Out of Africa-Out of Asia-Out of Africa

Roberta Estes recenty posted about the fact that Spencer & I will be revisiting The Journey of Man, fifteen years after he wrote the book and made the documentary.

As part of the preparation, I’m revisiting some uniparental results, in particular, recent ones. This preprint in bioRxiv Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago., caught my attention:

Background: After three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya. Results: The coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions: These results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements.

It was really hard for me to parse all the coalescene and phylogenies here. I know some readers are pretty well versed in this area so I’m curious about critiques and reactions to the above.

Why Confucianism matters

Human nature has not changed, within some broad parameters, across history. When I first became interested in topics such as ancient philosophy twenty years ago I recall being struck by the contemporary relevance of thinkers such as Aristotle. Previously my focus has been on the natural sciences, where the dead were just names, whose ideas had often been superseded and extended.

And yet when it came to ethics and moral living the philosophers and religious thinkers who flourished 2,000 years ago seem to have arrived at the primary issues at the general level, though progress and change occurred on the details (and continues to occur).

Why look to China? After all, there were ethical systems in the West. First, I’m not sure that the supernaturalistic religions work to bind elites together anymore due to lack of credibility. Christianity is getting weaker. My own personal hunch is that the current wave of Islamic assertiveness and violence is the paroxysm of a civilization confronting its irrelevance.

Second, Classical Antiquity had plenty of ethical systems, especially during the Hellenistic and Roman period. But Rome collapsed. There was a great rupture between antiquity and the medieval period. In contrast, the Confucian and Neo-Confucian system persisted down to the early 20th century in classical form and casts a strong shadow over East Asia even today. While Stoicism had personal relevance, Confucianism was designed to scale from the individual all the way to the imperial state.

The 1960s saw a radical transition to notional social egalitarianism in the West. This is the world I grew up and matured in. Arguably, I believed in its rightness, inevitability, and eternal dominance, until very recently. But I think that today that model is fraying and people are looking to find some mooring. In particular, I think we are in need of a rectification of names. From Wikipedia:

Confucius was asked what he would do if he was a governor. He said he would “rectify the names” to make words correspond to reality. The phrase has now become known as a doctrine of feudal Confucian designations and relationships, behaving accordingly to ensure social harmony. Without such accordance society would essentially crumble and “undertakings would not be completed.”

How are we supposed to behave with each given person? A lot of this is free-form and improvisational today, and it turns out that many people are not comfortable with this. Humans need scripts.

Finally, the world that Confucianism developed was highly stratified, though there was some chance of advancement. It was not a calcified caste system, but it was a hierarchical one. I believe that is the system that we are moving toward in the West, and it seems that a system that takes for granted non-egalitarianism, such as Confucianism, may benefit us.

Jiangsu, from the margin to the center

When I was eight years old I memorized all the capitals in the world…because (well, because a friend had done the same). I’ve always been into geography. But there is one thing I’ve been guilty about for nearly twenty years: I can’t point to all the provinces of China on a map and name them. For example, I only scored 83% in 2 minutes 10 seconds on Seterra’s China province quiz. For comparison, on the African countries quiz I got 100% in 1 minute 59 seconds. Obviously the latter is “harder” than the former, so it indicates my lack of focus.

To make up for my lack of fluency, I’m going to be reading Wikipedia entries of Chinese provinces and putting my reflections into this space. Readers who know more can also chime in in the comments.

I’m starting, for no particular reason, with Jiangsu. The coastal province north of Shanghai, it is not surprising that this is a wealthy region in a Chinese context. Shanghai is administratively distinct, but it seems that it’s core “native” culture is really that of southern Jiangsu. Even without Shanghai in the mix, Jiangsu would have about the 14th largest economy in the world if it was a separate and distinct nation.

Since I read Kenneth Pomeranz’s The Great Divergence about ten years ago I was not surprised at the fact Jiangsu was so economically vital. It had been the same in the 18th century when the lower Yangzi region became the heartland of Chinese economic growth and industry. But it seems that this region’s importance in trade and Smithian growth dates back at least to the Song dynasty, as the Grand Canal between north and south constructed during the Sui-Tang triggered development.

Originally Jiangsu was not part of China proper, as during antiquity it was inhabited by barbarian peoples. Of course, eventually, it was Sinicized, and when non-Chinese groups took over the North China plain Jiangsu and the Huai river served as a barrier to further southward expansion.

The duty to kill your friend

In the late 1980s Morgan Llwellyn wrote a novelization of the legends of Cu Chulainn, Red Branch.

One of the most dramatic passages involves the fight between Cu Chulainn and Ferdiad mac Daman. In the end Cu Chulainn kills Ferdiad (in a rather underhanded manner), because they were champions who represented rival tribal confederacies in Iron Age Ireland. But it was poignant in part because they were also very good friends.

