Month: March 2018

The origin of the Ashkenazi Jews in early medieval Europe

Posted on by Razib Khan


Last year’s The time and place of European admixture in Ashkenazi Jewish history is very close to the last word on the genetics of the ethnogenesis of Ashkenazi Jews. Here’s the author summary:

The Ashkenazi Jewish population has resided in Europe for much of its 1000-year existence. However, its ethnic and geographic origins are controversial, due to the scarcity of reliable historical records. Previous genetic studies have found links to Middle-Eastern and European ancestries, but the admixture history has not been studied in detail yet, partly due to technical difficulties in disentangling signals from multiple admixture events. Here, we present an in-depth analysis of the sources of European gene flow and the time of admixture events by using multiple new and existing methods and extensive simulations. Our results suggest a model of at least two events of European admixture. One event slightly pre-dated a late medieval founder event and was likely from a Southern European source. Another event post-dated the founder event and likely occurred in Eastern Europe. These results, as well as the methods introduced, will be highly valuable for geneticists and other researchers interested in Ashkenazi Jewish origins.

Roughly the Ashkenazi Jews are a half and half mix of a Middle Eastern population and various European groups. The majority of the European ancestry is “Southern European,” probably something like Italian. But, a minority of the European ancestry is like “Eastern European.” Additionally, the former admixture pre-dated the bottleneck, and probably dates to ~1000 A.D., while the latter event post-dates the bottleneck.

For years I had thought that Isaac Bashevis Singer’s excellent novel The Slave was interesting but implausible. The reason being that Ashkenazi Jews and their gentile neighbors did not mix by this time, as the European ancestry in Ashkenazi Jews dates to the Roman period.

These results reject that model…the tract-length evidence is persuasive to me that admixture with Slavs did occur.  Some Italian groups are more north shifted, but the most parsimonious explanation while the Eastern European like ancestry came in later is that it tracks Jewish migration into Germany and Poland-Lithuania later.

The dating of admixture is something I’m less sure of. At 625 to 1,250 years before the present, it puts the emergence of the Ashkenazi community firmly in the Christian era. I don’t want to get into too many details, but from what I have read the Church and local authorities frowned on Jews owning Christians slaves, and tried to suppress instances where Christian slave women became concubines to Jewish men or even Judaized.

I had long assumed that these records reflect elite paranoia. If the dates of admixture are right they may reflect a real concern and a phenomenon (the Y and mtDNA evidence strongly point to the likelihood that the pattern was generally partnerships between Jewish men and gentile women).

And to be frank they tell us less about Jews than they do about the nature of “Christian Europe” in the early medieval period. There is one school of Reform Protestant which takes a dim view of how deeply Christian medieval Europe ever was. I think these results support the thesis that Christianity was an elite religion whose grasp upon the masses was more tenuous and illusory than we might imagine. There is also the reality that the feudal Christian state never had totalitarian authority over the population.

In theory Jewish assimilation of Christians to their identity, Judaizing, could be a capital crime. But if these results are correct it was quite common in the formation of the early Ashkenazi community before it moved north and then east. This decentralization and relative weakness of the early medieval Church and state, the superficially of mass Christianity, might also explain how vast regions of France defected from orthodox Christianity for decades in the 12th century during the ascendancy of the Cathars.

On a final note, I decided to do a little probing on the Middle Eastern forebears of the Askhenazi. The paper says that Levantine populations are the most likely source, which is entirely expected. But I wanted more detail, so I used the Human Origins Array dataset. You can see on the PCA above that the Ashkenazi Jews are shifted toward the European (Basque) population away from Middle Easterners, but if you project the line outward it lands on Christian and Muslim Lebanese. Haber et al. last year showed that there was continuity between the modern Lebanese and Caananites, and the Jews were likely originally a form of Canaanite. Curiously, Palestinian samples in the data are strongly shifted away for the Lebanese, toward groups like Saudis.

