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

September 18, 2018

Open Thread

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

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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

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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


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.

Open Thread, 08/27/2018

Filed under: Open Thread — Razib Khan @ 8:00 am

DNAGeeks is dropping prices and offering free shipping on the phone microscopes for the rest of August. We’ll be putting the scopes on sale until the stock is cleared.

As I’m reading Imperial China 900–1800, I’m still thinking most of the readers of this weblog would benefit from doing so as well. There’s just so much within the book that is food for thought. Though you should read A History of the Byzantine State and Society as well!

Quillette has been producing some good material recently. I find it curious since a lot of scientists and Left-liberals more generally have been attacking it really vociferously recently. To be honest I think it’s kind of a sign that whatever Claire Lehmann is doing, she’s probably doing it well.

The critique some of the writing at Quilette is uneven is surely correct, but that’s true of lots of publications. In those cases, the authors take a hit, but the publications aren’t totally written off.

First, Progress and Polytheism: Could an Ethical West Exist Without Christianity? Well, since ancient China was predicated on ethics, obviously Christianity is not necessary, though it may be sufficient. I think more predictable is going to be the critique that Christianity is necessary for liberalism, as implicit in the argument in Inventing the Individuals: The Origins of Western Liberalism.

Second, The Dangers of Ignoring Cognitive Inequality. This is related to the piece in The American Conservative, The Recruitment Problem the Military Doesn’t Want to Talk About.

If you haven’t, please check out Consumer genomics will change your life, whether you get tested or not.

Genetics Society Medal 2019 – Deborah Charlesworth. Very deserved. One of the authors of Elements of Evolutionary Genetics.

Enrichment of genetic markers of recent human evolution in educational and cognitive traits.

Brian Resnick at Vox has been writing some decent stuff on genetics.

My WaPo review of David Quammen’s new book on evolutionary trees (and a comparison with other reviews). Like Jerry, I am confused as to why The New York Times assigned a literary reviewer with no science background to offer opinions on David Quammen’s The Tangled Tree: A Radical New History of Life.

Sometimes good conversations still occur on Twitter. Click for the whole thread. It’s worth it.

A CRISPR cure for Duchenne muscular dystrophy is closer after a trial in dogs.

Ancient encounters: How we came across the daughter of a Neandertal and a Denisovan.

Analysis of Polygenic Score Usage and Performance across Diverse Human Populations.

Why Elon Musk Reversed Course on Taking Tesla Private.

Apple Gives Series Order to Sci-Fi Drama Based on Isaac Asimov’s ‘Foundation’.

In ‘Small Fry,’ Steve Jobs Comes Across as a Jerk. His Daughter Forgives Him. Should We? Something was seriously wrong with Steve Jobs.

Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.

Immune genes are hotspots of shared positive selection across birds and mammals.

The Desperate Quest for Genomic Compression Algorithms.

Environmental factors drive language density more in food-producing than in hunter–gatherer populations.

After 32 episodes we have a general sense of what people like to hear about on our podcast. So far the top 5 in downloads have been:

The Golden State Killer and the Genetic Panopticon
The Neolithic Revolution
Lee Berger and the Dawn of “Big Data” in Paleoanthropology
The Genetics of Human Behavior
Barbarian Genetics

(not necessarily in that order!)

A random question: what politically liberal podcasts do you listen to? I started listening to Pod Save America and it’s just people talking Tumblr and hating Trump. That’s fine, but you can get that elsewhere….

August 20, 2018

Open Thread

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

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

August 19, 2018

Open Thread, 08/19/2018

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

Almost Human: The Astonishing Tale of Homo Naledi and the Discovery That Changed Our Human Story is a “deal” on Kindle. Recommended. Also, Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa.

Greece’s Bailout Is Ending. The Pain Is Far From Over. Seems to me that Greece is stuck in an unfortunate equilibrium (see the employment laws).

The Big Sort: Selective Migration and the Decline of Northern England, 1780-2018.