Most of you do not know me personally, obviously. But those of you who do know me from undergraduate years (and a few of those do read this blog!) also know that one of my closest friends from that time is now a Gender Studies professor at a major research university. We stopped being as close when she went to do her study abroad and we sort of drifted apart, but we are still friends on Facebook, and despite our sharp divergences on social and political issues I can’t exactly deny and negate the history that we had. That’s part of who both of us are today.

And yet we both implicitly know we’re on opposite sides in the culture war. And that’s fine by me. Not everything is political. And even if you have to do your duty in the end and stand with your own tribe when the rubber hits the road, you don’t need to deny the humanity in others.

Accepting that most people are damned, and liberal pluralism

Here is how I learned it. Once upon a time in the West, the Church aimed to save all of society by bringing everyone under the umbrella of the Truth. The shattering of Western Christendom with the Reformation caused a problem. If the Catholics were right, then the Protestants were damned, and if the Protestants were right, the Catholics were damned. You know all about the “Wars of Religion,” which occupied Europe in the 16th and 17th centuries.

Ultimately this led to the Westphalian system and a gradual acceptance that there would no longer be One True Religion in the West. Monarchs who even took a skeptical view on religion, such as Frederick the Great, arose in the 18th century. In this case, you had a Calvinist Hohenzollern dynasty which could not bring its Lutheran populace on board. In Saxony, you eventually had Catholic dukes ruling over a Protestant populace.

But another aspect of the collapse of universal Christianity in the West was the emergence of radical Protestant groups which understood most of society to be damned and beyond redemption. The separatism of the Amish is an extreme case of this. They don’t even attempt to convert anyone to their religion, which has turned into an ethnicity. This withdrawal of radical Protestants from attempting to force the temporal world to their will has expressed itself most fully in the United States of America, which never had a state-supported religion on the federal level, a radical innovation in its day.

This strain of Christianity is suspicious of the state and society in part because of the suppression their beliefs and practices by both the state and society in which they first emerged. But their relegation of the majority to the ranks of the damned also allows for a modus vivendi in this life. As a contrast, see this apologia for the Pope Pius IX behavior in the Mortara case in First Things, Non Possumus.

The basic argument seems to be that the Pope was motivated by the salvation which was being offered to the soul of the child baptized by the family’s maid. The curious thing is that the whole time I was reading the piece I was thinking about Islamists who would argue that coercive conversion of children of other religions to Islam is still good on the balance because they are now Muslims. The general way this wors is somehow a child is tricked into saying the shahada, and Islam enjoins that once converted one can not apostatize (the Kafir Kalash of Pakistan are suspicious of their children being around their Muslim neighbors because this has happened many times in the past to them).

Some of the same extreme “compassion” seems to be cropping up in American politics, as a deviation from the Truth is no longer tolerated. Pius IX was out of step with his time, as secular liberalism was on the rise. Today I wonder if that liberal in its own turn may have to give ground to a new totalitarianism.

Island demes in an empty world


As you probably know a new ancient genome paper was published last week in Nature, Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. There is at least one other involving Willerslev in the works for what it’s worth. Carl Zimmer has a good write-up in The New York Times, while Greg Cochran picked up the fact that the latest results show no evidence of “Australo-Melanesian” affinities that have been found in Amazonians.

The key issue here is that they found 11,500 year old remains from Alaska, one of which they sequenced at 17x coverage, which is rather good (not medical grade good, but really sufficient for a lot of population genomic work). It’s clear that the lineage represented by these remains is “basal” to that of other Native American peoples, whom David Reich’s group labeled “First Americans.” Later, the First Americans diverged into different populations, with the two in modern focus being a northern cluster, including the Aboriginal peoples of Canada and parts of the United States, and a southern one including everyone else. This does not mean that the Beringians were isolated outliers. There may have been many other peoples related to the Beringians who diversified, who went extinct as well. The settlement of Alaska by other peoples suggests to me that extreme conditions in the Arctic made it likely that there would be population turnover there. Also, the fact that these samples were located close to the source of settlement in the New World by modern humans makes their distant relation to all other New World populations unsurprising.

The big thing that the press is highlighting is the confirmation of the Beringian Standstill model, where modern humans percolated into the area between Siberia and Alaska, Beringia, and did not move east for thousands of years. Basically, the conditions were inclement toward human habitation on both sides of Beringia, while a relict modern human group likely occupied a pocket of more moderate climes for thousands of years, with minimal gene flow from the west, and blocked from migration to the east. Genetically the Beringia Standstill made sense for a long time…the divergence between Amerindian lineages and those of eastern Eurasia seemed too old to be accounted for by recent migration a bit more than 10,000 years ago (the old “Clovis first” hypothesis).

