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

July 31, 2017

Open Thread, 07/31/2017

Filed under: Open Thread — Razib Khan @ 1:25 am

Read a bit of The Unholy Consult. People who say George R R Martin’s work is too dark? They need to really read a bit of R. Scott Bakker, and Martin will seem to like someone who sees the world through rose-colored glasses.

I’m thinking of reading The Witchwood Crown later because I might need a pick-me-up after The Unholy Consult. I’ve also had The Wise Man’s Fear in my Kindle stack for over five years now, but I plan on reading it when Patrick Rothfuss finishes the series with book 3.

Speaking of fantasy, there is a lot of commentary on Game of Thrones. Always. Some of it is quite dumb. For instance, Game of Thrones and race: who are the non-white characters and where are they from in the books and show? To make a sound argument you actually need to know something about the books. The writer does not. For example, “The Targaryen monarchs, who ruled Westeros for hundreds of years but, thanks to their thing for incest, never really bred all that much with the locals.” This is false. Daenerys is only 1/8th Valyrian (at most). Half her recent ancestry is from a First Men house, the Blackwoods (though it surely has much Andal blood too). About 3/8th of her recent ancestry is Dornish, so a mix of Andal, First Men, and Rhoynish.

Second, George R. R. Martin published the first book in the series in 1996. It was on his mind for years before that. Obviously if he was writing these books today he’d tune them so they were more in sync with the cultural politics of the contemporary Left (since that is where his own personal sympathies lie). But it isn’t as if he can go back and rewrite the major characters and add some diversity which some of his fans might now want. The 1990s were a different time. I recall back on some message boards that Renly’s sexual orientation was an issue for some readers. Martin was arguably ahead of the times on that score.

There are fantasy works where the central characters are nonwhite. Both Judith Tarr in Avaryan series and Ursula K. Le Guin’s Earthsea series have been around for a while. And both these worlds have the added benefit of not being standard Tolkienesque medieval settings.

Inside Facebook’s Rapid Growth in Austin. Their presence is felt.

Kimura & Crow: Infinite alleles. Really great piece on the working relationship between Motoo Kimura and James F. Crow. About 11 years I emailed Crow 10 questions on a lark. He responded in less than a day. Also, Kimura and Crow’s An Introduction to Population Genetics Theory is worth getting (it’s cheap).

Divorce and Occupation. No surprise that there’s a correlation between income and divorce rate (negative). But some professions are outliers. Bartender and nurse anesthetists are above the trend line (more divorce than their income predicts). Clerics and actuaries are well below it.

Postdoctoral positions in human population genomics, nutrigenomics, & association studies at Cornell in Alon Keinan’s lab.

How evolution draws trade-offs.

The TakingHayekSeriously Twitter account has been passing along pieces and posts around the controversy surrounding Nancy Maclean’s Democracy in Chains: The Deep History of the Radical Right’s Stealth Plan for America. The book is ridiculous. So ridiculous that Vox published a piece Even the intellectual left is drawn to conspiracy theories about the right. Resist them.

I’ve been very loosely associated with libertarians because of my political sympathies for a long time. Years ago I actually visited The Center for Study of Public Choice where James Buchanan had his office because my friend Garett Jones had his office there. There’s no conspiracy here, or secret cabals under the radar. Libertarians are by and large a nerdy group of radicals fixated on stuff like the nonaggression principle. Just like you see on the internet. Kooky. Yes. But a cabal? Have you met libertarians? They don’t have the aptitude for that sort of coordination (Radicals for Capitalism is really the book to understand libertarianism, in particular because Buchanan and public choice theory have a minor role at best to play in libertarianism).

But that doesn’t matter. Democracy in Chains will validate the suspicions and beliefs of many people. And it’s a footnoted academic work. Unless it’s obvious fraud it’s going to be a success in influencing people.

Remember that Arming America won the Bancroft Prize for outstanding work of American history in 2000. Arming America was likely a work of fraud in large part. But its thesis, that America’s gun culture did not date to the colonial era, was congenial to the political ideology of many historians. Therefore even though it did not pass the smell test they gave the book rave reviews. I’d be surprised if  Democracy in Chains is a work of fraud. The author just doesn’t know what she’s talking about, but she is telling a story her audience wants to hear, with some academic credibility to boot (and so far historians have supposedly supported her).

The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods. I think these dynamics are going to be relatively common.

I must say, I don’t recommend All Things Made New: The Reformation and Its Legacy. The title suggests a broader work than it is. Far too much space is given to the English Reformation. Just thought I’d mention that.

Reading some of Big Gods: How Religion Transformed Cooperation and Conflict. Broadly agree with the thesis I think…but wondering about the replication of some of the experiments cited.

Also in my stack, The Red Flag: A History of Communism.

Andrew Sullivan notices in this week’s column that Islam seems to now be untouchable on the Left. This is going to too far, but liberals who express anti-Islamic sentiments are getting rather rare, and though privately many on the Left have serious issues with Islam (I know, because they tell me privately) they’re careful not to say it out loud lest they be attacked as racist. My own view is that there are 1.6 billion Muslims, so it makes sense for the Left to align with them. Isn’t world domination worth a hijab?

Don’t blame the Empire. Alex Tabarrok takes some deserved shots at Shashi Tharoor’s An Era of Darkness: The British Empire in India. The anti-colonialism tick often gets out of control among Indians, to the point where all evils are heaped upon the British. This is a major aspect of post-colonialism, which “erases” all identity-forming events before the arrival of Europeans.

Twitter lost 2 million users in the U.S. last quarter. Shit’s getting real Jack. If you use RSS, subscribe to my feed! I also have a mailing list, where I’ve sent out exactly one email so far. But if Twitter goes down….

Can 23andMe Tell Us If Jews Are A Race — And Is That A Good Thing? The author interviews scientists who know the science, but he still manages to garble and confuse everything. First, Ashkenazi Jews descend from a endogamous community which flourished in Central Europe probably no earlier than ~1000 AD. That is why a Ashkenazi Jewish cluster emerges naturally out of the population genetic data; there’s a real coherent demographic history being reflected. Whether that’s a “race” or not I’ll leave to the reader.

Second the story states that “Sephardic Jews are not considered a distinct population by either company, or by researchers — their genetic make-up is not sufficiently different from surrounding North African, Iberian and Greek populations.” This very misleading. To a great extent Sephardic Jews are rather distinct from the surrounding populations. There is some evidence of shared ancestry in Moroccan Jews with Moroccan Berbers (I know because I’ve looked at a lot of this data), but it’s a small proportion. Similar things can be said about most Sephardic communities. But, they are not nearly as coherent a genetic cluster as Ashkenazi Jews. There has been some gene flow and assimilation with many local Jewish populations (e.g., the Syrian Sephardic Jews absorbed a local Levantine Jewish community, which had its own liturgy until the 19th century).

Neanderthal-Derived Genetic Variation Shapes Modern Human Cranium and Brain. Many people skeptical of the robustness of this result.

July 30, 2017

The culture of reasoning: the Ummah shall not agree upon error

Because I watch Screen Junkies‘ “Honest Trailers” I get recommendations like the above from Looper, The Real Reason Why Valerian Flopped At The Box Office. Of course no one knows the ‘real reason’ Valerian flopped, aside from “it didn’t seem like a good movie.” The reality is that Valerian and the City of a Thousand Planets based on a French comic book and cast a 31 year old actor who looks like a haunted 15 year old. That’s all there is to say definitively. All the various failure points are overdetermined. But the video above gives you a lot of “reasons” if you want them in a list format in a British accent. All in the service of infotainment.

Hugo Mercier and Dan Sperber’s The Enigma of Reason offers up an explanation for you have things like “top 10 reasons” for pop culture artifacts of an ephemeral nature (for a preview, The Function of Reason at Edge).

I’ve mentioned this book a few times. I finished while in the Persian Gulf (I’ll blog that at some point soon), and have been ruminating on its implications, and whether to mention it further. The issue I’m having is that I am very familiar with Sperber’s work, and those who he has influenced, and research domains complementary to his. Even if I didn’t know all the details of the argument in The Enigma of Reason, in the broad sketches I knew where they were going, and frankly I could anticipate it. I suppose somewhat ironically I managed to infer and reason ahead of the narrative since I had so many axioms from earlier publications.

The Enigma of Reason comes out of a particular tradition in cognitive anthropology. What Dan Sperber terms the “naturalistic paradigm” in anthropology. This is in contrast to the more interpretative framework that you are probably familiar with in the United States. No one would deny that the naturalistic paradigm has scientific aspirations. That is, it draws from natural science (in particular cognitive anthropology as well as the field of cultural evolution), and conceives of itself as the study of natural phenomenon.

