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

November 12, 2018

Open Thread, 11/12/2018

Filed under: Open Thread — Razib Khan @ 7:03 pm

Fatal Discord: Erasmus, Luther, and the Fight for the Western Mind is an interesting book. Very much on the side of Erasmus. Like the author, I do think Erasmus turned out to be a beautiful loser. But ideas and biographies can have second acts.

How the GOP Gave Up on Porn. Basically, the war was lost. The curious thing about the pervasiveness of porn today is that arguably in many ways our modern society is more prudish than that of the 1970s and 1980s when the political activity around obscenity was very active.

Population genomics of grey wolves and wolf-like canids in North America.

The Summer’s Most Unread Book Is… From 2014. People don’t seem to finish non-fiction. Though for a lot of nonfiction books you don’t have to read every chapter, and they are very loose in a narrative sense.

Outlaw King Is a Lot Better Than You’ve Heard.

Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating.

If you need a paper, Sci-Hub.

Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference.

Shades of complexity: New perspectives on the evolution andgenetic architecture of human skin.

A Two-Player Iterated Survival Game.

Cultural Selection Shapes Network Structure.

A new blog, Academic Parents. Two of my kids were born during graduate school. I was not the primary caregiver at all, and obviously did not give birth to them. But it was somewhat difficult still. Can’t imagine if I was the one taking care of the newborn.

It’s also nice to see people starting blogs. Both Twitter and YouTube streaming have replaced the “voice” that blogging gave random people, but both media are relatively vapid and shallow compared to having to write down your thoughts.

Bob Trivers’ Natural Selection and Social Theory is now a free PDF. Highly recommend this book. Trivers is an engaging writer.

Last week I made a bet with a friend that Republicans would gain one seat in the Senate, and Democrats would gain the House. Looks like I won that bet.

 

November 4, 2018

Open Thread, 11/4/2018

Filed under: Open Thread — Razib Khan @ 12:46 am

So in a few days everyone can stop pretending to be cut-rate Nate Silvers.

My prediction: Dems will take the House. But Republicans will make a gain of +1 in the Senate.

Pakistan’s Hybrid Government and the Aasia Bibi Fiasco.. Basically, reasonable people in Pakistan are terrified about being openly reasonable, lest the crazy minority kill them. Another thing is that the details of what this woman did is irrelevant now, she’s a symbol. We’ve seen this in the United States: feelings don’t care about your facts.

DNA Sequencing Giant Illumina Will Buy Pacific Biosciences For $1.2 Billion – Exclusive CEO Interview. I think this is precautionary.

Half of Americans believe in ghosts…

Least-cost pathway models indicate northern human dispersal from Sunda to Sahul.

Inferring the ancestry of everyone. “We introduce an algorithm to infer whole-genome history which has comparable accuracy to the state-of-the-art but can process around four orders of magnitude more sequences.”

Largest genome-wide association study for PTSD identifies genetic risk loci in European and African ancestries and implicates novel biological pathways.

Many options, few solutions: over 60 million years snakes converged on a few optimal venom formulations.

Genetic Consequences of Social Stratification in Great Britain. This is obviously triggering discussion. But please note this preprint is the beginning of a conversation, not the closure on anything.

Species limits in butterflies (Lepidoptera: Nymphalidae): Reconciling classical taxonomy with the multispecies coalescent.

Again, Tim Blanning’s Frederick The Great is interesting as both biography and history of 18th century Prussia. The book has the subtitle “King of Prussia,” but if Blanning was in it for the clicks, it would be “The Gay Atheist Autocrat.”

October 28, 2018

Open Thread, 10/28/2018

Filed under: Open Thread — Razib Khan @ 1:35 pm

An old friend from college has a new book out, Augmented Mind: AI, Superhumans, and the Next Economic Revolution. This looks to be in Jim Miller territory.

Sex in humans may not be binary, but it’s surely bimodal. Jerry Coyne is a well known evolutionary biologist who is also a vocal atheist. He’s now emeritus from the University of Chicago, and so I feel he’s kind of “out of step” with the culture. For example, within this post, which I generally agree with, he uses the term “transsexual” when most academics would use “transgender” to mean what he means. A lot of biologists don’t comment on this issue for two reasons. First, it’s politically fraught and you can’t really win. Second, the terms, norms, and frameworks are changing fast and constantly, so that people don’t even know what they’re addressing.

Speaking of fraught, the first robust SNP hits for male nonheterosexual behavior were reported at ASHG. The preprint should be out in less than four months. Antonio Regalado has already reported on it, Genes linked to being gay may help straight people get more sex. We plan to interview one of the authors on our podcast.

Recently talked to some people from Andy Kern’s lab about implications of Wright-Fisher vs. non-Wright-Fisher models in terms of spatial heterogeneity. It really makes me excited for the “forward simulation revolution.” Talking to people in evolutionary genomics that isn’t focused on getting NIH grants for human research, and it is clear why Matt Hahn has stated that there’s already enough data produced for many years to come.

A Tentative OUT OF INDIA Model To Explain The Origin & Spread Of INDO-EUROPEAN LANGUAGES. I’m skeptical of the conclusion, but this post has a lot of interesting information. Additionally, I think that AASI ancestry is going to be found in the Indus Valley between 3000 and 2000 BC…but I’m not totally sure. Johanna Nichols’ work is recommended though.

The Fifth Column podcast talks to Sarah Haider. In general, I’m a fan of the podcast.

Recently I’ve been thinking about China and Saudi Arabia. Recently we’re looking skeptically at our elite’s ties with Saudi Arabia. But what about China? Many researchers and businesspeople “have” to work with China, and unlike Saudi Arabia, it seems implausible that we can “avoid” interactions. But there are plenty of human rights issues with the Chinese state. The only conclusion I draw is that people need to be careful about getting on their high horses. Researchers who criticize working with the Saudis or in Israel should also consider them working with Chinese colleagues who are under the purview of a problematic state…but that penalize their Chinese colleagues, and would be harder and harder to maintain over the years.

