The coming genetic invasion of history, and the rage to come

About ten years ago I reviewed Bryan Sykes’ book Saxons, Vikings, and Celts: The Genetic Roots of Britain and Ireland. It was what it was, a product of the Y/mtDNA era. Therefore, there were a fair amount of conclusions which in hindsight turn out to be wrong. Sykes, and other genetic historians, such as Stephen Oppenheimer, have annoyed historians for years with their genetic imperialism. More frequently, genetic research has been an accent or inflection on historical work. Peter Heather has integrated some genetic results in his earlier books, though you can ignore those and still obtain the general conclusions.

The recent work on near antiquity is a hint that that is going to be blown apart. Ancient DNA in the historical period has been a slow simmer for a while now. The reason is simple: ancient DNA returns more on the investment for prehistory, where there aren’t historical documents. Until recently ancient DNA techniques were expensive in a variety of ways. The industrial process described in Who We Are and How We Got There is going to change that.

In the near future, a large number of projects are going to surface which test hypotheses and conjectures offered by historians.

You would think that testing hypotheses, generally with demographic predictions, would be something that historians would welcome. The problem is that the test will mean some scholars are going to turn out to be wrong. People who spent decades building up a particular model or understanding of the past are going to have that torn away from them.

The normal human reaction is to get defensive. But the problem is that many historians are not well trained in genetic methods. In fact, many geneticists are not well trained in the abstruse statistical methods developed by scholars in ancient DNA.

We’ve seen some of the same from archaeologists. But archaeologists had models which were, to be frank, more speculative than those historians cling to. Even if a particular historical model may be wrong, it is likely there are reasonable grounds to have held onto to that position. If ancient DNA falsifies it the reaction will be even more strident I suspect.

Of course, geneticists need the help of historians. So when the bad feelings clear I think the synthesis will get us to a better understanding of the past.

The new post-genetic paradigm will come

Oftentimes the domain on which a technical framework is applied matters a great deal. Imagine, if you will, an explicit statistical test for a phylogenetic relationship between a set of extant populations, whereby one infers a group of ancestral populations. If the genus is Drosophila, it’s academic. Interesting, but academic. If the genus is Homo, then it gets complicated.

People care a great deal about the historical inferences made from human population genomic datasets. I say genomic, and not genetic, because the last ten years with genome-wide analyses and ancient DNA is very different from what we saw in the late 20th century and aughts. The definitive granularity is such that population genomics has touched upon very sensitive and precious issues, both in a scholarly and non-scholarly context.

A lot of the time I have my head down reading supplements where the statistical methods are. The reality is that this sort of science is cutting edge, and there are always later revisions. Usually you can see where those revisions might come from if you look at the detailed methods and conclusions that are found in the supplements. Also, you will find that that is where you see the limitations, and the reasons that the authors chose particular parameters.

To give you a sense of what I’m talking about, consider 2016’s Genomic insights into the origin of farming in the ancient Near East. The paper proper is 24 pages. But the supplemental text is 148 pages. There is a lot of interesting stuff in there, but I would just jump to page 125 and read the whole section there and down to the end. The method portion is important because you always need to take number values in results with a grain of salt. You see for example later work which refines fractions significantly when it comes to estimating admixture between a finite set of putative populations. And the last section seems likely to become a paper in and of itself at some point

But that doesn’t mean that the genetic inferences are not robust and come out of a vacuum. In the details the phylogenetic models being tested are going to be wrong on many particulars, but in relation to hypotheses being tested they are often entirely sufficient to reject to accept.

For example, there was long the idea that the Basque people of the western trans-Pyrenees region of Spain and France descended from pre-farming Europeans, and therefore the Basque language, which is an isolate, might have local roots which went back to the Pleistocene. Today, ancient DNA along with explicit testing of various phylogenetic scenarios makes it clear that the largest fraction of Basque ancestry derives from “Early European Farmers,” who represent a demographic pulse which radiated out of the Eastern Mediterranean and reached Spain 7,500 years ago. Of course Basques do have local hunter-gatherer ancestry, but these Mesolithic peoples themselves were the last in a sequence of very distinctive populations in Pleistocene Europe. Finally, Basques do have admixture from Indo-European peoples, just less than other people in Iberia.

Of course, genetics can’t tell us about languages. Using linguistic labels in population genetic papers is to some extent a lexical convenience, but it is also one we use because of the constellation of information we have. The last major demographic pulse into Iberia is associated with an ancestry which derives from Central Eurasia. This ancestry is copious in Northern Europe, but is also found in South Asia, and ancient DNA suggests its expansion occurred between 5,000 and 3,500 years ago. It also happens that the Indo-European languages are spoken in both India and Europe. The natural inference then is to make an association between this language family, and this demographic pulse.