Scott Atran’s In Gods We Trust: The Evolutionary Landscape of Religion comes out of this tradition, and some of the experimental literature in The Enigma of Reason seem very familiar from the earlier book (as well as Pascal Boyer’s Religion Explained). This is due to the fact that Atran goes to great lengths to show the ultimate nature of religion does not have to do with rational inferences as we understand them. That is, theological is a superstructure overlain atop a complex phenomenon which is not about philosophical reflection at all.

Of course the flip side can be true as well. When I was a teenager and younger adult I explored the literature on the existence of God a bit, from old classics like Thomas Aquinas’ arguments in Summa Theologica, to more recent and contrasting proofs of Norman Malcolm and Richard Swinburne (Michael Martin’s Atheism: A Philosophical Justification was actually a good sourcebook for high level arguments to theism).

When I read In Gods We Trust I realized that my earlier explorations were primarily intellectual justifications, and had little relationship why most people around me believed in God. And yet how did I become an atheist? For me this is a flashbulb memory. I was eight years old, in the public library. I was thumbing through the science books in the children’s section (particular, books on biology and medicine). The third row from the front of the stacks. And all of a sudden I had the insight that there wasn’t a necessary reason for the existence of God.

It all happened over the course of a minute or so. Mind you, I was never really religious in any deep sense. Something I’ve confirmed when talking to religious friends about their beliefs and how it impacts them. Though I nominally adhered to my parents’ religion when I was a small child, I was fascinated much more by science, and that really engaged most of my thoughts and guided my actions (contrastingly, going to the mosque was one of the most horribly boring things I recall doing as a small child).

My point here is that many of our beliefs are arrived at in an intuitive manner, and we find reasons to justify those beliefs. One of the core insights you’ll get from The Enigma of Reason is that rationalization isn’t that big of a misfire or abuse of our capacities. It’s probably just a natural outcome for what and how we use reason in our natural ecology.

Mercier and Sperber contrast their “interactionist” model of what reason is for with an “intellectualist: model. The intellecutalist model is rather straightforward. It is one where individual reasoning capacities exist so that one may make correct inferences about the world around us, often using methods that mimic those in abstract elucidated systems such as formal logic or Bayesian reasoning. When reasoning doesn’t work right, it’s because people aren’t using it for it’s right reasons. It can be entirely solitary because the tools don’t rely on social input or opinion.

The interactionist model holds that reasoning exists because it is a method of persuasion within social contexts. It is important here to note that the authors do not believe that reasoning is simply a tool for winning debates. That is, increasing your status in a social game. Rather, their overall thesis seems to be in alignment with the idea that cognition of reasoning properly understood is a social process. In this vein they offer evidence of how juries may be superior to judges, and the general examples you find in the “wisdom of the crowds” literature. Overall the authors make a strong case for the importance of diversity of good-faith viewpoints, because they believe that the truth on the whole tends to win out in dialogic formats (that is, if there is a truth; they are rather unclear and muddy about normative disagreements and how those can be resolved).

The major issues tend to crop up when reasoning is used outside of its proper context. One of the literature examples, which you are surely familiar with, in The Enigma of Reason is a psychological experiment where there are two conditions, and the researchers vary the conditions and note wide differences in behavior. In particular, the experiment where psychologists put subjects into a room where someone out of view is screaming for help. When they are alone, they quite often go to see what is wrong immediately. In contrast, when there is a confederate of the psychologists in the room who ignores the screaming, people also tend to ignore the screaming.

The researchers know the cause of the change in behavior. It’s the introduction of the confederate and that person’s behavior. But the subjects when interviewed give a wide range of plausible and possible answers. In other words, they are rationalizing their behavior when called to justify it in some way. This is entirely unexpected, we all know that people are very good at coming up with answers to explain their behavior (often in the best light possible). But that doesn’t mean they truly understanding their internal reasons, which seem to be more about intuition.

But much of The Enigma of Reason also recounts how bad people are at coming up with coherent and well thought out rationalizations. That is, their “reasons” tend to be ad hoc and weak. We’re not very good at formal logic or even simple syllogistic reasoning. The explanation for this seems to be two-fold.

First, reason is itself an intuitive process.

For the past few weeks we’ve had an intern at the office. I’ve given them a project using Python…a language they barely know. One of the things that is immediately obvious when going through pitfalls is that a lot of the debugging process relies on intuition one accrues over time, through trial and error. When someone is learning a programming language they don’t have this intuition, so bugs can be extremely difficult to overcome since they don’t have a good sense of the likely distribution of probabilities of the errors they’d introduce into the system (or, to be concrete, a novice programmer might not even recognize that there’s an unclosed loop, when that is one of the most obvious errors to anyone).

Second, reason is an iterative process which operates optimally in a social context. While  The Enigma of Reason reviews all the data which suggests that humans are poor at formal logic and lazy in relation to production of reasons, the authors also assert that we are skeptical of alternative models. This rings true. I recall an evangelical Protestant friend who once told me how ridiculous the idea of Hindu divine incarnations were. He was less than pleased with I simply switched his logic to a Christian context. But Mercier and Sperber suggest that these two features of loose positive production of reasons and tighter negative skepticism of those reasons come together in a social context to converge upon important truths which might increase our reproductive fitness.

The framework above is fundamentally predicated on methodological individualism, focusing in natural selection at that level. The encephalization of humans over the past two million years was driven by increased social complexity, and this social complexity was enabled by the powerful ability to reason and relate by individual humans. In some ways  The Enigma of Reason co-opts some of the same arguments presented by Robin Dunbar over ten years ago in Grooming, Gossip, and the Evolution of Language, except putting the emphasis on persuasion and reasoning.

At this point we need to address the elephant in the room: some humans seem extremely good at reasoning in a classical sense. I’m talking about individuals such as Blaise Pascal, Carl Friedrich Gauss, and John von Neumann. Early on in The Enigma of Reason the authors point out the power of reason by alluding to Eratosthenes’s calculation of the circumference of the earth, which was only off by one percent. Myself, I would have mentioned Archimedes, who I suspect was a genius on the same level as the ones mentioned above.

Mercier and Sperber state near the end of the book that math in particular is special and a powerful way to reason. We all know this. In math the axioms are clear, and agreed upon. And one can inspect the chain of propositions in a very transparent manner. Mathematics has guard-rails for any human who attempts to engage in reasoning. By reducing the ability of humans to enter into unforced errors math is the ideal avenue for solitary individual reasoning. But it is exceptional.

Second, though it is not discussed in The Enigma of Reason there does seem to be variation in general and domain specific intelligence within the human population. People who flourish in mathematics usually have high general intelligences, but they also often exhibit a tendency to be able to engage in high levels of visual-spatial conceptualization.

One the whole the more intelligent you are the better you are able to reason. But that does not mean that those with high intelligence are immune from the traps of motivated reasoning or faulty logic. Mercier and Sperber give many examples. There are two. Linus Pauling was indisputably brilliant, but by the end of his life he was consistently pushing Vitamin C quackery (in part through a very selective interpretation of the scientific literature).* They also point out that much of Isaac Newton’s prodigious intellectual output turns out to have been focused on alchemy and esoteric exegesis which is totally impenetrable. Newton undoubtedly had a first class mind, but if the domain it was applied to was garbage, then the output was also garbage.

A final issue, which is implicit in the emergence of genius is that it exists in can only manifest in a particular social context. Complex societies with some economic surplus and specialization are necessary for cognitive or creative genius to truly shine. In a hunter-gatherer egalitarian society having general skills to subsist on the Malthusian margin is more critical than being an exceptional mind.**

Overall, the take-homes are:

  • Reasoning exists to persuade in a group context through dialogue, not individual ratiocination.
  • Reasoning can give rise to storytelling when prompted, even if the reasons have no relationship to the underlying causality.
  • Motivated reasoning emerges because we are not skeptical of the reasons we proffer, but highly skeptical of reasons which refute our own.
  • The “wisdom of the crowds” is not just a curious phenomenon, but one of the primary reasons that humans have become more socially complex and our brains have larger.

Ultimately, if you want to argue someone out of their beliefs…well, good luck with that. But you should read The Enigma of Reason to understand the best strategies (many of them are common sense, and I’ve come to them independently simply through 15 years of having to engage with people of diverse viewpoints).

* R. A. Fisher, who was one of the pioneers of both evolutionary genetics and statistics, famously did not believe there was a connection between smoking and cancer. He himself smoked a pipe regularly.