Fast Hierarchical Bayesian Analysis of Population Structure.

The truth behind America’s most famous gay-hate murder. The media and the mainstream institutions basically colluded to create a narrative more politically convenient. Are we surprised?

15,000 Year Old Spearpoints Reveal Details About The Peopling Of The Americas.

When It Comes to Sleep, One Size Fits All.

Rare genetic sequences illuminate early humans’ history in Africa

October 21, 2018

Open Thread, 10/21/2018

Filed under: Open Thread — Razib Khan @ 11:20 pm

You may have noticed I haven’t been posting much. Busy with other things, like ASHG, work, family, etc. I don’t normally post “won’t be posting often” notices, as no one really cares much about blogs…but when I go into lower production mode people sometimes worry. No reason to worry.

Tim Blanning’s Frederick the Great: King of Prussia is an excellent book. So is The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815. Finally, Iron Kingdom: The Rise and Downfall of Prussia, 1600–1947. One of the most interesting things about Frederick the Great: King of Prussia is how Blanning recounts the importance of personally playing and repeatedly listening to music in the life of the German monarch. He was apparently a very competent flutist.

There was talk about ASHG about the Amy Harmon article, Why White Supremacists Are Chugging Milk (and Why Geneticists Are Alarmed). It seems most of the geneticists I know personally were contacted by Harmon at some point over the last two years. A lot of work went into this. Many of our quotes were obviously not used. That’s called journalism.

There was a period when many frog-Nazis were on Twitter brandishing a particular STRUCTURE bar plot (since frog-Nazism has been severely purged by Twitter I see this far less often). I understand that many journalists and people of the “chattering-thinking” classes are strongly influenced by what they see on Twitter in terms of their perception of what’s going on in the world.

Additionally, to be honest for many white people racism is somewhat an abstraction. They need to make recourse to instrumental variables. The SNL election night sketch which shows white liberals talking about how it’s never been so bad, and black comedians nodding along, illustrates a real trend, and that is that many white liberals feel like there has been a massive upsurge of racism over the past few years.* But as a nonwhite person who has lived in this country since the early 1980s, it is clear that America is far less racist than it was back then, and our society has been defined by a gradual decrease in racial prejudice. White support for laws banning interracial marriage went from about 25% in the 1980s to 10% in 2002, when the question stopped being asked because it was such a marginal viewpoint.

A story about the social and political of implications evolutionary population genetics is a reasonable one. And, it might make a somewhat interesting academic paper as well. But the prominence of this piece to me cuts to a deep disagreement about the nature of racial conflict and difference within human societies. Immanuel Kant’s abstract and intellectual reflections on race may be alarmingly white supremacist to many moderns, but the profitable character of exploitation of sugar and the utility of slavery in the West Indies, and the rise of the West in a much more robust manner as signified by the McCartney Mission in the 1790s, was far more important in shaping the emergence of a very vigorous white supremacist ideology in the late 19th century which culminated in Madison Grant and Lothrop Stoddard.

I enjoy discourses on the intersection of race and genetics as much as the next person. I write them myself. But the most concrete thing I can do for the “racial question” is what I’m doing already: participating in the amalgamation of very distinct pedigrees and producing Americans related to a much larger fraction of the world’s population. White Americans who believe in the cause of racial social justice and anti-racism can do something very easily if they so choose: select a non-white partner and produce mixed children. If you are already partnered up, encourage your children to do so. This will make a bigger difference than retweeting how great diversity is, while not living it in your own life. For white progressives, do understand that your nonwhite allies notice the overwhelming pallor of the types of people who become and remain your intimates. You spend an afternoon on a racially diverse panel. Why not spend life in a racially diverse manner? Because I am a political outsider to these issues nonwhites probably feel more comfortable telling me how they perceive you don’t have much skin in the game. An ounce of action is worth a pound of talk (also, you can proactively give money to nonwhite people from your own disposable income).

The above is not a troll at all. I’m not the sort of person who thinks that the type of person another human being becomes friends with, or partners with, is my business. Do as you wish. But if you accept the premises of most forms of anti-racist talk, then Norman Podhoretz’s 1963 essay which enjoins action still applies.

The Uralic podcast is up. Brown Pundits now have a podcast.

This Elizabeth Warren fact-check by the Daily Caller Foundation’s Emily Larsen is pretty good. Having to listen to political pundits talk about ancestry testing all week has been painful. More need for education….

ASHG photo that I find most amusing.

As most of you probably know, the human genome still has gaps. I felt this year more people talked about those gaps, and how to fill them in. Also, lots of African genetics (this was by plan).

May write some more tutorials soon. Depends on the time.

The Slow Burn podcast ended with talking about Juanita Broderick. The Broderick allegations really have shot into prominence over the last few years. But if the Republicans knew about them in detail, that does make their determination to impeach Bill Clinton far more comprehensible.

I don’t have much to say about the Khashoggi thing you haven’t heard elsewhere.

A new analysis of CEU mutation rates is there is an age effect, most mutations are paternal, and, there might be variation in increases in mutations with older individuals by family.

* Most of my white friends tend to point to particular media anecdotes. As a nonwhite person I have not perceived any difference, and I travel in various parts of the country. Your experience may vary.

October 16, 2018

Open Thread – Brown Pundits

Filed under: Open Thead,Open Thread — Razib Khan @ 12:24 pm

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

October 15, 2018

Open Thread, 10/15/2018

Filed under: Open Thread — Razib Khan @ 1:16 am


I pinned the above chart to my Twitter profile because I’m “trying to make it happen.” It was David Mittelman’s idea, and the data was courtesy of ISOGG, but putting it together as a graph has really brought home to people how the consumer genomic landscape has changed over the last half a decade.