Some observers note discordance between estimated fractions from paper to paper, but don’t seem to understand that the point isn’t to estimate fractions of ancestry as ends in and of themselves, but to estimate fractions of ancestry to expose and highlight demographic change (or lack thereof). We can say with a very high degree of certainty that the period between 3000 and 2000 BC witnessed massive demographic change in Northern Europe. Somewhat later there was a similar change in Southern Europe, but more demographically modest. These are simple facts.

There are some scholars, frankly often archaeologists, who dismiss the relevance of the genetic findings. But anyone who has read archaeology knows that there are many cases where researchers see demographic continuity, and posit in situ cultural evolution, where it is just as possible that a new people arrived. The reason ancient DNA has revolutionized our understanding of prehistory isn’t because it has brought us new knowledge, it has foregrounded old and buried knowledge. The knowledge being that migration matters.

But genetics is only a skeleton. A framework. True flesh on the bones of the story needs the input of archaeologists, linguistics, and other scholars. In Who We Are and How We Got Here David Reich expresses his ambition to construct a historical genetic atlas of the world. But that atlas will be all the poorer without the input from other fields besides genetics. Many archaeologists have gotten on board with genetics as a tool, but the reality is that there needs to occur the rejection of some theories precious to some scholars if there is going to be total buy-in. Eventually that will happen, and a new synthesis will arise.

Japan as a natural cultural experiment

History of Japan is a good survey for anyone curious about the topic because it is short enough to not be intimidating (this was a complaint from friends who I recommended read The Making of Modern Japan), but dense enough to actually be much more informative than a Wikipedia entry. Unlike many surveys of Japanese history, it does not operationally begin with Oda Nobunaga. The extensive treatment of the Nara and Heian period is something that I particularly appreciated since often these are explored only in specialist monographs with any depth.

One of the curious things about Japan is that since the conquest of the Emishi of northern Honshu around 800 AD, the Japanese lost an external frontier with another people. True, there were periods of endemic warfare between Japanese when central authority collapsed, but by and large, these conflicts were arguably less destructive than shocks from without would have been. Wars within cultural groups are highly destructive, but often they are governed by unified cultural scripts and mores.

In Strange Parallels: Mainland Mirrors: Europe, Japan, China, South Asia, and the Islands, the historian Victor Lieberman examines Japan as a case study of a “protected-zone” civilization. In Lieberman’s framework, the emergence of organized steppe nomadism in the years after the fall of Rome and China caused stress and chaos across what Nichols Spyman would term the “Eurasian rimland,” and what the ancients would have termed the civilized oikoumene. The same model crops up in Ian Morris’ War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots.

The development of the chariot during the Bronze Age was arguably an integrative force in the evolution of agricultural polities. Chariots were useful for the transport and deployment of elite warriors and archers. But, they were not utilized as shock troops, as would be the case with the rise of mounted cavalry. First emerging around 1000 BC on the western edge of the Eurasian steppe, by 0 AD the mounted cavalry had given birth to full-blown nomadism from Europe to China. To some extent, the only way that core civilizations on the Eurasian rimland could maintain themselves in the face of the pure nomadic assault was through co-option and assimilation. Arabs, Turks, and Mongols all swallowed up earlier settled civilizations. In the Near East, China, and India,  peoples of nomadic origin became the ruling classes, synthesizing and integrating with the traditions of those they conquered.

In contrast, much of Western Europe and Southeast Asia were protected from these incursions due to distance, topography, and climate. The German barbarians who took over the reins of power in the post-Roman world were agro-pastoralists, not nomads. In mainland Southeast Asia, the Tai incursions was a migration of agriculturalist warrior elites. The modern states of Cambodia, Vietnam, and Burma withstood the assaults and maintained cultural continuity with their past. In Western Europe, Ireland can be thought of as an analogous case, though the Viking shocks, and later Anglo-Normand conquest, disrupted its continuity.

Lieberman argues in Strange Parallels that these protected-zone societies are much more natural nation-states than elsewhere, in part because their organic identity from earlier cultural traditions persisted down to the modern era, as opposed to having been created anew through novel ideologies. And is it a surprise that of the European nations England, which has not undergone a mass invasion since 1066*, has one of the deepest self-conceptions as a nation-state?

Which brings us back to Japan: its imperial family dates at least the early 6th century AD. Though we don’t have verified dates before the Emperor Kinmei, it seems likely that the Imperial House of Yamato is quite a bit older than that. Unlike in the West then the Japanese have a much easier line of descent from antiquity for its elites. The persistence of the Japanese imperial family is a testament to the cultural prominence that the Yamato lineage has, with all of its ups and downs. In contrast, the arrival of waves of barbarians in other regions of the Eurasian rimlands produces a situation where taboos against taking official power eventually broke down. In the 5th century West Roman Empire, there was a taboo against barbarians or people of part-barbarian ancestry from becoming Emperor. Eventually, the barbarians got rid of the Emperor, and over the centuries became Emperors themselves. The same process is evident in the Islamic world, where the Arab Caliphs remained figureheads for Persian and Turkic potentates until they took over both de jure and de facto roles.

