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January 22, 2018

Populism leads to tyranny

Filed under: Politcs,Politics — Razib Khan @ 10:08 pm

I just listened to the authors of How Democracies Die on NPR. First, the book might well have been titled “The necessity of liberalism.” Basically, democracy without liberalism is clearly not democracy in their judgment.

But second, I was struck by their emphasis on the role of elites in dampening and diminishing the passions of the masses in a functioning modern democratic system. To a great extent, the authors were simply warning about what Fareed Zakaria termed “illiberal democracy” in The Future of Freedom over ten years ago.

Without elites acting as structural guardrails on the atavistic passions of the masses charismatic figures who channel their basest impulses can arise and gain popular approval of their autocratic behavior. The ancient Greeks could have told you that. Some things never change.

The rise of Chinese science and CRISPR

Filed under: Crispr — Razib Khan @ 9:52 pm

So as of now China is producing more scientific publications than the United States of America. But there’s quality and there’s quantity. I think most people would still American science is more cutting edge than Chinese science. And for cultural reasons that may stay true for a while longer.

But there is one area where China seems to be forging ahead and likely will make advances earlier than the USA: genetics, and genetic engineering in particular. The Wall Street Journal has a long piece, China, Unhampered by Rules, Races Ahead in Gene-Editing Trials. It turns out that Chinese have been doing human trials since 2015. Meanwhile, in the USA the greenlight has still not been given (though it seems close).

Honestly how quickly the Chinese are moving in human trials is alarming. Then again, this is a country with the highest number of executions in the world (some of this is sheer size, but it’s higher per capita than the USA). So we should keep perspective. There are many worse things that the Chinese are doing in relation to human rights that moving too fast in trials with cancer patients.

In any case, this comment jumped out at me:

In traditional drug development, too, human-trial rules can differ among countries. But China’s foray into human Crispr trials has some Western scientists concerned about the unintended consequences of using the wholly new tool—such as harm to patients—which could set back the field for everyone.

Western scientists the Journal interviewed didn’t suggest America’s stringent requirements should be weakened. Instead, many advocate an international consensus on ethical issues around a science that makes fundamental changes to human DNA yet still isn’t completely understood.

As a descriptive matter, I am highly skeptical of the possibility that “international standards” is going to involve the Chinese adhering to Western standards. If a genuine international consensus is going to emerge there has to be a give and take, which means that the very high threshold set for safety in human trials in the West may not apply in China.

January 21, 2018

The first ethical revolution

Filed under: axial age,History — Razib Khan @ 11:33 pm

My maternal grandfather was born in 1896. He died in 1996. He saw a great many changes in his life. If my children live 100 years what changes will they see? To the same extent? In the biological sciences, I suspect so. In particular, in the domain of stell cells and genetic engineering it strikes me that many revolutions will occur. My confidence when it comes to automation and AI is weaker, but the potential is great.

That being said, there probably won’t be flying cars or day-trips to the moon base.

Why? This may be a function of the nature of the low hanging fruit that we’ve picked in the area of physics with engineering application to technology. If you agree with the work of scholars such as Robert J Gordon there’s been a decrease in technological innovation which changes our lives over the past century so (see The Rise and Fall of American Growth). This isn’t for lack of trying. The institutional structures and organizational effort toward novel innovation are far more directed, conscious and planned than in the past (here’s a Planet Money podcast on how technological change is slower now, though not for lack of trying).

Arguably the only major technological revolution of this century is the smart-phone. And I don’t think that that’s something you can dismiss, the smart-phone has interposed itself today into our lives in some deep and fundamental ways.

But the point of this post is that perhaps human society periodically goes through phases of innovation. And then, there’s nothing.

Twenty years ago Julian Jaynes published The Origin of Consciousness in the Breakdown of the Bicameral Mind. Seventy years ago Karl Jaspers introduced the concept of the Axial Age. Both point to the same dynamic historically.

Something happened in the centuries around 500 BCE all around the world. Great religions and philosophies arose. The Indian religious traditions, the Chinese philosophical-political ones, and the roots of what we can recognize as Judaism. In Greece, the precursors of many modern philosophical streams emerged formally, along with a variety of political systems.

The next few centuries saw some more innovation. Rabbinical Judaism transformed a ritualistic tribal religion into an ethical one, and Christianity universalized Jewish religious thought, as well as infusing it with Greek systematic concepts. Meanwhile, Indian and Chinese thought continued to evolve, often due to interactions each other (it is hard to imagine certain later developments in Confucianism without the Buddhist stimulus). Finally, in the 7th century, Islam emerges as the last great world religion.

It has long puzzled me why all the great institutional faiths arose in about 1,000 years. And then not much since then (numerically Sikhs are marginal, while the fracturing of Christianity in the 16th still left the daughter sects recognizable and possibly reconcilable).

I think here perhaps an analogy to our technological conundrum applies. One reason we don’t have jetpacks and flying cars is that the limitations of physics make it difficult.  Some things may be physically possible, but the engineering costs are prohibitive. The several waves of life-transforming technological revolutions between 1750 and 1950 slowly started to ebb in the past generations. Why? It turns out that going from horse and human power, to fossil fuels, and nuclear power, were huge transitions in terms of gains in power. There may not be much to do at this point (fusion is perhaps the major exception).

Similarly, the reason that modern people can get a lot out of Marcus Aurelius’ Meditations, Confucius’ Analects, and the Bible, is that the ethical low-hanging fruit was picked. Recently there have been advances in domains such as the abolition of slavery, so it isn’t as if no progress has been made. But if you read about the Bronze Age world, you see one where human sacrifice is still routinely practiced, as opposed to being an aberration. The distance between 0 AD and 1000 BC is arguably greater ethically than between 0 AD and 2000 AD.

Living in large complex societies with social stratification posed challenges. A religion such as Christianity was not a coincidence, something of its broad outlines may have been inevitable. Universal, portable, ethical, and infused with transcendence and coherency. Similarly, god-kings seem to have universally transformed themselves into the human who binds heaven to earth in some fashion.

