Hinduism before India

Azar Gat is one of my favorite scholars. He does not seem to be one who bows before fashion. If you haven’t, I recommend War in Human Civilization a great deal.

With that being said, perhaps an overlooked work is his more recent Nations: The Long History and Deep Roots of Political Ethnicity and Nationalism. It is a reasonable antidote to Benedict Anderson’s Imagined Communities: Reflections on the Origin and Spread of Nationalism. Anderson’s book is apparently one of the most assigned works to undergraduates in the United States, and I saw it cited so often that I went ahead and read it to see if there was any “there there.” Alas, that was not to be. I have come to conclude that those who find profundity in Imagined Communities are superficial thinkers, and want “information for free.” That is, a theory that can explain history without having to learn many facts.

Gat’s Nations is not a simplistic argument that the specific nations we see around us today have deep roots in antiquity. The chasms between Arminius, Luther, and Bismarck, are great indeed. But for Gat the conceptual framework of nationhood is derived from primal constituents and extends itself naturally from a common human set of cognitive reflexes and the selective sieve of cultural evolution. A late Roman Republican politician could understand broadly the process of the formation of the creation of modern Italy from various constituent polities which shared a cultural affinity, just as the Roman Republic itself was a fusion of tribes.

This is on my mind because of a post over at Brown Pundits, India Never Existed. In the post, there is a quote from a scholar of South Asia who is seemingly at the center of constant controversy with “Hindu Twitter”:

In the old days, India was not united. And there was no cohesive Hindu identity. Literally, “Hindus” did not call themselves Hindus in premodernity.

So far as today, Hindutva is an ideology of hate, based on early 20th-century European fascism, that derides religious minorities.

Overall I think this is an unhelpful and polemical way to present the facts. I am not a Hindu nationalist. But neither am I secular Indian. In the Indian context “secular” means a very precise thing which is not covered simply by being an irreligious atheist (which I am). As an American who has an intellectual, but frankly no deep emotional, interest in South Asian affairs it is up to Indians to sort out their cultural and political conflicts. But, just as the “Out of India” Hindu nationalists strike me as in the wrong, it seems clear that some secular Indian intellectuals engage in polemics unfounded in fact, or shading the truth in a manner that serves their ideology rather than the facts on the ground.

A certain school of scholars, who seem to be engaging in a culture war against Hindu nationalists, present the genesis of Indian identity as a pure reaction to the engagement with Europe. That is, Indianness develops as a mimic of Englishness. Before 1800 there were  jatis, Muslims of various ethnicities, and curious minorities like Parsis, all coresident across South Asia, but there was no Hindu identity except as a disjoint set of characteristics and cultures which were not included amongst Muslims, Christians, Parsis, etc.

This view is extremely misleading. The genetic evidence seems clear that the ethnogenesis of modern South Asians dates to the period between two and four thousand years ago, between the last massive phase of admixtures between different continental elements, and the emergence of an endogamous caste system. The antiquity of caste is genetically attested and spans much of North and South India. As far back as the time of the Greeks and Persians, the people of the Indian subcontinent were known to those outside as a distinctive and coherent element, and the Hindu religious traditions certainly predate 1800. Adi Shankara, an 8th-century thinker who arguably outlined the core tenents tone of “elite Hinduism” as we know them today, was a Brahmin from the far South of the subcontinent.

It is true that the indigenous traditions of the Indian subcontinent were a diverse mix, and many communities (now termed “tribes”) were outside of the caste system and Hindu society. But by the time that Islam arrived in the subcontinent the influence of Brahmins had certainly spread a particular elite culture patronized by most rulers, with those who were skeptical often being devotees of religious groups more distinct from Hinduism (whether it be Buddhists or Jains). It is correct to point out that most people in the Indian subcontinent did not subscribe to Brahmin religious thought, but most of the population of Europe in 1000 AD practiced a very inchoate Christianity, and yet we do not hesitate to term this a Christian civilization, seeing as how much of the continent was bound together by a priestly elite which obtained sponsorship from kings and nobles.

To be frank, some of the anti-Hindutva scholars seem to be engaging in semantic games to win arguments with their ideological enemies. It is clear that Indian national identity in a political sense is recent, and is not analogous to that of China, which is ancient. But should one then say that a “European” identity did not exist in 1000 AD because most European polities were bound together by personal rule and the Christian religion, rather than geography and nationality as we understand it? It is clear that the outlines of what became Europe emerged in the wake of the Roman collapse, and the rise of Islam. Just because courtiers in the court of Charlemagne did not term themselves “Europeans” does not mean that the general outlines of Europeanness did not predate the ideological formulation in the early modern period, as Christians became Europeans.