The plot to the right, which shows a smoothed chart of the total number of kits over time, is also important.

I recorded a podcast for the Urbane Cowboys last week. It should go up today, so watch for it. I talked about a variety of topics, so I don’t know how it will drop in regards to editing.

Was talking to a friend about the importance of emotion in reasoning, or at least how emotion allows us to reason better. He asked about books, and Descartes’ Error came to mind. But I’ve read about critiques of its interpretation of the history of science and philosophy, though I think the big picture conclusion is probably still valid.

Will be at ASHG this week. Mostly I’m going to learn more about African genomics. Not as much on pop-gen as in previous years. If I approach your poster, don’t worry that I’m going to tweet or write about. Just be cool.

Noticed Tim Blanning’s massive survey of Frederick the Great is now less than $10 on Kindle. Because of the World Wars, I think we learn a lot less about Prussia from 1700 on than we otherwise would. Blanning’s The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815 is also excellent.

I’m listening to John Keegan’s A History of Warfare on Audible. To be honest I think I’m much better at reading than listening. This should be surprising. In courses, I generally prefer to learn from the textbook as opposed to listening to lectures. And I have a lot of experience reading over my lifetime. Less so listening.

Xuzi: The Complete Text has been a difficult read for me. I’ve gone back and reread passages several times. It is definitely on the discursive side. That being said, I have come to a strange observation: Xunzi’s view of religion is strangely similar to Ludwig Wittgenstein’s. Here from the Stanford Encylopedia of Religion:

He opposed interpretations of religion that emphasize doctrine or philosophical arguments intended to prove God’s existence, but was greatly drawn to religious rituals and symbols, and considered becoming a priest. He likened the ritual of religion to a great gesture, as when one kisses a photograph. This is not based on the false belief that the person in the photograph will feel the kiss or return it, nor is it based on any other belief. Neither is the kiss just a substitute for a particular phrase, like “I love you.” Like the kiss, religious activity does express an attitude, but it is not just the expression of an attitude in the sense that several other forms of expression might do just as well….

This seems similar to Xunzi’s belief that religious rituals were an important part of life, even if supernatural beings did not exist. Though Wittgenstein seems to have had some sort of fundamental mystical religious beliefs, whereas Xunzi was more of a naturalist.

The whale shark genome reveals how genomic and physiological properties scale with body size. Dim on comparative genomics. But I do like sharks.

Harvard and the Brigham call for more than 30 retractions of cardiac stem cell research. The medical science literature is going to yield a lot of problems sooner than later.

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

The Democrats Have a Latino Problem Hispanic voters were supposed to be the party’s future. It’s not working out that way.

Jason Collin’s on global fertility projections.

Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters.

Hidden ‘risk’ in polygenic scores: clinical use today could exacerbate health disparities.

Identity inference of genomic data using long-range familial searches. If they solve the Zodiac killer, forget about the worries.

Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.

Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics.

Existence and implications of population variance structure.

Megalakes in the Sahara? A Review.

On this week’s episode of The Insight we’re talking about the genetics of the Uralic peoples, and Finns in particular.

Have you been noticing more intrusive and stranger advertisements in the media? That’s because it’s in trouble. The whole sector. But you knew that.

October 9, 2018

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 6:28 pm

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

October 8, 2018

Open Thread, 10/8/2018

Filed under: Open Thread — Razib Khan @ 8:03 pm

Paul Romer won the Nobel. Not a big surprise. David Warsh’s Knowledge and the Wealth of Nations: A Story of Economic Discovery is pretty good. I recommend it. I would read it in concert with Hive Mind: How Your Nation’s IQ Matters So Much More Than Your Own and A Farewell to Alms: A Brief Economic History of the World (Warsh wrote a negative review of the second book and likely would not be a fan of the first).

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history. Bigger Yemeni data set. Yemeni and Levantine populations seem quite similar….

As you may not know Google+ was finally given an explicit sunset schedule. Google tried twice to tackle Facebook but failed both times. But it turns out that Facebook may never have a successor. A centralized social-graph has weaknesses, and younger cohorts seem to be creating segmentation. Their parents are on Facebook, so they have a nominal Facebook account. But the real action is on other platforms.

Life on the Dirtiest Block in San Francisco. Having drinks with friends at the top of hotels and high rise condominium complexes makes you forget that far below the homeless have come out and taken over the night.

Why most narrative history is wrong. First, this seems to be more about ‘popular’ history today, and the mainstream of past history. One reason contemporary academic history is so boring for most people is that it resists grand narrative temptation.

With that being said, this is more of an indictment on modern journalism.

Quantifying how constraints limit the diversity of viable routes to adaptation.

A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process.

Expanded Pre-Implantation Genomic Testing.

Fudged statistics on the Iraq War death toll are still circulating today. Do you remember this debate more than ten years ago? I do. The very assertion of these numbers distorted the discourse. This was just a prefiguring of the media landscape today. It’s mostly propaganda.

Phylogeny, ancestors and anagenesis in the hominin fossil record.

The genetic relationship between female reproductive traits and six psychiatric disorders.

In case my Twitter account gets deleted, remember you can subscribe to my RSS or follow my Facebook page.

October 3, 2018

Are there an other readers from 2002?

Filed under: Open Thread — Razib Khan @ 10:44 pm

As some of you know, this blog started in early June of 2002. I just noticed that two people left comments who date from the summer of 2002…which means I have people here who have been reading what I’ve been writing for 70% of my adult life. I know people drop in and out, but are there any others?

Just curious.

October 2, 2018

Open Thread – Brown Pundits

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

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

September 30, 2018

Open Thread, 9/30/2018

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

A new shirt, Vaccines Cause Adults. I think that’s pretty funny. Since I don’t have that sort of human, it wasn’t my idea. Obviously, Photo 51 t-shirts are still on the  DNAGeeks website.

