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February 21, 2018

The genetics of the Lombard folk migration

Filed under: barbarians,Germans,Lombards,Migration,Roman History,Romans — Razib Khan @ 9:13 am


There are many debates about the period after the fall of the Western Roman Empire in the late 5th century. For example, did it “fall” in the first place? I believe that the concomitant p0litical, social, and economic changes do warrant that word. But another question concerns the “barbarians,” who were mostly German peoples (there are some exceptions, such as the Iranian Alans and the Huns, whose specific provenance is unclear). Were they ethnically and politically coherent? Were they even peoples?

The extreme stylized positions might be outlined as follows:

– The barbarians who filled the political vacuum after the collapse of the late Roman state were coherent preexistent ethnic and political entities of German origin who migrated en masse and engaged in a folk wandering.

– Though their original provenance may have been in bands of German warriors from specific tribes, but the time they appear on the stage of history as we understand it, the barbarians were in fact a motley crew of opportunists of various origins, who adhered to a “barbarian” identity which was created de novo with the collapse of Rome. They were made by the collapse, they did not cause the collapse.

In the late 1990s, Norman Davies in The Isles presents an argument closer to the latter for the British Isles. That is, the Anglo-Saxon character of Britain was to a large effect a function of elite emulation and diffusion of a Germanic culture introduced by what was operationally a late Roman mercenary class. Davies alludes to texts which indicate a substantial native British population in Anglo-Saxon England centuries after the fall of Celtic kingdoms. This is in contrast to the apocalyptic vision of British monk Gildas, who depicts his Brythonic people fleeing before pagan Saxons and being driven into the sea. And, I have alluded to the possibility that the West Saxon monarchy, which later came to the center of English history during the Viking incursion, was in fact in origin Romano-British, rather than German (the early kings have Celtic names).

And yet England was always the most difficult case for cultural diffusion, because to a great extent Roman-British society did collapse. Both the British Celtic language and Christianity seem to have faded from the landscape, so the that the latter had to be reintroduced by Irish and continental European missionaries. Today, the genetics is more definitive, and it seems a substantial German migration did impact what became England, especially the east, what was the Saxon Shore. Though the majority of the ancestry of the people of England today seems to derive from people who were already resident in Britain in 400 A.D., a substantial enough minority seems to have greater affinities to people who were living in the stretch of land between the Netherlands and Denmark.

The case for mass migration on the continent of Europe (with the exception of much of the Balkans) is more difficult to make in a cut & dried fashion because the basic outlines of Romanness were much more intact in the centuries after the fall than in Britain. Though France and Lombardy may have names which derive from German tribes, there is not much that is German about these regions today, and frankly, even at the height of the barbarian rule when conquest and migration were fresh, the non-Roman overlay was likely a thin elite layer. Outside of Britan and the Balkans, the languages of the Roman Empire and the Christian religion maintained their dominance even after the fall of the Roman political order, a transformation of social norms, and the collapse of the economy.

And yet this does not deny the possibility of migration of peoples into this order. In Empires and Barbarians: The Fall of Rome and the Birth of Europe the historian Peter Heather argues that we must not neglect the likelihood that to some extent the arrival of the Germans was one of “folk wanderings.” That the identity of the Franks, Goths, and Lombards, did not emerge ad hoc and de novo through the accrual of military men around a tiny nucleus of German warlords and their retainers. That women and children were also part of the movement into the Roman Empire. Heather, in fact, depicts the Gothic arrival as one of destitute refugees fleeing the famine and chaos outside of the Pax Romana, and their subsequent militarization and rebellion as one forced upon them by the exigencies of their situation.

A new preprint on bioRxiv, Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics, clarify these arguments in the case of the Lombards, who conquered Italy in the 6th century. The abstract:

Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early Medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data was consistent with the proposed long-distance migration from Pannonia to Northern Italy.

The preprint has genetic and isotopic results from two graveyards associated with elite Lombards of the 6th century. The one in late antique Pannonia would be in modern Hungary. The one in modern Italy is near Turin. The late 6th century was a time of tumult in the Roman Empire, as both Italy and the Balkans were subject to massive turnovers of the ethnic and political orders. The movement into Italy from the northeast was a typical one, prefigured by the Goths and other Germans before the Lombards.

From what I know, as far as German barbarians went, the Lombards were rather “raw” and non-Roman (in contrast, some tribes, such as the Goths and Franks, had had relationships with the Roman Empire for generations before they decided to take it over). Though they were nominally Christianized, and elite Lombards persisted in practicing pagan rituals in Italy down to the 8th century, over 100 years after their conquest of the peninsula.

The authors used a lot of “best of breed” methods with their large data set, but the ADMIXTURE plot really illustrates the result fine enough. The blue is associated with Northwest European ancestry (British and white Utah samples), red with Italian ancestry (Tuscan), and green(ish) with Iberian (Spanish mostly). The very light blue is 1K Genomes Finnish. Panel B is the graveyard in modern Hungary, and panel C is the one from northern Italy.

There is a strong correlation in the graves with those being of Northern European ancestry, and having high status via grave goods. The individuals also exhibited some segregation in the graves. Northern European ancestry and Southern European ancestry individuals were clustered together. The Pannonian individuals, whether Northern or Southern European, don’t seem to resemble ancient or modern Hungarians. The isotope analysis indicates that many of the individuals were highly mobile.

Finally, the data was robust enough to do a pedigree analysis. It looks like a lot of these individuals are related. If you look at the plots you can see groups with the label “Kindred.”

There is so much detail in the results that I won’t recapitulate. Just read the preprint and make sure to check out the supplementary text. What I will say is this.

  1. The Lombard migration seems to have been a migration of people of Northwest European heritage into Southern Europe.
  2. The migration occurred during the lifetime of some individuals. These were highly mobile individuals.
  3. There were associated groups with the Lombards, who were genetically distinct, and likely of lower status. Their Southern European character is also distinct from the native population of Pannonia in the case of panel A.
  4. The Lombards themselves had Northern European ancestry which was somewhat heterogenous (probably different tribes and ethnicities). The shift away from Finnish ancestry probably indicates sampling more from western and opposed to central Europe.
  5. Admixture with the local populations and other post-Roman groups began early on.

