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

December 31, 2018

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:49 pm

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

The end of the year as we know it

Filed under: Open Thread — Razib Khan @ 3:25 pm
Another one is almost in the bag. Lots of interesting stuff this year, though probably the most important story in “world-historical” terms, the genome-editing of babies in China, hasn’t really ended. Ushering in 2019 with a $20.19 Tardigrade t-shirt New Years Eve sale at DNA Geeks. And 30% off everything with code WELCOME2019. I am […]

December 30, 2018

Judith Rich Harris, 1938-2018

Filed under: Judith Rich Harris,Psychology — Razib Khan @ 11:48 am

With hindsight, I judge Steve Pinker’s The Blank Slate: The Modern Denial of Human Nature as something of a high-tide in biologically informed realism in the psychological and behavioral sciences in the 21st century. A reread is bittersweet, knowing what has come to pass. But one of the best things about The Blank Slate is that he gave extensive publicity to Judith Rich Harris’ The Nurture Assumption. I like to think, perhaps hope, that her work influenced many “Generation X” parents.

In January of 2006 she answered 10 Questions for this weblog. Judy and her husband were always gracious and kind in their email correspondence with me. I can’t say that for many academics who are in the fullness of their health and well-being, something she struggled with for decades.

Her life made a difference. Read The Nurture Assumption and her follow-up book, No Two Alike: Human Nature and Human Individuality, to understand why.

December 29, 2018

Bangladesh elections

Filed under: Bangladesh,Bangladesh Elections,elections — Razib Khan @ 10:04 pm

Bangladeshis Must Choose ‘Lesser of Two Evils’ in Election:

Per capita income has increased by nearly 150 percent, while the share of the population living in extreme poverty has shrunk to about 9 percent from 19 percent, according to the World Bank.

Electricity generation has also increased drastically under Mrs. Hasina’s rule, helping to boost factory production and spreading out to homes in rural areas. The rates of maternal mortality and illiteracy have also declined.

Sultana Kamal, a Bangladeshi activist who was once close to Mrs. Hasina but has become increasingly wary of her, said a win by the current government would be seen as an indifference by voters to rights concerns.

From what I know most of my family generally supports the Awami League. My parents do, and I have an uncle who is an activist in that party. As an atheist I sympathize more with parties less keen on allying with Muslims who are excited to kill atheists. But….the Awami League seems to have gotten quite a big head, and Sheikh Hasina is becoming Bangladesh’s Indira.

If it’s the choice between economic growth and human rights, I think voters would choose the former. But I suspect that many will bet that economic growth is due to endogenous forces which are not controlled by the government, and will switch parties to rebalance the political system.

Variation in general intelligence and our evolutionary history

Filed under: Evolution,Intelligence,IQ — Razib Khan @ 9:16 pm

In a bit of “TMI”, I’m far more intellectually promiscuous than I am in my personal life. My primary focus on this blog, if I have one, is probably historical population genetics of the sort highlighted in David Reich’s Who We Are and How We Got Here. But I have plenty of other interests, from economic history to cognitive psychology. Like religion, I have precise and clear opinions about a topic like “intelligence.” Unlike many people with an interest in evolutionary genetics I have read psychometric work, am familiar with some of the empirical results, as well as being personally acquainted with people in the field of psychometrics.

A few days ago Nassim Nicholas Taleb opined on intelligence, and I was silent. Today some individuals who I know from within the field of cultural evolution, another one of my interests, discussed intelligence, and I was silent. I’ve said all I really have to say over 15 years, and it isn’t as if I reanalyze psychometric data sets. But, a question that Taleb acolytes (and presumably Taleb) have brought up is if intelligence is such an important heritable trait, why isn’t everyone much smarter?

Think of this as the second Von Neumann paradox. What I’m alluding to is the fact that we know for a fact that human biology is capable of producing a god-made-flesh. With all due respect to another Jew who lived 2,000 years earlier than him, I speak here of John Von Neumann. We know that he is possible because he was. So why are the likes of Von Neumann bright comets amongst the dust of the stars of the common man, rather than the norm?

First, consider the case of Von Neumann himself. He had one daughter and two grandchildren. That is, within two generations genetically there was less “Von Neumann” than there had been. Though his abilities were clearly mentat-like, from the perspective of evolution Von Neumann was not a many sigma individual. He was within the normal range. Close to the median, a bit below in fecundity and fitness.

Taking a step back and focusing on aggregate populations, the fact that intelligence seems to be a quantitative trait that is at least moderately heritable and normally distributed due to polygenic variation tells us some things evolutionarily already. In Principles of Population Genetics is noted that heritable quantitative traits are often those where directional selection is not occurring due to huge consistent fitness differentials within the population.