Patrick Wyman does not recommend The Silk Roads: A New History of the World. The killer observation for me is that whenever Patrick knew a lot about the topic the author was kind of wrong or off. This is an incredibly important sign for me. If you don’t have this still, you probably need to get to a point where you know enough about a topic. Just pick one, any topic. Additionally, he observes that 40% of the book deals with 20th and 21st century history. That’s also a big no-no for me. Contemporary history is well covered in our society. We have a presentism bias.

On the other hand, I would recommend Empires of the Silk Road. Christopher I. Beckwith is kind of cranky, but he’s learned and interesting.

Valerie Hansen’s The Silk Road: A New History is one I’d also recommend. It’s more focused on archaeology and the earlier period before 1000 AD. Hansen also lacks the long narrative ambition of Beckwith’s treatment, but if you want to know how Sogdian merchants rolled during the Tang dynasty, this is for you.

Buddhism and Islam on the Silk Road is also a good book, though its focus is rather narrow.

Lee Jussim asked on Twitter what counts as “white” today since so much social justice discourse (SJD) revolves around the concept. My response is basically “white” is what is necessary for you to win an argument (though another element now is that if you are Muslim you are not white, no matter how white you look, just like if you have a Spanish surname, you are not white either somehow). Here is how it works:

Italians are white: the ancient Romans were white people who oppressed and executed a marginalized person of color, a brown Palestinian named Jesus.

Italians are not white: Until after World War II Italians were actually not viewed as white, and had to “become white” (or, they had to become people who think they are white). They were even lynched!

The takeaway is that sophism is a feature, not a bug. That’s why I’m so good at faking this discourse.

He’s trolling us.

Global alliances and wheels within wheels. Talking about the concern that American Leftists have about Hindu nationalism. Though they seem sanguine about Islamism.

John Horgan interviews Bob Trivers in Jamaica. As usual with Trivers, it’s crazy. Though if you read his autobiography, Wild Life, there’s a lot that’s similar.

Of all Trivers’ books though, I would really recommend Natural Selection and Social Theory: Selected Papers of Robert Trivers. There’s a lot of science and biography in that work. Anecdotes about W. D. Hamilton in particular I enjoyed.

Variation in actual relationship as a consequence of Mendelian sampling and linkage.

What’s China’s new luxury status symbol? A curvy butt. Had a conversation with a friend who is a businessman in China. His female employees have butt-workout apps.

Gen­ome-edit­ing scis­sors will re­volu­tion­ise plant breed­ing, yet a pro­fessor fears EU countries will get side-tracked.

Margins – Save, annotate and share your papers with anyone.

An Empirical Demonstration of Unsupervised Machine Learning in Species Delimitation. The title is kind of weird. STRUCTURE? Also, I don’t really believe in automatic species delimitation. But it’s an effort.

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders.

Reproductive Longevity Predicts Mutation Rates in Primates.

Stronger and higher proportion of beneficial amino acid changing mutations in humans compared to mice and flies. I think I’ll blog this.

Reihan Salam has a new book out, Melting Pot or Civil War?: A Son of Immigrants Makes the Case Against Open Borders. The title is a bit overwrought, but Reihan is not. Obviously we share a lot in terms of our backgrounds and our opinions. And on questions regarding assimilation we’ve been on the same page for a long time.

Sexual selection, environmental robustness and evolutionary demography of maladapted populations: a test using experimental evolution in seed beetles.

The Blank Slateism of the Right. This is really about the Anglo-Right. American conservatives who come out of the liberal tradition are big fans of John Locke. That should tell you all that you need to know.

Robert Plomin’s Blueprint: How DNA Makes Us Who We Are is coming out soon. To be honest it looks like an updated version of Judith Rich Harris’ The Nurture Assumption.

Greg Cochran wrote up a review in Quillette with the expected title, Forget Nature Versus Nurture. Nature Has Won. Nathan Comfort in Nature wrote Genetic determinism rides again.

Stuart Ritchie was not happy with Comfort’s review:

The review is as bad as you’d think. He doesn’t seem to know the science, but that’s a feature, not a bug, for the sort of review he’s going to give. It’s useful for me because I can note who retweets and “likes” the review, as these are people who I will ignore on all things genetics indefintely.

A bigger question that I asked a few liberal academic friends: with all the concern over eugenics where’s the widespread objection among the usual hand wringers about noninvasive prenatal testing and widespread abortion of fetuses that test positive for Down Syndrome? In the Nordic countries nearly 100% of fetuses which test positive are aborted. In France about 75%. In the United states 70%.

My personal suspicion is that academics are much more concerned about future and vague eugenical specters. Not those activities done freely and through the proactive choice of people of their own class and likely liberal politics. Burn a few Robert Plomin’s at the stake, but make sure you don’t jeopardize your colleagues’ dreams of having a “healthy” baby.

Overlooked factors in the analysis of parole decisions. Basically it looks like the old result that judges are harsher before lunch is an artifact of who is seen before lunch (prisoners without attorneys tended to be seen before lunch).

Unless I have looked at the original study, I’m starting to just shy away from retelling results published through peer review. Studies really need to have sample sizes in the title. Small sample sizes are OK in some contexts, but so often they are used to get away with stuff.

September 25, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 12:22 pm

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

September 23, 2018

Open Thread, 9/23/2018

Filed under: Open Thread — Razib Khan @ 10:56 pm

Curious how many readers recognize the reference on the shirt to the left? You probably know if you’ve read The Double Helix. On the DNAGeeks website now.

Salon is stiffing freelancers of $150. I think this is more a commentary on the market for freelancers than Salon‘s always tenuous finances. The market-clearing price for a lot of web journalism/commentary is pretty low. Salon does this because it knows freelancers will tolerate and accept this behavior more often than not.

