact that the event occurred because they weren’t there to protect them. In Kazuo Ishiguro’s The Buried Giant, the author depicts a similar genocide in early 6th century Britain, which had the two-fold effect of traumatizing the warriors who came home to the slaughter of their families, as well as killing the young boys who would one day become fighters.

When inter-group conflict results in the killing of young women I think a Marxist materialist framework fails us. Yes, there is something animalistic and Malthusian in the competition for resources of premodern people. But humans personalize conflict and ideologize it.

The emergence of Han identity as autochthonous

Filed under: China,Historical Population Genetics,Sino-Tibetan — Razib Khan @ 10:00 pm

Reader Matt points me to two new papers on the linguistic phylogenetics of the Sino-Tibetan language families, Dated language phylogenies shed light on the ancestry of Sino-Tibetan and Phylogenetic evidence for Sino-Tibetan origin in northern China in the Late Neolithic. You should read Matt’s whole comment, but one thing he mentions is that by ~3,000 years ago, individuals who were genetically similar to modern Burmese were already present in the territory of modern Burma. Burmese are quite distinct from Cambodians or Vietnamese because there is a distinct “northern” element, which perhaps resembles Tibetans.*

Matt observes that this means the expansion of agriculture into Southeast Asia occurred through a few pulses in rapid succession, rather than gradually over time, as seems likely the case in Europe and South Asia (“Early European Farmers” to Corded Ware, or Iranian agriculturalists to Central Asian agro-pastoralists). Austro-Asiatic speaking groups pushed out from the highlands of southern China 4-4,500 years ago. Meanwhile, people from further north seem to have pushed into the uplands of the western portion of upland Southeast Asia 500 to 1,000 years after this. Further east, Austronesians were sweeping along the coast and expanding into the maritime fringe.

But I am not intending to talk about Southeast Asia. Rather, I want to focus on China. Or perhaps more precisely the region and cultures that became China. Both the above papers suggest that the diversification of the  Sino-Tibetan languages occurred around ~7,000 years ago. And, that they began expanding from the zone of inland China, the upper Yellow River basin, from the area occupied by the Yangshao culture. This would explain some peculiar genetic facts. First, the northern affinities of Tibeto-Burman groups in northeast India and in Burma itself (which might otherwise require later Tai migrations) mentioned above. But second, about ten years ago when the early work on EPAS1 and high altitude adaptation was done on Tibetans, their genetic relatedness to Han Chinese was surprisingly close! In fact, some estimate of divergence put it as recently as 3,000 years before the present (I think this was an underestimate, but it gets at the qualitative result).

Remember, this was still before the massive swell of publications which have transformed our understanding of the ubiquity of migration, admixture, and demographic expansion in the recent past across the Holocene. Today I suspect the best model to explain these affinities are that people on of modern greater Tibet descend in large part from the “Yangshao Diaspora,” and amalgamated with local peoples, whether indigenous hunter-gatherers of the plateau region or Indo-Europeans moving in from the west.

I’ll spare you the Bayesian phylogenetics, and the cautions about relying too much on lexicons (see a discussion on The Insight for more). But one interesting aspect of the trees generated by both papers is that the Chinese language tends to be basal in its position in relation to most of the other languages, and the region of China itself is relatively low in linguistic diversity. The basal position and the presence of core words which are associated with the millet zone of north-central China indicate that frontier Tibeto-Burman groups separated long ago from the ancestors of the Chinese dialects. The low linguistic diversity of China can be understood as a consequence of the Chinese Empire, which underwent demographic expansion from the Yellow River basin, and assimilated peripheral peoples over time (some of the southeast Chinese dialects suggest substrate influences).

Which brings me to the Yangshao culture and its centrality to the main stem of East Asian history. It flourished until 3000 BC. It was succeeded by the Longshan culture, which persisted until 1900 BC. Finally, the last great prehistoric culture of the region is the Erilitou. Due to both the oracle bones and various astronomical events associated with events recorded in Chinese history, history as such begins in the centuries before 1000 BC.