On Twitter, I implicitly defended Steven Pinker a bit. I think The Better Angels of Our Nature: Why Violence Has Declined will be noted as one of his most important books because many people were not, and are not, aware of positive trends in the aggregate. My personal experience is that many academic biologists, especially those with ecological backgrounds, are highly pessimistic. Basically, they are stuck in the 1970s.

There are reasons to be pessimistic, and I’m not as optimistic about the future as Pinker, but we first need to accept the facts as they are.

One of the strange things over the past five years or so has been the hatred I’ve seen directed at Steven Pinker by some academics. Consider this from the classicist in the thread above: “I’ve yet to come across *any* respective expert that doesn’t think Pinker’s popular books are garbage….” Or earlier this year I saw a German researcher on my Twitter timeline declare Pinker was pro-Nazi (based on a highly edited clip)!

Most interesting chart from Pew, How Millennials today compare with their grandparents 50 years ago.

The Nastiest Feud in Science: A Princeton geologist has endured decades of ridicule for arguing that the fifth extinction was caused not by an asteroid but by a series of colossal volcanic eruptions. But she’s reopened that debate.

“I will die here”: Death toll rises in southern India’s worst flooding in a century.

The importance of fine-scale studies for integrating paleogenomics and archaeology.

Forager-farmer transitions from East Asia to Sahul: Regional and Global Perspectives.

The Ginkgo Model of Societal Crisis.

530 House Projection.

A quantitative genetics model for the dynamics of phenotypic (co)variances under limited dispersal, with an application to the coevolution of socially synergistic traits.

The perils of intralocus recombination for inferences of molecular convergence.

The Insight is taking a break for a few weeks. Just want to note that I’m proud we have 32 episodes now! Subscribe on Apple Podcasts, Stitcher, or listen on the web.

I’ve asked people what podcasts they listen to before, but what blogs do you read? Honestly, I don’t read many anymore.

August 14, 2018

Open Thread, 08/14/2018

Filed under: Open Thread — Razib Khan @ 12:27 am

Weekly book recommendation, Power and Plenty: Trade, War, and the World Economy in the Second Millennium.

V. S. Naipaul has died. I never read his fiction. Perhaps I should. Suggestions? People always talk about A House for Mr. Biswas.

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations. ” We propose that it is time to contemplate the inclusion of polygenic risk prediction in clinical care, and discuss relevant issues.” Totally honestly, this is happening way faster than I had assumed it would.

Relatedness disequilibrium regression estimates heritability without environmental bias. A blog post on the topic: Relatedness disequilibrium regression explained.

Large-scale whole-genome sequencing of three diverse Asian populations in Singapore. Han (Southern) Chinese, Malays, and Indians (mostly Tamil).

Can Amazon Maintain the Spirit of ‘The Lord of the Rings’? I doubt it. One thing to remember is that George R. R. Martin was a screenwriter in Hollywood for a period. His writing is a more natural translation to modern visual media.

Only the Truth Will Prevent Harm. Sarah Haider. Enough said.

Deep Reads: How I learnt to love population genetics.

Important preprint. Expected patterns of local ancestry in a hybrid zone.

Salt and heart disease: a second round of “bad science”?

Last year, The Witchwood Crown was published. Haven’t read it. Any good?

August 13, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 10:59 pm

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

Open Thread

Filed under: Open Thread — Razib Khan @ 10:59 pm

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

August 6, 2018

Open thread, 08/06/2018

Filed under: Open Thread — Razib Khan @ 9:12 pm

In light of the recommendation of F. W. Motte’s Imperial China: 900-1800, I thought it would be useful to reiterate a minimal set of other books that are important in my intellectual development in relation to the history of China.

The Early Chinese Empires: Qin and Han. You need to start at the beginning, and this is that. To be fair, the Spring and Autumn period were a pretty big deal too, but I think a lot of their insights were distilled into what we see in the Qin-Han era. The Zhou and Shang are so distant that I’m not sure a real history could be written, as opposed to analysis of myth and archaeology (especially for the Shang).

