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May 30, 2017

The material over the ideological

Filed under: Economic History,Economics,History,Max Weber — Razib Khan @ 11:42 pm

I come not to praise or bury Max Weber. Rather, I come to commend where warranted, and dismiss where necessary.

The problem as I see it is that though a meticulous scholar, Max Weber is the father of erudite sophistry which passes as punditry. Though he was arguably a fox, his genealogy has given rise to many hedgehogs.

Weber is famous for his work on relating the Protestant ethic and capitalism (more precisely, Calvinism). In general I think Weber is less right than he is wrong on this issue. But the bigger problem is that Weber’s style of interpretative historical analysis also has spawned many inferior and positively muddled imitators, whether consciously or not.

To my mind the problems with Weber’s sweeping generalizations, interpretations, and inferences, are clearest on the topic of China. His assertions on the nature of the Chinese mind informed by Confucianism, and how it would relate to (and hinder) modern economic development are very hit or miss.

By the end of the 20th century things had changed in terms of the perception of how Confucianism might relate to capitalism. In the 1990s Paul Krugman famously argued that the East Asian economic miracle did not have to do with a particular model or cultural genius, but simply increases in capital investment and labor force participation (factor inputs). This was too stylized a fact. Though growth has slowed, I think it is undeniable that East Asian economic modernity is here to stay.

And some of that may be attributable to Confucianism in a distant causal sense, because the cultural sensibility does encourage the development of broad-based literacy through self-cultivation. In Strange Parallels Victor Lieberman notes the contrast between Vietnam, with its more Sinic cultural orientation, and the rest of Southeast Asia, with their Indic Theravada Buddhist cultures.

The Vietnamese elites’ orientation toward Confucianism meant that there was stratification in society, as there were constant upward and downward movements across class. The chasm between the Confucian literati and the peasantry was large. In contrast in Cambodia popular religion was relatively unifying due to its accessibility. But it is notable to me that Vietnam in particular is often perceived by those who travel in Southeast Asia to be an industrious and striving nation.

So yes, culture may matter. But simple economic forces, and material conditions, are incredibly important, and our understanding of their origins are more mysterious than we’d like to think.

This is on my mind because of the recent evidence of the power of the slave trade in the Islamic world. Islam gets a bad rap in relation to slavery. This is justified, as Muslim nations have been, and are, the most prominent perpetuators of institutional chattel slavery* in the modern and near-modern world. But it is also correct that in many ways de jure Islamic law gave slaves a degree of dignity and human rights which would not have been called for in Classical antiquity. Though the reality is slaves were often part of the Roman familia in many cases, ultimately they were still human tools, to be abused and disposed as one would domestic animals.

But the genetic data seem clear that African slavery increased greatly during the Islamic period, resulting in a much more human agony, as so many of the slaves died en route (males who were to be eunuchs had a high mortality rate as they had to be castrated before entering Muslim lands). This had nothing to do with the cruelty of Islam per se, but the overall development and advancement of the Eurasian oikoumene, and the role of African slave labor in its post 1000 A.D. economy.

In fact one might argue that the unity of the Islamic world, and its relatively uniform legal and cultural superstructure after the collapse of its political unity, was a factor in fostering the rise of the global slave trade. That is, Islam generated asabiya, social solidarity, within the group, but this ultimately was to the detriment of those who were outside of the group.

A similar story can be told about the New World slave trade. It flourished in the wake of the Reformation and the Renaissance, and just as European society was undergoing a cultural revolution which would usher in modernity. If one looked at the nature of European society in the 17th century, and its increasing moralism, and focus on personal piety, probity, and humanity, would we predict the expansion and scaling up of the European slave trade? No.

That dynamic was driven by economics (in the American case, the triangle trade).

Similarly, the mortality rates of slaves varied greatly by locale and the what they cultivated. The sugar islands were death traps. The rice farmers of coastal South Carolina lived relatively stable lives, even comparable to serfs. Those who grew tobacco were somewhere in the middle. All were under English jurisdiction. The mortality of Brazilian slaves was high, but nominally Roman Catholic jurisdictions were subject to more humanitarian codes. But the primary determinants of mortality, of humanity, were economic. Material, even if ideological variables had an impact on the margin (Rodney Stark has argued that the French legal system was more humanitarian in Louisiana, and one can see this in various vital statistics).

Obviously ideological and material forces interact and influence each other. My point here is to observe that too often public commentary gets caught up on the idea of the great idea driving history. But once we have some distance it is often obvious that on the proximate scale many of the patterns we see are constrained, driven, and conditioned, on material forces and parameters.

And yet ultimately those material forces through gains in productivity relax tight the pressures which constrain ideologically driven change and revolution. Slavery for example was long considered an institution that would always be with us in some form, but over the past few thousand years most societies have frowned upon it. Slave societies, whether ancient Roman or in the antebellum South, develop an unhealthy paranoia. With modern technologically driven economic growth the possibility of a post-slave economy seemed plausible, and opened the window for a practical abolition.

And here we are!

* I said “institutional chattel slavery” specifically to head off annoying nit-picking comments. Please don’t.

Ancient Egyptians: black or white?

Filed under: Egypt,Genetics,Historical Genetics,History — Razib Khan @ 9:20 pm

One of the most fascinating things about ancient Egypt is its continuity, and our granular and detailed knowledge of that continuity. We can thank in part the dry climate, as well as the Egyptian penchant for putting their hieroglyphs on walls and monuments (as well as graffiti!). And we can also thank the fact that both the ancient Greeks and Hebrews, Athens and Jerusalem so to speak, were deeply connected to and perceived themselves to be indebted to Egyptian civilization. Even before the translation of the Rosetta Stone and the deciphering of ancient Egyptian writing the Hebrews’ interactions with Egyptians, in particular in Exodus, mean that their memory would echo down through the millennia (the newly Christianized Irish interpolated Egyptian ancestry into their own genealogy).

The Greek relationship with Egypt was less fraught and at greater remove than the Hebrews. But the Classical period philosophers correctly perceived that Egyptian civilization was ancient, and preceded their own. Aegean-Egyptian connections were actually more longstanding than the Classical scholars knew, in Brotherhood of Kings: How International Relations Shaped the Ancient Near East, the correspondence in state archives which have been retrieved are rather clear that Minoan civilization was part of the orbit of Egypt early on. Though Egyptians never conquered the Aegean polities, mercantile and diplomatic connections were extremely old and persistent. The late Bronze Age eruption of barbarian Sea Peoples who attacked the whole civilized Near East may have been facilitated in part by the broad familiarity engendered by widespread trade networks.

The most recent book devoted to ancient Egypt I have read was Toby Wilkinson’s The Rise and Fall of Ancient Egypt. Synthesizing extensive written material with archaeology, perhaps the most impactful argument in Wikinson’s narrative was the persistence of the temple based institutions from the Old Kingdom down to the Ptolemaic era. Religious institutions carried on even with the shocks of Nubian and Libyan conquest in the post-New Kingdom period, down to Late Antiquity. The temple at Philae in southern Egypt was an active center of the traditional religion, and therefore the culture which dates to the Old Kingdom in continuous form, down to the 6th century A.D. (when it was closed by Justinian in his kulturkampf against ancient heterodoxies).

For various ideological reasons though many people are very curious about the racial characteristics of the ancient Egyptians. There are two basic extreme positions, Afrocentrists and Eurocentrists. Though I have not done a deep dive of the literature of either group, I’ve read a few books from either camp over my lifetime. In fact I believe the last time I read the “primary literature” of Afrocentrist and Eurocentrism was when I was an early teen, and it was rather strange because both groups seem to be recapitulating racial disagreements and viewpoints relevant to the American context, and projecting them back to the ancient world.

In college I stumbled upon Mary Lefkowitz’s Not Out Of Africa, a book length argument against the more sophisticated Afrocentrist views articulated in the wake of Martin Bernal’s Black Athena: The Afroasiatic Roots of Classical Civilization. Lefkowitz was a classicist, so many of her objections were exceedingly scholarly. The reality is that the best refutation of an Afrocentrist view of of ancient Egypt, which reduces to the idea that ancient Egyptians would be recognizably black African today, are the Fayum portraits. It is notable to me how similar these portraits are to modern Copts. In fact the actor Rami Malek, of Coptic background, looks strikingly like someone who stepped out of the Fayum portraits.

