The gray moral world of the Greeks

Listening to the Ancient Greece Declassified podcast on The Iliad was very interesting. As some readers know, I came across Greek mythology as a child. Though I began with Bulfinch’s Mythology, I did not stop there. Soon enough I moved beyond the juvenile material, and read darker, more violent and sexual material that to be entirely frank I was not prepared to comprehend.

Of course, Greek myths are not the only literature from the ancient world which contains adult material. Jonathan Kirsch’s The Harlot by the Side of the Road: Forbidden Tales of the Bible highlights those stories passed down from Hebrew tradition which are perhaps glossed over. The young David’s defeat of the giant Goliath is known to all schoolchildren. Less well publicized to the religiously illiterate American public is his adultery with Bathsheba (though obviously more observant people are quite aware of this aspect of his biography).

In the podcast above there is extensive discussion of the fact that the Trojans are not depicted as evil in The Iliad. As someone who came to maturity at the end of the 20th century, this struck me as somewhat strange as a child. I grew up on a diet of films about evil Nazi and Communist adversaries. The game of great powers for me was also fundamentally a moral one. We were the good guys. They were the bad guys.

In reading The Iliad it was difficult for me to understand why the Trojans were often depicted as such noble characters. And it wasn’t clear that the Greeks were good and moral. I particularly recall the vicious brutality of Neoptolemus, Achilles’ son.

This comes to mind because of late due to the popularity of George R. R. Martin’s work there has been a rise in popularity of gritty and morally gray works of speculative fiction. And when I read histories of World War I, it is also not entirely clear to me that the Central Powers were truly malevolent and dark forces. I do wonder if the second half of the 20th century was a world of exceptionally stark blacks and whites, of an almost Manichaean vision of conflict which emerged out of World War II, and continued with the rise of global Communism.

Fading to white by 2050

When our current attorney general, Jefferson Beauregard Sessions III, was going through hearings there was an incident where he held his Eurasian granddaughter in his lap, and some people in the media made some off-color remarks. This was to be expected since Jeff Sessions is a white southern male of a certain age. And his middle name is Beauregard.

But, what bothered me is the critiques were so 1968, not 2018. The reality is that 2018 is a year when many young men and women who grew up white segregationists in the 1950s and 1960s happen to have mixed-race grandchildren.

Which brings me to a new paper, What Majority-minority Society? A Critical Analysis of the Census Bureau’s Projections of America’s Demographic Future. In the author explicitly models the likely impact of interracial/ethnic marriage on projections of a “majority-minority” America.

Here are the essential bits:

What the example of infants demonstrates is the powerful growth of the mixed-white population in the projections. The size of this group (of all ages) rises threefold during the projections. By the 2050s, one of every three babies with white ancestry also has Hispanic or racially nonwhite ancestry; and these mixed infants are almost a fifth of all infants, of any ethnoracial background. Consequently, assumptions about the ethnoracial assignment of mixed minority-white individuals have a large impact on the projections. The Census Bureau’s assumption that they are not to be counted with whites determines the outcome of the majority-minority society by the mid-2040s.

The final point to bear in mind therefore is this: the critical role in the projections of individuals with mixed white-minority backgrounds means that our demographic future will not be exclusively determined by the usual demographic components: fertility, mortality, migration. It will also be shaped by sociological forces that influence the social locations of individuals who are situated by family background in between the major ethnoracial blocs of American society.

The paper highlights two critical, if not exhaustive, parameters: legal and social definitions of whiteness. Though connected, they are not identical.

It is now fashionable today to assert that white ethnic groups such as Irish, Italians, and Jews “became white” through assimilation. There is some clear truth in this. But, to the American government, they were always considered white, because they were allowed to be naturalized. The 1790 Naturalization Act limited the acquisition of citizenship to free whites. This was later expanded to people of African descent after the Civil War. But Asians were excluded.

In the early 20th century on the whole, though not exclusively, Arabs, mostly Christian, were allowed to be naturalized as white. But they were clearly a liminal case, and they were not always given citizenship. People from the Indian subcontinent were just on the other side of the line between white and nonwhite. Usually, they were not given citizenship, and when they were given citizenship, that was sometimes taken away due to the fact that the authorities determined they were Asian nonwhites.

As a contrast people from the south and east of Europe, and European Jews, were naturalized as white people. But, they were given citizenship somewhat begrudgingly and triggered a racial panic which helped to lead to the passage of the Immigration Act of 1924.