China between Empires: The Northern and Southern Dynasties. The period between the fall of the (Later/Eastern) Han and the rise of the Sui-Tang lasted many centuries. There wasn’t a precedent yet truly for the revival of a unitary Chinese state during this period. So a lot of cultural and political issues got hashed out over these 300+ years. Buddhism became a major cultural force, and the social and political fabric of Tang dynasty was stitched together (the Tang were a Han-Xianbei cultural mix, for example).

There are many histories of the Tang, which has a particular appeal in the modern era, but I like China’s Cosmopolitan Empire: The Tang Dynasty. For the more ambitious, I think S. A. M. Adshead’s T’ang China: The Rise of the East in World History is worth a read (this is expensive, so find a good library!).

The Age of Confucian Rule: The Song Transformation of China. Compared to the Tang the Song seem a bit dull, but a lot that defines modern China has its roots in this period, and not the Tang (which was somewhat atypical). For example, the meritocratic bureaucracy really got ingrained during the Song (though it has roots in the Han).

The Troubled Empire: China in the Yuan and Ming Dynasties. The title says it all. We’re coming into early modernity here.

And finally, China’s Last Empire: The Great Qing. These are the Manchus.

If you are wary of diving in headfirst, then I suggest John Keay’s book on China, but do not stop there. Keay is more conversant in the history and peoples of South Asia, so it’s not just best work in terms of thoroughness.

Why does any of this matter? First, because China matters to non-Sinologists in the 21st century, like the United States mattered to non-Americans in the 20th. That’s just a plain fact. It matters for the future. Second, if you take an interest in the human past China is a large proportion of that past. If you don’t know Chinese history, don’t talk to me about knowing history (similarly, you should know the history of the Near East and the Classical West, at a minimum, to really express an opinion to me about history in a broad sense and be taken seriously by me).

I would be interested in a recommendation on modern Chinese history, perhaps dating to after 1800. Someone besides Spence. And then also something on the Spring-Autumn period.

For a while I’ve been saying the new Rakhigarhi paper is going to be over-hyped in relation to what the science will tell us. The reason I say this is that The Genomic Formation of South and Central Asia really hit the major points in broad-strokes already. But in India Rakhigarhi is going to be a huge deal because:

1) it is a site in the Republic of India
2) it is from the mature Harappan phase

The results will confirm some beliefs, but it’s not a game-changer. A game-changer would be if we found someone who was half Corded-Ware in genetic ancestry from India in 2250 BC. Ultimately a lot of ancient DNA will probably come online in India over the next few years (hopefully?), and then the real action of mapping the details will begin. That’s exciting.

The Genomic Basis of Arthropod Diversity. This is a big preprint and a big deal.

Population size history from short genomic scaffolds: how short is too short?

I’ve started using my Facebook Page (as opposed to Profile). Mostly I’m going to use it push my content.

Workplace Wellness Programs Don’t Work Well. Why Some Studies Show Otherwise. Randomized controlled trials, despite their flaws, remain a powerful tool.

On Sarah Jeong. People need to never forget that NYC-DC elite journalists are a class. Their defense of her is a defense of their class interests. She’s a friend or acquaintance, and her social and political views, and writing style align with their own (or the writing they’d like to do more in public). Of course they are going to have her back and interpret everything she says charitably. She’s “their kind of people.” Someone like Protagoras, eh, I mean Jeet Heer, is inevitably going to tweet-storm about “contextualizing” her offensive statements.

Once you view elite national journalism as the voice of a self-interested class, as opposed to disinterested reportage, then it all makes sense.

Here’s Why It’s So Impossible to Get Reliable Diet Advice From the News. You should know all this. If you don’t, read it closely. It’s pretty obvious.

Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations. No surprise. Men on the move.

The fitness consequences of genetic variation in wild populations of mice. The Hoekstra lab is producing work in evolutionary biology that is always worth keeping track of.

Genetic draft and valley crossing. You had me at draft, but I want to marry you at “valley crossing.”

