At an inflection point of archaeology and genetics

People always ask me what to read in relation to the field of historical population genetics. In the 2000s there were a series of books which focused on the mtDNA and Y results from modern phylogeographic analysis. Journey of Man, Seven Daughters of Eve, The Real Eve, and Mapping Human History. But there hasn’t been much equivalent in the 2010s.

Why? I think part of the issue is that the rate of change has been so fast that scholars and journalists haven’t been able to keep up. And, the change is happening right now, so it would likely mean that any book written over a year would be moderately out of date by publication.

I noticed today that Jean Manco has an updated and revised version of her book, Ancestral Journeys: The Peopling of Europe from the First Venturers to the Vikings. This was needed, because the original book was written before some major recent findings, though after some preliminary ones. As Manco has observed herself it was feasible to replace speculations with facts.

Since it seems likely that George R. R. Martin’s next book will be published before David Reich’s, I think that’s all you got. Any suggestions would be welcome.

As for the flip side for history that might be useful to understanding the genetics results, J. M. Roberts The History of the World is the best cliff notes I can think of. It’s obviously a high level survey, but frankly that would improve the interpretation I see in some papers. The fact that much of the history has no contemporary relevance is pretty unimportant, since you want to focus on the older stuff, which is where ancient DNA really shows its metal.

At some point ancient DNA will start to exhibit diminishing returns. Then the long hard slog of interpretation and synthesis will have to begin in earnest.

Female Genital Mutilation IS a Muslim Issue. And, it’s a Medical Issue. And, it’s an African Issue. And, it’s a Human Rights Issue.


Slate has put up an extremely misleading article up, Female Genital Mutilation Isn’t a Muslim Issue. It’s a Medical Issue.

Articles such as the one above are why people end up eventually not believing the media at all. First, a few minutes of Googling will show that female genital mutilation (FGM) or female circumcision is not simply an issue related to African culture, and does have some relationship to Islam. From the article:

…The ancient, barbaric practice originated in pre-Islamic Africa and has endured irrespective of the prevalent religion of the area. Today, it is primarily a cultural problem in central Africa, with Muslim-majority countries such as Egypt and Somalia on the list alongside Christian-majority ones such as Ethiopia and Eritrea. Though much lower in comparison to many African nations, the practice is also seen in Iraq and Yemen.

I do have to wonder if this is one case where liberal progressive concern for not seeming to be racist against Africans by imputing upon them barbaric cultural practices is trumped by their concern not to disparage Islam by its promotion of barbaric religious practices. As Oliver Scott Curry has shown, a simple scatter plot illuminates the correlation between Islam and FGM, even though the practice is found among plenty of non-Muslim Africans.

Additionally, the chart has a lacunae. Do you know the country with the largest number of women in the world who are the victims of FGM? Indonesia! (obviously, not an African country, just the world’s largest Muslim country, famed for its moderate practice of Islam) Why Indonesia?

In about fifteen seconds of Googling you’ll get to an article on Wikipedia which states that of the Sunni schools of Islamic jurisprudence the Shafi considers female circumcision obligatory. The Hanbali school considers the practice strongly encouraged, while the Hanafi and Maliki schools consider it preferred.

If you look at a map of where the Sunni schools are dominant you see that much of East Africa and all of Southeast Asia are Shafi. Take a look at the correlation between the Shafi school and FGM on the map above (it may not be totally accurate, so take it with a grain of salt; the map suggests FGM doesn’t happen in Malaysia, but this VICE article says there are surveys that 93 percent of Muslim women have been subject to some form of circumcision).

The writer of the Slate piece is an American Muslim doctor, not a religious scholar. His family is from Pakistan. Therefore, unless they were Dawoodi Bohra he would have no real knowledge of FGM. Though it is preferred in the historical Hanafi tradition dominant among South Asian Muslims, it rare to nonexistent among them today (and may always have been so, as the Hanafi tradition originally was popular among culturally very different Persians and Turks). I know this from personal experience, as I come from a family with many members who are professional ulema, and this was never a practice that they mentioned or alluded to (in contrast to male circumcision).

When I first began to hear about female circumcision (now usually referred to as FGM) in the media I accepted the line that it was a cultural practice, usually with African associations. I accepted that line because I didn’t know any better, and trusted the media to not lie, and my own Islamic background didn’t suggest that this was a necessary practice of the religion. But some discussions with people and using something called the internet quickly made it clear that I did not understand what it was to be Muslim in Indonesia, much of Africa, or among Iraqi Kurds.