This long article from Huffington Post (and boosted on the editor in chief’s Twitter), Everything You Know About Obesity Is Wrong, is being widely shared on Facebook (I haven’t seen it much on my Twitter, but that’s because I follow mostly scientists).

Of course it’s really really light on the science of nutrition. Or should I say “science”? Because the truth is that nutrition science has a lot of problems, so there is space to criticize it. But that being said, this piece is being shared by people who seem to think that there is a conspiracy make it seem like being obese is unhealthy. But most of the article is about how cruel people are to the obese, especially medical professionals. There’s really little evidence presented that being obese doesn’t cause issues with morbidity and mortality. Quotes like this are representative: “But individuals are not averages: Studies have found that anywhere from one-third to three-quarters of people classified as obese are metabolically healthy.” That’s a huge interval. Why?

Ultimately the article should have been titled Everyone Is Cruel to Obese People and That is Wrong and Ineffective.

If you want some real nutrition science, What I learned about weight loss from spending a day inside a metabolic chamber.

I bought Early China: A Social and Cultural History. A lot of archaeology. But that’s what you get! I figure I should know more about Zhou China though. I think next I’ll try to read up on Neo-Confucianism, a topic I’ve been lax in because of my leaning toward “Han learning.”

Highly recommend Viet Nam: A History from Earliest Times to the Present. Most of the book does not deal with the Vietnam War. One curious thing I learned: the Vietnamese identity in the period around 0 AD was strong influenced by the influx of Yue people from southern China, as they imparted their culture and statecraft on the proto-Vietic populace. Of course on top of that came later Chinese migration, which resulted in the emergence of Vietnamese as a tonal language.

Though you’ll probably really want Phở as you read the book….

Also, I knew this, but Viet Nam makes it clear in all the gory details that the Austronesian Cham people of central and southern coastal Vietnam were undergoing the same shift to Islam from Hinduism that was occurring further south in the period after 1500. It seems rather clear that the emergence of a Cham sultanate on the model of Mataram or Johor never occurred because the Vietnamese conquered the Cham kingdom, and then assimilated or exterminated most of the natives. Many Cham fled to Cambodia, where they form the Muslim minority of that nation.

But, a small minority of Cham remain in Vietnam, and amongst these are a substantial Saivite Hindu community. It seems entirely possible that if the Cham had retained their independence as a nationality one would have seen total Islamicization, as occurred among the Malays. As is this, this process was retarded by Vietnamese conquest, and so some Chams still remain Hindu (the same process applies to the Philippines, where the native population was influenced by Hinduism first, and was in the first stages of Islamicization, when the Spaniards conquered the archipelago).

Indonesia: Peoples and Histories is worth a quick read. Not as dense and informative as Viet Nam: A History from Earliest Times to the Present.

Change in sexual signaling traits outruns morphological divergence in a recent avian radiation across an ecological gradient. Not a surprising result I guess.

This AJ+ video about “white feminism” is getting a lot of attention. Mostly because AJ+ is backed and owned by a conservative Salafist regime which runs an oligarchic state on the backs of dark-skinned South Asian indentured labor. I’ve spent a week in Qatar at a really nice hotel. I’ve never encountered service staff as solicitous and courteous in the United States. At some point I may write about how certain organizations and institutions use political movements as instruments…but I always feel this is so obvious.

Digging Into the Genetics of Drug Targets. Derek Lowe, the science blogger who has been blogging for the longest time. This is why it’s worth reading him.

Next week on The Insight we’ll be talking about Indian genetics, again. Partly in anticipation of the ancient DNA paper, which should drop any day now (I have no inside information). Question suggestions welcome.

Quantifying Heterogeneity in the Genetic Architecture of Complex Traits Between Ethnically Diverse Groups using Random Effect Interaction Models

Evolution and Selection of Quantitative Traits has finally been published in book form. It’s a good value on a pound-for-pound basis….

Individual selection leads to collective efficiency through coordination. The last sentence of the abstract is key: “This finding reveals a general principle that could play a role in nature to smoothen the transition to efficient collective behaviors in all games with multiple equilibriums.” You need to figure out ways to get to cooperation.

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. It seems within the Near East farming spread mostly through cultural diffusion. My suspicion is that that is due to the fact that it didn’t provide that huge of a demographic boost in its primitive form. Once the various farmer groups perfect their toolkit, they expanded into areas dominated by hunter-gatherers, not other farmers.

The Austronesian expansion actually makes me consider the possibility that we may never understand why the modern humans in the Near East ~55,000 years ago “broke out” and absorbed all the other hominin groups.

Cornell Just Found Brian Wansink Guilty Of Scientific Misconduct And He Has Resigned. If Wansink hadn’t become famous through his self-promotion, he could have continued on with his career. What he’s guilty of lots of people are guilty of, and the media and the public are complicit by demanding sexy and practical results.

Detecting archaic introgression using an unadmixed outgroup.

How Connected Is Your Community to Everywhere Else in America? This is incredible data journalism.

Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast.

Large-scale investigation of the reasons why potentially important genes are ignored.

Polygenicity of complex traits is explained by negative selection.

The effects of demography and genetics on the neutral distribution of quantitative traits.

When I’m working sometimes I listen to the Men of the West YouTube channel. It’s run by a Tolkienist who does some serious work in this area.

September 18, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 12:26 pm

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

September 17, 2018

Open Thread, 9/17/2018

Filed under: Open Thread — Razib Khan @ 10:13 pm

There are lots of things from Imperial China 900–1800 that I learned, though more often it simply deepened my knowledge. At this point, I am curious about something that is more like economic history (yes, I’ve read The Great Divergence). Recommendations?

