The union of being brown

Something which having this blog allows is to elaborate on theories/positions I’ve exposited for years on the Sepia Mutiny weblog. One of those ideas is an inclusive model of being brown (Desi). In set theory basically I’m suggesting that the set of those who are defined or self-define as brown/Desi can be reasonably modeled as the union of various other sets. In contrast, an exclusive model would posit that a brown person is an intersection of various other sets. Arguably some proponents of Hindutva explicitly adhere to this exclusive model, where only Hindu South Asians who are resident in South Asia are real browns. In contrast, in my model Bobby Jindal remains brown, despite him being American, and being a convert to an Abrahamic religion. Evangelical Protestant Gypsies in France are arguably brown; they may have some residual South Asian ancestry, and often retain many South Asian customs as well as Indo-Aryan language. People of European descent born and raised in India are also brown. They may not be typical in appearance, or even religion, but their upbringing in a South Asian milieu makes them at least as brown in my opinion, if not more so, than Diasporic browns. Adopted children who are of South Asian origin are also brown because of their indubitable ancestry through their appearance. It doesn’t matter if they have a Minnesota accent and are involved in the Lutheran youth group, and couldn’t tell Kolkota from Karachi from Kodaikanal.

But this inclusive model doesn’t deny that there are some brown people who are more prototypically brown. Hinduism is the South Asian religion par excellence. Islam is not, despite the largest numbers of Muslims in the world being resident in South Asia. All things equal being a Hindu gives one more of a brown stamp than being a Muslim. Similarly, being a Syrian Christian and not an evangelical Protestant in Kerala roots one in South Asia as opposed to a world wide Protestant community. There are white skinned pale brown people, but the reality is that the typical brown person is…brown-skinned.

This doesn’t mean that I’m the pope of brown people. You’re brown/Desi if you say you are in my book. But terms and categories need to have some utility. And this sort of way of classification and identification is I think instrumentally useful. It allows us to make comparisons. I would say, for example, that Zach is arguably more brown than I am despite his mixed ancestral heritage because of his manifestly clearer association with a South Asian nation, Pakistan, and his identification with many aspects of South Asian civilization. Myself, I admit frankly that I’m very alienated from South Asian high culture, and am drawn more to China and the West. But because of my ancestry it would be foolish for me to deny that I am South Asian.

2011, onward, ho!

I’m not big for introspection. So I’ll keep this plain & simple.

Thanks to Amos Zeeberg & Gemma Shusterman for taking care of the technical details of this weblog so I don’t have to deal with it. This is not a trivial matter; I’ve dealt with the technical upkeep of other weblogs for many years, and the time drain can be frustrating. Thanks to Erin Johnson, who kept house at ScienceBlogs for the first 25% of 2010. Big shout out to Ed Yong, who moved with me from ScienceBlogs, and to the whole blog crew who welcomed us.

Special thanks to Jason Goldman, Dave Munger, and Kevin Zelnio, who have given me perspective on science blogging and the world that is twitter, etc. Also Dr.Daniel MacArthur, whose copious re-tweets always seem to be accompanied by new followers (also, hope T. MacArthur enjoys his first full year). Shout out to Tyler Cowen, whose regular links have allowed this weblog to expand into the mindshare of those who read more than science weblogs. Also Reihan Salam, in the same vein. Finally, whoever reads me at the Atlantic and keeps linking to me periodically, I appreciate it.

The course of my blogging this year was strongly shaped by the ideas and thoughts of Greg Cochran, John Hawks, and Henry Harpending. Also Nick Patterson, though at further remove through his published works. Mad props to Dienekes Pontikos for the Dodecad Ancestry Project. Obviously thanks to the private foundations and governments who fund the awesome research which feeds the gullet of this weblog. 23andMe also for bringing genomics to the people.

Thanks to Ron Unz for the fellowship which allows me to focus fully on my intellectual endeavors, modest as they are.

To the commenters who keep the level of discourse high enough to periodically mitigate my misanthropy, much thanks. For all those of you who submit links from this weblog to digg, reddit, Facebook, etc., that too is appreciated. Traffic has never been a #1 priority, but I do take notice when some of my longer essays receive wide circulation. I’m amused when posts which I cobbled together in 30 minutes bring me over 100,000 page views.

Special mention of the various people associated with the old Gene Expression weblog. You know who you are.

A big shout out to the katz who allow me to post their pictures on the internet. And to all the “offline” friends, family, etc.: thanks for pulling me off the internet periodically. Though let’s watch what I eat & drink more closely from now on.

Finally, to all those who I haven’t mentioned, but should have, Happy New Year to you!!!!

A reminder, to follow me:

My total feed:

My twitter:!/razibkhan

The blog’s Facebook:

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My “home page”:

Mapping the “Green Sahara”

Guelta d’Archei, Chad. Credit: Dario Menasce.

