Open Thread, 04/28/2019

Reading The Race for Paradise: An Islamic History of the Crusades. A bit too many names and battles (narrative), rather than social and economic dynamics. But it’s a good inversion of the traditional narrative, and illustrates just how chaotic and fractions the Islamic world in the last decades of the 11th-century was. Western European society was coming back to Roman levels of density and complexity after 1000 A.D., and for various reasons, the last half of the 11th-century was a period of disunity in the lands of Islam, so the Crusades were timed very fortuitous for the Franks.

Speaking of the Crusades, Christopher Tyreman’s God’s War: A New History of the Crusades is one of my favorite books (I remember staying up to 3 AM on worknights reading this book). But for some reason, it has much worse Amazon reviews than Thomas Ashbridge’s The Crusades: The Authoritative History of the War for the Holy Land. Does anyone know why?

Interesting historical fantasy I stumbled across, The City of Brass. The author is a white ethnic woman from New Jersey who converted to Islam as a teen, and now has a last name which is associated with Bengali Brahmins (she also pronounces very peculiarly). The reviews are good, but I’m not a fan of historical fantasy. Mixing the real and fantastic doesn’t appeal to me.

Dante is still selling 30x WGS for $229 as of this writing. No, I have no idea how Dante works in regards to this price point. But apparently, it’s not a fraud.

Speaking of personal genomics, this week on The Insight I’ll be talking to Rodrigo Martinez, an officer at Veritas. Follow the link above to see the different ways you can subscribe.

Endgame is worth watching.

Speaking of podcasts and the like, I’m told that three people on a single Extremely Offline podcast that will go live next month will all have been podcasts on the Browncast. Can you guess who? It shouldn’t be too hard.

Evolutionary dynamics of culturally transmitted, fertility-reducing traits.

A genetic hazard score to personalize prostate cancer screening, applied to population data.

This thread is worth reading:

Gencove announces Phase I SBIR grant to validate polygenic risk score estimation from low-pass sequencing.

Angiosperm speciation speeds up near the poles. “Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness.”

The continuing impact of an ancient polyploidy on the genomes of teleosts. “…lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina.”

Darwin Devolves: The New Science About DNA That Challenges Evolution. Michael Behe has a new book out. Richard Lenksi has responded in detail on his weblog.

I read Darwin’s Black Box and Michael Denton’s Evolution: A Theory in Crisis 20 year ago. Not convinced. That being said, people without a scientific background can be impressed easily. I still remember the stupid reader who incredibly blown-away by the pig-headed sophistry in David Stove’s Darwinian Fairytales: Selfish Genes, Errors of Heredity and Other Fables of Evolution. I read the book because the reader was impressed, and the reader was someone who I didn’t have a strong opinion about. I came away concluding that the reader must be kind of a moron since the book itself was just plain ignorant in the literal sense.

I’m still trying to place a piece in The Federalist on evolution. They gave me a few suggestions. Friends who have read my draft were already impressed, so I’m 90% sure I can get this placed in the conservative media. I actually interviewed the author of this piece, Why One-Third Of Biologists Now Question Darwinism, for the Browncast. The podcast will go live tomorrow.

Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies. This is a really interesting paper. The citations are interesting too.

Efficient use of genomic information for sustainable genetic improvement in small cattle populations.

Direct-to-Consumer Genetic Testing and Potential Loopholes in Protecting Consumer Privacy and Nondiscrimination.

African genomics tells us about deep structure and history


Two interesting papers in Genome Biology that are open access, Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations and African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Since they are open access you should just read both of them.

I believe they are the first in a series of papers over the next few years using whole-genome analysis to understand the population structure within Africa, and how it relations to the people who branched off from Africans. Eventually, this will also lead to research focused on medical and population genomics, looking at characteristics and forces beyond phylogeny.

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Having a common name in a post-Dunbar’s number world

I’m not sure I believe the model outlined in Robin Dunbar’s Grooming, Gossip, and the Evolution of Language. I’m not even sure about the specific details of Dunbar’s number. But, the overall insight, that the vast majority of human history has been defined by small groups with people you see again and again had an impact on our psychology seems robust.

The connotations of the very word “stranger” are complex but generally lean to the negative. And I think that makes sense. One of the tasks of cultural norms and values is to figure out a way that strangers can be interacted with in non-zero sum relationships.

All of this is to preface a banal assertion about interaction in day-to-day life if you are a middle-class professional. I get a lot of emails from people with common names, and it’s a non-trivial cognitive load to figure out if I should pay attention or not. Names like “David”, “John”, and “Omar” are so common that I’ve actually ignored people I shouldn’t because I didn’t realize it was that David or Omar. I’ve almost even responded to the wrong person when two people with the same first name are emailing me at the same time.

In a premodern village or a Paleolithic hunter-gatherer tribe, having a common name on a population-wide scale wasn’t a big deal. The people you would address by name regularly was far less than 100 over a year. But in today’s world, some people have to interface with ten different strangers per day, along with all the “regulars.”