Which brings me to the social aspect of whiteness. By using the term “white” I think we’re eliding and masking the complexity of the dynamic at work. At different points in history the white American mainstream has had different perceptions of those white Americans who deviated from “typicality.” The migration of Irish and German Catholics in the decades before the 1850s triggered a very strong reaction. Similarly, the massive migrations around the turn of the 20th century also triggered a wave of nativism. At other points and periods deviation from “typicality” didn’t matter as much. For example, in the 19th century before the major wave of Jewish migration from the Russian Empire, there were three Senators of Jewish background, all from the South.

Though physically Irish, German and Polish Catholics were no more swarthy than Old Stock white Americans, their Catholicism was a major deviation from American norms. The early American Catholic Church in the 19th century was dominated by French priests and was relatively well integrated into the denominational landscape. The arrival of Irish Catholics, and the reformist Irish hierarchy, in the 1830s, transformed the demographics and cultural assertiveness of Roman Catholics. As a large religious minority in a normatively Protestant country, many leaders of the nascent Catholic community demanded some measure of corporate recognition, as had occurred in European lands. This triggered a massive backlash, leading to violent religious conflicts. Among the Catholics themselves, the Germans were leaders in an attempt to resist Anglicization, and maintain a separate German-speaking school system (the English-speaking Irish hierarchy quashed this separatism to mixed success).

Over the 20th century, the religious trajectory of both Jews and Roman Catholics was to adhere to Protestant norms. Ethnographic research on late 20th century Roman Catholics shows that many of them have internalized a “Protestant” conception of Christian identity and affiliation, being confessional, congregational, and individual in their beliefs. The social assimilation into the mainstream whiteness of “white ethnics” was to a great extent due to their accommodation to the broad outlines of American public religion.

But what has been made can be unmade. Though American Jews are predominantly secular, there been a level of exoteric de-Christianization of the Reform movement, as well as an ideological reaffirmation of Jewish nationhood. In American Catholicism, the consensus of the mid-20th century has flung apart, with wholesale secularization and quasi-Protestantization on one hand, the emergence of highly sectarian counter-cultural traditionalists and integralists on the other hand.

Ironically, with the collapse of a narrow set of cultural mores defining typical white Americans, white American identity has become more racialized. Ethnic and historical differences between various Old Stock groups, such as Southerners and Yankees, become collapsed and bracketed into the catchall of “white privilege.” Clear class differences between rural Appalachian whites and Yankee Brahmins get papered over due to the overwhelming presence of systemic white supremacy. The aristocracy of skin which began to emerge in the early 19th century as a siren call of white racial democratic populism ironically reemerges in the rhetoric of 21st century, as all non-whites, of all class and ethnic backgrounds, are a subject people crushed underneath the behemoth of white supremacy.

But let’s take a step back. Earlier I alluded to the distinction between legal and social norms. Today we need to also acknowledge that social and ideological norms differ, and are diverse. The ideological framework is that systemic white supremacy oppresses marginalized “people of color.” The latter category is highly inclusive, ranging from well educated Asian Americans to working-class Latino immigrants, as well as highly assimilated “white presenting” people of various ethnicities who “identify” as “people of color.” The ideological framework treats them as interchangeable elements in the algebra of oppression, but socially and culturally this is bullshit and totally unrealistic.

One of the reasons that certain quarters of academia have made it their job to debunk the “Asian American model minority myth” is that Asian Americans in various ways are not oppressed and marginalized by systemic white supremacy. The emphasis on a catchall Latino/Hispanic identity in the United States runs up against the fact that this group runs the gamut from people who are no different physically from Africans Americans to those who look totally white, and others who have various degrees of indigenous ancestry. Like the African American/black category there’s a logic to inclusion, capturing all possible individuals that might fit into the class to maximize numbers. But the Latino/Hispanic category is arguably much more culturally diverse than that which encompasses American blacks. The same is obviously true in a more clear way for “Asian Americans,” which includes people from Pakistan to Japan. But the logic of political, social, and cultural mobilization requires the creation of these meta-ethnic identities which bind people together.

But when you leave the political and ideological realm, social realities are very different. A dark-skinned Latino is treated very different than a white Latino in many situations. Though South and East Asians are both “Asian American,” socially and culturally they are very distinct, and South Asians are perceived in the American context to be atypical Asian Americans. There is a high level of social and cultural segregation among various Asian ethnicities, though some level of sub-regional pan-Asian identity does emerge among American born Asian Americans (e.g., East Asians and South Asians may create broader social communities where traditional ethnic boundaries break down).