I have read no book length refutation of the Eurocentrist, usually Nordicist, perspective. Mostly because this is a view associated with white supremacism, and that ideology is generally attacked on normative, not positive, grounds. But the visible evidence of the Fayum portraits is a strong refutation of the Nordic model. Of course, there is the reality that we now know that the Nordic phenotype, and the genetic components which congealed into that typical of Northern Europe today, was only coming into existence when the Old Kingdom of Egypt was already a mature civilization.

Of course both Afrocentrists and Eurocentrists will reject the evidence of the Fayum portraits became they came from the Roman era, and they would argue that the demographic nature of Egyptians changed quite a bit between that period and the end of the New Kingdom. And they are not incorrect that the period between the arrival of the Romans and the fall of the New Kingdom was characterized by a great deal of change. There were Libyan dynasties, Nubian dynasties, and periods of rule by Assyrians, Persians, and Macedonians. Large colonies of Greeks, Macedonians, and Hebrews-becoming-Jews were also resident in Egypt. Especially, but not limited to, the urban areas.

But now we have ancient DNA! Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods:

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Because modern people care about the Afrocentrist question, the extent of Sub-Saharan African ancestry is highlighted in this paper. I do not think this is actually the most interesting aspect. But I’ll get to that. Since this post will be read by a fair number of people I’ll talk about the relationship of ancient and modern Egyptians to (Northern) Europeans and Sub-Saharan Africans.

The figure to the left is looking at 90 ancient Egyptian mitochondrial genomes (and some modern ones in the two rightmost columns). Since mtDNA is copious it was relatively easy to extract and analyze.  Haplogroup L, the red to orange shades in the bar plots, are associated without dispute with Sub-Saharan Africa. Haplogroup U6, M1 and a few others may be “back to Africa” variants of different periods (they are generally found in Afro-Asiatic groups).

What you can see is that somewhat more than half of Ethiopia’s mtDNA lineages are L, in keeping with the whole genome estimate of Sub-Saharan African ancestry in most Cushitic populations. In Egypt there is a difference over time; haplogroup L goes from low frequencies to much higher frequencies in modern periods. The ~20% fraction in the modern samples is in line with the population wide admixture one sees in modern Egyptians of Sub-Saharan admixture.

I actually recomputed the haplogroups to a finer granularity from the supplements for readers who know this stuff well. Here they are:

 

Haplogroup Count
H 2
H13c1 2
H5 2
H6b 2
HV 3
HV1a’b’c 4
HV1a2a 3
HV1b2 2
HV21 2
I 5
J1d 2
J2a1a1 2
J2a2b 2
J2a2c 4
J2a2e 3
K 16T 2
K1a 2
K1a4 2
L3 2
M1a1 4
M1a1e 2
M1a1i 2
M1a2a 2
N 2
N1’5 2
N1a1a2 2
R 3
R0 2
R0a 2
R0a1 2
R0a1a 3
R0a2 3
R0a2f 2
R2’JT 2
T 3
T1a 3
T1a2 2
T1a5 4
T1a7 7
T1a8a 2
T2 3
T2c1 2
T2c1c 2
T2e 2
U 2
U1a1 2
U1a1a3 2
U3b 3
U5a 2
U6a 2
U6a2 2
U6a3 2
U7 4
U8b1a1 3
U8b1b1 2
W3a1 2
W6 2
W8 2
X 2
X1 2
X1c 2

A quick inspection of mtDNA haplogroup frequencies shows that ancient Egyptians are not typical of modern Europeans. Not that much H, and lots of T, J and K. What that does remind me of are Early European Farmers. These people, who brought agriculture to Europe from Anatolia contributed a large fraction of the ancestry of modern Southern Europeans, and a lesser component to Northern Europeans.

But ultimately what’s great about this paper is that they have ancient autosomal DNA. That is, genome-wide results.

They got three samples of reasonably high quality. More precisely: “Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs.”

You can see the three samples on this bar plot. What is interesting is that they’re all pretty similar.

What you can see here is that to a great extent ancient Egyptians were descended from a population closely related to Natufians, or Natufians themselves. This easily explains the mtDNA affinity to Neolithic farmers: Natufians and Anatolian Neolithic populations were sister populations. The f3 statistic which looks at shared drift shows an affinity of ancient Egyptians with ancient farmer populations with Near Eastern provenance, but also with modern Sardinians. This is a common pattern, as ancient groups do not have later migration waves, with the Sardinians the modern population closest to this.

You see in the bar plot that northern Levantine populations are placed between Anatolian Neolithics and Natufians, as one might expect based on their geographical position and gene flow between these two regions. Additionally, the cyan color is associated with eastern farmers from the Zagros. I’ve already talked about gene flow from this area to the Levant recently. If you compare the Bronze Age Sidon samples I think you’ll see broad affinities with these Late Period Egyptians.

The PCA gives us results consonant with the model-based clustering. If you plot the genetic variation of ancient Egyptians they’re closest to Neolithic eastern Mediterranean populations. No great surprise.

Not the modern Egyptians. Why? It’s pretty clearly because modern Egyptians are shifted toward Sub-Saharan Africans. But there is also another component: modern Egyptians have more of the cyan eastern farmer component. What could this be?

An immediate thought comes to mind. We focus a great deal on Sub-Saharan African slavery. One reason is that it is visible. Black Africans are physically distinct from most Middle Eastern populations. But Egypt was long the center of another slave trade: “white slaves” from the Caucasus. Circassians. For hundreds of years Mamluks were recruited from the Caucasus as military slaves. They eventually became the ruling class of Egypt, until their decimation in the 19th century under Muhammad Ali (who himself was an Albanian Ottoman who never learned to speak Arabic well).

As noted in the paper earlier work looking at patterns in ancestry tracts and LD decay had made it obvious that much of the admixture of Sub-Saharan ancestry in Egypt, as in much of the Middle East, is relatively recent. In particular, it dates to the Islamic period, when trade and conquest took on new dimensions in Africa and north into Central Asia. One way ethnic minorities like Assyrians and Lebanese Christians differ from their Muslim neighbors is that they have much lower fractions of Sub-Saharan African ancestry, and no East Asian component. The latter might surprise, but remember that Central Asian Turkic slaves have been prominent in Muslim armies since at least the 9th century.

But some of the Sub-Saharan ancestry in Egyptians is old. The ancient Egyptian samples have it. To have none of it would seem strange, considering the history of contact between Nubia and Egypt, dating back to the Old Kingdom. Second, there is evidence of low levels of Sub-Saharan African gene flow into Southern Europeans. How did that happen? The highest fractions are in Spain, and can there be attributed to the Moorish period. But that explanation does not hold in much of Italy, where there are a few percent of haplogroup L. This probably is due to south-to-north gene flow across the Mediterranean during the Classical period. Some of the peoples on the south shore of the Mediterranean almost certainly already had some Sub-Saharan African admixture.

Not getting into the details of it, there are ways to explicitly model gene flow into a target population from donors defined by a phylogeny. In this case the authors tested various models of gene flow from Sub-Saharan Africans and Eurasians (non-Africans) to generate allele frequency patterns we see in modern Egyptians and ancient Egyptians.

What they consistently found is that modern Egyptians are about twice as much Sub-Saharan African as ancient Egyptians. The proportions for modern Egyptians ranged from ~10 to ~20 percent Sub-Saharan African against a Eurasian background, with a bias toward the higher values (depending on which populations you put into the phylogeny for non-Africans), and ~0 to ~10 percent for the ancient Egyptians, again with a bias toward the higher values. The pattern is consistent in these tests.

An issue here is that we’re going off three samples. That being said, the authors observe that despite differences in contamination/quality and time period they’re very concordant with each other. If I had to bet I think Old Kingdom samples would have somewhat less Sub-Saharan and eastern farmer ancestry. But the basic pattern persisted down to the Roman period, and was only shifted by admixture due to slavery.

And not to belabor the point, but a paper from a few years ago which had some Copt samples looks familiar in its broad outlines. You see that the Copts have very little Sub-Saharan African ancestry, though it does seem to be evident (the marker set is in the hundreds of thousands of SNPs). Additionally, they are quite distinct from the Qatari Arab sample.