How old? This paper suggests that the portion of Native American ancestry which indicates an affinity to East Asians stopped exhibiting gene flow from that source around ~25,000 years ago, after diverging around ~36,000 years ago. This points to the fact that after modern humans came to dominate eastern Eurasia they began to diversify rapidly after 40,000 years ago, but gene flow between different populations did not always allow them to drift apart…at least initially. The ancestors of Native Americans and East Asians may have been in extremely separate locations by ~25,000 years ago, whether it be on the fringes of eastern Siberia, or somewhere in southern China (there is no reason that the modern Chinese have to have had ancestors resident on the North China plain before the Last Glacial Maximum).*

One aspect here I want to emphasize is that our image of a world thickly populated with humans may mislead us in our intuition about how patchy occupation was ~25,000 years ago. Yes, humans may have left artifacts all over the world, but that doesn’t mean that there weren’t centuries or millennia of no occupation, or, that meta-population dynamics were such that extinctions were common. For decades in population genetics there has been talk of “clines vs. clusters,” but if human population densities were far lower, or occupation patchier, then clines may have become much more important recently with high density than in the past.

Finally, back to the Australo-Melanesian issue. Either there is a lot of population structure in ancient Beringia to be explored, with diverse quasi-Asiatic groups, or there was an Australo-Melanesian group already in South America.

* Ancient North Eurasian ancestry came into Beringians ~20,000 years ago. Two groups which merged during the middle of the Last Glacial Maximum.

South Asian Genotype Project update

Just a quick update. I know I haven’t been responsive, but I’ve been traveling and spending time with the family and working a lot for the past few weeks. I’m going to make some revisions to my pipeline as well. I will get back to generating results soon (as in a week or so). So please keep sending data to contactgnxp@gmail.com.

The global elite is the only elite now

When I read Beyond the Global Culture War ten years ago it was interesting, but I was unconvinced. The author, Adam K Webb, has a peculiar political typology where the liberal democratic “end of history” is seen in a very negative light, part of an atomistic and dehumanizing trend across human history which has only come to prominence of late (in the past it was exemplified by atheistic and hedonistic cults, such as the Carvaka). A strange thing to someone reading in the mid-2000s is that Webb has good things to say about the Islamic Republic of Iran, and its vision for society.

It is important to remember that the clerical elite which dominates Iran are not know-nothings. Much of Shia Islam explicitly integrates and accepts the validity of ancient Greek philosophy. In contrast, mainstream Sunnis have been skeptical of philosophy’s value since the time of Al-Ghazali. Shia Islam, therefore, preserves intellectual threads which date back to the 8th and 9th centuries of the Abbassid Caliphate, which have become attenuated within Sunni Islam. Though Sunni Islam is not anti-intellectual per se, it is not surprising that the most austere and anti-humanistic sects, such as Salafism, come out of that tradition (in contrast, extreme Shiism gave rise to the Bahá’í religion).

Khomeini studied and admired both Plato and Aristotle. Many people have seen similarities between the novel republican-theocratic hybrid state of the Islamic Republic and Plato’s Republic, with Shia clerics taking the place of philosopher-kings. Webb suggested that the Islamic Republic was led by a ruling class of clerics who had a vision of the good for their society, and that was a good thing. This, in contrast to the regnant neoliberal consumer capitalism promoted by the likes of Thomas Friedman in a vulgar fashion, and Francis Fukuyama in a more implicit and subtle manner.

In Beyond the Global Culture War Webb argues for the likelihood of a resurgent movement of nationalisms based around public virtue and a vision of the “good society” which is more than just the sum of capitalist transactions between consenting adults. He imagined that despite their differences, Muslim, Buddhists, Christians, Confucians, and Hindus, could all come together as one against secular neoliberalism.

After 40 years at the helm as I am writing this the “virtuous” ruling class of Iran is under serious stress, in large part because of individual corruption at the elite levels, as well their commitment of the body politic to international adventurism. And even the best-laid plans and aims succumb to a diminishment of enthusiasm and zeal.

And yet nevertheless some of the theses of Beyond the Global Culture War are more relevant now than they were when the book was written. First, the neoliberal order of infinite plentitude and a universal middle class collapsed in the financial crisis of 2008. Though the global order continues on neoliberal precepts, it is more a matter of not knowing what the alternative could be, rather than genuine enthusiasm. Second, nationalism and localist movements which cut against the grain of global democratic liberalism have become vigorous. China shows no signs of embracing democratic liberalism, India is home to a Hindu nationalist movement that has the reins of power, and right-wing political movements are on the march in Europe. Third, a genuine international global elite has taken on greater solidity since the financial crisis, because they understand that their interests are more important in concert than the nation-states which they are notionally citizens of.

