Open Thread, 03/18/2019

Going back to finishing Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not. My general attitude so far is that I’m skeptical, but the author presents a plausible thesis. Additionally, the book is worth reading because of its engagement with the whole literature in this area. It’s got a good bibliography you can follow-up.

We had Shadi Hamid on the Brown Pundits podcast. Really appreciate Shadi’s interest in engaging with a diverse array of people. A real intellectual for our time, and unfortunately all too rare in many places these days (I think Shadi should go on the Extremely Offline podcast, even though he is extremely online).

There’s a Fake Outrage Machine on the Right, Also. Basically, they’re trying to get a professor fired for saying in some forum several years ago that cops should be killed. This is egregious, but one of the features of academia, as it is today, is that egregiousness is defended.

Some people are making the analogy to the professor who is under fire at Sarah Lawrence, who wrote an op-ed suggesting there needs to be more intellectual diversity in academia. That’s a pretty weird comparison, but I guess it tells you something. If you are conservative your very existence is scary. If you are on the Left, suggesting people should be killed is scary. But look, there are literal Communists in the academy. No one is demanding they be fired, and unless you add all sorts of caveats being a Communist often means you believe in violent revolution against a class of people. Being liberal in the broad sense is illustrated only when it’s hard, not when it’s easy.

A conservative assault on academia may need to occur, but it shouldn’t be around small things like a professor here and there. Go for the money. That’s the heart. Crazy professors are like stray strands of hair.

The Stanford professor who rejected one of Elizabeth Holmes’ early ideas explains what it was like to watch the rise and fall of Theranos. If you listened to The Dropout, you get the feeling that Dr. Phyllis Gardner was the hero we didn’t deserve. It must have been difficult to watch what has happened over the past 15 years for her. She knew it was fake all along.

Immune Gene Diversity in Archaic and Present-day Humans. Starting to think that the low diversity and population sizes of northern humans were a long-term problem, and one reason they were absorbed by southern modern humans. Not totally sure though.

Jomon genome sheds light on East Asian population history.

Shared polygenetic variation between ASD and ADHD exerts opposite association patterns with educational attainment.

The Scandals of Meritocracy. Virtue vs. competence. Would you rather have a boss who is evil but competent, or good but incompetent? The reality is you have to balance the two. Richard Nixon was probably smarter that Dwight Eisenhower in raw g, but Eisenhower was probably a better person.

Indian population is growing much faster in the north – and the south is paying the price. Much of South India is below replacement. Kerala’s fertility is similar to Japan’s. The Gangetic core of North India is well above replacement. The state of Bihar has 100 million people and a total fertility rate of 3.41. That’s similar to Pakistan’s.

Classic Mechanism of Epigenetic Inheritance Is Rare, Not the Rule. Some geneticists are in “but we all knew that” mode. But the reality is that going by the popular press the public doesn’t know that. The unfortunate reality is that scientific revolutions don’t come around that often.

DNA Friend. Amusing parody site.

Genome-Wide Polygenic Risk Scores and prediction of Gestational Diabetes in South Asian Women.

Fooled By Randomness is my favorite Nassim Taleb book.

Graham Coop has released a textbook, Population and Quantitative Genetics. Since I periodically get emails to delete comments from kids in high school and college, I knew younger people read this weblog. I’d recommend a resource like this to see if you are really interested in population and quantitative genetics.

Check out the Population Genomics blog.

A History of the Iberian Peninsula, as Told by Its Skeletons.

Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula.

Population histories of the United States revealed through fine-scale migration and haplotype analysis. White Americans are the garlic people.

The Ubiquitous Sequencing Age

Several years ago Yaniv Ehrlich published A Vision for Ubiquitous Sequencing. We’re inching in that direction. In The Atlantic Sarah Zhang has a piece, An Abandoned Baby’s DNA Condemns His Mother, while The New York Times just came out with, Old Rape Kits Finally Got Tested. 64 Attackers Were Convicted:

Still, even with such successes, the problem of untested rape kits persists. Advocates for rape victims estimate that about 250,000 kits remain untested across the country.

Unfortunately, until recently, the ‘forensic genetics’ employed rather primitive 1990s technology. But that’s changing, though both money and expertise need to be brought to bear. Companies such as Gencove and Othram are bringing that expertise to a broader market, with the latter company focusing specifically on the forensic market.

So ubiquitous sequencing is happening. Soon. What does that mean? We need to think about privacy. We need to think about data. We need to reflect on the broader implications of this world beyond specific targeted tasks such as forensic identification.