And the way these various ethnicities relate to the mainstream, that is, white America, differs. The paper above asserts that one of the major issues is the binary framework of white vs. non-white in social, political, and legal discussions is not realistic. For the purposes of the Census people of mixed background, racial and ethnic (Hispanic/non-Hispanic) are coded as “minority.”  For all practical purposes, this is a legal fiction. The fact is that people of non-Hispanic white background, and part Asian or Latino/Hispanic background, do not unambiguously identify as minorities, nor does society treat them as such. That being said, they are still somewhat atypical, as evidenced in the literature review in the paper above.

The main exception to the ambiguity is the case of black Americans and people with black ancestry. In the United States today individuals with visible African ancestry tend to be coded as black, irrespective of blood quantum, in accordance with the rule of hypodescent. Originally a way to maintain racial hierarchy and purity, hypodescent has been tacitly accepted as a method by which black Americans maintain their demographic numbers in the face of possible erosion. This is not an abstract matter. In much of Latin America, some African ancestry does not entail a black identity necessarily.

A growing proportion of mixed-race Americans should transform our understanding of racial dynamics that might emerge in the middle of the 21st century. As it is, many of the frameworks operational in both a legal and ideological sense derive from a mid-20th-century milieu, when the United States was a biracial nation. The black American struggle for legal equality in the 1960s was relatively successful, and ethnic activists in other minority groups saw in it a model to emulate.

But to not put too fine a point on it, 2018 is not 1968. About 30% of white Americans claim that a close relative is in a relationship with a person of another race of Latino/Hispanic ethnicity, while 8% of white Americans are in a relationship with a person of another race or of Latino/Hispanic ethnicity. A substantial number of “white presenting” mixed-race people have matured in a mostly white environment but have close relatives who are clearly non-white. To give an explicit example, a person who is 1/4th Chinese and has blonde hair and blue eyes can both identify and be seen as white, but also feel a very strong and visceral connection to their Asian ancestry and heritage. This is something new in the American context, as to become white in the past was to “pass” and disavow and disengage the contamination of non-white heritage.*

As the decades pass many more people will have complex and multi-valent identities. To some extent, this is tacitly understood. But elite ideological discourse and legal frameworks have not caught up. They probably should. Our conception of political and ideological alignments predicated on theories of demography-as-destiny may need to take into account details of demography which are not imagined in our current models….

* Perhaps with the exception of Native American ancestry. Neither Will Rogers nor Charles Curtis disavowed their native ancestry.

Tibeto-Burmans in Bengal, and Indians in ancient Malaya

Thanks to the Singapore Genome Variation Project, and some data from Lynn Jorde‘s lab, I added some Tibetans and Malays for a pooled data set of East, Southeast, and some South Asians. The marker density was 70,000. I was curious to explore the various contributions of ancestry from eastern Eurasians into northeast South Asia.

The Tibetans, in particular, seem to be a common “source” population in a lot of places. There are fewer than 10 million Tibetan people, proper, today. But the impact of Tibetan or quasi-Tibetan people historically has been much greater than their current numbers might suggest. Additionally, Tibetans occupy a very wide geographical range, far outside of the Tibetan Autonomous Region of modern China. The majorit of ethnic Tibetans live outside of its political boundaries. The terms “Sino-Tibetan” and “Tibeto-Burman” are both ethno-linguistic terms which point to the affinities of Tibetans in a broader East and Inner Asian context. Not only was the Tibetan Empire of the 7th to 9th centuries a major geopolitical power, but the Tangut state which dominated much of modern Gansu for centuries had Tibetan affinities.

Meanwhile, in the northeastern quadrant of South Asia, Indo-Aryan languages are dominant today. But, Tibeto-Burman, Tai, and Austro-Asiatic languages are all important as well (or at least present). As noted in Strange Parallels, the Tai are most recent arrivals in Southeast Asia proper. This is known from history.

For Southeast Asia various archaeological, philological, and now genetic, data suggest that Austro-Asiatic languages arrived with the first farmers, who emigrated from what is today southern China, in the range of 4,000 years ago. The arrival of Tibeto-Burman languages and peoples to Southeast Asia surely precedes that of the Tai, which dates to 1,000 years ago, but likely postdates the arrival of Austro-Asiatic groups.*

The situation in northeastern South Asia is somewhat confused in terms of period of arrival of the various groups. A few years ago a paper on cholera genetics in Bangladesh reported analysis which indicates that the ancestors of eastern Bengalis received an admixture pulse of East Asian ancestry about 1,500 years ago. And, that a pulse model would suffice. An immediate explanation that came to mind is that these Bengalis mixed with Munda people, who have substantial East Asian ancestry, and speak an Austro-Asiatic language.

In The Genomic Formation of South and Central Asia one model for the emergence of Munda people that fits the data is:

1) An admixture of East Asian people (presumably, Austro-Asiatic farmers), with “Ancestral Ancestral South Indians” (AASI). AASI being indigenous South Asians who lack any West Eurasian ancestry.