The ethnocultural distinctiveness of the Lombards is clear from the textual evidence. The genetic data here confirm that in totality. But, The Geography of Recent Ancestry Across Europe, also highlighted a lot of deep population structure within modern Italy, and could not discern much impact of barbarian migration outside of the Balkans across their data set. Why?

It is rather clear that there were population declines across the West Roman Empire in the years after the Gothic Wars. If you read the textual evidence you imagine some sort of catastrophe going on. In human terms it was catastrophic. On the scale of economics, it was catastrophic. But in terms of population genetics, the long-term impact was not that extreme. The local population structure was not much altered because the Roman population base was so high that even a large decline did not induce bottleneck effects, and the German elite was also small enough it did not much perturb the underlying structure which had roots back to the period before the Roman Empire. Even in the first generations of Lombards in Italy, which is the Collego data set reflects, there was intermarriage between German people and others.

The demographic impact of the German migrations was huge on culture, politics, and economics. But it was not huge on population genetics.

February 19, 2018

A celebration of Cheddar…Man

Filed under: Ancient DNA,Cheddar Man — Razib Khan @ 7:39 am


It’s been a lot of cheddar the past few weeks. Or should I say Cheddar Man, the 9,150 year old Mesolithic subfossil from the area of Cheddar Gorge in England. This individual is important because it’s the oldest remain of such high quality found in Great Britain. And, in the late 1990s, as reported in Bryan Sykes’ Seven Daughters of Eve and elsewhere, the Cheddar Man subfossil was genotyped for mtDNA, the maternal lineage. There were, and are, lots of controversies about the validity of that result due to contamination being common in those early years of ancient genetics.

But today we have Cheddar Man’s whole genome. The preprint is finally out, and I’m digesting. Additionally, there has been a Channel 4 documentary, and a few weeks of media hype all around the implications of Cheddar Man.

This is an exciting time for genetics, history, and heritage. Since Britain is a major center of interest for these topics, it’s not surprising that Cheddar-mania has taken off. To mark this occasion DNA Geeks commissioned a design of Cheddar Man using Prince as a model. That might seem strange, but it probably is appropriate given Cheddar Man’s other-worldly and ambiguous appearance. You can get t-shirts and framed prints.

I’ll probably be posting about the Cheddar Man preprint, which really transcends Cheddar himself, tonight or tomorrow.

February 16, 2018

Winds of Winter not likely in 2018

Filed under: Fantasy — Razib Khan @ 9:25 pm

George R.R. Martin Throws Even More Cold Water on Winds of Winter Dreams.

Basically, it looks like he will come out with a different book first. It’s hard to imagine him squeezing out the next book in A Song of Ice and Fire before that in 2018.

There were two years between A Game of Thrones and A Clash of Kings. Two years between A Clash of Kings and A Storm of Swords. Five years between A Storm of Swords and A Feast For Crows. Finally, six years between A Feast For Crows and A Dance of Dragons.

If the next book was released now, it would be more than six years. It looks like we’ll go beyond seven years.

The trend is not promising. I’m pretty sure I’m not the only person who is, was (?), a big fan of the series go through the five stages of grief. It is what it is.

February 15, 2018

White modern Northern Europeans are genetically more like brown South Asians than brown(ish) ancient Northern Europeans were

Filed under: Human Population Genetics — Razib Khan @ 8:01 am

The Guardian has a piece by Arathi Prasad, Thanks to Cheddar Man, I feel more comfortable as a brown Briton. Dr. Prasad is a geneticist, so the science is pretty decent (she’s probably seen the documentary ahead of time too).

But there is a curious quirk here and it reveals something about human psychology: modern Britons are genetically much closer to South Asians, like Arathi Prasad, than these ancient darker-skinned Britons. The plot to the left illustrates this (it’s using the Dystruct package). The far right of the top panels represent South Asians. You can see Europeans pretty clearly. Let’s note two things:

1) Modern Europeans (except for Sardinians) share an orange “steppe” component with most South Asians (these are no doubt Indo-European migrations of the Bronze Age)

2) The brown element represents European hunter-gatherers. This element is found at varying quantities across Europe, with the lowest fractions in Sardinians. Though present in South Asians (this may or may not be an artifact to be honest), it’s not present at very high frequencies.

One always has to be careful about taking these proportions as literal representations of ancestral populations. They are not. But what they show is that modern Northern Europeans and South Asians have been touched by the same population movements over the past 5,000 years, and so are genetically much closer than the people who lived in Northern Europe and South Asia 5,000 years ago.

Humans are a visual species. In a pre-modern environment, physical cues were important for group identity, though I suspect just as much due to scarification and tattooing as phenotypic differences due to biology. The fact that Cheddar Man, and Paleolithic hunter-gatherers in Western Europe more generally, probably resembled modern South Asians more than they do modern Northern Europeans (I think they were more likely to be olive-brown than dark-brown, but I’m not confident), is more salient to human folk biology than the fact that modern Northern Europeans are much closer genetically to South Asians than the more “brown” ancient Northern Europeans.

Stuff like this always reminds me of the deep wisdom in Artur C. Clarke’s Childhood’s End. The ultimately benevolent alien species which mentored humanity shielded us from their physical appearance because the knew we’d find it horrifying. The substance of what they did for us, who they were, was going to be less important to immature humans than the fact of what they looked like.

Note: Fst between Sindhi from Pakistan and WHG (Cheddar Man was one) is 0.087. Sindhi from Pakistan and English is 0.023. English to WHG is 0.058 (source). Fst can not be naively interpreted as “genetic distance.” But, this gets at the fact that Mesolithic European hunter-gatherers were very distant from modern South Asians. And widespread gene flow and admixture over the past 5,000 has compressed a lot of genetic differences which were starker across geography in the past.

February 14, 2018

Ancient DNA and Dystruct

Filed under: Human Population Genetics — Razib Khan @ 10:56 pm


There’s a new preprint, Inference of population structure from ancient DNA, which uses explicit demographic models to make inferences about ancestry. I haven’t dug into the guts of the math, but, the outputs are quite interesting.

