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

May 20, 2018

Open Thread, 5/20/2018

Filed under: Open Thread — Razib Khan @ 3:40 pm

Warren Treadgold’s The University We Need: Reforming American Higher Education is going to come out in early July, but I’ve written my review. Don’t know when NRO will post it. In general, I’m positive. Though Treadgold has some ideological issues with Leftism in the academy, much of the book is apolitical and shines the light structural problems with contemporary academia.

It’s not a secret that I’m a fan of the author’s earlier work, A History of the Byzantine State and Society. So I checked some of the footnotes in The University We Need, and it turns out he’s a skeptic about the accolades given to Chris Wickham’s Framing the Early Middle Ages. Myself, I think both of these huge books are worth reading.

Bernard Lewis has died. He gets a lot of bad press from people like Edward Said of Orientalism fame, and over the last 20 years has become inextricably connected to neoconservatives who cheered on our nation’s foreign adventures. But a lot of his work is pretty interesting, especially the earlier stuff. I like The Middle East: A Brief History of the Last 2,000 Years.

On The Number Of Siblings And p-th Cousins In A Large Population Sample. I can’t say I follow all the mathematical details but jump to equation 7. But this preprint heavily informs Edge & Coop’s How lucky was the genetic investigation in the Golden State Killer case?

The Coming Wave of Murders Solved by Genealogy. The horse has left the barn and the great rush is on. Ultimatley this all going to be a normal part of forensic work soon enough.

I’m not sure that there’s a single fact yet in The Rise and Fall of American Growth: The U.S. Standard of Living since the Civil War that’s surprised me. Is this because so much of this stuff has now percolated across our culture (e.g., the increased demand for horses in the late 19th century due to complementarity with railroads).

That being said there is a lot of specific detail that’s of interest. For example, the proportion of households with telephones during the Great Depression dropped, but those with radios kept increasing as a fraction of the American populace. The reason is that telephones were rented and required recurrent payments, which many families could no longer afford, while radios were purchased once, after which usage was free.

I don’t know much about Jordan Peterson. Curiously the people who talk to me about him the most are moderate liberals who are annoyed about the demonization of him by the further Left. I don’t have much to say, except it’s shocking how many patrons he has, and, the Left-media attacks on him probably are making him more popular.

Men are far more dangerous than women:

Problematic anti-Semitism bill passes in South Carolina:

The Act, which if not challenged in court and struck down as unconstitutional, will require South Carolina’s public institutions of higher education to “take into consideration the [State Department’s] definition of anti-Semitism for purposes of determining whether the alleged practice was motivated by anti-Semitic intent” when “investigating, or deciding whether there has been a violation of a college or university policy prohibiting discriminatory practices on the basis of religion.”

Heavy-handed suppression of anti-Semitism on campus is going to lead to more, not less, anti-Semitism. You know why.

Genetic analysis of Sephardic ancestry in the Iberian Peninsula.

Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles.

A New Way for DTC? Nathan Pearson, Root Deep Insight.

Was Kevin Cooper
Framed for Murder?

Farmers, tourists, and cattle threaten to wipe out some of the world’s last hunter-gatherers.

May 13, 2018

Open Thread, 05/13/2018

Filed under: Open Thread — Razib Khan @ 9:23 pm

The University We Need: Reforming American Higher Education is a funny book. The author, Warren Treadgold, is someone I know from his magisterial A History of the Byzantine State and Society. One of the complaints about A History of the Byzantine State and Society is that it’s too dry and academic. The University We Need is not dry at all, unless you are referring to the mordant wit on display.

Since I’ll be reviewing The University We Need for NRO I won’t say much more than that, except that Treadgold is most definitely in a “gives no fucks” mood. Yes, he attacks administrators as you’d expect, but he also slams Hillsdale, the professoriate, and students. He also has opinions about cafeteria food!

Italy’s 5 Star, League Reach Deal to Govern Nation. This sort of Left-Right hybrid to me illustrates that we’re in a “crisis of capitalism,” or more precisely a crisis of Western civilization. Italian total fertility rate is ~1.40. The rest is commentary.

Localizing and classifying adaptive targets with trend filtered regression. In Who We Are David Reich talks about his ambition to create a sort of encyclopedia of human genomic history. But once that history is established, we’ll need to move on to understanding selection. This preprint looks like it will be important.

23andMe Hits Ancestry.com With Patent Suit Over DNA Kit. One thing they are doing is suing over notifying about identity-by-descent. The “non-obvious” reason for awarding the patent is apparently the notification.

Intellectual property is a joke. But it’s also big business.

This week on the podcast we talked about the grandmother hypothesis with Kristen Hawkes. I should have been more aggressive in jumping in to get her to clarify what “life history theory” was. Live and learn.

We are now at 20 podcasts. If you can, please subscribe with iTunes or Stitcher. Also rate us highly and leave positive views if you can!

Carl Zimmer’s podcast has been recorded already, but won’t be dropped until close to when She Has Her Mother’s Laugh is published. We’re also recording a podcast with Patrick Wyman of Tides of History. This should be “evergreen”, at least on the scale of a year, so expect that in June or later.

The next few weeks we’re going to go it alone with just Spencer and myself, talking about a few topics we’re both interested in. It’s a good change of pace. We’ve got some ideas for what we’re going to talk about in June. I think it is most definitely important to follow-up on the Indo-Aryan podcast, which we actually recorded in July of 2017, though we didn’t drop it until 2018.

There was an interesting fiasco on Twitter recently where some semi-prominent people asserted that Andrew Sullivan was against gay marriage. This is really bizarre because Sullivan was a major proponent of the idea before it was ever mainstream, and for a period also got resistance from the more radical anti-bourgeois faction of the gay rights movement.

Anyway, the mistaken tweets occurred because Sullivan is transforming into a hate-figure on the Far Left, and a lot of people are Twitter are stupid and ignorant, so they just inferred facts from their theory that Sullivan is right-wing. Some of these people retracted the falsehood grudgingly but as usual you can see that retweets and likes are/were more evident on the original tweet.

The point is repeating all this is this is how “knowledge” is created now. If you have a prominent Twitter account it’s trivial to inject falsehoods into the debate. I’ve seen people doing this pretty consciously several time (this is really common in anonymous/pseudo accounts).

At the Brown Pundits weblog, I put up a post on this strange Slate piece on how the 1990s TV show Friends is contributing to sexism and homophobia in India. Though ostensibly about India, and narrated by an immigrant from India, the piece is about preoccupation within American culture in 2018.

A publication like Slate is going to get a lot of clicks if they post something about misogyny and homophobia in Friends, but how to make it novel? Pretend it’s actually about India! To me, this is to journalism to science fantasy is to science fiction.

Societies and cultures in relative decline and undergoing stagnation tend to undergo a period of involution. Narcissism writ-large.

I also wrote a post on Brown Pundits on why India did not become mostly Muslim. Need to think a lot more on this. Not all the comments were dumb.

Reading the coalescent chapter in Molecular Population Genetics, and it’s amusing to note that the coalscent’s big advantage over forward-simulations in terms of computational horsepower needed isn’t really that big of a deal today. Even a few years back this was a huge issue. This is like in phylogenetics where everyone runs Bayesian stuff, where 15 years ago people were having a hard time imaging max-likelihood!

While reading Molecular Population Genetics I keep hearing the author’s voice in my head. I think this has to do with the fact that I know the author before I read his books. This didn’t happen when I read She Has Her Mother’s Laugh because I had read Carl Zimmer before I got to know Carl in person. At least that’s my theory (The 10,000 Year Explosion was all in Greg Cochran’s voice).

Reading too much about Rome. So Carthage Must Be Destroyed is in the stack.

A systematic assessment of ‘Axial Age’ proposals using global comparative historical evidence. The argument here is that the “Axial Age” wasn’t a singular time period, but a continous event that spanned thousands of years. I think this is probably right, though “ages” are conceptually useful mental bookkeeping. This is similar to the idea that age cohorts are a real thing, but generations are not.

The Infectious Enthusiasm of Breaking the Bee.

Detection of shared balancing selection in the absence of trans-species polymorphism.

Self domestication and the evolution of language.

I need to set aside a day to catch up on the South Asian Genotype Project (SAGP). Also, figure out which plugin is causing the 500 errors.