Open Thread, 03/14/2019

Again, recommend Nature’s Metropolis: Chicago and the Great West. Great book.

Creating Christian Marriage in Early Islamic Arabia:

…perhaps the earliest, of a churchman saying definitively that marriage isn’t marriage without a specific Christian ritual comes from an unexpected corner of the late antique world: the Persian Gulf island of Dayrin (modern Tarut in Saudi Arabia) under the rule of the early Muslim caliphate. On this island in 676, Patriarch George I—chief bishop of the Church of the East, one of the two main churches of the Syriac Christian tradition—issued a canon that only unions that received a priestly blessing would be recognized as legitimate, lawful marriage….

…Patriarch George’s writings suggest that East Arabian Christians habitually drank at Jewish taverns and participated in “pagan” funerals—pagan, that is, in their “un-Christian” ostentatiousness. Significantly, interreligious mixing extended into family relations too. George complains of Christian women marrying “pagans,” here meaning Muslims….

I’m not a total revisionist. But not the date. 676. Contrary to traditional Islamic historiography I think it is highly plausible, even probably, that these men would not have been “Muslims” as we’d conceive of them. Rather, Islam, as we’d understand it really, makes sense only from 750 AD and later, with the emergence of the Sunni ulema, the turn against philosophy in mainstream Islam, and the focus on religious legalism. No Bukhari, no Islam.

This brings me to another issue that emerged in a discussion with a reader about Brown Pundits. Some Hindus say that their religion is founded in the Vedas. Similarly, though traditional most Muslims (Shia and Sunni) ground their faith in customs and traditions which accrued organically in the centuries after the death of Muhammad, they will assert that the fundamental basis of their religion goes back to Muhammad and that Islam qua Islam exploded out of the deserts of Arabia under the Rashidun.

From the perspective of the nonbeliever, I think both narratives miss important cultural genealogical features of the development of “Hinduism” and “Islam.” Hindus believe that their religion is the tradition of the Aryans. I hold that the Aryan, Indo-European, traditions that are present within Hinduism are calcified fossils, artifacts which symbolic meaning, but that the core of Dharmic traditions, whether Hindu or Buddhist or Jain, are not fundamentally from the Indo-Europeans. Some intellectual historians suggest that the Sramanic traditions, the counter-Hindu movements, are a revolt of the indigenous non-Aryan components. But I think the same is arguably true of Puranic Hinduism. All of these religions are qualitatively different from the sacrificial ritualism of the pastoralist Aryans.

Similarly, with Islam it is no secret that I am sympathetic with the argument that the emergence of the mawālī, non-Arabs, within Islam after 750 A.D. fundamentally transformed from the religion. Whereas proto-Islam under the Umayyads crystallized was the cult of the ruling caste, an Arab peculiarity, under the Abbasids, who saw the waxing of Iranian culture within the Caliphate, Islam became the religion of the state, and eventually the dominant element of the society. Though I would argue that the influence of Iran and Turan on Islam is probably quantitatively less than that of non-Aryan India on Hinduism, the transformation is great enough that I think one can make a similar case that Islam, a post-Christian Arab ruling sect, was “hijacked” by Iranian and Turanian modalities under the Abbasids.

Again, to be clear, I am not interested in “explaining” to Muslims or Hindus that “actually….” their religion isn’t what they think it is. I’m trying to get a better sense of cultural development and relatedness from the perspective of non-believers.

Biotic interactions affect fitness across latitudes, but only drive local adaptation in the tropics. This surprised me at first blush.

A week ago I had a conversation with Thomas Chatterton Williams for the BrownCast. One thing that we both agreed on: we hate Twitter, but we can’t leave it. Also, lots of people on Twitter are very stupid. I used to think commenters on this blog were stupid, but the reality is that you are geniuses among the dull compared to the Twitter mobs.

Why Elites Dislike Standardized Testing. The reality is that the gains to test-prep are not that great. ETS works really hard on this. But if you read Twitter or many mainstream commentators they act as if test-prep is driving the inequalities. It’s not. The world is full of bullshit.

The Life History of Human Foraging: Cross-Cultural and Individual Variation. Very important paper.

A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background Rate Variation. I don’t know much about the details of phylogenetic methods, but the first author is an old grad school classmate of mine. He knows his shit.fopen

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution.

Genomic architecture of phenotypic plasticity of complex traits in tetraploid wheat in response to water stress.

Siete Habanero Sauce, 4.5 stars out of 5.0

Tried out Siete Habanero Hot Sauce today. I really like it!