I understand it’s a hot potato politically, but if I didn’t have a dog in this fight I’d say that the contention that Palestine and Jordan (look at the Jordanian sample positions) underwent some population turnover is likely true (though I’d be curious about the data on Palestinian Christians).

The peopling of the Indian subcontinent at the dawn of knowing

Posted on by Razib Khan

A few people have been pointing me to a new paper, A Bayesian phylogenetic study of the Dravidian language family, which implies that the Dravidian language family diversified ~4,500 years ago. I don’t have much to say about the paper itself since it aligns with my own conclusions, but it’s well outside of any field that I can judge (though it does use standard phylogenetic packages I’ve used).

Recently I’ve been going back to old posts of mine on South Asian population genetics because no matter how much some people drag their feet on this question, we’re pretty close to knowing how South Asians came to be. Here’s what I said in December of 2010:

Who were the Indo-Iranians? I lean toward the proposition that they do derive from the Andronovo culture of the Eurasian steppe. This would date the entrance and expansion of Indo-Aryans in northern India 3-4,000 years ago. I also contend that the dominant element of ancestry among modern South Asians is not Indo-Aryan. Rather, it is an ancient stabilized hybrid of pre-agricultural societies in the Indus valley and Neolithic farmers who originated from what is today western Iran and eastern Anatolia. Therefore, I posit that the “Aryanization” of the Indian subcontinent is properly modeled as the same processes which led to the emergence of an Anatolian and Rumelian Turkish identity; a small elite population which forces an identity shift among the majority.

Where was I wrong? Where was I right?

Even looking at ADMIXTURE plots which don’t always give an accurate sense of population history it seemed likely that “Ancestral North Indian” (ANI) was not one thing. Some South Asian populations seemed to have much stronger affinities to West Asian populations. And in particular those from highland West Asia, toward the Caucasus. These include groups in southern Pakistan, but also to some extent in South India. In contrast, other groups had affinities with Eastern European populations, in particular, high caste North Indians, and to a lesser extend Indo-European peoples more generally.

I think I got the dynamic correct. Subsequent analyses comparing ancient DNA from the Caucasus and Iran suggest that all South Asians have a lot of shared drift (ergo, ancestry) with highland West Asians, while a smaller subset has high shared drift (ergo, ancestry) with pastoralists from the Eurasian steppe. The groups match up with what the ADMIXTURE plots were suggesting.

There was more than one pulse of ANI-like ancestry and that one of them was like West Asians and one more like Europeans. Remember, this is before we knew the acronyms ANE, WHG, and EEF. Or CHG and Eastern Middle Eastern Farmers and Western Middle Eastern Farmers.

But, I think I was wrong about the magnitude of the admixture. This was before ancient DNA had revolutionized our understanding of population movement and turnover. I was still resisting the mass migration of a whole folk across huge distances. I’m more open to that now. I am not sure I still believe the very high steppe fractions implied in some of the recent analyses, but it’s certainly higher than I would have believed back then.

Finally, the recent diversification of the Dravidian languages supports the model that their current distribution is not primordial. Rather, they probably expanded relatively recently from the northwest of the subcontinent. Probably earlier than the Indo-Aryan expansion into the Gangetic plain, but not that much earlier.

Additionally, because the Dravidians were not primordial, but expanding only somewhat ahead of Indo-Aryans, they were part of an interactive social-cultural sphere with the Indo-Aryans. I think the very high frequency of R1a1a-Z93 in some non-Brahmin South Indian groups, even tribal ones, suggests to me that the expansiveness of some paternal Indo-Aryan kin networks across the whole subcontinent.

Addendum: Much of the attention goes to the ANI dynamics. But though recent work attests to the overwhelmingly diversity, and basal character, of South Asian mtDNA lineages, we can’t be entirely sure that they are indigenous without ancient DNA. If a migration from the east at the Pleistocene-Holocene boundary was characterized by gradual diffusion of groups with reasonable effective population sizes they could have brought over their diversity.