May 7, 2018

Open Thread, 5/07/2018

Filed under: Open Thread — Razib Khan @ 11:29 pm

Longtime readers are well aware that A History of the Byzantine State and Society is one of my favorite books. To understand the Middle East right before the arrival of the Mongols and the emergence of the Crusader states, one has to understand the expansion of Byzantium in the early 11th century, and it’s subsequent regression in the late 11th and 12th centuries. In 2005 I actually did a 10 questions with the author, Warren Treadgold.

So I’m very excited to be reviewing his new book, The University We Need: Reforming American Higher Education, for NRO.

Had a chance to read Matt Hahn’s Molecular Population Genetics. The con is that it’s an $80 book that’s 350 pages. This is not a replacement for Principles of Population Genetics or Introduction to Quantitative Genetics. Rather, as alluded to by the title there’s a lot of focus on molecular evolutionary and population genetics. Imagine a population genetics book written with an assumption that you know what a SNP-chip is and have access to genome-wide sequence data. In some ways, it’s similar to Rasmus Nielsen’s (and Slatkin) An Introduction to Population Genetics. But these books reflect the authors.

For example, if you look up “site frequency spectrum” in An Introduction to Population Genetics there are seven pages. In Molecular Population Genetics there is one page on this topic. Anyone familiar with the work of these researchers would totally expect this. If you are a pop-gen nerd, there’s really no debate. You need to get Molecular Population Genetics or steal it from a friend. But a bigger question is why I recommend seemingly esoteric books to my readers. I say seemingly because understanding the population genetics in the generality makes a lot of the detailed more specifically interesting stuff much more comprehensible.

The readership of this weblog is small but self-selected. If you consider yourself an intellectual person and have some disposable income and leisure you should be developing yourself in various ways outside of the professional sense.  If you are reading this weblog you are likely to be the type of person who wants to understand things not just because one gets paid to understand things, but because understanding things is an end unto itself.

I am privileged to be paid to explore various topics related to certain intellectual interests (human population genomics), but I believe that something would be seriously wrong with me if I limited my inquiries to this narrow topic. Therefore I read a fair amount of history, and take an interest in topics like cognitive science and Biblical scholarship. Part of my attempt on this weblog to is to add population genetics to the list of interests of people who are professionally not engaged with the topic, whether they be in closely related fields (e.g., a theoretical ecologist) or in a totally different line of work (union organizer).

The Neutral Theory in Light of Natural Selection. This review is free. One of the great things about this is that it kind of revived a corner of science Twitter which had started to go into senescence (Patrick Phillips has been at the center of several of these discussions).

Related to our podcast topic from this week, Doc Edge and Graham Coop have read the definitive formal take, How lucky was the genetic investigation in the Golden State Killer case? The TL;DR version is not that lucky. They show formally that with a database of ~1 million individuals with SNP-data it’s likely that you’ll get relative matches that might be useful. More precisely, a database of ~1 million means that there is a ~90% chance of at least one 3rd cousin match. There’s even a 25% chance of a 2nd cousin match! A database of ~5 million gives a 75% chance of a 2nd cousin match, and ~10 million gives a 90% chance of a 2nd cousin match. These are around the range of the databases of 23andMe and Ancestry right now.

As the authors say: “it’s a question of deciding the circumstances under which we as a society want these familial searches to be used.”

Tales of Human Migration, Admixture, and Selection in Africa.

The evolutionary history of human populations in Europe. Preprint by Iosif Lazaridis.

There is a certain number of traditional liberals with a libertarian bent who I’ve always admired. Nadine Strossen is one of those (Wendy Kaminer is another). Strossen is out with a new book, HATE: Why We Should Resist It with Free Speech, Not Censorship (Inalienable Rights). It strikes me this is conservative in the literal sense in that she is attempting to defend a late 20th-century liberalism which is now on the wane.

The Liberal Media Can Have Ideological Diversity Without Conservatives. Two sections jump out at me. First, “the social conservative’s view on fetal personhood is unfalsifiable — and does boast a significant constituency — but it doesn’t generally lend itself to novel or engaging debates.” The issue with abortion is not about debating, as much as it is important to not always put forward writers who implicitly assume that the pro-choice position is the only view that one might entertain. I’m skeptical of some of the leaps that pro-life writers make based on their political position…but then, I’m not pro-life. It’s important to at least know the views of other people.

Second, the author suggests that Left-wing socialists who believe that the people should control the means of production (as opposed to simply redistributive socialism as is the case in Scandinavia) should be given a fair hearing, though they observe “concentrating financial power in the state apparatus has often been an invitation to tyranny.” Yeah. That.

Pretty straightforward establishment liberals, such as Matt Yglesias, are starting to assert that publications like The Atlantic and The New York Times are equivalent to National Review, in their ideological valence (the argument being that they shouldn’t have to hire conservatives since they’re liberal publications). Conservative critics have long asserted this, but now liberals are agreeing.

Conservatives have lost the universities and the press. Both these institutions don’t even make a pretense at evenhandedness at this point. The broadly liberal center is eroding. I suspect that people like Nadine Strossen will be viewed in the future like Cato the Younger.

Stuff You Missed in History Class podcast, Mohenjo Daro. People don’t really know much.

Interviewing Carl Zimmer for the podcast this week. Taking suggestions for questions to ask him (we have a finite time so might not get it in….)


April 29, 2018

Open Thread, 04/29/2018

Filed under: Open Thread — Razib Khan @ 10:05 pm

One of the strange things about getting old is that your friends start to become kind of a big deal. Matthew Hahn has a new book out, Molecular Population Genetics. If there is one single reason I keep blogging, it’s to get awareness of the field of population genetics to spread beyond the small circle who are “in the know.” I joked on Twitter that buying this textbook is like spending money to talk to Matt about pop-gen, and that’s surely worth it.

Another one for the stack!

Speaking of worth it, Kyle Harper’s The Fate of Rome: Climate, Disease, and the End of an Empire is definitely worth a read. Not done, and I’m not sure it’s better than The Fall of Rome: And the End of Civilization. Perhaps my issue is that exogenous shocks are to be expected in my view of the world. Though the details in The Fate of Rome are novel, the general thesis and framework were what I’d assumed were taken for granted.

What Happens When Geneticists Talk Sloppily About Race. I don’t think that David Reich was sloppy…though the op-ed was edited in a way that was confusing. That being said I’ve heard through the grapevine that some prominent human population geneticists may write a response to David’s op-ed, which is something I want to see. Part of me still thinks that these vigorous public discussions are important (another part of me just thinks that when Sulla or Marius take over all this old-fashioned fixation on truth will be irrelevant).

One thing stated in the piece above is that regular people have a Platonic model of race. This is true. But it is also a fact that geneticists have not done a good job of explaining to the educated public what population structure is, and why it’s not trivial or arbitrary. I know this from personal experience over 15 years interacting with people about genetics online (some of the funniest interactions are on Facebook where a person of professional class background/status “genetics-splains” me about how I don’t understand the extent [lack] of human genetic variation and how arbitrary population cluster identity is).

With The Genomic Formation of South and Central Asia I obviously think we have the broad outlines of the peopling of South Asia in hand. There will be lots of detailed elaborations of how/what happened, but I think the big picture is nailed down.

That being said some of the objections remind me a lot of Creationist tendencies. Creationists often focus on weak points and hammer in on them over and over.

One of the weird things about Indian genetics is that a lot of people think new research will overturn Hindu nationalism. But I know several Hindu nationalists, and privately they tell me that most Hindu nationalists don’t care about these abstruse issues, and many of the more intellectual ones don’t have a major problem with the science.

GEDmatch, Ysearch and the Golden State Killer.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.

Bracketing phenotypic limits of mammalian hybridization.

A few people have asked about the podcast. We skipped a week, but we’ll be back. Taking some feedback in relation to various aspects of the show. A common issue seems to be that my voice is too quiet though Spencer’s is “just right.”

Again, if you use Stitcher or iTunes please remember to give us positive reviews and 5-stars!

If you have ideas for shows, we’re game.

April 24, 2018

Open Thread, 4/24/2018

Filed under: Open Thread — Razib Khan @ 12:23 am

Finished She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. To be honest I was pleasantly surprised that the narrative wasn’t overly fixated on the ‘perversions.’ Sometimes it’s hard to move past that.