A bigger framework is that we can see patterns across societies in time and space, and draw analogies and inferences. Human social and political institutions are commensurable. The development of Europe in the wake of the fall of Rome and the shock of the barbarian invasions is neatly analogous to the emergence of native Indian religious traditions in the wake of the shock of the arrival of Muslim Turks. There are differences, but Europe and Europe’s experience is not sui generis. One could state that France “did not exist” until the French Revolution, and the 19th century drives toward assimilation of local dialects and the emergence to prominence of “standard French.” But it is clear that something “French” clearly motivated the elites, Protestant and Catholic, who battled in the 16th and 17th centuries, at the intersection of religion and nationality. Even though most peasants had a rural and local identity, the stage was set for the national passions which inflamed the Revolutionary regime of the 1790s.

Similarly, the Indian republic has had its issues, but it is not a coincidence that it has managed to maintain continuity and integrity through all its ups and downs. Indian identity is clearly somewhat an artificiality because a unified Indian state was imposed relatively late in history, and only for a short period by a Mughal elite which was not in cultural solidarity with the diversity of its subjects. But across the cultural diversity, there is a level of affinity which has historical roots. An analogy here can be made to Indonesia, a diverse archipelago which was never a unitary state, but whose cultural cohesiveness is a product of history rather than politics. The regions of India and Indonesia, Kashmir and the northeast for India, and the eastern islands for Indonesia, are those regions with less cultural affinity and oftentimes no shared history with the central elite.

My understanding of these sorts of issues are informed by two things:

  • Specific attention to details of history, which is hard to obtain without just reading
  • A general understanding of human social development informed by evolutionary anthropology

Some systems of thought constrain comprehension in a semantic straightjacket. So, for example, there are those who would argue that “religion” in a Western context is qualitatively different from “religion” in an Eastern context. I think this is ridiculous. All religions exhibit cognitive features, which are the outcomes of our evolutionary history, which is shared. There is the idea that a nation-state has to be understood as a crisp definition which emerges in the period between the Peace of Westphalia and the French Revolution. That the nation-state was born in Western Europe, and all successor nation-states the world over are derived from Western European ideas.

There is some contingent truth to this. Modern nation-states are fundamentally Westphalian. The language and the framework of modern diplomacy are European. In particular, it comes out of the second half of the 17th century. But the European nation-state is not sui generis, and diplomacy was not invented by Europeans. The concept of a geographically delimited polity associated with a standing army and civilian bureaucracy is not just something particular to early modern Europe. The Romans, Chinese, and Muslims created such political systems. The Roman system collapsed in Western Europe, while the later European system overwhelmed the Chinese and Muslim political systems.

But even in their accession to the European forms, native societies retained their uniqueness. Their own deep roots. This is evident in both China and Japan, whose political systems outwardly are replicas of European ideologies and frameworks. The Islamic Republic of Iran is a peculiar hybrid of European and indigenous. When Western scholars deride Hindutva as based on “early 20th-century European fascism”, they remove from Indians any agency. As if Hindu nationalism is simply a curry-flavored form of European fascism. Like Baathism, Chinese Nationalism after the purge of the Communists, and the military regime of interwar Japan, there were clear influences from Europe, but all exhibited strong indigenous roots and bases as well.

There are things particular, and things general. It was almost inevitable that a traditionalist Hindu renaissance would develop long before the ferment of right-wing ideologies in early 20th century Europe. The small-scale decentralized Indian cultural complex which weathered the storm of Islamic rule was unlikely to ever maintain itself in the face of modernity (contra Gandhi). It was going to evolve in various directions, and one of them would be reactionary, even if that reaction was toward an imagined past which synthesized future hopes informed by the present with past solidities.

The past was very different. And other cultures are very different. But they are not incomprehensibly different. Outside of Europe the antecedent of the present is not simply the past of Europe. Other societies differ from Europe and reacted in various ways to the colonial experience, but the European shock is not the sum totality of what they are and what they will be. The terms and concepts we use to scaffold our comprehension of the world around us are important in their details, but they are not what we are comprehending. Just because we see the past darkly through the mirror does not entail that we should simply refashion the past in our easier imaginings.

All your GWAS belong to us


Very interesting preprint, A global view of pleiotropy and genetic architecture in complex traits. Nothing too surprising, but worth a read.

After a decade of genome-wide association studies (GWASs), fundamental questions in human genetics are still unanswered, such as the extent of pleiotropy across the genome, the nature of trait-associated genetic variants and the disparate genetic architecture across human traits. The current availability of hundreds of GWAS results provide the unique opportunity to gain insight into these questions. In this study, we harmonized and systematically analysed 4,155 publicly available GWASs. For a subset of well-powered GWAS on 558 unique traits, we provide an extensive overview of pleiotropy and genetic architecture. We show that trait associated loci cover more than half of the genome, and 90% of those loci are associated with multiple trait domains. We further show that potential causal genetic variants are enriched in coding and flanking regions, as well as in regulatory elements, and how trait-polygenicity is related to an estimate of the required sample size to detect 90% of causal genetic variants. Our results provide novel insights into how genetic variation contributes to trait variation. All GWAS results can be queried and visualized at the GWAS ATLAS resource (http://atlas.ctglab.nl).