A certain type of anti-Islamic and anti-Muslim thinker infers from the Quran all that is Islam. This is simply not a valid way to go about understanding the history of Muslims and their modern cultures. And yet you have the Muslim writer in Slate asserting “Further, there is no religious sanction for the procedure found in the Quran.” (actually, there is no sanction for the almost universal practice of male circumcision among Muslims in the Quran either)

This reference misunderstands how Islam and most Muslims have related to their religion historically. The Quran is not equivalent to the Christian Bible. Rather, it is more like the Hebrew Bible to Rabbinical Jews. It is a starting point, but not the ending point. Religious practice is more often dependent upon Hadith, Sunnah, and later commentaries by learned jurists, as well as interpretations by living jurists.

From the viewpoint of many Muslim Americans this is a ridiculous way to look at the religion. As an atheist I would assert descriptively that their view of Islam has mapped itself upon a phenomenology of religion which derives directly from American confessional Protestantism, but that’s a digression. For the vast majority of the world’s Muslim, observant or not, devout or not, the religion as transmitted and interpreted by the ulema through these extensive post-Quranic materials and subsequent commentaries is what serves as the intellectual superstructure for belief and practice. The wisdom of the ummah and ulema.

Does this mean that FGM is “uniquely Islamic”? Obviously it is not. As an atheist I don’t think there’s any real essence to a religion in any case. A religion is what people say a religion is. For whatever reason Shafi ulema have asserted that their interpretation of the Islamic religion is such that FGM is obligatory. The fact that over 90% of Muslim women in the 90% Muslim nation of Indonesia have been subject to FGM, and that it is a Shafi nation, is not a coincidence. Nor is it a cultural holdover form the pre-Islamic period. That Iraq Kurdish Muslims, who are Sunni and Shafi, and are the locus of FGM in that nation, is not a coincidence.

Despite the often historically positive comments in relation to FGM in other Sunni traditions, the prevalence of the practice is low to nonexistent in nations dominated by the other traditions. That does show that there is no determinative relationship, and traditions can be reinterpreted.

Additionally, among many Christian groups, and among non-Shafi Muslims, FGM is prevalent in Africa. Looking at the history of the Shafi school much of its jurisprudence was elaborated under the Mamluk Sultans of Cairo. FGM has a long history in Egypt, so without further research I have the suspicion that the strong emphasis on the practice within this school is a function of its history in this region of East Africa.

Overall, I think it is wrong to assert that FGM is necessarily or uniquely about Islam. But, it clearly may be sufficiently about Islam, and denying that many hundreds of millions of the worlds Muslims accept as authoritative religious rulings which enjoin the practice upon them as meritorious is simply promoting falsehood.

The claims made in the Slate piece come from a Kevin Drum piece which show that clearly Islam is not uniquely associated with FGM in Africa. That’s fine as far as it goes, but I think this post has shown that there is some association between Islam and FGM. I don’t expect a Muslim American doctor to actually know about the historical details of why different schools of Islam law have different opinions…because Islamic law is pretty unimportant and trivial in America to most Muslims, who follow a few major orthopraxic norms (e.g., don’t drink, don’t eat pork, etc.). I do wish though that the editors at Slate had looked a bit more closely at this piece in a critical-rational manner.

But I don’t expect the media at this point to be critically rational about these sorts of things. The conclusion was one which the editors were probably happy with, so they didn’t look too closely.  That’s fine. But some of their readers will spend more than five minutes on the factual questions.

Addendum: Unlike in Judaism, circumcision in Islam is not necessarily obligatory (among the Hanafi and Maliki it is simply high preferred). As I note above it is not mentioned in the Quran. There probably wasn’t a need because all the peoples of Arabia were circumcised when the Quran was compiled.

Addendum II: Unlike the editors of Slate, and probably the Muslim American author above (who I assume spends more time fruitfully catching up on oncology journals rather than treatises on Islamic law), I knew off the top of my head the distribution of schools of Islamic law geographically, as well as the soft spot the Shafi had for FGM. So Indonesia did not surprise me at all.

But what do I know? I’m just a humble geneticist, not someone who went to j-school to learn how to report!

The civilization before history

A forgotten civilization?

No, I am not talking about Atlantis or Hyperborea or Lemuria. Nothing made up here. Nor am I talking about the real Neolithic cultures highlighted in War Before Civilization. I alluding to the period between 3500 and 3100 BCE in the Near East when the city of Uruk was the nexus for and a source of a massive cultural and mercantile expansion. I’ll quote Wikipedia:

Around 3600 BC, during the Middle Uruk period, Uruk trade networks started to expand to other parts of Mesopotamia, and as far as North Caucasus. According to archaeologist Konstantine Pitskhelauri, this expansion started even earlier, at the end of the 5th millennium BC, and continued in the 4th millennium.