The second wave of social-ethical transformation occurred in the early modern period, starting in Europe. My own opinion is that economic growth triggered by innovation and gains in productivity unleashed constraints which had dampened further transformations in the domain of ethics. But the new developments ultimately were simply extensions and modifications on the earlier “source code” (e.g., whereas for nearly two thousand years Christianity had had to make peace with the existence of slavery, in the 19th century anti-slavery activists began marshaling Christian language against the institution).

We may be living in the 21st century, but we’re still living by Iron Age ethics. And that’s not surprising.

Notes on South Asian genetics, 2018

Filed under: Genetics — Razib Khan @ 9:50 pm
A “pure” Tamil Brahmin, Chandrasekhar

In the post below Zach observes that the progressive author of a piece criticizing Ajit Pai has to note she too is a Gaud Saraswat Brahmin. Of course, she is progressive and opposes casteism no doubt. But to me “caste-dropping” that you are a Brahmin is like criticizing standardized testing, while observing that you also aced your standardized test. Not that that matters. Or that it proves anything.

But I’m posting this because there was a section on the genetic purity of Gaud Saraswat Brahmin’s of Karnataka. It caught my attention because I knew it was likely false. I’ve looked at South Indian Brahmins, and they generally look like they have gene flow from other South Indians. Also, if you use something called your eyes you can see that some South Indian Brahmins do not look like pure Indo-Aryan specimens at all.

Several years ago my friend Zack collected a bunch of data via his Harappa project. We’ve come further since then, but it’s still one of the best sources of information we have. Looking at the data there, and elsewhere, we can say a few things about South Asian genetics.

  • Jatts are different. I don’t know much about Jatts personally, aside from the fact that they are quite proud of being Jatt online. But in Zack’s data, and my own analysis in the SAGP, Jatts are highly inflated for “European-like” ancestry compared to populations around them. They have the highest proportions in their part of South Asia. Even higher than Pathans.

If you asked me to say why, at this I do think Jatts do have a more recent gene flow than other groups in South Asia. If you talk to Jatts online about their history, you will know what their hypothesis for this exotic element is.

  • Brahmins are different from other South Asians, and from each other. It will surprise no one that Brahmins are often somewhat different from non-Brahmins genetically. But, they also differ from each other.

Both South Indian and Bengali Brahmins mixed with the local population. Probably on the order of ~25% of the ancestry of these two Brahmin communities can be attributed to the local substrate. But, if you correct for East Asian admixture Bengali Brahmins are actually quite similar to the Brahmins of the Gangetic plains to the west. This comports with history.

A similar fraction seems reasonable for South Indian Brahmins, though perhaps more. The key issue that I have in this case is that the “European-like” proportion of South Indian Brahmins is about half of that of North Indian Brahmins. This would indicate half dilution. The admixture was probably from the higher end of the non-Brahmin caste hierarchy.

To get a sense of what I’m talking about, here are some percentages:

Ethnicity Dataset N SIndian Baloch Caucasian NEEuro NEEuro ratio
ap-brahmin xing 25 49% 36% 3% 6% 6%
iyengar-brahmin harappa 8 47% 37% 4% 6% 6%
iyer-brahmin harappa 11 47% 37% 5% 5% 5%
brahmin-tamil-nadu metspalu 2 47% 38% 6% 5% 5%
tn-brahmin xing 14 47% 38% 6% 4% 5%
karnataka-brahmin harappa 5 46% 35% 5% 6% 7%
oriya-brahmin harappa 2 45% 35% 2% 8% 9%
kerala-brahmin harappa 1 43% 39% 4% 6% 6%
brahmin-uttar-pradesh metspalu 8 42% 36% 5% 12% 12%
bengali-brahmin harappa 8 41% 33% 5% 10% 11%
up-brahmin harappa 4 39% 37% 7% 11% 12%
bihari-brahmin harappa 1 39% 38% 5% 11% 12%
rajasthani-brahmin harappa 2 34% 36% 8% 12% 13%
punjabi-brahmin harappa 3 34% 39% 10% 11% 11%
kashmiri harappa 3 30% 37% 14% 9% 10%
pashtun harappa 7 19% 34% 20% 11% 13%
maharashtrian harappa 6 46% 35% 5% 5% 6%
tamil-nadar harappa 5 57% 31% 2% 0% 0%
gujarati-patel harappa 2 55% 41% 0% 0% 0%
bengali harappa 11 47% 27% 2% 4% 5%
ap-reddy harappa 6 54% 36% 3% 0% 0%

Don’t take the percentages as literal populations.

  • Some groups that think they are special are not so special. Kashmiri Pandits, for example, fancy themselves as somewhat better than other South Asians, often because of their West Asian or even European physical appearance. But the genetic data indicates ancestrally they’re not surprising in any way in the context of their geographic locale.
  • Geography is not that predictive. Well, it sort of is. But you see that groups like Chamars in Uttar Pradesh are similar to South Indian populations.

Open Thread, 01/21/2018

Filed under: Open Thread — Razib Khan @ 3:24 pm

Don’t know when I’ll get to Kyle Harper’s book, The Fate of Rome: Climate, Disease, and the End of an Empire, but it looks very interesting (Patrick Wyman interviewed him for his podcast).

One thing though: climate always changes. It’s how organisms react to that change and why that is perhaps more informative. The way the Roman political order reacted the way it did to the exogenous environmental shocks had more to do with the nature of the Roman political order than the sui generis character of the shocks (they were going to happen….).

If you haven’t subscribed to my podcast with Spencer Wells, The Insight, you should (so far it’s on iTunes, Google Play and Stitcher). We’re coming out with episodes every week now. The next one will include Spencer’s recollections of the Paleolithic period of personal genomics, before 2005. We’re also recording a podcast with Gencove’s Joe Pickrell on ancestry testing this week.

DNA Geeks has more Gene Expression themed gear now, including a redesigned “Are you genotyped” shirt.

A new blog, mtDNAwiki.