What seems to be obvious is that Western Eurasia has a much richer set of models to choose from than elsewhere. European, Middle Eastern and South Asian populations exhibit the greatest difference between Dystruct and Admixture.

Five things paleogenetics tells us about the human past

Filed under: Human Population Genetics — Razib Khan @ 10:25 pm

Since I’m flogging Enlightenment Now, I thought perhaps I should remind readers that Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past by David Reich is out in 1.5 months. For years people have asked me about a book to read to understand what genetics has to say about human history. This is that book.

And yet before you get there, what do you need to know?

Here are five things you should know. Five things that we know with a very high degree of certitude.

  1. Many (most?) modern populations clusters we perceive as clear and distinct date to the last 5,000 years. To give a concrete example, the genetics that we find to be typical of Northern Europeans only comes into being ~5,000 years ago, with the Corded Ware populations. To my knowledge none of the prior populations along the North European plain exhibit the mix of characteristics and ancestries typical of modern Northern Europeans in any way, shape, or form.
  2. Concomitantly, many of the physical characteristics we find typical of modern populations are probably relatively recent configurations due to natural selection.
  3. Non-African populations, whether European, Middle Eastern, South Asian, (South)East Asian, Amerindian or Oceanian, derive from a population expansion that dates to ~50,000 years BP. These populations experienced a bottleneck on the order of 1,000 to 10,000 breeding individuals.
  4. Modern humans are old. Population structure within Africa of modern humans dates to at least 200,000 years before the present, and perhaps even earlier.
  5. Population turnover was ubiquitous. Change was the only constant.

February 13, 2018

How Craigslist stays at 1 by not moving on from the year 2000

Filed under: Technology — Razib Khan @ 9:53 pm

In the open thread, I made a casual comment that I’ve become a bit more skeptical of market efficiencies lately. Remember, in the perfect market, the profit of the firms should converge upon zero. Is this to anyone’s benefit? Obviously, it is to the benefit of the consumer. But what happens in the long term when firms can’t make any money?

This crossed my mind recently in regards to Craigslist. Craigslist is notoriously no-frills and reflects an aesthetic and functionally stuck in the year 2000. The founder, Craig Newmark, is a pretty weird person. The company has 50 employees and does not maximize profit. But Newmark and Craigslist have had a culturally huge impact. They destroyed the newspaper classifieds.

And yet Craigslist stays stuck in the year 2000. This was obvious to me when they went after Padmapper. Padmapper was clearly a service which added value to Craigslist. And yet today I wonder if this behavior by Craigslist actually allows it to continue providing the services it does.

Imagine that Craigslist opens up its API and all sorts of other web applications develop around it. What I can imagine is that Craigslist would become the locus of massive and highly efficient arbitrages. Consider programs which match buyers and sellers in a way which minimizes the “deals” that sellers can today gain from buyers who are naive. Perhaps instead of two people going into an exchange, an ecosystem of “runners” who would transport products.

My thoughts on this are vague and cloudy, but perhaps reduced efficiency and rationality actually means Craigslist can persist for far longer?

When Western Near Eastern Farmers carried North Eurasian Y chromosomes into Central Africa

Filed under: Afro-Asiatic,Human Population Genetics,R-V88,R1b — Razib Khan @ 9:24 pm


Whenever you look at a map which shows the distribution of Y chromosomal haplogroup R1b you see two areas where the frequency seems very high. First, Western Europe has a very high frequency. Before 2010 it was commonly assumed that R1b was the heritage of late Pleistocene European hunter-gatherers. Around 2010 deeper analysis suggested perhaps that this was not so, and that the deepest divisions in the phylogeny of Eurasian R1b could be found to the east. The high frequency of this haplogroup then may have been an artifact of the Holocene.

Ancient DNA has confirmed this hypothesis. The high frequency of R1b in Western Europe seems to date to the Bronze Age. Though R1b is not found exclusively in Indo-European peoples and existed at low frequencies in Pleistocene Europe, its current ubiquity in Europe seems likely related to demographic turnover between 3 and 5 thousand years ago.

If I had to bet I think R1b, like R1a, originates among the North Eurasian people who mixed with West Eurasians and Amerindians. The Ma’lta boy, for example, seems to have been a basal R.

But notice a secondary mode of R1b in Africa. This is R-V88. The highest frequencies of this Y chromosomal haplogroup are found in Chadic speaking populations. Chadic is a basal group in the Afro-Asiatic language family. A few years ago a paper was published using autosomal DNA on Chad populations and suggested that Eurasian backflow occurred in deep antiquity. From that paper:

We estimate that [autosomal] mixture occurred 4,750–7,200 ya, thus after the Neolithic transition in the Near East…In Chad, we found a Y chromosome lineage (R1b-V88) that we estimate emerged during the same period 5,700–7,300 ya

A new paper, The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages, really gets to the origin of R-V88, with a massive Y data-set. There’s a lot of other Y lineages that are surveyed in this work, but in the supplements, the figure makes it clear that Sardinian R-V88 is basal to star-like African topologies. The implication here is that the African lineages derive from European ones.

The autosomal paper found Chad populations (though the one in question was not Chadic speaking) seem to share drift from Sardinians in particular. Looking at ancient genomes Early European Farmers seem to have been the primary donor population. Additionally, the coalescence of the African lineages seems to date to 5 to 6 thousand years before the present.

Though not definitive, the association of Afro-Asiatic populations with R-V88 is strongly suggestive to me of the possibility that some western Near Eastern Farmers spoke Afro-Asiatic languages.

Enlightenment Now is out, so there goes my weekend….

Filed under: Enlightenment Now,human nature,Intellectual history,Steven Pinker — Razib Khan @ 2:38 pm

Steven Pinker’s Enlightenment Now: The Case for Reason, Science, Humanism, and Progress is now out. I plan on reading it this weekend front to back.

Over the past few years, it’s not a secret that I’ve become more skeptical of the possibilities for humanism and progress. The case for reason and science are obviously clear, but that’s because reason and science aren’t fundamentally normative issues. Humanism and progress are grounded in norms.