That being said, I have my biases. I like them hot. It’s moderately hot…it won’t burn a hole through your alimentary system, but it will kick you gently in the mouth. Second, it’s not a very sweet sauce, but a savory one. That makes sense in light of the avocado oil.

But the most exceptional and pleasant aspect of Siete Habanero Hot Sauce is the fact that somehow the spice kicks in later on. Instead of barging in the front door you can taste the creamy avocado before there is a “finish” of habanero spiciness. It’s something I always look for in a hot sauce since it allows for full flavor appreciation.

Swidden rice farming does not lead to high population density

Admixture on K = 5

I’ve been looking at the data from the recent Munda paper. Standard stuff, admixture, treemix, and f-statistics.The northern Munda samples were collected in Bangladesh. So I thought: I can test the hypothesis that the East Asian ancestry in Bangladesh is to a large part Santhal. After looking at it every which way, I think that in fact, the Munda may not have ever been very populous in much of northeast India. The Santhal is just not a good donor population to Bengalis, at least not when comparing mixes such as Dai + Tamil.

Additionally, the Santhal are really not that well modeled by mixing South Asians with any particular Southeast Asian group, though it works. I think that’s suggestive of the possibility that the Austro-Asiatic group which gave rise to the Munda don’t exist in their current form anywhere in Southeast Asia. Additionally, the Lao samples that are provided in the new paper I think may have Indian ancestry via admixture from Austro-Asiatic Mon or Khmer groups.

Basically, there is so much bidirectional gene flow that I think it’s really hard to get a grip on what’s going on. Additionally, the Burmese and northeast Indian populations (e.g., the Mizos) clearly have a strand of ancestry that derives from relatively recent migrants that came down from the region of eastern Tibet, and perhaps Sichuan or even further north. And this component shows up in Bengalis as well.

On top of this, there is the “Australo-Melanesian” substrate that is present all across Southeast Asia, and probably was present in modern southern China in the early Holocene, which has distant affinities with the “Ancient Ancestral South Indians” (AASI).

At this point, I keep my own counsel. But there may be an interesting story to tell related to how efficient and effective different forms of agriculture were, and how that interplayed with genes and language.

Genes, memes, and Mundas

The Munda languages of the northeastern quadrant of the Indian subcontinent are quite interesting because they are more closely related to the Austro-Asiatic languages of Southeast Asia than to the Indo-Aryan or Dravidian languages which are spoken by their neighbors. The Munda are usually classified as adivasi, which has connotations of being an ‘original inhabitant’ of the Indian subcontinent.

More concretely, the Munda have traditionally operated outside of the bounds of Sanskrit-influenced Hindu civilizations, occupying upland zones and governing themselves as tribal units, rather than being a caste population.

What the field of genetics tells us is that there are really no true aboriginal inhabitants of the Indian subcontinent in an unmixed form. That is, the vast majority of people in the Indian subcontinent have a substantial contribution of ancestry from the wave of migration out of Africa that occupied the southeast fringe of Eurasia beginning ~50-60,000 years ago. The modern adivasi generally are defined more by their social-cultural position within the landscape of Indian culture, as opposed to their long-term residence in the subcontinent.*

The term is a particular misnomer for the Munda because of the evidence that they are intrusive to the subcontinent from Southeast Asia. We have ancient DNA and archaeology which indicates that upland rice farmers, likely Austro-Asiatic, arrived in northern Vietnam ~4,000 years ago. This makes it unlikely to me that they were in India much earlier. The Y chromosomal data indicate that the paternal ancestry of the Munda derives from Southeast Asians, not the other way around.

A new genome-wide analysis of the Southeast Asian fraction of Munda ancestry suggests that it can be as high as ~30%. The paper is The genetic legacy of continental scale admixture in Indian Austroasiatic speakers:

Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000–3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.29/0.71 are Lao people from Laos and Dravidian speakers from Kerala in India. The South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian genetic component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

The paper already came out as a preprint many months back, so I’ve already mentioned it. The big finding, to me, is that it uses genome-wide methods to estimate an admixture in the range of ~4,000 between the southern Munda Southeast Asian and South Asian ancestral components. It also confirms something that has been pretty evident for nearly ten years of genome-wide analysis of South Asian population genetics: the Munda have less West Eurasian ancestry even after you account for the Southeast Asian admixture than any mainland Indian population outside of the Tibeto-Burman fringe.

In Narasimhan et al. the authors present a model that fits the data where:

  1. The proto-Munda mix with an “Ancient Ancestral South Indian” (AASI) population that has no West Eurasian admixture in India’s northeast
  2. Then, mix more with an “Ancestral South Indian” (ASI) population that has some West Eurasian admixture

Read More

Minding the base rate fallacy

In the near future, I’m pretty sure that most pregnancies will begin with a non-invasive genomic analysis (OK, that’s not how they will really begin, but you get what I’m saying). Far more extensive than what you get now no doubt.