An Ethnolinguistic and Genetic Perspective on the Origins of the Dravidian-Speaking Brahui in Pakistan. Have not read. Though I anticipated the conclusion over 5 years ago.

I contribute regularly to the Insitome Blog. So, No genetic test will tell you if you are Hispanic or Latino, was written after watching days of DNA-test reveals on YouTube. There’s a lot of education that needs to be done! As the Regional Ancestry product rolls out results expect many more blog posts (and probably explainers in podcast/video format at some point).

The convergences between the racialist Right and the identity politics Left have always been sad. But now that both are the waxing it’s quite sinister. For example, both would agree that science is Eurocentric in some deep way. And, both pay close attention to marriages which are racially mixed to draw broader lessons.

How genetics is unlocking the secrets of ancient human migration. On the Scandinavian hunter-gatherers.

Adaptation is subtle, and that’s the problem

Filed under: Adaptation,Human Population Genetics — Razib Khan @ 1:09 pm

The figure above is from a very important new preprint, Human local adaptation of the TRPM8 cold receptor along a latitudinal cline. A marker in 09TRPM8, rs10166942, seem to be correlated with adaptation to cold.

The abstract:

Ambient temperature is a critical environmental factor for all living organisms. It was likely an important selective force as modern humans recently colonized temperate and cold Eurasian environments. Nevertheless, as of yet we have limited evidence of local adaptation to ambient temperature in populations from those environments. To shed light on this question, we exploit the fact that humans are a cosmopolitan species that inhabits territories under a wide range of temperatures. Focusing on cold perception, which is central to thermoregulation and survival in cold environments, we show evidence of recent local adaptation on TRPM8. This gene encodes for a cation channel that is, to date, the only temperature receptor known to mediate an endogenous response to moderate cold. The upstream variant rs10166942 shows extreme population differentiation, with frequencies that range from 5% in Nigeria to 88% in Finland (placing this SNP in the 0.02% tail of the FST empirical distribution). When all populations are jointly analysed, allele frequencies correlate with latitude and temperature beyond what can be explained by shared ancestry and population substructure. Using a Bayesian approach, we infer that the allele originated and evolved neutrally in Africa, while positive selection raised its frequency to different degrees in Eurasian populations, resulting in allele frequencies that follow a latitudinal cline. We infer strong positive selection, in agreement with ancient DNA showing high frequency of the allele in Europe 3,000 to 8,000 years ago. rs10166942 is important phenotypically because its ancestral allele is protective of migraine. This debilitating disorder varies in prevalence across human populations, with highest prevalence in individuals of European descent, precisely the population with the highest frequency of rs10166942 derived allele. We thus hypothesize that local adaptation on previously neutral standing variation may have contributed to the genetic differences that exist in the prevalence of migraine among human populations today.

The mechanism and adaptive story make sense. They used several methods which corrected/accounted for population structure, and noted that the allele frequency difference was still significantly predicted by variation in latitude (though not temperature).

In the plot above you can see that South Asian populations share allele frequency distributions closer to East Asians, though genetically they are somewhat closer to Europeans. Looking at the haplotype structure this variant looks to be old variation that has been under selection in Eurasia. Additionally if you look at the frequencies it doesn’t look like the sweeps are completing. Since migraines are one correlated side effect that probably makes sense.

The problem I have with this preprint is a simple one. The SNP seems to be in the HGDP browser (it’s in your 23andMe genotype if you have one, I checked). The geographic distribution doesn’t look as clear as it does in the 1000 Genomes data. In particular in the New World populations the latitudinal cline is reversed from what we’d expect.

These sorts of objections are pretty typical. And they authors did do a sophisticated statistical analysis…but sometimes visual inspection of the raw frequencies is still important when the effect is subtle. Over the next decade there is going to be a lot of sophisticated analysis of adaptation, because the low hanging fruit has been picked. But we need to still look over the results with care….

The rich can afford to not steal

Filed under: Psychology,Replication crisis — Razib Khan @ 12:07 pm

Pardis Sabeti has an op-ed in The Boston Globe, For better science, call off the revolutionaries. In it, she contrasts and compares the changes in social psychology and genetics over the past 15 years. In the former, you have had the replication crisis, while in the latter you saw the confirmation that many candidate-gene studies were not robust and replicable.

Sabeti observes that while there has been a great deal of vehemence in the change in social psychology, in genetics people have taken the overturning of the old studies in stride, and not personalized it.

I think we can all agree that personal attacks, vehemence, and Jacobin behavior is counter-productive to what science aims to be. This applies outside of the context of the replication crisis in social psychology. The problem emerges when you ask what the alternative strategy is to overturn an entrenched order.

Though it’s implied in the piece, the reason that geneticists could be more graceful probably has more to do with the situation they were presented with in the 2000s. The rise of genomics and computation generated a surfeit of data and the ability to analyze that data. Repeated gains in power and precision mean that every overturned orthodoxy gave rise to many more research opportunities. An established researcher whose candidate-gene study was overturned had bigger fish to fry than defend turf which was small potatoes set next to the possibilities of the “post-genomic” future.*

In other words, the difference here is situational. I was aware there was a problem in social psychology by the middle-2000s, because I had friends and acquaintances who were graduate students in the field. They complained about all the things that we now know were problems. It was one of those “open secrets” where less powerful people couldn’t speak the truth, and more powerful people who benefited from the status quo had no incentive to change the norms. I really don’t know how this was going to change in a gentle fashion.

* Compare the arguments between selectionists and neutralists in the 1970s vs. now. The reality is most people just want to analyze the data, not argue about theoretical issues. That’s because we have data.

January 20, 2018

South Asian Genotype Project, update

Filed under: South Asian Genetics,South Asian Genotype Project — Razib Khan @ 10:08 pm

I’ve been working on the South Asian Genotype Project. Again, if you are interested: send me a 23andMe, Ancestry, or Family Tree DNA raw genotype file to contactgnxp -at- gmail.com.

