Open Thread – 10/18/2020 – Gene Expression

Taking a break from the book club, I’m finishing up books that I never finished though started. So, The Turks in World History. Recommended. Not so deep as to confuse, but not so casual as to be Wikipedia.

In Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past the citation goes to For whatever reason I notice a lot of academics check, rather than this weblog. I mention this because is an aggregator that accesses all my RSS, so if I publish something somewhere else, it will be loaded on that website (e.g., if I publish in NRO, City Journal, etc., it automatically gets pushed to the aggregator). I created the website for the total content feed, but just pointing it out for those who like bookmarks rather than RSS feeds. The stylizing isn’t great, but I doubt most readers of this weblog are here for the styling.

The Five Deadly Sins of the Left. The author, Ruy Teixeira, was behind the emerging Democratic majority hypothesis.

Statistics used to infer inter-breeding between humans and Neanderthals are strongly predicted by flanking sequence heterozygosity.

Want to remind readers of Cabellero’s Quantitative Genetics. Excellent book, and pretty affordable and up-to-date.

With Covid-19 Under Control, China’s Economy Surges Ahead. Every time I post something like that someone says (on Twitter): “Actually China’s economy is all fake.” As someone who has been paying attention to China’s economy for 20 years, and frankly been very skeptical of a lot of their numbers, this assertion goes into the true-but-trivial category. There’s a lot of fakery. But that’s irrelevant to the qualitative fact that Chinese prosperity in 2020 is a fact.

The Crypto State? How Bitcoin, Ethereum, and other technologies could point the way to new systems of governance. This is in City Journal. I’ll be having something out in CJ again soon.

New Research (not by me!) on Kids, Babies, Day Care & Schools. It’s hard to navigate between “the sky is falling” and “it’s just the flu bro.” I think Emily Oster has been trying hard to do so. There’s a lot of politicization in public health, so I listen to her since I think she aims to be as free as possible.

He is undoubtedly the most influential intellectual in America today. And, he is also one of the stupidest. I’ve told my eight-year-old daughter some of his ideas, and she looked at me incredulously. Then again, she’s on the order of 2.3 standard deviations or so above Dr. Kendi’s intelligence. In any case, he’s so dull he has no idea when he expresses thoughts which, as Oliver Trialdi pointed out, suggest he’s joining the “Intellectual Dark Web.”

How Mark Zuckerberg Learned Politics. A few years ago Zuck rediscovered spirituality. All this indicates a future public profile much bigger than toady.

Steven Pinker’s obituary for Judith Rich Harris. She was a friend of this blog, and I always enjoyed corresponding with her and her husband.

Not All Identities Are Created Equal.

Introduction to Social Science Genetics.

The Next China? India Must First Beat Bangladesh. Indians are kind of jumping the shark over this…but, yeah, it’s a bad sign that on a per capita basis Bangladesh will surpass India. But, the real story is India has many regions that lag way behind. Maharashtra, where Mumbai is, has a higher per capita income than Bangladesh and a far larger GDP. But states like Bihar and Uttar Pradesh are huge, and poorer than Bangladesh.

The Age of Confucian Rule: The Song Transformation of China. This is an excellent book. Recommend it to everyone.

Ancient DNA from Guam and the Peopling of the Pacific. Look like the Lapita. I used to play “ratball” with a guy from Guam named Tulio back when I was 15.

Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context.

The rate of whole-genome duplication can be accelerated by hybridization.

Empirical variance component regression for sequence-function relationships.

8 Million Have Slipped Into Poverty Since May as Federal Aid Has Dried Up. I’m against austerity. COVID-19 has been a disaster for the economy, and it’s “no one’s fault.” Not going to lie, I suspect a debt crisis is in our future, but I doubt that this stimulus will be dispositive in either direction.


Week 2, Gene Expression book club

The second chapter of Not Born Yesterday: The Science of Who We Trust and What We Believe is short. Much of it is re-warmed evolutionary biology, with a focus on ethology. If you’ve read Amotz Zahavi’s The Handicap Principle: A Missing Piece of Darwin’s Puzzle or Dugatkin & Reeve’s Game Theory and Animal Behavior this will be a quick and easy chapter. Basically, the issue being explored here is that social cognition and conformity run up against the fact that there is an incentive to “cheat”, and communication is a two-way street.

Zahavi was the 20th century’s most eloquent expositor of the “handicap principle.” The idea that you need “hard-to-fake” signals to accurately convey information. So, for example, huge antlers are honest signals of robustness and genetic health, even though they are nonfunctional, and reduce individual fitness (it’s easier to find and catch animals with antlers). The idea that people are gullible and credulous in terms of communication and information processing runs afoul of the reality that communicators are incentivized to deceive you to optimize their own fitness (or, just “free rider” off communication altruism of conspecifics).