The Japanese have a different experience. At the beginning of their history, they were a cohesive culture expanding into the post-Jomon frontier. Though reinforced with an elite migration of Koreans and Chinese prior to the Fujiwara period, unlike polities across Eurasia the Japanese ruling class have been uniformly and continuously of the same ethnicity and identity as the populace which it ruled.** And, unlike the Vietnamese or Koreans, they have not been subjected to conquest and hegemony by China. They have long been of the Sinic sphere, not within the Sinic sphere.

Between Korea and Japan, there is a 200 km distance by water. In contrast, between England and France, there are about 30 km. This greater distance explains the relative isolation of Japan in comparison to England when it comes to continental affairs. Proto-historical expeditions in Korea, or Hideyoshi’s adventure, are exceptions, not the rule.  Official contacts between Japan and China often had gaps of centuries.

This is not to say that Japan was not influenced by the continent. Obviously, Buddhism, Chinese writing, and the wholesale transplantation of Tang culture during the Fujiwara period attest to the early influences, while later on even during the Tokugawa era there were influences from Western thought via the Dutch. Rather, the Japanese are a natural experiment of a people who have repeatedly engaged with the world on their own terms, and developed their own culture organically to such an extent that they put their ancient tribal animism, Shinto, as the state religion during their phase of modernization!

In answer to the question “why is Japan different?” I would say this is a peculiarity of geography, close enough to be influenced culturally, but distant enough to be politically isolated.

* I think the Dutch invasion under William of Orange really was an invasion. But its impact was mild due to broad local support.

** Contrast this with ethnically distinct ruling elites in the Near East, India, and China, as well as cosmopolitan ruling families in Europe. Even England was for several centuries ruled by a nobility which spoke French.

 

Carthage (and others) must be read

The first half of Richard Miles’ Carthage Must Be Destroyed: The Rise and Fall of an Ancient Civilization is useful, but there’s less of a focus on the culmination you know is coming, the Punic Wars. For a history of that, I’d actually recommend Adrian Goldsworthy’s The Fall of Carthage: The Punic Wars 265-146 BC (one of the best descriptions of Cannae).

By utilizing archaeology and generating an inferred cultural history of Carthage, Miles does a great job contrasting the Punic mercantile republic with Rome. Aside from the penchant to name their leading citizens Hanno, Hannibal, and Hamilcar (to the point it’s hard to keep track of who is who), the most notable aspect of ancient Carthage seems to be its tendency to crucify generals who fail in battle. The Carthaginians come off as cartoon villains, even setting aside the child sacrifice. This is probably partly history being written by the winners, but it’s clear that still, Rome, in particular, was unique in its public spiritedness and social cohesion.  This, despite the fact that Rome and Carthage had both converged on a system of an oligarchic republic during the height of their rivalry.

Ancient history, and reading about other cultures, is illuminating about the human condition because different peoples in different exigent circumstances seem to react mostly the same but to wildly different outcomes.

For China, I don’t know of a better treatment in survey form than John King Fairbank’s classic. I also have a very soft spot for Jaques Gernet’s A History of Chinese Civilization. Fairbank’s book is more narrative history with some cultural fat on the bones. Gernet is more a cultural history with an exoskeleton of narrative diplomatic history.

For Rome, there are many recent books. But I still really like Michael Grant’s big thick survey, History of Rome. I don’t know about Greece since I haven’t read Greek history much since I was a child. Though Grant has some books on Greece too.

Finally, Michael Axworthy’s Empire of the Mind should be on a “to read” list. It’s a little off the beaten path because it’s a history of Iran. It’s got only superficial coverage of the recent past and tries to go deep into the psyche of what makes Iran Iran. I think it is fair to say that the book ends of concluding that Iran, as we understand it today, is hard to detach from the Safavid period (when it become Shia).

I think these civilizations of the Eurasian oikoumene are good places to start to understand the human condition because so many people were peasants and those ruled by peasants over the past 10,000 years. I would recommend a book on India, but those are mostly religious books. Islam comes a little late, as does Northern Europe. Much of Eurasia and Africa had no written language. If you understand China, Persia, and Rome, you’ll understand a lot. And probably enough.

Book recommendations welcome.

A shock is a surprise because it’s a shock

Reading Thomas Childer’s The Third Reich: A History of Nazi Germany reminds me a lot of reading The Red Flag: A History of Communism. These strange and extreme ideological systems seem likely to be eternally marginalized…until they aren’t. The dream of revolution is a fantasy until it isn’t. The rot within these societies, their anomie and disharmony, could be papered over and suppressed for a time. But the revolution took root in rich soil fertilized by the decay and necrosis of the old order.

Human social and cultural systems go through the evolutionary process in a gradual fashion. But quite often they don’t. In fact, compared to biological systems I’d say cultural evolutionary processes are more nonlinear and protean. We may attribute this to exogenous shocks, but with hindsight, we often see that there were endogenous parameters setting the system up to collapse with the first “push” from the outside or an unexpected variable.