Breaking it down, if being very smart was much, much, better than being of average smarts, then everyone would become very smart up to the physiological limit and heritable genetic variation would be removed from the population. Characteristics with huge implications for fitness tend not to be heritable because natural selection quickly expunges the deleterious alleles. The reason that fingerprints are highly heritable is that the variation genetically is not much impacted by natural selection.

The fact that being very intelligent is not evolutionarily clearly “good” seems ridiculousness to many people who think about these things. That’s because if you think about these things, you are probably very good at thinking, and no one wants to think that what they are good at is not evolutionarily very important. The thinking man cannot comprehend that thinking is not the apotheosis of what it is to be a man (similarly, the thinking religious man sometimes confuses theological rumination with the heights of spirituality; reality is that man does not know god through analysis, man experiences god).

So let’s talk about another quantitative trait which is even more heritable than intelligence, and easier to measure: height. In most societies males, in particular, seem to be more attractive to females if they are taller. As a male who is a bit shorter than the American average, it is obvious that there is some penalty to this in social and potentially reproductive contexts. And yet there is normal variation in height, and some populations seem to be genetically smaller than others, such as the Pygmy peoples of the Congo rainforest. Why?

Though being a tall male seems in most circumstances to be better in terms of physical attractiveness than being a short male, circumstances vary, and being too tall increases one’s mortality and morbidity. Being larger is calorically expensive. Large people need to eat more because they have larger muscles. Selection for smaller size in many marginalized rainforest populations is indicative of the fact that in such calorically challenging environments (humans in rainforests have to work hard to obtain enough calories in a hunter-gatherer context), the fitness gain due to intrasexual competition is balanced by reduced fitness during times of ecological stress as well as individual correlated responses (very large males die more often than smaller males).

Additionally, for height I mentioned the sexual component: there does not seem to be a necessary association with higher reproductive fitness with being a tall woman. Though this is subject to taste and fashion, there is likely some antagonistic selection across the two sexes at work, where tall men are the fathers of taller daughters, whose reproductive fitness may actually be lower than smaller women. And vice versa, as short men may produce more fit short daughters (though again, this depends on ecological context and cultural preconditions).

Being very large impacts fitness through the genetic correlation of size with other characteristics. Very large males are subject to higher risk for sudden tears in their lungs, or suboptimal cardiac function. Humans select chickens to be very large in the breast for food, but these chickens can barely walk, and may not be able to reproduce without assistance. Evolution in a quantitative genetic sense may then be all about trade-offs.

So let’s go back to intelligence. What could be the trade-offs? First, there are now results presented at conferences that very high general intelligence may exhibit a correlation with some mental pathologies. Though unpublished, this aligns with some prior intuitions. Additionally, there is the issue where on some characteristics being “species-typical” increases reproductive fitness (an average size nose), while in other characteristics being at an extreme is more attractive (very curvy women with large eyes and small chins; secondary sexual characteristics). Within intelligence, one could argue that being too deviated from the norm might make socialization and pair-bonding difficult. Here is an anecdote about the genius Von Neumann:

Neumann married twice. He married Mariette Kövesi in 1930. When he proposed to her, he was incapable of expressing anything beyond “You and I might be able to have some fun together, seeing as how we both like to drink.”

Apparently having a very fast analytic mind which can engage in abstraction and conceptual manipulation does not mean that one can come up with anything better than that when it came to procuring a mate. And procuring a mate is one of the only “good” things from an evolutionary perspective.

The human mind is neither universally plastic, nor it is a prefabricated set of specialized modules. It is a mix of both. We clearly have some “pre-loaded” code, such as the ability to recognize faces intuitively and rapidly (which a small proportion of the population lacks). But other competencies develop over time, co-opting neurological architecture that grew organically for other purposes. In Reading in the Brain Stanislas Dehaene recounts how the region which specializes in the ability to recognize letter shapes is a preexistent visual-spatial module, probably developed for ecological adaptation to environments where recognition of various organic and inorganic objects was of fitness relevance (obviously now tied in to regions of the brain geared toward verbal comprehension). Dehaene even seems to suggest there may be a trade-off between various cognitive capacities when comparing individuals from urban developed societies and individuals from non-literate small-scale societies.

As human societies have specialized over the last 10,000 years a small number of people who naturally were on the end of a particular distribution in abstraction-and-analysis ability began to preferentially fill exotic niches that had previously not existed. From all we can tell the ancient polymath Archimedes was a Von Neumann for his age. Archimedes seems likely to have been of aristocratic background, and part of the class of leisured intellectuals. The fact that he had such innate talent and disposition, combined with his life circumstances, was simple happenstance.