Consider Rupert Murdoch. Born an Australian, but now an American citizen. He has media properties of note across many nations. He has daughters who are half ethnically Chinese, granddaughters who are part Ghanaian, and other grandchildren who are being raised British (and are descendants of Sigmund Freud!).

Murdoch may be an extreme case, but his life and ties are not atypical for the global oligarchic class. Below them is the global professional caste which moves between nations as needed, and views themselves citizens of the world. They are foot-soldiers in keeping the machinery of internationalism chugging along. The banker in New York arguably has more in common in terms of public and private interests with the banker in London or Shanghai than they do with the citizens who reside in the hinterlands of the nation-states in which they live.

And yet nation-states exist, and nationalism is robust through popular democratic means. Just as Franklin Delano Roosevelt was viewed as a traitor to the patrician class from which he came, so some demagogues will come out of the oligarchic class to elevate the importance of the nation above their own class interests. But perhaps India gives a better sense of nationalism and its tension with its global elite: Hindu nationalism is rooted in upper caste middle-class Indians, but their origins are often sub-elite or petite bourgeois. They are often less fluent in international English, as opposed to the nascent national language, Hindi. India’s negotiation between being part of the international order of liberal democracies, and something deeply native and distinctive, may be illustrative of the future.

I am not one who believes that the nation-states were “invented” by the French in the last decade of the 18th century. But, the nation-state was given more salience and centrality in the 19th century, as multi-ethnic monarchies were seen as archaic and outmoded, and liberal nationalism captured the spirit of the day. The trend toward nationalism ironically became international. Though some nation-states were artificial and have failed their original promise, many have come to become part of the international order.

The nation-state is now part of our diplomatic heritage, and there is no movement for “world government” in any concrete sense. Though there are international governmental institutions, their solidity is similar to that of taxonomic ranks above that of species. They have some reality and utility, but they’re not nearly as relevant or distinct as species.

Over the next few years, we will start to see how the nation-state, and the resurgent nationalisms, deal with the reality of a supra-nation without a state, the cosmopolitan global overclass. At the pinnacle of the global overclass are the oligarchs. This group has always been of internationalist bent due to their reliance or positions in finance and trade. But in the past few centuries, national patriotism was a feature present even among oligarchs. To some extent, the national and personal interest were comingled. The House of Morgan did not intervene to stabilize the American economy purely out of patriotism. But the fiscal health of the United States was seen as necessarily tied to the health of the House of Morgan. And it is also true that during the great age of globalization before 1914 this class was still characterized by a powerful robust nationalist ethos which would be unthinkable today.

Tom Friedman was wrong. The world is not flat. The world is multi-textured. In the United States Obama’s presidency did not herald a post-racial era, but a more racial era! Similarly, despite the financial collapse, there is a shadow across the world of a global class which operates in a flat neoliberal landscape where the acid of capitalism has eaten away at local national affinities and affiliations in anything beyond a legal and convenient sense. The dream of lives on for some, and those “some” count a lot more individual than the multitudes who have soured on the universal global order.

Predictions for 2018

I don’t normally do year-end stuff. But I figured, why not? After all, I put up a post at my work blog about the major things that happened in historical human pop gen this year.

Indian population genomics will move forward notably. The ancient DNA work really feels like vaporware sometimes. Some of the researchers involved reach out to journalists (people of my acquaintance) and leave tantalizing clues, but they disappear off the face of the earth. I assume that some sort of Indo-Aryan intrusion from Central Asia will seem clear from the data and results, though the Indian media and intellectual class will claim the opposite. In this way they are just like the American media and intellectual class; if the evidence does not fit just say that the evidence says the opposite of what it does. People will believe because they want to believe.

The current protests in Iran won’t go anywhere. Someone with guns needs to be on the side of the protestors. That’s it. Also, if a group with guns ends up favoring them, the West will find that anti-clerical Iranians are quite nationalistic and not necessarily liberal democrats.

The Democrats will win the House of Representatives. I think there’s about a 50/50 chance that they’ll get the Senate.

The United States will be in a recession by the last quarter of 2018. We’re overdue. All OECD countries are growing, to the point where Brent crude prices are going up. This isn’t sustainable, especially since many developed nations have been kicking the bucket down the line.

Personal genomics is going to be more of a presence as the year progresses. I was surprised by all the attacks from the tech-press on direct to consumer genomics over the past few months. That indicates to me that the industry is getting big enough to be a click-bait target.

George R. R. Martin will publish Winds of Winter.

More ancient DNA from the New World. This has been in the works for a while. I’m really skeptical that they won’t be able to push it out in 2018.

Twitter will continue to not be able to find its way. Basically, it can’t win, and won’t win.

More work in complex trait genetics published. This is has been long in the works, so this I know for a fact. Whatever the results, don’t worry, it will confirm all your priors no matter what those priors are.