A return of the gods

I have mentioned Alister McGrath’s The Twilight of Atheism: The Rise and Fall of Disbelief in the Modern World several times on this weblog. When I first read this book, about twelve years ago, its overall argument seemed unpersuasive. It was already clear then that the United States was going through a wave of secularization, which has seen a massive expansion in the number of “religious nones” in the past generation. It was during this period that books such as Richard Dawkins’ The God Delusion became a cultural phenomenon.

As an empirical matter disbelief has not fallen in the modern world. On the contrary.

But McGrath was getting at something when he exulted in the possibilities for traditional religion in a “post-modern” context, where objective science was no longer privileged. In the middle 2000s, this seemed like a strange contention to be making. Books such as Higher Superstition: The Academic Left and Its Quarrels with Science were still on our cultural radar. The “Science Wars” were over. Science had won.

But when one war is won, the seeds for the next are sown. Over at Why Evolution is True, Jerry Coyne has a post up, Princeton’s course on how marginalized scientists can produce “different ways of knowing”. The entire post is a rather predictable product of someone who has a late 20th-century positivist viewpoint on these issues. For Coyne science is fundamentally transcultural and universal. As a paleoliberal Jerry also lacks the semantic nuance to navigate today’s progressivism very well, with its attention to lexical detail and precision. Coyne means well, but he sometimes comes off as a visitor from the 20th century.

It’s hard for me to think that Jerry Coyne would disagree with the idea that science is a cultural product, and so is refracted through cultural considerations. Rather, Coyne likely wants to emphasize the universal and objective nature of the scientific enterprise, at least in the ideal. As such, those who hold this rarified, idealistic, and practically not realized concept of science tend to imagine the scientific worker as a bare ratiocination machine. A contrasting view, more popular today, is to acknowledge that science is a human enterprise which has been subject to bias and distortion due to the particular socio-cultural perspectives brought to the enterprise by scientists.

A decade ago the latter view was not nearly as well articulated within science, among practicing scientists (though it was found outside of science). Therefore, Coyne could easily have expressed such dismissive attitudes and been indulged. But the times have changed. Viewpoint matters more now.

In The Twilight of Atheism McGrath argues that the idea of objective reality as highly attainable gave succor to triumphalist positivism. With its fading away the high tide of positivism will recede…and it does seem that that has occurred since he wrote his book. I am speaking particularly within science, with Jerry Coyne’s type of positivism being viewed suspiciously by many younger and mid-career researchers.

Thirteen years ago a sociologist of science, Steve Fuller, supported the Intelligent Design movement because he argued that scientists were biased by their subjective perspectives. At the time he was laughed out of court (literally). But it does have to be acknowledged that religious conservatives are an extremely underrepresented group within the natural sciences.

To this Jerry Coyne would simply appeal to his very strident transcultural and universalist views on science. Even if a disproportionate number of scientists are atheists and liberals, reality is what it is, and despite the bias objectivity wins out. But what does seem like the majority viewpoint (at least vocally) within science now is that representation of different experiences matters a great deal. This group would have to make a different argument as to why the enormous underrepresentation of religious conservatives within science does not matter in the least in relation to the questions being explored and the theories being proffered. As I do not hold this position (I lean more toward Coyne), I won’t attempt to outline what that argument would be.

Rather, I want to move back to the “twilight of atheism.” Secularization is real. But is it irreversible? Though it might seem glib to contend that the critical rationalism engendered by science erodes away at the authority of religion, the correlation does seem a real one. But if diversity of epistemology becomes the standard position, if sciences’ special and authoritative role within modern society is dethroned, I do wonder if a “reenchantment of the world” might become possible. If what is good and true is a function of feeling and power, of sentiment and moral suasion, then religion clearly is going to be in the game.

Few of the people who wish to pull science off its artificial pedestal would be sympathetic to the resurgence of religion, but that might be irrelevant….

Donald Knuth in the Galactic Library!

If you are a nerd you have been waiting for George R. R. Martin to complete his A Song of Ice and Fire series. But if you are a next level nerd, what you’ve been waiting for is for Donald Knuth to finish The Art of Computer Programming.

If you’ve never heard of Knuth, The New York Times has a nice profile up, The Yoda of Silicon Valley-Donald Knuth, master of algorithms, reflects on 50 years of his opus-in-progress, “The Art of Computer Programming”. When you first encounter Knuth and his life you get a sense of what it means to live and breath the life of the mind (Paul Erdos seems in the same category).

But this got me to thinking: if human civilization collapses would The Art of Computer Programming make it through to the successor societies? Enough people have memorized large sections of the Bible and the Koran, and various other religious and mythic works, that we’d be able to reconstruct them (and they would be passed down orally in rough form). It is unlikely that all the books would be destroyed. Similarly, great works of literature such as Shakespeare are widely read and internalized by the public.

This is not the case for a lot of detailed technical knowledge. From what I know the paper we use today is relatively perishable. If our civilization collapsed, it isn’t assured that low volume publications wouldn’t simply disappear as the books degrade beyond recognition without being copied (and without our modern technology digital storage will disappear).