Today we live in a different age. Specialization, and the post-industrial economy, put a premium on competencies associated only with individuals on the “right tail” of the IQ distribution. Similarly, our genetic background predisposes many of us to obesity because the modern environment is “obesogenic.” The reality is that obesity was not an issue for almost all of human history, so genetic variation (often behavioral/cognitive) that is associated with obesity today was not so associated with it in the past. There could be no selection against obesity when it wasn’t a trait within the population.

Just as the modern environment is potentially “obesogenic,” it is also potentially “intelligenic.” Here’s what I’m talking about, The Science Behind Making Your Child Smarter:

The research also lends insight into why many apps and training programs aimed at raising IQ fail to produce lasting effects, says Elliot Tucker-Drob, an associate professor of psychology at the University of Texas at Austin, and co-author of the study.

Raising IQ may require the kind of sustained involvement that comes with attending school, with all the practice and challenges it entails. “It’s not like you just go in for an hour of treatment a week. It’s a real lifestyle change,” he says


To be a “nerd” is a lifestyle only possible in the modern information-rich environment. The Flynn effect is evidence that changing environments can shift the whole distribution. But just as with obesity or adult-onset diabetes risk, there is also heritable variation latent across the genome that seems to affect one’s response to the intelligenic environment.

Humans have large brains for our size. We are smarter than other primates. But evolutionary genetics today seems to be coming to the conclusion that it wasn’t a quantum jump, but gradual selection and change. Having a very low intellectual capacity was probably correlated with low fitness in the past (though small brains are calorically less greedy). But, having a very high general intelligence does not seem to have resulted in that great of a gain in social or cultural status in comparison to being of normal intelligence. In fact, if the genetic correlation is such that it’s associated with some higher risk for mental instability, it could simply be that a form of stabilization selection over time kept humans within the “normal range” because that was evolutionarily optimal. Be smart enough. But not too smart that you are weird.

And, as theorists from cultural evolution have observed, we are a “hive-mind” which leverages collective wisdom. Most of us don’t have to derive mathematical equations, we can use the formula provided to us. Though it’s useful to have a few people around who can invent statistics that the rest of us use…

Tony Joseph’s Early Indians

Filed under: ancient india,Early Indians — Razib Khan @ 1:58 am

My review of Tony Joseph’s new book, Early Indians: The Story of Our Ancestors and Where We Came From, is now up at India Today.

In general, I liked the book, and have only minor quibbles with Joseph’s reportage of the genetic results. He has very particular interpretations of results on some questions, but his core audience of Indians will be focused on this, not the minutiae of D-statistics. For example, it seems to me that he gave a great deal of emphasis to the aboriginal heritage of South Asians in quantity and impact. This is a defensible stance, but it’s not a necessary one dictated by the results from the data.

The non-genetic assertions I had less background on, and so did some literature review by following Joseph’s copious citations. In these “fuzzier” fields it is harder to establish a consensus from what I can see (the number of opinions of linguists on any topic seems to equal the number of linguists!). The downside is certain conclusions are not there yet. The upside is there is still scholarship that will be done.

Overall, get Early Indians. But read with some caution and use it as a sourcebook for follow-up queries.

Making Sense of Roman History: A Reading List

Filed under: Books,Roman History — Razib Khan @ 1:42 am

Inspired by Tanner Greer, I’ve decided to put together a list of books that I think will useful to understanding the Romans from the perspective of a non-specialist without a background in Latin, or Classics more broadly (I am in this category obviously).

First, I’m a big fan of Michael Grant’s History of Rome. Grant was a historian who wrote a great many books for the popular audience, and his History of Rome is a comprehensive survey. I’ve read it multiple times. Mary Beard’s SPQR: A History of Ancient Rome is a more contemporary take which covers a similar period. But I’m not sure it’s as useful if you have less background than Grant’s more traditional sequence.

Robin Lane Fox’s The Classical World: From Homer to Hadrian covers a lot more than Rome, but what it does cover that is Greek is essential to understanding Rome.

Adrian Goldsworthy’s The Fall of Carthage: The Punic Wars 265-146 BC is a good read on a classic topic. Goldsworthy is a military historian, and it shows. To be frank I haven’t read many treatments of the republican period, since so much of it is back-loaded to the decades before the principate. But Goldsworthy’s Caesar: Life of a Colossus illuminates this critical juncture in Roman history well enough.

There are so many nearly novel-like treatments of figures from the Second Triumvirate and the Julio-Claudians that I’m not going with anything conventional: try Agrippina: Sex, Power, and Politics in the Early Empire. Colin Wells’ The Roman Empire focuses on the imperial peight up until the middle of the 3rd century. If you’ve read the survey above then you know why Gwyn Morgan’s 69 A.D.: Year of Four Emperors is important to read.