Of course, I’ve long been more and more partial to the Scottish Enlightenment, which is more conservative and cautious than that of the French. In the current year, I’m a conservative liberal. But I am gloomy on the prospects for liberalism in the near term future.

Seth Largo distills may of my core intuitions:

February 11, 2018

Open Thread, 2/11/2018

Filed under: Open Thread — Razib Khan @ 9:51 pm


The podcast that Spencer Wells and I are doing, The Insight, now has got eight episodes up. It’s nice that people are stumbling upon it now. Additionally, we’re pretty satisfied with the uptake. So far. To break out of our “core” audience we need more people to know about us.

First, please subscribe via iTunes, Stitcher or Google Play. Second, mention the podcast on social media. Tell your friends. Third, we have the next two or three podcasts planned, we’re still taking suggestions for ideas and possible guests (so far we’ve had John Hawks and Joe Pickrell on).

I now have Amazon Associates for Canada and the UK. The links to US Amazon items I post on this page should now change depending on your IP.

Cheddar Man changes the way we think about our ancestors. This is a pretty good article. But a few points. First, anyone who followed the literature would have predicted that Cheddar Man would contribute ~10% of the genomes to modern Britons and that he would lack alleles for light skin, but have them for blue eyes. I can’t believe any of the researchers were shocked in light of the La Brana etc. results. Second, we’re not extremely confident that he had very dark skin after the past few years when it’s clear pigmentation genetics involves more than just a few major loci. Seeing as how selection methods have detected lots of sweeps for skin lightening alleles over the last 5,000 years in Northern Europe, it seems implausible that they were as light as modern Northern Europeans, but not necessarily dark.

Spencer and I will probably an episode of The Insight on Cheddar Man after the documentary is out on the 18th (and the paper, probably in Nature).

I’ve blogged on female circumcision/FGM before. There are variations of opinion within Islam on this practice. It is mandatory, meritorious, or there is no comment. Muslims from areas where this is not practiced, such as South Asia or the Maghreb, naturally assume that this is a “cultural practice” that has nothing to do with Islam.

This is simply false. The Shafi school of Sunni Islamic jurisprudence considers female circumcision obligatory, for example. The complicated issue is that a) not all women subject to female circumcision/FGM are Muslim, for instance, in Africa, including Egyptian Copts b) not all Muslims are subject to the practice, obviously. These facts allow all sorts of confusions and obfuscations to emerge.

But the bigger issue is that if you are not Muslim it is not really coherent to say that something is a “cultural” practice as opposed to a “religious” one. Religion is part of the culture, and to a great extent on the reflective conscious scale the defining element of culture. Muslims disagree as to the religious acceptability of many practices. Those disagreements are cultural because Islam is cultural.

Land of Promise is a book I’ve mentioned many times. It’s one whose premises rub me the wrong way: the vigorous mixing of state fiat with the market. I’m not a fan of “industrial policy.” And yet I read the book because Michael Lind, the author, knows his history, and he’s honest about it.

I do think on some level I’m rethinking my commitment to the free market as opposed to institutions, and the short-term benefits of market efficiency set against the long-term advantages of social stability. That’s probably part of a general trend toward conservatism away from libertarianism.

Let’s Ban Porn. Don’t laugh. It took some boldness for The New York Times to publish something as laugh-out-loud implausible. But in the end, I think porn is the symptom. Really we as a culture don’t agree on what sex is supposed to be about. Without that agreement, porn is a sideshow.

Also, the proliferation of porn in the last 20 years hasn’t led to the explosion of sex crimes that critics on the Left and Right would have predicted.

Some of you may wonder about DNA Geeks. What’s the deal? Well, I can tell you that we are building a nice brand, and periodically there are traffic spikes. And the microscope is killing it.

The main sadness for me is that the ratio of R1b to R1a t-shirts sold is like 20:1. But I guess it’s quality over quantity?

While I was taking a Twitter break I got a few DMs about the latest controversy about hours worked by academics:

The stupidest thing on science twitter is how crazy and nasty people get over the idea that you have to work hard in science to succeed. Everybody knows you have to work hard and long to succeed, and yet everyone is willing to outright lie about the truth, lest you be publicly destroyed.

It’s pretty clear some people work fewer hours than other people and do fine. It’s also clear that other people have higher sweet spots in terms of return-on-time-worked. The problem is when people presume there’s a one-size-fits-all formula. I think it would be best if people reacted with a little more charity to those who extrapolate from what’s worked for them.

February 8, 2018

Unlurking thread

Filed under: Open Thread,Unlurk — Razib Khan @ 6:46 pm

Basically, a thread to unlurk if you want.

Reflecting on Journey of Man 15 years later

Filed under: Podcast,The Insight — Razib Khan @ 6:44 pm

Journey of Man, Spencer Wells’ book and documentary, came out 15 years ago. To a great extent the impact of TV is such that one can argue it introduced genetic anthropology to a whole generation.

A lot has happened since then. On this week’s The Insight we review what’s happened since then, and how Spencer, who started out a conventional academic scientist, became a documentarian.

If you subscribe on iTunes, Sticher or Google Play, make sure to post a review.

February 7, 2018

Preference falsification in our time and evermore

Filed under: Epistemology — Razib Khan @ 11:31 pm

One of the main reasons I listen to the Secular Jihadists podcast is that there’s an earnest honesty from the hosts which is fading from our society in public discourse. Though I’m not a “New Atheist” personally (just an atheist), I don’t mind, and even appreciate, people who can discuss the reality that according to the Sunnah, Muhammad, PBUH, was a child rapist and sex slaver by the norms of the current year.

As I am not Muslim and I don’t wish to emulate Muhammad I don’t have to reconcile traditional Islam’s understanding of him with modern norms (not that Muhammad is special, Moses was a child slaughterer). But I am also not sure that airing the reality of Muhammad’s life is productive, or forwards any broader conversation. But the fact of the traditions of his life is trueIf facts are never aired, then facts fade from comprehension, and people may confuse polite ommissions with reality.

Because attitudes toward Islam have been ideologized honesty about the religion in public is dangerous, as the truth is a weapon in partisan games. For example, a few months ago I noticed Jerry Coyne had linked to an old post of mine on why being Muslim is not a racial thing on Twitter. Curiously, Twitter flagged the post as sensitive.