** From what we know about Blaise Pascal and Isaac Newton, their personalities were such that they’d probably be killed or expelled from a hunter-gatherer band.

July 29, 2017

The passing onto to better things…faster and faster

Filed under: iPhone,Technology — Razib Khan @ 2:15 am

As many of you know, Apple is doing away with the iPod Shuffle. One curious thing is that I’ve noticed several people buying these devices in the last week through my Amazon referrals. At $50 the price point isn’t high, but it does seem a bit much for an obsolete technology.

Which made me reflect on how quickly technologies become obsolete now. As the few people who read this blog and know me in real life are aware, between 2007 and 2014 I went everywhere with a Shuffle. I always had a backup Shuffle. This is not because I’m an audiophile. I’m not. I listened to podcasts.

Arguably the emergence of smartphones made the Shuffle redundant, but I found that the Shuffle was more portable than a smartphone. Ultimately what made me dump the Shuffle is that I went full d-bag and started doing the bluetooth thing. All of a sudden it didn’t matter where the phone was. I still have a Shuffle, but it’s in a drawer somewhere. Perhaps I have a backup too. I don’t recall.

I probably stuck with the Shuffle longer than most. As an old(er) person I’m reflecting now how fast “ubiquitous” technologies are getting obsolete. Faster and faster.

As a child of the 1980s VCRs were part and parcel of our technological furniture. By the early 2000s VCRs were in decline, with DVD rentals surpassing VHS in 2003. Cassettes were eclipsed by CDs in the early 1990s after a two decade reign, but CDs really didn’t master the space for more than ten years (at least in the USA). DVDs had a similarly short “moment.”

How much more can change though? Some of the transition occurred because smartphones, in particular the iPhone, swallowed up whole sectors (audio and photography). Other changes are due to the utilization of high speed internet for video. We got rid of our television in 2004, and for a while there I felt “out of the loop” on a lot of water cooler conversation. But now television has come to me, as binge watching on Netflix has become common.

What will change next?

Generation X

Filed under: Beastie Boys — Razib Khan @ 1:03 am

July 28, 2017

The Indo-Aryan question nearing resolution

Filed under: Genetics,science — Razib Khan @ 5:50 pm

India Today published my review of the current state of the genetics and genomics of the Indian subcontinent, and what it can tell us about the ethnogenesis of South Asians generally. In the piece I tried to be very circumspect and stick to what we know with a high, if not perfect, degree of certainty. Here I will add some comments where I reduce the threshold of certainty somewhat. That, I’m going to include here my beliefs where I think I’m right, but in some details wouldn’t be surprised if I was wrong.

First, the title is Aryan wars: Controversy over new study claiming they came from the west 4,000 years ago. Writers don’t get to choose titles, and this is not one I would have chosen. But I am not in a position to care or know what draws clicks. Let’s note that this “controversy” is restricted mostly to India. Outside of India it’s not controversial, but a matter of the science, because people don’t have any political or social investment in the topic. It reminds me of debates about genetics and intelligence in the West, where emotions get overwrought and lies fly wildly with abandon.*

Second, there is a reference in the figures to an “Out of India” (OIT)  model. That is, the Aryans migrated out of India, and implicitly the Indo-European languages derive from South Asia. I don’t think this theory has any support at all. That is, I think it is rather clear that proto-Indo-European probably emerged neither in Europe proper, nor in South Asia, but in the Inner Eurasian spaces between. But for an Indian audience ignoring OIT would seem a peculiar lacunae, so there was a reference added to the figure on that account (I pushed back against this, but do not make ultimate decisions on figures).

But I do think it was plausible up until 2009’s Reconstructing Indian History to suggest that most modern South Asian ancestry dates to the Pleistocene. In this framework the Indo-Europeanization of the subcontinent was primarily a cultural one, where small groups of Central Asians imposed their language on the native population. What the genome-wide work has shown is that South Asians are the product of a large-scale mixing process between a population very distant from West Eurasians (“Ancestral South Indians”, ASI) and a population which was indistinguishable from other West Eurasians (“Ancestral North Indians”, ANI).

Since ANI is indistinguishable from West Eurasians I hold it is clearly a West Eurasian population in provenance. Those who reject this position from a scientific perspective believe that there could have been some sort continuous zone of “ANI-like” habitation from northwestern South Asia up into northern Inner Eurasia (and perhaps toward West Asia as well) dating from the late Pleistocene. I do not that believe this is plausible, and I will tell you that prominent researchers who I have brought up this idea to are somewhat incredulous.**

Third, there are major unresolved issues genetically in relation to the dates and the total number of mixing populations. I am quite confident saying around half of the total South Asian genomic ancestry today derives from populations who were living outside of South Asia on the Holocene-Pleistocene boundary 11,700 years ago. Much of that ancestry probably flourished between the Caucasus and Zagros mountains. The remainder somewhere in the vast swath of territory between the Baltic and Siberia (perhaps further south, toward the Pamirs?).

But I am not confident of the relative balances of contribution to the ANI. It does seem that the northern component, which is derived in part from the southern component, is much more prominent in upper castes and northwestern populations. In contrast the southern component is found throughout the subcontinent.

In Genomic insights into the origin of farming in the Near East there is analysis of South Asia in the supplements. The author concludes that ANI can not be modeled as a single population (Zack Ajmal and I were saying this in 2010). The top hits for the sources of ANI tend to be the genomic sample from the Zagros, in western Iran (before subsequent admixture with Levantine farmers), and a population similar to the Yamna culture the steppe. The issue seems to be that later steppe populations which harbor a fair amount of “Early European Farmer” ancestry (e.g., LBK in Central Europe) due likely to back migration aren’t good model fits.

Below are two plots, one showing a scatter of South Asian groups with their Iran_N (a sample from ~10,000 years ago) vs. Yamna (from ~5,000 years ago), and another with the ratios.


DO NOT TAKE THE PROPORTIONS LITERALLY.  My intuition that these models are overestimating the proportion of steppe ancestry, but my confidence in my intuition is low.

There are two groups enriched for Iran_N ancestry.

  1. Lower caste groups, especially from South India.
  2. Populations in southern Pakistan.

The reasons I differ. If you have done genetic analysis of the Pakistani populations it seems quite obvious that unlike other groups in South Asia Pakistani groups facing the Arabian sea across from Oman have genuine Near Eastern ancestry. This affinity declines as you go north in Pakistan rather rapidly. Notice though one South Indian group: Jews from Cochin. This population clearly has recent Near Eastern ancestry.

The Kharia are an Austro-Asiatic Munda group. For whatever reason Austro-Asiatic groups seem to consistently have very little steppe ancestry. The Mala are Dalits from South India. The further up you go on the modal Iran_N-Yamna cline you see the populations are either upper caste, or, they are from the far northwest of the subcontinent.

The conclusion I derive from this is that first there was an early migration of West Eurasian populations consisting of Iranian farmers. This group mixed with the ASI element. The Indo-Aryans, who probably correlates with the Yamna-like component, arrived later as an overlay (and nearly half of their ancestry was derived from Iranian farmers). Then many South Asian populations have modifications on this base model of compound ANI + ASI; Munda and Bengali have later East Asian ancestry, while populations on the Arabian sea have Near Eastern ancestry.

Fourth, the story in India Today leans heavily on Y chromosomes R1a1a. It is true we are Lords of the Steppe and destined to drive out enemies before us. But, it is not the primary story. And yet Y chromosomal phylogenies are easy for the public to understand. But they only make sense in light of the above framework. R1a1a is found in South Indian tribal populations. It seems likely that Indo-Aryan paternal lineages were highly invasive across the subcontinent, just as they were in Europe. In many cases they likely extended far beyond domains where Indo-European acculturation occurred.

I’m probably wrong on some of the details. But I suspect the final story will not be so different from this.

Finally, I will mention the cultural element here. There is a fair amount of the discussion of the form “so you are saying the ancestors of Indians are Europeans?” or “does this mean Hinduism is not Indian?”

The piece was about genetics and demography, not my opinions about culture. So I will say this:

  1. The “West” as an entity is no older that Classical Greece. 500 BC. My own personal position, strongly held, is that the West should indicate cultures and societies which descend from the European societies which adhered to the Western Church around ~1000 AD (some nations, like Lithuania, became absorbed into this cultural complex hundreds of years later). So Russia is not the West. And Merovingian Francia is not the West.
  2. Indian civilization of what we term the Hindu variety coalesced in the period between between 500 BC and 500 AD, from before to the Mauryas up to the Guptas. Obviously the period before 1000 BC was important in setting the ground-work, but I do not believe it was Indian as we’d understand it in anything but the geographical sense, nor was it Hindu in any way we’d recognize it today (similarly, Shang dynasty China was not China as we’d understand, which came into being after 500 BC).