I think different people will benefit from reading the book differently. If you are a layperson a serial reading from front to back is optimal. She Has Her Mother’s Laugh is a long book, so this will take a while. But you need to do this to get situated. If you are a geneticist, you may benefit from jumping around chapters, and sampling what people in other fields are doing. Additionally, some geneticists would actually benefit from reading the historical chapters.

Started reading The Fate of Rome: Climate, Disease, and the End of an Empire. Yes, it’s very good. Will see if it’s better than The Fall of Rome: And the End of Civilization after I’ve finished.

Thanks for whoever reviewed the podcast I cohost on iTunes and Sticher. If you haven’t done so, please do so!

Appreciate the feedback so far.

Found out today that India Today posted my review of Who We Are a few weeks ago! Pretty funny I didn’t see it.

Meanwhile, The Genetic History of Indians: Are We What We Think We Are? It looks like Indian scientists are bending before reality: ““How do I say it? See, I am a nationalist,” Rai says over the phone. “People will be upset. But that’s how it is. All the studies are showing that people came here from elsewhere.”

A friend asked again “how do I learn population genetics?” My opinion has not changed in the 15 years I’ve become interested in the field, read Principles of Population Genetics. If you need a gentle introduction, Population Genetics: A Concise Guide is probably that. But I read Principles of Population Genetics in 2004 without any formal training in the field. It’s not that difficult if you put time into it.

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. Gotta do it on flies first!

California, Coffee and Cancer: One of These Doesn’t Belong. The cancer warnings in California are treated as a joke by the population. Unfortunately, there are real carcinogens out there.

Genomic SEM Provides Insights into the Multivariate Genetic Architecture of Complex Traits.

April 17, 2018

Open Thread, 4/17/2018

Filed under: Open Thread — Razib Khan @ 3:01 am

Almost done with She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. To be honest I’m a little relieved that there wasn’t that much focus on the “perversions” of heredity. Lots of interesting stuff. This is definitely a book that scientists and lay people could benefit from.

Carl is a great writer so he makes rather abstruse concepts clear and engaging to nonspecialists. As for those of us who have our noses close to the ground, we sometimes lose the bigger perspective. There is a lot of interesting research that he surfaces in She Has Her Mother’s Laugh that I wasn’t very familiar with, though I had probably read about it or seen it in one of his columns (or Ed Yong’s).

Met a lot of cool people, and touched base with others who I knew ahead of time, at the AAPA 2018. Compared to ASHG or even SMBE the conference was very white. I guess that’s why there were all the diversity sessions?

Lee & I

I had a lot of discussions with Lee Berger about science on a broad philosophical level. Unfortunately, specialization is such that it can be hard to communicate across disciplines such as human genomics and paleoanthropology. But as Lee brings enough samples into the open to do some real statistics I think that will change how constrained to the elect paleoanthropological knowledge is.


Lee’s son introduced me to the concept of South African barbecue. I haven’t had any yet, but I’m curious about it.

Lee will be on this week’s episode of The Insight. Again, please subscribe on iTunes, Stitcher, Google Play. The last episode with Stuart Ritchie was our most successful yet in terms of traffic. We’re suspecting that Lee’s episode will do quite well as well. People keep finding the podcast by chance. We really need reviews to get featured by iTunes!

Spencer and I will probably shift back to a two-person conversation next week. We should probably do an AMA again soon.

Was There a Civilization On Earth Before Humans? Very interesting piece, especially for those of us who have read science fiction. But my issue is straightforward: humans have scrambled biogeography so much in such a short amount of time. I think any other industrial species would have done the same. Even after they went extinct, the phylogeographic chaos they wrought would remain.

It seems very likely that all Australian marsupials descend from one South American ancestor species. The explosive emergence of very different placentals all across Australia simultaneously in the fossil record would be quite suspicious (or red deer descendants in New Zealand).

I spent some time with the people who were associated in some way with the Reich lab a fair amount during the AAPA meeting. I also talked to a few friends about what they thought about David’s op-ed and book. It’s no surprise that there are legitimate human population geneticists considering writing a response of some sort. It’s also no surprise that even critics of David within the population genetics community think that the Buzzfeed op-ed was so bad that it makes it harder for them say something, as the water has been nuddied.

In some ways the reaction has made one of David’s major points: population geneticists need to offer their unvarnished opinions, rather than cosigning people in other fields who mangle their findings.

Some people feel that David “threw me under the buss” in his now infamous chapter. I don’t see it that way.

As many of you know (if you subscribe to my total content feed you know) I have a few other blogs, one of them Brown Pundits. It actually receives substantial traffic from India now. It will be “interesting” to say the least.

A population genetic interpretation of GWAS findings for human quantitative traits. Stuck in the weeds of ancient DNA these past few years I haven’t been paying attention to the storm of GWAS and PRS approaching.

Signatures of negative selection in the genetic architecture of human complex traits.

April 9, 2018

Open Thread, 04/10/2018

Filed under: Open Thread — Razib Khan @ 10:32 pm

About ~2/3 of the way through She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. It’s what you’d expect from a Carl Zimmer book, threading history with rock-solid attention to science. So far he’s actually been a really good, if popular, history of science. I say popular not pejoratively, but because the thematic and chronological structure isn’t academic, but hinges on more personal stories, whether it Carl’s own family, or people, famous and not so famous, with genetic issues that passed on down through the generations.

The book isn’t out yet, but you can pre-order of course. The current plan is to get Carl on The Insight (Stitcher, Google Play and web).

Speaking of which, it’s doing really well right now.

Because I’ve been pestering you, some of you have left nice feedback for us, which is pretty important over the long-term. I’ll probably keep on this until we reach 100 reviews on iTunes.

Last week’s episode on the topic Jewish genetics is the biggest one so far in terms of single-week downloads, and this week’s conversation with Stuart Ritchie should also pull in some interest. We talk a fair amount about Stuart’s book, Intelligence: All That Matters, and depressing topics such as the decline in fluid intelligence over a lifetime.

We’ll probably be revisiting intelligence and genetics with a future guest soon, but in the short-term we’ll pivot toward paleoanthropology since the AAPA is going on this week. I don’t know anything about bones so I’m going to mostly check out the pop-gen sessions, and then ask John Hawks for a core-dump at some point near the end of the week for the rest.

Because most people are ignorant heathens the “read the supplements” t-shirt did not sell well. But I got one for myself (we don’t comp ourselves, so I paid for it fair and square!).

Many rely on Twitter and Google Scholar, but I want to remind people of Pubchase and SciReader. They’re still useful to finding things right outside of your core zone of interest.

I mentioned the book The Invention of Humanity before. I was reading it before switching to Carl’s book (I want to prep for a podcast and I’m also going to give the book to someone else), and it’s OK, but it has the same problem as Inventing the Individual: intellectual history which engages in a sequence of inferences and asserts their validity by fiat without any argument.

There’s a lot to learn from books like this, but that mostly involves facts, rather than arguments (whose premises and method I generally find unpersuasive).

Randall Parker said he liked The Fate of Rome better than The Fall of Rome. On that recommendation, I got The Fate of Rome, as  The Fall of Rome is arguably my favorite history book of all time.

We’ll see.

Ezra Klein and Sam Harris had a podcast debate. I didn’t learn much new in this debate aside from how the two view each other (lots of commentary on the comments of the other).

But one thing I have to say is that Sam Harris’ contention that America’s racial caste system was not historically rooted in a biological conception of racial hierarchy is a point I agree with. By the late 19th and early 20th century, the public rhetoric was based on such an understanding, but that understanding developed organically over time with the emergence of taxonomy and then evolutionary biology in the 18th and 19th centuries.

Its origins are far more ancient, and arguably primal.

Though Daniel Walker Howe’s magisterial What Hath God Wrought is not about race fundamentally, it is a useful work to try and get a sense of how our modern conceptions of the white supremacist republic may mislead us in terms of how it was initially conceived (as on many things, white nationalists and people on the extreme cultural Left agree on many things about early America, where I think they are being anachronistic).