So what did I say? You can see….

Obviously, I didn’t say anything too crazy. Rather, the text flagger probably saw “race” and “Islam” and wondered if I this was frog-nazi talk. But more generally there has been heightened sensitivity around Islam and Muslims over the past 17 years, and frank discussion of the religion is now difficult. I recall watching the PBS’ To the Contrary in the 1990s and at one point there was a discussion about Muslim women and their plight. The most stridently Left on the regular panel, Julianne Malveaux, stated plainly that there was perhaps something about Islam which was constitutively anti-woman.

I happen to disagree with the idea that there is anything constitutively anti-woman about Islam, but that’s because I take a very dim view of religious essentialism. But it’s not an unreasonable assertion given the huge body of shariah where women are given inferior status in relation to men. Malveaux wasn’t crazy. And none of her fellow panelists said much in relation to her observation about the essential anti-feminism of Islam. It was the 1990s and anti-religious outbursts by a very Left-wing person wasn’t surprising. Islam was a religion, ergo….

Today the situation is different. I doubt Malveaux would say something similar in public. And I assume that her panelists, especially the conventional liberals, would come to the defense of Islam if she did. This despite the fact that privately many liberals will admit that Islam and women’s rights do not exactly correlate too well. I have a friend who chides Islamophobes on Facebook who will state it is a “fucked up religion” in personal conversation (and to be entirely frank, this is really common from non-Muslim South Asians in the West, who tend to come from Islamo-skeptic backgrounds and yet cultivate strong SJW public personas).

What I’m alluding to here is the ubiquity of preference falsification. The term was popularized in Timur Kuran’s Private Truths, Public Lies: The Social Consequences of Preference Falsification. Chinese “Communism” today is arguably just one huge game of preference falsification. Late stage Soviet Communism was also preference falsification writ large.

The Secular Jihadists don’t engage in preference falsification, and I find that refreshing because it’s so rare. I don’t agree with their New Atheist beliefs on a lot of the details, nor do I share their liberal politics, but I know where I agree and disagree. There’s no reading between the lines. They say what they mean and mean what they say.

While listening to podcasts and viewing YouTubes one thing I’ve come to realize is that Far Left and Far Right views are more interesting because the two groups are so marginal they don’t have an incentive to preference falsify. I disagree with both perspectives, but it’s honest disagreement. When I listen to mainstream Center Left and Center Right folks it’s generally much more boring. They are keen on telling truths that won’t rock the boat and will make the fewest waves. They will lie, omit, and manipulate, to also minimize rocking the boat.

Back in the 2000s Andrew Sullivan came up with the “Yglesias Award”, named after Matt Yglesias, now of Vox. From the page about the award: “This award…is for writers, politicians, columnists or pundits who actually criticize their own side, make enemies among political allies, and generally risk something for the sake of saying what they believe.” Can anyone imagine him criticizing his own side today? Vox and its coterie of writers have become well-off on cozying up to establishment power. They are now the system. Or at least one of the two primary systems (the Right and Left).

There is an equivalent on the Right. Back in the 2000s The Weekly Standard wrote some positive pieces on Intelligent Design. This was strange because The Weekly Standard was a flagship journal of neoconservatism, and so decidedly secular and urban, with a large contingent of Jewish writers and editors. In contrast, Intelligent Design was being pushed forward by evangelical Protestants, and to a lesser extent a small number of conservative Catholics. At the time most people understood that The Weekly Standard was engaged in coalition building. Privately no one there probably found Intelligent Design creditable, but they were part of a coalition of people who took these ideas seriously and sincerely. Though on some level everyone understood what The Weekly Standard was doing, the important thing was that it did what it did in public, and expended some of its capital among secular intellectuals to support religious conservatives as a costly signal to its commitment to the Right.

One reason that Heather Mac Donald began to speak out about atheism and the Right in the 2000s is that she’s a sincere person and was aggravated by the juxtaposition in public respect for religion that conservative intellectuals were prone toward, despite many of them privately having little use for faith.

There’s another dynamic where preference falsification and revealed preferences are connected. I recently observed that Joe Kennedy III seems to be evidence of the royal family of the Democratic party getting whiter while the party gets browner. Joseph P. Kennedy and Rose Kennedy now have many great-grandchildren, such as Joe Kennedy III. Most are no doubt liberal Democrats who think diversity is great and good. But take a look at who these Kennedys are marrying. Since they’re a prominent family, their weddings are noted in the public record. Though the Kennedy’s of the current generation say the correct thing for liberals about racial diversity in public, their private choices are more in alignment with being in sympathy with a white ethnostate.

Why does any of this matter? As I said above, if the public lying is ubiquitous enough, people begin to confuse polite ommissions or accepted public distortions with reality. Eventually the public and private come into alignment. An analogy to religion is appropriate. All of the living descendants of Moses Mendelssohn descend from Christian branches of his lineage. The conversion in the early 19th century of prominent German Jews to Christianity was often a conscious act of assimilation, or a means toward professional advancement. There is evidence that some of these individuals were never sincere Christians in a deep theological sense, and many people understood this. But over time the preference falsification in these families faded, and they became sincere Christians in public and private.

Now consider the case of sex differences. One of the reasons I post on sex differences on strength is to remind people who de facto preference falsify about the truth, and expose newbies to the truth who might otherwise confuse falsification-by-omission with the truth. By this, I mean that over the past generation sex differences are not an issue that many among the cultural elite (on the Left) want to talk about in depth. Most people know that there are differences in strength, though they may be fuzzy on the details. But some younger people actually confuse the lack of attention to sex differences with the fact of no sex differences, and take maximal gender social constructionism at face value!

Because the truth is not fashionable preference falsification will become more and more common. Demands for politeness by omission will become more strident and all-encompassing.  Old-fashioned positivists and empiricists who naively make testable truth claims will still exist, but their prestige will be low. Instead of truth being telos, an ends, it will become purely techne, a means or artifice.

