The past was not PG

The Week has published a screed against the low moral quality of Game of Thrones, Game of Thrones is bad — and bad for you. Obviously there is something to this insofar as one can see a coarsening of entertainment, or at least a decline in the stylized aspects of the depiction of reality.

But one of my initial reactions is that much of the narrative that we value from the past was not particularly PG. If you read The Harlot by the Side of the Road: Forbidden Tales of the Bible you see that the “Good Book”, in fact the only book many read front to back by many after the Reformation in Protestant Europe, has some quite unsavory tales. The story of Judah and Tamar in particular is hard to digest from a modern Western perspective because many of the elements are understated and workaday. Greek mythology is no better obviously. From Zeus raping Leda, Achilles throwing a fit because his sex-slave was taken away, to the tradition of Agamemnon sacrificing Iphigenia.

In some cases the shocking aspect of ancient stories is because moderns have different values. Slavery and concubinage were taken for granted during the period that the Hebrew Bible and Classical mythology crystallized into the forms which came down to us. In other cases I presume that it was unlikely that small children were going to ever read the original stories themselves, so sexual elements that might confuse were probably omitted in some oral tellings.

This is not to say that Game of Thrones is a modern masterpiece. But some of the disquieting, and frankly perverse, aspects of the narrative are only shocking if your standard is the relatively antiseptic literary fiction which one finds between the Regency and the cultural revolution of the 1960s. That is the aberration in human history, while gritty genre fiction much closer to primal human storytelling.

Open Thread, 07/09/2017

I’m a sucker for the aesthetics of Norden. Why? I wonder if part of it is that the fringe of Northern Europe is a science fictional setting. The long dark nights during the cold winter, and the twilight during midsummer. The sun may be bright, it never gets too high in the sky. The 13th Warrior wasn’t the best movie, but it was evocative. One of the problems with the film depiction of the Lord of the Rings trilogy is that New Zealand seems too bright and airy (and also not decayed enough).

Because of the SMBE meeting I haven’t made much progress on The Enigma of Reason. Much of it has been reviewing the literature in cognitive psychology and reasoning which I’m familiar with (system 1 vs. system 2, Wason reasoning task, etc.). Though it is leading me up to the main thesis.

I remember years ago Matthew Yglesias mentioned he was going to do a bit more reading of books, as opposed to news, to differentiate himself from other pundits. Today he admitted he wasn’t going to make a show of having an informed opinion about the Frankfurt School. I suggested he take time out to read The Dialectical Imagination: A History of the Frankfurt School and the Institute of Social Research, 1923-1950. The modern campus Red Guards don’t know anything about Adorno, Marcuse, or Horkheimer. But the outlines of contemporary project toward cultural revolution and exaltation of the marginalized are all there. Rather than being the origin modern radical movements, I suspect that the Frankfurt School simply provides a useful tool and framework to go about its project.

I do know that some politically moderate scientists who read The Dialectical Imagination, and saw campus politics in a totally different, and more intelligible, light.

Joe Pickrell’s new company, Gencove, Improving ancestry estimates in South Asia.

I said on Twitter that “easiest way to make housing affordable for non-rich is to build more houses for the rich so they won’t buy houses built for non-rich.” What do I mean? It’s all about supply. The well-off will always be first in line for any supply of housing. If you allow for copious development, vertically and horizontally, then the rich can purchase the luxury condos and mansions that they crave, while the middle class and lower class can buy up the more normal housing stock.

The Austin skyline, then and now.

Yazidi sex slave had to choose between son and escape from Isis.

Bangladeshi students test into elite schools. This story is about the entrance examinations for the elite public high schools of New York City. In 2010 the average Bangladeshi family in New York City had a household income of $37,000. I believe in the near future the entrance exams will not be the only criterion for gaining admission. The reality is that Asian American students lack “leadership” and are not “well rounded,” and all the Asian American applicants “look the same.”

A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes.

Racism Is Everywhere, So Why Not Move South? This article is written in the context of black Americans. But the insights are general. Houston has a cost of living that’s at the national average. It’s the fourth largest city in the United States, and there is a lot of good phở because of the large Vietnamese community.