Though I do think religious and literary works have value, to be frank it seems that any sufficiently advanced civilization has to converge upon similar narratives to encapsulate the sort of normative framework around which a society can function. For example, cannibalizing other human beings “because you can” always seems to be understood to be in the “bad” category. Some level of generosity toward the downtrodden is usually classed in the “good” category. I don’t think this is arbitrary, I think it’s an interaction between social complexity beyond the tribal scale, and our cognitive architecture which has first-order “natural tools” to deal with clan-based dynamics, but not supra-clan systems.

In contrast, a lot of technical knowledge, what we bracket into “natural science”, is quite counter-intuitive, and has appeared in one single civilization, that of early modern Europe. I’m particularly thinking of the fruitful synthesis of mathematical formalism and empirical testing which has characterized natural philosophy since Galileo. The historical record is clear that proto-scientific thinking in various forms emerges in many societies, with disparate threads in the same culture even (e.g., empiricism and mathematical formalism were present, but not fused, in the Classical world). But the combination in early modern Europe that kick-started modernity as we know it is rare, and takes a fortuitous combination of circumstances to allow for its flowering.

I hope that the Long Now Foundation has figured out a way to inscribe various technical texts on long-lasting tablets (perhaps stone?) and store them somewhere!

Open Thread, 12/17/2018

DNAGeeks is doing the last holiday push.

The new WordPress post editor kind of sucks. Installed a plugin to get rid of it. I guess it’s easier if you aren’t comfortable in HTML and want to do complex layouts, but I think the site is OK as is (though perhaps I need a better degradation to mobile?).

A lot of people have been telling me that The Three-Body Problem is good. Thoughts?

The latest Brown Pundits podcast, episode 5 on China. Soon Tanner Greer of Scholar’s Stage will be on!

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. The paper points to the fact that it seems that a Caucasus-related ancestry that has been seen in early Bronze Age Greece also seems to have impacted southern Italy and Sicily. There’s a paper that will come out soon with ancient samples from Sicily and Sardinia that confirms this. The same Caucasus-related ancestry is found in the steppe expansion, but that too came into Italy through the north.

Lund professor freed student from Islamic State war zone. One of the craziest stories I’ve read this year.

The untold story of how India’s sex workers prevented an Aids epidemic. About twenty years ago or so there were a lot of stories about how India was going to be the next major locus of HIV infection. That hasn’t occurred.

This week on The Insight Spencer & I talked about African genetics. Already a very popular episode.

Don’t blame Trump for the demise of The Weekly Standard. I’m still shocked that The American Conservative is still around, while The Weekly Standard is not. In general, I think reliance on a patron means you need to be careful about your heterodoxies. Life is about trade-offs. Scott McConnell has a reflection on the passing of The Weekly Standard, What The Weekly Standard Has Wrought:

If the Iraq war was sold to the American establishment by a small elite, the price was borne by many. Estimates of the fiscal costs run from $1 trillion to as much as $3 trillion, (if you credit Nobel prize recipient Joseph Stiglitz’s calculations, which include the long-term care costs for American soldiers with lifelong and life shattering injuries). The human costs to the soldiers and their families was substantial. Throughout the Mideast, the number of people killed, wounded, or turned into refugees by the invasion was staggering. The American “regional dominance” touted by the Standard proved entirely fanciful.

It is hard for younger people to remember what the years after 9/11 were like. The center-Left was broadly in support of the initial invasion of Iraq, though with some qualms, and ultimately turned against it. The Right was different. Aside from a few people at The American Conservative and stubborn individuals like Greg Cochran, by and large, there wasn’t any strong dissent from one of the most disastrous foreign policy decisions in American history. It is striking to me that so many of the people associated with The Weekly Standard are now given “strange new respect” by “resistance liberals” when they backed a war with such consequences (though to be fair, the center-Left which now pays homage to The Weekly Standard were usually in favor of the war before they were against it).

Another Clever Proxy for Quantitative History. If you don’t know who Peter Turchin is, familiarize yourself!

As 2018 turns to 2019 some of you may be wondering about books you should read. If you haven’t, Who We Are and How We Got Here is still very relevant.

Two books on history which will blow your mind, The Fall of Rome and The Fate of Rome. These are works that take material and environmental conditions seriously.

F. W. Mote’s Imperial China is highly recommended as well.

David Warsh’s Knowledge and the Wealth of Nations is well written. If you want to get a sense of ‘endogenous growth theory.’

Justin Fox’s Myth of the Rational Market is good too. There was a period in the second half of the 2000s when a lot of good popular books on economics and finance were coming out (for obvious reasons).

The Twilight of Atheism: The Rise and Fall of Disbelief in the Modern World. This book is less crazy reading today than it was years ago when I read it. Some of the predictions have been born out.

If you are looking for scientific biography with heft, I recommend Sewall Wright and Evolutionary Biology.

Wittgenstein’s Poker. An enjoyable read. If you don’t know much about Wittgenstein or Popper aside from sketches, it might be a good place to start (a bit too soft on Wittgenstein and hard on Popper from what I recall by the way, at least for my taste).