Unfortunately the data for this paper just published is not on the European Nucleotide Archive. I really want to dig a little deeper into it.

What are the takeaways here? Egypt has been the sink for a lot of migration and gene flow over the past several thousand years, and probably earlier. Not surprising considering that it was relatively wealthy in the aggregate. The Natufian population that the Late Period Egyptians resemble the most did not have Sub-Saharan African ancestry according to earlier research. These Late Period Egyptians do have some. This is reasonable in light of the long interaction with Nubia which is historically attested. Similarly, there was clearly gene flow from Southwest Asia. This is again historically attested, especially in the Nile Delta (though foreign garrisons of mercenaries are recorded in Upper Egypt as well).

The Roman period probably did introduce some gene flow from Southeast Europe and Southwest Asia. But these populations are not that distinct from Egyptians.

Similarly, the Islamic period also brought in different peoples from Arabia and the Caucasus. But the most salient dynamic during the Islamic period was a massive trans-Saharan slave trade (though the Caucasus impact may have been comparable, and I think these results support the proposition that it was).

It seems entirely likely that the Copts are descended from a mix of Roman era Egyptians. Not only do they resemble the people in the Fayum portraits, but the circumstantial genetic data is that they have fewer “exotic” components which increased in frequency during the Islamic era. This would be exactly parallel to ethno-religious minorities in the Levant and Iraq.

One curious element to me is the suggestion gene flow before ~5,000 BCE between Sub-Saharan Africa and the lower Nile valley was low. If it hadn’t been low, it seems unlikely that the fraction of Sub-Saharan ancestry (or shift in that direction in relation to other Eurasians) in Copts would be so small.

So what explains the lack of earlier gene flow? I think the answer is going to be the fact that the human demographic landscape is characterized by lots of local population extinctions. As ancient DNA sampling coverage gets better and better meta-population dynamics are coming into focus, and we see gene flow, and die offs, in several areas. It is fashionable to say that human population variation is characterized by clines. But much of this clinal aspect is an outcome of the period after massive admixture over the last ~10,000 years.

And yet it may not be that the period before the Holocene was not clinal. Rather, it may be that large depopulations of areas of human occupation fragmented clinal ranges, and resulted in new range expansions from “core” zones.

About ~8,000 years ago there was a major desertification period in the Sahara desert. Many trans-Saharan populations may have gone extinct during this time due to rapid climate change. Eventually repopulation may have occurred from outside of the Sahara, so that post-Natufian Levantines and Sub-Saharan Africans from what today call the Sahel pushed up and down the Nile drainage basic respectively, meeting in the zone of Nubia on the boundary of history and prehistory.

Unlike many other areas of the world we have a long attested record of Egyptian history. As we get more mummy samples it seems likely that we’re get a crisper, clearer, picture. And the time transects will not be narrative blind; we already know the general arc of Egyptian history. If, for example, we see a new ancestral component around ~1500 B.C., in Egypt it’s not mysterious what this might be: the Hyksos.

This is just the prologue to a fascinating book that will be written over the next decade.

Related: Blog post analyzing one Copt’s results suggests that Sub-Saharan admixture is more like Dinka than Yoruba (in contrast, Muslim Egyptians have a mix of both, the latter probably coming during the Islamic slave trade, while the former is probably ancient admixture).

Citation: Schuenemann, V. J. et al. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8, 15694 doi: 10.1038/ncomms15694 (2017).

May 29, 2017

Open Thread, 5/29/2017

Filed under: Open Thread — Razib Khan @ 11:45 am


The above talk from David Reich is very good. Highly recommended.

Chris Wickham’s Medieval Europe is pretty good, though it is very similar to his The Inheritance of Rome and Framing the Early Middle Ages.

Rod Dreher finds out it is highly like he has some African ancestry from a slave ancestor. This seems to be detected in 1 out of 10 whites using reasonable thresholds. Probably that that means that genealogically much more than 10% of Louisiana whites have lines of descent from people who were mixed-race slaves (though in French areas it might be mediated often by mixing with “free people of color”).

May 28, 2017

Bitter Libyan Fruit

Filed under: International Affairs,Libya — Razib Khan @ 11:35 am

In Mary Beard’s excellent SPQR: A History of Ancient Rome she describes an “empire of obedience” that emerged in the 2nd and 1st centuries BC. This refers to the often ad hoc arrangements of Roman rule and hegemony which preceded the explicit imperial period, when domination was bureaucratized and formalized.

Sometimes it seems that the United States is an empire of obedience, though we do operate through formal institutions such as NATO and the IMF. There’s an ad hoc schizophrenic aspect to it all.

In Across The Chasm Of Incommensurability many of the commenters seem to be focusing Chinese susceptibility to government propaganda. But my post was in large part pointing to the fact that Americans themselves are often blinkered and biased, though we often exhibit a conceit of all knowing objectivity.

On Twitter I said the following:

People immediately thought I was alluding to the Manchester bomber. Actually I wasn’t. I was thinking about the Copts killed in Egypt (including children) by ISIS-affiliated militants with basis in Libya.

This is not a one off. Since the overthrow of the Gaddafi regime Libya has been an incubator for terrorism. Its current political landscape is anarchic, with rival militias jockeying for power. Libya happens to be right next to the most populous Arab nation. This is not a good recipe for stability in the region.

Some commentators, such as Daniel Larison, have been arguing against the intervention since the get-go. But in general the media seems to have taken a policy of benign neglect toward what’s going on within Libya.

The Western powers take it upon themselves protect the people from their own governments. This is fair enough. But what Iraq showed us is that not all peoples are ready to be Jeffersonian Democrats. This is a fact.

The Roman “empire of obedience” gave way to one of direct rule. That was the only way to keep the chaos in check. Imperialism and colonialism are not fashionable today, but if Western governments keep intervening that seems the only way to keep the chaos at bay.

May 26, 2017

The Canaanites walk among us: ancient DNA edition

Filed under: Ancient DNA,Bronze Age,History — Razib Khan @ 2:09 pm

Ancient DNA from here to there:

Ancient DNA has illuminated many things, but there is a logic as to what topics and questions it tackles. The focus on northern Eurasia is clearly a function of the probability of preservation, though techniques of extraction are getting better and better. I can’t imagine how we’d ever get a sample out of a moist tropical environment, but I won’t be surprised if something is obtained from a cave in southern Africa or high in the Tibesti in the near future.

But another parameter is time since the demographic events in question. Too ancient, and the probability of success is too low(ok, time is a parameter in much of science!). It seems plausible that in idealized circumstances we’re going to push beyond the one million year barrier. And yet too recent is also a problem (or not a problem!). For humans and even non-humans we have lots of corroboration about questions we might ask about the recent past. You could use “ancient DNA” to trace the migration of Mormons across the Intermontane West, but why would you?

So you see the earliest ancient DNA work on humans was biased toward testing models about gene flow and ancestry tens of thousands of years in the past, between modern humans and archaic lineages. Obviously we don’t have oral history or written texts from this period, and archaeology will only get us so far.

More recently the time depth has been getting shallower and shallower. Both David Reich and Eske Willerslev’s work on European prehistory is liminally historical. By this, I mean that what is prehistory in Europe is a historical period in the Near East. We may not have written records from the Corded Ware or Bell Beaker cultures, but we do have plenty of them from contemporaneous Near Eastern groups.

The Cauldron of Peoples:

There are still questions to be asked about European prehistory, but the gaps are getting narrower and narrower. Scholars are finally devoting resources to other regions of the world. Last year Iosif Lazaridis’ The genetic structure of the world’s first farmers finally opened up the box that was the prehistory of the Near East. This was important, because much of prehistory and history began in the Near East. Farmers from this region seem to have moved into Europe, South Asia, Central Eurasia, and Africa. To understand the population histories of these areas one needs to understand the population history of the Near East.

What Lazaridis et al. found this that there were at least two major groups of very genetically distinct Near Eastern farmers at the dawn of agriculture. Once group faced the eastern Mediterranean, while the other seems to have flourished on the slopes of the Zagros. Western and eastern farmers respectively. It is important to note that these two groups were very genetically distinct. If we sampled these two groups of farmers, who faced each other across northern Mesopotamia, in any modern population survey we’d assume that the genetic distance meant that they were sampled from different continents or very distant regions of Eurasia.