As you likely know, much of China proper was not Sinicized until after the fall of the Han dynasty. Deep into historical time the Yangzi river valley and Sichuan were culturally liminal to the orbit of the expanding Chinese civilization, but not of it (perhaps like early Macedonia, influenced by the more complex civilization, but still distinct and barbaric). Further south the territory had more in common ethnolinguistically with much of Southeast Asia. The Sinicization of the south that occurred in the period between 0 and 1000 AD was not just cultural, but also demographic. Looking at modern Chinese their genetic variation for the Han is quite a bit lower than many might expect. The Han of provinces such as Guangdong in the far southeast is not closer to the Vietnamese than they are to the Han of the Yellow River plain, despite geographic proximity to the latter (some of this might simply be due to homogenizing gene flow back and forth).

An aspect of East Asian historical demography and genetics that stands out to me is that in China itself there isn’t a very strong signature of admixture between distinct lineages that you see in Europe or South Asia (or even West Asia). By this, I mean the fact that the Uygurs are about 50/50 West and East Eurasian. Or that South Asians are mixed between West Eurasians and an ancient indigenous lineage. Or, that the disparate West Eurasian ancestors of Europeans, and the Basal Eurasian component, were all quite distinct before being threaded together. True, many northern Han have detectable West Eurasian ancestry (5% or less), but I think this can be attributed to Turkic and Mongolic peoples, who have higher fractions of this ancestry (probably from Indo-Europeans that they absorbed).

Modern Chinese show much more affinity to the Devil’s Gates samples from the northeastern border with Russia dated to 7,700 years ago than modern Western Europeans do with people present 7,700 years ago (or modern Indians would with people of a similar date). This may illustrate the particular geographic advantages of the upper Yellow River basin over 4,000 years, from 3000 BC down to 1000 AD, when both Chinese economic and cultural power shifted to the Yangzi river valley**. The arrival of the light chariot after the 2000 BC attests to contacts to the west, but the genetic imprint has always been relatively minor. Contrast this to the vast steppe zone between Pannonia and the Altai, where there were multiple reflux events as peoples migrated in both directions at various peoples.

China is different from the other nations of the Eurasian oikomene. The “Rimland.” Some of this goes very deep, and probably the best understanding has to involve a consideration of the physical and human geography of the region, and its relative isolation from broader forces in Eurasian history.

Many peoples claim to be autochthons. The ancient Athenians for example. But the people of the Han civilization developing in the centuries after 1000 BC in the Yello River basin could likely make a more plausible case of being descendants of local hunter-gatherers who were “always there”, and eventually settled down to farm.

* One of the reasons I am convinced that Bengalis have Tibeto-Burman, and not simply Austro-Asiatic, East Asian ancestry is that this northern component can be seen in modern Bengalis, who are about 5-20% East Asian in ancestry.

** The economic power had shifted by 700 AD, but Xian in the north remained the capital until the fall of the Tang.

May 5, 2019

2019 Brown Pundits Reader survey

Filed under: Brown Pundits Survey,Survey — Razib Khan @ 4:54 pm

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


One of the strange things is the comments on this weblog make it seem like many more of the readers are South Asian than is really case (or care about the India-Pakistan conflict). I wish more of you would speak. I’m brown, but I speak on Chinese history. It’s my history too. In a cosmopolitan post-national world the global chattering class should consider Terrence’s insights and be less bashful.

Open Thread, 05/05/2019

Filed under: Open Thread — Razib Khan @ 3:12 pm

I don’t know what’s going on with the plugins on this website, but one of them is causing the issues with memory. Will keep looking into it.

Starting to read The Human Swarm: How Our Societies Arise, Thrive, and Fall. This book, along with Nicholas Christakis’ Blueprint: The Evolutionary Origins of a Good Society, book and E. O. Wilson’s The Deep Origin of Societies were negatively reviewed in Nature. Knowing who the reviewer was it was predictable, just like it the review of Robert Plomin’s book was predictable when you saw who it was assigned to. I don’t think this is a coincidence.

A useful book, India: Brief History of a Civilization.

The Secular Jihadist podcast did an interview (for patrons only) with Tom Holland. Not sure I’ll read In the Shadow of the Sword: The Birth of Islam and the Rise of the Global Arab Empire because one thing that always comes through is how little we know about the first century of Islam once one applies the critical-rationalist lens that is taken for granted in Western historiography (and yes, I’ve read Robert Hoyland’s work).

You Will Never Smell My World the Way I Do.