The Coming Anarchy. This book was wrong. But it can still illuminate in the wrongness.

If you haven’t gotten a copy of Principles of Population Genetics, not too late. Not a book you need to read front to back. Just read a chapter here and there.

With Christmas coming up, I don’t know how much time or inclination I’ll have to blog. So happy holidays to everyone if you don’t see me around much!

How the Catholic Church Created Our Liberal World. These arguments are not new. I first encountered them in Adam Bellow’s In Praise of Nepotism. I’m not totally convinced…I wonder if the rise of capitalism and modernity in Western Europe was over-determined. One thing to note is that the largest gradient of genetic variation in Europe is north-to-south. Northern Europe from Ireland to Russia is relatively uniform. But the socio-cultural gap between west and east is striking and derives in large part from the difference between a Latin Christian West, and an east which was not Latin and usually Orthodox Christian.

Running AdmixTools through R – admixr

One of the reasons that I don’t post AdmixTools results too much is that the framework requires more statistical “deep thought” than just popping out a PCA or even running some model-based clustering. Read the methods supplements of one of the Reich lab’s papers, and you’ll see what I’m getting at. But a more prosaic reason is that I generally work in the plink format, and format conversion, as well as editing parameter files, is a pain. In general, I don’t do much “exploratory AdmixTools” stuff for a reason.

Martin Petr has made the second excuse a lot less of an excuse. His admixr package gives one an easy interface into AdmixTools. In particular, it allows one not to have to edit parameter files so much. It took me about ~15 minutes to get it downloaded and running. I’m on a Mac and for R use RStudio.

– remember to install wget if you are on a Mac (this will show up if you want to use online datasets)

– You need to make sure to set the path to AdmixTools. In the RStudio console, I just entered:

Sys.setenv("PATH"="~/MyPath/To/AdmixTools/bin/")

If you can get AdmixTools installed in the first place, admixr should be very easy.

A pagan psychology does not a pagan society make

Ross Douthat has a column in The New York Times, The Return of Paganism: Maybe there actually is a genuinely post-Christian future for America. He concludes:

That embarrassment may not last forever; perhaps a prophet of a new harmonized paganism is waiting in the wings. Until then, those of us who still believe in a divine that made the universe rather than just pervading it — and who have a certain fear of what more immanent spirits have to offer us — should be able to recognize the outlines of a possible successor to our world-picture, while taking comfort that it is not yet fully formed.

Thirteen years ago I also stumbled in such an inchoate direction in a post, A Prayer For The Emperor. Douthat in fact linked to this post from his perch at The American Scene, though he may not recall it.

I think Douthat is making a distinction implicitly in The New York Times column between a pagan psychology, which bubbles up out of human innate cognitive architecture, and a pagan religious society, which takes the cognitive froth and reshapes it into collective ritual and belief.

Human intuitions regarding the supernatural seem to be fundamentally animistic. We imbue places and animals with spirit. In general, I agree with the scholars who argue that this is an outcome of “overactive agency detection.” A world filled with the illusion of life and danger may induce more stress and anxiety, but in the Darwinian context, excessive vigilance is a virtue, not a vice.

“Religion nerds” like Douthat and Rod Dreher actually have a fair amount in common in their assumptions and cognitive style with hyper-rational atheists such as Armin Navabi (Navabi comes out of a “religion nerd” background). As Roman Catholic Christians Douthat and Dreher must give a nod to the mystical, and Dreher, in particular, has asserted the importance of the sensory in reawakening his religious faith. But both scaffold, channel and discipline their supernatural intuitions into very precise streams. Similarly, Navabi’s understanding of religion is as a system.

One of the elements of the religious systems developed over the past 3,000 years in complex societies characterized by specialization, and the emergence of a literate ruling class (or at least a ruling class which makes recourse to a literate caste), is that animistic and spirit-soaked component of religion has receded. Some intellectual historians have argued that the atheism of early modern Europe can be understood as the logical conclusion of a rationalist streak within Reformed Protestantism, which reduced the supernatural singularly to God and his host. Whereas other forms of Christianity perceived the world as filled with false gods who were faces of genuine demons, the rationalist form of Reformed Protestantism dismissed false gods as human inventions. This diminution of the supernatural then might lead one to the next logical step, banishing even God from the universe!

I do not think this was a special event in world history. We are all aware that the same tendency was pregnant within Hinduism, Buddhism, and in Chinese societies, with certain sects and factions pushing toward atheism and materialism. In the world of early Islam skeptics also existed, often drawing from the older traditions of the Classical World. Strangely, it is in the European Christian world that the supernatural-skeptical tradition was mostly absent. One might suppose this might have something to do with near monopoly of the religious class on intellectual activity in Western Europe for many centuries. Those who were personally skeptical likely kept that to themselves due to their vocation.

But these currents have always floated above the populace, whose practice and beliefs were much more demotic. The existence of religious reform and revival, and zealous cults, within most societies is due in large part to the deviationism that characterizes the religious sentiments of the populace at large. Though the mythos, ritual, and panoply of the great religions attract the people to them, the reality is that all these could exist without the formal and rationalist element which is necessitated by the systematizing tendencies of the intelligentsia.