This finding suggest that the clinal patterns of variation in much of today’s world may be a consequence of massive population admixture between groups which had heretofore exhibited deep population structure. Why such deep structure existed and persisted is an interesting question, but at this point it is important to note descriptively that the past 10,000 years have seen a massive reduction of this structure due to gene flow between populations.

In the Near East Lazaridis et al. found that there was significant reciprocal gene flow between the western and eastern regions of the Near East after the emergence of farming, down to the historical period. This is one reason that estimates of “farmer” ancestry in modern Europeans always gave very low estimates: the reference populations no longer existed in unmixed form in the Near East. The peoples who brought agriculture to Southern Europe were related exclusively to the western farmers of the Near East, a population which no longer exists in unmixed form in that region of the world (ergo, among modern groups Sardinians are the closest proxies we have).

The Age of Bronze:

But there is much that occurred after prehistory in the Near East. We know this because we have extensive records going back 4,500 years, and even earlier. And though put into written form in the first millennium before Christ, the Hebrew Bible also records the deeds and names of people who have come and gone well before the Classical Age.

A new preprint on biorxiv sheds some light on a critical transitory period, Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences:

The Canaanites inhabited the Levant region during the Bronze Age and established a culture which became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole-genomes from ~3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalogue modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with massive population movements in the mid-Holocene triggered by aridification ~4,200 years ago. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations such as the Persians and Macedonians.

The period between 1700 and 1800 BCE in the Near East saw many changes and was a sort of nexus. Sumer had fallen, the Hittites had not emerged as a superpower, while Egypt was not heavily involve in the game of kings as of yet. The system of international relationships described in Brotherhood of Kings had not crystallized. That was for the late Bronze Age.

But some of the pieces we were to recognize were already in place. An Amorite Babylon under Hammurabi established the contours of the culture and polity we’d recognize down to the Persian conquest. In Egypt the Middle Kingdom was going into decline, and the Hyksos interregnum would give rise to the New Kingdom, which would become a major player in the Levant (and probably is the model for much of the Egypt we see described in the Bible).

The admixture plot above reflects the five individuals from Sidon dating to about ~1750 BCE. They are about a 50:50 mix of western and eastern farmer. Though they seem to be genetically rather similar to modern Lebanese (the authors sampled Lebanese Christians in particular), there have been some changes between the Bronze Age and the modern period. In particular, a genetic component that seems to be related to the Eurasian steppe is present in modern Lebanese. Explicit admixture estimates give a range of 5-10% mixing into a ~90-95% Bronze Age ancestral background.

This seems to establish basic continuity between the Bronze Age and the modern period. Totally unsurprising. Remember that Italy exhibits deep population structure that dates back to at least 2,000 years ago, and probably earlier. It is likely that much of the same applies to the Near East. Though looking at Muslim populations one can see minor and non-trivial contributions of populations which moved in after Islam (Sub-Saharan and East Asia segments are clear signs of slavery impacting Muslims that would not apply to ethno-religious minorities), most of the ancestry broadly is deeply rooted back to antiquity.

Because of sampling issues one can’t estimate admixture between eastern and western farmers just from looking at ancient DNA transects. We don’t have the density that we have in Europe (yet). So the authors used a more classic inference technique looking at decays of linkage disequilibrium in the genome. In short you can see how many generations that a pulse admixture between two populations occurred by looking at correlations of variants across the genome. The authors arrive at the intervals above, and in particular focus on the period that seems to overlap with the rise and fall of the empire of Sargon of Akkad and correlated with a climatic disruption.

I suspect they are wrong here. First, it seems pretty clear to me that LD based admixtures assuming a pulse event have a bias toward underestimating values. There are theoretical reasons for this. So usually I pad the mid-point value across the interval on these estimates.

One thing that ancient DNA has told us is that often the less complex the society, the more demographic turnover you have. All things equal then we would expect turnover to be an older event, as simple societies are succeeded by complex ones. The succession of complex societies by other complex societies is often less disruptive for the masses because this transformation is more a matter of elite replacement.

By ~2200 BCE the Near East was already quite complex. I believe that the massive western-eastern farmer admixture occurred between 3600 and 3100 BCE, during the Uruk Expansion. The evidence of lower Mesopotamian influence and demographic settlement in places as far afield as Anatolia, the Caucasus, and Syria, are well attested from the archaeology of this period. This was was a time when a very complex and sophisticated civilization emerged almost de novo across much of the Near East. I believe that a prehistoric expansion of Sumerian civilization mediated the merging of eastern and western farmers, though some of the mixing pre-dates and post-dates the Uruk Expansion and collapse (e.g., the movement of western farmer ancestry into Mesopotamia seems certain to have occurred through the arrival of groups like the Amorites).

Additionally, buried in this preprint is evidence of major Y chromosomal turnover. We’ve seen this  before. The prominence of haplogroup J in Bronze Age and modern Levantines seems to be due to eastern farmer migration. In fact, adding haplogroup J and R together we get the inference that more than half the paternal lineages of Lebanese today are not from western farmers native to the area.

Beyond the Bronze Age:

What about the second ancestral component? Drilling down on the Y chromosomes of the Levant, R1b seems to far outnumber R1a, though the R1a clades are all of the Asian/Scythian Z-93 branch which is dominant in Central Asia and the Levant. The R1a may have come with the Persians, but in region of the western Levant for several hundred years after the period of the Bronze Age Sidon samples there was a state, the Mitanni, which clearly had an Indo-Aryan ruling class.

An Aegean influence occurred multiple times. First, at the end of the Bronze Age many of the “Sea Peoples” were clearly of Aegean origin, and so may have brought steppe-like ancestry. Second, there was the long period under Hellenistic and Roman rule, when Greek and non-Greek ethnic identity existed side by side, and movement occurred in both directions. I think only ancient DNA will answer this question, and it may be that there were multiple post-Bronze Age inputs of genes which shaped modern Levantines.

After Babel:

The curious thing that many of these studies are telling us is two-fold:

  1. Most of the population genetic structure we see around us dates to the Bronze Age, on the borderlands between history and prehistory. I think we can start to set this as a strong prior. It holds true for the Near East, Africa, South Asia, Japan and Southeast Asia. We’ll see about core East Asia, but I think probably it is true there too.
  2. Selection has continued, so that alleles for lactose tolerance and lighter skin have changed in frequency even since that period. The derived allele for SLC45A2 is found at about 2/3 frequency in modern Lebanon, but was absent in these five Sidonians. Though the sample size is small, this was somewhat surprising, and suggests that they were a swarthier people than modern Lebanese.

Addendum: I have said little here about Afro-Asiatic languages, as I don’t know enough about this topic.

May 25, 2017

Why many academic departments should be replaced with “think tanks”

Filed under: academia — Razib Khan @ 3:56 pm

Glenn Loury has an important essay up on his website, Self-Censorship in Public Discourse: A Theory of “Political Correctness” and Related Phenomena”. A classic “read the whole thing.” But I want to highlight one section:

Sociologist James Coleman, perhaps the world’s leading scholar of educational policy, recalls that in 1976 the president and a number of prominent memembers of the American Sociological Association (ASA) tried to have him censured for the “crime” of discovering, and announcing, that citywide busing for school desegregation purposes caused White flight. This claim had been denied for years prior to Coleman’s research, and far reaching social policies had been erected on the presumption that it was not true.

40 years later the same attitude is prevalent in much of sociology and has spread to anthropology and other fields. The reality is that the idea of objective scholarship is an illusion. We all know that “think tanks” exist to promote certain ideas and viewpoints, often due to funding strings attached. I know of people who have changed their views, and so have had to change their affiliation (or, simply not published in areas that they knew would not be well received by their institution).

Academia, with the freedom of tenure should be different. But it’s not. The reason it’s not is that it is a social enterprise, and the esteem of one’s colleagues is more important than the abstract idea of freedom to explore what you want. There are strong incentives in many disciplines to toe a particular line, and humans are conformists and they do as they’re expected to.

If all debates come down to politics and power, then putting them in the domain of think tanks makes it more honest and clean.

At an inflection point of archaeology and genetics

Filed under: Genetics,History — Razib Khan @ 1:54 pm

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.