But, non-invasive prenatal tests (NIPT) is already ubiquitous for a variety of conditions, in particular, those that result in visible changes in the karyotype. Down syndrome is probably the most well-known instance of this, though there are others. Denmark funds NIPT through public monies, and Down syndrome has almost disappeared among children born.

With all that being said, the presentation of results from these tests must be accompanied by some statistical scaffold or primer. Here is a post from someone with a background in computational genetics, How I learned to stop worrying and love Bayes’ Theorem:

At my 9 week doctor’s appointment, my doctor brought up the option of genetic testing, specifically non-invasive prenatal DNA testing. As a geneticist doing bioinformatics, I thought how cool it is that we can test for chromosomal abnormalities from the blood of the mother. The idea is that there are fetal DNA floating around in the mother’s blood and so inferences about whether there is an excess of a particular chromosome can be made by examining the mother’s blood…

Fast forward 2 weeks, I was at a FedEx store faxing my medical record to the doctor’s office at UCLA (I was in Boston for an internship for a few weeks during my first trimester) when I got a phone call from my doctor in Boston. This was the most difficult phone conversation I have ever had in my life. Over the phone, she told me that the NIPT test came back that my baby was high risk (40% chance) for Trisomy 13 (or Patau’s syndrome). My heart dropped….

Some of you see the title of this post. And you see the title of the post I linked to. So you know the conclusion and the moral of the story.

If you are still confused, please do read the post, and afterward please do repeat the phrase “base rate fallacy” to yourself multiple times, because it will prevent you from getting confused. It’s in the class of “news we’ll need to use” in the near future.

The new Amazon Tolkien series will be set during the Second Age

So it’s confirmed, the new Amazon Tolkien series will be set during the Second Age. This seems like a fine choice, since some of the characters that we know and “love,” such as Sauron, Galadriel, and Elrond, will be major players, and the framework for the Third Age which is the backdrop that we’re familiar with will be set.

Additionally, as noted in the reactions, the fact that much of the action could take place on Numenor is probably a good thing for character development and dramatic tension. Numenor is the byword for hubris in Tolkien’s legendarium and opens up a path for a more complex and realistic take on character development than may have been possible during the more mythological First Age.

And of course, the series could culminate in a set-piece battle to end all battles.

The beginning of the end of Game of Thrones and the hanging thread of A Song of Ice and Fire


Even if marginally, A Storm of Swords is the highest rated of George R. R. Martin’s books on Amazon. In the judgment of many people, which includes me, it is the best of his books. It was also the highpoint of interest in the series. For various reasons, it was published several months earlier in the UK than in the USA. So I special ordered the UK edition and received it in June of 2000, about 1.5 years after I began reading the series in the last weekend of January 1999.

Since I began writing this blog, in 2002, I have written now and then about my interest in the series, and frustration and patience with the delay in the books being published. The first three books were published in 1996, 1999, and 2000. The fourth book came out in 2005. The fifth, 2011. We’re now eight years along, and Martin is still working on book six.

For the longest time, I had no interest in watching the television show, since the books were far ahead of them, and I planned on watching the HBO series after George R. R. Martin wrapped up A Song of Ice and Fire. I had long assumed that the penultimate book would be published ~2016 so that the gap between the end of the HBO series and the novels would not too drawn out. Obviously, that did play out.

With the show Game of Thrones to conclude this year, there is a bittersweet aspect to those of us who have been reading the books for nearly a generation. There has been something of a “fork” so that many details of the show now differ from the books, and the HBO series, in fact, outrun Martin’s writing so much last year that much of the storyline was somewhat improvised. But the conclusion is said to be broadly the same between the television series and the book. Which means if and when we read the books we’ll know where it ends.

Open Thread, 03/05/2019

Thanks to everyone who has gotten a membership. Still working out a few kinks and trying to enable yearly billing and Papyal (I’m messing up something on the Paypal API). Since someone asked, here is my Patreon for the Brown Pundits podcast.

Speaking of that, I’ll be posting a conversation with an Indian middle-class Dalit soon (already posted for patrons), as well as interviews pending for Thomas Chatterton Williams and Shadi Hamid.

The Insight will have Alicia Martin on this week, and then Lara Cassidy on Irish genetic history, as well as something on historical linguistics by Asya Pereltsvaig. Yeah, we’re preloaded for the next month! Then the current plan is to talk about deep ancient structure in our complex species.