Going back to where this post started, “ex-Muslims” is a particular affront to the modern order of things. Their existence is an offense, and uncomfortable to most Muslims. Their witness as to Islam’s illiberality is highly inconvenient for the modern Western Left, which maintains a public alliance with Islam. And yet most of these individuals are committed to Left social progress in all areas outside of Islam.

My prediction is that Left critics of ex-Muslims will become more and more vociferous. Not because they believe in their case. Rather, they know that marginalizing this one group despite the injustice of that course of action is an excellent “hard-to-fake” signal of their sincerity and commitment to their Muslim allies.

No one understands the targets of selection in humans (except disease)

Filed under: Human Population Genetics,Natural Selection — Razib Khan @ 9:43 pm

I’m proposing on an upcoming episode of The Insight that we should talk about natural selection in the context of humans. The reason is that there seems to be a lot of it. It may even be ubiquitous. But, in most cases which aren’t trivial, we have no good idea what’s going on.

By not being trivial, I mean when there is selection on loci implicated in immunological variation in response, it’s pretty clear what’s going on. Infection by pathogens is arguably the reason that humans have sex, where some sort of frequency-dependent selection is obvious.

When it comes to something like lactose tolerance (lactase persistence), the genomic evidence seems indisputable that there was natural selection (a very long haplotype in Eurasia sweeping up in frequency recently). And there’s a reasonably plausible story. The adoption of agro-pastoralism by disparate populations across the world has produced similar adaptions, albeit via different genetic pathways. But, it isn’t as if we have experimental or ecological evidence as to the differential fitness of humans “in the wild” on this trait. Does milk sugar really make that huge of an impact? (disease kills, its selective power is clear)

Then, you have cases like pigmentation where there are numerous explanations which part of the story, but not most of it. And finally, you have situations like the EDAR variant among East Asians and Amerindians where selection seems likely, but there is zero plausible explanation of what the target of selection is.

February 6, 2018

The genome of “Cheddar Man” is about to be published

If you are American you have probably heard about “Cheddar Man” in Bryan Sykes’ Seven Daughters of Eve. If you don’t know, Cheddar Man is a Mesolithic individual from prehistoric Britain, dating to 9,150 years before the present. Sykes’ DNA analysis concluded that he was mtDNA haplogroup U5, which is found in ~10% of modern Europeans, and which ancient DNA has found to be overwhelmingly dominant among European hunter-gatherers. But for years there has been controversy as to whether this result was contamination (after all, if it’s found in ~10% of modern Europeans it wouldn’t be surprising if the DNA was contaminated).

Today that is a moot point. On February 18th Channel 4 in the UK will premier a documentary that seems to indicate genomic analysis of Cheddar Man’s remains have been performed, and he turns out to be exactly what we would have expected. That is, he’s a “Western Hunter-Gatherer” (WHG) with affinities to the remains from Belgium, Spain, and Central Europe. These WHG populations were themselves relatively recent arrivals in Pleistocene Europe, with connections to some populations in the Near East, and with unexplored minor genetic admixture from an East Asian population. Their total contribution to the ancestry of modern Europeans varies, with lower fractions in the south of the continent, and the highest in the northeast.

Overall, the consensus seems to be that in Western Europe the genuine descent from indigenous hunter-gatherers passed down through admixture with Neolithic farmers, and then the Corded Ware and Bell Beaker groups, is around ~10%. This is the number that shows up in the press write-ups. But, there are some researchers who contend it is far less than 10%, and that that fraction is misattribution due to early admixture with relatives of these hunter-gatherers as steppe and farmer peoples were expanding.

Phylogenetics aside, one of the major headline aspects of the Cheddar Man is that reconstructions are now of a very dark-skinned and blue-eyed individual. Some of the more sensationalist press is declaring that the “first Britons were black!” As far as the depiction goes, this is literally true. The reconstruction is of a black-skinned individual in the sense we’d describe black-skinned.

But on one level it is entirely expected that this is what Cheddar Man would look like. The hunter-gatherers of Mesolithic Western Europe were genetically homogenous. They seem to derive from a small founder population. And, on the pigmentation loci which make modern Europeans very distinctive vis-a-vis other populations, SLC24A5, SLC45A2 and HERC2-OCA2, they were quite different from anything we’ve encountered before. First, these peoples seem to have had a frequency for the genetic variants strongly implicated in blue eyes in modern Europeans close to what you find in the Baltic region. The overwhelming majority carried the derived variant, perhaps even in regions such as Spain, which today are mostly brown-eyed because of the frequency of the ancestral variant. Second, these European hunter-gatherers tended to lack the genetic variants at SLC24A5 and SLC45A2 correlated with lighter skin, which today in European is found at frequencies of ~100% and 95% to 80% respectively.

The reason that one of the scientists being interviewed stated that there was a “76 percent probability that Cheddar Man had blue eyes” is that they used something like IrisPlex. They put in the genetic variants and popped out a probability. The problem is that the training set here is modern groups, which may have a very different genetic architecture than ancient populations. Recent work on Africans and East Asians indicate that the focus on European populations when it comes to pigmentation genetics has left huge lacunae in our understanding of common variants which affect variation in outcome.

East Asians, for example, lack both the derived variants of SLC24A5 and SLC45A2 common in Europeans but are often quite light-skinned. A deeper analysis of the pigmentation architecture of WHG might lead us to conclude that they were an olive or light brown-skinned people. This is my suspicion because modern Arctic peoples are neither pale white nor dark brown, but of various shades of olive.

As far as blue eyes go, it is reasonable that these individuals had that eye color because that trait seems somewhat less polygenic than skin color. There are darker complected people with light eyes, from the famous “Afghan girl” to the first black American Miss America, Vanessa Williams. The homozygote of the derived HERC-OCA2 variant seems relatively penetrant. From what I recall the literature indicates many people with blue eyes are not homozygotes on this locus for the derived haplotypes, but those who are homozygotes for the derived haplotypes invariably have blue eyes.

Addendum: It isn’t clear in the press pieces, but it looks like they got a high coverage genome sequence out of Cheddar Man. They refer to sequencing, and, they seem to have hit all the major pigmentation loci. This indicates reasonable coverage of the genome.