If I was a parent considering names, this would be something that I would take into account. It’s probably not optimal to have a very rare name, because people might misspell it or misremember it, though it will be salient. But having a very common name can also be annoying, to the point where many people with common names now go by their middle name or a nickname. Rather, a familiar but not-so-common name is probably optimal.

To give an example, the name “Dennis” is not too common for people my age (as opposed to “David”). If I get an email from a “Dennis” there is only one or two people it could be.

The Genetics Of The St. Thomas Christians, part 2

Last year I posted The Genetics of the St. Thomas Christians. Recently I got some more samples. Of these, four were clearly self-identified as Southist/Knanaya Christians (as opposed to Northist Christians). The Knanaya are a bit different in their traditions than the broader much larger St. Thomas Christian community.

In the PCA above the bottom left are Middle Eastern groups. Druze and Yemeni Jews. Toward the top are Lithuanians. Green are Iranians. From the bottom right, up a diagonal axis, you see south-north Indian cline from low caste Telugu Christians, to Jatts from Punjab.

It does seem in relation to the other more generically labeled St. Thomas Christians the four Knanaya show some noticeable Middle Eastern shift.

Here’s an admixture plot:

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College educated conservatives are divided on evolution


A few years ago an academic friend of mine mentioned offhand that it must be difficult for me to be an evolutionary biologist (of sorts) and a conservative (of sorts). As someone in touch with many “elite conservatives” (people who work at think-tanks and the like), that’s not true at all. Though Creationism has substantial support at the grassroots (the only time I have encountered evolution-skepticism in the last ten years has been from people who grew up fundamentalist), the reality is that at the elite levels in the conservative movement it is not a widespread position.

But, conservatives are still divided. Looking at the General Social Survey EVOLVED variable, and limiting to non-Hispanic whites, you see that while there is nearly total unanimity among self-identified liberals with college educations or higher that humans developed from animals, college-educated conservatives are split.

If you run some regressions you will see a lot of this is due not to politics, but to what politics is correlated with. Self-identified conservatives are much more likely to be religious conservatives. Those conservatives who are not religious conservatives are not very skeptical of evolution.

But one issue that I am wondering about: if most elite conservatives have no issue with evolution, and even college-educated conservatives are split down the middle, why is there so little “balance” at conservative publications? That is, periodically there is a report or opinion favorable to Intelligent Design published. But there is rarely a counter-response, even though attitudes amongst the readership are surely mixed?

I may personally attempt to change this a bit by submitting “pro-evolution” pieces here and there. We’ll see how that works out.

The expansion of modern humans ~50,000 as part of a regular Poisson process

Last of the giants: What killed off Madagascar’s megafauna a thousand years ago?:

The first job is to understand exactly when the megafauna died out.

Radiocarbon dating of over 400 recent fossils demonstrates that animals under 22 pounds lived on Madagascar throughout the last 10,000 years. For animals over 22 pounds, there are abundant fossils up to 1,000 years ago, but relatively few since. The biggest decline in number of large animals occurred rapidly between A.D. 700 and 1000 – practically instantaneous given the long history of their existence on the island.

According to new dates on fossil bones with cut marks on them, humans arrived on Madagascar 10,500 years ago, much earlier than previously believed. But whoever these early people were, there’s no genetic evidence of them left on the island. New analysis of the human genetic diversity in modern Madagascar suggests the current population derives primarily from two waves of migration: first from Indonesia 3,000 to 2,000 years ago, and later from mainland Africa 1,500 years ago.

So it seems that people lived alongside the megafauna for thousands of years. How did the humans interact with the large animals?

Our new study found dozens of fossils with butchery marks. Cut and chop marks provide compelling evidence as to which species people were hunting and eating. Evidence of butchery of animals that are now extinct continues right up to the time of the megafaunal crash. Some people on Madagascar hunted and ate the megafauna for millennia without a population crash.

The abrupt land use change might hold some clues. The transition from a forest-dominated ecosystem to a grassland-dominated ecosystem appears to be widespread….

This research about Madagascar is important. If it turns out correct, I think it gives us deep insights about the expansion of modern humans outside of Africa ~50,000 years ago, and why their arrival resulted in the extinction of so many other human lineages. A generation ago we might have posited that some massive bio-behavioral change is what triggered this, but I am coming closer to the idea that cultural changes are punctuated enough that that may actually explain things. The culture changes first, then genes follow the culture.

Perhaps one might posit a model with massive turnovers in the hominin lineage due to this cultural dynamic occurs periodically, as if it’s a Poisson process.

Open Thread, 04/12/2019

Just a reminder for people to check in on The Insight this week. Lots of talk about Denisovans between Spencer and myself. We’ve also got a follow-up podcast scheduled with a researcher working in Denisovan genomics in a few weeks (we’re on Spotify now by the way).

Our three new hires at George Mason economics. These look good.

Sri Lanka Suicide Bombings Targeting Christians Kill Hundreds. The most likely culprits seem to be a jihadist group active in southern South Asia.

A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences. I think the “Crusader genes” are hard to find in the Near East because the collapse of the Latin kingdoms was gradual enough that “Franks” and their scions mostly managed to get out and go back to Western Europe.

Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants.

Anxious Times In Pakistan’s Pagan Valley.