Large masses of Uruk migrants settled in the South, and later in the North Caucasus. The sites in this general area include Habuba Kabira in Syria, and Arslantepe in Turkey. Uruk expansion to the northeast included sites like Godin Tepe in Iran. Tepe Gawra, in northwest Iraq, is another important site with deep stratigraphy that includes the Uruk period in later layers. Hamoukar is a large site in northeastern Syria that has been recently excavated; it includes Uruk and pre-Uruk layers.

Uruk enclaves have also been identified at Tell Brak and Nineveh in northern Mesopotamia, and on the Syrian Euphrates at Qrayya, and Jebel Aruda. On the Euphrates in Anatolia, Uruk enclaves were found at Hassek Hoyuk, Samsat, and Tepecik (Elazığ Province, near Keban Dam).

Sargon of Akkad is usually asserted to have been the first empire-builder in history, in that his rulership extended across many ethnicities, from the Mediterranean to the Persian Gulf. The Four Corners of the World he claimed. But the Sargonid system lasted for but a century, and successor Mesopotamian hegemonies did not extend beyond the land of two rivers until the rise of the Neo-Assyrian Empire over 1,000 years later.

In contrast, the Uruk culture persisted for hundreds of years, far longer than successor polities in that area in the 3rd millennium. It was also more expansive than even than Sargon’s empire.

There has long been a debate about the nature of the Uruk expansion. What is ideology? Was it trade? Was it migration? Was it conquest?

Empire of power, empire of ideas

Since we do not have writing to tell us a narrative we can never know definitively, at least until ancient DNA clears up the demographic questions. In Babylon: Mesopotamia and the Birth of Civilization the author points out that Communism spread across many societies without invasion (though in some cases there was external invasion; ask the Germans). Similarly, many religions have also spread without external invasion. Christianity’s spread to Armenia, Ethiopia, Georgia, and Ireland, occurred relatively gradually and synthesized without indigenous cultural forms due to broad-based diffusion as well as elite adoption so as to integrate into the Christian world system. But there is something very distinct about the Uruk expansion in contrast to the above examples: some of the cities seem to be replica copies of Uruk in toto.

If it was an ideological movement of emulation by local elites only there should have been at least some synthesis even these narrow regions of Uruk-outside-of-Sumeria. In fact there seem to have been small pieces of Uruk society scattered across the Fertile Crescent (and beyond!) during this period, embedded in wholly culturally alien territory. Additionally, there is some circumstantial evidence for fighting and conquest.

Now that we know there were massive migrations during the Neolithic and Bronze ages across the Near East and Europe, I think we should update our estimations of the alternative hypotheses. In light of radically decreasing genetic distance between the eastern and western portions of the Fertile Crescent since the rise of agriculture it seems implausible to think that the Uruk expansion might not have at least been partly mediated by the movement of people. People moved. So did ideas.

That being said, as observed in Babylon: Mesopotamia and the Birth of Civilization, the recession of the Uruk hegemony after ~3100 BCE was extreme in its totality and rapidity. Heretofore longstanding zones of Uruk civilization outside of southern Mesopotamia disappear immedlately. Peasant ways of life which had flourished in the local regions during earlier periods reappear as the city-states disappear. Not only does the way of life defined by the Uruk period retreat, but the sole overarching preeminence of Uruk in what became Sumeria disappears, to be replaced by a millennium of jostling between rival city-states, Uruk (Erech in the Bible), Ur, Kish, and Lagash.

Later analogs to the Uruk collapse

Does this remind you of something? The Late Bronze Age was characterized by a collapse of civilization as well, with a regress to old centers such as Babylonia, Assyria, and Egypt. Smaller polities on the Levantine coast emerged in the wake of the decline of the earlier empires, while Greece and Anatolia went into “Dark Ages,” as the Mycenaean citadel society descended into barbarism and the Hittite domains totally collapsed.

The city-states of Classical Greece were fundamentally different from the Mycenaean citadel-culture that had preceded them centuries earlier. The Greek civilization of the Bronze Age had adopted many of the forms of the Minoan society based in Crete and extending around the Aegean. Aesthetically, and in terms of their writing system. Mycenaean civilization was fundamentally one of rough hewn barbarians grafted onto a beautiful well developed canopy of Minoan motifs. And the Minoans themselves were clearly influenced by the broader constellation of Near Eastern civilizations, from the Hittites to the kingdom of Cyprus and down to Egypt.

