Open Thread, 10/15/2018


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 shouldn’t 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.

Xunzi: 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 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.

On Eve of Harvard Bias Trial, Dueling Rallies Show Rifts Among Asian-Americans. The pro-Harvard Asians seem to have memorized zingers from Between the World and Me. They may be pro-social justice, but they’re still Asians, so no creativity!

Open Thread, 10/8/2018

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.

ASHG Meeting next week.

Max Boot is making the rounds promoting his new book, The Corrosion of Conservatism: Why I Left the Right. I haven’t read the book, but having listened to him on various podcasts, one thing that annoys me about this guy: his faction of maximalist neoconservatives and war-hawks in the post-9/11 era were cheering on the mass psychosis which led to this nation backing multiple military adventures. In particular, I’m talking about the invasion of Iraq, which cost $2 trillion dollars, 4,500 American soldiers’ lives, and hundreds of thousands of Iraqi lives.

Instead of starting in 2015, he should start in 2003.

Are there an other readers from 2002?

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.

Open Thread, 9/30/2018

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 indefinitely.

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.

Open Thread, 9/23/2018

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.

Open Thread, 9/17/2018

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. The liberal moment is probably passing. If you have opinions you want to spread, then try to convince those with power. They will make people agree with you.

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.

Open Thread, 9/09/2018

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, due 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.

On simulation, and genealogies.

Open Thread, 09/02/2018

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.

I don’t read many blogs. Honestly, there aren’t many blogs. The Scholar’s Stage is one I do read.

Open Thread, 08/27/2018

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. In fact, I see a fair amount of undergraduate college-level material being shared around when they agree with someone’s politics; people only get intellectual snobby when they disagree with the conclusion (this is a big move by Protagoras on the Prairie).

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….

Has anyone been getting page-load errors? I’ve been getting a lot fewer (once a month, rather than once every few days). I think the memory issues may have cleared….

Open Thread, 08/19/2018

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.