What we see in the decline of the customary Christian sects and denominations in American society is in some ways a loss of the power of cultural elites. Arguably this period of the dominance of several forms of Christianity was itself a temporary period, with the early republic characterized by a large proportion of unchurched and free-thinkers, as well as a plethora of radical sects. The decades after World War II were an exception, which we took to be the new normal.

The broader decline in trust in institutions, the popularization of culture, and the disdain toward elites, has manifested now a turning away from organized religion. But the populace still wants to believe, and in their hearts they have deep and strong intuitions about the universe. Whether the universe has purpose, it feels like it has purpose. Individuals and subcultures develop ad hoc beliefs and practices to channel these feelings and sentiments, but there is no broad social system or identity to bind them together into a formal whole.

A “harmonized paganism”, as Douthat may say, may not manifest because a it needs a harmonious society, and that is not something we have. State paganism needs a powerful state with a self-confident elite culture. State paganism needs an Emperor, to be the axis mundi between Heaven and Earth. Elite Western Christianity is collapsing, but it being replaced popular paganism, and that is because elite high culture no longer has the prestige it once did, and all is demotic. The ancient world was not a mass society, it was a culture defined by rules, and bound by ritual. The consumer society is driven bottom-up decision making, the impulse of the mob.

What we are seeing is the reemergence of hunter-gatherer animism writ large.

Open Thread, 12/10/2018

Merry Christmas & Happy Holidays!

Just a heads up that DNA Geeks is running a holiday sale on the microscopes with free shipping (until stocks are sold out).

Also, updating a plugin broke the site, so I had to deactivate and reactive all the plugins. For whatever reason, the ‘related posts’ plugin also no longer works. Does anyone click those links? Might have to find a replacement.

Models of archaic admixture and recent history from two-locus statistics.

Incidence of Dementia over Three Decades in the Framingham Heart Study. Decreased incidence.

China Launches First-Ever Mission to the Moon’s Farside.

Fourth Brown Pundits podcast, “the Golden Age of Islam”. Here are the iTunes and Stitcher links. Would appreciate subscriptions+reviews.

America’s New Religions. I dislike overuse of the term “religion.” And I’m generally skeptical of the idea of “political religion” as a useful term, as opposed just mass movement. But I think I”m coming around.

When it comes to religion, I take for granted that you’ve read a book like In Gods We Trust. That being said, I do wonder about the psychological research used to support some of the conclusions in the field of the cognitive anthropology of religion in the wake of the “replication crisis.” Some of the stuff, like depictions of eyes making you more ethical don’t seem to be robust findings.

On The Insight this week we talked Game of Thrones. Yes, I do think meiotic drive is the best rational explanation for the persistence of Valyrian characteristics.

More data from the Estonian Biocentre. Also, the title of a paper, “Multiple deeply divergent Denisovan ancestries in Papuans” which is clearly in review.

The presence and impact of reference bias on population genomic studies of prehistoric human populations.

Genetically Modified People Are Walking Among Us.

Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila.

Criticizing Islam is turned into “hate speech” on Facebook. The problem is that the “big platforms” like Twitter and Facebook are so big and diverse that it’s not that hard to “game them” and engage in speech policing. Facebook is really about family photos now. And Twitter is best done non-ironically if you have more than a trivial following.

George R.R. Martin takes time off from not writing his book to laud New York pizza.

Why We Miss the WASPs. The reactions seem to be driven by people who were not clear what the narrow connotations of “WASP” originally was.

Anti-Zionism Isn’t the Same as Anti-Semitism. I pretty much agree, though operationally the lines between ‘anti-Zionism’ and ‘anti-Semitism’ bleed over pretty easily.

Models uncovering African population genetic history


In a deep sense, we know a lot more about the population genetic history of England at the fine-grain than we do about the whole continent of Africa. That’s going to change in the near future, as researchers now realize that the history and emergence of modern humans within the continent was a more complex, and perhaps more multi-regional, affair than had been understood.

Because of the relative dearth of ancient DNA, there has been a lot of deeply analytic work that draws from some pretty abstruse mathematical tools operating on extant empirical data. A series of preprints have come out which use different methods, and arrive at different particular details of results, but ultimately seem to be illuminating a reoccurring set of patterns. Dimly perceived, but sensed nonetheless.

Here’s the latest offering, Models of archaic admixture and recent history from two-locus statistics. I can’t pretend to have read the whole preprint (lots of math), but these empirical results jumped out at me:

We inferred an archaic population to have contributed measurably to Eurasian populations. This branch (putatively Eurasian Neanderthal) split from the branch leading to modern humans between ∼ 470 − 650 thousand years ago, and ∼ 1% of lineages in modern CEU and CHB populations were contributed by this archaic population after the out-of-Africa split. This range of divergence dates compares to previous estimates of the time of divergence between Neanderthals and human populations, estimated at ∼650 kya (Pr¨ufer et al., 2014). The “archaic African” branch split from the modern human branch roughly 460 − 540 kya and contributed ∼ 7.5% to modern YRI in the model (Table A2).