In the subject please put:

  1. “South Asian Genotype Project”
  2. The state/province your family is from
  3. Ethnolinguistic group
  4. If applicable, caste

I changed the reference populations because the earlier ones were too complicated. You can see the population averages from public data sets for some groups.  The results for project members are here. I re-ran everyone who has sent data in so far. I’ll leave commentary for later.

At this point, I think the easiest way to update project members is to create a mailing list. If you are have submitted genotypes, please join:

Subscribe to the South Asian Genotype Project

* indicates required

The eastern edge of the sea of grass

Filed under: Historical Population Genetics,Magyars — Razib Khan @ 1:50 pm

A new preprint, Mitogenomic data indicate admixture components of Asian Hun and Srubnaya origin in the Hungarian Conquerors, throws a rather large sample of medieval mtDNA samples at the question of the ethnogenesis of the Magyar people. The context here is that Maygars speak a non-Indo-European language, with a distant relationship to the Finnic ones, but genetically are not much distinguished from their neighbors.

But the differences are not non-zero, ‘best of breed’ methods can pick up a small fraction of exotic ancestry.

The results above are based on samples from cemeteries of the Magyar elite. These are people who identified with a steppe confederacy which coalesced in the 9th century in the Volga region, and in 895 conquered the region of Central Europe which we now term Hungary. In the 10th century, the Magyar tribes were an alien and predatory force within Europe, pagan and exotic. They were, in fact, the latest in a long time of mobile Central Asian horsemen, going back to the Scythian, Sarmatians, Huns, and Avars.

What the data from these results confirm is that a substantial proportion of the maternal lineages of the Hungarian nobility were East Eurasian. Their genetic profiles, in fact, resembled Scythians who had mixed with Altaic peoples, even if they were not descended from those people. What this suggests is that the Magyar conquest elite was part of a broader landscape of ethnolinguistically distinct, but interconnected, steppe confederations. The preprint gives great space to the likelihood that a substantial proportion of the Magyar elite was in fact Turkic in origin.

This leads to one of the major assertions of the paper: the distinctive linguistic identity of modern Hungarians is a legacy of the Hunnic period, and not the Magyar conquest. From what I can tell they didn’t have older DNA, so I don’t know how they came to this conclusion, except that the conquest Magyars were small in number, and seem to have been decimated over time (Mongol invasion, the battle of Mohacs).

January 18, 2018

The Dravidianization of India

Filed under: Dravidian,India Genetics,India genomics,Indo-Aryan — Razib Khan @ 9:36 pm

On this week’s The Insight Spencer Wells and I talk about the Indo-Aryan arrival to South Asia. This was recorded very early last summer, and I’m rather unguarded (it’s well before I had the piece published in India Today).

I think 2018 will finally be the year that a lot of South Asia will be “solved.” There has been some foot-dragging on papers and results, but that can only go so long.

All that being said I suppose I should make some suppositions I have arrived at on this topic more explicit, as in a discussion with an Indian friend he admitted had no idea about some of my views, though he reads this weblog when I expressed them. That’s because they are speculative and my confidence in them is weak, though you can infer my opinions if you look very closely.

The figure to the left is from Genomic insights into the origin of farming in the ancient Near East, a paper published about a year and a half ago. You see various South Asian populations being modeled as a mixture of four different source populations. The Onge are an Andaman Islander population (and the closest we can get to the aboriginal peoples of South Asia). Iran_N represents Neolithic Iranians, the canonical “eastern farmer” population. Steppe_EMBA represent Yamnaya pastoralists, who are themselves modeled as a mixture of Eastern European Hunter-Gatherers (EHG) and southern population which has affinities with the Iran_N cluster. EHG in their turn seems to exhibit ancestry from Western European Hunter-Gatherers (WHG), whose heritage dates to the late Pleistocene, and Ancient North Eurasians (ANE), who flourished in Siberia, and contributed ancestry to populations to the west and east (including the ancestors of Native Americans).

When I first saw this specific figure I was incredulous. I had long thought that “Ancient North Indians” (ANI) were a compound of two elements, one related to the farmers of West Asia (Iran_N), and the other steppe Indo-European (Steppe_EMBA/Yamnaya). But the fraction of Yamnaya/Indo-European/Indo-Aryan ancestry seemed far too high.

A few years later I am not less certain about my skepticism. The fractions here in the details are debatable. Within the text of the paper, the author admits that the true ancestral populations are probably not represented by the model. But they are close. In most cases, the “Han” ancestry is probably indicative of the fact that the non-ANI component of South Asian ancestry is most closely related to the Onge, but is significantly different nonetheless.

The ratio of Iran_N and Steppe_EMBA is the key. Here is a selection from the paper:

Group Iran_N Steppe_EMBA Ratio
Jew_Cochin 0.53 0.23 2.27
Brahui 0.60 0.30 1.98
Kharia 0.13 0.07 1.97
Balochi 0.57 0.32 1.75
Mala 0.23 0.18 1.25
Vishwabrahmin 0.25 0.20 1.21
GujaratiD 0.29 0.28 1.04
Sindhi 0.38 0.38 1.00
Bengali 0.22 0.25 0.91
Pathan 0.36 0.45 0.81
Punjabi 0.24 0.33 0.72
GujaratiB 0.27 0.38 0.72
Lodhi 0.21 0.29 0.72
Burusho 0.27 0.43 0.64
GujaratiC 0.23 0.37 0.61
Kalash 0.29 0.50 0.58
GujaratiA 0.26 0.46 0.57
Brahmin_Tiwari 0.23 0.44 0.51

Any way you slice it, a group like the Tiwari Brahmins of Northern India have more Onge-like ancestry than most of the groups in Pakistan. But also observe that the ratio toward Steppe_EMBA is more skewed in them than among even Pathans or Kalash.  The Lodhi, a non-upper caste population from Uttar Pradesh in north-central South Asia are more skewed toward Steppe_EMBA than Pathans.