The strangest part of this chapter is that Mercier threw in a reference to Haig’s theories about mother-offspring genetic conflict due to different life-history incentives. The mother is optimized to not invest too much into the fetus so that resources are left for future offspring, while the fetus is incentivized to extract as much as possible (within reason; the offspring is related to future progeny, though in most mammals that might be 0.25 and not 0.50). All this is true, and it’s a robust area of science, but I thought this chapter would have benefited from more discussion of ethology and behavior, and less on evolutionary genetics.

Basically, the takehome here is that the gullible should be selected against…

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God is back! (in Russia)

For over ten years I have been making fun of John Micklethwait and Adrian Wooldridge’s 2009 book God is Back: How the Global Revival of Faith Is Changing the World. There are several reasons for this, but the primary one is that anyone who was looking at the data could see the period between 2000 and 2020 has witnessed a massive secularization in the most powerful nation in the world. Being generous to the metrics for religion, the United States has become twice as secular in a single generation (i.e., 10% “no religion” in 1990 vs.
20% in 2020).

This was a surprise to social scientists. If you read Rodney Stark and William Sims Bainbridge’s The Future of Religion: Secularization, Revival and Cult Formation, written in the mid-1980s, descriptively it seems that the United States went through a cultural change in the 1960s where many marginal Christians ‘defected’ to irreligion, “New Religious Movements”, or nominal adherence (e.g., no church attendance), but that by the 1970s that trend had played itself out and a ‘new normal’ equilibrium had been established.

This is the story you are told in Barry Kosmin’s 1993 One Nation Under God: Religion in Contemporary American Society, based on the 1990 “Religious Identification Survey.” America was an 85:5:10 nation. 85% Christian, 10% “Nones” and 5% “Other religion” (the largest proportion of these being Jews). Samuel Huntington’s last book, Who Are We?: The Challenges to America’s National Identity, assumes this as a background condition. But by the time that the book was published, there was already evidence in the data, including from Kosmin’s follow-up surveys, that the old equilibrium was changing.

Rodney Stark, who by the 2000s had become a semi-Christian apologist, who has a “supply-side” religious framework which argues that secularization couldn’t happen anymore, actually came out with research trying to show that actually American’s weren’t getting more irreligious. But these attempts seem to have stopped by 2010 when scholars couldn’t ignore the writing on the wall.

By the end of the 2000s, Robert Putnam assembled the data and presented a causal hypothesis in American Grace: How Religion Divides and Unites Us. Putnam and his coauthor offer a simple story: as American Christianity became politicized in a polarized culture war, many defected. This is the case particularly for those with more liberal or Left ideologies, and younger people. Whether you believe this story is irrelevant to the descriptive reality. And 2016, with the election of Donald J. Trump, illustrates that secularization has even started to work its way into the Republican party.

And it’s not just America, though to be frank, we’re the most important dynamic. Despite the fact that the 2000s were focused on Islamic terrorism, the Arab world is now undergoing mass disillusion with religion. Believe it or not, “New Atheism” is still relevant in the Muslim world! Richard Dawkins is viewed negatively by much of the Western intelligentsia today for his dim view of Islam, but he is still a heroic figure to freethinkers in the Muslim world. It’s still 2006 in places like Bangladesh or Algeria. Religious violence against freethinkers is actually a sign of secularization because freethinkers are getting bold enough to express their views in public.

Then there is China. In 2003 Jesus in Beijing: How Christianity Is Transforming China And Changing the Global Balance of Power was published. Written early in the George W. Bush administration this book was catnip for Christian conservatives, presenting the vision of a China which was substantially Christian, and whose conservative Protestant Christianity would result in a pro-Israel orientation!

I’ve tracked the numbers and read some books on the topic of religion in China today, and overall it’s a complicated story. Obviously, China is not undergoing “secularization,” but neither are mainland Chinese becoming devout Christians in the same way that the religion is dominant (if still a minority) in a place like South Korea. Jesus in Beijing suggests that 10% of Chinese were Christian by the year 2000, but the best estimates put the figure close to 5% today (more conservative estimates would put it at 2%…it’s complicated not just because of “high churn” “House Churches”, but because some “Christians” are pretty heterodox. Google “Eastern Lightning”). There is a revival of “traditional religion” in China as well. But, I don’t think anyone can assert that China is more religious in a deep sense any more than they were in 2000.