I think most readers now get a sense I am rather pessimistic about concepts such as public reason and getting the populace on board with ideas through persuasion. But, self-styled intellectual elites should still try to cultivate less stupidity and ignorance than is the case today. We’re led too often in the public arena by fools who can’t do their own data analysis, haven’t read the history books they were assigned in college, and whose goal is to seem smart enough to trick the masses than actually impress themselves with what they’ve achieved. Though I guess for most people impressing oneself is about the bank account.

The Rakhigarhi publication is supposed to be here within a month or so. But that’s what I was told a month or so ago. At this point I don’t expect to be surprised. We need to think about archaeology, linguistics, and mythology.

For your amusement:

Genetic influence on social outcomes during and after the Soviet era in Estonia. Heritability increases with meritocracy. That’s what you’d expect.

Slope or correlation, not variance explained, allow estimation of heritability.

Viktor Orban: Hungary PM re-elected for third term. 70% of the vote went to right-wing nationalist parties. Europe’s mainstream elite shouldn’t blame the people, they’re the ones who are promoting the worship of democracy as the only legitimate form of government. They need to blame themselves.

Comparison of phasing strategies for whole human genomes. Not a big surprise if you’ve tried this, but if you haven’t, a must read.

It looks like modal extra-pair paternity rates in human populations are in the range of 1-2%. Sorry aspiring cuckolds!

April 1, 2018

Open Thread, 4/2/2018

Filed under: Open Thread — Razib Khan @ 10:38 pm

DNA tests for IQ are coming, but it might not be smart to take one. I talked to Antonio about this piece a few times. I didn’t have much to say with any insight. These tests aren’t ready for primetime because the prediction is pretty weak/worthless.

With a lot of this stuff realized phenotype is what matters. If I took a test and it said my predicted IQ was 90, or if I took an IQ test and it said that I was in the 15th percentile from the bottom, I wouldn’t reconsider whether I’m dumber that most people seem to think I am. I’d think that the tests were dumb.

Like genetic screening more generally this sort of stuff will become more important for newborns in the future because you don’t have a realized phenotype. Siblings different in intelligence. Some of this is random, but some of it surely dependent on genes. If children have different talents or competencies I suspect many parents will want to know as early as possible (my two oldest are young, but it’s already pretty obvious that my son is much stronger on visuospatial skills while my daughter has a better ability to abstract in a general sense).

Ancient DNA tracks the mainland extinction and island survival of the Tasmanian devil. The main issue I have with all these studies is the importance they put on climate. Climate changes. Often. That’s usually not a sufficient condition for extinction. People and the animals they bring around are.

I guessed that the supplements shirt would not be popular, judging by how many questions I get that would be answered by reading the supplementary text!

That being said, I bought one for myself. Of course, I would! (I’m going to post a photo of me wearing it when I get)

A Financial Times story about the Kalash. I filled in some dumb surveys and it allowed me to read for free.

When Gmail Launched On April 1, 2004, People Thought It Was A Joke. I’m starting to worry about our reliance on platforms. And that includes Gmail.

How to Talk About ‘Race’ and Genetics. David Reich responds.

There has been a lot of talk on “science Twitter” about the David Reich situation. Some of it in public. And some of it in private DMs. I am heartened personally to see that most people are defending him because he does not deserve the patronizing abuse that’s being directed at him.

I am not much in touch with David, though we have met in person, and exchanged a few emails about his work. It’s not breaking any confidence for me to say that he did not write Who We Are and How We Got Here to become famous. The book will sell well, but it’s not written in a manner that will make him rich. In any case, among his peers, he is already quite famous after all. As he noted in the introduction to Who We Are and How We Got Here he wrote it to speak to those outside of the community of human population geneticists who read and write scientific papers.

Since David has such a high-status people within the community are very careful about what they say about him if they have strong criticisms. Not only is it hard to argue that he’s ignorant of the science (after all, he is one of the major producers of science!), but he’s a powerful figure embedded in a powerful institution.

This is why when you examine the list of 60+ signatories to this op-ed in Buzzfeed, How Not To Talk About Race And Genetics, there are very few working geneticists on the list. I heard a rumor that there were actually a few genetic anthropologists willing to sign, but who didn’t agree with the final text and withdrew. And good for them, because this op-ed is a confused mess.

But, to be frank it’s entirely to be expected from a certain type of scholarship. Like many, I have expressed some concern and annoyance that geneticists engage in imperialism without consulting historians and archaeologists. But these are real disciplines with real facts and theories, whether those facts are undermined, and the theories shown to be false. There is something real to be grasped at. The Buzzfeed op-ed, in contrast, is by turns patronizing, incoherent, or just false.

The conversation has been bracing, but I’m not sure it’s moving toward any synthesis.

Complex traits are probably subject to Kurzweil’s The Law of Accelerating Returns. Stuff is moves slow, then faster, and then we’re slammed against a new world before we can adjust.

Here’s a poll I created:

Detecting signatures of positive selection along defined branches of a population tree using LSD. The day will come with ancient DNA papers will start to slow down in their rate of release and I’ll have to catch up on the selection literature (though to be fair, there’s only so many real targets of selection we’ll pick up).

Comparison of Genotypic and Phenotypic Correlations: Cheverud’s Conjecture in Humans.

Back to reading Enlightenment Now.

March 26, 2018

Open Thread, 3/26/2018

Filed under: Open Thread — Razib Khan @ 9:17 pm

Does anyone have a galley or review copy of She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity? The book is long, and review copies are in short supply. Would be nice if I could see it before it’s released at the end of May. Just use my contact email if you have a copy.

Pretty excited about it! The use of the word “heredity” is a clue to me that this is going to be a book with a really long historical narrative.

How Genetics Is Changing Our Understanding of ‘Race’. Everyone is talking about this David Reich op-ed in The New York Times. Well, at least in my corner of Twitter.

It’s adapted from a chapter of Who We Are and How We Got Here. That chapter is both more subtle and more punchy than the op-ed. Anthropologists will probably dislike it even more than they dislike this op-ed because Reich does not pull punches (though contrary to the impression you might get from the op-ed he clearly prefers to use “ancestry” rather than the word “race”).

There’s not much to say about the op-ed.

I think it’s more interesting to perceive the dynamics of scientific culture at work in the reaction. The Reich lab is an eminent one, and its Diaspora includes other elite institutions now. He is affiliated with Harvard Medical School and the Broad.

Friends of mine who operate outside of human genetics characterize this subfield within genetics as one with sharp elbows and a mafia-like network of pedigree laboratories and superstar professors. It’s probably worse in the explicitly biomedical area, but population geneticists who don’t work on humans still say human population geneticists are different (we’re talking averages here).

There were many criticisms of the op-ed from human population geneticists…but they were subdued, restrained, and often prefaced by praise for Reich’s scientific chops or his generosity as a collaborator. Both true of course. There was also praise.

But the op-ed illustrated the reality of some unpalatable propositions. In Who We Are and How We Got Her David Reich himself makes it clear that some of the ideas he’s mooting are not palatable to him. If it wasn’t clear from the op-ed already.

But it also I believe it illustrated what I like to say about academia from what little I’ve seen and experienced within it: it is a highly feudal culture defined by patronage networks and an ordered understanding of the relationship of superiors to subordinates. As they say: “You come at the king, you best not miss.”

If he was someone less connected, less at the peak of his powers, I believe that David Reich’s reputation would be ground up in a sausage machine. This op-ed reminds me of nothing more than Symmachus’ plea for an old way that is fading before the new. Symmachus was rich and famous. He could dissent from the ascendant orthodoxy that was “passing on to better things.” But his class of the old pagan elite was at its dusk.

Most of the more vociferous criticisms are coming from anthropologists because it’s a different field with an alternative nobility of blood and status. David Reich can be thought of as an alien warlord who as trespassed the boundaries of their kingdom. But Reich is also aiming at the very foundations of their rule, so they can do no other but unleash the dogs of war.

Speaking of that book, my review is up at National Review Online. Hope to contribute more in the future to that publication! Doesn’t look like Kevin Williamson is getting fired from The Atlantic, so there’s space in those pages.

I’ll probably talk more about the book in a spoilerish way next week so that people who purchased the book can read it.

Efficiently inferring the demographic history of many populations with allele count data and Recovering signals of ghost archaic admixture in the genomes of present-day Africans. These deserve close readings.