Why One-Third Of Biologists Now Question Darwinism. I’m writing a response to this piece for The Federalist. Rather than a response to Intelligent Design, I want to represent what evolutionary biology really is.

Evidence for Early European Neolithic Dog Dispersal: New Data on South-Eastern European subfossil dogs from Prehistory and Antiquity Ages.

Gene Wolfe, death of a master

Gene Wolfe, Acclaimed Science Fiction Writer, Dies at 87. Wolfe’s prose could be challenging to read. I actually read The Book of the New Sun trilogy twice because of some elements of impenetrability in the style, though there’s a reason Wolfe was acclaimed. In general, I’m not a fan of “science fantasy” or the “dying Earth” genre, but Wolfe really made it work.

One thing about Wolfe that is of interest is that like J. R. R. Tolkien he was a Catholic convert, whose religion influenced his work. Arguably more directly and consciously in the case of Wolfe. But it is subtle enough that it doesn’t distract or warrant notice. In fact, I’d argue that Severian is much less clearly a Jesus-figure than Paul in the Dune series to the naive reader.

I’m not someone who minds authors telegraphing their viewpoints and ideologies into narratives, no matter what it is. But I think there’s no point in putting it into “speculative fiction” if it’s too direct. For example, I think one reason C. S. Lewis’ Narnia cycle is less popular than Tolkien’s work is that it reads as Christian fantasy, rather than fantasy with inflections from the author’s Christian viewpoint.

Wolfe, like Tolkien, had strong personal views. But he did not let them saturate his stories. The Christian outlines and themes in The Book of the New Sun are clear after someone points them out. But they aren’t salient at all when you are reading it without foreknowledge.

Let the genomic die fly!


A new “polygenic risk score” (PRS) paper is making some waves, Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood. Since it is open access I suggest you read it.

But basically, they took ~2 million common variants (there are about ~100 million common variants in the world population) in ~300,000 individuals in 4 cohorts, and used it to predict weight. A genome-wide polygenic score statistic. The correlation with BMI of the score is 0.29. This is pretty modest. But it seems to me that the biggest and most important finding is that it seems to capture a lot of the people at the tails of the distribution.

I’m becoming more and more convinced that the best things these PRS scores can do in the near-term is to identify people who are possibly at these tails. In a complex trait context, the tails are where for diseases a lot of the people who are going to have issues later in life exist. People with BMI in the range 25-30 may have a modest increase in risks, but someone who is very obese, with BMI above 35, is at much greater risk. Over 40% of the people in the top decile here were obese. Only 10% of people in the bottom decile were.

This research comes out of the context of earlier work on the heritability of BMI. It’s around 0.75 or so. That means it runs in families. Combined with the fact that in the recent past, or in other nations, there is a great variation in median size and distribution, one can intuit that genetic dispositions and environmental context both help explain the variation we see around us. The modern American environment is clearly obesogenic. When most of the American population were involved in physical jobs on farms the environmental context was very different.

Over the next few years, there risk scores for BMI will get better, and expand to other populations. One thing that some people are pointing out is that we know it’s heritable, so why not just look at your family? As many of you know, Mendelian segregation means that siblings may have quite different risk profiles on the genomic level. Polygenic risk score prediction is I think going to be extremely interesting and informative in the case of traits which are known to be found within families across generations (e.g., autism), but don’t seem to impact everyone. Perhaps we’ll find for a given characteristic expression is random, due to some life event or cofactor such as infection. Or perhaps we’ll find that differences among siblings have some genetic basis in variants inherited from parents?

Addendum: One of the authors, Sek Kathiresan, has been answering questions on Twitter.

The telos of modern humans

Credit: Luke Jostins

Next week’s episode of The Insight is going to be on Denisovans. It’s a long one because so much has come out in the last few months on the specific topic, as well as the broader framing issues (e.g., the discovery of a new human species on Luzon).

One of the major points Spencer and I discussed is how important it is to understand general trends in the hominin lineage, that is, humans, before the great expansion ~60,000 years ago. For example, Neanderthals and Denisovans were very different in their paleoecology and biogeography. Neanderthals seem relatively homogeneous (probably due to repeated mass die-offs). In contrast, the “Denisovans” look to have been very deeply diverged within their clade. If the latest work is correct, and some Denisovan lineages split more than 400,000 years ago and persisted down to >100,000 years ago, then the differences between Denisovans may have been considerably greater than between any modern human lineages. For example, the Khoisan diverged from all other humans ~200,000 years ago, and there are possible deeper lineages, but not that much deeper.

Right now what you know about the Denisovans are from genomes in the Altai region. Imagine if we extrapolated to all modern humans from Altaians? It seems entirely likely that the Denisovan lineage was very diverse because it occupied very diverse territory geographically.

But diversity aside, one of the things I like to point out to people, is that there was an overall trend of encephalization among hominins. Neanderthal brains were growing larger too. We need to understand the natural history of all human lineages to understand what happened 60,000 years ago. I am coming to the conclusion that it wasn’t some incredible miracle of a behavioral big bang, but the inevitable outcome of systemic forces in hairless ape evolution that started ~2 million years ago.