Which brings me to Russia. Recently the World Values Survey came out with its 2017-2020 “wave.” You can find out many interesting things from this website (also, you can pull down the raw data). For example, ~20% of mainland Chinese in the survey believe in God. The figure is 80% for self-identified Protestants and Muslims in China (the sample sizes are ~50 for these two groups), the same proportion as self-identified Buddhists (N~250 for that religion)!

But, what is striking me to is that over the past 30 years Russia has become far more religious, while the USA has gotten less religious. Here are results for selected nations (the exclusion only makes a difference for Japan):

These results pass the qualitative “smell test.” The USA and Spain have both gotten more secular in the last generation. While Russia seems to have embraced religious social conservatism under Vladimir Putin.

We need to be careful about how we interpret these data. For example, if you ask if people “belong” to a church, 90% of Russians say they do not. The figure for Americans is 40%. And 32% of Americans are avowed “active members” as opposed to 3% of Russians. Russians have a strong identity with Orthodox Christianity in 2020, but they are not actively practicing Christians in a way that American Protestants would recognize.

One question you might ask is that is this about age effects? No. If anything, very young Russians seem a bit more secular.  It seems that the generation that came of age under Gorbechev and Yeltsin was raised without religious identity, has proactively embraced it as adults as they have aged.

Is God back? Not necessarily. But the average is definitely over.


Has China won by beating coronavirus?

About three weeks ago the Chinese reported a few instances of community spread in Qingdao. Five days ago a story broke that there were now 13 individuals. The government said they would perform 9 million tests.

Today the results came back on 7 million tests. None of them were positive. It turns out that the 13 positive individuals were traced back to a hospital that quarantined people who had tested positive abroad. Ultimately there was “less to see” here than we originally thought since it is reasonable that now and then COVID-19 might leak out of the quarantine hospitals.

In February I was doing some “back-of-the-envelope” calculations and they suggested that a bad-case (but not worst-case) scenario was 250,000 deaths in the USA. We are probably already there in terms of excess deaths. I wasn’t pessimistic enough. It is not implausible that we’ll reach 500,000 deaths, though the combination of social distancing, monoclonal antibodies, and infections of those at lower risk first before herd immunity, and probably next year vaccination, will mean we’ll be in the 300,000-400,000 range of excess mortalities.

The situation in China is different. And surprisingly so. It seems that the 1.4 billion Chinese have successfully implemented the “contain and crush” strategy. They crushed the virus in Wuhan. But then they also crushed the virus when it resurged in Manchuria and a district of Beijing. All the powers of an authoritarian state were brought to bear, but it seems likely that the public has a high degree of compliance in China.

Of course, this elicits the standard skepticism of China’s numbers, which I initially shared. The reason I believe that the Chinese have contained COVID-19 is that the people in China themselves seem to think it is contained. You can watch how “normal” people behave in public. You can contact ex-pats who live in China. Life is back to where it was.

Then there are stories like this, China Box Office Poised to Surpass U.S. as World’s Largest Moviegoing Market Amid Pandemic. There is enough economic data to suggest that China is “back to normal” in terms of exports and imports. Yes, perhaps they are lying about their data as they were before, but it is as if they are in “before-times.”

Finally, is there a moral to this story? You can draw your own conclusions in terms of comparisons. I’m happy that the Chinese seem to have COVID-19 under control, but I’m worried about America’s comparative state and social capacity…


To my sons: be a man as Poitier is!

The death of Olivia de Havilland made me very sad. For many years I had tracked the passing of various “Golden Age” movie stars. I myself don’t remember this period, but their fame and films haunted the last decades of the 20th century. These were the artistic ‘classics’ of my youth, and the human witness of that period decayed and dying in their turn, one by one.

Of the very oldest there seems to me to be three prominent women and one prominent man now that remain aliive. Of the former, Eva Marie Saint, June Lockhart, and Angela Lansberry (I date Betty White’s real fame to a much later phase in her career). And then, there is Sidney Poitier.

Poitier has always held a special place in my heart. As a small child, I remember watching his films such as To Sir, With Love, and Lillies of the Field, with great interest. Poitier was a striking figure, a black man with very dark skin who modeled a sort of dignified and earnest Western manliness. Unlike black actors such as Harry Belafonte, Poitier’s visage exhibited no glimmer of Europe. His very appearance was unapologetically black with no compromises. But his mien, his bearing, was universal and admirable, reaching out across the chasm of external difference, bringing home the common virtues which bind us.

The 21st century

In this way, he exemplified a particular conservative and traditional attitude toward race and culture which I have always been personally sympathetic to. Integration into the fabric of society as a man on his own terms, rather than separation as a people apart.

That was always my goal. Whether I succeeded or not is a different matter, though that might be due to my own eccentricities rather than the broader culture.