I assume everyone on this blog has heard about my podcast and are sick of hearing about it. But there are still people who follow me on Twitter who haven’t.

Since nothing has changed in a while, more positive reviews on iTunes and Sticher, please.

I think you’ll enjoy the interview with Stuart Ritchie, though that won’t post until further into April.

In a few days, I’ve going to have a post up on a new shirt which I pushed for at DNAGeeks (we got an artist to do something). But for now, check out the GNXP-helix themes hats and beanies.

The Battle of the Blue Cat Café How an anti-gentrification boycott became a proxy war between the radical left and the alt-right. Hits a little close to home.

The basic outline is that gentrification in East Austin is transforming lower class & lower-middle-class black and Latino neighborhoods into middle and upper-middle-class white neighborhoods. This makes some people really angry because they don’t want their neighborhood to change.

I’ve had some “interesting” discussions about this with locals with deeper roots. It’s fashionable to bemoan gentrification, but when I bring up my experience as an immigrant, and how that naturally results in change and transformation of neighborhoods, people get uncomfortable. The emotions deployed against gentrification aren’t that different from the emotions used against immigration. In many ways, the East Austinites who are being “displaced” can be psychologically analogized to middle and lower-middle-class Trump voters who feel they’re being “displaced.” Both groups feel they are being marginalized by people who are changing the world that their ancestors created with their own labor. And they probably are.

I don’t have a good answer to this. The free-market person in me says that gentrification has to happen, and the neighborhoods are going to change no matter what. But another part of me actually understands the argument by making an analogy to the national level: too much migration into a polity can result in a transformation of its institutions and dispossession of its majority. Pretty soon East Austin will mean something very different from what it has traditionally meant.

If you haven’t had wood ear salad, you haven’t lived. I highly recommend it as one of the major experiences of Sichuan cuisine (and of course don’t go to the place if their green beans are not recommended.

March 19, 2018

Open Thread, 3/19/2018

Filed under: Open Thread — Razib Khan @ 3:31 pm

Some people have asked me what I think about Imagined Communities: Reflections on the Origin and Spread of Nationalism. I haven’t finished it, but now I understand why it is one of the most assigned books for undergraduates: it’s concise yet facile superficiality would appeal to a know-it-all twenty year old. What’s more disturbing, though I guess not surprising, is that Imagined Communities communities is a book that I’ve seen name-checked for years by various public intellectuals. Did they read the book?

It’s not that the book is incredibly wrong. It’s just that there’s not that much there in my opinion.

Been enjoying sampling the Philosophize This! podcast.

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Haven’t blogged it because I haven’t read the supplements.

Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project.

Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase. This is big.

‘Serial Bomber’ Is Suspected in Explosions That Have Put Austin on Edge. Twitter was useless yesterday as most of the people seemed more enraged at the media for not laying the blame on white supremacists or Muslim radicals, as opposed to those getting killed or injured.

Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits.

Feeling like I should reread The End of History and the Last Man. Feels like history has started again….

Some people ask me about how I read fast. Part of the answer is that I read a lot in a specific area at the same time. Also, you can read fast if you know a lot about a topic. For example, a substantial portion of Who We Are and How We Got Here involves going over four and three population tests. I know what those are, so I read those sections quickly.

Finally going to hunker down and figure out which plugin is causing the 500 error on this website.

Just a reminder, please subscribe to the podcast on iTunes or Sticher and review it (positively). I’ll stop with the flogging when people no longer tell me “Oh, I didn’t know you had a podcast!”

This week we’ll I’m interviewing Milford Wolpoff (that is, what’s going live).

March 14, 2018

Open Thread, 3/14/2018

Filed under: Open Thread — Razib Khan @ 8:46 pm

I finally met my old friend Ramez Naam in the flesh. Ramez’s publisher sent me his book More Than Human: Embracing the Promise of Biological Enhancement in 2005. One thing led to another, and somehow he’s guest blogging on Gene Expression!

CRISPR as we know it did not exist in 2005. Things have really changed since then, and for the better, at least from the perspective of genetic engineering. It’s as if some of the stuff in More Than Human is coming to life.

I also recommend his book The Infinite Resource: The Power of Ideas on a Finite Planet.

Ramez is more optimistic about the future than I am, though cautiously so. I hope he’s right, and I’m wrong. I fear he’s not.

My concern is not with technological innovation. That will happen. It’s with maintaining social stability due to the immiseration of what was the middle class in developed societies. Also, the bourgeois version of the New Class seems to lack empathy toward the future lumpen….

SEC Charges Theranos Founder Elizabeth Holmes With ‘Massive Fraud’. “Fake it ’till you make it” will keep happening if there are no follow-up criminal charges. Holmes may not have gotten away the con, but she was a paper billionaire for a while and funded R & D with the cash that they raised on lies. One moral some are going to take away is that she took a big risk and failed, but it was one that perhaps needed to be taken.

Adaptive landscape of protein variation in human exomes.

Genetic dissection of assortative mating behavior.

Conor Lamb Wins Pennsylvania House Seat, Giving Democrats a Map for Trump Country. I’m pretty bullish on a Democrat takeover of the house. The country will swing back. That being said, I’m also bullish on the idea that the Democrats are their own best enemy, and divisions and lack of coherency in their plan going forward will mean they won’t be able to capitalize on their electoral windfalls over the next few years.

This week’s episode of The Insight is up, 23andMe, the FDA, and Our Genomic Future. We have some potential guests lined up. One of whom is Stuart Ritchie, author of Intelligence: All That Matters.

Please subscribe via iTunes or Stitcher, and leave us 5-star reviews! 

St. Patrick’s Day is coming up. I’ll be avoiding drunk people on the streets of Austin. But I also want to point out that my “side-hustle” DNA Geeks has an M222 t-shirt available. In case you don’t know, that’s the legendary Niall of the Nine Hostages’ possible haplogroup (a sublineage of R1b). About 10% of Irish men are M222.

‘Tomb Raider’: Fans Slam Criticism of Alicia Vikander’s Body. There are two points that I want to make. First, at 5’5 inches, Alicia Vikande is of a very normal height (Angelina Jolie was two inches taller). She’s not physically imposing, and she has a very narrow waist as well. Her figure is “boyish.” Second, since the 1990s there has been a shift in male action stars toward being more shredded/athletic as opposed to jacked-up and exaggerated in their physicality. This is a very different Lara Croft for a very different time.

I decided to check out the new public library today. Saw the book The Invention of Humanity: Equality and Culture Differences in World History. I hate the overuse of the term “invention” in book titles, but when I noted the beginning covered China, I got it. Too often books that are Eurocentric turn out to be more data than narrow/inference, and they rig the data ahead of time to support their thesis (see, Inventing the Individual).

I also got Constructing the World (a David Chalmers book), The Bible and Asia: From the Pre-Christian Era to the Postcolonial Age, Creators, Conquerors, and Citizens: A History of Ancient Greece, The Third Reich: A History of Nazi Germany. That’s ranked in order of likelihood that I’ll get through them.

Also, Philip Jenkins has a new book, Crucible of Faith: The Ancient Revolution That Made Our Modern Religious World. Jenkins is a great scholar, I admire his work a lot. But I think I’m going to take a break from religious history, since I know a fair amount about the topic.

Polygenic scores and tea drinking.

Exposing flaws in S-LDSC; reply to Gazal et al.. Working your way through this literature is often pretty useful, so start at this commentary.

National Geographic has a special on race and what not. One piece being shared is kind of interesting, These Twins, One Black and One White, Will Make You Rethink Race. Here’s an important quote:

In genetic terms, skin color “is not a binary trait” with only two possibilities, Martin notes. “It’s a quantitative trait, and everyone has some gradient on this spectrum.”

Historically, when humans have drawn lines of identity—separating Us from Them—they’ve often relied on skin color as a proxy for race. But the 21st-century understanding of human genetics tells us that the whole idea of race is a human invention.