Here is a fact I learned from Imperial China 900–1800 that might be of interest: in the late 17th century the expanding Manchu Empire (which had conquered China) and Russia began to jostle for power in Inner Asia, and the Khalkha Mongols, the Mongols proper, were deciding which side to align with. I had long known that the Khalkha Mongols had aligned with the Manchus. What became the Manchu imperial line had a genealogical relationship with the Mongols, as they would often take wives from a particular group of Mongol tribes (Kangxi Emperor’s paternal grandmother was a Mongol). Imperial China makes it clear that Mongol cavalry units were critical elements of the Manchu military machine, and as the Manchu assimilated into the Han culture they became arguably even more important as a population which could provide militarily ready men at a moment’s notice.

But a more interesting aspect of the Manchu alliance with the Mongols are the ethnoreligious implications, and what they wrought across Inner Asia. The Khalkha had become Tibetan Buddhists by the time the Manchus conquered China. According to Imperial China, their religious leaders argued for the furtherance of their alliance as junior partners to the Manchus as opposed to the expanding Russians in part because the Manchus were more respectful of Buddhism. Mind you, the Manchus were not themselves Tibetan Buddhists, though they were always keen to co-opt the various prominent Tibetan lamas. But, they had earlier practiced Chinese and Korean forms of Buddhism (as the Jurchens) and seemed resistant to Tibetan Buddhism in comparison to the Mongols.

The Russian Empire was obviously dominated by an Eastern Orthodox Christian elite. But, eventually, they made accommodations with various minority religions, including Buddhism. But, Buddhism, Islam, Judaism, and non-Orthodox Christianity were all subordinate religions. Historically non-Orthodox ethnic groups invariably suffered erosion due to the social advancement which conversion to Orthodoxy entailed. From the viewpoint of meta-ethnic identity, the Manchus were clearly superior to the Russians, as the Manchus tended toward more neutrality in religion than the Russians.

Dzungaria in red

And yet there are two conditions that need to be highlighted here. The Manchus were responsible for the ethnic cleansing of the Mongol Dzungar tribes in the 18th century. The Dzungars were the last great Inner Asian polity to challenge the gunpowder empires. They were arguably the final flowering of the steppe and its way of war. Unlike the Khalkha Mongols the Dzungar tribes, who were Oirat, were not part of the Mongol expansion under Genghis Khan. Ethnically somewhat distinct, the Dzungar nevertheless were Tibetan Buddhists, just like the Khalkha.

The 18th-century wars to destroy the Dzungar polity and exterminate or scatter its people occurred with the assent and aid of the Khalkha Mongols, who were ethnically close and religiously identical. Some of the Dzungar even fled westward, to joint co-ethnics under Russian rule in the Kalmyk Khanate. The region of Xinjiang that today is labeled “Dzungaria” had very few Mongols after the wars against the Dzungars. Nor did it have many people who we today would call Uygurs. Rather, post-genocide Dzungaria was occupied by nominally Muslim Kazakh and Kirghiz people, while today it has become a magnet for Han and Hui people as Urumqi has become Central Asia’s largest city.

Why am I reviewing all of this? To show how complicated the idea of alliances and affinities based on civilizational identity can be. The reality is that religion and ethnic identity do matter somewhat, but on the medium-scale, they are not as important informatively as on the extremes. Obviously traditionally ethnoreligious groups exhibited ingroup affinity. Buddhist Mongols lived with Buddhist Mongols. Muslim Mongols often assimilated to becoming Turks, while Mongol tribes which had experimented with Islam but eventually became Buddhist lost their Islamic connections. And, on the largest temporal scales and on the margin broader ethnoreligious affiliations matter. Buddhists from as far away as Japan protested to the Taliban when they were mooting the idea of destroying the Bamiyan Buddhas. Christians focus on the persecution of Christians in China. The Mongols, Oirat and Khalkha, became heavily involved in Tibetan politics after their conversion.

Details matter.

A very long post from me, Between the saffron and scimitar, inspired by a lot of the comments we get at Brown Pundits. About six months ago I said something about the Kali Yuga on Twitter in a joking manner, and someone responded: “isn’t that an alt-right meme.” Well, it turns out that some alt-right people are Evola-loving pagans, though I doubt most are. But the idea of the Kali Yuga kind of predates the alt-right in the Hindu tradition, though a lot of people don’t know anything about Hinduism. Similarly, many Indian Hindus (religious or not) have weird perceptions of the origin of any ideas that are also found in Islam…and my name does not help in the way they reflexively respond when I express ideas that might be found in Islam.

But the reality is that it is hard to tease apart Indian culture today from the various influences that domination by Muslims left, even if said Indians are self-consciously anti-Muslim. This is to many people somewhat offensive. I think a good analogy might be some conservative white Americans who don’t want to admit that for many decades white supremacy was considered part and parcel of American patriotism, and constitutive to American nationalism. That arguably has long-term impacts, though unlike many on the Left I do not think that it is an all-pervasive miasma which touches every aspect of American life in 2018.

Pew has a new religious typology out. Not much in the report is surprising.

Here is a surprise to me though: New Age beliefs are more common among the orthodox Christian/religious groups than among the secular subset that is dominated by atheists and agnostics.

There are some interesting distinctions between the “Religion Resisters” and “Solidly Secular.” The latter is 65% male, while the former is majority female. The latter is more educated, wealthier, and more likely to be concentrated in the Northeast and Midwest, while the former is more often in the West. The “Solidly Secular” are the type of people who would be New Atheists. The “Religion Resisters” are actually somewhat more liberal socially and politically issues than the “Solidly Secular.”

Another Pew report suggests that Americans with no religious affiliation have nearly as many Christian beliefs as Europeans who say they are Christian. This is not because those with no religious affiliation in the USA are very Christian. Rather, it’s because European “Christians” are a lot less orthodox than you might expect.

The Next Financial Crisis Lurks Underground Fueled by debt and years of easy credit, America’s energy boom is on shaky footing. Basically, the argument is that the fracking boom, which has driven American fossil fuel supply to the point where we now surpass Saudi Arabia, is an artifact cheap credit pumping money into the system.