Classical Greece was very different, mostly doing away with the autocratic kingships of the Bronze Age, as well as adopting a different form of writing from the Phoenicians. Linear B was impenetrable to them. All the scribes had died without passing their knowledge.

Though Homer and the broader corpus of Greek mythology clearly preserves elements of the Bronze Age society (translation of Mycenaean Linear B tablets makes it clear that many of the Classical gods had roots in the the pantheon of the Bronze Age), the Classical Greeks had forgotten their Mycenaean past (before Linear B was translated it was assumed by most that it was not Greek, but rather a mainland extension of Minoan civilization). The cyclopean masonry typical of Mycenaean citadels were believed by Greeks of the later period to have been constructed by…cyclops.  This method had been forgotten in the several hundred year Greek Dark Age. The battles depicted in the Iliad are clearly those between petty Dark Age warlords, not the kings of old (though the prominence of Mycenaean cities such as Pylos and Mycenae were recalled).

The point here is that Mycenaean Greek civilization, which was created to a great extent by imitating a non-Greek prototype, collapsed, after which there was total regression to peasant barbarism. The Greek civilization that emerged later was much more distinctive, and less imitative, than the initial incarnation.

The Sumerian Dark Age and its aftermath

Unlike the case with the Mycenaeans, I believe that Uruk expansion to the west, north, and east, was mediated by migration and conquest from the source. Mycenaean civilization was modeled upon, and strongly inflected by, Minoan civilization, which was modeled upon Near Eastern polities. But they were never total replicas of each other. Though there were certainly mercantile connections and colonies of Near Easterners in the Aegean, it seems likely that these later cases of influence were genuine instances of cultural diffusion. We have writing to back-up our presuppositions.

In contrast, the nature of the Uruk expansion indicates transplantation in totality and exact replication of the original society. To me this reminds me of Roman colonies. Unlike cultural diffusion, the colonies of Latin speaking Roman citizens in regions of southern Gaul, Iberia, and North Africa, served as entry-points for Romanitas. But this Romanization could be reversed. This was certainly the case in southern Britain, which had a fully developed Latin Roman urban society, but collapsed back to barbarism with the retreat of the legions. Arguably it was also the case in the hinterlands of the Balkans, with modern Vlachs and Romanians being the descendants of the Latin peasants.

It is not difficult then to assume that if there was some exogenous shock to the Uruk system ~3100 BCE, the isolated colonies would quickly whither. Just as the urban centers of southern Britain were replaced by fortresses of semi-barbaric British elites, so the subjugated hinterland cultures, which had persisted, quickly filled the vacuum left by the collapse of the Uruk polity. Eventually, just as Classical Greece developed its own distinct indigenous civilization in the broader commonwealth of eastern Mediterranean polities, so Ugarit, Ebla, Mari, the city-states of Hatti, and Urartu, came into the light of history in the 3rd millennium organically.

Forgotten Antediluvian Sumeria

In Babylon the author suggests that the flood legend allows them to partition their own literate civilization, which developed after 2900 BCE, from the fallow two century period after the collapse of the Uruk ascendancy. Could the the Sumerians have forgotten the greatness of the 4th millennium in a few centuries? I believe that they might have.
The Uruk ascendancy of the 4th millennium, if it took political form, would have have exhibited none of the totality and dominion of a modern nation-state. Rather, like the Maurya Empire, and many antique polities, it would have been defined by numerous strongpoints extending out from a dense and well networked core. In the outer zones of control the dominion would have consisted primarily of close supervision of the interstices between territories occupied by indigenous tribal chiefdoms, who may have given nominal fealty to the local governor appointed from Uruk. A collapse would have consisted proximately of the destruction or abandonment of the strongpoints, and ultimately the forgetting of the period of alien hegemony by the local populations.

At that time core Sumeria was an oral society, and in the centuries after the Uruk expansion there were major changes to many aspects of its physical superstructure, and therefore one presumes the ideologies underpinning the control of the population by the elite. Without written records the quasi-imperial past might have become muddied very quickly if there was a transition of elites. The peasants would have had no great incentive to remember the Uruk hegemony, while the nouveau elites may have wanted to created their own legends, rather than be haunted by the earlier greatness.

The many civilizations before writing

My forebears?

The Uruk ascendancy should not be a surprising idea when we think about it in the context of world “history.” The civilization of the Indus valley was certainly a civilization, but its script remains undeciphered. Though they were likely symbolic in some manner, it is quite possible that they were not a fully fleshed representation of language in the way cuneiform was. Most of the examples of the script are exceedingly short.