If you’ve read this blog you know I’ve blogged about “black and white twins” for over ten years. Also, I think a lot of the debunkings of race are pretty facile. But that’s not what I want to talk about. Rather, one of the things that are unmasked unwittingly in pieces such as this is how deeply Eurocentric these conversations are. It’s as if public intellectuals and journalists that write on this topic either don’t know any non-white families or they pretend that they don’t. The “humans” and “Us” implicitly points to white European systems of racial classification (e.g., East Asians relied on skin color somewhat, but since they are not much darker than white Europeans, they also included hair color, to distinguish the Dutch from the Portuguese, and large noses and body hair, to distinguish from themselves).

Twins with different skin tones are striking. But almost any South Asian, black American, or Latino, or Southeast Asian, or even East Asian, can tell you that there is a wide range of pigmentation within many families. Basically, unless you are in a homogeneous European social environment, where most everyone has very light skin on a global scale, you will see the variation of pigmentation within families. Both my parents have large sibling cohorts, and in both of them there are cases where the difference in complexion between siblings is in the same range as the two fraternal twins highlighted in the piece.

Of course, journalists who work for National Geographic or The New York Times know people of varied ethnicities and probably see that there is pigmentation variation within those families. They just pretend as if they don’t for these sorts of pieces which debunk race, and the readers pretend they don’t know this information as well as they take it in in a self-satisfied manner and nod sagely.

I haven’t had much time to read Enlightenment Now: The Case for Reason, Science, Humanism, and Progress. But those who say it’s quite like The Better Angels of Our Nature seem correct from how how far I’ve gotten.

My timeline has been swarming with debunkings of Enlightenment Now from all ideological angles. The best responses to these can usually be found in Saloni’s timeline (from her), who is “Pinker’s bulldog.”

Ex-Muslim TV‘s Twitter account is irritated that some of its stuff is now labeled “sensitive material.” The day before this came up I noted that one of my posts that Jerry Coyne retweeted about Islam and apostasy was also labeled “sensitive material.”

Basically if Muslims find it offensive, it might be subject to scrutiny from Twitter. This may or may not be defensible from Twitter’s perspective in a business sense, or ethically. But it’s just the reality we have to deal with, though I would like to know which school of Islamic jurisprudence Twitter relies on to gauge sensitivity and offense. I suspect it will be the Hanafi fiqh due to its liberal utilization of qiyas, which allow’s Del Harvey’s minions more free play.

The nation-state is dying. What will come out of its ashes? I suspect empire by another name….

March 6, 2018

Open Thread, 4/6/2018

Filed under: Open Thread — Razib Khan @ 1:03 am

Eden in the East is a weird book. Written in the late 1990s before modern-day genomics, its central thesis about the origin of Southeast Asian people in Pleistocene Sundaland seems likely to be wrong (at least most of their ancestry). But the author, a polymath medical doctor, marshals an enormous amount of archaeological and textual data supporting old ideas of cultural diffusionism, much of it plausible.

Despite my skepticism of the general theses promoted, reading Eden in the East is useful insofar as you need data and interpretive sieve for the swell of ancient DNA.

The University of Wisconsin-Stevens Point is eliminating many majors and adding new ones. This is eliciting a lot of outrage on Twitter.

Public universities are funded by the public. If they aren’t fulfilling the public role then things will have to change. Unlike many people, I don’t shed too many tears about the elimination of some of these majors because most graduates of them are stupid and uninformed (some of them actually have a less accurate view of the world coming out than before they arrived at university).

Here’s the breakdown:

Expanding programs Change into majors Discontinuing the programs
Chemical Engineering Aquaculture/Aquaponics American Studies
Computer Information Systems Captive Wildlife Art – Graphic Design will continue as a distinct major
Conservation Law Enforcement Ecosystem Design and Remediation English – English for teacher certification will continue
Finance Environmental Engineering French
Fire Science Geographic Information Science Geography
Graphic Design Master of Business Administration Geoscience
Management Master of Natural Resources German
Marketing Doctor of Physical Therapy History – Social Science for teacher certification will continue
    Music Literature
    Political Science
    Sociology — Social Work major will continue


Let’s set aside the fact that some of these programs, such as sociology and American Studies, are often de facto political action outfits. As someone who has talked to people who have history degrees from universities of various prestige and stringency, institutions of higher learning are doing a really shitty job inculcating knowledge into these kids. Or love of the topic. Also, their critical faculties aren’t the best. Too much critical theory, not enough critical thinking. Recitation doesn’t cut it.

Aquaculture and aquaponics is a vocational program of study which isn’t sexy, but at least it aims to impart skills. That’s what a lot of these kids need.

So my buddies at DNA Geeks unveiled a new t-shirt, Pipe(tte) Dream.

I kind of thought it was funny, but it turns out there’s some demand for stuff like this. Is bench biology still a thing? I guess so…. Anyway, if you are interested, click on through!

Evolutionary inferences about quantitative traits are affected by underlying genealogical discordance. This is an important preprint. Read it.

The Silicon Valley elite’s latest status symbol: Chickens. Some of the people caught up in this are quite self-aware: Citroen’s 19-year-old son, Luca, who grew up around the family business, puts it this way: “Being able to say you have chickens says, ‘I have a back yard,’ and having a back yard says, ‘I have space.’ And having space means you have money, especially when it comes to Silicon Valley real estate.” Chickens are a “hard to fake” signal of wealth. Yeah (the Romans had sacred chickens).

My main hope is that some of these rich Silicon Valley hobby-farmers pick up a copy of Introduction to Quantitative Genetics. It would do them some good (and perhaps the world?).

Do any readers have a review copy of She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity? It’s Carl Zimmer’s new book and the publisher is out of galleys.

Speaking of reviews, I’ll be writing one up for Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past for a publication most of you have heard of. Have to put the “writer hat” back on for a bit. Between my job, my intellectual interests, and family, I haven’t put much effort into that.

You probably know that Antifa went after Christina Sommers:

To be honest these forays by centrists (Sommers is a registered Democrat with libertarian leanings, similar to Steven Pinker) into the academy are starting to remind me of those ridiculous “debates” that Jews had to have with professional anti-Jews (mostly apostates) in the courts of medieval European monarchs. There were the outward forms of debate, but everyone knew what it was about (since Sommers and Pinker are from Jewish backgrounds perhaps that’s apposite).

Similarly, when the campus Left is against some speaker many people roll their eyes, and the administration makes the usual noises, but you know that the protestors are going to get a slap on the hands no matter how obnoxious or aggressive they are. For most academics, for various reasons, there are no enemies on the Left. Communists and Communist sympathizers like Angela Davis can be fulsomely praised with no worries about reputation, but those academics who think Sommers or Pinker are making reasonable points have to furtively communicate on secret direct message groups.

That’s where we are.

I now understand why Benedict Anderson’s Imagined Communities has been assigned to so many undergraduates: it’s a short and simple book. It’s depressing but unsurprising that it could be so influential. More on that later.

The criticisms that Enlightenment Now doesn’t really delve into the intellectual archaeology of the Enlightenment are spot on. But this seems a case where the title is a bit off, but the text itself is solid. I have seen on Twitter quotes about how Pinker has apologia for the Tuskegee experiment. My prior at this point about these sorts of invidious accusations is that they’re lies. For a variety of reasons, people lie about Steven Pinker. That’s sad, but we live in a world where liars prosper, so it shouldn’t be surprising.

My podcast with Spencer, The Insight, has been pretty successful so far. I just submitted it to a bunch of podcast directories this weekend to cover bases. Our goal is to get highlighted by iTunes, so if you haven’t, subscribe and leave a good review! (also, there are only three reviews on Stitcher so far)

We interviewed Chris Stringer a few weeks ago. This week we’re trying to get Milford Wolpoff recorded (to be posted next week). We have some ideas about guests we might have on. Currently, we want to mix personal genomics/biotech, genetics, and paleoanthropology. I think I want to mix in some straight history at some point, since so much ancient DNA is starting to percolate into that field.

Retweets Are Trash. Basically, the argument is that if you get rid of RTs some of the toxic effects of Twitter are dampened. Skeptical, but hopeful.

How Twitter Lost The Internet War. The most important part is the assertion that Twitter has a lot of tech-debt that it hasn’t retired or discharged, and that’s why it hasn’t been able to solve its troll problem in a non-manual manner. I have a hard time crediting this. But perhaps that’s how it is?