I think biography is a pretty good way to get a sense of particular periods. With that in mind, Frank McLynn’s Marcus Aurelius: A Life and David Potter’s Constantine the Emperor are useful, if a bit plodding and overmuch for the casual student.

The Fall of Rome: And the End of Civilization, The Fate of Rome: Climate, Disease, and the End of an Empire, and The Fall of the Roman Empire: A New History of Rome and the Barbarians are all critical contemporary analyses of the end the Roman polity. Written from an archaeological, environmental scientific, and narrative historical angles, they give different viewpoints on the same questions. These are all more or less responses to the sort of work written by Peter Brown a generation earlier, The Rise of Western Christendom: Triumph and Diversity, A.D. 200-1000, which argues against the idea of the fall. From a different perspective (the barbarian), The End of Empire: Attila the Hun & the Fall of Rome, though to be frank this book is as much about Aetius as it is about Attila.

Life and Leisure in Ancient Rome is one of the many books on the topic of “daily life” during this period and place. You should read at least one of these. I’m not a humanist in Tanner’s league, so you won’t get poetry recommendations from me, but Aupelius’ The Golden Ass is the only complete surviving Latin novel. It’s rather weird. You surely know the list of eminences of the Latin poets, but Ovid’s Metamorphoses induced less labor than Virgil’s Aeneid. I recall thinking Virgil was a bit too “try hard.” Unlike The Fall of Rome: And the End of Civilization and History of Rome, both of which I’ve read more than half a dozen times front to back, with literature I usually read once, and don’t retain too much. I’m a Philistine!

Rome and China: Comparative Perspectives on Ancient World Empires and Rome and Jerusalem: The Clash of Ancient Civilizations are interesting comparative analyses. If you had to pick the two, I’d go with the first, but that’s because purely intellectual histories are not as interesting to me.

Historical fiction isn’t always accurate, but it really brings the dramatis personae alive. Colleen McCoullough’s First Man in Rome series is excellent, especially the first few novels. Everyone knows Robert Graves’ I, Claudius. But my teenage-self really enjoyed Allan Massie’s Let the Emperor Speak, about Augustus, and Tiberius: The Memoirs of the Emperor. Gore Vidal’s Julian: A Novel is well written and engaging, though a little light on history (not surprisingly there is a lot of editorializing by Vidal through Julian).

You have in some way read the works of Seutonius,Tacitus, and Livy because they are the foundation for so much of the narrative works written today. They are also the source material for fiction and dramatizations. If you want to “go back to the sources”, give Ammianus Marcellinus a try. He’s overlooked, and he’s excellent.

Rodney Stark wrote The Rise of Christianity: How the Obscure, Marginal Jesus Movement Became the Dominant Religious Force in the Western World in a Few Centuries back when he was a scholar and not a polemicist. I’m skeptical of some of his conclusions, but his thinking here is rigorous.Robin Lane Fox’s Pagans and Christians is complementary to The Rise of Christianity. Finally, Michelle Salzman’s The Making of a Christian Aristocracy: Social and Religious Change in the Western Roman Empire is worth a deep read.

Some of the New Testament is interesting too. I especially think that the material attributed to St. Paul, a Roman citizen, is worth reading.

And finally, St. Augustine is worth a read. City of God is interminably long, but Confessions is more compact, and the beginning of a whole genre which eventually culminated in James Frey.

December 28, 2018

Open Thread, 12/28/2018

Filed under: Open Thread — Razib Khan @ 5:49 pm

Last open thread of the year. Been busy with life obviously. Won’t be posting this on Sunday as usual, but just making up for missing the pre-Christmas weekend.

Battling the Gods: Atheism in the Ancient World is an interesting book because it’s more about the nature of religion in the ancient world than unbelief. Much of the text is preoccupied with the transition that occurred with Christianity’s dominance in the West. Probably good to pair with The Rise of Western Christendom: Triumph and Diversity, A.D. 200-1000.

No Invasion Or Migration, But Interaction: What This New Genetic Study Suggests About Prehistoric India. I heard the usage of the word “interaction” was being pushed by some Indian researchers as early as a year ago. It’s less provocative than the term “invasion” and perhaps even “migration.” But a word is a word. Science is not mathematics or religion, where terminology is substance.

The piece linked here puts an incorrect gloss on the research it’s reporting on in my opinion. It is highly likely that about 50% of the ancestral contribution to the population of the Indian subcontinent today was not resident within the Indian subcontinent before 10,000 years ago. We’ll see as more ancient DNA comes out.