These positions mean that I think nationalist passions are in the “not even wrong” category. Indian Hindu civilization is indigenous by definition, since it was synthesized in situ on the edge of historical perception and attestation (for the record, I think Adi Shankara was critical in the completion of a crystalized self-conception of Hindu religio-philosophical thought, but its origins predate him). Similarly, Indian civilization was not seeded by white Europeans because white Europeans were only coming into being in Europe when the Indus Valley civilization was collapsing.

That is all (for now).

Addendum: The first tranche of ancient DNA should be out in a few months. Also, there is another paper on Indian genetics in the work from the usual suspects. There won’t be anything totally surprising (or so I’ve been told).

* By lies, I mean the contention that intelligence is an “invalid” instrument in relation to predictiveness, or, if it is valid, it is not genetically heritable. People routinely lie about these facts in discussion or spread lies because there are socially preferred positions which they conform to. Similarly, many questions about Indian history seem to hinge on widely promoted lies.

** This model needs to also confront the massive mixing of the last 4,000 years. If it is true then it is ASI which is mostly likely intrusive, because it is not creditable that these two populations were in nearby proximity for tens of thousands of years without exchanging genes.

The Indo-Aryan migration to the Indian subcontinent

Filed under: India Genetics,Indian Genetics — Razib Khan @ 7:45 am

The piece is up at India Today. The headline and title are of course optimized for clicks. I would, for example, say that the Indo-Aryans came from the west, not the West.

In the course of writing this it has become clear that many people have very specific commitments on this issue. I think it is clear I do not. Genetic inference methods have wide shoulders of confidence in particular dates. So I’ll leave it to those with more archaeological knowledge to argue over specific date. But it strikes me that the dates point to a likelihood that much of the expansion and diversification of Indo-Aryans may precede their expansion into the Gangetic plain ~1500 BCE, the date preferred by many scholars.

Apparently we shouldn’t have to wait too long for ancient DNA from Rakighari (months, not years). But I doubt that will settle anything, as opposed to being preliminary and setting off new debates.

July 26, 2017

18,000 years BC (the film)

Filed under: Dog Evolution,Human Evolution,Paleolithic — Razib Khan @ 5:42 pm

Alpha, set 20,000 years ago in Europe, was apparently originally titled “Solutrean.” The change is probably for the best. It will come out next spring. I really hope that this movie is good and does well. It isn’t often that you have something which takes place during the Last Glacial Maximum.

The plot seems to reflect the what you might read in Pat Shipman’s The Invaders, but it’s about 20,000 years too late for her model to work. One of the major criticisms of the idea that dogs and modern humans operated as a team is that it seems way too early. But of late there have been suggestions that the date is earlier than we’d previous thought in relation to when dogs as we understand them arose: Ancient European dog genomes reveal continuity since the Early Neolithic. Here’s the relevant section: “By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000–40,000 years ago.”

Please note though that the divergence of the dog lineage from the ancestors of modern wolves is a distinct question and process from domestication as such as we understand it. Though it seems likely these events didn’t occur too far apart in time.

The future will be genetically engineered

Filed under: Genetics,Genomics — Razib Khan @ 4:04 pm

If the film Rise of the Planet of the Apes had come out a few years later I believe there would have been mention of CRISPR. Sometimes science leads to technology, and other times technology aids in science. On occasion the two are one in the same.

The plot I made above shows that in the first five years of the second decade of the 20th century CRISPR went from being an obscure aspect of bacterial genetics to ubiquitous. Friends who had been utilizing “advanced” genetic engineering methods such as TALENS and zinc fingers switched overnight to a CRISPR/Cas9 framework.

As I’ve said before the 2010s are the decade when “reading” the genome becomes normal. We really don’t know what the CRISPR/Cas9 technology is capable of. It’s early years yet. With that, First Human Embryos Edited in U.S.. Technically they’re single celled zygotes. The science itself is not astounding. Rather, it is that the human rubicon has been passed in the United States. As indicated in the article there has been some jealousy about what the Chinese have been able to do because of a different cultural and regulatory framework.

There are those calling for a moratorium on this work (on humans). I’m not in favor or opposed. Rather, my question is simple: if CRISPR/Cas9 makes genetic engineering cheap, easy, and effective, how exactly are we going to enforce a world-wide moratorium? A Butlerian Jihad?

Note: I know that people are freaking about humans + genetic engineering. But most geneticists I know are more excited about the prospects of non-human work, since human clinical trials are going to be way in the future. Over 20 years since Dolly it’s notable to me that no human has been cloned from adult somatic cells yet.

July 25, 2017

On the precipice of the Kali Yuga

Filed under: China,History — Razib Khan @ 2:04 am

The idea of decline is an old one. See The Idea of Decline in Western History for a culturally delimited view. But whether it is Pandora opening her box or Eve biting the apple, the concept of an idyllic past and the ripeness of imminent decline seems baked into the cake of human cultural cognition. It was always better in the good old days.

Of course there is the flip side of those who presume that the Eternal City will continue as it always was unto the end of time. Meanwhile, cornucopian optimists of our modern era, such as Steve Pinker, are the historical aberration. But they are influential in our age.

Tanner Greer has a profoundly pessimistic post up, Everything is Worse in China, which is getting some attention (as I’ve stated before Tanner’s blog in general is worth a read). Rod Dreher has two follow up posts in response. First, A: Confucius, Basically, which is somewhat an answer to Tanner. And then an email from Tanner himself. It is here that he suggests to Rod’s readers Xunzi: The Complete Text. That is all for the good (for a broader view, A Short History of Chinese Philosophy).

Readers can probably read between the lines that I have been gripped somewhat by Sinophilia of late. I am rather pessimistic about the state of American culture and the prospects for the American republic as we have known it. I don’t see any of the major political factions offering up a solution for the impending immiseration of the middle class.

So I look to the east. Much of the history of the world has been a history of Asia, and it seems we are going to go back in that direction. If we are pessimistic about China, to a great extent we are pessimistic about the world.

Perhaps then we need to abandon the idol of the nation-state, or in China’s case the nation-civilization. Rod Dreher has the Benedict Option for orthodox Christians* But we need to think bigger. Men and women of civilized inclinations may need to band together, and form secret societies shielded from the avarice of the institutional engines which channel human passions toward inexorable ends. We need a strategy for living as civilized people in an anarchic world, an archipelago of oligarchy in the sea of barbarism. Sooner, rather than later.

History comes at you fast.

* I mean here Trinitarian Christians of a traditionalist bent, not Eastern or Oriental Orthodox Christians.

Ancient Europeans: isolated, always on the edge of extinction

Filed under: Europe,Human Genetics,Scandinavia — Razib Khan @ 12:19 am

A few years ago I suggested to the paleoanthropologist Chris Stringer that the first modern humans who arrived in Europe did not contribute appreciable ancestry to modern populations in the continent (appreciable as in 1% or more of the genome).* It seems I may have been right according to results from a 2016 paper, The genetic history of Ice Age Europe. The very oldest European ancient genome samples “failed to contribute appreciably to the current European gene pool.”

Why did I make this claim? Two reasons:

1) 40,000 years is a long time, and there was already substantial evidence of major population turnovers across northern Eurasia by this point. You go far enough into the future and it’s not likely that a local population leaves any descendants. So just work that logic backward.

2) There was already evidence of low population sizes and high isolation levels between groups in Pleistocene and Mesolithic/Neolithic Europe. This would again argue in favor of a high likelihood of local extinctions give enough time.

This does not only apply to just modern humans, descendants of southern, likely African, populations. Neanderthals themselves show evidence of high homogeneity, and expansions through bottlenecks over the ~600,000 years of their flourishing.

The reason that these dynamics characterized modern humans and earlier hominins in northern Eurasia is what ecologists would term an abiotic factor: the Ice Age. Obviously humans could make a go of it on the margins of the tundra (the Neanderthals seem less adept at penetrating the very coldest of terrain in comparison to their modern human successors; they likely frequented the wooded fringes, see The Humans Who Went Extinct). We have the evidence of several million years of continuous habitation by our lineage. But many of the ancient genomes from these areas, whether they be Denisovan, Neanderthal, or Mesolithic European hunter-gatherer, show indications of being characterized by very low effective population sizes. Things only change with the arrival of farming and agro-pastoralism.