How Sexually Dimorphic Are Human Mate Preferences? The blogger and twitter named “Yeyo” (the new one is a fake) raised my consciousness to the fact that in terms of upper body muscle mass human males and females are extremely dimorphic.

On Twitter, I joked that people should send me money via Paypal as recompense for my “emotional labor” as a PoC who has to educated people. No one sent me money. #whitePeopleAreRacistForReal! If you are an anti-racist white person who reads my blog, you should send me money, or you are a racist! How do you feel when you read about Cameron Whitten’s shakedowns of white liberals? I think they’re hilarious, and more power to him. He’s a total con artist, but I would appreciate these people going broke.

July 30, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 11:00 pm

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

Open Thread

Filed under: Open Thread — Razib Khan @ 9:14 pm

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

July 29, 2018

Open Thread, 07/29/2018

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

Reading Imperial China 900–1800 it is interesting how the Khitan seem to have chosen to develop a written script that was not based on that of the Chinese, to resist the cultural assimilation that would have inevitably occurred. Through that choice they reduced their short-term efficiency, but probably enabled their long-term persistence as a people. Certainly the Khitan seem to have remained less Sinicized on the even of Jurchen conquest than the Jurchen were on the eve of the Mongol conquest (though the Jurchen conquered North China, so they had a bigger demographic imbalance). That the Khitan continued nomadic ways is clear as they managed to reassemble to the west and fond the Qara-Khitai. The Manchu descendants of the Jurchen who conquered China seem to have been thoroughly Sinicized after a few centuries as well.

DNAGeeks going “full nerd”. If you don’t know why UGA is funny, learn some genetics! Trust me, it’s good for you. Look how I turned out.

Last Friday for whatever reason I watched Mission Impossible: Fallout. I don’t really watch films except for Marvel and DCEU stuff (I need to keep up with the culture). But I was in the mood, and I hadn’t watched a Mission Impossible since the 1996 one. Apparently Tom Cruise is really into parkour. And though Cruise has aged really well, so has Michelle Monaghan. At least Ving Rhames is still around.

I used to listen to Chapo Trap House now and then. Still do now and then. There is some stuff I agreed with, some stuff I don’t agree with that I think needs to be said, and, they are often kind of funny. But unless you are on the same political wavelength I think they do get a little stale, because they’ve got an agenda, and they need to keep revisiting the same themes. It’s a feature, not a bug.

But listen below where they contextualize the “supposed crimes” of Communism:

The issue isn’t that avowed socialists are engaging in whataboutism in relation to Communism. That’s kind of what I expect. It’s that Chapo Trap House is still part of the respectable broader Left to center-Left cultural Zeitgeist. And they’re contextualizing literal Communism.

This is the sort of stuff that pisses conservatives off whenever we point out double-standards of respectability of radical Left politics as opposed to the radical Right. If someone contextualized Nazism as a reaction to Versailles and hyper-inflation they’d be de-platformed in a second. Meanwhile, Chapo pulls in $100,000 per month on Patreon.

A special treat this week on The Insight (Apple Podcasts, Stitcher and Google Play). We talked with James Lee, lead author of Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. In the next few months we have at least one more interview relating to behavior genomics work. This is a field where stuff is happening.

Though I hope ancient DNA will start popping back up in the fall.

Big Pharma Would Like Your DNA: 23andMe’s $300 million deal with GlaxoSmithKline is just the tip of the iceberg. This was always the plan.

Out of Africa by spontaneous migration waves. Not sure if I buy this model, but we’re at more model-building stage.

A Large Body of Water on Mars Is Detected, Raising the Potential for Alien Life. This is cool.

Episode 856: Yes In My Backyard. I relate to the NIMBY activist. It’s a generational and local vs. migrant issue. Not a typical class one.