Differential gene expression is associated with degeneration of mating-type chromosomes in the absence of sexual antagonism.

Multilevel selection in groups of groups.

Insights about variation in meiosis from 31,228 human sperm genomes.

When do individuals maximize their inclusive fitness?

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

Meta-analytic evidence that sexual selection improves population fitness.

Rumbles in religion and cultural evolution

Filed under: History,Religion — Razib Khan @ 12:28 am

A few months ago I posted Society Creates God, God Does Not Create Society, which was a write-up of a paper in Nature, Complex societies precede moralizing gods throughout world history. The study was of interest to me because it seemed to test the hypothesis and argument presented in Big Gods: How Religion Transformed Cooperation and Conflict. Their conclusion using the Seshat historical database was in the negative in relation to the hypothesis. That is, big societies gave rise to big gods, big gods did not seem to give rise to big societies.

Now a different group of researchers, some of them associated with the model of big gods leading to big societies, have shot back with an intense critique of the paper in preprint form, Corrected analyses show that moralizing gods precede complex societies but serious data concerns remain.

There seem to two critical issues that these authors want to highlight: problems in analysis, and problems in the underlying data. In terms of the analysis, the authors suggest that because the Seshat database relies on written evidence it is going to be biased toward more recent dates because writing tends to be found later in social development and complexity. They reanalyzed the data by pushing the emergence of big gods back by a century and found the direction of the effect reverse. In other words, they are saying that the result was not robust. A second issue that impacted the analysis is that the authors of the preprint assert that since so many missing values from preliterate societies were recoded as an absence of big gods what the results are showing is a negative correlation of missing entries with complex societies.

A second broader issue seems to be a suggestion that Seshat itself is riddled with too many errors to be reliable.

As someone deeply interested in the scientific question I don’t have a strong opinion as to what’s going on here (though I am probably a bit skeptical of the idea that Seshat is without much value considering the time and effort I know Peter Turchin and his collaborators have put into it). Feelings seem to be getting heated online, but I’m hoping that open-science will win in the end.

Peter Turchin and Patrick Savage have put up preliminary responses. No doubt there will be more back and forth. But one major improvement over many historical discussions is that this is playing out transparently through data analyses, then the standard “historian here, let me assert my expertise here to shut you down….” (a lot of historians on Twitter behave in a mendacious manner in my opinion, because I often know enough about many historical topics to see exactly how they are laundering their credentials to support sophistry in a manner that is opaque to their trusting audience).

May 4, 2019

Batch effects in the 1000 Genomes data?

Filed under: 1000 Genomes,Genome — Razib Khan @ 4:37 pm

This is an important preprint, Legacy Data Confounds Genomics Studies:

Recent reports have identified differences in the mutational spectra across human populations. While some of these reports have been replicated in other cohorts, most have been reported only in the 1000 Genomes Project (1kGP) data. While investigating an intriguing putative population stratification within the Japanese population, we identified a previously unreported batch effect leading to spurious mutation calls in the 1kGP data and to the apparent population stratification. Because the 1kGP data is used extensively, we find that the batch effects also lead to incorrect imputation by leading imputation servers and suspicious GWAS associations. Lower-quality data from the early phases of the 1kGP thus contaminates modern studies in hidden ways, it may be time to remove or upgrade such legacy sequencing data from reference databases.

Despite the fact that there are hundreds of thousands of high-quality whole genomes sequenced today, the 1000 Genome Project looms very large as a diverse reference set. As noted in this preprint the sequencing was done a while back, so some of the data is of relatively low coverage (so the variant calls may not be confident). And, I think many of us have seen publications which have left us scratching our heads a little over the years, so this preprint really comes at the right time.

May 3, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 11:29 pm

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

Is the Asian American sex difference in outmarriage due to adoption of girls from East Asia?

Filed under: Interracial Marriage,race — Razib Khan @ 12:31 pm

I was revisiting the statistics on intermarriage rates of various Asian American ethnicities on the Asian Nation website drawn from the 2010 census. And something weird jumped out at me: the absolute number of 1.5 and 2nd generation “Asian American” women of some ethnicities is way higher than for others. For Korean Americans, it’s almost a 1:2 ratio of men to women.