May 24, 2017

Across the chasm of Incommensurability

Filed under: China,Epistemology,India — Razib Khan @ 11:23 am

The Washington Post has a piece typical of its genre, A Chinese student praised the ‘fresh air of free speech’ at a U.S. college. Then came the backlash. It’s the standard story; a student from China with somewhat heterodox thoughts and sympathies with some Western ideologies and mores expresses those views freely in the West, and social media backlash makes them walk it back. We all know that the walk back is insincere and coerced, but that’s the point: to maintain the norm of not criticizing the motherland abroad. The truth of the matter of how you really feel is secondary.

Tacit in these stories is that of course freedom of speech and democracy are good. And, there is a bit of confusion that even government manipulation aside, some of the backlash from mainland Chinese seems to be sincere. After all, how could “the people” not defend freedom of speech and democracy?

Reading this story now I remember what an academic and friend (well, ex-friend, we’re out of touch) explained years ago in relation to what you say and public speech: one can’t judge speech by what you intend and what you say in a descriptive sense, but you also have to consider how others take what you say and how it impacts them. In other words, intersubjectivity is paramount, and the object or phenomenon “out there” is often besides the point.

At the time I dismissed this viewpoint and moved on.

Though in general I do not talk to people from China about politics (let’s keep in real, it’s all about the food, and possible business opportunities), it was almost amusing to hear them offer their opinions about Tibet and democracy, because so often very educated and competent people would trot out obvious government talking points. In this domain there was little critical rationalism. One could have a legitimate debate about the value of economic liberalization vs. political liberalization. But it was ridiculous to engage with the thesis that China was always unitary between the Former Han and today. That is just a falsehood. Though the specific detail was often lacking in their arguments, it was clearly implied that they knew the final answer. I would laugh at this attitude, because I thought ultimately facts were the true weapon. The world as it is is where we start and where we end.

Or is it? From the article:

Another popular comment expressed disappointment in U.S. universities, suggesting without any apparent irony that Yang should not have been allowed to make the remarks.

“Are speeches made there not examined for evaluation of their potential impact before being given to the public?” the commentator wrote.

“Our motherland has done so much to make us stand up among Western countries, but what have you done? We have been working so hard to eliminate the stereotypes the West has put on us, but what are you doing? Don’t let me meet you in the United States; I am afraid I could not stop myself from going up and smacking you in the face.”

Others were critical not of Yang’s comments but of the venue in which she chose to make them.

“This kid is too naive. How can you forget the Chinese rule about how to talk once you get to the United States? Just lie or make empty talk instead of telling the truth. Only this will be beneficial for you in China. Now you cannot come back to China,” @Labixiaoxin said.

There is a lot of texture even within this passage. I do wonder if the writers and editors at The Washington Post knew the exegetical treasures they were offering up.

To me, there is irony in the irony. Among the vanguard of the intelligensia in these United States there is plenty of agreement with the thesis that some remarks should not be made, some remarks should not be thought. Especially in public. The issue is not on the principle, but specifically what remarks should not be made, and what remarks should not be public. That is, the important and substantive debates are not about a positive description of the world, but the values through which you view the world. The disagreements with the Chinese here are not about matters of fact, but matters of values. Facts are piddling things next to values.

So let’s take this at face value. Discussions about Tibetan autonomy and Chinese human rights violations cause emotional distress for many Chinese. I’ve seen this a little bit personally, when confronting Chinese graduate students with historical facts. It’s not that they were ignorant, but their views of history were massaged and framed in a particular manner, and it was shocking to be presented with alternative viewpoints when much of one’s national self-identity hinged on a particular narrative. Responses weren’t cogent and passionate, they were stuttering and reflexive.

Now imagine the psychic impact on hundreds of millions of educated Chinese. They’ve been sold a particular view of the world, and these students get exposed to new ideas and viewpoints and relay it back, and it causes emotional distress. Similarly, for hundreds of millions of Muslims expressing atheism is an ipso facto assault on their being, their self-identity. This is why I say that the existence of someone like me, an atheist from a Muslim background, is by definition an affront to many. My existence is blasphemy and hurtful.

And the Chinese view of themselves and their hurt at insults to their nationhood do not come purely from government fiction. There’s a factual reality that needs to be acknowledged. China was for thousands of years was one of the most significant political and cultural units in the world. But the period from 1850 to 1980 were dark decades. The long century of eclipse. China was humiliated, dismembered, and rendered prostrate before the world. It collapsed into factious civil war and warlordism. Tens of millions died in famines due to political instability.

In the late 1950s and early 1960s between 20 to 50 million citizens of the Peoples’ Republic of China starved due to Mao’s crazy ambitions. This is out of a population of ~650 million or so. Clearly many Chinese remember this period, and have relatives who survived through this period. A nation brought low, unable to feed its own children, is not an abstraction for the Chinese.

On many aspects of fact there are details where I shrug and laugh at the average citizen of China’s inability to look beyond the propaganda being fed to it. And I am not sure that the future of the Chinese state and society is particularly as rosy as we might hope for, as its labor force already hit a peak a few years ago. But the achievement of the Chinese state and society over the past generation in lifting hundreds of millions out of grinding poverty have been a wonder to behold. A human achievement greater than the construction of the Great Wall, not just a Chinese achievement.

But it is descriptively just a fact that nations which have been on the margins and find themselves at center stage want their “time in the sun.” The outcomes of these instances in history are often not ones which redound to the glory of our species, but it is likely that group self-glorification and hubris come out of a specific evolutionary context.

There are on the order of ~300 million citizens of the United States. There are 1.3 billion Chinese. If offense and hurt are the ultimate measures of the acceptance of speech than an objective rendering might suggest that we lose and they win. There are more of them to get hurt than us.

But perhaps the point is that there is no objectivity. There is no standard “out there.” Once the measuring stick of reality falls always, and all arguments are reduced to rhetoric, it is sophistry against sophistry. Power against power. Your teams and views are picked for you, or, through self-interest, or, your preferences derived from some aesthetic bias. Sometimes the team with the small numbers wins, though usually not.

Discourse is like a season of baseball. At the end there is a winner. But there is no final season. Just another round of argument.

Ten years ago I read Alister McGrath’s The Twilight of Atheism. I literally laughed at the time when I closed that book, because the numbers did not seem to support him in his grand confidence about atheism’s decline. And since the publication of that book the proportion of people in the United States who are irreligious has increased. Contrary to perceptions there has been no great swell of religion across the world.

But on a deep level McGrath was correct about something. Much of the book was aimed at the “New Atheism” specifically. A bold and offensive movement which prioritized the idea of facts first (in the ideal if not always the achievement), McGrath argued that this was a last gasp of an old modernist and realist view of the world, which would be swallowed by the post-modern age. He, a traditional Christian, had a response to the death of reason and empiricism uber alleles, his God of Abraham, God of Isaac, and the God of Jacob. Primordial identities of religion, race, and nationality would emerge from the chaos and dark as reason receded from the world.

With the rise of social constructionism McGrath saw that the New Atheists would lose the cultural commanding heights, their best and only weapons, the glittering steel of singular facts over social feelings. On the other hand, if facts derive from social cognition, than theistic views have much more purchase, because on the whole the numbers are with God, and not his detractors.

And going back to numbers. The Washington Post is owned by Jeff Bezos. And China is a massive economic shadow over us all. Anyone who works in the private sector dreams of business in China. Currently Amazon is nothing in China. What if the Chinese oligarchs made an offer Bezos couldn’t refuse? Do you think The Washington Post wouldn’t change its tune?

When objectivity and being right is no defense, then all that remains is self-interest. Ironically, cold hard realism may foster more universal empathy by allowing us to be grounded in something beyond our social unit. In the near future if the size of social units determines who is, and isn’t, right, than those who built a great bonfire on top of positivism’s death may die first at the hands of the hungry cannibal hordes. Many of us will shed no tears. We were not the ones in need of empathy, because we were among the broad bourgeois masses.

In the end the truth only wins out despite our human natures, not because of it.

Applying intelligence to genes for intelligence

Filed under: Behavior Genetics,Genetics,Intelligence — Razib Khan @ 12:10 am

Carl Zimmer has an excellent write up on the new new Nature study of the variants associated with IQ, In ‘Enormous Success,’ Scientists Tie 52 Genes to Human Intelligence.