I’ve been asked to submit a chapter on a book on Indian genetics, primarily relating to the “Aryan question.” I’ve gotten most of it written, but it’s really annoying to have to wait until the Rakhigarhi preprint/paper is out. The general finding will be no surprise to a reader of this weblog. Don’t think it will be published in the USA. Perhaps I’ll post the draft at some point if the copyright allows.

Replicability of introgression under linked, polygenic selection. “Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.”

July 23, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 9:12 pm

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

Open Thread, 07/23/2018

Filed under: Open Thread — Razib Khan @ 3:12 am
Sale Code: GET20

Doing a Summer Sale at DNAGeeks, 20% off with the GET20 code. I believe GNXP-helix themed stuff is still the most consistent/popular item.

Reading T. N. Ninian’s Turn of the Tortoise: The Challenge and Promise of India’s Future. It’s a relatively dry book with an academic orientation. No complaint from me. So far the most interesting, and unfortunate, thing I’ve learned is that Indian men will take a 50% pay cut to work in a white-collar as opposed to blue-collar manufacturing job. Ninan contends that this may be due to caste aversion to manual labor. Men who have lower-paying white-collar jobs have better marriage prospects than those who have higher-paying blue-collar jobs.

James Gunn Fired From ‘Guardians Of The Galaxy’ Franchise Over Offensive Tweets. I’ve seen some people suggesting that you need to evaluate the “whole person” and that “people grow.” These are almost always the same people who gleefully crucify anyone to the Right of Alexandria Ocasio-Cortez for anything they’ve ever said in any context. I see no end to this cyber-Maoism until cultural “mutually assured destruction” becomes reality. To maintain civilization we must be barbarians!

Someone on Twitter suggested replacing libraries with bookstores and Amazon. This elicited outrage. I have opinions on this because I’m confident that among the population I’ve been a top 1% utilizer of libraries over my lifetime. I’ve seen slowly as libraries transform from book repositories to internet access portals and community centers. But, a minority of the population using the library is still using it for books.

And of that minority, many are nerdy kids for whom the library is a window upon the whole world. True, the internet is great, but the internet is broad and shallow. The minority of overutilizers of the book lending function of the library probably make a big impact in other ways later on in their life.

Before the age of 12, I probably had my parents buy me about a half a dozen books, ever. I bought more as a teen, and as an adult, I probably buy/purchased half the books I’ve read. This is a “think of the children” issue. Libraries are distribution centers for essential free “gateway drugs” of cognition. Not for most. But for those who care.

Last week on Secular Right I wrote On the semiotics of secularism and nakedness of village atheism in the culture war. As I told a friend of mine, people were tweeting almost word-for-word the exact same Islamophilic sentiments in the Left-progressive Twittersphere (he was one of them). Reactions to Richard Dawkins have become tribal measuring sticks. It’s tiresome for many apostates from the Islamic religion. Most Left-progressives don’t care about Islam or Muslims that much. They just care that they’re “tolerant” and follow their crowd as to who is, and isn’t, marginalized (1.8 billion Muslims, marginalized!).

Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians.

If you liked the Stuart Ritchie podcast from a few months back, you need to listen this week. If you subscribed I don’t need to remind you. Also, if you are subscribed to my total content RSS or follow my “gnxp posts” Twitter, you know I’ve been pushing my work-blog content into those feeds now (since people keep complaining that they’re missing them). Initially, I kept my work-blogs more “lay-friendly,” and they are still more soft-touch than the stuff I put here, but I’ve noticed that the more technical one still get shared a lot. I’ll have a write-up of a paper that’s going to be quite big (mega-sample size) out on the work-blog this week.

Looks like a justification for the two-fold cost of sex (the male part):

Inferring Continuous and Discrete Population Genetic Structure Across Space. This was out as a preprint a while back. These issues require more thought than people in pop-genomics have been doing.

Here’s What Happens To Your Body When You Eat Super Hot Peppers.

Neandertal fire-making technology inferred from microwear analysis.

Black American Culture and the Racial Wealth Gap:

… Consistent with the Nielsen data, they found that blacks with comparable incomes to whites spent 17 percent less on education, and 32 percent more (an extra $2300 per year in 2005 dollars) on ‘visible goods’—defined as cars, jewelry, and clothes….