So I looked at the inmarriage rate of various ethnicities by for women, and it turns out that there is a ~0.90 correlation between the rate and the ratio. Basically, when there is a huge surplus of women to men of the same ethnicity these women tend to marry men of other ethnicities.

This is not a deep interest of mine, but I do know that the number of girls adopted from many Asian nations tends to exceed the number of boys. Adoptees, in general, are already much more likely to marry out of the racial category that their physical appearance codes, but if there was a massive sex ratio difference that would probably exacerbate the issue.

The main reason I’m posting on this is that there is a huge literature, and lots of talk, about how Asian American men are emasculated, and the issues with regards to interracial dating being unbalanced in this community. I think that that is probably still a valid point, but I’m not sure that the interracial marriage statistics reflect the magnitude of the issue. Rather, perhaps it is just an artifact of adoption patterns and the large representation of adoptees in cohorts for certain ethnicities?

Statistics on Asian American interracial marriage statistics

Filed under: data — Razib Khan @ 11:55 am

I really don’t know what to make of some of the contentions in Zach’s post below, What’s wrong with fetishizing white men? (also, posting videos which Hindi means I have no idea specifically what is going on in the video) Some of this is probably due to differences between the UK and the USA. But there are some statistics from the 2010 USA Census.

The website Asian Nation has tabulated the outmarriage rates by generation (foreign-born vs. US-raised) and various Asian American ethnicities. You can see the results below as I’ve repackaged them to focus on inmarriage of various subgroups, stratified by sex.

Some notes

1) “Asian Indian” only includes people who are Indian nationals or whose ancestors were from the Republic of India. It excludes other South Asian nationalities (I am not “Asian Indian” for example). But since other South Asian nationalities are a very small number in the USA I think that’s fine.

2) The statistics are generated from subsamples of the Census. I would be a bit cautious on outmarriage rates for groups like Asian Indians and Koreans where in 2010 the number of those born or raised in the USA was still rather small compared to the foreign-born/raised population. One reason Indian Americans showed extremely low outmarriage rates in the early 2000 Census results is that there was a massive swell of immigration in the Clinton era from Indians, so the foreign-born immigrants overwhelmed the signal.

3) Both the Japanese and Chinese have multi-generational communities in the United States. There are large numbers of highly assimilated Japanese and Chinese Americans whose roots in East Asia are as far back as their grandparents, or even earlier. I think it is noticeable that there is sex balance here.

4) I know a lot of you like bullshitting. I will be doing other things for a while so not monitoring comments much. But if I come back and have to see 1,0000-word personal thoughts which are factless and emotional I will just delete them, even if you are a long-time commenter.

May 2, 2019

An Islamic view of the Crusades

Filed under: Crusades,History — Razib Khan @ 1:34 am

I should say a thing or two about The Race for Paradise: An Islamic History of the Crusades. It turns out that the Islamic perspective on the Crusades and Muslim-Christian conflict is pretty much exactly what you might infer from the Christian perspective. That is, the narrative in The Race for Paradise is surprisingly unsurprising. In fact, there was too much narrative, as many of the chapters were a sequence of names and battles.

I’m not someone to say that social, cultural, and economic history are the only histories that matter. But, they are often the sorts of information that you can’t easily find online in Wikipedia summaries. In contrast, diplomatic and military history can be found in other sources. So I felt The Race for Paradise a bit thin on matters social, cultural and economic, though the author did make an attempt here and there. If you read this book I would recommend you skip over a lot of the standard narrative and just find those chapters.

Additionally, for such a short book, I will warn you that you’ll not get just the conflict in the Near East. Substantial portions are taken up by the Crusades in Iberia and the conquest of Sicily, and there is an end section on the reaction to the Ottomans. Curiously, there was only perfunctory mention of the Baltic Crusades, but then, this is an Islamic view, so that actually makes sense

If you are really interested in the topic, I really recommend God’s War and The Northern Crusades.

Ultimately, I will conclude from reading The Race for Paradise that despite the strong distinctions that the Dar-ul-Islam and Christendom made between each other after the fall of Rome and before the rise of modernity, the two are hard to understand individually without considering the other. The familiarity of the narrative in The Race for Paradise is that Islamic civilization, unlike that of India or China, is not comprehensible on some level without the referents of the Christians, who were there before Islam, and amongst whom many Muslim societies emerged from.