Diving into Chinese philosophy

Posted on by Razib Khan

Back when I was in college one of my roommates was taking a Chinese philosophy class for a general education requirement. A double major in mathematics and economics (he went on to get an economics Ph.D.) he found the lack of formal rigor in the field rather maddening. I thought this was fair, but I suggested to him that the this-worldy and often non-metaphysical orientation of much of Chinese philosophy made it less amenable to formal and logical analysis.

I recalled this when a friend of mine, from an Indian background, asked what I would recommend for him to learn a bit about Chinese philosophy. What I suggested was that he read A Short History of Chinese Philosophy, and then read The Analects and something like Confucius: And The World He Created.

As someone who lives in the West from a Hindu background, I didn’t think it was worth it for him to explore Chinese Buddhism, or even Neo-Confucianism, which emerged out of the reaction and accommodation with Buddhism.

Thoughts? Recommendations?

Henan, the heart of China

Posted on by Razib Khan

I haven’t posted on one of these in a while. Mostly because I don’t know what to say about Henan. Henan is where China began. As noted in Wikipedia four of the eight ancient capitals of China are located in this province, in the heart of the North China plain. Chineseness, as we understand it, coalesced in this province. The first historical dynasty, the Shang, had the core of their domains in Henan. Though we don’t have historical evidence of earlier legendary Chinese dynasties, many believe that they are likely recollections of the archaeological cultures which flourished in Henan before the Shang (e.g., the Eritlou culture as the Xia).

Originally a land of millet, Henan is China’s number one wheat producer. Whereas the staple of the south is rice, in the North China plain is it noodle.

The agricultural focus of Henan indicates its relative lack of development. In some ways, it resembles Bihar and eastern Uttar Pradesh in India, which were the core of South Asian polities at the dawn of recorded history, but are now backwaters. With 94 million people Henan is China’s third most populous province, but it turns out that more people in China have origins in Henan (103 million) than any other province. This reflects nearly 10 million migrants who work in other provinces, generally coastal ones.

Being the locus and origin of Han Chinese culture it is no surprise that the province is overwhelmingly ethnically Han. But curiously it also seems to have an overrepresentation of Christians compared to other Chinese provinces.

Carl Zimmer profile of the Reich group at work

Posted on by Razib Khan

The New York Times has a review up (sort of) of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, David Reich Unearths Human History Etched in Bone. But since Carl has been covering the publications coming out of the Reich lab for many years now it’s kinds of a survey of the whole operation and how David and company go where they are.

The last few paragraphs are pretty tantalizing:

As of last month, Dr. Reich’s team has published about three-quarters of all the genome-wide data from ancient human remains in the scientific literature. But the scientists are only getting started.

They also have retrieved DNA from about 3,000 more samples. And the lab refrigerators are filled with bones from 2,000 more denizens of prehistory.

Dr. Reich’s plan is to find ancient DNA from every culture known to archaeology everywhere in the world. Ultimately, he hopes to build a genetic atlas of humanity over the past 50,000 years.

“I try not to think about it all at once, because it’s so overwhelming,” he said.

Three years ago I was having a discussion with someone from Reich’s group and mentioned offhand that in terms of getting data I give the nod to Eske Willerslev’s group of researchers, though I thought the people around David and Nick Patterson tended to perform a deeper analysis. Three years is a long time, and as the results since then have shown, the “SNP capture” methodology is very cost effective. They might not get the whole genome sequences of individuals, but they get lots of individuals. And for a lot of population genomic analysis, you want lots of individuals more than the whole genome sequence.

But not all. The more ancient individuals probably have a lot of variation “private” to them and their population, so you don’t know all the neat polymorphisms you might miss.