Patrick Wyman, who sometimes comments on this blog, has a great Fall of Rome podcast.

The Sad, Sexist Past of Bengali Cuisine. Really upper caste Bengali Hindu cuisine.

Utilities fighting against rooftop solar are only hastening their own doom. Not surprised. I have been following Ramez Naam’s commentary on this for years. He’s been on this.

Islamophobes are attacking me because I’m their worst nightmare. Linda Sarsour.

I thought Hillary would win the election. But I told a long-time reader of this weblog who is a Democratic operative that BLM activists getting in Bernie Sanders’ face did not presage well for the direction of the party. Linda Sarsour as the face of progressivism is a massive boon for the Right and Republicans.

Sarsour has left a trail of obnoxious and offensive comments on Twitter. So have many people. For me personally the biggest issue is possible solidarity with Rasmea Odeh. The PFLP is the literal definition of a terrorist organization (though a Marxist, not Islamic, one). But the reality is that her enemies on the Right know that she and her compatriots in the “woke” movement would never exhibit charity toward their political opponents, so they are attempting to destroy her because they know she would do the same to them. That’s where we are in American politics today. You destroy your enemies, or they destroy you. Let’s have fun until the last battle though!

A combined analysis of genetically correlated traits identifies 107 loci associated with intelligence. I guess I’ll start paying attention to when they can explain ~25% of outgroup sample variance. They’re already further than the 7% in this preprint, though that will take a little longer to publish.

Procedures for enumerating and uniformly sampling transmission trees for a known phylogeny.

A reanalysis of Schaefer et al. does not indicate extensive CRISPR/Cas9 mediated off-target editing events.

Evolutionary Action of de novo missense variants across pathways prioritizes genes linked to autism and predicts patient phenotypic severity.

The search for Eden opens up new vistas

The end of Eden

A particular conception of the “Out of Africa” model of human origins died in this decade. This model hooked into preexistence narratives about “Adam” and “Eve”, utilizing Y and mitochondrial DNA lineages passed down through direct male and female lines respectively. Its most extreme manifestation could be exemplified by Richard Klein’s ideas in the early 2000s outlined in his book The Dawn of Human Culture.

For Klein the chasm between Homo sapiens sapiens, humans, and other hominins was vast. A physical anthropologist who surveyed with skill the rapid expansion and proliferation of modern human cultures over the past ~50,000 years, Klein relied on a particular evolutionary model to explain how this occurred. He posited that humankind emerged in East Africa as a punctuated speciation event, triggered by a mutation which allowed for the development of fully elaborated recursive language.

The difference between our own lineage and our relatives in this framework was huge. To not put too fine a point on it, Neanderthals and other archaic humans were animals. We, Homo sapiens sapiens, were humans qua humans.

Though Klein was a paleoanthropologist, he gained great support from a school of molecular evolution which arose in the 1970s and 1980s under Allan Wilson. Wilson’s initial fame arose because he utilized a “molecular clock” analysis of primates to contend that the divergence of our human lineage from great apes was much more recent than paleontologists had believed. Eventually new fossil finds confirmed the molecular phylogeny. After this event Richard Leakey has stated paleoanthropologists were reluctant to challenge molecular results.

Wilson later focused on recent on human origins, utilizing mitochondrial DNA, which is passed down directly through the maternal lineage. In this way they found that African mtDNA lineages were very diverse, and that non-African lineages were nested within the broader tree of African lineages.

The conclusion from this finding was that modern humans arose in Africa and spread to other parts of the world. This conclusion in general has been confirmed.

But over the years more and more evidence has accumulated that the story is more complicated than the original narrative that all modern humans descend from a small bad of East Africans who populated the whole world ~50,000 years ago.