Everyone who is literate knows that the Sahara desert is the largest of its kind in the world. The chasm in cultural, biological, and physical geography is very noticeable. Northern Africa is part of the Palearctic zone, while the peoples north of the Sahara have long been part of the circum-Mediterranean population continuum. The primary continuous habitable corridor is that of the Nile valley. And yet scholars have long known that there has been variation in the climatic regime of the Sahara. The pharaohs of ancient Egypt seem to have hunted a wider range of fauna than is to be found in the deserts surrounding the current Nile valley, perhaps relics from a more humid period. Rock art in some regions of the desert indicate aquatic life, and species more characteristic of the savanna. And yet we should not think of the Sahara as a recent phenomenon; it does seem to be geologically ancient, despite periodic humid interregnums.

ResearchBlogging.orgA new paper in PNAS attempts to map the hydrography of the Sahara over the Holocene, as well as back to the Pleistocene. The ultimate aim seems to be to better frame the geographic constraints on the expansion of humanity from its African homeland, and refute a simple projection from the present to the past. In this case, it is the existence of the Nile as a verdant and habitable watercourse which connects the north and south, and bisects the continuous desert. Ancient watercourses and biogeography of the Sahara explain the peopling of the desert:

Evidence increasingly suggests that sub-Saharan Africa is at the center of human evolution and understanding routes of dispersal “out of Africa” is thus becoming increasingly important. The Sahara Desert is considered by many to be an obstacle to these dispersals and a Nile corridor route has been proposed to cross it. Here we provide evidence that the Sahara was not an effective barrier and indicate how both animals and humans populated it during past humid phases. Analysis of the zoogeography of the Sahara shows that more animals crossed via this route than used the Nile corridor. Furthermore, many of these species are aquatic. This dispersal was possible because during the Holocene humid period the region contained a series of linked lakes, rivers, and inland deltas comprising a large interlinked waterway, channeling water and animals into and across the Sahara, thus facilitating these dispersals. This system was last active in the early Holocene when many species appear to have occupied the entire Sahara. However, species that require deep water did not reach northern regions because of weak hydrological connections. Human dispersals were influenced by this distribution; Nilo-Saharan speakers hunting aquatic fauna with barbed bone points occupied the southern Sahara, while people hunting Savannah fauna with the bow and arrow spread southward. The dating of lacustrine sediments show that the “green Sahara” also existed during the last interglacial (∼125 ka) and provided green corridors that could have formed dispersal routes at a likely time for the migration of modern humans out of Africa.

This paper was written before the Denisovan admixture results shifted the necessity to genuflect so explicitly to Out of Africa. But its results are interesting nonetheless, since they don’t depend too deeply on a paleoanthropological model. Rather, by surveying biogeogeography and geologic data they produce a sense of how the Sahara exhibited climatic flux over the past 100,000 years as a function of time and space. The latter is important because the Sahara is not an amorphous sandy waste. Rather, it exhibits a great deal of topographical variation:

Credit: T L Miles

In the Tibesti mountains the highest peaks are ~11,000 feet above sea level (3,400 meters). Because of the aridity of the Sahara in general even these elevations does not induce sufficient precipitation to produce a “green mountain” effect, common in other arid parts of northern Africa and Arabia. But in a regime of slightly only higher precipitation and milder temperatures (remove 3 degrees fahrenheit per 1,000 feet against latitude controlled sea level temperature) one can imagine the Tibesti having been much more biologically productive in the past. Consider this from the Tassili n’Ajjer region of southern Algeria:

Because of the altitude and the water-holding properties of the sandstone, the vegetation is somewhat richer than the surrounding desert; it includes a very scattered woodland of the endangered endemic species Saharan Cypress and Saharan Myrtle in the higher eastern half of the range.

The range is also noted for its prehistoric rock paintings and other ancient archaeological sites, dating from neolithic times when the local climate was much moister, with savannah rather than desert. The art depicts herds of cattle, large wild animals including crocodiles, and human activities such as hunting and dancing….

The main thrust of the paper seems to be to refute the common assumption that an eternal Nile served as the north-south corridor for African fauna, including humans. Here is the reason:

Reanalysis of the Saharan zoogeography…suggests that many animals, including water-dependent creatures such as fish and amphibians, dispersed across the Sahara recently. For example, 25 North African animal species have a spatial distribution with population centers both north and south of the Sahara and small relict populations in central regions. This distribution suggests a trans-Saharan dispersal in the past, with subsequent local isolation of central Saharan populations during the more recent arid phase. If a diverse range of species (including fish) can cross the Sahara, it is impossible to envisage the Sahara functioning as barrier to hominin dispersal. The zoogeography of the Nile suggests that it was a much less effective corridor…Only nine animal species that occupy the Nile corridor today are also found both north and south of the Sahara….

There are also isolated pieces of evidence which refute a Nile-only model: Saharan oases which have endemic species of crocodiles. The existence of “desert crocodile” populations is a signal of a more well-watered past, with a subsequent retreat into isolated oases (some of these populations did go extinct in the 20th century though). In some ways this is a problem. Simple models make simple predictions, and are easier to test. But if simple models are false, that is an even greater problem.