With that gripe submitted, it’s pretty incredible that the Reich lab has 3,000 ancient samples in the pipeline for analysis. In Who We Are and How We Got Here David Reich outlines just how he and his collaborators transformed the artisanal process of data generation from ancient DNA into a rationalized and commoditized factory process.

Open Thread, 3/19/2018

Posted on by Razib Khan

Some people have asked me what I think about Imagined Communities: Reflections on the Origin and Spread of Nationalism. I haven’t finished it, but now I understand why it is one of the most assigned books for undergraduates: it’s concise yet facile superficiality would appeal to a know-it-all twenty year old. What’s more disturbing, though I guess not surprising, is that Imagined Communities communities is a book that I’ve seen name-checked for years by various public intellectuals. Did they read the book?

It’s not that the book is incredibly wrong. It’s just that there’s not that much there in my opinion.

Been enjoying sampling the Philosophize This! podcast.

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Haven’t blogged it because I haven’t read the supplements.

Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project.

Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase. This is big.

‘Serial Bomber’ Is Suspected in Explosions That Have Put Austin on Edge. Twitter was useless yesterday as most of the people seemed more enraged at the media for not laying the blame on white supremacists or Muslim radicals, as opposed to those getting killed or injured.

Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits.

Feeling like I should reread The End of History and the Last Man. Feels like history has started again….

Some people ask me about how I read fast. Part of the answer is that I read a lot in a specific area at the same time. Also, you can read fast if you know a lot about a topic. For example, a substantial portion of Who We Are and How We Got Here involves going over four and three population tests. I know what those are, so I read those sections quickly.

Finally going to hunker down and figure out which plugin is causing the 500 error on this website.

Just a reminder, please subscribe to the podcast on iTunes or Sticher and review it (positively). I’ll stop with the flogging when people no longer tell me “Oh, I didn’t know you had a podcast!”

This week we’ll I’m interviewing Milford Wolpoff (that is, what’s going live).

The western wolves are back, did you notice?

Posted on by Razib Khan

Tensions rise on the range after wolf kills cow in California for the first time in a century:

A wolf has killed a California rancher’s cow for the first time in more than 100 years, raising tensions in the newly reclaimed wolf country in California’s rugged northeastern corner.

California now has two packs in the north. This isn’t world-altering. Perhaps it was inevitable. But sure crept up on me.

Oregon now has nearly 100 wolves. There’s even a pack which wanders the mountains above the town I grew up in!

The gray wolf habitat is forest, so much of California won’t see a swarming of wolves because it is desert or cultivated. But it seems very unlikely that the Shasta pack doesn’t presage an expansion of wolf territory west toward the Pacific, and then down into vast timberlands reaching toward San Francisco. And wolves will surely move south along the western edge of the Sierras.

 

Denisovans, Neanderthals, Yetis, oh my!

Posted on by Razib Khan

An excellent open access paper is out in Cell which explores the distribution of archaic hominin, and in particular Denisovan, ancestry, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture:

Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

Before you get caught up in the results, you should check out the methods. They’re pretty ingenious. Though with novel results like this people also really need to work their way through them as well (the authors present a lot of simulation results to validate the method, so I’m sure that will convince most; it certainly sways me).

The plots at the top of this post show the different distribution of Neanderthal and Denisovan admixture, by matching regions of the genome that they’ve identified as archaically introgressed. The ultimate logic is to look for variants which aren’t found in Africans, and are found in non-Africans, and scan over segments of the genome hoping that you can pick up the haplotypes that would slowly be chopped up over time through recombination that came in from Neanderthals or Denisovans.

At the top-left of the figure, you see “Northwest Europeans.” The segments tend to concentrate at the bottom-right of the panel. That means that they match the Neanderthal reference sequence to a high degree, but not the Denisovan. This makes sense since everything we know from earlier work indicates that Northwest Europeans don’t have Denisovan ancestry.

On the bottom-right you see Papuans. They’re very out of place because they are the only population in the list where Denisovan ancestry is greater than Neanderthal ancestry. This is visible in the match patterns.