But we know something about the Indus people in part because we know that they traded with Sumeria, and there were people from this culture who were resident in Sumerian towns. Clearly Sumer viewed these people as peers, albeit aliens.

Another example would be the Inca. Before the Spanish overthrew their empire, it stretched from Columbia to central Chile. Because we have Spanish records, and memories of the Inca nobility who were assimilated into the post-conquest order, we know that this was not simply an ideological expansion. It was a military one. And one of demographic transplantation and imposition. Though there still debates, it seems most likely that the Inca did not have true literacy.

The ultimate point is that ancient people were far more organized and cohesive across large territories than we likely give them credit for. Let me finish with this article from last year in Science, Slaughter at the bridge: Uncovering a colossal Bronze Age battle:

About 3200 years ago, two armies clashed at a river crossing near the Baltic Sea. The confrontation can’t be found in any history books—the written word didn’t become common in these parts for another 2000 years—but this was no skirmish between local clans. Thousands of warriors came together in a brutal struggle, perhaps fought on a single day, using weapons crafted from wood, flint, and bronze, a metal that was then the height of military technology.

And yet chemical tracers in the remains suggest that most of the Tollense warriors came from hundreds of kilometers away. The isotopes in your teeth reflect those in the food and water you ingest during childhood, which in turn mirror the surrounding geology—a marker of where you grew up…Just a few showed values typical of the northern European plain, which sprawls from Holland to Poland….

Further clues come from isotopes of another element, nitrogen, which reflect diet. Nitrogen isotopes in teeth from some of the men suggest they ate a diet heavy in millet, a crop more common at the time in southern than northern Europe.

Ancient DNA could potentially reveal much more: When compared to other Bronze Age samples from around Europe at this time, it could point to the homelands of the warriors as well as such traits as eye and hair color. Genetic analysis is just beginning, but so far it supports the notion of far-flung origins. DNA from teeth suggests some warriors are related to modern southern Europeans and others to people living in modern-day Poland and Scandinavia. “This is not a bunch of local idiots,” says University of Mainz geneticist Joachim Burger. “It’s a highly diverse population.”

As University of Aarhus’s Vandkilde puts it: “It’s an army like the one described in Homeric epics, made up of smaller war bands that gathered to sack Troy”—an event thought to have happened fewer than 100 years later, in 1184 B.C.E. That suggests an unexpectedly widespread social organization, Jantzen says. “To organize a battle like this over tremendous distances and gather all these people in one place was a tremendous accomplishment,” he says.

Standardized metal weaponry and the remains of the horses, which were found intermingled with the human bones at one spot, suggest that at least some of the combatants were well-equipped and well-trained. “They weren’t farmer-soldiers who went out every few years to brawl,” Terberger says. “These are professional fighters.”

Curiouser and curiouser….

Why the rate of evolution may only depend on mutation

Sometimes people think evolution is about dinosaurs.

It is true that natural history plays an important role in inspiring and directing our understanding of evolutionary process. Charles Darwin was a natural historian, and evolutionary biologists often have strong affinities with the natural world and its history. Though many people exhibit a fascination with the flora and fauna around us during childhood, often the greatest biologists retain this wonderment well into adulthood (if you read W. D. Hamilton’s collections of papers, Narrow Roads of Gene Land, which have autobiographical sketches, this is very evidently true of him).

But another aspect of evolutionary biology, which began in the early 20th century, is the emergence of formal mathematical systems of analysis. So you have fields such as phylogenetics, which have gone from intuitive and aesthetic trees of life, to inferences made using the most new-fangled Bayesian techniques. And, as told in The Origins of Theoretical Population Genetics, in the 1920s and 1930s a few mathematically oriented biologists constructed much of the formal scaffold upon which the Neo-Darwinian Synthesis was constructed.

The product of evolution

At the highest level of analysis evolutionary process can be described beautifully. Evolution is beautiful, in that its end product generates the diversity of life around us. But a formal mathematical framework is often needed to clearly and precisely model evolution, and so allow us to make predictions. R. A. Fisher’s aim when he wrote The Genetical Theory Natural Selection was to create for evolutionary biology something equivalent to the laws of thermodynamics. I don’t really think he succeeded in that, though there are plenty of debates around something like Fisher’s fundamental theorem of natural selection.

But the revolution of thought that Fisher, Sewall Wright, and J. B. S. Haldane unleashed has had real yields. As geneticists they helped us reconceptualize evolutionary process as more than simply heritable morphological change, but an analysis of the units of heritability themselves, genetic variation. That is, evolution can be imagined as the study of the forces which shape changes in allele frequencies over time. This reduces a big domain down to a much simpler one.