For two obvious reasons we happen to have many ancient European genomes. First, many of the researchers are located in Europe, and the continent has a well developed archaeological profession which can provide well preserved samples with provenance and dates. And second, Europe is cool enough that degradation rates are going to be lower than if the climate was warmer. But if Europe, as part of northern Eurasia, is subject to peculiar exceptional demographic dynamics we need to be cautious about generalizing in terms of the inferences we make about human population genetic history. Remember that ancient Middle Eastern farmers already show evidence of having notably larger effective population sizes than European hunter-gatherers.

Two new preprints confirm the long term population dynamics typical of European hunter-gatherers, Assessing the relationship of ancient and modern populations and Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. The first preprint is rather methods heavy, and seems more of a pathfinder toward new ways to extract more analytic juice from ancient DNA results. Those who have worked with population genomic data are probably not surprised at the emphasis on collecting numbers of individuals as opposed to single genome quality. That is, for the questions population geneticists are interested in “two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage.”

I encourage readers (and “peer reviewers”) to dig into the appendix of Assessing the relationship of ancient and modern populations. I won’t pretend I have (yet). Rather, I want to highlight an interesting empirical finding when the method was applied to extant ancient genomic samples: “we found that no ancient samples represent direct ancestors of modern Europeans.”

This is not surprising. The ‘hunter-gatherer’ resurgence of the Middle Neolithic notwithstanding, Northern Europe was subject to two major population replacements, while Southern Europe was subject to one, but of a substantial nature. Recall that the Bell Beaker paper found that “spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years.” This means that less than 10% of modern Britons’ ancestry are a combination of hunter-gatherers and Neolithic farmers.

And yet if you look at various forms of model-based admixture analyses it seems as if modern Europeans have substantial dollops of hunter-gatherer ancestry (and hunter-gatherer U5 mtDNA and Y chromosomal lineage I1 and I2, associated with Pleistocene Europeans, is found at ~10% frequency in modern Europe in the aggregate; though I suspect this is a floor). What gives? Let’s look at the second preprint, which is more focused on new empirical results from ancient Scandinavian genomes, Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. From early on in the preprint:

Based on SF12’s high-coverage and high-quality genome, we estimate the number of single nucleotide polymorphisms (SNPs) hitherto unknown (that are not recorded in dbSNP (v142)) to be c. 10,600. This is almost twice the number of unique variants (c. 6,000) per Finnish individual (Supplementary Information 3) and close to the median per European individual in the 1000 Genomes Project (23) (c. 11,400, Supplementary Information 3). At least 17% of these SNPs that are not found in modern-day individuals, were in fact common among the Mesolithic Scandinavians (seen in the low coverage data conditional on the observation in SF12), suggesting that a substantial fraction of human variation has been lost in the past 9,000 years (Supplementary Information 3). In other words, the SHGs (as well as WHGs and EHGs) have no direct descendants, or a population that show direct continuity with the Mesolithic populations (Supplementary Information 6) (13–17). Thus, many genetic variants found in Mesolithic individuals have not been carried over to modern-day groups.

The gist of the paper in terms of archaeology and demographic history is that Scandinavian hunter-gatherers were a compound population. One component of their ancestry is what we term “Western hunter-gatherers” (WHG), who descended from the late  Pleistocene Villabruna cluster (see paper mentioned earlier). Samples from Belgium, Switzerland, and Spain all belong to this cluster. The second element are “Eastern hunter-gatherers” (EHG). These samples derive from the Karelia region, to the east of modern Finland, bound by the White Sea to the north. EHG populations exhibit affinities to both WHG as well as Siberian populations who contributed ancestry to Amerindians, the “Ancestral North Eurasians” (ANE). There is a question at this point whether EHG are the product of a pulse admixture between an ANE and WHG population, or whether there was a long existent ANE-WHG east-west cline which the EHG were situated upon. That is neither here nor there (the Tartu group has a paper addressing this leaning toward isolation-by-distance from what I recall).

Explicitly testing models to the genetic data the authors conclude that there was a migration of EHG populations with a specific archaeological culture around the north fringe of Scandinavia, down the Norwegian coast. Conversely, a WHG population presumably migrated up from the south and somewhat to the east (from the Norwegian perspective).

And yet the distinctiveness of the very high quality genome as inferred from unique SNPs they have suggests to them that very little of the ancestry of modern Scandinavians (and Finns to be sure) derives from these ancient populations. Very little does not mean all. There is a lot of functional analysis in the paper and supplements which I will not discuss in this post, and one aspect is that it seems some adaptive alleles for high latitudes might persist down to the present in Nordic populations as a gift from these ancient forebears. This is no surprise, not all regions of the genome are created equal (a more extreme case is the Denisovan derived high altitude adaptation haplotype in modern Tibetans).

Nevertheless, there was a great disruption. First, the arrival of farmers whose ultimate origins were Anatolia ~6,000 years ago to the southern third of Scandinavia introduced a new element which came in force (agriculture spread over the south in a few centuries). A bit over a thousand years later the Corded Ware people, who were likely Indo-European speakers, arrived. These Indo-European speakers brought with them a substantial proportion of ancestry related to the hunter-gatherers because they descended in major fraction from the EHG (and later accrued more European hunter-gatherer ancestry from both the early farmers and likely some residual hunter-gatherer populations who switched to agro-pastoralism**).

For several years I’ve had discussions with researchers whose daily bread & butter are the ancient DNA data sets of Europe. I’ve gotten some impressions implicitly, and also from things they’ve said directly. It strikes me that the Bantu expansion may not be a bad analogy in regards to the expansion of farming in Europe (and later agro-pastoralism). Though the expanding farmers initial mixed with hunter-gatherers on the frontier, once they got a head of steam they likely replaced small hunter-gatherer groups in totality, except in areas like Scandinavia and along the maritime fringe where ecological conditions were such hunter-gatherers were at advantage (War Before Civilization seems to describe a massive farmer vs. coastal forager war on the North Sea).

But this is not the end of the story for Norden. At SMBE I saw some ancient genome analysis from Finland on a poster. Combined with ancient genomic analysis from the Baltic, along with deeper analysis of modern Finnish mtDNA, it seems likely that the expansion of Finno-Samic languages occurred on the order of ~2,000 years ago. After the initial expansion of Corded Ware agro-pastoralists.

The Sami in particular seem to have followed the same path along the northern fringe of Scandinavia that the EHG blazed. Though they herd reindeer, they were also Europe’s last indigenous hunter-gatherers. Genetically they exhibit the same minority eastern affinities in their ancestry that the Finns do, though to a greater extent. But their mtDNA harbors some distinctive lineages, which might be evidence of absorption of ancient Scandinavian substate.

I’ll leave it to someone else to explain how and why the Finns and Sami came to occupy the areas where they currently dominate (note that historically Sami were present much further south in Norway and Sweden than they are today). But note that in Latvia and Lithuania the N1c Y chromosomal lineage is very common, despite no language shift, indicating that there was a great deal of reciprocal mixing on the Baltic.

Overall the story is of both population and cultural turnover. This should not surprise when one considers that northern Eurasia is on the frontier of the human range. And perhaps it should temper the inferences we make about other areas of the world.

* You may notice that this threshold is lower than the Neanderthal admixture proportions in the non-African genome. Why is this old admixture still detectable while modern human lineages go extinct? Because it seems to have occurred with non-African humans had a very small effective population, and was mixed thoroughly. Because of the even genomic distribution this ancestry has not been lost in any of the daughter populations.

** Haplogroup I1, which descends from European late Pleistocene populations, exhibits a star phylogeny of similar time depth as R1b and R1a.

July 23, 2017

Open Thread, 07/23/2017

Filed under: Open Thread — Razib Khan @ 4:49 pm

Finished The Enigma of Reason. The basic thesis that reasoning is a way to convince people after you’ve already come to a conclusion, that is, rationalization, was already one I shared. That makes sense since one of the coauthors, Dan Sperber, has been influential in the “naturalistic” school of anthropology. If you’ve read books like In Gods We Trust The Enigma of Reason goes fast. But it is important to note that the cognitive anthropology perspective is useful in things besides religion. I’m thinking in particular of politics.

I haven’t been blogging much since I was abroad on a business trip. Specifically to the Persian Gulf. I’ll say more later, though I am going to be vague on geography since I’d rather not mix these two streams of my life (also, to be clear, this is not related to my day job).

One Family, Many Revolutions: From Black Panthers, to Silicon Valley, to Trump. I had known of this connection before, between Ben Horowitz, the Silicon Valley VC guy, and David Horowitz, the right-wing provocateur. The elder Horowitz’s contention that one needs to play dirty to get anywhere is a position that I believe has more support today than it did ten years ago. The culture has come to him.

Don’t Believe in God? Maybe You’ll Try U.F.O.s. No surprise.