And one of the curiosities of humans is our tendency to maintain public fictions all the while knowing that private realities are different. With the chaos of the 1st century B.C., social unrest, the rise of successive strongmen, it was clear to observers of the time that the Roman Republic was sick. The final victory of Augustus and the end of the “republican” chaos is often depicted as a relief for most Romans and their subjects, with the exception of a few aristocrats who were pushed into a purely servile and ceremonial role.

Still, the public fiction continued. Augustus famously was the “first citizen,” princeps. The term imperator became more ubiquitous with the reign of Vespasian a century later, as the Roman Empire recovered from the fall of its first royal dynasty. Nevertheless, the forms of the Republic were maintained despite the reality that Rome had become an autocracy. Only around 300 AD did princeps fall into disuse. Diocletian began to exclusively use the term dominus. Lord.

Other public fictions persisted even then. The office of consuls, which date to Roman prehistory, was maintained down to the 6th century A.D., the reign of the Justinian. The last of the Roman Emperors coincidentally who grew up as a native Latin speaker.

Obviously, the tendency toward public fictions is not an artifact of Rome. To a great extent, Constitutional Monarchies are public fictions. When around 200 A.D. the emperor Septimius Severus did away with the fiction that the laws enacted were derived from the will of the Senate of Rome, he did away with a practice that had maintained a republican facade for centuries. The shocks and violence of the 3rd century, when the Roman system almost collapsed, was the coup de grace. Though Diocletian and the military emperors which came after him were never self-styled kings, due to the taboo around the term in Roman society, their forms and manners were inherited by the monarchs of medieval Europe. The radiant crown that Westerners perceive to be prototypical of the form is a Roman inheritance was popularized by the sun-worshipping emperors of the late 3rd century. Julian the Apostate, a reactionary who abhorred the new, did away with many of the imperial accretions added by his recent predecessors, with all the pomp, ceremony and glamor that that entailed (though his reign was an aberration in more ways than that as a beared pagan convert). The Romans never had kings, but showed kings how to be kings in substance and style.

In the pre-modern world, these fictions were quite resilient. The Zhou dynasty persisted centuries after it no longer had any power to speak of. The Abbassid Caliphs were kept as puppets in Mamluk Egypt for 250 years before the Ottoman conquest. The Merovingian dynasty’s last 100 years was to be as symbolic puppets for the lords of the Franks. The last Mughals lived over a century after the power of the dynasty, if not its glamor, had faded from memory.

The moral of the story is that public fictions can last quite a bit longer than the reality from which they are spun. With hindsight, the chaos and disrepute ushered in by the reign of Commodus clearly signals the end of the old Roman Empire with its republican fictions. But that was not clear then. The frog continued to boil, until from the outside barbarians threw in a dash of scalding water. Only then did the skin peel. But the frog had long been dead.

Why the world before 1450 matters

It is no surprise that I am not excited by the proposal to focus AP History in the United States on the period after 1450. Overall I agree with many of the comments made in T. Greer’s tweet thread. Though I have a concurrent opinion with many history teachers who oppose the change, my opposition is for different reasons. To be frank I don’t care about “showing our black and brown and native students that their histories matter—that their histories don’t start at slavery”.

Though my leanings are toward positivism, that is, I think history is an empirical discipline, even with a potential scientific scaffold, I understand that with finite time and resources your choices are conditional on your viewpoint. When I grew up in the American North the Civil War was taught with facts, but the arrangement and emphasis of those facts were not flattering to the Confederacy. I think objectively this isn’t hard from a modern perspective. But, the fact that some Union regiments were raised in the area where I grew up is certainly relevant

But this old-fashioned biased perspective still gave the nod to the importance of objectivity in some deep way. And though I was an immigrant who was routinely asked “where I was really from”, there was also an understanding that I needed to know this particular Union history, because it was the history which I inherited.  It was our history, which set the objective preconditions of the world in which we lived. The sharply critical cast of modern history teaching has its roots in this fundamental understanding. History may often have had propagandistic overtones, in that it inculcated, but the facts still mattered, and sometimes they were at counter-purposes to the narrative (e.g., the Abolitionists were clearly in the minority even in the North; good history teachers didn’t lie about this).

The idea that one’s history, “their” history, is rooted in descent is common sense. But it’s also an idea which brings together frog-Nazis and Critical Race Theorists. Because of the closeness of the past few hundred years, the histories will be contested on the grounds of ideology. All narratives are contested, but emotion and effort vary in the contestation. The way to push through the contestation is to flood the zone with facts, with robust models. But this isn’t feasible for high school students, many of whom simply want to obtain a good AP score so they never have to take a history course again.