South and East Asian populations exhibit a pattern with high (relative) levels of Neanderthal matches, but also a minor amount of Denisovan matching. This aligns with earlier work, which reported low levels of Denisovan admixture among populations with eastern Eurasian ancestry broadly.

The surprise is that the variation in matching to the Denisovan Altai genome exhibited a north-to-south cline. In particular, Northeast Asian populations seem to have a mix of two types of Denisovan. One, which is close to the Denisovan sequence that is normally used as a reference, and one which is diverged from it. The Papuans and South Asians seem to have Denisovan ancestry which is not so much like the Altai sample. This is not very shocking of course.

Finns barely miss the p-value cut-off (Bonferroni-corrected threshold), but they clearly have some Denisovan from East Asian gene flow, and some of it looks to be similar to the Altai Denisovan. Curiously, the Vietnamese (Kinh) don’t show any Altai Denisovan, but the Dai do. The Japanese have a lower proportion of the Altai Denisovan than the two Han Chinese samples. And very strangely the 1K Genomes samples from the New World, a substantial proportion of which have Amerindian admixture, show no Denisovan.

Pontus Skoglund immediately made a very interesting observation:

And Alexander Kim followed up:

In the thread to Skoglund’s original comment Africa Gomez notes that the authors suggest that high linkage disequilibrium in New World populations, due to recent admixture between diverged groups, may reduce the power to detect the Denisovan ancestry. So perhaps that’s that?

But for a moment, let’s set that aside. The best evidence right now is that the Denisovan admixture into Papuans, and therefore South Asians, occurred not too after the Neanderthal admixture event. That mixture is reasonably well dated because of ancient genomes which are closer to the period of admixture. But what about the second event with the Altai Denisovan? If what Skoglund says is true the date for that might be closer to the Last Glacial Maximum, and not when modern humans came to dominate the region. And I say dominate because there’s evidence that anatomically modern humans may have ventured quite far into eastern Eurasia before they finally swept aside more established lineages.

A few years back researchers found that one of the mutations that allow for Tibetan high altitude adaptation seems to have come in from a Denisovan genetic background. Spencer Wells, who knows a thing or two about Central Asia, has always half-seriously suggested that the legends of the Yeti derive from populations of archaic humans who persisted in the uplands of the heart of Eurasia.

But perhaps they weren’t pure Denisovans in any case. Work out of David Reich’s lab has suggested that Denisovans themselves, or at least the Alta Denisovan, harbors a deep ancient lineage diverged from modern humans, Neanderthals, and Denisovans, in low fractions. The “Altai Denisovan” admixture may have come into Northeast Asians via a mixed population, which arose when modern humans came to dominate eastern Eurasia, but only transmitted the Altai Denisovan ancestry later.

A preview review of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past

Posted on by Razib Khan

So I read the final version of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. It’s good. You can finally set aside The History and Geography of Human Genes, though with the rate of change in the field of ancient DNA I wouldn’t be surprised if there was a major revision of Who We Are and How We Got Here in two to four years.

I’m writing up a full reaction for National Review Online, so I’m not going to say too much here in specifics. And, since the book is still not out for a bit over a week I think it would be kind of rude of me to spill the beans on anything too juicy (though if you read this blog closely there won’t be any huge reveals).

So let me say something in the generality first. I’ve told the story of my friend Barry* before. Barry is a smart guy. He has a Ph.D. in the physical sciences from an eminent university in the Boston area. Barry works as a senior research engineer at a major semiconductor firm. Barry is interested in many things about the world. In 2011 I mentioned in passing to Barry over dinner that researchers had published in Science last year the fact that most humans alive today carry appreciable Neanderthal DNA. Barry was shocked. This was news to him. When I expressed shock that someone like Barry would be ignorant of this fact, Barry suggested perhaps I needed to expand my horizons as to the nature of things that the typical educated and interested person knows about science at any given time. That’s fair enough.