Fracking isn’t profitable at current oil prices. I think the author is probably a little too pessimistic, because technology does get better, and increased crude oil prices will probably show up at some point to fuel further investment.

One of the best things about the fracking boom is I don’t have to listen to friends yammer on about “peak oil” in all-knowing tones. That being said, how are books like Confronting Collapse maintaining such high Amazon star rankings? Is it a fraud? Or do these sorts of pessimistic tomes just always sell well?

A thing I’ve noticed since I’ve shifted to mostly reading on Kindle: I read in a more sequential fashion. Obviously, I can still jump chapters, but the reality is that I don’t do it much. Is it just me?

Genomic prediction of cognitive traits in childhood and adolescence. This claim is important: “Polygenic scores for educational attainment and intelligence are the most powerful predictors in the behavioural sciences and exceed predictions that can be made from parental phenotypes such as educational attainment and occupational status.” I’m assuming this is the sort of stuff in Robert Plomin’s new book, Blueprint: How DNA Makes Us Who We Are.

Going to try and get a review copy for National Review.

E-book Sales Fell 10% in 2017:

Adult fiction remained the most popular e-book category–44% of sales in the category were in the digital format–but e-book sales in the segment dropped 14% from 2016, to 108 million units.

E-books have a much smaller share of the adult nonfiction market, 12%, but sales in the segment rose 3% last year, to 38 million units, NPD reported.

The steepest decline in e-book sales last year was in the children’s category, where sales fell 22%. In children’s, the digital format accounted for only 5% of all sales last year. E-book sales were down 8% in the young adult category, falling to 4 million units sold. The format comprised 18% of all young adult unit sales last year.

Makes sense that it would decline in the children’s category. When it comes to reference textbooks, I still go paper. It’s just easier for me to look things up.

Numbers did not add up in the passport revocation story. Unfortunately, this is a pattern in the media. Stuff that happened in the Obama administration was not reported…but when it continues in the Trump administration it becomes teh Nazi!

Genomic history of the Sardinian population. As Spencer and I alluded to on last week’s episode of The Insight, L. L. Cavalli-Sforza and colleagues did a really good job in their sampling. “Low effective migration rates separate these provinces from a broad area that extends to the mountainous Gennargentu massif region, including inland Ogliastra to the west. The Gennargentu region is also where some of the Sardinian individuals in the HGDP originate (A. Piazza, personal communication). We find that the HGDP Sardinian individuals partially overlap with our dataset and include a subset that clusters near the Ogliastra subpopulation.” That is, the HGDP Sardinians are among the more “EEF” Sardinians.

A Game of Thrones: The Graphic Novel is on sale for Kindle. I don’t even know if I’d want to read a novel in graphic form. But then I’m not a very visual person. Some of the original books actually had a few illustrations. But not that many. For the record, Eddard Stark in my head will always look somewhat like the actor Bill Campbell, not Sean Bean.

Eight Decades of Ethnic Dilemmas: Iconic sociologist Nathan Glazer on the problems of group identity, affirmative action and Donald Trump. It’s incredible to me that Nathan Glazer is still around and intellectually active. To a great extent I’m sympathetic to many of the views he expresses in this article. He’s in the same class as Thomas Sowell for me, though to be entirely frank Sowell has gotten a little too predictably partisan with age for my taste.

Inferring Continuous and Discrete Population Genetic Structure Across Space. An important paper.

Gibraltar Neanderthal Genomes on the way….

Bacteria in a Dinosaur Bone Reignite a Heated Debate.

Dating genomic variants and shared ancestry in population-scale sequencing data. When I see Gil McVean on the author list I read.

Two Psychologists Four Beers. Podcast with Alice Dreger. One of the co-hosts seems to have disappeared for most of the podcast. I assume he was just drinking beer. The last third where Dreger talks about journalism is probably the most novel.

Also, Dreger admits that she probably would have defended Bret Weinstein and Heather Heyer with vigor if she had not been so exhausted and drained by her own academic controversy, as she was forced out of her Northwestern position.

I will add on a personal note that I feel some fatigue and exhaustion because many of my friends in academia expect me to “speak up” about topics that are too politically sensitive for them to broach. I’m OK with doing that…but I have my limits, and other peoples’ third rails are not the burning passion of my life.

To be frank, I’m pretty skeptical about the future of the republic of letters and intellectual life in the West. At least in public.

For example, Thousands of scientists publish a paper every five days.

The Many Indian Genomes.

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations.

An Ancient Crosshatch May Be the Earliest Drawing Ever Found. Looks like well-done steak to me.

By the way, the consistently shared drift between Basques and Sardinians, especially highland Sardinians, should make us lean toward the non-Indo-European hypothesis for Paleo-Sardinian.

September 10, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 8:58 pm

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

September 9, 2018

Open Thread, 9/09/2018

Filed under: Open Thread — Razib Khan @ 8:55 pm

DNAGeeks is now promoting some “helix” themed polos. If you click through, you’ll see a 25% discount code.

Listened to Carl Zha and Nathan Myers‘ podcasts. About China and the Silk Road.

The podcast Two for Tea with Iona Italia and Helen Pluckrose has an interview with my friend Sarah Haider.

Zha pointed me to this report, Massive Numbers of Uyghurs & Other Ethnic Minorities Forced into Re-education Programs, which is the source for the number in articles like this: U.N. Panel Confronts China Over Reports That It Holds a Million Uighurs in Camps. It’s short, but if you don’t want to read, there are major reasons to be skeptical of the 1 million figure as being credible. I think it’s likely that the Chinese government is targeting Uyghurs for re-education, partly because there’s a long history of that sort of thing. But the Kashgar region, in particular, strikes me as extremely unrepresentative, do its particular nature (far more Uyghur and Muslim than any other area of China).

Some people have asked me about books about Central Asia. Here are some I’ve found interesting, The Silk Road: A New History, Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present, and Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane.