Dissenters from Eden

There were always geneticists who were skeptical of the neat Out of Africa with total replacement model. In Origins Reconsidered Richard Leakey recounts a conference in 1992 where he was pigeon-holed by geneticists who thought there was no reason to accept without dispute the mitochondrial Eve narrative. Over the years talking to some older geneticists I can say that Leakey was reporting a real undercurrent of irritation with the confidence that Allan Wilson’s group and their fellow travelers projected in relation to their model. Nordborg 1998 On the probability of Neanderthal ancestry reflects some of the technical objections to inferring too much from one locus when it came to the possibility of other components of ancestry.

When genome-wide analyses in the middle 2000s became feasible, a visible counter-culture within genetics argued that total replacement was not supported by the data. In 2006 Wall & Hammer published Archaic admixture in the human genome. They concluded that “Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively.” They were not that far off with European populations. As far as Africa goes, that is a question that will be explored in detail in the next few years.

That analysis though has only 44 citations. I have had debates on Twitter with how exotic and marginal these ideas were. In general it is safe to say that they were not exotic and marginal in the community of human evolutionary population geneticists. But that’s not a large set. Both John Hawks and Milford Wolpoff have indicated a lot of marginalization for models outside of the narrow window of Out of Africa with total replacement. From everything I’ve heard about the run up to the 2010 publication of the Neanderthal genome many of the principal researchers, including Svante Paabo, were totally surprised by the evidence of admixture into modern lineages. Wolopff even emailed me after I reviewed the paper to suggest that it felt so good to come out of the wilderness and have some of his views accepted.

Anagenesis and punctuation?

But were Wolpoff’s views accepted? The revised model actually kept much of the Out of Africa framework in place, except it added the wrinkle of assimilation of some archaic lineages. The dominant signal in the non-African genomes seems to have come from an African lineage which left around ~50,000 years ago.

The classical multi-regional model that Wolpoff was associated with, whereby modern humans evolved across the whole world from local archaic lineages, but maintained species cohesion through gene flow, was not supported. Rather, the archaic admixture of Neanderthals and Denisovans into Oceanians pointed to local continuities, which was a broader position of multi-regionalism. But this is not speciation without branching, anagenesis.

Nevertheless, there was another aspect of Out of Africa with replacement that needed revision. Though not explicitly outlined in many framings, one aspect implicit is that the dynamics that Africa and Eurasia were subject to during the emergence of modern humans were the same.

But that doesn’t seem to be the case. The ancestors of all non-Africans went through a major population bottleneck. On the order of ~1,000 individuals (this is a very large bottleneck actually, and I’ve seen numbers as low as 100, though that seems on the small side; calculating effective population size ~50,000 years ago can be tricky). The same is not true of African populations. Though many of them show signals of population declines during the Pleistocene, the extreme uniform bottleneck which characterizes all non-Africans, from Iberia to Australia to Patagonia is just not evident in Sub-Saharan African populations.

In other words, the Out of Africa event did not apply within Africa. Here’s an excerpt of an email I sent to Carl Zimmer in December of 2010 (he was updating the second edition of The Tangled Bank):

…it may be that there was no rapid antique population expansion in Africa which was analogous to [the] out of Africa migration. IOW, non-Africans are just a branch of Northeast Africans, and the Bushmen and other groups were already differentiated by that point. So you could theoretically remove the arrows within Africa! I think this is a subtle and tendentious point, so probably best to leave that as it is. But remember how deep the basal branching of the Bushmen was in the Denisova paper? It WAY predates any possible out of Africa migration by multiples.

Which brings me to the current year and the present time. The recent paper which utilized an ancient genome from South Africa to push back the date of the diversification of African lineages to about ~250,000 years before the present was not entirely surprising to me. Every time I talked to people who had access to African whole genomes their dates kept getting pushed back further and further into the past.

And of course we now have fossil confirmation that human populations which seemed to be anatomically modern (or close) were already present ~300,000 years ago in Morocco. The New York Times has a good overview of the work, Oldest Fossils of Homo Sapiens Found in Morocco, Altering History of Our Species. I read the papers and the commentaries and don’t have much to add, nor do they add much for non-specialists in my opinion (since we can’t really judge the morphology too well, nor do we have a detailed understanding of the fossil record). In one of the Nature letters the authors conclude in the abstract that “The emergence of our species and of the Middle Stone Age appear to be close in time, and these data suggest a larger scale, potentially pan-African, origin for both.”