2) A mix of this component with “Ancestral South Indians” (ASI), with consists of AASI and a minority ancestry of West Eurasian farmer from Iran.

Presumably there other models which fit the data as well, but even with naive admixture analysis it was long evident to anyone who looked at the Munda were atypical. The Turan/East European ancestry that one can find with classical model-based admixture at various levels in various South Asian populations is always absent in the Munda. Not only that, but they had very high fractions of modal South Asian ancestry combined with the East Asian component.

So can the East Asian ancestry in Bengalis be explained by the Munda? I’ve posted on this topic before, and every time I come to the same conclusion, probably not. Now that I have Tibetan and Malay samples to define a northwest-southeast transect I can say that again, more definitively.

At K = 10 in the admixture plot above you notice that the cluster modal in Malays and Cambodians accounts for almost all the East Asian ancestry in the Austro-Asiatic Munda sample. In Bengalis that component is found, but so is the proportion modal in Tibetans, and also in Han Chinese. The same pattern is found in the Burmese, but with much higher fractions. In fact, let’s compare average fractions between Bengalis and Burmese.

Han Tibetan Austro-Asiatic
Bengali 3% 4% 4%
Burmese 16% 34% 28%

The Han-model component is kind of general. We can’t reject the possibility I think from these proportions that the East Asian ancestry in Bengalis is exactly the same as that in Burmese…though based on Y chromosomal data I do think there is some Munda ancestry in Bengalis. Additionally, Munda people are found in some numbers even today in Bengal, into Bangladesh (the Santhals).

Looking at results from a three-population test the Tibetan(like) contribution to Bengalis seems likely:

outgroup pop1 pop2 f3 f3-error z
AustroAsiatic Dai Telegu -0.00187497 0.00012171 -15.4052
AustroAsiatic Telegu Lahu -0.00182418 0.000124765 -14.6209
AustroAsiatic Malay Telegu -0.00135077 0.0001035 -13.0508
AustroAsiatic Han Telegu -0.00138827 0.000112488 -12.3415
AustroAsiatic Telegu Kinh -0.00158805 0.000130918 -12.1301
AustroAsiatic Miaozu Telegu -0.00142974 0.00011907 -12.0076
AustroAsiatic Telegu She -0.0015296 0.000127609 -11.9866
AustroAsiatic Cambodians Telegu -0.00135761 0.000119312 -11.3786
AustroAsiatic Telegu Tujia -0.00137567 0.000125184 -10.9892
AustroAsiatic Telegu Naxi -0.00106498 0.000123643 -8.61336
AustroAsiatic Telegu Japanese -0.000991272 0.000116507 -8.50824
AustroAsiatic Yizu Telegu -0.00111008 0.000133985 -8.28514
AustroAsiatic Telegu Han_N -0.000844919 0.000122055 -6.92243
AustroAsiatic Telegu Tibetan -0.000414633 0.000109922 -3.77207
AustroAsiatic Telegu Hezhen -0.000428829 0.000116739 -3.67339
AustroAsiatic Xibo Telegu -0.000504054 0.000138498 -3.63943
AustroAsiatic Telegu Burmese -0.000335967 0.000108207 -3.10485
Bengali AustroAsiatic Iranian -0.00331738 7.5938E-05 -43.6853
Bengali Miaozu Telegu -0.00250784 6.12097E-05 -40.9712
Bengali Han Telegu -0.00250669 6.11899E-05 -40.9658
Bengali Telegu Tibetan -0.0022997 5.672E-05 -40.5448
Bengali Telegu Japanese -0.00240064 6.02193E-05 -39.865
Bengali Dai Telegu -0.00253233 6.53283E-05 -38.7632
Bengali Malay Telegu -0.00212941 5.51377E-05 -38.6199
Bengali Xibo Telegu -0.0023685 6.24874E-05 -37.9036
Bengali Telegu Han_N -0.00241445 6.40346E-05 -37.7054
Bengali Telegu Burmese -0.00205009 5.43997E-05 -37.6857
Bengali Telegu Naxi -0.00249315 6.66967E-05 -37.3804

OK, so what do we do with this, and how does it make sense? If you read a book like Land of Two Rivers, you won’t have any sense that an admixture between a Tibeto-Burman people, and Indo-Aryan speakers, occurred in eastern South Asia 1,500 years ago. To a great extent this is “prehistoric,” hidden from us, even if by that period mentions of the fringes of modern Bengal exist in Classical Indian sources. It is clear that many of the people who lived in Bengal were not part of Aryan society.  The later Vedic sources assert this explicitly, mentioning non-Aryan tribes beyond the march.