Peter Frankopan’s The Silk Roads: A New History of the World is supposedly good, but I haven’t read it.

I don’t know the last time I linked to Salon. I subscribed to Salon premium in 2002…but I’m pretty sure I let it lapse early in my blogging. But here I go, A witch hunt or a quest for justice: An insider’s perspective on disgraced academic Avital Ronell. There’s a lot of “score settling” in this piece…the author hired Ronell, who turned on him and swallowed his department.

A certainly number of professors have, are, and will, engage in sexually inappropriate relationships with their graduate students. Ronell seems likely to be in that class, but the more interesting aspects are of the story are:

1) That prominent fashionable professors, such as Zizek and Judith Butler have defended her (Butler had a follow-up equivocation, but who knows, perhaps it’s just performative).

2) Ronell is a certain type of academic who everyone who has been in academia has heard of or experienced. The depiction in the Salon story makes her seem like a total psychopath who suborns the mission of the institution toward the service of her self-aggrandizement.  This is a certain type of professor. A certain type of business person. A certain type of middle manager. We all know of these people. It’s not surprising that they exist in the academy. But, I do wonder if the transparent fixation on style above substance in the field of scholarship, “deconstruction”, that Ronell operates within allowed her selfish and narcissistic tendencies to flourish in a manner it wouldn’t have if she was engaging in supervising laboratory work or archival research.

Alibaba’s Jack Ma, China’s Richest Man, to Retire From Company He Co-Founded.

Will Saudi Arabia Cease to Be the Center of Islam?. This piece cites The Idea of the Muslim World: A Global Intellectual History. I think it underestimates the cultural prestige of West Asians within Islam.

Should all babies have their genomes sequenced? Moot point.

The genetic history of the Iberian Peninsula over the last 8000 years:

The Iberian Peninsula, lying on the southwestern corner of Europe, provides an excellent opportunity to assess the final impact of population movements entering the continent from the east and to study prehistoric and historic connections with North Africa. Previous studies have addressed the population history of Iberia using ancient genomes, but the final steps leading to the formation of the modern Iberian gene pool during the last 4000 years remain largely unexplored. Here we report genome-wide data from 153 ancient individuals from Iberia, more than doubling the number of available genomes from this region and providing the most comprehensive genetic transect of any region in the world during the last 8000 years. We find that Mesolithic hunter-gatherers dated to the last centuries before the arrival of farmers showed an increased genetic affinity to central European hunter-gatherers, as compared to earlier individuals. During the third millennium BCE, Iberia received newcomers from south and north. The presence of one individual with a North African origin in central Iberia demonstrates early sporadic contacts across the strait of Gibraltar. Beginning ~2500 BCE, the arrival of individuals with steppe-related ancestry had a rapid and widespread genetic impact, with Bronze Age populations deriving ~40% of their autosomal ancestry and 100% of their Y-chromosomes from these migrants. During the later Iron Age, the first genome-wide data from ancient non-Indo-European speakers showed that they were similar to contemporaneous Indo-European speakers and derived most of their ancestry from the earlier Bronze Age substratum. With the exception of Basques, who remain broadly similar to Iron Age populations, during the last 2500 years Iberian populations were affected by additional gene-flow from the Central/Eastern Mediterranean region, probably associated to the Roman conquest, and from North Africa during the Moorish conquest but also in earlier periods, probably related to the Phoenician-Punic colonization of Southern Iberia.

The Insight will be putting up a podcast on the life and science of L. L. Cavalli-Sforza. Spencer worked with Cavalli-Sforza as a postdoc at Stanford in the late 1990s.

September 3, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 8:57 pm

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

September 2, 2018

Open Thread, 09/02/2018

Filed under: Open Thread — Razib Khan @ 6:07 pm

John Hawks’ write-up, The man who tried to catalog humanity: Luigi Luca Cavalli-Sforza chased Darwin’s dream of a tree of humankind, is worth reading in full. With some hindsight, it’s pretty clear that L. L. Cavalli-Sforza was way ahead of his time in terms of ambition and vision.

But he was also someone who paid attention to details. I have heard it said that Cavalli-Sforza could be very knowledgeable about where and from whom he obtained samples. The “Sardinians” in the HGDP dataset, for example, are not arbitrary, but “more Sardinian” than the random sample of Sardinians that you might find else.

Second, his multidisciplinary perspective allowed him to have deep and powerful insights, even if they in the details there was a lot he got wrong. In 2007 a friend of mine whose lab was collaborating with Cavalli-Sforza’s group told me how amusing and peculiar the younger researchers thought his fixation on agriculture was. But, it’s quite clear to me that the last decade has vindicated his intuition that shifts in “mode of production” have been critical to the arc of human evolution and diversification.

The Asian-American Age: At the movies and in court, a rising minority claims the spotlight. One of the problems with the idea of “Asian-American leaders” is that these leaders are very non-representative of Asian-Americans more generally. For example, Indian Americans who write and do journalism with an ethnic (but American) focus are very liberal. But the average Indian American, even if Democrat, generally don’t know what “Critical Race Theory” is and are not worked up over “intersectionalism.”

A Generation Grows Up in China Without Google, Facebook or Twitter.

New paper ignites storm over whether teens experience ‘rapid onset’ of transgender identity.

Adaptive evolution of sperm proteins depends on sperm competition in a pair of Lepidoptera.

4500-year-old DNA from Rakhigarhi reveals evidence that will unsettle Hindutva nationalists. I do wish that the Indian reaction wasn’t so ideologically polarized. There are the standard dumb Hindu nationalist responses…but a lot of the ‘secularists’ (that’s the term I see in their Twitter bios) barely understand the science either, and are selectively trumpeting the results as buttressing some ideological point.

And from me in India Today3 strands of ancestry

Pornocracy.

August 27, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 8:56 pm

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

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