It is important for me to reiterate that the key is to focus on ratios and not exact percentages. Though the Steppe_EMBA fraction did strike me as high, glimmers of these sorts of results were evident in model-based clustering approaches as early as 2010. The population in the list above most skewed toward Iran_N are Cochin Jews. This group has known Middle Eastern ancestry. But next on the list are Brahui, a Dravidian speaking group in Pakistan. There is a north-south cline within Pakistan, with northern populations (Burusho) being skewed toward Steppe_EMBA and southern ones (Sindhi) being skewed toward Iran_N. Additionally, Iranian groups such as Pathans and Baloch likely have had some continuous gene flow with Middle Eastern groups, probably inflating their Iran_N.

Trends I see in the data:

  1. There is a north-south cline within Pakistan with Steppe_EMBA vs. Iran_N
  2. There is a north-south cline within South Asia with Steppe_EMBA vs. Iran_N
  3. There is caste stratification within regions between Steppe_EMBA vs. Iran_N
  4. Though not clear in this table, there are strong suggestions that Indo-European speaking groups tend to be enriched in Steppe_EMBA, all things equal (e.g., the Bengalis in the 1000 Genomes look a lot like the middle-caste Telugus in the 1000 Genomes when you remove the East Asian ancestry…except for a noticeable small fraction of a component which I think points to Indo-European ancestry)

What does this mean in terms of a model of the settlement of South Asian over the past 4,000 years? One conclusion I have come to is that Dravidian speaking groups are not the aboriginal peoples of the subcontinent. Rather, their settlement across much of South Asia is very recent. Almost as recent as Indo-Aryan habitation. In First Farmers the archaeologist Peter Bellwood proposed this model, whereby Indo-Aryans and Dravidians both expanded across South Asia concurrently. Though I think elements of Bellwood’s model that are incorrect, it’s far more correct in my opinion than I believed when I first encountered it.

Why do I believe this?

  1. The Neolithic begins in South India in 3000 BC.
  2. Sri Lanka is Indo-European speaking
  3. The Dravidian languages of South India don’t seem particularly diverged from each other
  4. There is ancestry/caste stratification in South India even excluding Brahmins (e.g., Reddys and Naidus in Andhra Pradesh look somewhat different from Dalits and tribals)
  5. Some scholars claim that there isn’t a Dravidian substrate in the Gangetic plain
  6. R1a1a-Z93, almost certainly associated with Indo-Aryans, is found in South Indian tribal populations
  7. Using LD-based methods researchers are rather sure that the last admixture events between ANI and ASI (“Ancestral South Indians”) populations occurred around ~4,000 years ago

Here is my revised model as succinctly as I can outline it. The northwest fringes of South Asia, today Pakistan, and later to be the home of the Indus Valley Civilization (IVC), was populated by a mix of indigenous populations, a form of ASI, when West Asian agriculturalists arrived ~9,000 years ago from what is today Iran. These were the Iran_N or “eastern farmer” groups. The West Asian agricultural toolkit was serviceable in northwestern South Asia for reasons of climate and ecology, but could not expand further east and south for thousands of years.

There is where the first admixture occurred that led to a population was mixed between ANI and ASI. These people lacked Steppe_EMBA. They were pre-Indo-European. They were almost certainly not all Dravidian speaking. The Burusho people of northern Pakistan, for example, speak a language isolate (in India proper you have Nihali and Kusunda)

By ~3000 BC this proto-South Asian (in a modern sense) population began to expand, while the IVC matured and waxed. Eventually, the IVC waned, fragmented, and disappeared.

Around ~2000 BC, or perhaps somewhat later, Indo-Aryans arrive in South Asia. The situation at this stage in not one of a primordial and static Dravidian India, on which Indo-Aryans place themselves on top. Rather, it’s a dynamic one as the collapse of the IVC has opened up a disordered power vacuum, and a reconfiguration of cultural and sociopolitical alliances.

In the paper above the author alludes to the pervasiveness of both Iran_N and Steppe_EMBA ancestry in South Asia, including in South India. “Indo-European” Y chromosomal lineages are also found among many South Indian groups, albeit at attenuated proportions region-wide. In Peter Turchin’s formulation, I believe that “Indo-Aryan” and “Dravidian” identities became meta-ethnic coalitions in the post-IVC world. Genetically the two groups are different, on average. But some Dravidian populations assimilated and integrated Indo-Aryan tribes and bands, while Indo-Aryans as newcomers assimilated many Dravidian populations.

The reason that the ratio of Iran_N to Steppe_EMBA does not decline monotonically as one goes from west to east along North Indian plain is that Indo-Aryans were not expanding into a Dravidian India.  Dravidian India was expanding only somewhat ahead of Indo-Aryan India, and in some places not all at all. In the northwest fringe of South Asia there had long been a settled population of peasants with West Asian ancestry with Iran_N affinities. In contrast to the east the landscape was populated by nomadic tribal populations with ASI affinities. North Indian Brahmins may have more Steppe_EMBA than some populations in Pakistan and more ASI because they descend from Indo-Aryan groups who absorbed indigenous ASI populations as they expanded across the landscape.

Dravidian groups as they expanded also assimilated indigenous populations. This explains some groups with very high fractions of ASI. Their ASI ancestry is a compound, of an old admixture in Northwest India, and also later assimilation in South India. The presence of R1a1a-Z93 in these populations reflects the integration of some originally Indo-Aryan groups into the expanding Dravidian wavefront.

Where does this leave us?

  1. The Indo-Aryan vs. Dravidian dichotomy is not one of newcomers vs. aboriginals. It is of two different sociocultural configurations which came into their current shape in the waning days of the IVC. That is, it is less than 4,000 years old
  2. The two populations were clearly interacting closely around the time of the collapse and disintegration of the IVC and post-IVC societies. There has been gene flow between the two
  3. ~4000 years ago ANI and ASI populations existed in their “pure” form, but that is because ASI aboriginals still existed to the south and east of the IVC, while Indo-Aryans were a new intrusive presence in the Indian subcontinent

January 17, 2018

Runs of homozygosity are not good for your functioning

Filed under: Population genomics,Runs of Homozygosity — Razib Khan @ 8:20 pm

A must read review in Nature Reviews Genetics, Runs of homozygosity: windows into population history and trait architecture. Because it’s a paper on runs of homozygosity, James F. Wilson is on the apper.