The first Indians. An extract from a new book to be published in India. I have a review written for India Today (not online yet). To my surprise, it’s already selling on Amazon, Early Indians : The Story of Our Ancestors and Where We Came From. As per the subhead, it is clearly geared toward a subcontinental audience.

Polygenic risk scores: a biased prediction?

Polygenic adaptation to an environmental shift: temporal dynamics of variation under Gaussian stabilizing selection and additive effects on a single trait.

Genomic Prediction of Complex Disease Risk.

Analysis of 100 high coverage genomes from a pedigreed captive baboon colony.

Most retweeted social science in 2018.

Five Amazing Things We Learned About History From Ancient DNA In 2018.

Inside Facebook’s Secret Rulebook for Global Political Speech. This has been reported before. But it’s finally entering the mainstream because I think the mainstream realizes that there is no longer any mainstream that’s controllable by the Western establishment. In the 1990s some non-Western governments, such as Saudi Arabia, made the argument for enforcing much stricter censorship on the internet. Instead, American standards generally won out, though there were attempts to create regional gardens. Ironically (or not), it is a private American corporation which is enforcing the “lowest common denominator” non-offensive speech, albeit haphazardly and capriciously.

1) Some anti-war conservatives were observing issues with how we recruit our military back in the 2000s when neocon adventures were at high tide. These are the type of people who might know the implications of the Marian reforms in recruitment in the late Republic, and how it empowered generals. Not sure Matt Yglesias is part of that set, though perhaps I’m wrong.

2) Most “centrist” types are usually anti-“identity politics” liberals or moderates who “come from the Left.” That’s why the issues in academia loom large and those in the military don’t. They don’t know many people in the military, just like much of the intelligentsia.

3) The Left dominates the academy, while the Right is the conventional orientation of the American officer corps. Social liberals are probably somewhat more intelligent and intellectual than social conservatives. Social conservatives are probably somewhat more courageous and patriotic than social liberals. But the difference is not enough to account for the disproportionate representation across the professional groups. This is probably a matter of self-selection and sorting.

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.

One of the reasons that Scholars Stage is one of the few blogs I still read, Making Sense of Chinese History: A Reading List. Will second Imperial China.

In case you missed it, Tanner was a guest on this week’s BrownCast, the Brown Pundits podcast.

As for my other podcast, The Insight, very proud that we closed 2018 with 44 episodes total now! That’s not quite one a week, but it’s not that far off.

Amy Harmon of the NYT on Race & Genetics, Women in Science. If you enjoy listening to white liberals talk about racism and science. Since all white people are “racist” I guess it makes sense to have experts weigh in. They certainly are never shy about explaining racism to me.

David Frum mentioned offhand that in 2019 he is thinking about doing YouTube commentary on books, etc. My response is simple: in terms of data density, it’s written >>> audio > video (with obvious audio). But in terms of the nominal number of people you read, it’s probably flipped. I have experience with all formats for what it’s worth.

Also, reflecting on my life and how I allocate time…and if whatever I’m doing here is “worth it to me,” I do want to give readers a heads up that I’m wondering about ways I can increase remuneration from this weblog beyond the trivial (e.g., some sort of gating for readers who follow me regularly).

Finally, this current domain has been active again for about a year now. Here are the top 10 posts of 2018:

Why The Chinese Don’t Buy Deodorant
Intercourse and Intelligence
Making What Harvard Is About Transparent
The Maturation Of The South Asian Genetic Landscape
Traits of men who prefer breasts, booty, or legs
Elizabeth Warren Carries Native American DNA
The Great Genetic Map And History Of China
The Origin Of The Ashkenazi Jews In Early Medieval Europe
The Genome Of “Cheddar Man” Is About To Be Published
White People Are Not Gods, They Bleed

December 24, 2018

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:47 pm

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

December 23, 2018

Drivers of selection for ghosts in the genome

Filed under: Archaic admixture,Evolutionary Genetics — Razib Khan @ 12:44 am

A new preprint on bioRxiv, Strong selective sweeps before 45,000BP displaced archaic admixture across the human X chromosome, is suggestive of an exciting new phase in human evolutionary genomics. Basically, leveraging whole-genomes in diverse populations to explore selection dynamics.

The authors looked at X chromosomes in males for reasons of technical tractability. Human males carry a single X chromosome, so it’s easy to determine the sequence of genetic variants across a physical stretch of DNA (females, with two X chromosomes, require phasing). The X is interesting for two other reasons: it is present in females about 2/3 of the time (because they have two copies), and, is subject to really strong selection in males 1/3 of the time. Basically, males exhibit no recessive dynamics on the X chromosome because we carry only one. This means that genetic variants which are “recessive” in their expression to selection in females are expressed in males.