Rather, I think history before 1450 is critical not because it is relevant to a diverse student body due to genealogical affinity, but because common human universal themes are easier to perceive in more distant peoples whose actions and choices don’t have as strong a direct connection to the lived present. Consider the Classical Greeks. It is reasonable to assert that the genesis of the West as we understand it has to be traced at least in part to the Ionian flowering of the 5th century, and to Athens in particular. But it is not reasonable to make Classical Greeks a stand-in for modern Europeans, whose Christianity (at a minimum culturally) would be alien, and whose origins are from peoples who the ancient Greeks would term barbarians.

The Classical Greeks are profoundly alien to moderns, rupturing excessive identity, though that didn’t stop 19th century Romantics! Athenian democracy is very different from the modern democracies, with its participatory character and the large class of excluded residents. But Athenian democracy, and Classical Greece more generally, also highlight deep universal aspects of the human condition. It speaks more forcefully to many students because the mental clutter of the past few centuries, and their ideological baggage, are removed from the picture.

Additionally, cross-cultural comparisons of similarities and differences in the ancient and medieval world are useful because they are less overshadowed by the “Great Divergence”, and the post-1800 European breakout. While the world before Classical Greece was one of strange and isolated polities in a vast barbarous world, the world after 1450 points strongly in our mind’s eye to a state where Europe occludes our entire view. The problem is not slavery, because the age of European supremacy saw the abolition of slavery.

Obviously, even the period before 1450 can be fraught. Consider the rise of Islam, and the crystallization of the West as Christian Europe in tension with the rising civilization to the south, and the receding pagan wilderness to the north and east. There are plenty of opportunities for debate, disagreement, and ideological axes to grind. But contrast the same argument around the Arab-Israeli conflict or Sykes-Picot Agreement.  The fact is that pushing the past further back into the past muddles modern preoccupations. And that’s a feature, not a bug.

Our Edo period future?

The second season of Westworld has some scenes set in Edo period Japan. To spoil things for you there is apparently a scene-by-scene re-creation of a plot arc from the first season of the show set in the American West. Watching this scene, and comparing it to the earlier version, I can’t but help feel that the Edo period setting is more grand and refined. If the first season’s violent attack was brutalist, the scene above is more neoclassical.

Then again, Edo Japan and the American West are perhaps antipodes of second-millennium civilization. Where the 19th century American West was anarchic, chaotic, and creative, the Edo period in Japan was notable for its stability, order, and the perception that it was a culture in chrysalis. Old forms may have been reinvented, but those forms were treasured.

The context for the Edo period is that 16th century Japan was a dynamo. Not always in a good way. The islands were riven by internal warfare. The Japanese were known to be a piratical race by the Ming dynasty, and the 16th century ended with the warlord Hideyoshi’s disastrous invasion of Korea. Prefiguring Japanese ability to imitate the West in industriousness they developed a skill in the making of guns, while Roman Catholic Christianity had great success in the southern island of Kyushu.

Eventually, Tokugawa Ieyasu set the stage for Japan’s nearly three hundred year exile from the congress of nations, turning his back on Hideyoshi’s adventurousness. Of course, it is false to assume that the Japanese were totally insulated from the outside world. Not only did they connect with the West through the Dutch, but the Japanese maintained a more intense relationship with Korea. Even in the 17th and 18th century, a movement of “Western Learning” persisted through the interaction with the Dutch (though arguably late Confucian influences may have been more significant).

The violent suppression of Christianity in the 17th century and the emergence of a static caste system strikes modern sensibilities as brutal, barbaric and regressive. But the Edo period’s reduction in distribution and production of lethal firearms shows the upside of a conservative and controlling social land political elite. Violence continued, but it was relatively controlled and channeled.

We think of the future as endlessly protean and dynamic. But science fiction offers up an alternative possibility far more like Edo period Japan: technologically stagnant, culturally conservative. Frank Herbert’s Dune was set in the context of a universe where there had been a religious jihad against artificial intelligence. Meanwhile, Isaac Asimov’s Foundation series was originally based on imperial Rome, but later incarnations admitted that the better model was imperial China. Just as in the Dune series, the Foundation universe had to grapple with humanity’s protean and chaotic violence, which threatened to take down our civilization periodically due to enthusiasms.

The Edo period stretches from the early 17th century down to the middle of the 19th. All in all this is not a bad run. Our own republic’s 250 year anniversary will be on us in 2026.

Migration at the roof of West Asia

Click to see the full figure

The figure to the left is from The genetic prehistory of the Greater Caucasus. If you are a regular reader of this weblog, or Eurogenes, you can figure out what’s going on, and keep track of the terminology. But in 2018 I think we’re getting to the end of the line in making sense of “admixture graphs” in relation to West Eurasian population structure. The models are just getting too complicated to keep everything straight, and the distinct-populations-subject-to-pulse-admixture seems to be an assumption that may not necessarily hold.

To get a sense of what I’m talking about, the above preprint focuses on populations in and around the Caucasus region. One of the major reasons that this is important is that the Caucasus was and is to some extent a continental hinge, connecting Eastern Europe and the Pontic steppe, to the Near East. The Arab Muslims pushed north of the Caucasus, and came into conflict with the Khazars, while Cimmerians and Scythians moved south from the Pontic steppe.