If you are the product of a first cousin marriage, you have lots of runs of homozygosity. That’s because some of you will have large sections of the genome where both of the homologous chromosomes come from the same individual and are identical. In populations with small populations, this occurs not through recent inbreeding, as much as the reduced genetic diversity cranking up the frequency of some haplotypes over and above others.

The review covers all the bases, from distributions of runs of homozygosity in modern populations to ancient ones, as well as their functional consequences.

To the left, the plot shows that some populations, such as the Makrani of Pakistan, have fewer numbers of runs of homozygosity, but long ones when they have them. The populations on this part of the diagram are part of the “inbreeding belt.” In contrast, there are other populations with lots of runs of homozygosity, but they’re shorter. These are usually part of the “bottleneck belt,” where bottlenecks and small long-term effective populations have produced greater levels of homozygosity even on the genotype scale.

Perhaps the most interesting point though is that runs of homozygosity strongly correlate with changes in the values of a complex trait. In general, inbreeding is not too good, because recessively expressing deleterious alleles get exposed, and runs of homozygosity are a proxy for that.* This is why more exogamy in the Middle East and India may be such a social good.

* There may be confounds here. More educated and smarter people may marry those more distant from them geographically due to mobility.

January 14, 2018

Open Thread, 1/14/2018

Filed under: Open Thread — Razib Khan @ 10:43 pm

Steven Pinker is one of my favorite public intellectuals. The Language Instinct is probably my favorite book from Pinker.

Last week I started seeing scientists who I respect(ed) starting to tweet that Steven Pinker, a moderately liberal academic of Jewish background, is a fan of Neo-Nazis. This stuff started to litter my timeline since I follow many scientists on Twitter. To find all the links and commentary, start with Jerry Coyne, who is a friend of Steve’s. All I have to say is that a substantial portion of the science Twittersphere is OK with bracketing Steven Pinker with Neo-Nazis. True fact.

I read Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts two years ago. I don’t remember much about that book though.

CBC under fire for documentary that says first humans to colonize New World sailed from Europe. There is less evidence for the Solutrean Hypothesis now than there was 20 years ago (in a relative sense). We also now know from ancient DNA that almost no Solutrean ancestry is present in modern Europeans.

If you don’t believe me, read this paper, The genetic history of Ice Age Europe.

At least most of my Twitter followers don’t seem to be anti-Pinker.

Having a hard time saying anything about Anhui of note. Perhaps that says something?

Turning cheesecake into a weapon of war

Filed under: Cultural Evolution,Evolutionary Psychology — Razib Khan @ 10:23 pm

Steven Pinker and many other evolutionary psychologists believe that music is cognitive cheesecake. That is, we have a lot of cognitive faculties working in concert, and musical appreciation and ability emerge out of the synthesis. But there wasn’t direct selection for music, as such. Musical appreciation then may not be adaptive.

And yet like reading and writing music clearly co-opts part of the human brain in terms of functional localization. There are people with brain injuries who can not speak well who nevertheless can sing well, and can communicate through song.

But perhaps most important, just because a trait did not emerge due to natural selection, does not entail that it might not be subject to later selection. One can make arguments that musical ability was adaptive at some point in human existence on the individual scale. But I have something else in mind: music is functionally important in war. Military marching bands did not arise coincidentally, music as an accompaniment to the march and a way to communicate and rouse the troops to action have been part and parcel of winning and executing battle. Music triggered social change in the 1960s.

I think much the same is probably true of religion.  My own position is that the shamanic/primal form of religious belief bubbles up out of our cognitive architecture as a side effect of other processes. But this byproduct can be co-opted by cultural evolutionary selection, and reshaped into something with functional utility.

The genetics of the St. Thomas Christians

Filed under: Indian Genetics,Nasrani,St. Thomas Christians — Razib Khan @ 10:08 pm

First, I have to say I appreciate everyone who keeps sending data to the South Asian Genotype Project. Basically, I’m automating the pipeline, finding ways to merge data from a host of sources, but also figuring out how to refine the analysis.

But until then, today I decided to do some more manual analysis of three St. Thomas Christian samples I have (also called Nasranis). The reason is that there were some questions on Twitter in relation to the genetics of this group, and though three is not a great sample size, it’s better than nothing.

The St. Thomas Christians are a diverse group of people of various denominations in the southern state of Kerala who have various origin stories. Though today the St. Thomas Christians have a range of denominational and sectarian affinities, their origins probably have something to the Church of the East.

These Christians also have origins about among the local Brahmin community, Jews, and West Asian settlers. To be honest, whenever people tell me about the Brahmin origins unless they were recent converts I discount this because there are about ten times as many St. Thomas Christians in Kerala as there are Brahmins. There is a small Jewish community in the area, and this region of India was long part of the Indian Ocean trade network of the Arabs.

I merged the three Nasrani samples with a lot of other populations. Zooming in on the South Asians, if you look at the PCA plot to the left (click it), you’ll see that they are not in the same cluster as the South Indian Brahmins (Brahmins from the four South Indian states are very similar to each). But, in comparison to non-Brahmin South Indians, they do seem Brahmin shifted.

As I have observed before these South Indian Brahmins can be thought of as more than 50% North Indian Brahmin, but the remainder being South Indian non-Brahmin. Aside from exotic exceptions (Parsis, Bengalis), most South Asians exist on an ANI-ASI “cline,” with lower caste South Indians being at one end of the cline (more ASI), and populations in the far northwest, such as the Kalash, being at the other end (more ANI). The PCA would suggest that the Nasrani are more ANI-shifted than a generic South Indian group, but less so than South Indian Brahmins.

Using Treemix to detect gene flow events, what I found is that the Nasranis look like a generic South Indian group. There’s no evidence of gene flow from Middle Eastern populations (Jews, Persians).

I did some f-3 tests and there isn’t anything conclusive I see to suggest Middle Eastern gene flow into the Nasranis fro that avenue.