Turkey Is Turning Into the Next Pakistan. Being totally honest, it’s hard for me to believe that the media hasn’t been underplaying this story. Back when ISIS was a thing, Turkey was turning a blind eye to thousands of foreign fighters that were streaming into Syria. Even if Turkey isn’t pro-Islamist (and it kind of is), they are clearly backing Sunni Islamists who will impose a nasty majoritarianism if they ever win. Not that the anarcho-communist Kurds we’re backing would be any better in the long run.

Ultimately in Syria, I can’t begrudge ethnoreligious minorities for siding with the Assad regime against the rebels. And, I can’t begrudge the Sunni population their reliance on militants who are more fierce and principled in defending them and their interests against the government. But we’ve been through Iraq twice. Our Saudi ally has birthed monsters over the past generation. We turned a blind eye when our ally of convenience in the 1980s, Iraq, engaged in gas attacks against Iran and the Kurds.

We need to learn, and just stop. Stop!

On the lookout for Kindle deals in books. Here’s what I got recently:

* The Rise and Fall of Communism.
* Carthage Must Be Destroyed: The Rise and Fall of an Ancient Civilization
* The Sleepwalkers: How Europe Went to War in 1914.

I have a lot of books on Communism that I need to read!

Interesting paper, Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome.

The 500 errors on this site are due to a plugin and some of the issues with porting this blog over a few months ago. I need to allocate a day to figure this out, but I’ll do it. The same issues with the South Asian Genotype Project. I will update it. But I need to have four or five uninterrupted hours, and that’s just hard to come by.

SXSW should be interesting this week. As per usual I’ll avoid most of the festivities.

February 25, 2018

Open Thread, 02/25/2018

Filed under: Open Thread — Razib Khan @ 9:48 pm

Reading Enlightenment Now. Seems fine enough. Will say more when I get done.

I will say it’s strange to see how many people really hate the book (presumably without reading it?) and hate Steven Pinker. And curiously, it’s a pretty broad and ecumenical hate, from the respectable Left to the respectable Right. There is also more measured criticism on the merits from academics.

Land of Promise, by Michael Lind, is a book I’ve mentioned several times. It is broadly within the mainstream “big government Left.” But, I don’t think I’ve observed that it ended on a curious note. It used the term “chain migration” and argued for a shift toward skilled migration. Lind also asserts that low skill immigration pushes down wages of low skill Americans.

Land of Promise came out in 2012. The 2008 financial crisis looms large. But we’ve moved a lot when it comes to immigration even since then… Not sure if the editors would let Lind leave that section in if he was writing today because it’s pretty much consonant with Donald Trump’s positions.

The Inside Story Of How An Ivy League Food Scientist Turned Shoddy Data Into Viral Studies. Another story from Buzzfeed on the Wansink story. Some assertions:

* Brian Wansink is a “good person” by normal definitions.

* His ultimate aim as a scholar is something most people would agree with. That is, he wants people to eat healthier.

* Any single aspect of his behavior in this article, p-hacking, recycling papers to lower ranked journals, sloppiness, and trying to get the media to pay attention to his research, is not that exceptional. It’s the magnitude and synergistic complementation.

* There are serious issues with the incentives for academics today, whether it be within the field (quantity of publications as opposed to quality), and the media (publish stuff that the media wants to believe).

The Wansink affair is a really great illustration of the symptom. But the structural problems are still there.

Reading a bit of the The Classical World: The Foundations of the West and the Enduring Legacy of Antiquity. But really I think perhaps Robin Lane Fox’s The Classical World: An Epic History from Homer to Hadrian does it better. But we’ll see.

Picked up Stephen Oppenheimer’s Eden in the East: The Drowned Continent of Southeast Asia. The thesis seems kind of crazy, but I’m curious and doing some research for a future podcast.

Tania Joya did an interview, ISIS Ex-Wife Speaks to the Secular Jihadists.

Tania gets a lot of space in Graeme Wood’s The Way of the Strangers: Encounters with the Islamic State, but she’s apparently writing her own book. I’m pretty curious, because Tania and I have a lot in common, but are also different in many ways. She grew up in a British Bangladeshi household, and one of the major things she mentions in the interview is how oppressively capricious and controlling her parents were. To be honest I related to this…but as a male, I’m sure my experience was much milder. Additionally, British Muslim communities are isolated and regressive in a way that American Muslim communities never are (in fact, outside of a few places like Hamtramck, Michigan, there aren’t American Muslim communities as such). That also comes through in what Tania says.

Spencer wrote a blog post today which is worth checking out, R.I.P. Great Leap Forward, which reflects his own historical progression and understanding on this topic. Our podcast with Chris Stringer should be up Wednesday night (so subscribe), and we touched on this somewhat (it was recorded before the paper landed, though Chris already knew about it). We’ll be talking to Milford Wolpoff this week, so we’ll see what he thinks.

One thing I want to mention offhand. Back in the 2000s, I had some online exchanges with “Mencius Moldbug”. They weren’t exactly hostile, but ultimately I dismissed him because he got a lot of details wrong. And, to be honest, I was kind of annoyed by his stupid cultists who would leave comments. Moldbug himself was and is a smart guy, but some of his acolytes were not.

In 2018 I do have to say that I think that though Moldbug was wrong on a lot of details, and still is, he had insight into something more general which I lacked. My deep pessimism about bourgeois liberal democratic civilization and the state of intellectual culture draws from the same well that he drew from, though I disagree on a lot of the details to this day (I also now am much more open to radical Leftist critiques as well).

I bring this up partly because one of the things that convinced me to ignore Moldbug was his rejection of data which conflicted with his priors. For about 10 years it has been rather obvious to me looking at the literature and my own data analysis that most ancestry in Southern Italy and Sicily does not derive from migration from the east which dates to Roman antiquity.

The blogger at Eurogenes has posted the result from a Sicilian Bell Beaker individual. You can see that modern Sicilians are shifted away from the Bell Beaker Sicilian, who is more skewed toward the EEF cluster. But it’s pretty obvious that the shift has not been predominant. Modern Sicilians tend to have some ancestry which is certainly North African, and perhaps Greek. And the Sub-Saharan African in some individuals, which probably arrived during the Islamic period, is hard to miss. But most of their ancestry seems to date to before the Roman period.

And Sicily is the “best case” for predominant replacement in Italy.

DNAGeeks is now selling a Neanderthal shirt which honors their artistic abilities.

I put a poll up on Twitter asking about the species status of Neanderthals. I am a lumber, so I’m between two and three.

It’s kind of weird that people are explaining that there are “species concepts” to me in the comments. I thought answer 3 makes it pretty clear I’m aware of that.

I watched Black Panther. I liked it. It looks like it will make a lot of money. I wouldn’t be surprised if it results in copy-cat films. They probably won’t make a lot of money because they won’t be good films, and then Hollywood will go back to doing what it always did.

Also, I found out that there’s another Mission Impossible film. Tom Cruise is the new Dick Clark of our era.

Apparently, there isn’t a character for the word “problematic.” That’s good.

But I’m reading Judith Butler’s Gender Troubles soon. You might find that strange, but I’ve read Christian and Muslim apologetis too.

February 11, 2018

Open Thread, 2/11/2018

Filed under: Open Thread — Razib Khan @ 9:51 pm

The podcast that Spencer Wells and I are doing, The Insight, now has got eight episodes up. It’s nice that people are stumbling upon it now. Additionally, we’re pretty satisfied with the uptake. So far. To break out of our “core” audience we need more people to know about us.

First, please subscribe via iTunes, Stitcher or Google Play. Second, mention the podcast on social media. Tell your friends. Third, we have the next two or three podcasts planned, we’re still taking suggestions for ideas and possible guests (so far we’ve had John Hawks and Joe Pickrell on).

I now have Amazon Associates for Canada and the UK. The links to US Amazon items I post on this page should now change depending on your IP.

Cheddar Man changes the way we think about our ancestors. This is a pretty good article. But a few points. First, anyone who followed the literature would have predicted that Cheddar Man would contribute ~10% of the genomes to modern Britons and that he would lack alleles for light skin, but have them for blue eyes. I can’t believe any of the researchers were shocked in light of the La Brana etc. results. Second, we’re not extremely confident that he had very dark skin after the past few years when it’s clear pigmentation genetics involves more than just a few major loci. Seeing as how selection methods have detected lots of sweeps for skin lightening alleles over the last 5,000 years in Northern Europe, it seems implausible that they were as light as modern Northern Europeans, but not necessarily dark.