Genetic variation is concrete currency with which one can track evolutionary process. Initially this was done via inferred correlations between marker traits and particular genes in breeding experiments. Ergo, the origins of the “the fly room”.

But with the discovery of DNA as the physical substrate of genetic inheritance in the 1950s the scene was set for the revolution in molecular biology, which also touched evolutionary studies with the explosion of more powerful assays. Lewontin & Hubby’s 1966 paper triggered a order of magnitude increase in our understanding of molecular evolution through both theory and results.

The theoretical side occurred in the form of the development of the neutral theory of molecular evolution, which also gave birth to the nearly neutral theory. Both of these theories hold that most of the variation with and between species on polymorphisms are due to random processes. In particular, genetic drift. As a null hypothesis neutrality was very dominant for the past generation, though in recent years some researchers are suggesting that selection has been undervalued as a parameter for various reasons.

Setting the live scientific debate, which continue to this day, one of the predictions of neutral theory is that the rate of evolution will depend only on the rate of mutation. More precisely, the rate of substitution of new mutations (where the allele goes from a single copy to fixation of ~100%) is proportional to the rate of mutation of new alleles. Population size doesn’t matter.

The algebra behind this is straightforward.

First, remember that the frequency of the a new mutation within a population is \frac{1}{2N}, where N is the population size (the 2 is because we’re assuming diploid organisms with two gene copies). This is also the probability of fixation of a new mutation in a neutral scenario; it’s probability is just proportional to its initial frequency (it’s a random walk process between 0 and 1.0 proportions). The rate of mutations is defined by \mu, the number of expected mutations at a given site per generation (this is a pretty small value, for humans it’s on the order of 10^{-8}). Again, there are 2N gene copies, so you have 2N\mu to count the number of new mutations.

The probability of fixation of a new mutations multiplied by the number of new mutations is:

    \[ \( \frac{1}{2N} \) \times 2N\mu = \mu \]

So there you have it. The rate of fixation of these new mutations is just a function of the rate of mutation.

Simple formalisms like this have a lot more gnarly math that extend them and from which they derive. But they’re often pretty useful to gain a general intuition of evolutionary processes. If you are genuinely curious, I would recommend Elements of Evolutionary Genetics. It’s not quite a core dump, but it is a way you can borrow the brains of two of the best evolutionary geneticists of their generation.

Also, you will be able to answer the questions on my survey better the next time!

America’s great Saudi foreign policy sin

The future past

Periodically on my Twitter feed there is mention of the new series, The Handmaid’s Tale. The New York Times has a typical positive review. The author attempts to assert its contemporary relevance, ending with ‘the new “Handmaid’s Tale” enters the culture as its own kind of Offred-like resistance, pushing back against a reality that somehow got ahead of the show’s own imagination.’

This is not the 1980s. Or the early 2000s. The President of the United States is a nominal Christian at best. Maggie Haberman, who covers Trump for The New York States had this to say about his relationship to Mike Pence:

…When Trump and Pence were first getting to know each other, the one thing that Trump had relayed to people, according to several advisers I spoke to at the time, was that he was a little uncomfortable with how frequently Pence prayed. And Pence is fairly devout about his praying. Trump is not a serious churchgoer and in an anomaly for a presidential candidate, very rarely went to church services when he was running….

We live in an age of massive secularization, even on the conservative Right. Ergo, the rise of a post-religious Right predicated on ethnic identity, whether implicitly or explicitly. Though Donald Trump and the Republicans in Congress are going to rollback a few of the victories of the cultural Left, there is no likelihood of turning back the clock on the biggest win of the last generation for that camp, gay marriage.

Also, don’t watch the series, read the book. Books are usually better. While I’m recommending reading, while Atwood’s work gets a lot of attention (it’s already been made into a film back in 1990), I want to suggest Pamela Sargent’s The Shore of Women for those curious about a different take on broadly similar themes. Flipping the framework of The Handmaid’s Tale on its head Sargent depicts a far future gynocracy, as opposed to a near future patriarchy. Additionally, The Shore of Women  has echoes of the bizarre 1970s film Zardoz.

I’ve always felt the Sargent is an underrated writer (also see Ruler of the Sky, a novelization of the life of Genghis Khan). Her output is not high volume, but it is high quality.

But this post is not about The Handmaid’s Tale, and the specter of an anti-feminist dystopia. Rather, it will be on the reality of an anti-feminist dystopia which exists in our world, which also happens to be religiously totalitarian and oligarchic. I am talking about the great ally of the United States of America in the Middle East, the kingdom of Saudi Arabia.

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Aryan marauders from the steppe came to India, yes they did!