Someone like Barry is a perfect audience for Who We Are and How We Got Here. Barry hasn’t taken much biology, so the review of concepts such as recombination (even if the author doesn’t use that word) and mutation are useful. But more importantly, Who We Are and How We Got Here catches someone like Barry up to the state-of-the-art knowledge that we have in terms of human history, deep and prehistoric.

But it’s not just Barry. I’ve talked to plenty of people who work in evolutionary genomics who are not totally up-to-speed on the ancient DNA revolution. They too would benefit from reading Who We Are and How We Got Here front to back. I know people who work in the field of cultural evolution, who would also benefit from reading Who We Are and How We Got Here. I know behavior geneticists who would benefit from reading  Who We Are and How We Got Here. And so forth.

If you can’t find it in yourself to read 200-page supplements top to bottom, Who We Are and How We Got Here also is what you need.

Last summer I had the pleasure of having lunch with the author of Who We Are and How We Got Here, David Reich. If you read the prose it’s hard not to hear his precise and careful words echoing in your mind. Who We Are and How We Got Here is not rich with the same stylistic flourish and engagement as one might find in a popularization by Steven Pinker or Richard Dawkins. And I don’t think that was its intent, judging by how much space is given over to the four-population test! This is a serious book that is earnest in focusing on the substance of the science first, second, and last.

David expressed his discomfort with the opportunity cost that writing this book entailed for him when we spoke. While focusing on the book for the past few years he hasn’t had much time to do original analysis himself. His body language indicated the deep discomfort this caused him, and in Who We Are and How We Got Here he admits frankly that devoting himself to the book resulted in him not performing many analyses and publishing many papers.

One reason to write Who We Are and How We Got Here is that a book will reach outside the circle of those consuming and participating in the ancient DNA revolution. And a revolution it is! David Reich is already a highly eminent academic by any measure.  Who We Are and How We Got Here will do nothing to elevate his standing among his peers, because amongst them his stature is measured by the scientific papers published and projects in which he is involved.

So why make the sacrifice and write this book? Let me quote David Reich himself:

…I finally thank several people who repeatedly encouraged me to write this book. I resisted the idea for years because I did not want to distract myself from the science, and because for geneticists papers are the currency, not books. But my mind changed as my colleagues grew to include archaeologists, anthropologists, historians, linguists, and others eager to come to grips with the ancient DNA revolution.

I would expand the purview here more broadly: all public intellectuals should know about the human past in its fullness. It’s a shadow that hangs over us and frames our arguments about the present. How we came to be where we are matters unless you are the most clinical of logicians. If you are Gilbert Ryle, turn away!

In Who We Are and How We Got Here Reich recounts an encounter with an impudent undergraduate at MIT who wondered at the end of a lecture how it was he got funding for his abstruse projects. He responded with the standard pitch that goes into NIH grant proposals, that to understand human disease, one must also understand human population structure, and to understand human population structure it helps to understand human population history. After recollecting this anecdote Reich observes that he wishes he had responded differently. He concludes:

The study of the human past-as of art, music, literature, or cosmology-is vital because it makes us aware of aspects of our common condition that are profoundly important that we heretofore never imagined.

To me, this goes back to the Greek distinction of techne vs. telos. Science as an instrument in expanding the limits of human longevity and health is important, but it is not the only thing that science is capable of. If we turn science into pure instrument, we lose something essential and integral in its purpose.

These are old, ancient, universal disagreements. In ancient China, there were groups of philosophers who outlined a vision that had little use for the fripperies of the past. Legalists who wished to turn the whole society into an instrument of production and power, for whom techne was prominent. The Legalists expressed a cold calculating face of practicality and instrumentality, but the universal altruists who followed Mozi ultimately had some of the same inclinations. How could men make merry with music when there was still suffering in the world? Shouldn’t nonproductive cultural practices be curtailed before we achieve the Utopia of plentitude?