The fact that the X is disproportionately found in females also means that all sorts of intra-genomic conflict driven by sex occur on this chromosome. You will know this if you read Matt Ridley’s excellent The Red Queen.

The specific result here is that the authors found a common family of haplotypes in males on the X chromosome outside of Africa whose homogeneity is indicative of a very strong sweep. From the text:

The identified selective sweeps are as strong or even stronger than the most dramatic sweeps previously found in humans. Ten sweeps span between 500kb and 1.8Mb in more than 50% of non-Africans (Table S2). The strongest sweep span 900kb in 91% of non-Africans and affects 53% of non-Africans across a 1.8Mb region. For comparison, the strongest sweep previously reported surrounds the lactase gene and spans 800kb in 77% of European Americans (24). The selection coefficient on the genetic variant driving this sweep was estimated to 0.15 (24) suggesting even stronger selection for several of the X chromosome sweeps we have identified.

The swept regions we identify here may be recurrent targets of strong selection during human evolution. To investigate this possibility, we intersect our findings with our previously reported evidence of selective sweeps in the human-chimpanzee ancestor (16).We find a strong overlap between the sweeps reported here and regions swept during the 2-4 my that separated the human-chimpanzee and human-gorilla speciation events (17, 25) shown as grey regions in Figure 2 (Jaccard stat.: 0.17, p-value: <1e-5) (Materials and Methods). This suggests that the identified regions of the X chromosome are continually subjected to extreme positive selection.

A selection coefficient of 0.15 is eye-popping. Selection coefficients of 0.01 are reasonable. For humans, anything in the 0.10 range is more like a weird artifact than a true result. But here it is. The fact that the regions overlap with earlier targets of selection during the speciation event that led up to our lineage is clearly of interest.

Looking more closely at the regions of the X which was subject to the selection, they found almost no archaic ancestry. That is, the ~1% Neanderthal ancestry that is expected across the X chromosome is almost absent in these segments derived from the selection event. The inference is made that perhaps then these sweeps occurred due to introgression from a sister modern human lineage, perhaps an earlier wave out of Africa which never mixed with Neanderthals. The archaeology is compelling now that these people existed, and there are tentative suggestions from genomics which attests to their presence as well (e.g., modern human admixture into the Altai Neanderthals).

Looking at the 45,000-year-old Siberian genome the authors found the same signatures that they see in other non-Africans. This means the event had to happen between 55 and 45 thousand years ago, after the Neanderthal admixture (which is found all around these zones in the genome), but before geographical diversification and expansion of the modern human lineage.

The authors conclude:

We hypothesize that our observations are due to meiotic drive in the form of an inter-chromosomal conflict between the X and the Y chromosomes for transmission to the next generation. If an averagely even transmission in meiosis is maintained by a dynamic equilibrium of antagonizing drivers on X and Y, it is possible that the main bottlenecked out-of-Africa population was invaded by drivers retained in earlier out-of-Africa populations. If this hypothesis is true, the swept regions represent the only remaining haplotypes from such early populations not admixed with Neanderthals.

Meiotic drive is a segregation distorter. A form of intra-genomic selection which is potentially very powerful. Some hypothesize that alleles normally subject to meiotic drive sweep through the population so fast that researchers underestimate the phenomenon’s ubiquity because they haven’t caught sweeps in action.

This strange evolutionary genetic process then may have preserved a genetic relic within the human genome. But on Twitter Iosif Lazaridis suggests that perhaps the donor population were “Basal Eurasians,” and all non-Africans may have some Basal Eurasian ancestry, with Near Easterners exhibiting more than baseline ancestry (presumably through later admixture).

December 22, 2018

Brown Pundits – Episode 6, Chinese history, pop culture and strategy, with Tanner Greer

Filed under: Podcast — Razib Khan @ 11:21 pm
The latest BP Podcast is up. You can listen on Libsyn, iTunes and Stitcher. Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe at one of the links above. Thanks to everyone who reviewed the podcast! Please leave more 5-star reviews. If this podcasts interests enough people I’ll be getting us on other platforms. This week a very special episode of Brown Pundits’ BrownCast with Tanner Greer of The Scholar’s Stage, one of my favorite weblogs. If I’m a philosopher in the armchair, Tanner is a practitioner in the field. He lived for several years in China, and his observations have a contemporary salience that our discussion last week probably lacked.