43 Senators Want to Make It a Federal Crime to Boycott Israeli Settlements. Here are the sponsors. I’ve never felt so sympathetic toward BDS….

My piece in India Today on South Asian genetics is hitting the printing press this week.

July 17, 2017

Castes are not just of mind

Filed under: Caste,Human Genetics,India — Razib Khan @ 8:31 pm

Before Nicholas Dirks was a controversial chancellor of UC Berkeley, he was a well regarded historian of South Asia. He wrote Castes of Mind: Colonialism and the Making of Modern India. I read it, along with other books on the topic in the middle 2000s.

Here is Amazon summary from Library Journal:

Is India’s caste system the remnant of ancient India’s social practices or the result of the historical relationship between India and British colonial rule? Dirks (history and anthropology, Columbia Univ.) elects to support the latter view. Adhering to the school of Orientalist thought promulgated by Edward Said and Bernard Cohn, Dirks argues that British colonial control of India for 200 years pivoted on its manipulation of the caste system. He hypothesizes that caste was used to organize India’s diverse social groups for the benefit of British control. His thesis embraces substantial and powerfully argued evidence. It suffers, however, from its restricted focus to mainly southern India and its near polemic and obsessive assertions. Authors with differing views on India’s ethnology suffer near-peremptory dismissal. Nevertheless, this groundbreaking work of interpretation demands a careful scholarly reading and response.

The condensation is too reductive. Dirks does not assert that caste structures (and jati) date to the British period, but the thrust of the book clearly leaves the impression that this particular identity’s formative shape on the modern landscape derives from the colonial experience. The British did not invent caste, but the modern relevance seems to date to the British period.

This is in keeping with a mode of thought flourishing today under the rubric of postcolonialism, with roots back to Edward Said’s Orientalism. As a scholar of literature Said’s historical analysis suffered from the lack of deep knowledge. A cursory reading of Orientalism picks up all sorts of errors of fact. But compared to his heirs Said was actually a paragon of analytical rigor. I say this after reading some contemporary postcolonial works, and going back and re-reading Orientalism.

To not put too fine a point on it postcolonialism is more about a rhetorical posture which aims to destroy what it perceives as Western hegemonic culture. In the process it transforms the modern West into the causal root of almost all social and cultural phenomenon, especially those that are not egalitarian. Anyone with a casual grasp of world history can see this, which basically means very few can, since so few actually care about details of fact.

Castes of Mind is an interesting book, and a denser piece of scholarship than Orientalism. Its perspective is clear, and though it is not without qualification, many people read it to mean that caste was socially constructed by the British.

This seems false. It has become quite evident that even the classical varna categories seem to correlate with genome-wide patterns of relatedness. And the Indian jatis have been endogamous for on the order of two thousand. From The New York Times, In South Asian Social Castes, a Living Lab for Genetic Disease:

The Vysya may have other medical predispositions that have yet to be characterized — as may hundreds of other subpopulations across South Asia, according to a study published in Nature Genetics on Monday. The researchers suspect that many such medical conditions are related to how these groups have stayed genetically separate while living side by side for thousands of years.

This is not really a new finding. It was clear in 2009’s Reconstructing Indian Population History. It’s more clear now in The promise of disease gene discovery in South Asia.

Unfortunately though science is not well known in any depth in the general public. The ascendency of social constructionism is such that a garbled and debased view that “caste was invented by the British” will continue to be the “smart” and fashionable view among many elites.

July 16, 2017

Open Thread, 07/16/2017

Filed under: Open Thread — Razib Khan @ 2:07 pm

I know that Game of Thrones is premiering tonight, but just wanted to remind readers that R. Scott Bakker’s The Unholy Consult will be out in a week. The author, R. Scott Bakker, has a blog, Three Pound Brain. He has some strange ideas…much of which I can’t make heads or tails of. But that’s OK, I enjoy his fiction, I don’t worship his philosophy.

I’m traveling, so not much time to comment. But let me say that I’m sad to see that Maryam Mirzakhani has died.

If you want to get a sense of the historical background of the framework within which I write much of this blog, you might find Will Provine’s The Origins of Theoretical Population Genetics of interest.

Tucker Carlson Goes to War Against the Neocons. I know that most people on the Left don’t like Tucker Carlson now because of his recent political postures, but back in the 2000s he was known as a quite heterodox (read: not partisan and boring) commentator. And I have to say that it is nice for someone to say what may of us, including former supporters of the Iraq invasion, think now and then when we recall the period before 2011.

July 14, 2017

The past was not PG

Filed under: Bible,Culture,Game of Thrones,Mythology — Razib Khan @ 9:34 am

The Week has published a screed against the low moral quality of Game of Thrones, Game of Thrones is bad — and bad for you. Obviously there is something to this insofar as one can see a coarsening of entertainment, or at least a decline in the stylized aspects of the depiction of reality.

But one of my initial reactions is that much of the narrative that we value from the past was not particularly PG. If you read The Harlot by the Side of the Road: Forbidden Tales of the Bible you see that the “Good Book”, in fact the only book many read front to back by many after the Reformation in Protestant Europe, has some quite unsavory tales. The story of Judah and Tamar in particular is hard to digest from a modern Western perspective because many of the elements are understated and workaday. Greek mythology is no better obviously. From Zeus raping Leda, Achilles throwing a fit because his sex-slave was taken away, to the tradition of Agamemnon sacrificing Iphigenia.

In some cases the shocking aspect of ancient stories is because moderns have different values. Slavery and concubinage were taken for granted during the period that the Hebrew Bible and Classical mythology crystallized into the forms which came down to us. In other cases I presume that it was unlikely that small children were going to ever read the original stories themselves, so sexual elements that might confuse were probably omitted in some oral tellings.

This is not to say that Game of Thrones is a modern masterpiece. But some of the disquieting, and frankly perverse, aspects of the narrative are only shocking if your standard is the relatively antiseptic literary fiction which one finds between the Regency and the cultural revolution of the 1960s. That is the aberration in human history, while gritty genre fiction much closer to primal human storytelling.

July 13, 2017

When white people were “ethnic”

Filed under: Religion — Razib Khan @ 3:22 pm

In the period between 2005 and 2010 I spent a fair amount of time reading about American history. And one aspect which interested me was the nature of the assimilation of white Americans of non-Protestant background, in particular Roman Catholics and Jews. This was triggered by reading The Impossibility of Religious Freedom, where the author argues that the modern American conception of church-state separation is difficult to understand in practice unless religion is defined as something similar to low church American Protestantism

Though the American founding was famously eclectic and tolerant, as befitted a republic designed by men with elite Enlightenment sensibilities, it was culturally without a doubt Protestant in heritage, if not belief. The American Revolutionary Zeitgeist was steeped in British-influenced anti-Catholicism. In keeping with the same sort of Protestant populism which inspired the Gordon riots a broad swath of American colonial opinion was critical of the Quebec Act for giving French speaking Catholics a modicum of religious liberty and equality before the law.

Despite this historical context the relationship between the Roman Catholic population and the American republic in the early years was relatively amicable. Most of the priests were French Canadians, and Catholic population was highly assimilated and integrated. The great change occurred with the arrival of large numbers of Roman Catholic Irish, as well as a Irish American clerical ascendency which drew upon a revival in the Church in Ireland.

John T. McGreevy’s Catholicism and American Freedom is probably the best history of the religion in the United States that I read during that period. Not because it’s comprehensive, it’s not. Rather, because it focuses on the tension between the Church and the American republic and society, and how it resolved itself, and how that resolution unravelled.

Periodically people in the media make allusions to the ability of the American republic and culture to assimilate Catholics and Jews, and how that might apply to Muslims today. The discussion really frustrates me because there is almost never an acknowledgement that Roman Catholics experienced various degrees of low-grade persecution during periods of the 19th century. The Ursuline Convent riots are just the most sensational incident, and the Know Nothing movement turned into a political party.

The expansion of public schooling in parts of this was country tied to anti-Catholicism. But the Catholics did not take this passively. The emergence of a whole counter-culture, and parochial schools, suggested that they were ready to fight back to maintain their identity. The powerful Irish clerics who served as de facto leaders of the Roman Catholic faithful seem to have wanted to establish a modus vivendi with the American government which recognized the Church’s corporate role in society. By and large American elites and culture rejected this attempt to import a European style model to the New World.

By the late 19th century a movement began in the American Roman Catholic Church which became labeled the Americanist heresy. Despite its official condemnation I would argue that “Americanism” eventually became the de facto ideology of most American Roman Catholics. As Catholics conceded and assimilated toward American liberal and democratic norms in their everyday life, the hostility from the general public declined, and by the middle of the 20th century Will Herberg’s Protestant, Catholic, Jew articulated a vision of religious harmony among white Americans.