Its seems every post on Indian genetics elicits dissents from loquacious commenters who are woolly on the details of the science, but convinced in their opinions (yes, they operate through uncertainty and obfuscation in their rhetoric, but you know where the axe is lodged). This post is an attempt to answer some questions so I don’t have to address this in the near future, as ancient DNA papers will finally start to come out soon, I hope (at least earlier than Winds of Winter).

In 2001’s The Eurasian Heartland: A continental perspective on Y-chromosome diversity Wells et al. wrote:

The current distribution of the M17 haplotype is likely to represent traces of an ancient population migration originating in southern Russia/Ukraine, where M17 is found at high frequency (>50%). It is possible that the domestication of the horse in this region around 3,000 B.C. may have driven the migration (27). The distribution and age of M17 in Europe (17) and Central/Southern Asia is consistent with the inferred movements of these people, who left a clear pattern of archaeological remains known as the Kurgan culture, and are thought to have spoken an early Indo-European language (27, 28, 29). The decrease in frequency eastward across Siberia to the Altai-Sayan mountains (represented by the Tuvinian population) and Mongolia, and southward into India, overlaps exactly with the inferred migrations of the Indo-Iranians during the period 3,000 to 1,000 B.C. (27). It is worth noting that the Indo-European-speaking Sourashtrans, a population from Tamil Nadu in southern India, have a much higher frequency of M17 than their Dravidian-speaking neighbors, the Yadhavas and Kallars (39% vs. 13% and 4%, respectively), adding to the evidence that M17 is a diagnostic Indo-Iranian marker. The exceptionally high frequencies of this marker in the Kyrgyz, Tajik/Khojant, and Ishkashim populations are likely to be due to drift, as these populations are less diverse, and are characterized by relatively small numbers of individuals living in isolated mountain valleys.

In a 2002 interview with the India site Rediff, the first author was more explicit:

Some people say Aryans are the original inhabitants of India. What is your view on this theory?

The Aryans came from outside India. We actually have genetic evidence for that. Very clear genetic evidence from a marker that arose on the southern steppes of Russia and the Ukraine around 5,000 to 10,000 years ago. And it subsequently spread to the east and south through Central Asia reaching India. It is on the higher frequency in the Indo-European speakers, the people who claim they are descendants of the Aryans, the Hindi speakers, the Bengalis, the other groups. Then it is at a lower frequency in the Dravidians. But there is clear evidence that there was a heavy migration from the steppes down towards India.

But some people claim that the Aryans were the original inhabitants of India. What do you have to say about this?

I don’t agree with them. The Aryans came later, after the Dravidians.

Over the past few years I’ve gotten to know the above first author Spencer Wells as a personal friend, and I think he would be OK with me relaying that to some extent he was under strong pressure to downplay these conclusions. Not only were, and are, these views not popular in India, but the idea of mass migration was in bad odor in much of the academy during this period. Additionally, there was later work which was less clear, and perhaps supported an Indian origin for R1a1a. Spencer himself told me that it was not impossible for R1a to have originated in India, but a branch eventually back-migrated to southern Asia.

But even researchers from the group at Stanford where he had done his postdoc did not support this model by the middle 2000s, Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. In 2009 a paper out of an Indian group was even stronger in its conclusion for a South Asian origin of R1a1a, The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system.

By 2009 one might have admitted that perhaps Spencer was wrong. I was certainly open to that possibility. There was very persuasive evidence that the mtDNA lineages of South Asia had little to do with Europe or the Middle East.

Yet a closer look at the above papers reveals two major systematic problems.

First, ancient DNA has made it clear that there has been major population turnover during the Holocene, but this was not the null hypothesis in the 2000s. Looking at extant distributions of lineages can give one a distorted view of the past. Frankly, the 2009 Indian paper was egregious in this way because they included Turkic groups in their Central Asian data set. Even in 2009 there was a whole lot of evidence that Central Asian Turkic groups were likely very different from Indo-European Turanian populations which would have been the putative ancestors of Indo-Aryans. Honestly the authors either consciously loaded the die to reduce the evidence for gene flow from Central Asia, or they were ignorant (the nature of the samples is much clearer in the supplements than the  primary text for what it’s worth).