Because the disciplines of Confucius won the ancient culture wars the Legalists and Mohists are remembered as crass caricatures. But the Confucian respect and reverence for accumulated human wisdom, the customs, and folkways of the past, were wise, insofar as a Confucian system persisted in China for over 2,000 years.** They gelled with deep human dispositions.

If we are to view human beings more than production and consumption machines shackled to the modern capitalist hedonic treadmill, then we need to consider the past as part of who we are. It is part of the treasury of human existence, which is more than just feelings of the present, but echoes down through the generations, through family lines, and cultures, and even in our genes. Humans without root float freely, but they are never truly free.

* I’m changing names, though if you know me from college or know me personally, you know who I’m talking about.

** Obviously this is a coarse generalization, one could argue that Legalism was laundered through State Confucianism!

Open Thread, 3/14/2018

Posted on by Razib Khan

I finally met my old friend Ramez Naam in the flesh. Ramez’s publisher sent me his book More Than Human: Embracing the Promise of Biological Enhancement in 2005. One thing led to another, and somehow he’s guest blogging on Gene Expression!

CRISPR as we know it did not exist in 2005. Things have really changed since then, and for the better, at least from the perspective of genetic engineering. It’s as if some of the stuff in More Than Human is coming to life.

I also recommend his book The Infinite Resource: The Power of Ideas on a Finite Planet.

Ramez is more optimistic about the future than I am, though cautiously so. I hope he’s right, and I’m wrong. I fear he’s not.

My concern is not with technological innovation. That will happen. It’s with maintaining social stability due to the immiseration of what was the middle class in developed societies. Also, the bourgeois version of the New Class seems to lack empathy toward the future lumpen….

SEC Charges Theranos Founder Elizabeth Holmes With ‘Massive Fraud’. “Fake it ’till you make it” will keep happening if there are no follow-up criminal charges. Holmes may not have gotten away the con, but she was a paper billionaire for a while and funded R & D with the cash that they raised on lies. One moral some are going to take away is that she took a big risk and failed, but it was one that perhaps needed to be taken.

Adaptive landscape of protein variation in human exomes.

Genetic dissection of assortative mating behavior.

Conor Lamb Wins Pennsylvania House Seat, Giving Democrats a Map for Trump Country. I’m pretty bullish on a Democrat takeover of the house. The country will swing back. That being said, I’m also bullish on the idea that the Democrats are their own best enemy, and divisions and lack of coherency in their plan going forward will mean they won’t be able to capitalize on their electoral windfalls over the next few years.

This week’s episode of The Insight is up, 23andMe, the FDA, and Our Genomic Future. We have some potential guests lined up. One of whom is Stuart Ritchie, author of Intelligence: All That Matters.

Please subscribe via iTunes or Stitcher, and leave us 5-star reviews! 

St. Patrick’s Day is coming up. I’ll be avoiding drunk people on the streets of Austin. But I also want to point out that my “side-hustle” DNA Geeks has an M222 t-shirt available. In case you don’t know, that’s the legendary Niall of the Nine Hostages’ possible haplogroup (a sublineage of R1b). About 10% of Irish men are M222.

‘Tomb Raider’: Fans Slam Criticism of Alicia Vikander’s Body. There are two points that I want to make. First, at 5’5 inches, Alicia Vikande is of a very normal height (Angelina Jolie was two inches taller). She’s not physically imposing, and she has a very narrow waist as well. Her figure is “boyish.” Second, since the 1990s there has been a shift in male action stars toward being more shredded/athletic as opposed to jacked-up and exaggerated in their physicality. This is a very different Lara Croft for a very different time.

I decided to check out the new public library today. Saw the book The Invention of Humanity: Equality and Culture Differences in World History. I hate the overuse of the term “invention” in book titles, but when I noted the beginning covered China, I got it. Too often books that are Eurocentric turn out to be more data than narrow/inference, and they rig the data ahead of time to support their thesis (see, Inventing the Individual).