We chose a separate population trio to validate our inference and compare levels of archaic admixture with different representative populations. This second trio consisted of the Luhya in Webuye, Kenya (LWK), Kinh in Ho Chi Minh City, Vietnam (KHV), and British in England and Scotland (GBR). We inferred the KHV and GBR populations to have experienced comparable levels of migration from the putatively Neanderthal branch. However, the LWK population exhibited lower levels of archaic admixture (∼ 6%) in comparison to YRI, suggesting population differences in archaic introgression events within the African continent (Table A3).

To be frank I’m not sure as to the utility of the term “archaic” anymore. I sometimes wish that we’d rename “modern human” to “modal human.” That is, the dominant lineage that was around ~200,000 years ago in relation to modern population ancestry.

Skull from Iwo Eleru, Nigeria. Photo credit: Katerina Harvati and colleagues CC-BY

But, these results are aligned with other work from different research groups which indicate that something basal to all other modern humans, but within a clade of modern humans in relation to Neanderthal-Denisovans, admixed with a modern human lineage expanding out of eastern Africa. The LWK sample is Bantu, and has a minority Nilotic component that has West Eurasian ancestry. This probably accounts for the dilution of the basal lineage from 7.5% to 6%.

I wouldn’t be surprised if the final proportions differ. And other research groups have found deep lineages with African hunter-gatherers. My own view is that it does seem likely that one of the African human populations that flourished ~200, 000 years ago expanded and assimilated many of the other lineages. The “Out of Africa” stream is one branch of this ancient population. But it seems possible that the expansion was incomplete, and that other human lineages persisted elsewhere until a relatively late date.

A genetic history of the human race is not controversial science nor is it fraught

Recently I was talking to a journalist about genetic genealogy, and we both agreed that soon Christine Kenneally’s The Invisible History of the Human Race: How DNA and History Shape Our Identities and Our Futures will need an update. Though published in 2015, much of the research in The Invisible History of the Human Race dates to much earlier.  In the last few years, personal genomics has gone from a sector of millions to tens of millions. In years after 2020 it will go to hundreds of millions.

And yet I’m not sure the educated public is ready to understand what a genomic future is going to look like.

This is why I think that the Elizabeth Warren DNA story is important to get right. The reality is that this isn’t really about Elizabeth Warren’s ancestry, it’s a story at the intersection of high politics and culture wars, and genetics is getting caught in the undertow. Recently I heard Ben Shapiro comment that Warren likely had “maybe 1/1024th Native American.” Actually, I think it’s very likely she has 0.5 to 1% Native American ancestry (read this Elizabeth Warren DNA post for why I say that) Not to be trite, but facts don’t care about Ben Shapiro’s feelings. I know he’s not a fan of Warren, but he shouldn’t be laundering misrepresentations.

Even in the comments of this website motivated reasoning cropped up when the original Warren story became a national sensation. Many on the Right side of the spectrum laughed at the results and interpreted them in the least generous terms. The falsehoods and misunderstandings promoted by the media, often inadvertently because most journalists don’t have the skills to navigate the science, were injected into the conservative memesphere.  Shapiro has admitted, to his own chagrin, his lack of science background, and I suspect if I explained it to him he wouldn’t use “maybe 1/1024th Native American” line. He doesn’t need to. If you are a conservative there are many reasons to be critical of Elizabeth Warren.

But I can’t blame Shapiro too much. He was reacting to this story in The New York Times, Elizabeth Warren Stands by DNA Test. But Around Her, Worries Abound. In this piece, the attacks on Warren are coming from the Left and Native American activists. There is a real story here. The Boston Globe has published an editorial warning her not to run. The air has changed around her.

From the piece in The Times:

Warren’s presidential ambitions, she has yet to allay criticism from grass-roots progressive groups, liberal political operatives and other potential 2020 allies who complain that she put too much emphasis on the controversial field of racial science — and, in doing so, played into Mr. Trump’s hands.

Ms. Warren’s allies also say she unintentionally made a bigger mistake in treading too far into the fraught area of racial science — a field that has, at times, been used to justify the subjugation of racial minorities and Native Americans.

There is “racial science” like there is “evolution science” or “Creation science.” The term is not used by any scientist that I know of, but comes up by critics and polemicists. The New York Times, whether consciously or not, is going to convince a lot of scientifically illiterate people who don’t read their science pages that there is a field of “racial science” (using the term “race science” liberally is a thing on the Left…reminds me of social conservatives who used to call everyone who was not an evangelical Protestant a “non-Christian”)

Here’s what went on in the Warren case is:

  1. Not scientifically controversial
  2. But scientifically new

Here is a review, A comprehensive survey of models for dissecting local ancestry deconvolution in human genome which looks at “20 methods or tools to deconvolve local ancestry.” There may be disagreement on the best method for various reasons, but there is no disagreement that local ancestry deconvolution is possible. It is not controversial. In fact, it is rather important in areas such as admixture mapping for diseases.