I’ve been thinking about Twitter, comments, papers, books, and blog posts recently. And the audacious argument in Christopher Beckwith’s Warriors of the Cloisters: The Central Asian Origins of Science in the Medieval World. Beckwith renames what we know as the scholastic method as the “recursive argument method.” His contention is that this method developed in the viharas, colleges, of Central Asian Iranian Buddhism before the rise of Islam. With the conversion of these Buddhist peoples to Islam, their intellectual traditions were assimilated into the Islamic one. While the vihara became madrassas, which spread from the Islamic east to the west, the disputation techniques were never fully integrated into Islamic civilization, even though Central Asian Iranians such as Avicenna continued the tradition. Eventually, the tradition did take root in the Latin West, being transmitted by Islamic civilization.

Here is the Wikipedia definition of scholasticism:

Scholasticism is not so much a philosophy or a theology as a method of learning, as it places a strong emphasis on dialectical reasoning to extend knowledge by inference and to resolve contradictions. Scholastic thought is also known for rigorous conceptual analysis and the careful drawing of distinctions. In the classroom and in writing, it often takes the form of explicit disputation; a topic drawn from the tradition is broached in the form of a question, opponents’ responses are given, a counterproposal is argued and opponents’ arguments rebutted. Because of its emphasis on rigorous dialectical method, scholasticism was eventually applied to many other fields of study.

Scholasticism is basically enforced nerdiness. Beckwith argues that modernist humans have abandoned this tradition, and he argues that postmodernism is really just a form of late-stage modernism. While in scholasticism the method and substance of the argument are critical, in postmodernism the individual who is making the argument is arguably even more important.

If a wealthy white male and a poor black woman entered into the argument as to whether “income inequality was bad for society,” we (post)moderns would place a great deal of weight upon who the disputants were, no matter the substance of their arguments.

The recursive argument technique is thorough, exhaustive and requires space. One can see scholasticism playing out in the form of a book-length argument, or in an extended paper. But it is almost impossible to imagine that its well-structured method could be format could be fitted to the comments of an article or blog post, let alone Twitter.

Twitter, in particular, is extremely well suited for a who/whom style of argument. Aside from threading it lacks the ability to structure arguments in a complex manner, and, its 280 character limit enforces a level of brevity at the single tweet scale. Deep substantive disagreements are almost never hashed out on Twitter because the platform does not have the capacity, goodwill or no. Rather, short rhetorical bursts and quips are optimized to lift the spirits of conferences in fellowship, ostracize heretics, and demonize the opposition. The laconic sophist is the ideal user of the platform.

Linkage disequilibrium in subdivided populations. Nei hath spoken.

Statistical Thinking from Scratch: A Primer for Scientists. Coming this summer, something new for your dead-tree collection.

Hierarchical clustering of gene-level association statistics reveals shared and differential genetic architecture among traits in the UK Biobank.

Ant collective behavior is heritable and shaped by selection.

Testing for correlation between traits under directional evolution.

Constraint-based analysis for causal discovery in population-based biobanks.

H.I.V. Is Reported Cured in a Second Patient, a Milestone in the Global AIDS Epidemic.

Theranos: How a broken patent system sustained its decade-long deception.

Interesting how similar his take is to some moderns:

Medicare should stop blocking access to next-generation sequencing for people with hereditary cancer.

PARASITES MEDIATE CONDITION-DEPENDENT SEXUAL SELECTION FOR LOCAL ADAPTATION IN A NATURAL INSECT POPULATION.

Will be reading This View of Life: Completing the Darwinian Revolution soon. Hope to have the author on the podcast at some point.

Very heartened to see the author of This View of Life: Completing the Darwinian Revolution, David Sloan Wilson, rejecting attempts to smear and taint Bret Weinstein with guilt by association. Wilson expressed an old-fashioned liberal sense of fair play and decency which seemed totally out of place in a place like Twitter.

Some of the idiots on Twitter once asked me “I wonder how it makes you feel that Ann Coulter retweeted you” in relation to a tweet that “blew up” (I don’t remember what it was). Now Illan Omar is having her words retweeted by the froggish sect for obvious reasons. How does it make her feel? I assume whatever her feelings are they are sincere and deeply felt, and whatever agreements frogs might have with her is neither here nor there to her. At least she cares about the substance of her beliefs, whether you think they are good or bad, not vague posturing associations.

The cult of feeling and naked emotive reflex reigns supreme today. Reason, for ill or goodwill, is at least bracing in its clarity.

The game is on. Let the disputes begin!