The elephant in the room is the relevance to the “Indo-European controversy.” Colin Renfrew long ago posited that the Indo-European languages derive from West Asian farmers who expanded into Europe as early as ~9,000 years ago. A rival theory is that Indo-Europeans spread out of the Pontic steppe ~4,000 years ago. In 2015 two major papers suggested that the steppe was a major source of Indo-European expansion. Case closed? This preprint suggests perhaps not.

But we’ll get to that later. What do the results here show? The prose is a little hard to tease apart, but the major issues seem to be that in antiquity, or at least the period they’re focusing on, much of the gene flow seems to have been south (Near East) to the north (through the Caucasus, and out to the north slope). To some extent, we already knew this: the Yamna people of the Pontic steppe have “southern” ancestry from the Near East that earlier East European/Pontic people do not. In this preprint, the authors show that groups such as the Maykop of the north slope of the Caucasus carry Y haplogroups such as G2, and not the R1 lineages commonly found in the steppe. David W. suggests that this confirms that Near Eastern gene flow into the steppe was female-mediated.  This is plausible, but I would caution that Y chromosomes alone can be deceptive, due to the power of particular patrilineages. We’ll probably rely on the X chromosome to make a final judgment.

The plot below shows many of the relationships as a function of location and time. The green component is modal among “Iranian farmers,” the orange among “Anatolian farmers,” and the blue among “Western hunter-gatherers.”

A major aspect of this preprint is that it has to work hard to differentiate two Anatolian farmer-like signals: the first, from Anatolian farmers proper, and the second from the descendants of European farmers, who themselves are a mix of Anatolian farmers with a minority ancestry among the hunter-gatherers. The answers would probably be totally unintelligible if not for archaeology. It’s clear that the steppe people had contact with both European and Near Eastern farmers and that later East European groups that succeeded the Yamna were subject to reflux from Central Europe, and received European farmer ancestry.

Another curious nugget in their results is that there was early detection of both Ancestral North Eurasian (ANE) ancestry and, some East Eurasian gene flow (related to Han Chinese). One of their individuals carries the East Eurasian variant of EDAR, which today is only found in Finns, though it was found in reasonable frequencies among the Motala hunter-gatherers of Scandinavia. Additionally, Fu et al. 2016 found that the ancestors of Mesolithic hunter-gatherers received some gene flow from Eastern Eurasians as well (also in the supplements of Lazaridis et al. 2016).

The authors admit that there is probably population structure among ANE and undiscovered groups of East Eurasians who were traversing the Inner Asian landscape. I think this is all suggestive of some long-distance contacts, though the intensity and magnitude increased a lot with high-density societies and the mobility of pastoralism.

Much of the genetic mixing in the Near East, and to some extent in the trans-Caucasian region, seems to date to the 4th millennium. This is technically prehistory, but it is also the Uruk period. This was a phase of Mesopotamian culture expansion between 4000 and 3100 BC which resulted in replicas of Uruk style settlements as far away as Syria and southeastern Anatolia. There is even evidence of Uruk-related migration to the North Caucasus.

The Uruk experienced abrupt and sudden collapse. Uruk settlements outside of the core zone of Mesopatamia disappear.

It’s the final paragraph that warrants discussion:

The insight that the Caucasus mountains served not only as a corridor for the spread of CHG/Neolithic Iranian ancestry but also for later gene-flow from the south also has a bearing on the postulated homelands of Proto-Indo-European (PIE) languages and documented gene-flows that could have carried a consecutive spread of both across West Eurasia…Perceiving the Caucasus as an occasional bridge rather than a strict border during the Eneolithic and Bronze Age opens up the possibility of a homeland of PIE south of the Caucasus, which itself provides a parsimonious explanation for an early branching off of Anatolian languages. Geographically this would also work for Armenian and Greek, for which genetic data also supports an eastern influence from Anatolia or the southern Caucasus. A potential offshoot of the Indo-Iranian branch to the east is possible, but the latest ancient DNA results from South Asia also lend weight to an LMBA spread via the steppe belt…The spread of some or all of the proto-Indo-European branches would have been possible via the North Caucasus and Pontic region and from there, along with pastoralist expansions, to the heart of Europe. This scenario finds support from the well attested and now widely documented ‘steppe ancestry’ in European populations, the postulate of increasingly patrilinear societies in the wake of these expansions (exemplified by R1a/R1b), as attested in the latest study on the Bell Beaker phenomenon….

But instead of tackling this let’s focus on the paper that came out of the Willerslev group, The first horse herders and the impact of early Bronze Age steppe expansions into Asia. This is a final manuscript in Science. That means it was probably written before The Genomic Formation of South and Central Asia. When it comes to South Asia, the results from the two publications are consanant. There is no conflict.*

More interesting are the results in West Asia, and the linguistic supplement. In the authors note that tablets now indicate an Indo-Aryan presence in Syria ~1750 BC. Second, Assyrian merchants record Indo-European Hittite, or Nesili (the people of Nesa), as early as ~2500 BC.