I also got Constructing the World (a David Chalmers book), The Bible and Asia: From the Pre-Christian Era to the Postcolonial Age, Creators, Conquerors, and Citizens: A History of Ancient Greece, The Third Reich: A History of Nazi Germany. That’s ranked in order of likelihood that I’ll get through them.

Also, Philip Jenkins has a new book, Crucible of Faith: The Ancient Revolution That Made Our Modern Religious World. Jenkins is a great scholar, I admire his work a lot. But I think I’m going to take a break from religious history, since I know a fair amount about the topic.

Polygenic scores and tea drinking.

Exposing flaws in S-LDSC; reply to Gazal et al.. Working your way through this literature is often pretty useful, so start at this commentary.

National Geographic has a special on race and what not. One piece being shared is kind of interesting, These Twins, One Black and One White, Will Make You Rethink Race. Here’s an important quote:

In genetic terms, skin color “is not a binary trait” with only two possibilities, Martin notes. “It’s a quantitative trait, and everyone has some gradient on this spectrum.”

Historically, when humans have drawn lines of identity—separating Us from Them—they’ve often relied on skin color as a proxy for race. But the 21st-century understanding of human genetics tells us that the whole idea of race is a human invention.

If you’ve read this blog you know I’ve blogged about “black and white twins” for over ten years. Also, I think a lot of the debunkings of race are pretty facile. But that’s not what I want to talk about. Rather, one of the things that are unmasked unwittingly in pieces such as this is how deeply Eurocentric these conversations are. It’s as if public intellectuals and journalists that write on this topic either don’t know any non-white families or they pretend that they don’t. The “humans” and “Us” implicitly points to white European systems of racial classification (e.g., East Asians relied on skin color somewhat, but since they are not much darker than white Europeans, they also included hair color, to distinguish the Dutch from the Portuguese, and large noses and body hair, to distinguish from themselves).

Twins with different skin tones are striking. But almost any South Asian, black American, or Latino, or Southeast Asian, or even East Asian, can tell you that there is a wide range of pigmentation within many families. Basically, unless you are in a homogeneous European social environment, where most everyone has very light skin on a global scale, you will see the variation of pigmentation within families. Both my parents have large sibling cohorts, and in both of them there are cases where the difference in complexion between siblings is in the same range as the two fraternal twins highlighted in the piece.

Of course, journalists who work for National Geographic or The New York Times know people of varied ethnicities and probably see that there is pigmentation variation within those families. They just pretend as if they don’t for these sorts of pieces which debunk race, and the readers pretend they don’t know this information as well as they take it in in a self-satisfied manner and nod sagely.

I haven’t had much time to read Enlightenment Now: The Case for Reason, Science, Humanism, and Progress. But those who say it’s quite like The Better Angels of Our Nature seem correct from how how far I’ve gotten.

My timeline has been swarming with debunkings of Enlightenment Now from all ideological angles. The best responses to these can usually be found in Saloni’s timeline (from her), who is “Pinker’s bulldog.”

Ex-Muslim TV‘s Twitter account is irritated that some of its stuff is now labeled “sensitive material.” The day before this came up I noted that one of my posts that Jerry Coyne retweeted about Islam and apostasy was also labeled “sensitive material.”

Basically if Muslims find it offensive, it might be subject to scrutiny from Twitter. This may or may not be defensible from Twitter’s perspective in a business sense, or ethically. But it’s just the reality we have to deal with, though I would like to know which school of Islamic jurisprudence Twitter relies on to gauge sensitivity and offense. I suspect it will be the Hanafi fiqh due to its liberal utilization of qiyas, which allow’s Del Harvey’s minions more free play.

The nation-state is dying. What will come out of its ashes? I suspect empire by another name….