The science isn’t that hard to explain at a high level. The figure to the left is from a new paper that recently came on the genetics of the New World (using ancient DNA). What you see is that some human populations are isolated from other human populations. For example, the last common substantial ancestry of Native American populations before 1492 and Northern Europeans dates to the period between 20,000 to 40,000 years ago.

Tens of thousands of years of genetic separation result in genetic distinctiveness. This is a standard old population genetic model. When populations come back together and mix, that daughter population is clearly going to be genetically a mix between the two parent populations. But the human genome is a sequence of three billion distinct base pairs, and the mixing exhibits discrete patterns within the genome.

Humans are diploid, which means we have two copies of each gene. These genes are aligned along homologous chromosomes. One homolog you inherit from the father and one homolog you inherit from the mother. These two homologs are the basis for Mendel’s Law of Segregation.

When sex cells, sperm and eggs, are formed they carry only one of the homologs. They are haploid, with single gene copies. If they weren’t, you’d end up tetraploid instead of diploid. You get one gene copy from the mother and one gene copy from the father.

But, before the formation of sex cells, during meoisis, the homologs undergo recombination. In humans that means that there is swapping between stretches of homologous chromosomes. The average human has between 20 and 40 recombination events across the genome. A concrete way to think about it is that the individual who is producing sperm or egg is taking the chromosomes they inherited from their parents, and mixing them together, so the final set of chromosomes are a synthetic combination of the chromosomes of grandparents.

Purple segments half-identical to paternal grandfather

To make this concrete, to the left is a partial depiction of one of my children’s chromosomes, and the relatedness to my father. The purple regions are genomic stretches where the child is half-identical to the paternal grandfather. The light gray sections have no genetic descent from my father. The reason is that one of the homologs is from the maternal side. The other homolog is from me, and could be from either my father or my mother. Where the purple alternates with light gray, you see clearly where recombination events happened, as maternal and paternal homologs broke and paired together to produce sperm with novel chromosomes (e.g., my contributed chromosome 11 is 90% my father, 10% my mother…while chromosome 19 is more balanced.

But that’s not the only way to look at recombinations. To the right is an ancestry painting for 23andMe from a friend of mine who is ~25% East Asian and ~75% Northern European. On their chromosome you see two homologs. The blue segments are Northern European. The dark brown segments are East Asian. Notice the alternation between European and East Asian on one of the homologs: this chromosome is almost certainly from the parent who is 50% East Asian and 50% European. There was a recombination event where an “East Asian” homolog, inherited from the parent of East Asian origin, recombined with the “European” homolog, inherited from the parent of European origin.

The resultant chromosome is something new in a physical sequence, with alternating segments of East Asian and European ancestry. Just as the whole genome has an imprint of the genetic history of a population, so sequences of the genome also exhibit distinctiveness due to their origins. Because each generation introduces recombination events, the lengths of these distinct ancestry blocks can tell you how many generations in the past the admixture may have happened.

That’s the theory. The new aspect is that genomic technology has allowed science to assess patterns of local ancestry to a much greater extent than was possible even 15 years ago. With hundreds of thousands of genomic positions, variants, scientists are now able to map regions of the genome to an incredible level of granularity, deploying theoretical understanding of Mendelian and population genetics that dates back to the 20th century.

To look at Elizabeth Warren’s genome, and discover that a small segment of a particular length derives from a Native American population, is not a “controversial field of racial science.” This sort of analysis is now becoming de rigueur in much of medical genetics in larger part because population history has a major impact on disease risk susceptibility. To be fair, doing a local ancestry deconvolution on populations which are much, much, closer genetically due to recent shared history is difficult. But Warren’s is not one of those cases!

Honestly, I don’t know what the outcome of The New York Times calling this “racial science” is going to be, seeing as how it seems likely in the next few years >100 million Americans will have likely done ancestry tests. Many scientists, fairly, do criticize of the interpretations of these tests, and how the public perceives them. But the underlying models and methods are workaday.

It is the interpretation, and how they interact with social and political values, is fraught. The link in the phrase “controversial field of racial scienceactually goes to an article where social and political commentators and activists react to Warren’s decision to take the DNA test. There is no discussion of the science at all. It’s controversial because of what they believe the implications are, not because the science is faulty or unsound.

For example, many (though not all) Native Americans object to the idea of using genetic science to shed light on the status of particular individuals as Native American or not. The decision to take this DNA test, in an environment where many already privately grumbled about Warren’s claims, was obviously clearly a political and public relations misstep. But that does not speak to whether the science itself is sound or unsound.

Conservatives will be highly skeptical of Warren because of her policy positions. And, if the above article is correct, it seems that some of the Left is now against her on the grounds of her impolitic foray into Native American identity. That is all fine, and not much of a concern of mine. But when non-science journalists get their hands on a science story, they tend to mess it up, and that is a problem in the long-term. The sands of politics and society are protean, and always shifting. Science is something more solid, and we should not try to muddy the waters.