December 21, 2018

Pathans between Hind and Iran

Filed under: Genetics — Razib Khan @ 2:47 pm

There was a comment below on the positions of Pathans genetically in relation to South Asians and Iranians. The “Pathan” samples are from Pakistan, while “Pashtun” are from Afghanistan. What you can see is that the “Pathan” samples are more like Punjabis, while Pashtuns are like Tajiks. The Iranian samples are from western Iran. You can see that the Pakistani Pathans are definitely a little closer to UP Brahmins than to Iranians. The Afghans are a bit closer to Iranians than UP Brahmins.

Here’s Treemix:

With 4 migrations:

With 6 migrations:

The power of the nameless

Filed under: Hinduism — Razib Khan @ 11:56 am

From the Wikipedia entry for Angkor Wat

The initial design and construction of the temple took place in the first half of the 12th century, during the reign of Suryavarman II (ruled 1113 – c. 1150). Dedicated to Vishnu, it was built as the king’s state temple and capital city. As neither the foundation stela nor any contemporary inscriptions referring to the temple have been found, its original name is unknown, but it may have been known as “Varah Vishnu-lok” after the presiding deity.

And more:

Cambodia was first influenced by Hinduism during the beginning of the Kingdom of Funan. Hinduism was one of the Khmer Empire‘s official religions. Cambodia is the home of the holy temple of Angkor Wat, the largest Hindu temple in the world. The main religion adhered in Khmer kingdom was Hinduism, followed by Buddhism in popularity. Initially the kingdom revered Hinduism as the main state religion. Vishnu and Shiva were the most revered deities, worshipped in Khmer Hindu temples….

Cham Hindus, an ethnic group in Vietnam influenced by Indic culture 1,000 years ago, are still Hindu to this day. Similarly, the people of the Indonesian island of Bali maintain continuity with the Hindu traditions of Java.

Now, consider this comment from the usual suspect:

Professor Truschke is also correct in stating that “Hinduism” is in many ways a constructed category. It was the British who used it as an umbrella term in the census for anyone who didn’t declare their religion to be something that the colonial power recognized (like Islam). Previously, people may have described themselves as worshipping a particular god.

It is curious that this person who protests for the honor of the Islamic religion casually asserts that the Hindu religion was created as a category by the British! While his religion taps at deep truths and must be respected, he can dismiss the faith of 800 million as a British fiction. The glamor of fashionable nonsense never ceases to attract this one like a moth to the flame.*

In any case, where have I heard this before? From the Wikipedia entry on caste:

There are at least two perspectives for the origins of the caste system in ancient and medieval India, which focus on either ideological factors or on socio-economic factors….

This school has focused on the historical evidence from ancient and medieval society in India, during the Muslim rule between the 12th and 18th centuries, and the policies of colonial British rule from 18th century to the mid-20th century….

This view, which emphasizes the colonial experience, is encapsulated by Nicholas Dirks’ Castes of Mind. A debased form of this is that “well acktchually…did you know the British invented caste?”

The genetic reality has falsified this. Evidence from places such as Andhra Pradesh indicates that the endogamy which is the hallmark of caste/jati dates back to 1,500 to 2,000 years ago. This is not to deny that the category and its organization was not influenced by the British, and likely earlier the Muslims, but its ultimate basis seems to be one which is deeply rooted in South Asia.

Now consider this map:

1941 British religious census, 75% of India is non-Muslim

After many centuries of rule by a religiously Muslim elite, the majority of Indians still retained a non-Muslim identity. The legacy and prestige of Islamicate conquest-elites were such that the 1857 rebellion against the British co-opted a Mughal as a figurehead, so persistent was their glamor. And yet the majority of Indians still cohered around an identity that was called “Hindu,” originally a term for Indian.

Without any knowledge of the puranas, or the elaboration of the Vedanta centuries before Islam became a permanent feature of the South Asian landscape, the fact that most Indians remained non-Muslim after centuries of Islamic rule indicates that there was a systematic social-religious system to which they adhered. The fact that they exported this social-religious system in fragments and essentials to Southeast Asia over 1,000 years ago indicates that Hinduism as we understand it was not simply a British reification!

It is sometimes common among people who follow the Abrahamic religions to classify Hinduism as “pagan.” Though theologically there is some justification for this, to be frank, this is more an aspersion than a description, bracketing Indian traditions with small-scale primal religions which were prevalent outside of Eurasian oikoumene.

Ethnographic evidence indicates that much of “Islamic Africa” was minimally Islamicized until the 20th century. Rather, local elites patronized ulema, whose remit was sharply delimited. It was modern transportation and public health that allowed for greater central integration across regions such as the Senegal. Sufi orders, in fact, benefited from European colonization in many regions of Africa because the only “high religion” tradition that was available locally was Islam, and so many heretofore pagan or nominally Muslim tribes were assimilated into the high culture matrix that was nearest to them.