Next, they asked if education accounted for the differences in financial habits by limiting the comparison to middle-aged families with advanced degrees. Surprisingly, they found that the racial gap in financial health-scores didn’t shrink; it widened. Highly-educated Asian families scored 3.49, comparable whites scored 3.38, comparable Hispanics scored 2.94, and comparable blacks remained far behind at 2.66. Thus, the study authors concluded, neither “periodic shortages of time or money” nor “lower educational attainment” were the driving forces behind the differences in financial decision-making.

Elizabeth Holmes’ Downfall Has Been Explained Deeply-By Men. The author of this Wired piece is Virginia Heffernan, who I know for having an impeccable pedigree, but whose writings are substantively often total tripe. Heffernan, who has a Ph.D. in English from Harvard, once wrote a weird piece titled Why I’m a creationist, which begins “As a child I fell in love with technology, but I have to admit I never fell in love with science.”

In any case, Holmes’ case is clearly one where a person from a upper-class WASP background with Stanford connections leveraged all that into a lot of money. Heffernan’s attempt to transform it into a gendered issue is totally predictable, but also incredibly reductive.

New criteria for sympatric speciation in the genomic era.

Gene expression drives the evolution of dominance. Old debates made new.

Nathan Lents’ new book, Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes, looks interesting. Here’s a write-up by Lents’ in Skeptic.

Though I do wonder if Creationism as a cultural force has lost some steam. After all, conservative Protestants are probably more worried about their catastrophic losses in the culture wars right now than somewhat abstruse meta-scientific questions. I mean, I have more Twitter followers than The Discovery Institute!

If you want to analyze Tibetan genotypes, I converted some files I found in the Jorde lab website to plink. It has an OK overlap with HGDP.

What podcasts do you listen to?

Also, the India ancient DNA story should get a major breakthrough within the next week or so. “Watch this space” and all that.

July 16, 2018

Open Thread, 07/17/2018

Filed under: Open Thread — Razib Khan @ 11:57 pm

History of Japan: Revised Edition. As I said, a pretty good and short history. Recommended.

CRISPR/Cas9 gene editing scissors are less accurate than we thought, but there are fixes. I know the focus is on human genetics. And rightly so. But this isn’t going to be as much of an issue in animal and plant breeding.

Patterns of speciation and parallel genetic evolution under adaptation from standing variation.

Genome-wide analysis in UK Biobank identifies over 100 QTLs associated with muscle mass variability in middle age individuals.

Amazon told me R for Everyone: Advanced Analytics and Graphics was on sale. Great. But I already own it. That being said, I can tell you it’s a pretty good book.

Genome doubling shapes the evolution and prognosis of advanced cancers.

Against Moral Equivalence. “The talking heads trafficking in examples of U.S. interference neglect to mention that the goal of American policy has always been to prop up anti-totalitarian, pro-market leaders.” I dislike the tendency of American conservatism to conflate anti-authoritarian and pro-market. The two are distinct (I’m pro-market for what it’s worth, but capitalism is amoral, even though it leads to greater human well-being).

Large randomized controlled trial finds state pre-k program has adverse effects on academic achievement.

Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan.

Confronting Implicit Bias in the New York Police Department. Implicit bias stuff is sketchy science. But people want solutions for social problems.

How Social Science Might Be Misunderstanding Conservatives. I got introduced to the “authoritarian personality” in college. I didn’t think much about it, but over the years it seemed pretty clearly a bit rigged. But whatever. Then I read The Dialectical Imagination: A History of the Frankfurt School and the Institute of Social Research, 1923-1950. That’s where it comes from. Enough said, right?

Tides of History is a great podcast. Now Patrick Wyman is talking about the “Hundred Years War.”

Should I post “open threads” anymore? It seems that the number of comments keeps dropping. Really “everything” is moving to Twitter nowadays though Twitter is a wasteland.

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