Finally, I ran ADMIXTURE in supervised mode. Here are the average results for a set of South Asian populations (mean values):

Group Druze Georgian Han Iranian Telugu Yemenite Jew
Bangladeshi 1% 2% 12% 1% 83% 1%
Chamar 0% 0% 3% 0% 97% 0%
Gujurati_Patel 0% 1% 0% 10% 89% 0%
UP Kshatriya 0% 3% 1% 21% 76% 0%
Nasrani 0% 4% 1% 12% 83% 0%
Pathan 0% 4% 1% 55% 40% 0%
Piramalai_Kallar 0% 0% 2% 0% 97% 0%
SI_Brahmin 0% 4% 1% 16% 78% 0%
Telugu_Reddy 0% 3% 0% 0% 94% 3%
UP_Brahmin 0% 4% 1% 26% 69% 0%
UP_Kayastha 0% 0% 1% 20% 79% 0%
Velama 1% 1% 0% 2% 96% 0%
West_Bengal_Kayastha 0% 0% 7% 8% 85% 0%

In these data the Nasrani do look shifted in the same direction as South Indian Brahmins, though less so. Observe that there is no clear Middle Eastern signal in the Nasrani above and beyond what you see in South Asians. This, despite the fact that Indian Jews show a very strong signal of admixture from the Middle East. At this point I am confident in rejecting Nasrani St. Thomas Christian origins in a converted Jewish community, or one with a large degree of West Asian admixture.

Though the genetic profile of these three individuals does not support clear descent from South Indian Brahmins, I can not reject the model of Brahmin admixture into this community. On the contrary, a plausible model would see to be that various South Indian groups, including Brahmins, contributed to the Nasrani community over the centuries.

To be continued….

January 12, 2018

From the content to the creator

Filed under: Blog — Razib Khan @ 9:24 pm

The science fiction writer S. M. Stirling has a problem with his series centered around the Domination alternative history because readers often confuse the narrative of the alternative history for the author’s endorsement of its arc and philosophy. You see, the novels and stories depict a world where a quasi-Nazi ghoulishly Nietzschean race termed the Draka eventually rise to conquer the whole world. Similarly, the fantasy writer Brandon Sanderson has had problems with readers who are curious why he has sympathetic atheist characters, despite he himself being a devout Mormon.

Obviously, some writers focus on what they know and have experienced. Jhumpa Lahiri comes to mind. She has said that she has no plans to delve beyond the purview of her West Bengali story arcs. But other writers like to explore viewpoints which are startlingly novel and at variance with those of themselves. This is probably particularly true of speculative fiction. Part of being human is the ability to do this with varying levels of fluency.

It is important in any case not to confuse the writer with what they are writing about.

Some of the same applies to what I talk about on this blog. This is clear and obvious when I’m considering the selection coefficient of a novel allele. But what about the Iranian regime?

  1. I am not personally a fan of the regime.
  2. I also believe it is important to describe it accurately and in its own terms.

Some of the latter is for instrumental reasons: if you are to defeat the enemy you must understand it. Even in the early 9/11 years, this was clear, but many people resisted this attempt, as emotions were quite raw. Islamist radicals were viewed in almost metaphysical terms, as forces of nature, evil essences of the universe. The reality though is that they are embodied creatures with needs, wants, and delusions, just like any other.

Ultimately I’m generally pretty frank with my views on a topic if I have them and want to express them. I’m not being cryptic. In some cases, I don’t want to interject my own personal views (which most can infer or know in any case). In other cases, I don’t have a strong opinion.

What religion is

Filed under: Religion — Razib Khan @ 8:38 pm

It’s been about 10 years since I addressed this topic. Largely because I have no new thoughts. But probably after 10 years, it’s useful to revisit/clarify on this topic to clarify confusions, since people have a lot of opinions on this topic.

People mean different things when they mean “religion,” and the different meanings are not contradictory, nor in conflict.

At the lowest level in terms of individual cognition religion emerges from deep intuitions about the nature of the universe. Colloquially one might say that religion bubbles out of our unconscious.

In relation to social units, say the clan or tribe, religion consists of these intuitions about the nature of the universe and the world around us, bound together with rituals and verbal descriptions and narratives. These rituals and communal narratives help forge some sort of group Weltanschauung that has a functional utility in terms of inter-group competition and relations. Here religion steps out of the individual and becomes an expression of collective consensus.

As human societies became more complex the role of religious professionals became more elaborated. The common role of a shaman can be thought of as a magician, one who manipulates and operates in the domain of the supernatural. Shamans are common and ubiquitous in pre-state societies (even if a tribe does not have a “professional” shaman, someone takes on the role when needed). The priest adds on top of this institutional authority, often supra-clan or tribal. No king, no priest. Eventually, though the shaman-priest took on the role of the metaphysician. The metaphysician generates abstract principles and rationales, which can transcend the tribe or ethnicity, and allows religion to generate meta-ethnic civilizational identities in the service of priestly functions.

So in the post-Axial Age, the religious professional is often shaman, priest, and philosopher.

In relation to my post about why I am not a New Atheist, New Atheists, and the hyper-verbal expositors of modern organized religion, often tend to reduce religion to a branch of philosophy with some textual revelatory buttress. By refuting the philosophy of religion, they think that they refute religion in toto.  But what they refute is only the latest and most elaborated structural expression of the religious phenomenon.

What about the priest? Though I am wary of the term “political religion,” due to semantic confusion, it seems clear that the function of the priest can be stripped of its supernatural valence. Many of the most objectionable characteristics of religion for people of liberal orientations derives from the institutionalized priestly functions. Unfortunately, the persistence of the priest in the absence of gods, shamanic powers and metaphysical justification opens the doors to secular totalitarianism.

Finally, it seems almost impossible to stamp out the shaman. Shamanism is like music. You can banish it through institutional sanctions, but once those sanctions disappear, shamanism reappears.