The contrast with Dharmic and Chinese paganism is instructive. Only in areas where the local “high religion” tradition was moribund (e.g., Korea) or nascent (what became the Philippines) did Christianity gain widespread purchase. In the “pagan” hinterlands of the Indonesian archipelago Muslims and Christians, and later a modified form of Hinduism, gained mass conversions from peoples previously untouched by central governance.

Persistence of native Dharmic religious traditions despite Muslim cultural prominence is strong indirect evidence of a resilient high religious tradition despite debates as to its name.

Related post: Hinduism before India.

* The same person dismisses revisionism about 7th century Islam, which he takes to be authoritatively historical, while accepting at face value the idea that Hindus had no self-conception as a coherent identity before 1800.

Hinduism before India

Filed under: History,India,Nationalism — Razib Khan @ 2:25 am

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

All your GWAS belong to us

Filed under: genome-wide association,GWAS — Razib Khan @ 12:30 am

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

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

December 19, 2018

The Insight Show Notes — Season 2, Episode 10: 2018 in genomics

Filed under: Genomics,science — Razib Khan @ 10:34 pm

The Insight Show Notes — Season 2, Episode 10: 2018 in genomics

This week we reviewed the “big stories” in 2018 in genomics. There were a lot of possibilities, but we narrowed down the list.

First, we discussed Neanderthal art. And, it’s ramifications for the “Great Leap Forward” in behavioral modernity.

The second story involves the post-Roman barbarian migrations. With the relative cheapness of ancient DNA techniques, researchers are expanding the purview of their topics to more recent periods, in particular domains where written and archaeological evidence are not clear.

Next, we talked about the sequencing of an F1 of a Denisovan male and a Neanderthal female. That is, this individual had a mother from one group of humans, Neanderthals, and a father, from another, a Denisovan. The probability of discovering such an individual seems low, and they researchers stumbled upon this! No one like this is present today. But was it different in the past?

The fourth story was the discovery of the Golden State Killer through DNA pedigree analysis. Serial killers beware!

Then we discussed the polygenic risk score of educational attainment. With more than 1 million samples, 2018 saw the next step in the intersection of genetics and traits.

Citation: Khan, Razib, and David Mittelman. “Consumer genomics will change your life, whether you get tested or not.” Genome biology 19.1 (2018): 120.

2018 was the year that the consumer genomics went mainstream, with more than 20 million customers. The sector has finally broken out of nerd culture into pop culture.

It was also the year that DNA came to politics, as Elizabeth Warren released genetic results that indicated some amount of Native American ancestry.

Finally, the year in DNA ended with the “CRISPR babies” story.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

The Insight Show Notes — Season 2, Episode 10: 2018 in genomics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

December 18, 2018

A return of the gods

Filed under: Epistemology — Razib Khan @ 2:02 am

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

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

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

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

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

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

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

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

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

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

The year personal genomics got personal

Filed under: Genetics,Genomics,Technology — Razib Khan @ 1:12 am

The data for the above chart was assembled from press reports of various personal genomic companies with a public profile. So the values act as lower bounds. Additionally, the total numbers are from a comment in Genome Biology that I coauthored in the middle of 2018. Since then many more millions of people have been genotyped.

When Spencer Wells began The Genographic Project in 2005, genetic genealogy was an obscure and niche product. Today, consumer genomics has become a meme. Between January 1st of 2016 and January 1st of 2019, the total number of individuals who have purchased genotyping array kits increased 10-fold! From 2.5 million to closer to 25 million. An extrapolation would give a figure of 250 million individuals genotyped by January 1st of 2021.

This is at the root a story of science and technology. In 2005 it was rare for researchers to have access to the data of individuals who had tens of thousands of markers typed. By 2015 millions of Americans had purchased genotype arrays tested on themselves with hundreds of thousands of markers. From barely in the ivory tower, to the mass market. It has now become a business and cultural story. As 2018 ends the consumer genomics industry is now maturing, and expanding outward into the broader culture, as families now talk about their ancestry testing results over the holidays.

What does 2019 have in store? It is not implausible to imagine that the 50 million marks will be surpassed. At that point what was once a tool of the hobbyists will have left its stamp on the mainstream, and the public will begin to dictate what the “killer apps” of the sector are going to be.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

The year personal genomics got personal was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

December 17, 2018

Donald Knuth in the Galactic Library!

Filed under: Donald Knuth,Future,History — Razib Khan @ 4:57 pm

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

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

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

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

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

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

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

Open Thread, 12/16/2018

Filed under: Open Thread — Razib Khan @ 1:10 am

DNAGeeks is doing the last holiday push.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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