I currently believe that southern and eastern South Asia were touched by the expansion of Indo-Aryan/Dravidian speaking people after 4,000 years ago. This would make sense in light of the Vedic memory. I also suspect that Austro-Asiatic Munda people arrived after 4,000 years ago into a landscape where the population was AASI, without any West Eurasian influence. By 500 BC it seems that Indo-Aryan culture at least arrived on the edge of Bengal. At this date I suspect most of the tribes living in Bengal were probably already Munda. If the argument in The Rise of Islam and the Bengal Frontier is correct that much of eastern Bengal was not intensively cultivated until after 1000 AD. The period between 500 AD and 1000 AD was also the only one in ancient or medieval India where Bengal was home to the paramount hegemonic power in South Asia, a state ruled by the Pala dynasty.

Meanwhile, Tibeto-Burman people seem to have arrived to the east around 200 BC in the Irrawaddy basin. Rice cultivation in this region dates to 1500 BC. This is 500 years after rice cultivation arrived in northern Vietnam. Presumably then around 200 BC and later there was a transition from Austro-Asiatic languages to Tibeto-Burman langauges (the Mon may be intrusive from Thailand). Somehow I suspect that between 0 and 500 AD a group of Tibeto-Burmans moved up to the coast and arrived in eastern Bengal. Mixing with the native Munda they were probably absorbed by the expansion of Indo-Aryans eastward triggered by the political dominance of the Pala dynasty.

But was the gene flow in one direction? This seems unlikely. All the Burmese samples have South Asian admixture. This can be explained by proximity. But there are signatures of this in Cambodia, and the Malay samples I selected were part of a tight cluster. It seems that the Malay samples also have substantial South Asian admixture. The Indian Ocean economy and Diasporas between 0 AD and 1000 AD, after which Muslims and later Europeans became dominant, is a lacunae in our understanding. The presence of Malagasy and clear Austronesian influence in East Africa indicate a east to west migration. But Indian genetic signatures are found through Southeast Asia as well. Some of this can be chalked up to proximity (Burma) and colonial era contact (Malaysia), but Cambodia is too far for either to be plausible. Curiously, this influence is mostly lacking in Vietnam, or the interior of Southeast Asia. This is strongly suggestive of maritime trade contact. The regions where Indic culture were strong are the regions where there is a genetic signature of South Asians.

At this point I think I’ve established enough about South Asia and Bengal to move on from that. In the future I’m more curious about exploring contacts between South Asia and Southeast Asia, and how it left a cultural and biological impact.

* The 4,000 year date I arrival from the genetic sample and culture which emerges in northern Vietnam’s Red River Valley, and marks the transition between hunter-gatherers to agriculture.

The dual engines of modern science

A few years ago Armand Leroi wrote The Lagoon: How Aristotle Invented Science. Some people immediately made a critique that actually, science, as we understand it, is really the creation of early modern Europe. That Aristotle and his fellow Ancients, or physicians and astronomers of early medieval Islam, or the scholastics of the high Middle Ages, didn’t “really” do “science.”

I think most of us understand where this critique is coming from. But, even if you grant the objection if Aristotle was alive today, would he be a scientist? Of course, he would go into science! And, he would probably a good one. Perhaps a great one. Why? Because he had the curiosity, cognitive skills, and, there is a culture that would allow him to flourish. To me, the biggest difference between early modern Western science, as it emerged in the 17th and 18th centuries, and what came before, is that it was a cultural concert of thinkers, a vast constellation of minds and minions.

In contrast, much of ancient science was driven by singular geniuses.

This brings me to the massive replication effort that just got published:

There are lots of angles to this story. Mostly good. But Jonathan Haidt pointed out how important this makes collaboration and a culture of truth-seeking within the enterprise. Alexandra Elbakyan has stated that her scientific activism is driven by “communist ideals.” And though I dislike Communism, I do think there is something fundamentally communistic about science. In Uncontrolled Jim Manzi points out that within the world of science there are very strong norms about honesty. A major issue with scientific fraud is scientists are trusting.

But then there is the von Neumann factor: geniuses can accelerate and open up whole landscapes of research. They do a “different kind of science.” It’s less culturally embedded, and less social and incremental. They are the sparks which fly in the darkness. Ratiocination machines of a different kind and ken from mortal man.

The moral of the story, if there’s any, is that modern science is a synthesis of these two aspects. There is the “industrial” aspect of scale, efficiency, and incrementalism. One step at a time into the darkness, cautious and continuous. This is science that Adam Smith would be proud of. International, specialized, and efficient. Optimized.