Spencer and I will probably an episode of The Insight on Cheddar Man after the documentary is out on the 18th (and the paper, probably in Nature).

I’ve blogged on female circumcision/FGM before. There are variations of opinion within Islam on this practice. It is mandatory, meritorious, or there is no comment. Muslims from areas where this is not practiced, such as South Asia or the Maghreb, naturally assume that this is a “cultural practice” that has nothing to do with Islam.

This is simply false. The Shafi school of Sunni Islamic jurisprudence considers female circumcision obligatory, for example. The complicated issue is that a) not all women subject to female circumcision/FGM are Muslim, for instance, in Africa, including Egyptian Copts b) not all Muslims are subject to the practice, obviously. These facts allow all sorts of confusions and obfuscations to emerge.

But the bigger issue is that if you are not Muslim it is not really coherent to say that something is a “cultural” practice as opposed to a “religious” one. Religion is part of the culture, and to a great extent on the reflective conscious scale the defining element of culture. Muslims disagree as to the religious acceptability of many practices. Those disagreements are cultural because Islam is cultural.

Land of Promise is a book I’ve mentioned many times. It’s one whose premises rub me the wrong way: the vigorous mixing of state fiat with the market. I’m not a fan of “industrial policy.” And yet I read the book because Michael Lind, the author, knows his history, and he’s honest about it.

I do think on some level I’m rethinking my commitment to the free market as opposed to institutions, and the short-term benefits of market efficiency set against the long-term advantages of social stability. That’s probably part of a general trend toward conservatism away from libertarianism.

Let’s Ban Porn. Don’t laugh. It took some boldness for The New York Times to publish something as laugh-out-loud implausible. But in the end, I think porn is the symptom. Really we as a culture don’t agree on what sex is supposed to be about. Without that agreement, porn is a sideshow.

Also, the proliferation of porn in the last 20 years hasn’t led to the explosion of sex crimes that critics on the Left and Right would have predicted.

Some of you may wonder about DNA Geeks. What’s the deal? Well, I can tell you that we are building a nice brand, and periodically there are traffic spikes. And the microscope is killing it.

The main sadness for me is that the ratio of R1b to R1a t-shirts sold is like 20:1. But I guess it’s quality over quantity?

While I was taking a Twitter break I got a few DMs about the latest controversy about hours worked by academics:

The stupidest thing on science twitter is how crazy and nasty people get over the idea that you have to work hard in science to succeed. Everybody knows you have to work hard and long to succeed, and yet everyone is willing to outright lie about the truth, lest you be publicly destroyed.

It’s pretty clear some people work fewer hours than other people and do fine. It’s also clear that other people have higher sweet spots in terms of return-on-time-worked. The problem is when people presume there’s a one-size-fits-all formula. I think it would be best if people reacted with a little more charity to those who extrapolate from what’s worked for them.

February 8, 2018

Unlurking thread

Filed under: Open Thread,Unlurk — Razib Khan @ 6:46 pm

Basically, a thread to unlurk if you want.

February 4, 2018

Open Thread, 2/4/2018

Filed under: Open Thread — Razib Khan @ 9:56 pm

One of the things that reading Land of Liberty has prompted in me is the need to read Matt Stoller’s book, when it comes out. Land of Liberty in many ways was a historical foil of Stoller’s article, How Democrats Killed Their Populist Soul.

And yet both exhibit an intellectual honesty which I generally find lacking in the modern pundit class, agree or disagree.

Steven Pinker’s new book, Enlightenment Now: The Case for Reason, Science, Humanism, and Progress, is now being published a few weeks earlier. Apparently this now one of Bill Gates’ favorite books.

I’m a big fan of Steven Pinker. But I’ve become much more pessimistic than him over the past few years. Here’s hoping that Enlightenment Now turns that around.

DNA Geeks has a total site redesign! Check it out.

I haven’t been saying this on the podcast yet, but you should be subscribing to it on iTunes, Stitcher, and Google Play, and review and rate it. Spencer and I have a certain audience already, and we’d like to expand it.

This has probably always been so, but I’m really getting tired by the emergence of different verbal ticks in various socio-political subcultures. For example, when liberals say “my dude” -“bros”, it’s dismissal-by-identity. Both NRx, and what is now called the Altright, also have their own subculture languages, which makes understanding what they’re trying to say hard for outsiders. A feature or a bug?

Taking a Twitter break for a week.

January 28, 2018

Open Thread, 01/28/2108

Filed under: Open Thread — Razib Khan @ 10:07 pm

For various reasons we focus Classical Greece and Rome, but neglect the Hellenistic period, with the exception of the biography of Alexander. If you want to read something besides Alexander to Actium, check Dividing the Spoils.

A heads up, this week on The Insight we’ll be talking to Joe Pickrell of Gencove. The main topic will be DNA and ancestry.

Is the United States the new Saudi Arabia? This stuff is crazy if you read books about “Peak Oil” in the 2000s. Also, I really don’t ever want to hear about this stuff from random guys who read these books and thought they had all the answers ever again.

DNA Geeks is now gearing toward more general STEM and items for children. The 100x LED Microscope for Mobile Devices has been quite popular, and shipping is right now free. Also, we have European vendors for our t-shirts, so shipping is cheaper and faster.

Following many liberals on Twitter has confirmed my right-wing identity, though modified by policy beliefs. In particular, far Left people, such as Matt Stoller, seem to make coherent criticisms of capitalism and what it has wrought. Criticisms which I don’t always have a good answer for.

In contrast, moderate liberals, with their mild platitudes and thin policies are not persuasive, but their adherence to sex/race identity politics and smearing of all those to the Right of them as white supremacists means that it’s pretty obvious all of those who are “Other” need to band together as one when the time comes. We hang together, or we’ll go to the re-education camps separately.

The Follower Factory. This makes sense.

Why Ursula Le Guin Matters.

Nicholas Christakis is being treated pretty unfairly. I don’t expect that he’ll get satisfaction. This isn’t the age for honorable men.

Big Data Comes to Dieting.

The new gnomAD is pretty dope.

Dissecting historical changes of selective pressures in the evolution of human pigmentation. Not sure of the demographic model.

January 21, 2018

Open Thread, 01/21/2018

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

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

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

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

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

A new blog, mtDNAwiki.

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

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

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

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

January 14, 2018

Open Thread, 1/14/2018

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

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

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

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

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

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

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

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

December 30, 2017

Predictions for 2018

Filed under: Open Thread — Razib Khan @ 10:31 pm

I don’t normally do year-end stuff. But I figured, why not? After all, I put up a post at my work blog about the major things that happened in historical human pop gen this year.

Indian population genomics will move forward notably. The ancient DNA work really feels like vaporware sometimes. Some of the researchers involved reach out to journalists (people of my acquaintance) and leave tantalizing clues, but they disappear off the face of the earth. I assume that some sort of Indo-Aryan intrusion from Central Asia will seem clear from the data and results, though the Indian media and intellectual class will claim the opposite (in this way they are just like the American media and intellectual class; if the evidence does not fit just say that the evidence says the opposite of what it does).

The current protests in Iran won’t go anywhere. Someone with guns needs to be on the side of the protestors. That’s it. Also, if a group with guns ends up favoring them, the West will find that anti-clerical Iranians are quite nationalistic and not necessarily liberal democrats.

The Democrats will win the House of Representatives. I think there’s about a 50/50 chance that they’ll get the Senate.

The United States will be in a recession by the last quarter of 2018. We’re overdue. All OECD countries are growing, to the point where Brent crude prices are going up. This isn’t sustainable, especially since many developed nations have been kicking the bucket down the line.

Personal genomics is going to be more of a presence as the year progresses. I was surprised by all the attacks from the tech-press on direct to consumer genomics over the past few months. That indicates to me that the industry is getting big enough to be a click-bait target.

George R. R. Martin will publish Winds of Winter.

More ancient DNA from the New World. This has been in the works for a while. I’m really skeptical that they won’t be able to push it out in 2018.

Twitter will continue to not be able to find its way. Basically, it can’t win, and won’t win.

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