The world of Islam and the world of Westen Christianity view each other as exotic cousins. Not as aliens.

May 1, 2019

The natural history of song – a human universal

Filed under: Human Evolution — Razib Khan @ 11:18 pm

“I am human, and I think nothing human is alien to me.”
– Terrence

One of the bizarre things about modern cultural anthropology is that its tendency toward extreme relativism means that it engages in so much “thick description” that generalities of humanity disappear in the avalanche of prose. A deep sense of ontological incommensurability creeps into the discussions of cross-cultural patterns. The prestige, what there is, of academic anthropology, then infects normal people, so that some can say that religion, as understood in the West, is qualitatively different from religion understand in the East. With a straight face.

I think this is wrong and leads us down a path to intellectual nihilism (well, actually, we’re at the end of that path today aren’t we!).

This sort of thing applies to other cultural phenomena as well. Consider music and in particular song. A new preprint uses the Human Area Relation Files (an ethnographic database) to statistically analyze patterns in songs across many societies, A natural history of song:

What is universal about music across human societies, and what varies? We built a corpus of ethnographic text on musical behavior from a representative sample of the world’s societies and a discography of audio recordings of the music itself. The ethnographic corpus reveals that music appears in every society observed; that variation in musical behavior is well characterized by three dimensions, which capture the formality, arousal, and religiosity of song events; that musical behavior varies more within societies than across societies on these dimensions; and that music is regularly associated with behavioral contexts such as infant care, healing, dance, and love. The discography, analyzed through four representations (machine summaries, listener ratings, expert annotations, expert transcriptions), revealed that identifiable acoustic features of songs predict their primary behavioral function worldwide, and that these features fall along two dimensions, melodic and rhythmic complexity. These analyses show how applying the tools of computational social science to rich bodies of humanistic data can reveal both universal features and patterns of variability in culture, addressing longstanding debates about each.

The figure at the top reports the three largest components of variation, formality, arousal, and religiosity. Not surprisingly, some types of songs are more weighted toward one feature than another. Lullabies are not particularly religious, arousing, or formal.

Interestingly, the vast majority of variation in songs is found within societies, not between them. There is some difference, with some societies lacking formal songs, at least in the ethnographic record. But, this illustrates that the basic repertoire for this cultural feature was probably present by the late Pleistocene in our species.

Songs seem to be aspects of human behavior which are both consumption and production goods. That is, on the individual and social level we consume songs for pleasure. On the individual level songs are essential parts of the parental toolkit to soothe the infant beast. They also serve a purpose in society to generate cohesion and produce fellow feeling. This is clear in a confessional religious context, but consider that drummers were important elements of the Ottoman war machine. Human cultural phenomena are so often multivalent that they need to be inspected and examined from a variety of dimensions.

I’m not a very musical person myself, so there is obviously individual variation in the ability to appreciate or produce music. But the basic cognitive toolkit seems to emerge out of a concert of neurological processes, somewhat distinct from common language (as evident by aphasics who can sing but can not speak).

It’s a Denisovan world, and paleoanthropology just lives in it!

Filed under: Human Evolution — Razib Khan @ 9:07 pm

Unless you’ve been sleeping under a rock, you may have seen a new paper, A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. The reason it is a big deal is that except for a fragment of a skull reported on at a conference, this is the first remains outside of Denisova cave identified as “Denisovan.” Part of the identification was morphological. Both this find and those in Denisova cave, are characterized by very large teeth.

But the really interesting aspect is that they used analysis of proteins to place this sample phylogenetically. You can see the results above. Proteins don’t degrade as fast as DNA, from what I know, so this isn’t surprising. This individual, from high altitude Tibet, dated to at least 160,000 years ago, is in the same clade as the Denisovan that has been sequenced in the broader context of hominin evolution. This is not a rock-solid inference…there wasn’t that much informative variation (I believe Janet Kelso said on Twitter that one particular position where the Denisovan were derived compared to all other hominins in particular matched this paleo-Tibetan sample). But, if you had to guess, it does seem likely that this was an individual related to the Denisovans that we’ve come to know and love.