Why SpaceX matters

Filed under: SpaceX,Technology — Razib Khan @ 8:37 pm


Unless you were sleeping under a rock today you saw what SpaceX did. I don’t really follow Musk closely. My friends in Silicon Valley speak highly of him. He shares an interest in some of the same topics I do (he’s a fan of Nick Bostrom’s Superintelligence). But in general on an analytical level I think he’s a long-term thinker who may seem crazy, but actually is simply less pedestrian in his focus than the typical billionaire.

T. Boone Pickens has given hundreds of millions of dollars to Oklahoma State University…with the majority going to its athletic programs. And yet to my knowledge, Pickens’ philanthropy has attracted less opprobrium than Musk’s focus on quixotic topics such as hostile strong AI. Musk is weird. Pickens just furthers the cause of traumatic head injury so that his fellow Okhlahomans can cheer on Saturday.

Today at work one of my coworkers hooked up the conference screen to the coverage of the SpaceX launch and landing. I had one eye on the screen…when I saw the descent of the two boosters which landed successfully. I literally jumped out of my chair and ran over to watch them land. It was like seeing a CGI “artist’s conception” of the future of space travel come to life!

As many of you know I am not a fan of Joseph P Kennedy II. When I was a child in the 1980s he gave on the floor of the House of Representatives where he argued against funding for space exploration because of the opportunity cost in relation to social spending. His delivery was quite appallingly poetic from what I recall, something like “why must we take food from the poor so that spaceships can sail high above us?”

Because I was a science nerd with a child’s lack of understanding of the “real world,” where some people were poor and destitute, my reflex was very negative. I still remember Kennedy’s pained expression and can feel my rictus of rage. I probably didn’t appreciate the substance of Kennedy’s argument, but the spirit of it was clear to me.

Some might argue that we don’t need to make a choice. But what if we did? What if space didn’t return much on our investment?

These are fundamentally ancient arguments. In China, during Warring States periods there was a stylized debate between the partisans of Mozi, who we can characterize as a utilitarian, and the followers of Confucius, as to the value of frivolities such as music. Those who aligned with Mozi were fixated on human well-being on the most general and universal scale possible. Music and other cultural productions were pure aesthetic consumption which took away from labor which might otherwise have gone into alleviating human suffering. In the end, history weighed in on the side of the Confucians…with the exception of Communist revisionists in the 20th century.

Musk, and Jeff Bezos, envisage us as an inter-planetary (and perhaps extra-planetary) species. This is laudable so as to avoid the risk of mass extinction on a single “lifeboat Earth.” But perhaps humans becoming inter-planetary is like art? Perhaps it is part of our telos?

These are ideas explored in science fiction. In Against the Fall of Night Arthur C. Clarke writes about a human race which is immortal and geriatric, inward-looking and lacking the spirit of curiosity that defines us, except for a young boy named Alvin. Francis Fukuyama’s End of History and the Last Man prophesies a pedestrian future untouched by the chiliastic passions we see today in Islamic fundamentalism or the dragons of pre-liberal nationalism awakening. Space offers a way out of these two visions of conflict and ennui.

There is also a deeper evolutionary historical framework for understanding why we are fascinated by the possibilities of space, crazy as they are. Our own modern human lineage was the first to cross over from Sundaland to Sahul. No matter whether you accept a new date of 65,000 years BP, or the more traditional date of 45,000 years, modern humans show up in Australia very early after their exit en masse from Africa.

These humans crossed 90 kilometers of open sea. In Guns, Germs, and Steel Jared Diamond proposed that Australia may have been settled by a pregnant woman who clung to a floating tree branch. Genetics tells us this is false. Oceanian peoples went through a bottleneck, but not such an extreme one.

The implication is that the proto-Oceanian people who left Sundaland for Sahul did so as a unit, impelled by some cultural human prerogative. We may think that going to Mars is crazy, but we know Mars exists. What would have driven these proto-Oceanian peoples eastward into the great blue ocean? And how did they go east during the Pleistocene, before seafaring traditions?

The lesson from prehistory is that modern humans are a crazy species. We journey across the deep blue sea into the unknown. To a great extent, this is irrational for the groups and individuals who engage in this activity. The vast majority of voyagers probably expired. And yet something within us kept pushing some of us until we made it. In a different lingo, one might say that staying home, focusing on safety and comfort, is a local maximum. International space agencies and private firms such as Lockheed Martin were chasing the local maxima. That was safe and defensible. Only someone as crazy as Elon Musk would push SpaceX into an endeavor which was insane and likely to fail. And yet sometimes humans don’t fail, and crazy is actually saner than we could ever imagine.

February 5, 2018

Neanderthal introgression in the ancient DNA age

Filed under: Human Population Genetics — Razib Khan @ 9:45 pm

Over the past ten years or so the idea of “adaptive introgression” in the human context has gone from seeming ludicrous to banal. When I first began entertaining this idea in 2006 some commenters literally heckled me, because the idea of admixture with Neanderthals seemed so ludicrous. Then, in 2010 the maturation of the field of ancient human DNA confirmed that it was likely non-Africans had Neanderthal admixture. Over the next few years, specific instances of introgression were discovered (e.g., EPAS1 from a Denisova-relative).

Today the whole landscape of adaptive introgression from other lineages is now being mapped. An open access paper in Molecular Biology and Evolution, Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans, examines the distinction between the immediate sweep of an introgressed allele after admixture, and later selection on alleles which are segregating neutrally within the absorbing population.

The authors developed a statistic which detected “immediate adaptive introgression (iAI).” Instances where alleles increased in frequency immediately after the admixture in the modern human background from Neanderthals (or possibly other archaics?).

One interesting gene was LYPD6B. This seems to have been subject to selection immediately, and it’s widely distributed in modern non-Africans. This locus controls “cholinergic signaling in the brain” and the authors suggest that the “results suggest that selection on this introgressed haplotype may have been due to beneficial behavioral and/or physiological traits.” The other possible cases of iAI seem mostly involved immune response, not entirely surprising.