Second, Y chromosomal marker sets in the 2000s were constrained to fast mutating microsatellite regions or less than 100 variant SNPs on the Y. Because it is so repetitive the Y chromosome is hard to sequence, and it really took the technologies of the last ten years to get it done. Both the above papers estimate the coalescence of extant R1a1a lineages to be 10-15,000 years before the present. In particular, they suggest that European and South Asian lineages date back to this period, pushing back any possible connection between the groups, and making it possible that European R1a1a descended from a South Asian founder group which was expanding after the retreat of the ice sheets. The conclusions were not unreasonable based on the methods they had.  But now we have better methods.*

Whole genome sequencing of the Y, as well as ancient DNA, seems to falsify the above dates. Though microsatellites are good for very coarse grain phyolgenetic inferences, one has to be very careful about them when looking at more fine grain population relationships (they are still useful in forensics to cheaply differentiate between individuals, since they accumulate variation very quickly). They mutate fast, and their clock may be erratic.

Additionally, diversity estimates were based on a subset of SNP that were clearly not robust. R1a1a is not diverse anywhere, though basal lineages seem to be present in ancient DNA on the Pontic steppe in some cases.

To show how lacking in diversity R1a1a is, here are the results of a 2016 paper which performed whole genome sequencing on the Y. Instead of relying on the order of 10 to 100 SNPs, this paper discover over 65,000 Y variants worldwide. Notice how little difference there is between different South Asian groups below, indicative of a massive population expansion relatively recently in time which didn’t even have time to exhibit regional population variation. They note that “The most striking are expansions within R1a-Z93 [the South Asian clade], ~4.0–4.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the western steppes into the Indian sub-continent.

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10 Things About Ancient History You Should Really Know

For this “10 things” I am going to constraint the historical period to the period before 1000 BCE. Basically all that came before Greece and Rome (from a Western perspective).

1) The Bronze Age Near East had its own equivalent of a Westphalian system. See The Brotherhood of Kings.

2) Even in the 3rd Millennium BCE the world was quite international. There are references in Sumerian tablets to expatriate communities of merchants from Meluhha. Meluhha almost certainly referring to what we call the Indus Valley civilization.

3) The relationship between Sumerians and Akkadians prefigures the relationship between the Greeks and Romans. Mesopotamia had long had Semitic speaking groups like Akkadians, as evidenced by their prominence in lists of rulers to an early date, but in the most antique period Sumerians were dominant. Over time though Sumerians disappeared as a distinct ethnicity, and the language was preserved as one of liturgy for thousands of years after their extinction.

4) The longstanding antagonists of Sumer, the nation of Elam in southwest Iran, persisted for 1,500 years after the Sumerians left the scene. They were finally absorbed by the Medes and Persians in the 6th century BCE.

5) Because cuneiform tablets can be baked and preserved our documentary evidence from some earlier periods in Near Eastern history is much better than more epochs, simply due to preservational differences.

6) The Hittite polity, which lasted for nearly 1,000 years as the dominant rival of many other Near Eastern powers, was analogous in some ways to the Hungarian kingdom, with a very distinct ruling class. The Hittites called themselves the Nesa, and ruled over various non-Indo-European popualtions, in particular the Hatti.

7) Sumeria likely had a larger population than the same area after the Mongol sack of Baghdad (there may also be an issue with salinization of lower Mesopotamia over time).

8) The Biblical Philistines may in part have been Bronze Age Greeks (bonus: the political units of Bronze Age Greece may have been larger than during the Classical period because bronze forging requires more mobilization of resources than iron).

9) Pleistocene “megafauna” survived into the Bronze Age.

10) Indo-Europeans of an Indo-Aryan variant called the Mittani were the ruling class in much of the territory ruled by ISIS for the past few years. They even worshipped Indo-Aryan gods.

Addendum: I invite readers to give me better suggestions. I’m not an ancient historian, just an enthusiast!

Evolutionary game theory and international relations

The North Korea Paradox: Why There Are No Good Options:

Denny Roy, a political scientist who studies Asian security issues, told me last fall that North Korea “intentionally employs a posture of seemingly hyper-risk acceptance and willingness to go to war as a means of trying to intimidate its adversaries.”

This puts the world in a quandary: How could any outside threat possibly exceed the risk that North Korea already takes on itself? How could any concession remove the North Korean weakness that drives its behavior?

Basically North Korea is a weak state. Its only leverage is to hold the world hostage and act crazy. Unfortunate, but true.

But this piece reminded me a lot of stuff that John Maynard Smith described in Animal Signals. Sometimes it is the weaker and more vulnerable animals which have to engage in high risk agonistic competition, so that they can show more fit individuals that there is going to be a significant cost in initiating hostilities.

It also reminds me of high school. If you are smaller than average, it is best to make it clear to larger bullies that you won’t be passive. You may lose the fight, but by escalating rapidly you can dissuade a bully from targeting you, as opposed to someone who is more likely to be an easier victim.

Of course, bullies need to be “rational” actors here….