As suggested in earlier work Hittite remains don’t suggest steppe influence. David W. says:

The apparent lack of steppe ancestry in five Hittite-era, perhaps Indo-European-speaking, Anatolians was interpreted in Damagaard et al. 2018 as a major discovery with profound implications for the origin of the Anatolian branch of Indo-European languages.

But I disagree with this assessment, simply because none of these Hittite-era individuals are from royal Hittite, or Nes, burials. Hence, there’s a very good chance that they were Hattians, who were not of Indo-European origin, even if they spoke the Indo-European Hittite language because it was imposed on them.

The main aspect I’d bring up with this is that in other areas steppe ancestry has spread deeply and widely into the population, including non-Indo-European ones. It is certainly possible that the sample is not needed enough to pick up the genuinely Hittite elite, but I probably lean to the likelihood that the steppe signal won’t be found. It seems that the Anatolian languages were already diversified by ~2000 BC, and perhaps earlier. Linguists have long suggested that they are the outgroup to other Indo-European languages, though this could just be a function of their isolation among highly settled and socially complex populations.

Two alternative models present themselves for these results. The Anatolian Indo-European languages expanded through elite diffusion,  part of the same general migrations that emerged out of the Yamna culture ~3000 BC. The lack of a steppe signal may be due to sampling bias, as David W. suggested, or, more likely in my opinion, simple dilution of the signal. Second, the steppe migrations were one part of a broader palette of population movements and cultural diffusions, and the Anatolian Indo-Europeans are basal to the efflorescence of the steppe derived branches.

The evidence of the explosion of Indo-Aryans in the years after 2000 BC in West and South Asia, as well as the expansion of Iranians across vast swaths of Inner Asia during the same period, suggest to me that Indo-Iranians are most definitely part of the steppe pulse. The connection to the Sintashta charioteers presents itself, and, connections to the Uralic languages indicates incubation in the trans-Volga region.

In West Asia, the Indo-Aryans crashed themselves against the most advanced civilizations of their time. Like the Bulgars, and unlike the Hittites, Indo-Aryan Mitanni was totally absorbed by their non-Indo-European Hurrian substrate. Indo-Aryan linguistic influence was preserved in their names, their gods, and in particular words relating to chariots. And yet in 2017’s Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences, the authors observe:

We next tested a model of the present-day Lebanese as a mixture of Sidon_BA and any other ancient Eurasian population using qpAdm. We found that the Lebanese can be best modeled as Sidon_BA 93% ± 1.6% and a Steppe Bronze Age population 7% ± 1.6% (Figure 3C; Table S6). To estimate the time when the Steppe ancestry penetrated the Levant, we used, as above, LD-based inference and set the Lebanese as admixed test population with Natufians, Levant_N, Sidon_BA, Steppe_EMBA, and Steppe_MLBA as reference populations. We found support (p = 0.00017) for a mixture between Sidon_BA and Steppe_EMBA which has occurred around 2,950 ± 790 ya (Figure S13B).

This needs to be more explored. The admixture could have come from many sources. I am curious about the frequency of R1a1a-z93 among modern-day Syrians and Lebanese.

For me these arguments can only be resolved with a deeper understanding of linguistic evolution. The close relationship of Indo-Aryan and Iranian languages is obvious to any speaker of either of these languages (I can speak some Bengali). A divergence in the range of 4 to 5 thousand years before the present seems most likely to me. But the relationship of the other Indo-European languages is much less clear.

One of the arguments in Peter Bellwood’s First Farmers is that the Indo-European languages exhibit a “rake-like” topology with the exception of Indo-Iranian, which forms a clear clade. To him and others in his camp, this argues for deep divergences very early in time.

It is hard to deny that the steppe migrations between 4 and 5 thousand years ago had something to do with the distribution of modern Indo-European languages. But, it is harder to falsify the model that there were earlier Indo-European migrations, perhaps out of the Near East, that preceded these. Only a deeper understanding of linguistic evolution, and multidisciplinary analysis of regional substrates will generate the clarity we need.

* I’m going to skip the Botai angle in this post.

Abraham on the shoulders of Zoroaster (and others)

Yesterday on Twitter I made a quip about “linear Western models of time.” A friend pointed out that that was actually “Judeo-Christian.” I was going to agree…but then I realized something: I vaguely recalled that eschatology and millenarianism were things that some have hypothesized came into Judaism from Zoroastrianism.

The historical context is straightforward. The Babylonians took the Jews to Mesopotamia, where they were strongly influenced by the local cultures. Mesopotamia for most of the period before the Islamic conquest was dominated by Iranian polities, the Achaemenids, Parthians, and Sassanids. Though the non-Iranian populace of Mesopotamia never took to Zoroastrianism, which was considered somewhat the ethnic religion of Iranian peoples,* it has hard to imagine they were not influenced by the religion.