But perhaps the bigger issue is that there may be a lot of selection on segregating variants that came in from Neanderthals. That is, introgression may be more important for selection on standing variation. This is is probably the dominant mode of adaptation in humans in any case. Think of it is portfolio diversification.

Speaking of variation, there’s a paper in the works which suggests that admixture with Neanderthals replenished some of the genetic diversity that the Out-of-Africa modern lineage lost:

“They left many beneficial variants behind in Africa,” says evolutionary genomicist Tony Capra of Vanderbilt University in Nashville, who reported the results. “Interbreeding with Neandertals provided an opportunity to get back some of those variants, albeit with many potentially weakly deleterious Neandertal alleles as well.”

In the long run sex always wins

Filed under: Uncategorized — Razib Khan @ 7:33 pm

Carl Zimmer has an incredible piece up, This Mutant Crayfish Clones Itself, and It’s Taking Over Europe:

All the marbled crayfish Dr. Lyko’s team studied were almost genetically identical to one another. Yet that single genome has allowed the clones to thrive in all manner of habitats — from abandoned coal fields in Germany to rice paddies in Madagascar.

In their new study, published in the journal Nature Ecology and Evolution, the researchers show that the marbled crayfish has spread across Madagascar at an astonishing pace, across an area the size of Indiana in about a decade.

Basically, it looks like a crayfish mutated and now is able to reproduce clonally. That is, it’s asexual. Also, because of its chromosomal structure, it’s no longer inter-fertile with the species from which it emerged.

As it happens there are a fair number of lineages which have sexual and asexual species. Asexual species seem to be much younger. The implication then is that they’re going extinct and emerging over and over again.

February 4, 2018

Open Thread, 2/4/2018

Filed under: Open Thread — Razib Khan @ 9:56 pm

One of the things that reading Land of Liberty has prompted in me is the need to read Matt Stoller’s book, when it comes out. Land of Liberty in many ways was a historical foil of Stoller’s article, How Democrats Killed Their Populist Soul.

And yet both exhibit an intellectual honesty which I generally find lacking in the modern pundit class, agree or disagree.

Steven Pinker’s new book, Enlightenment Now: The Case for Reason, Science, Humanism, and Progress, is now being published a few weeks earlier. Apparently this now one of Bill Gates’ favorite books.

I’m a big fan of Steven Pinker. But I’ve become much more pessimistic than him over the past few years. Here’s hoping that Enlightenment Now turns that around.

DNA Geeks has a total site redesign! Check it out.

I haven’t been saying this on the podcast yet, but you should be subscribing to it on iTunes, Stitcher, and Google Play, and review and rate it. Spencer and I have a certain audience already, and we’d like to expand it.

This has probably always been so, but I’m really getting tired by the emergence of different verbal ticks in various socio-political subcultures. For example, when liberals say “my dude” -“bros”, it’s dismissal-by-identity. Both NRx, and what is now called the Altright, also have their own subculture languages, which makes understanding what they’re trying to say hard for outsiders. A feature or a bug?

Taking a Twitter break for a week.

February 3, 2018

Why the Chinese don’t buy deodorant

Filed under: earwax,Human Population Genetics — Razib Khan @ 11:30 pm

 
In human populations a SNP in ABCC11 is correlated with two salient traits: 1) wet or dry earwax 2) body odor. When I had my first son sequenced before his birth the main variant of phenotypic consequence that I noticed (aside from him being a heterozygote on KITLG), was that he carried a derived mutation on this position. Meaning that he was going to have dry earwax and fewer issues with body odor.

My wife and I are both heterozygotes. This is not too surprising. The derived variant is actually greater than 50% in Bengalis in the 1000 Genomes (in South India the derived variant is also around ~50%), while about ~25% of Northern Europeans are heterozygotes.

This genetic story came to my mind again because of this article in The New York Times, Aiming at China’s Armpits: When Foreign Brands Misfire:

There’s another reason few Chinese consumers buy deodorant: basic biology.

Scientists in recent years have shown that many East Asians, a group that includes China’s ethnic Han majority, have a gene that lowers the likelihood of a strong “human axillary odor” — scientist-speak for body stink.

That lowers the likelihood that they will use deodorant to begin with, according to a 2013 study by researchers at the University of Bristol and Brunel University in Britain, after a survey of nearly 6,500 women of various backgrounds.

“It is likely that deodorant usage is not widely adopted because there is, for much of the East Asia population, no need for it,” it said. (For those curious about such matters, that same genetic difference also leads to drier earwax.)

A friend of mine in undergrad of East Asian background told me once that she had never worn deodorant. So this shouldn’t be very surprising.

Today I found a paper, A missense variant of the ABCC11 gene is associated with Axillary Osmidrosis susceptibility and clinical phenotypes in the Chinese Han Population, which explicitly probes the correlation between body odor (“Axillary Osmidrosis”) and the SNP in question in the Han Chinese population.

The chart below makes the association obvious:

The correlation between carrying the G, ancestral, allele, and body odor is very strong. Though it is imperfect. Going through this literature human smells are clearly a polygenic trait (see The effect of ethnicity on human axillary odorant production). That being said, this case-control study in a Han population shows ABCC11‘s importance in at least East Asian populations (earlier work in Japan showed that those with body odor tended to have wet earwax and carry the G allele as well).

In regards to the genotype proportions the authors observe:

The excessive heterozygosity observed in AO individuals is probably due to the effect of selection, particularly nonrandom mating against AO phenotype.

This doesn’t make sense to me. Wouldn’t people who have body odor tend to pair up in a society where they are a minority? The authors note that the excess of heterozygotes was observed in earlier studies too.

If you dig into the frequencies it seems that the derived mutation is absent among populations in Africa without recent Eurasian back-migration. I looked it up, and it’s segregating in ancient Eurasian samples, with Ust Ishim being a heterozygote. It is curious that in no population has the derived frequency swept to fixation, nor has the ancestral variant fixed in other groups (such as in Europe).

I strongly doubt that there is any selection on this locus due to earwax or body odor. It is a pleiotropic locus, there are other effects from the mutation. One of those other effects is probably the target of any selection. And in regards to selection, it seems likely that that would be a balancing sort since neither the ancestral nor the derived variant are fixed in most populations.

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