These different aspects of religiosity exist and persist simultaneously in most contexts, but sometimes in tension. Philosophers and priests often take a dim view of shamanic religiosity. In organized religion of the modern sort shamanism is marginalized, or highly constrained and regulated in sacraments. But the recession of state-sponsored Christianity across much of the West has arguably resulted in a resurgence of shamanism, and the proliferation of diverse supernatural beliefs which had previously been suppressed (much of East Asia is characterized by relative weakness of philosophical religion but the strength of shamanism).

Jade Eggs anyone?

The relevance of all this in relation to New Atheism is that New Atheism seems to posit a religious “Blank Slate.” That is, children are indoctrinated in religion at a small age, previous to which they had been atheists. Part of this is due to the fact that the philosophical-metaphysical aspect of religion is quite clearly indoctrination, and often of a superficial sort at that (judging by how weak most believer’s grasp of theology is). But the communal and psychological aspects are not indoctrination, as much as specific instantiations of general human sentiments, dispositions, and intuitions. The erasure of a Christian, Buddhist or Islamic religious orientation will not necessarily leave in its wake a mind primed for scientific naturalism. Rather, it will simply be one shorn of Axial-Age accretions, reverted back to the shamanic age…

As someone who is an atheist, I have never had strong intuitions that lead me to find shamanism plausible. Additionally, the philosophical arguments are wanting for me in relation to God, though they are interesting (thanks to reader Thursday I’m reading Edward Feser’s work). Finally, obviously, I take a dim view of the conformity and structure which the priests attempt to impose upon us.  But I do not presume I have typical.

Personal genomics question: am I related to my 5th cousins?

Filed under: DTC personal genomics — Razib Khan @ 1:06 pm

There are some personal genomics questions I get over and over via email. I thought I would post an answer so that Google could pick it up.

One of them usually has do with if someone is “really” related to someone who comes up as a 5th cousin on a DTC service. What does “really” mean?

Graham Coop has done the formal work to show that it’s highly likely all our genealogies intersect some point in the recent past. Several years ago in his paper with Peter Ralph, The Geography of Recent Genetic Ancestry across Europe, they used genetic data to infer just how closely European lineages coalesced with each other over the past few thousand years.

But that’s not the question people are really asking about. They are asking, does this DNA match increase the probability that I’m somehow related to this person?

In general, I think not. For example, I regularly get queries from South Asians about distant matches with Europeans. Does this mean they are European? No. I think what it means is:

1) There are lots of Europeans in the database, so a false positive match is likely to be European, even if you are non-European.

2) At short genetic distances, the segments are really mostly some sort of false positive.

January 11, 2018

Why I am not a New Atheist

Filed under: atheism,Atheist,New Atheism — Razib Khan @ 9:32 pm

Since this comes up now and then I thought I’d put up a quick and short post why I am not a “New Atheist.”

I am an atheist. But I have two major disagreements with the New Atheist tendency. One of them is descriptive and the other is prescriptive.

For the past fifteen years or so I have been strongly convinced that the cognitive anthropology of religion has a lot to say in explaining why most people have historically been religious. The thesis, outlined in books such as In Gods We Trust and Religion Explained, is that humans have strong innate cognitive dispositions which often synthesize together to produce intuitions that dispose them toward belief in the supernatural.

In contrast, a caricature of the New Atheist position would be that religion was written down in a book, and is a meme copied into human brains. As such, it is a meme which can be undone with enough social and cultural suasion. New Atheists, like the village atheists of yore, seem to think one can argue others out of their religiosity.

Fundamentally I do not think this is correct. Nor do I think that religious beliefs have much to do with logic or reason. Religion is a complex phenomenon which is rooted in supernatural intuitions and then evolves further in a cultural context, with some possible functional utility as a group-marker.

Second, I do not think religion is the “root of all evil”, and so see no need to convert the world to atheism. Obviously, the horror of Communism illustrates that removing supernatural religion does not remove the human impulse to atrocity.

More recently, I have been convinced that truth and knowledge is a minor value to most humans, including elites. Lying is pretty ubiquitous, and most people are rather satisfied with big lies girding social norms and conventions. One may try to avoid “living by lies” in private, but actually promoting this viewpoint in public is ridiculously self-destructive. Most people could care less about the truth, while elites simply manipulate facts to buttress their social positions and engage in control.

In other words, the New Atheists seem to think that it’s a worthy to aim to enlighten humanity toward views which they believe align with reality.

At this point, I care about converting the common man to a true understanding of reality as much as I care about a cow grokking trigonometry. I don’t.

Note: I am not anti-New Atheist either! I think they play a role in the ecology of ideas. Also, I don’t really care if people get their feelings hurt. I hurt feelings all the time. To paraphrase George Constantza, you get a few New Atheists running around, and I’m not looking so bad.

Zhejiang, the heart of Jiangnan

Filed under: China,Zhejiang — Razib Khan @ 2:47 pm

Zhejiang is the province to the south of Jiangsu, and the heart of Jiangnan, the lower Yangzi river area. As noted in my previous post this region is notable for its economic productivity and wealth, which dates back more than 1,000 years, and persists down the present. Like Jiangsu, Zhejiang is outside of the core area of the rise of Han civilization, but by the 1st millennium A.D. became a redoubt of Chinese civilization in the face of non-Chinese incursions into the north.

Zhejiang is also the location for one of the major centers of Christianity in China, Wenzhou. On the order of ten percent of this city’s population is Christian.

Out of Africa-Out of Asia-Out of Africa

Filed under: Human Population Genetics,Out of Asia,Out-of-Africa — Razib Khan @ 1:58 pm

Roberta Estes recenty posted about the fact that Spencer & I will be revisiting The Journey of Man, fifteen years after he wrote the book and made the documentary.

As part of the preparation, I’m revisiting some uniparental results, in particular, recent ones. This preprint in bioRxiv Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago., caught my attention:

Background: After three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya. Results: The coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions: These results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements.

It was really hard for me to parse all the coalescene and phylogenies here. I know some readers are pretty well versed in this area so I’m curious about critiques and reactions to the above.

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