And then there are the startling breakthroughs. Sometimes those breakthroughs are genius and insight. Consider the story of the emergence of String Theory outlined in Lee Smolin’s The Trouble with Physics. Smolin is a skeptic of String Theory, but in the book, he describes how rapidly it took the scientific world by storm, just by force of its insight and elegance.

In contrast, there are cases such as CRISPR, where several different groups seem to have “stumbled” onto it (this resembles the “rediscovery” of genetics in the early 20th century). The genius here is less in the humans than in what nature had invented, and what humans discovered through trial, error, and luck. Nevertheless, in a few years, CRISPR radically transformed the possibilities in “genetic engineering.”

Going forward, big collaborative science will keep lumbering on. It will play the role that it has played for decades, driving translation, laying the seedbed for innovation. Normal science. But every now and then a spark will fly, and a new flame will explode. Genius still has a role to play in the firmament of human advancement.

The Limits of My Language are the Limits of My Stupidity

I think about this quote from 1984 literally every day:

Don’t you see that the whole aim of Newspeak is to narrow the range of thought? In the end we shall make thoughtcrime literally impossible, because there will be no words in which to express it. Every concept that can ever be needed will be expressed by exactly one word, with its meaning rigidly defined and all its subsidiary meanings rubbed out and forgotten.” (1.5.23, Syme)

And more:

“It’s a beautiful thing, the Destruction of words. Of course the great wastage is in the verbs and adjectives, but there are hundreds of nouns that can be got rid of as well. It isn’t only the synonyms; there are also the antonyms. After all, what justification is there for a word, which is simply the opposite of some other word? A word contains its opposite in itself. Take ‘good,’ for instance. If you have a word like ‘good,’ what need is there for a word like ‘bad’? ‘Ungood’ will do just as well – better, because it’s an exact opposite, which the other is not. Or again, if you want a stronger version of ‘good,’ what sense is there in having a whole string of vague useless words like ‘excellent’ and ‘splendid’ and all the rest of them? ‘Plusgood’ covers the meaning or ‘doubleplusgood’ if you want something stronger still. Of course we use those forms already, but in the final version of Newspeak there’ll be nothing else. In the end the whole notion of goodness and badness will be covered by only six words – in reality, only one word. Don’t you see the beauty of that, Winston? It was B.B.’s idea originally, of course,” he added as an afterthought. (1.5.23, Syme)

1984 is a great book. But do you remember how it ended?

Cave bears live on in brown bears, and were vegetarians (what!?!?!)

Unless you’ve been asleep you are aware of another megafauna ancient DNA discover, Partial genomic survival of cave bears in living brown bears:

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

A sad thing about this publication is that brought to my attention that these ancient cave bears were mostly herbivores. It makes me view The Clan of the Cave Bear differently!

I assume most readers of this weblog are not surprised. We know that various extant and extinct members of the elephant lineage have mixed. By a strange coincidence (or perhaps not?) the fraction of cave bear DNA in modern brown bears seems very similar to the fractions of Neanderthal DNA we seen in modern lineages. The authors infer that the gene flow may also have been bidirectional, so various bear lineages had multiple and complex interactions over hundreds of thousands of years. Something notable is that the divergence between cave and brown bears is considerably deeper than that between Neanderthals and modern humans. If the latter can be dated to around 750,000 years ago, with large intervals on either side, the bears apparently separated into separate species 1.2 to 1.4 million years ago.

The greater time depth is of interest to the authors. From The New York Times:

“We did not expect to find this at all because they’re really quite diverse in terms of their evolution,” Dr. Barlow said.

The team was also able to determine that the genes flowed both ways between species, with the cave bears also carrying some brown bear DNA. The most recent transfer of genes came from the cave bear to the brown, the study found.

Brown bears are more closely related to polar bears than they were to cave bears from whom they diverged more than a million years ago, he said. Cave bears were largely herbivores, while brown bears are meat-eaters and about 20 percent smaller than cave bears, with more delicate bones. A brown bear would probably have looked “wimpy” next to a cave bear, he said.

The expectation here is conditional on the idea that bears which occupy different ecological niches probably won’t hybridize even if they overlap in range.

All that being said, when Greg Cochran started talking about archaic admixture into modern lineages in 2005 I read up on the mammalian hybridization literature and came to the conclusion that a priori there was no reason why Neanderthals and modern (African) humans couldn’t have produced fertile offspring. Big mammals tend to occupy a lot of territory, and different big mammal lineages overlap. It seems rather common for gene flow to occur between them. There is evidence of jackal and coyote introgression into Eurasian wolves, for example.