It should be rather obvious from the above that I believe this religious harmony was achieved in large part through concessions that American Catholics made to the folkways of the United States. You see the same dynamic in Jonathan Sarna’s American Judaism. Second, in Catholicism and American Freedom McGreevy lays out the great unravelling of the Catholic hierarchy’s understanding with American society which occurred in the 1960s, as social liberalism went far beyond what even the most progressive Roman Catholic intellectuals were ready to countenance. And in this cultural revolution Catholics were shocked to find that their Jewish allies made common cause with mainline Protestants and post-Protestants.

The reason I am writing this is that the American landscape today is different in deep ways from that of the 19th and early 20th century. The lessons of Catholic and Jewish assimilation to a Protestant understanding of religion were achieved through bitter conflict, and the rejection of a corporatist accommodation between the American government and religious minorities, as was achieved in several European countries. The modern ideas of religious pluralism are fundamentally different from the explicit understanding of Protestant supremacy which ruled the day a century ago, and only slowly faded with assimilation of non-Protestants.

July 11, 2017

23andMe ancestry only is $49.99 for Prime Day

Filed under: 23andMe,D.T.C. Personal Genomics,Personal genomics — Razib Khan @ 11:10 am

23andMe has gone below $50 for “Prime Day”! For those of us who bought kits (albeit more fully featured) at $399 or even more this is pretty incredible. But from what I’m to understand these sorts of SNP-chips are now possible to purchase from Illumina for well less than $50 so this isn’t charitable.

At minimum a way to get a raw genotype you can bank later.

July 10, 2017

The sons of Ham and Shem

Filed under: Afro-Asiatic,History — Razib Khan @ 1:33 am

Recently I had the pleasure of having lunch with David Reich and he asked me about my opinions in relation to the Afro-Asiatic languages. I thought it was a strange question in that I get asked about that in the comments of this weblog too. Why would I have any particular insight? I gave him what I thought was the likely answer: Afro-Asiatic languages probably emerged from the western Levant. The ancient textual evidence indicates that to the north and east of Mesopotamia the languages were not Semitic. Though Akkadian, a Semitic language, was present at the dawn of civilization, Sumerian was the dominant language culturally in the land between two rivers, and it was not Semitic. As Lazaridis et al. did not detect noticeable Sub-Saharan African ancestry in Natufians, or later Near Easterners, I have become skeptical of any Sub-Saharan African origin for Afro-Asiatic.

But after the earlier post I made a few mental connections, and so I’ll put something up which pushes forward my confidence on a few issues. They lean predominantly on Y chromosomes. I understand that this sort of phylogeography has been shown to be not too powerful in the past, but in the scaffold of the ancient DNA framework it can resolve some issues.

About a decade ago study of Adolf Hitler’s paternal lineage (through male relatives) indicated that his haplogroup was E1b1b. Though reports that Hitler was non-European, because this is a very common lineage in non-Europeans, as well as Jews, were incorrect, it does turn out that Hitler’s paternal lineage is not associated with the Indo-European migrations. That is, unlike me, Adolf Hitler does not descend from the All-father, but rather one of the men who were conquered and assimilated by the steppe pastoralists.

But E1b1b is an interesting lineage. First, it is very common in much of Africa, especially the north. Second, it is common among the Natufian people according to Lazaridis et al. In contrast the Neolithic Iranian farmers seem to have harbored haplogroups J. Today the Near East is a mix of the two, which makes sense in light of the fact that reciprocal gene flow has occurred in the last 6,000 years.

Looking at E1b1b frequencies you notice a few things. The highest frequencies with large N’s are in the Cushitic and Berber languages. Haplogroup J has a different distribution, being skewed more to West Asia. In Ethiopia E1b1b is more common, but J is far more prevalent among the Semitic Amhara than the Cushitic Oromo. Though it is subtle autosomal DNA makes it clear that the Semitic speaking populations in Ethiopia-Somalia have more Eurasian ancestry than the Cushitic ones. I believe this is evidence of the multiple migration pattern discerned earlier.

If you go further south in East Africa and compare E1b1b and J you see a skew in the ratio. E1b1b declines in frequency, but J basically disappears. Among the Masai, who have a clear minor West Eurasian ancestral component, albeit far less than Ethiopians, 50% carry E1b1b. Among the Sandawe, who are a language isolate  with clicks, but exhibit Cushitic genetic affinities, 34% carry E1b1b. Among their Hadza hunter-gatherer neighbors, 15% do so. Among many Khoisan groups the frequency of E1b1b is 10%. Most of these groups exhibit no J haplogroup. This aligns easily with what Skoglund was reporting earlier: the first pastoralists had no “eastern farmer,” but did have “western farmer.” The Natufians were E1b1b. The wider reach of E1b1b in Africa in comparison to J is likely due to the fact that the admixed pastoralists were pushing into relatively virgin territories. Later Eurasian backflow events, which brought Semitic languages, encountered a much more densely populated Africa.

The hypothesis I present is that after the descendants of the Natufians made the transition to farming, some immediately pushed into areas of Africa suitable for farming and/or pastoralism. They quick diversified into the various Berber and Cushitic languages. The adoption of Nilo-Saharan languages, and later Khoisan ones, was simply the process of successive and serial admixture into local populations as these paternal lineages introduced their lifestyle. In the Near East many distinct Semitic languages persisted across the Fertile Crescent, and for whatever reason the various non-Semitic languages faded and Semitic ones flourished.

The great Bantu expansion was massive

Filed under: History,Human Genetics,Punt — Razib Khan @ 12:01 am

Lots of stuff at SMBE of interest to me. I went to the Evolution meeting last year, and it was a little thin on genetics for me. And I go to ASHG pretty much every year, but there’s a lot of medical stuff that is not to my taste. SMBE was really pretty much my style.

In any case one of the more interesting talks was given by Pontus Skoglund (soon of the Crick Institute). He had several novel African genomes to talk about, in particular from Malawi hunter-gatherers (I believe dated to 3,000 years before the present), and one from a pre-Bantu pastoralist.

At one point Skoglund presented a plot showing what looked like an isolation by distance dynamic between the ancient Ethiopian Mota genome and a modern day Khoisan sample, with the Malawi population about $\frac{2}{3}$ of the way toward the Khoisan from the Ethiopian sample. Some of my friends from a non-human genetics background were at the talk and were getting quite excited at this point, because there is a general feeling that the Reich lab emphasizes the stylized pulse admixture model a bit too much. Rather than expansion of proto-Ethiopian-like populations and proto-Khoisan-like populations they interpreted this as evidence of a continuum or cline across East Africa. I’m not sure if this is the right interpretation of the plot presented, but it’s a reasonable one.

Malawi is considerably to the north of modern Khoisan populations. This is not surprising. From what I have read Khoisan archaeological remains seem to be found as far north as Zimbabwe, while others have long suggested a presence as far afield as Kenya. Perhaps more curiously: the Malawi hunter-gatherers exhibit not evidence of having contributed genes to modern Bantu residents of Malawi.

Surprising, but not really. If you look at a PCA plot of Bantu genetic variation it really starts showing evidence of local substrate (Khoisan) in South Africa. From Cameroon to Mozambique it looks like the Bantu simply overwhelmed local populations, they are clustered so tight. Though it is true that African populations harbor a lot of diversity, that diversity is not necessarily partition between the populations. The Bantu expansion is why.

Of more interest from the perspective of non-African history is the Tanzanian pastoralist. This individual is about 38% West Eurasian, and that ancestry has the strongest affinities with Levantine Neolithic farmers. Specifically, the PPN, which dates to between 8500-5500 BCE. More precisely, this individual was exclusively “western farmer” in the Lazaridis et al. formulation. Additionally, Skoglund also told me that the Cushitic (and presumably Semitic) peoples to the north and east had some “eastern farmer.” I immediately thought back to Hogdson et al. Early Back-to-Africa Migration into the Horn of Africa, which suggested multiple layers. Finally, 2012 Pagani et al. suggested that admixture in the Ethiopian plateau occurred on the order of ~3,000 years ago.

Bringing all of this together it suggests to me two things

  1. The migration back from Eurasia occurred multiple times, with an early wave arriving well before the Copper/Bronze Age east-west and west-east gene flow in the Near East (also, there was backflow to West Africa, but that’s a different post….).
  2. The migration was patchy; the Mota sample dates to 4,500 years ago, and lacks any Eurasian ancestry, despite the likelihood that the first Eurasian backflow was already occurring.