I am the father of two young sons. Men who will grow up in this century, nurtured by its cultures, tempered by its traumas. I worry about them. And yet sometimes I think of someone like Poitier, who experienced a level of racism simply due to his physical appearance that we couldn’t even imagine, and yet who became something of a role model and figure of admiration, even to brown children of immigrants new to this country.

Let your bearing be reverent when you are at leisure, be respectfully attentive in managing affairs, and be loyal towards others. Though you be among barbarians, these may never be cast aside.


Prime Day!

It’s “Prime Day” (well, the second). I know it has nothing to do with Prime Day as such, but I really do recommend all of you read Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. It’s getting out of date here and there, but it’s essential in 2020 if you are interested in the human past.

I’m surprised how two years on there hasn’t been much else that’s come out.

Now in regards to Prime Day, Kindle Fire is on sale. I recently cracked my primary Fire so I was using a backup. I realized that the backup was too heavy, and instead of getting one of the big Kindles I got a smaller one that’s lighter. I don’t really use the Kindles for surfing the web or watching movies, I have computers or smartphones for that. I have a paperwhite, but I do most of my reading on the fire.

I know some people don’t like reading on an e-reader, but it does make me much faster.


A more nuanced model for the settling of the Americans

The genomic formation of First American ancestors in East and Northeast Asia:

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000-18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia.

Read the preprint. I’ll note three things

– The authors suggested that differentiation between American native lineages occurred in eastern Siberia, not Beringia. In other words, there’s a lot of ancient structure in the New World that dates to the Last Glacial Maximum

– Speaking of ancient structure, using the new methods in this paper they detect more pervasive “Australo-Melanesian” ancestry in lower quality ancient remains. It seems clear ta this point that this isn’t about Australo-Melanesian, as much as genetic variation in East Eurasia during the Pleistocene that we have a poor grasp of at this point

– In Europe ancient DNA quickly converged on the trihybrid model of Mesolithic hunter-gatherers, and early farmers, and steppe pastoralists. The tsunami of ancient DNA has fleshed out a lot of details, but the basic framework has been in place for five years. The situation in other parts of the world seems to be more unsettled and dynamic. More sophisticated models and more ancient DNA keeps returning surprise on the margin


Open Thread – 10/11/2020

I notice that Europe: The Struggle for Supremacy, from 1453 to the Present is on sale. Am I a sucker for cheap Kindle books with high page counts? Yes. But I stopped eating out over the past year, so what’s a few dollars here and there?

Chris Wickham’s Medieval Europe is also on sale. If you can afford Framing the Early Middle Ages: Europe and the Mediterranean, 400-800, get that. But this is a decent book.

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Week 1, Gene Expression book club

Not Born Yesterday: The Science of Who We Trust and What We Believe starts rather quickly and succinctly out of the gate. The author reviews the extant literature and folk wisdom that humans are gullible, and not suspicious of people trying to swindle them. To a great extent, this is the mainstream view now, with the emergence of the “heuristics and biases” literature, and the field of “cultural evolution” which is rooted in the idea of social cognition.

Social cognition basically means instead of thinking things through yourself you allow the community to decide. As a hadith states, the Ummah shall not agree upon an error. It’s cheap, easy, and good enough. But, this reliance on community means that irrational herds can erupt, and the opportunity arises for ‘cheaters’ to game these systems of information flow (think ‘affinity scams’).

The first chapter of Not Born Yesterday is a capsule of the view not taken in this book, so I assume the best is yet to come.

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Gene Expression Book Club – it’s off to the races!

So I’ve started reading the two books we selected:

Autumn in the Heavenly Kingdom: China, the West, and the Epic Story of the Taiping Civil War

Not Born Yesterday: The Science of Who We Trust and What We Believe

Chapter 1 for both of them is very short, so I assume most of you will not flake out on this. I may go ahead, but as you know I will be posting every Friday night. If you have a blog, post your own  impressions and I will link that up. If you have a comment, put in a comment. If you are an “oral” expositor, I suppose I could link to a podcast.

The page for the book club will be updated over the next five months.

Hugo Mecier follows me on Twitter, so I’m going to try and see if he’s willing to do a livestream early in 2021 about Not Born Yesterday. I don’t know Stephen Platt, but am hoping to do the same thing with him if he’s open to it.

Remember, you only need to read one book. But really both are doable. I’m going to be reading some other things since one chapter a week is so leisurely.

As for why I’m doing the book club and just totally pessimistic about Western civilization:

There are barbarians all around us. Just look. These people are no different than censorious religious radicals in the past. Except for religious radicals at least had some notional broader vision of the world and the good. These people only care about their own individual feels. Power uber alles.