So I  guess I’m not that surprised. And David Quammen’s new book, The Tangled Tree, presents a rather non-revolutionary message from where I stand. Though perhaps it hasn’t gotten out to the “public.” The complexity and multi-textured reality of the “species problem” is pretty clear to any biologist who work’s on population-level data.

Open Thread, 08/27/2018

DNAGeeks is dropping prices and offering free shipping on the phone microscopes for the rest of August. We’ll be putting the scopes on sale until the stock is cleared.

As I’m reading Imperial China 900–1800, I’m still thinking most of the readers of this weblog would benefit from doing so as well. There’s just so much within the book that is food for thought. Though you should read A History of the Byzantine State and Society as well!

Quillette has been producing some good material recently. I find it curious since a lot of scientists and Left-liberals more generally have been attacking it really vociferously recently. To be honest I think it’s kind of a sign that whatever Claire Lehmann is doing, she’s probably doing it well.

The critique some of the writing at Quilette is uneven is surely correct, but that’s true of lots of publications. In those cases, the authors take a hit, but the publications aren’t totally written off. In fact, I see a fair amount of undergraduate college-level material being shared around when they agree with someone’s politics; people only get intellectual snobby when they disagree with the conclusion (this is a big move by Protagoras on the Prairie).

First, Progress and Polytheism: Could an Ethical West Exist Without Christianity? Well, since ancient China was predicated on ethics, obviously Christianity is not necessary, though it may be sufficient. I think more predictable is going to be the critique that Christianity is necessary for liberalism, as implicit in the argument in Inventing the Individuals: The Origins of Western Liberalism.

Second, The Dangers of Ignoring Cognitive Inequality. This is related to the piece in The American Conservative, The Recruitment Problem the Military Doesn’t Want to Talk About.

If you haven’t, please check out Consumer genomics will change your life, whether you get tested or not.

Genetics Society Medal 2019 – Deborah Charlesworth. Very deserved. One of the authors of Elements of Evolutionary Genetics.

Enrichment of genetic markers of recent human evolution in educational and cognitive traits.

Brian Resnick at Vox has been writing some decent stuff on genetics.

My WaPo review of David Quammen’s new book on evolutionary trees (and a comparison with other reviews). Like Jerry, I am confused as to why The New York Times assigned a literary reviewer with no science background to offer opinions on David Quammen’s The Tangled Tree: A Radical New History of Life.

Sometimes good conversations still occur on Twitter. Click for the whole thread. It’s worth it.

A CRISPR cure for Duchenne muscular dystrophy is closer after a trial in dogs.

Ancient encounters: How we came across the daughter of a Neandertal and a Denisovan.

Analysis of Polygenic Score Usage and Performance across Diverse Human Populations.

Why Elon Musk Reversed Course on Taking Tesla Private.

Apple Gives Series Order to Sci-Fi Drama Based on Isaac Asimov’s ‘Foundation’.

In ‘Small Fry,’ Steve Jobs Comes Across as a Jerk. His Daughter Forgives Him. Should We? Something was seriously wrong with Steve Jobs.

Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.

Immune genes are hotspots of shared positive selection across birds and mammals.

The Desperate Quest for Genomic Compression Algorithms.

Environmental factors drive language density more in food-producing than in hunter–gatherer populations.

After 32 episodes we have a general sense of what people like to hear about on our podcast. So far the top 5 in downloads have been:

The Golden State Killer and the Genetic Panopticon
The Neolithic Revolution
Lee Berger and the Dawn of “Big Data” in Paleoanthropology
The Genetics of Human Behavior
Barbarian Genetics

(not necessarily in that order!)

A random question: what politically liberal podcasts do you listen to? I started listening to Pod Save America and it’s just people talking Tumblr and hating Trump. That’s fine, but you can get that elsewhere….

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

A plague of pastoralists

There are many reasons to read Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa. One of them is to know, understand, and express wonderment, at what the Tutsis of Central Africa achieved in the five years before and after the year 2000. What they did was awesome, and horrific.

The Congo is the size of Western Europe, and for a period 3 million Tutsi controlled the whole region. These were no two-bit warriors. They hijacked a plane from eastern Congo and landed it far to the west to launch a second front in the war.

It may seem strange, but I thought of this while reading Imperial China. The Jurchen, who became the Jin Dynasty, conquered northern China in a decade, in a furious frenzy, about 900 years ago. These people are ethnically related to the Manchus and emerged out of a coalition of hunting, fishing, and farming tribes only in the decades before 1000 AD. Taking up nomadism, they quick overwhelmed first the Khitan people, and then swept over the Yellow River plain, toppling the Northern Song Dynasty.