Early Islamic chronicles describe a religious culture in Mesopotamia in the early centuries after Muhammad that would be both familiar and alien. The familiar aspect would be the dominance of various forms of Christianity and Judaism among the Semitic speaking population. The form of Judaism which came to be dominant by the medieval period was strongly influenced by Jewish thinkers in late antique Mesopotamia, who operated with a certain freedom that Jews under Christian rule did not have. Though Christians in Mesopotamia tended to be Oriental Orthodox, whether it be what we would today term Jacobite or the Church of the East, they were Christian.

But the exotic aspect is that many other religious groups, inflected with Zoroastrian and pagan beliefs, were also present. The pagans of Harran persisted down to the Islamic period because of the protection that they had received from the Persian emperors during the Byzantine period. Though groups like Mandeans and Yazidis seems exotic to us today, they were probably part of the bubbling matrix of beliefs which produced novel religious movements rather regularly (ghulat Shia sects like the Alawites probably have laundered some of these old beliefs into modern outwardly Muslim groups).

Manicheanism, for example, seems to have emerged at this intersection of religions. The prophet himself was from a heterodox (from our perspective) Christian background, but his new religion integrated aspects of Christianity, Zoroastrianism, and Buddhism, as well as agnosticism which seems to have channeled Neoplatonic conceptions of the corruption of this world.

The important point here is that this was not a unique confluence of events. Centuries before the Roman Empire, exiled Judaeans were in contact with Zoroastrians in Mesopotamia. The dislocation probably helped force their shift away from belief in a geographically delimited tribal god, local to Palestine, toward a more mature monotheism. But they were also introduced to new ideas which seem to be derived from Zoroastrianism: angels, the prominent role of Satan as God’s foil, an elaborated heaven, and eschatology, seem to be derived from the milieu of Zoroastrian influenced culture.

But were they? One of the major themes, perhaps the most interesting one, in The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies, are the common Mesopotamian motifs which seem to pervade the West Eurasian oikoumene, from Europe to South Asia.

Perhaps the Zoroastrian influence on the Abrahamic religions is less about the creative genius of the Iranian peoples as they impinged upon the older civilizations of West Asia, as it is about their absorption and synthesis of far older motifs?

Again, this sort of synthesis, cooption, and appropriation should be unsurprising. The more and more I’ve dug into the early history of Islam, the more I’ve come to the conclusion that subjugated Iran & Turan held captive the uncouth Arab and brought the arts to the rustic desert nomads! Actually, that appropriation of a classicist jibe misleads as to my view of the early Arab conquerors of Persia. I suspect they were primarily civilized peoples on the margins of the Persian and Roman world, not raw Bedouins. But, many of the aspects of Islam that we think of as constitutive to the religion probably only dates to the Abbasid period and later, when Iranians of Zoroastrian, Christian, and Buddhist background dominated the culture (e.g, the emphasis messianism in Shia Islam probably is accentuated by Zoroastrian influences, while Sunni Islam’s focus on learning of the ulema in a formal sense may be modeled on Central Asian Buddhist monastic forms).

Ultimately the reason I’ve brought this up is that many things that we in the modern world find beautiful or good are said to be contingent on the nature of Christianity, and Christianity is contingent on Jewish thought. Quite often this is false. I used to watch Bible documentaries where David Wolpe was a frequent guest. Wolpe was wont to say that the genius of the Jews was the invention of ethical monotheism. If I had to bet I think this is just wrong. My own suspicion is that on the probability the Jewish shift toward ethical monotheism in their conception of their tribal religion was given a strong push sufficiently, if not necessarily, by the widespread currency of proto-Zoroastrian ideas in Persian Babylon (and later Ctesiphon).

The idea of linear time is often connected liberal individualism and the possibility of progress. The caricature is that the “Judeo-Christian tradition invented progress,” ergo, liberalism, science, etc. This sort of reductive causal model has always struck me as implausible, in part because most of the people (thought not all!) who make this assertion know very little outside of our their own tradition, so they are easily impressed by its uniqueness due to its singular hold on their imagination.

I’m not presupposing here that Zoroastrianism was a necessary condition for the emergence of many traits unique to Judaism. It seems likely that something like ethical monotheism was going to be “invented” somewhere (note that millenarianism seems to have developed in China independently before the first “Western” influences, such as Buddhism and Manichaeanism).

This speaks to the thesis of whether history is driven by unique ideas, or structural forces. They aren’t exclusive, nor are they unrelated. Peter Turchin and others have suggested that ethical metaphysical/religious systems were nearly inevitable with the maturing of large multi-ethnic imperial polities. I believe that evolutionary psychology allows us to understand why those ethical systems were broadly similar in the generalities. The human quest for cosmic justice is just an elaboration of our intuitions about fair-play in a Paleolithic tribal band.

* Zoroastrianism was more successful in the Caucasus, probably because Caucasian elites were integrated into the military elite of the Iranian states.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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