The issue with intelligence is that it’s a highly polygenic trait for which measurement is not always trivial. You need really large sample sizes. It’s about ten times less tractable than height as a quantitative trait. There are still many arguments about its genetic nature (though a majority position that it’s not rare variants of large effect seems to be emerging).

But all in good time.

Science is divided into many different fiefdoms, and people don’t always talk to each other. For example I know a fair number of population genomicists, and I know behavior geneticists who utilize quantitative genomic methods. The two are distinct and disparate groups. But the logic of cheap sequencing and big data is impacting both fields.

Unfortunately when you talk to population genomicists many are not familiar much with psychology, let alone psychometrics. When it comes to the behavior geneticists many come out of psychology backgrounds, so they are not conversant in aspects of genetic theory which harbor no utility for their tasks at hand. This leads to all sorts of problems, especially when journalists go to get comments from researchers who are really opining out of domain.

Some writers, such as Carl Zimmer, are very punctilious about the details. Getting things right. But we have to be cautious, because many journalists prefer a truth-themed story to the truth retold in a story format. And, some journalists are basically propagandists.

Over the next five years you will see many “gene and IQ” studies come out, with progressively greater and greater power. Read the write-ups in The New York TimesScience, and Nature. But to my many readers with technical skills this is what you should really do:

  1. pull down the data.
  2. re-analyze it.

My plain words are this: do not trust, and always verify.

I’m a big fan of people educating themselves on topics which they have opinions on (see: population genetics). If intelligence is of some interest to you, you should read some things. Arthur Jensen’s classic The g Factor: The Science of Mental Ability can be quite spendy (though used copies less so). But Stuart Ritchie’s Intelligence: All That Matters and Richard Haier’s The Neuroscience of Intelligence are both good, and cheaper and shorter. They hit all the basics which educated people should know if they want to talk about the topic of intelligence in an analytical way.

May 23, 2017

The co-location of the creative class

Filed under: Arcology,geography — Razib Khan @ 2:10 pm

I have never read Richard Florida’s The Rise of the Creative Class. There are a few reasons for this. First, his thesis was so ubiquitous in the 2000s that a distillation was easy to be had for free. People would write about Florida’s ideas. And he’d talk about it constantly in interviews.

Second, what was true about his model struck me as obvious, and what was not made it less significant. Single professionals in the knowledge economy are not by and large young Mormons who marry young and want to move into spacious tract homes in the suburbs as soon as possible. Rather, they will spend a significant part of their 20s and 30s expending and consuming in and around large cities, and want to be in circumstances where they can meet other like-minded people in similar situations.

But you can’t just create these cities by putting up bike paths. There’s no easy way to mimic what occurred in Silicon Valley. The Valley has a combination of structural (Stanford is there) and contingent factors (California has no non-compete clauses) that help it. It may be that in the modern world there are actually greater returns to locating in an ideapolis which is more expensive.

I recently had a conversation with a friend about academic research. What proportion in a given field of novel and innovative findings are produced by the top 10 institutions? The percentage varies by field and person to person, but I’ve gotten numbers ranging from 40 to 90% from people in different fields. In other words, research productivity is described by a power law as a function of institution.

Similarly, there will be one Silicon Valley, and everyone else will have the scraps. Information technology has not made the landscape flat. The visceral and concrete aspect of “being there” is even more of an advantage in a world where everyone is accessible via email and social media.

This article in Wired, Can the American Heartland Remake Itself in the Image of Silicon Valley? One Startup Finds Out, makes it pretty clear that it doesn’t matter how cool Denver is, it’s going to be hard if you aren’t in Silicon Valley.

The importance of geography and co-location is why I propose that a project for the 21st century should be the construction of a massive arcology between Long Beach and San Diego. Perfect weather on the coast and mountains inland. Aim to house the entire United States population there to start out with.

May 22, 2017

America with the evil empire

Filed under: Foreign Policy,Saudi Arabia — Razib Khan @ 12:11 pm

Before Donald Trump’s speech in Saudi Arabia my eyes were already preparing to start rolling. If there is one thing that brings Americans of all political stripes together, it is contempt for our alliance with Saudi Arabia. Nevertheless, the American ruling class reaffirms and reiterates our alliance with the passing of every administration like clockwork.

The Saudi alliance useful. It is financially lucrative for the small minority of Americans who are part of the international elite. It helps sustain some intellectuals and think tanks in Washington D.C. And in the bigger game of geopolitics the Saudis have been aligned thoroughly with the United States since after World War II.

But no one is under any great illusions about what the Saudi regime is. When Trump says “For decades, Iran has fueled the fires of sectarian conflict and terror” we have to laugh at the audacity of the lie. Starting in the late 1970s Iran did try to assert leadership of international Islam…but to do so it had to dampen sectarian consciousness, because 90% of the world’s Muslims are Sunni. Iran does support other Shia movements (though in general other Twelver Shias; the alliance with ghulat sects is opportunistic, as is that of the almost-Sunni-Zaydis of Yemen), and has had a very close relationship with Hezbollah for generations. But it has engage in this with a relatively soft touch with pretenses, because the Shia are outnumbered.

In contrast, Saudi Arabia does not need to pretend. The Saudi government and populace has been fomenting and exporting sectarian hatred for generations. Sectarian hatred even predates oil as an export of the peninsula. In 1802 the Wahhabis under the Saudis sacked Karbala. The Shia of eastern Saudi Arabia live under what is perhaps best analogized to Jim Crow for Americans.

After 9/11 many average Americans asked “why do they hate us?” This is a big question with many answers.

Here is one. For various reasons our government is allied  with a neo-medieval monarchy. Most Americans are not too aware of foreign policy, international affairs, and geography. But if you are a well informed citizen of Iran, you know exactly what Saudi Arabia is.

Many Muslims who are Sunni also know what Saudi Arabia is. Many Sunnis rue the day that oil enriched the monarchies of the Arabian peninsula, because they believe that it transformed the nature of modern Islam. This is overdone; the Wahhabis of the 18th century in Arabia can be paired up with the Deobandis of 18th century India, or the revivalism of the Sokoto caliphate in the 19th century in the Sahel. But on the margin and in quantitative degrees it is hard to deny that oil wealth has helped shape the ideological topography of modern day Sunni Islam.

The robust American alliance with one of the most extreme regimes in the world makes a farce of our rhetoric of freedom and democracy. But Americans being who we are, we continue to engage in that rhetoric despite the reality that we quickly compromise when the national interest demands it. The strength of the American-Saudi alliance from administration to administration suggests there is far more than what we see above the surface. The rumors that some Muslims spread that the House of Saud has some of the biggest wine cellars in the world illustrates the reality that that regime is very willing to violate the spirit and letter of the laws which it promotes in public.

But the alliance is always a black mark in our American self-perception that we’re a moral superpower. Most Americans don’t realize it, but in the Muslim world it something that people take note of.

May 20, 2017

Open Thread, 05/21/2017

Filed under: Open Thread — Razib Khan @ 10:36 pm

Sorry database was down yesterday. Something weird happened that my scripts couldn’t pick up and I was traveling. Will update the scripts as needed.

Winning the battle against post modernism by losing the war for the soul of science

Filed under: Epistemology,Science Wars — Razib Khan @ 1:18 am


Over 20 years ago Paul Gross and Norman Leavitt wrote Higher Superstition: The Academic Left and Its Quarrels with Science. To me the book was revelatory and a shock; my own experience with “anti-science” was mostly with Creationists. This was only a few years before the Sokal affair.

In the wake of that it seems that the excesses of the “post modern” Left receded. When you review the “science wars” it is also notable that it is an elite affair, with a strong French inflection (Sokal’s book Fashionable Nonsense was actually originally published in French!).

With the rise of “big science” like the Human Genome Project the fuss about social constructionism in science seemed a bit silly. Onward and upward!

But change is in the air. There is a “new Sokal affair,” A new academic hoax: a bogus paper on “the conceptual penis” gets published in a “high quality peer-reviewed” social science journal. The abstract goes like so:

Anatomical penises may exist, but as pre-operative transgendered women also have anatomical penises, the penis vis-à-vis maleness is an incoherent construct. We argue that the conceptual penis is better understood not as an anatomical organ but as a social construct isomorphic to performative toxic masculinity. Through detailed poststructuralist discursive criticism and the example of climate change, this paper will challenge the prevailing and damaging social trope that penises are best understood as the male sexual organ and reassign it a more fitting role as a type of masculine performance.