And yet this is not an isolated occurrence. Consider the rapid expansion of Arabs in the 7th century. Within 20 years Persia had fallen, and much of the Roman East was under their rule. The Mongols of the 13th century are an even more striking example, swallowing state after state.

Contrast with these instances the expansion of Rome or Russia. These polities grew in a piecemeal fashion, step by step. There was no explosion, just a long fuse.

My thoughts are inchoate. But it is a very strange reality that the Tutsis are traditionally pastoralists, and have been characterized by a great deal of mobility. Perhaps there is something on a psycho-cultural level which makes them more comfortable with the high-risk daring operations that they attempted and often completed during the years of the Great War of Africa. Farmers, that is peasants, are famously and justifiably characterized as extremely conservative (do some reading about how long it took potatoes to be adopted as a crop in Eastern Europe!). But nomads? I don’t think there is a similar stereotype.

And, to be entirely frank, the peculiar explosiveness of mobile pastoralist peoples that emerge out of obscurity may shed some light on the process whereby prehistoric pastoralists in Eurasia seem to have left such a strong cultural and genetic legacy….

The Fall of Gondolin and the transformation of Tolkien’s world

In a little over a week, The Fall of Gondolin will be released. This is on the heels of the publication of Beren and Lúthien last year, and The Children of Húrin in 2007. I notice that both of these two books are “Kindle Deals” right now, so they are probably anticipating that getting more people to buy these two books will gin up demand for The Fall of Gondolin.

If you’ve read The Silmarillion these novels are not going to be original. Rather, they’re for the Tolkien completists. But though Tolkien was a traditional conservative who did not look kindly upon the forces of the free market, I think the fact that Amazon is going to use his work, his world, as source material means that old stories are going to be recycled. Tolkien’s son, Christopher, who at over 90 years of age is nearing the end of his time guarding his father’s legacy. I wonder if these last novels are parting salvos by him before he loses total control.

I was not too interested in Beren and Lúthien and The Children of Húrin. But The Fall of Gondolin is a genuinely more epic tale.

The films in the 2000s were pretty good in my opinion, but what Amazon will do is probably going to totally reimagine how Tolkien’s vision is perceived by a new generation. Reading these novels might be a way to reacquaint oneself one last time with what these works of fantasy meant to people and were meant to be.

There could be 100 million genotyping kits sold by January 1st 2020

The figure to the right is from the comment David Mittelman and I wrote for Genome Biology, Consumer genomics will change your life, whether you get tested or not. The original numbers are from ISOGG, which does a great job collating information from a variety of sources. When final revisions for the comment were due, we only found data up to 5/1/2018.

That being said, I thought it would be useful to generate a chart where I combined and smoothed the results from the various companies. It is clear that the period after 2016 is when you see massive takeoff and adoption, driven first by Ancestry, but later by 23andMe joining the race. The other companies have been increasing their sales as well, with new players such as MyHeritage making a big play.

All this makes me wonder: what does the future have it store? Year-to-year the total number of kits in circulation were doubling in 2013 and 2014. That rate dropped to ~1.6-fold increases in 2015 and 2016. A lot of this is due to 23andMe turning away from customer acquisition (more marketing always leads to more sales). With 23andMe competing with Ancestry again in 2017 one saw a >2.5-fold increase in the number of kits sold.

My back-of-the-envelope calculations indicate that around 1.8 million kits were being sold per month between the big players in the first in the first 4 months of 2018. That’s about 18 million kits this year. That means 29 million kits total in circulation by January 1st of 2019. The wildcard here though is that this space is “consumer”, which means that a disproportionate number of kits are going to be sold between Halloween and Christmas. Extrapolating from the period between January 1st to May 1st, as I’m doing above, could be way too conservative.

The sales in markets outside of the USA, along with customer acquisition through marketing, need to keep increasing up until January 1st of 2020 for there to be 100 million kits sold. But I think it’s very possible. I’m on the bubble of saying even likely. The wholesale price of arrays (the chips) keeps decreasing, so the price point of the consumer product is also decreasing. This isn’t a situation where the market is growing linearly, it’s exponential. A few positive shocks here and there 100 million by January 1st of 2020 may seem conservative.

Addendum: There has been some confusion in the media between sequencing and genotyping platforms. These are different technologies. Genotyping platforms, SNP-arrays, are targeting a genome-wide subset of polymorphisms. 23andMe’s current chip seems to probe about 630,000 markers. The whole genome consists of 3 billion bases. In the 2020s sequencing will probably replace targeted genotyping arrays in consumer products, but it will probably really come to the fore first in the medical space.