This suggest to me anagenesis. Has multi-regionalism come back, but no within Africa?

Parameters, not paradigms

John Hawks has put in his two cents, and it’s always worth paying attention. My major take home is that we don’t know a lot even though we know more, and we need to be careful here. The genome blogger from the 2000s who has been relatively quiet over the last five years, Dienekes, resurfaced, dismissing the idea of pan-African anagenesis and asserting an Out of North Africa viewpoint. He’s been talking about this model since 2011, so there’s nothing new here. In January of 2011 he asserted that “Africa was home to a structured population.” That is what we are seeing today.

The publication of the Nature letters triggered a lot of discussion on Twitter. When I was involved it mostly consisted of Aylwyn Scally and Pontus Skoglund, with John Hawks, Chris Stringer, and others jumping into the stream. Here are some points which are of note:

1) Most people now suspect that large scale population structure within Africa over the past few hundred thousand years is a major story.

2) But there is an assumption that collapsing of that structure through gene flow was not reciprocal. That is, some populations likely expanded at the expense of others. The arguments are whether the assimilation of the secondary groups is on the order of a few percent, as seems to be the case in Eurasia, or a much higher fraction.

3) Because the phylogenetic distance between within African lineages is likely smaller than between Neanderthals and modern humans, as well as the likely similar census sizes and technological toolkits, I contended that it is not unreasonable to guess that as much as 20% of the ancestry of a daughter population of an expanding group could be from the local substrate. There was no great objection to this guess.

4) Remember, even simple mtDNA phylogenies as far back as the 1980s, as well as paleontological analyses of fossils, indicated that an Out of Africa movement into Eurasia. This was such a strong signal in the data that it was clear with even relatively little to go on. The situation for within Africa is not analogous, suggesting to me that an extreme model of replacement or gene flow across persistent demes in local regions is not tenable.

5) Ultimately, the issue will resolve on parameters of admixture and the nature of demographic expansion in the details. Instead of a tree, we will conceive of this as a graph, a trellis with lengths of different thicknesses.

6) Hawks brought up the fact that one reason classic multi-regionalism did not work is that the Fisher wave of expansion of favored genes is slower than the migration of humans. When I suggested it does not seem that the genetics of gene flow in plants, which do resemble classical multi-regionalism, were a good analogy for humans, Skoglund contrasted the sessile nature of the taxon in contrast to mobile humans. I did point out though that after favored alleles moved through migration into a population, there was often in situ selection. He agreed.

7) A key issue that both Hawks and Dienekes emphasize is that we don’t know the role that extremely diverged lineages from our own ancestors play in our story. That is, were there many modern human populations across Africa, interspersed with other human species? Or was there one modern human population that mixed with other species? We don’t really know the details of all of this.

8) I expressed skepticism of the idea of “behavioral modernity.” My reason for being skeptical is that the origin of modern humans is not as neat as we like to think, and the origin of “behavioral modernity” is also not as neat as we like to think. When the consensus was that humans emerged as a punctuated de novo event, ensouled by the Lord God on High 50,000 years ago (or, coming down from the skies as in Battlestar Galactica or in Larry Niven’s Ringworld), the idea of behavioral modernity kind of made sense. But it’s all more confused now (in any case, in Clive Finlayson’s The Humans Who Went Extinct he seems to be arguing that much of modern culture was invented by Gravettians, well after the Out of Africa event).

The consensus seems to be that rather than focusing on a set of human universals as behaviorally modern, we should look at the demographic patterns of the past to infer when our own lineage came into its distinctive being. Those of you who have read me for a while know this is already congenial to me, Luke Jostins’ plot of the encephalization of all hominin lineages over the past million years was suggestive to me long ago that our own lineage is not so special. Rather, something like us was probably inevitable so long as an asteroid didn’t wipe out large mammals once Homo erectus spread across the globe. Humanity is a destiny, not a lineage.

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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