The whole paper is pretty amusing.

First, I have to admit that this is not equivalent to the Sokal Affair, because the journal is far less reputable than Social Text. Part of the story are lower standards in academic publishing, and the fact that “peer review” is a lot sloppier and error prone that many in the general public think. The authors made up citations, and the peers did not catch them.

Another element of this may be that these sorts of fields are so diffuse that it’s hard to get good peers who understand what you are saying. One reason specialist journals of reasonable prestige get good peer reviews is that the reviewers work in basically the same field. You can’t make up citations in that situation.

But ultimately the fact that people like Jerry Coyne are promoting this also highlights that twenty years after Alan Sokal’s hoax the science wars were not won. The problem with the tactics of the social constructionists in the 1990s is that they were too showy and swung for the fences. Over the past twenty years the way that this sort of constructionist narrative has succeeded is that first it has to colonize and dominate disciplines outside of science, and then leverage progressive causes which scientists on the whole are onboard with in any case. Instead of undercutting science, the new tactic is to be pro-science rhetorically, but to constraint and delimit. Accept the idea of scientific reality, but simply demand it conform to your one’s own preferences (this by the seems to be the stance of Creationists).

May 19, 2017

Pegging the human expansion of out of Africa

Filed under: Paleoanthropology — Razib Khan @ 11:38 pm

Genetic science is good at many things, but precise dates have not always been its strong suit. There are many reasons for this, and the possibility of variable mutation rates puts a major a barrier in our ability to get absolute precision. From what I can archaeology is a little better here, despite all the problems that this discipline has.

Early human occupation of a maritime desert, Barrow Island, North-West Australia:

. In this first major synthesis we focus on the dating and sedimentology of Boodie Cave to establish the framework for ongoing analysis of cultural materials. We present new data on these cultural assemblages – including charcoal, faunal remains and lithics – integrated with micromorphology, sedimentary history and dating by four independent laboratories. First occupation occurs between 51.1 and 46.2 ka, overlapping with the earliest dates for occupation of Australia. Marine resources are incorporated into dietary assemblages by 42.5 ka and continue to be transported to the cave through all periods of occupation, despite fluctuating sea levels and dramatic extensions of the coastal plain.

The best current work sees to suggest that unlike most world populations Australians have not experienced much turnover. That is, the first settlers are the ancestors by and large of the current native populations. If this is correct we’re getting some really clear lower bound values for the date of Neanderthal and Denisovan admixture into our lineage.

The eternal Axial Age

Filed under: History — Razib Khan @ 11:17 pm

As I have noted before one of the most interesting aspects of ancient Greek history is that in many ways the socio-political identities and outlook of the Hellenic people before and after the Bronze Age were probably as distinct as that between hunter-gatherers and agriculturalists. That is, the citadel culture of the Mycenaeans was constructed out of recognizable elements. Take one dollop Near Eastern autocracy, add a dash of semi-civilized barbarian warlord, and finish off with the tincture of brutalist post-Minoan aesthetic, and you have the pirate kings of Achaea, who so plagued the kings of the Hittites and later transformed themselves into the “Sea Peoples.”

The story of what happened after the end of the Bronze Age is somewhat well known to us, because the roots of our civilizations are clear in the ideas which emerged in the period between 1000 BCE and 0 CE. The basis of the institutional religions which we see around us date to the Axial Age. Judaism, Christianity, Islam, Hinduism, and arguably Daoism, Confucianism, Buddhism and Zoroastrianism, either arose or ripened in the one thousand years after the birth of Christ, but from a naturalistic perspective the bases of these traditions are present in the early Iron Age. To be concrete about what I’m getting at, Judaism over its history truly takes shape in the centuries leading up to, and subsequent to, the compilation of the Babylonian Talmud. But the disparate threads of Rabbinical Judaism were already there in the centuries before Christ; they were simply synthesized and extended later on.

Much the same can be said about science. On the one hand, a narrow view of science is that it is the cultural product of a group of individuals who began collectively exploring aspects of the natural world in the 17th century. Eventually this contingent cultural enterprise spread across the whole world. But the roots of the scientific enterprise can also be seen in the Pre-Socratic philosophies. It was already there 2,500 years ago. But the victory of Platonism, and later the rise of Hellenistic ethical systems, and finally the ideological uniformity imposed by Christianity, dampened the efflorescence of heterodox speculations which flourished for the few centuries around 450 BCE. The steam went out of the scientific enterprise, and it never truly became science as we understand it in the modern world. But pieces of it that came together later on were familiar to us of old.

And then there are the political innovations. The Greeks gave us all their different varieties; democracy, oligarchy, the mixed monarchy-oligarchy of Sparta. The Romans had their republic, and even during the imperial period rejected the institution of ‘kinship,’ though all the powers of a king were eventually accrued to the emperors.

But political debate existed outside of Greece and Rome. In China political and ethical philosophy were intertwined, the tension between Legalism and Confucianism would continue down through the ages after the official ascendancy of the latter during the Former Han. In India there was a variety of forms of governance characterized by differing levels of centrality before the conquest of the Mauryas set the horizons and template for much of the rest of South Asian history.

Democracy and republics faded. Republican governments eventually made periodic revivals. During the period of the American Revolution many were skeptical of the idea of such a geographically expansive state such as the United States being able to maintain a republican form of governance. The shift toward a more democratic self-identity in the early 19th century with the rise of Jacksonian populism was even more shocking, because for much of history democracy was seen as a failed Greek experiment which often devolved into illiberal mob rule.

I recall 15 years ago Steven Pinker observing that one reason philosophy has made little progress is that what one could not make progress in was consigned to philosophy, while the natural and social sciences waxed in their ability to model and explain the world around us. This is uncharitable to philosophy in many ways, but it gets at something real: we haven’t pushed much further beyond the Greeks on foundational questions. Similarly, Islam is the last major religion to have emerged, and the theology of Christian churches and the metaphysics of Buddhism and Hinduism are all one to two thousand years old. Instead of progress we’ve seen shifts back and forth in fashion. Reworking of templates, not the creation of new things.

Over the past few centuries we have witnessed something different than this. The birth of the modern. The explosion of democracy and liberalism, and economic well being through massive gains to welfare and well being to the non-elites. Between 1800 and 1970 the wage gap between the skilled and unskilled in Western societies shrank. Seen from the first half of the 1960s the future was shiny, infectious disease was going to be unknown, and robots would allow us a life of leisure.

Though we do have iPhones and other shiny devices, and nerds like me can consume lots information on the web, things have not quite worked out in exactly the way predicted. Yes, China and much of the developing world has improved in terms of vital statistics. And it looks like space commerce may finally arrive in the next decade. But we do not have a Mars colony in 2017, let alone a Moon colony.

Economic productivity combined with a demographic transition mean that extreme deprivation is slowly being strangled. But inequality flourishes, and the wage gap between the skilled and unskilled began to increase after 1970 in the developed world. Whereas at one point the Whiggish perception that history was progressive, and that it would end in some quasi-utopian terminus, was self-evident, today many are not as certain. The unipolar geopolitics of the 1990s has given way to a new farcical world of the “Great Game,” while secular Arab nationalism has faded to irrelevance in the face of a resurgence Islamic identity.

History does not move in cycles where the future reenacts the past. But much of the modular furniture of existence seems to be 2,000 years old. The Salafi movements the world over are fundamentally products of modernity, or the reaction to various elements of European modernity. Their roots pre-date the 20th century, and go back to revivals in the Arabian peninsula in the 18th century which parallel a reconstruction of self conscious orthodox Islam in India as the Mughal order was collapsing. But ultimately they are refurbishing the furniture put together by Ibn Hanbal in the 9th century, who himself might have been comfortable among Judaean Zealots. The Taliban are simply the Maccabees of our age.

From an American perspective the reality, the necessity, of the spread of democracy and the expansion of liberalism seem self-evident. Inevitable. Along with technology and science, it all seemed to hang together. In the 1990s the future was arriving as scheduled.