Finally, there is an important twist that the high altitude adaptation in Tibetans due to EPAS1 seems to have arrived from an introgressed haplotype from Denisovans. Perhaps then the introgression occurred 40 to 50 thousand years ago, as modern humans replaced Denisovans. The majority of the ancestry of Tibetans though seems to share rather recent Holocene origins with groups such as the Han Chinese. Therefore, rather than absorption of an old substrate in Tibet, it could be that you are looking at a variant widely found in the northern Denisovans.

I’ve been talking a lot about Denisovans recently. Why? It seems that the investigations prompted by the original surprise sequencing of 2010 are finally yielding results. But one thing that is clear is that our understanding of the origin of our lineage, and how various hominins interacted with each other, and who they were, is much sketchier than we might like to think. Though the Tibetan and Denisova cave Denisovans were both robust, if the lineage began to diversify ~400,000 years ago, that’s certainly enough time for various morphological types to have emerged in different parts of Asia.

It could simply be we’ll never be able to specifically understand a lot of the detailed processes that occurred in terms of how different hominin groups related to each other. But, we will probably be able to get a better general picture in the near future. As Spencer mentioned in our podcast last week, the Neanderthals in some ways may have been atypical for ancient hominins, and not a good guide to the long term trajectory of the Denisovans.

What is a “Brown Pundits” podcast?

Filed under: Podcast — Razib Khan @ 4:42 pm

One of the interesting things about asking people whether they would come on this blog’s podcast is that they often say “I don’t know if I’d be that interesting to the audience….” More specifically, there isn’t always a South Asian “hook” to some of the episodes.

But the name of the podcast is “Brown Pundits” because this podcast was started by a few brown guys. Not because we discuss purely “brown” things.

The Insight Show Notes — Season 2, Episode 25: The $1,000 Genome

Filed under: Genetics,Medicine,Podcast — Razib Khan @ 2:56 pm

The Insight Show Notes — Season 2, Episode 25: The $1,000 Genome

Citation: Rodrigo Martinez
If you haven’t, please fill out The Insight listener survey.

This week on The Insight (Apple Podcasts, Spotify, Stitcher and Google Podcasts) Rodrigo Martinez of Veritas Genetics talks about the $1,000 genome. Though the reality is we’re well beyond the $1,000 genome, which Rodrigo unpacks in detail.

Rodrigo has been at the forefront of reimagining what genomics can do. Those more interested in his ideas should see his blog post, Next in the Genomics Revolution: The Era of the “Social Genome”.

We discussed the difference between genotyping vs. sequencing, what clinical grade means, and what Veritas’ place in the ecosystem is.

J. Craig Venter

Rodrigo also tells us how a chance encounter in Mexico with J. Craig Venter in the late 1990s resulted in his interesting career path within the nascent field of genomics. One of the major themes of the podcast has been how we’ve observed genomics transform in the last generation, from blue-sky science that cost billions of dollars, to commodity data generation, and finally into the phase of value-add interpretation.

While some researchers have focused on generating the genetic data, much of Rodrigo’s focus has interpretation..been how that data is stored and represented: The Geography of the Genome. And of course, we talked about the famous chart produced by the NIH, which illustrates the cheapening of genomic data.

He talks about how the graph of “cost per genome” doesn’t explain why adoption has exploded in the last few years, rather than earlier.

The decline in genomic costs

There was an extensive discussion about how sequencing, in particular, is going to add more value than the genotyping platforms that are introducing the public to genomics. Basically, genotyping platforms looking for variation that we know exists. Sequencing is the total information of the ACGT read, therefore it allows you to discover things you didn’t even know existed!

Rodrigo envisages genomics moving from the “read” era to the “read/write” era, and finally to the “social” era. Clearly, the genome itself is not the “killer app,” but we don’t know what it will be. We talk about how interpretation and support services are going to be the primary sectors where most of the activity in genomics is going to occur, as raw sequencing becomes a commodity service.

Some of those services are going to be clearly medical. For example, drug-gene interactions. But the key insight is we don’t know the shape of the most likely use cases because information technology is so difficult to predict!

Though internal projections at Veritas indicate that they will have sequenced 1 million individuals by 2021.

Two comments in Genome Biology from 2013 and 2018:

The Insight Show Notes — Season 2, Episode 25: The $1,000 Genome was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

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