Skoglund will soon have the preprint out.

July 9, 2017

Our civilization’s Ottoman years

Filed under: Culture,International Affairs,international relations — Razib Khan @ 9:29 pm

Some right-wing intellectuals are wont to say that multicultural and multiracial empires do not last. This is not true. Historically there are plenty which lasted for quite a long time. Rome, Byzantium, and the Ottomans, to name just a few of the longest. But, though they were diverse polities modern liberal democratic sensibilities would have been offended by them. That is because these empires were ordered and centered around a hegemonic culture, with other cultures accepted and tolerated on the condition of submission and subordination.

The Ottoman example is the most stark because it was formally explicit under the millet system by the end of its history, though it naturally evolved out of Islamic conceptions of the roles of dhimmis under Muslim hegemony. For 500 years the Ottomans ruled a multicultural empire. Yes, it decayed and collapsed, but 500 years is a good run.

I bring up the Ottoman example because I was having a discussion with a friend of mine, an academic, and he brought up the idea that the seeming immiseration of the middle to lower classes in developed societies will lead to redistributive economic policies. Both of us agree that immiseration seems on the horizon, and that no contemporary political movement has a good response. But I pointed out that traditionally redistributive socialism seems most successful in relatively homogeneous societies, and the United States is not that. American society is diverse. Descriptively multicultural. There would be another likely solution.

Eleven years ago Amartya Sen wrote a piece for The New Republic which could never get published in the journal today, The Uses and Abuses of Multiculturalism. In it he looked dimly upon the emergence of plural monoculturalism. Today plural monoculturalism is the dominant ideal of the identity politics Left, with cultural appropriation in vogue, and separatism reminiscent of the 1970s starting to come back into fashion. Against plural monoculturalism he contrasted genuine multiculturalism. I think a better word for it is cosmopolitanism.

The Ottoman ruling elite was Sunni Muslim, but it was cosmopolitan. The Sultan himself often had a Christian mother, while during the apex of the empire the shock troops were janissary forces drawn from the dhimmi peoples of the Balkans. This was a common feature of the Islamic, and before them Byzantine and Roman empires. The ruling elites exhibited a common ethos, but their origins were variegated.

Many of the Byzantine emperors were not from ethnic Greek Chalcedonian Christian backgrounds (before the loss of the Anatolian territories many were of Armenian, and therefore non-Chalcedonian, origin). But the culture they assimilated to, and promoted, as the core identity of the empire was Greek-speaking and Chalcedonian, with a self-conscious connection to ancient Rome. I can give similar examples from South Asia or China. Diverse peoples can be bound together in a sociopolitical order, but it is invariably one of domination, subordination, and specialization.

But subordinate peoples had their own hierarchies, and these hierarchies interacted with the Ottoman Sultan in an almost feudal fashion. Toleration for the folkways of these subordinate populations was a given, so long as they paid their tax and were sufficiently submissive. The leaders of the subordinate populations had their own power, albeit under the penumbra of the ruling class, which espoused the hegemonic ethos.

How does any of this apply to today? Perhaps this time it’s different, but it seems implausible to me that our multicultural future is going to involve equality between the different peoples. Rather, there will be accommodation and understandings. Much of the population will be subject to immiseration of subsistence but not flourishing. They may have some universal basic income, but they will be lack the dignity of work. Identity, religious and otherwise, will become necessary opiums of the people. The people will have their tribunes, who represent their interests, and give them the illusion or semi-reality of a modicum agency.

The tribunes, who will represent classical ethno-cultural blocs recognizable to us today, will deal with a supra-national global patriciate. Like the Ottoman elite it will not necessarily be ethnically homogeneous. There will be aspects of meritocracy to it, but it will be narrow, delimited, and see itself self-consciously above and beyond local identities and concerns. The patriciate itself may be divided. But their common dynamic will be that they will be supra-national, mobile, and economically liberated as opposed to dependent.

Of course democracy will continue. Augustus claimed he revived the Roman Republic. The tiny city-state of Constantinople in the 15th century claimed it was the Roman Empire. And so on. Outward forms and niceties may be maintained, but death of the nation-state at the hands of identity politics and late stage capitalism will usher in the era of oligarchic multinationalism.

I could be wrong. I hope I am.

Open Thread, 07/09/2017

Filed under: Open Thread — Razib Khan @ 8:29 pm

I’m a sucker for the aesthetics of Norden. Why? I wonder if part of it is that the fringe of Northern Europe is a science fictional setting. The long dark nights during the cold winter, and the twilight during midsummer. The sun may be bright, it never gets too high in the sky. The 13th Warrior wasn’t the best movie, but it was evocative. One of the problems with the film depiction of the Lord of the Rings trilogy is that New Zealand seems too bright and airy (and also not decayed enough).

Because of the SMBE meeting I haven’t made much progress on The Enigma of Reason. Much of it has been reviewing the literature in cognitive psychology and reasoning which I’m familiar with (system 1 vs. system 2, Wason reasoning task, etc.). Though it is leading me up to the main thesis.

I remember years ago Matthew Yglesias mentioned he was going to do a bit more reading of books, as opposed to news, to differentiate himself from other pundits. Today he admitted he wasn’t going to make a show of having an informed opinion about the Frankfurt School. I suggested he take time out to read The Dialectical Imagination: A History of the Frankfurt School and the Institute of Social Research, 1923-1950. The modern campus Red Guards don’t know anything about Adorno, Marcuse, or Horkheimer. But the outlines of contemporary project toward cultural revolution and exaltation of the marginalized are all there. Rather than being the origin modern radical movements, I suspect that the Frankfurt School simply provides a useful tool and framework to go about its project.

I do know that some politically moderate scientists who read The Dialectical Imagination, and saw campus politics in a totally different, and more intelligible, light.

Joe Pickrell’s new company, Gencove, Improving ancestry estimates in South Asia.

I said on Twitter that “easiest way to make housing affordable for non-rich is to build more houses for the rich so they won’t buy houses built for non-rich.” What do I mean? It’s all about supply. The well-off will always be first in line for any supply of housing. If you allow for copious development, vertically and horizontally, then the rich can purchase the luxury condos and mansions that they crave, while the middle class and lower class can buy up the more normal housing stock.

The Austin skyline, then and now.

Yazidi sex slave had to choose between son and escape from Isis.

Bangladeshi students test into elite schools. This story is about the entrance examinations for the elite public high schools of New York City. In 2010 the average Bangladeshi family in New York City had a household income of $37,000. I believe in the near future the entrance exams will not be the only criterion for gaining admission. The reality is that Asian American students lack “leadership” and are not “well rounded,” and all the Asian American applicants “look the same.”

A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes.

Racism Is Everywhere, So Why Not Move South? This article is written in the context of black Americans. But the insights are general. Houston has a cost of living that’s at the national average. It’s the fourth largest city in the United States, and there is a lot of good phở because of the large Vietnamese community.

Patrick Wyman, who sometimes comments on this blog, has a great Fall of Rome podcast.

The Sad, Sexist Past of Bengali Cuisine. Really upper caste Bengali Hindu cuisine.

Utilities fighting against rooftop solar are only hastening their own doom. Not surprised. I have been following Ramez Naam’s commentary on this for years. He’s been on this.

Islamophobes are attacking me because I’m their worst nightmare. Linda Sarsour.

I thought Hillary would win the election. But I told a long-time reader of this weblog who is a Democratic operative that BLM activists getting in Bernie Sanders’ face did not presage well for the direction of the party. Linda Sarsour as the face of progressivism is a massive boon for the Right and Republicans.

Sarsour has left a trail of obnoxious and offensive comments on Twitter. So have many people. For me personally the biggest issue is possible solidarity with Rasmea Odeh. The PFLP is the literal definition of a terrorist organization (though a Marxist, not Islamic, one). But the reality is that her enemies on the Right know that she and her compatriots in the “woke” movement would never exhibit charity toward their political opponents, so they are attempting to destroy her because they know she would do the same to them. That’s where we are in American politics today. You destroy your enemies, or they destroy you. Let’s have fun until the last battle though!

A combined analysis of genetically correlated traits identifies 107 loci associated with intelligence. I guess I’ll start paying attention to when they can explain ~25% of outgroup sample variance. They’re already further than the 7% in this preprint, though that will take a little longer to publish.

Procedures for enumerating and uniformly sampling transmission trees for a known phylogeny.

A reanalysis of Schaefer et al. does not indicate extensive CRISPR/Cas9 mediated off-target editing events.

Evolutionary Action of de novo missense variants across pathways prioritizes genes linked to autism and predicts patient phenotypic severity.

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