In 2017 the Russian experiment with Western democratic forms has not turned out how we wanted. Though China is economically liberal, it is not democratic. The global capitalist elite were as surprised as everyone else by 2008, and in the wake of that shock they have persuaded themselves that there is no need for a fundamental rethink of the institutions that they’ve developed over the past 70 years since the Bretton Woods Agreement.

As the Western economic elite continues to persist in denial, the cultural elite has been making a broad push to sweep post-1960s social liberalism throughout the world. This, all the while that Western societies have been demographically stagnant, and Western economic power has been declining in relative terms.

We are in the late stages of the long 20th century. The institutions and mores of the post-World War II are still with us, like Zeitgeist zombies. But the combination of global capitalism, individualism, democratic values always constrained by oligarchic preferences, and the universal acid of Critical Theory infused identity politics, does not hang together in a robust fashion. In most of the world if people have to pick between their ‘sexual identity’ and their ‘religious identity’, I think it will be the latter (assuming they concede that a sexual identity is a thing). In the early 20th century Marxists had to confront the fact that internationalism was not capable of overcoming nationalism. In the 21st century the identity politics of individual self-actualization and self-definition will likely confront 2,000 year old identities.

Ideologues dream of final victories. Of ideologies sweep through the world, from sea to sea. Global Communism. A world-wide capitalist order defined by free trade and free movement of peoples. China and India converting to Christianity and finally ending the civilizational conflict between Christendom and Islam, as Muslim MENA is constricted between Christian Europe, Africa, and Asia.

But pluralism has defined the last few thousand years. The final victory has been elusive. The old ideologies and religions do not die, they evolve, they reinvent, they repurpose. The stories are different in each age, but they live in a shared universe of characters who also repeat similar plot elements.

The second century BC was a strange time for the Roman republic. It was an empire in all but name. The ancient enemy Carthage was no more. But destitution was also coming to some of the Roman people. This resulted in reformers attempting to right the ship of state. The brothers Gracchi attempted to help the plight of the Roman poor with redistribution.  Marcus Livius Drusus expanded the franchise to non-Roman Italians. Political redistribution if you will. Gaius Marius began as a necessary general, but ended as a chaotic autocrat. The social cohesion of the Roman republic was breaking down. Faction began to dominate all of public life.

Into situation stepped Sulla. Sulla is not a contingent man. Sulla is a type. A reaction, usually a vain and futile attempt to hold the past together, and push it into the future, by brutal means. Sulla arises when social elites lose faith in the present, and attempt to recreate institutions from an idealized past.

Sulla is efficient. Cruel, but certain in his rightness. Sulla is not a clown. He is not narcissistic, for Sulla does have ideals, even if you hold that those ideals are cruel or callous. Sulla is a piece of furniture, found in many places at many times. The United States of America has not seen Sulla yet. I believe it will.

May 18, 2017

A problem with Fellowship of the Ring

Filed under: Fellowship of the Ring — Razib Khan @ 10:50 pm

Do you notice something off with this scene? Can you guess what bothers me?

Tales of the Chinese future past

Filed under: China,Chung Kuo — Razib Khan @ 10:00 pm

In the first half of the 1990s I was an avid reader of David Wingrove’s Chung Kuo series. This is before I knew much about Chinese history, or much about life to be honest. This vast epic future history is set in a world where a resurgent China dominates the world. Wars of genocidal extermination against the black and brown peoples, as well as the Japanese, have left the ethnographic topography rather simpler. Europeans exist as a subaltern race in the techno-Confucian order.

The Chinese hegemony erases the true history of the human past and promulgates a fictional alternative history, which the populace accepts as the truth. In this telling the semi-legendary Chinese general who was turned away by the Parthians 2,000 years ago continues westward, and ultimately China conquers Rome. All institutional organized religion is obliterated from existence and memory; no Christianity, no Buddhism. It is as if the Former Han dynasty had access to 21st century technology.

Earth is ruled by a small oligarchy of virtuous monarchs. Progress is dampened in the interests of social stability. The world is explicitly stratified into classes, though there is some mobility upward and downward within a single generation. They know their world’s history is a foundation of lies, but lies are seen as critical to social harmony and stability. The truth may set people free, but this is not a world where freedom is the primary value. Rather, stability and social harmony are prized.

Though Wingrove’s narrative is not without some sympathy for the dominant social order in terms of what it was attempting to achieve (they were not Legalists, but rather moralists), ultimately the most sympathetic protagonists channel the values of the late 20th century West. Truth, progress, and individualism.

Reading this series in the first half of the 1990s as a teenager it all seemed fantastical. Liberalism, Western liberalism, was inevitable as humanity’s terminal state. We all knew that. As the Chinese grew wealthier the expectation by many was that they would begin to inch toward Western norms and institutions, just as the collapsing Soviet Union was. The very concept of a jarring lateral shift in norms, values, and Weltanschauung, was quite literally the stuff of science fiction!

I now believe that I was very wrong about many things back then, and David Wingrove’s fertile imagination grasped far deeper, and perhaps troubling, possibilities about the arrow of history. In 2011, after a 15 year hiatus, Wingrove returned to this series with a prequal, Son of Heaven. It is perhaps an appropriate time for me at this juncture to revisit this world, and even look at it with more sympathy as an adult than I did as a child.

Of course I’ll also be re-reading my Xunzi. In translation I feel as if I’m missing but, but my hope is that re-reading will allow me to gain insight. Unfortunately I am hopeless at languages, otherwise I would attempt to learn to read Mandarin at this advanced age.

Notes on my social media fast

Filed under: Facebook,Social Media,twitter — Razib Khan @ 9:19 pm

I turned on StayFocused last Thursday and set it for a week. I locked myself out of Twitter and Facebook.

Because so many people now message via Twitter and Facebook I did check via Chrome on my phone once a day. But I didn’t check the stream of messages at all.

Obviously a lot has happened in the news over the past week. Being off Twitter meant I found out about thinks a bit more slowly. But that’s OK.

I’m back on Twitter. But I am not going to reinstall it on my phone. I try and be accessible to people and respond to them…but over the years it has gotten too much. I get tagged in so many conversations. From now on I’m much more likely to ignore them.

There are still things Twitter is useful for. Things I want to say that are easier to say there. But most of the “conversations” are not worth it. Many of them are circle-jerks. In other cases a sincere person like Nicholas Christakis has to show almost Job-like patience with others who don’t play by rules of fairness and charity.

Facebook is a different case. I don’t use it to chatter with people. Rather, I post about my children or what I’m eating. I like baby pictures and see what’s happening in peoples’ lives who I know in some way. I missed it, but not that much. But I also now think it is far less toxic (in part because I’ve “trained” Facebook not to show me all the political arguments and such). I think this week has given me insight into why Facebook is so much more popular and valuable than Twitter.

On the balance when it comes to intellectual discourse, I think Twitter has made things worse.

To be a scientific intellectual today

Filed under: Career,Genetics — Razib Khan @ 2:41 pm

George Busy has put up note about changes in his career path, Meditation on the Caltrain. I took offense to this section:

On top of this, there was the burgeoning realisation that no one actually reads the academic papers that I write. This is no moot point: writing papers is the main purview of a research scientist, and the central way we both communicate our results and measure success. However, compared to the proportion of the world’s population who can read, the number of people that had sat down to ingest my latest, dense, and fascinating (to me at least) treaty on the population genetics of Africa, three years in the making, was minuscule. The words of a colleague rang in my head: “99.9% of scientific papers just don’t get read”.

His most recent paper, Admixture into and within sub-Saharan Africa, was great. I meant to blog it, but got busy with other things. To be frank the fact that someone like George Busy is having trouble in the academic market is sobering. He has produced good and prominent work, and has been attached to groups which have some prominence. Of course grant approvals and job prospects have a stochastic element. But his experience shows that talent and good work is just a necessary, not sufficient, condition.

It looks like Busby will land in Silicon Valley with one of the two companies that do a lot of work on ancestry. Good for him. I think it does behoove those of us with intellectual pretensions to wonder what we’re doing out in the world. And, it also behooves academics to wonder what they’re doing with their job security. Sometimes it is important to tell the truth and explore topics even if people don’t care, or don’t want to listen. Otherwise, why fund anything that’s not practical with the public fisc?

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