Here are the figures which outline the primary results from geology and biogeography:

There are two primary inferences made in regards to humans:

1) The Holocene inference seems to be that Nilo-Saharan populations have their origins in the societies which expanded north and south along the liminal zone of the Sahara. The authors argue that Nilo-Saharan populations on isolated oases in the northern Sahara are relics from the past expansion in the early Holocene. This sounds plausible, but it would be nice to explore this in more depth via linguistic and genetic analysis. With the rise of the camel and Islam a trans-Saharan trade in humans may have resulted in a great deal of trans-location of whole populations from one area to another. Concurrent with the Nilo-Saharans who pushed north the authors also suggest that savanna hunters moved south. I am not clear who these people are from the paper, and the mapping between archaeology and linguistics here seems more tentative.

2) A deep history inference also seems to be that trans-Sahara population movements were feasible in a period around 120-100 years BP, but not 50-60 years BP. The distinction here matters because the latter is a relatively young age for the Out of Africa migration, while the former is an older one. If the latter view is correct then the only plausible route of migration is probably the coastal fringe of the Horn of Africa. If the former view is correct then a whole host of possibilities confront us, because the hydrography of the Sahara may have been constrained, but there were several avenues of migration.

In regards to #2, a clement phase, and then resealing of the genetic barrier, may align well with recent models which posit a non-trivial period of separation between Africans and non-Africans after the Out of Africa migration. In other words early modern humans may have followed the pattern of many species, with  an expansion into, and beyond, the Sahara, and then a subsequent separation of two populations by a resurgent desert. The difference is that the daughter population isolated on the far side of the desert eventually “broke out” from the margins of the African homeland to the rest of the world.

Citation: Drake NA, Blench RM, Armitage SJ, Bristow CS, & White KH (2010). Ancient watercourses and biogeography of the Sahara explain the peopling of the desert. Proceedings of the National Academy of Sciences of the United States of America PMID: 21187416

Friday Fluff – December 31st, 2010

FF3 1. First, a post from the past: Golden ideas.

2. Weird search query of the week: “young girls gone mature”.

3.Comment of the week, in response to Slouching toward idiocracy:

JWM and Dave Both hit on key concepts here.

Its not just cats, cattle and humans, in fact the relative brain size of almost all domesticates is smaller then their wild ancestors . This just part of a suite of changes that characterize domesticates. Including reduced size, a more pronounced forehead, a shorter foreface, overall increased morphological diversity, a wider range of coat colors, long hair, curly hair, naked skin, and reduced dentition. Most of these characteristics are seen in modern humans relatives to our ancestors. Compared to erectines and neanderthal and even early AMH modern humans are less skeletally robust, have shorter forefaces and larger foreheads and smaller teeth in more crowded jaws. Compared to chimps we are characterized by being having naked skin, long hair of an astonishing variety of color and form and increased morphological diversity even within genetically homogeneous populations.

The belyaev Domestic fox experiments, provides a very intriguing clue as to why this might be. Belyaev was able to induce all of the morphological changes typical of domestic animals in foxes by breeding for a single characteristic, Tameness. Tameness can be conceived of as openness to novel social situations and strangers. This is characteristic of all juvenile animals but rare in adult wild animals. Selection for this trait seems to effect developmental genes which have major effects in morphology resulting in these typical patterns of morphological change.

Domestic animals are generally less intelligent then their wild ancestors but they appear to have domain specific capacities for social learning and thinking that their wild ancestors don’t

I suspect that the development of just such capacities as been one of the primary selective patterns behind the development of modern humans. We may have lost some individual brain power but without the evolution of those social capacities I doubt we would have ever been able to harness that brain power to build civilization. I also think it’s quite likely that the selective environment of civilization has selected for a horde new adaptions on traits like IQ and time preference which would have not been as advantageous for our paleolithic ancestors.

4) Was 2010 exciting for you?

5) And finally, your weekly fluff fix:

On to 2011….

Predictions, expectations, etc.

More use of the term “polytypic”.

Ötzi turns out to have Near Eastern affinities.

The Hobbits finally have some genetic material successfully analyzed.

Many, many, more human origins stories spun out of control by the press. Without a rock-hard interpretative framework like “Out of Africa” there is less “functional constraint.”

Facebook peaks in terms of cultural influence. Its user base and profits will continue to grow, but there will be a new “It” company.

The economy will grow faster than economists’ expectation. I don’t have great hope or insight, but economists’ forecasts are usually wrong, and lean toward conventional wisdom. The conventional wisdom is that we’ll muddle along.

More about exomes.

The blurring between blog and mainstream media will continue.

The segmentation of the blogosphere will continue.

Barack H. Obama will be profile as the “comeback kid” by conventional wisdom peddlers by the end of 2011.

People will start to get annoyed by the proliferation of “social media” firms, and the bubble will burst.

23andMe will have 200,000 customers by 2011.

Perl 6 will go prime-time, but it will be clear that working on IBM-time meant that they missed their window of opportunity.

Top 10 Gene Expression posts of the year

According to Google Analytics, they are:

10 – 1 in 200 men direct descendants of Genghis Khan.

9 – Most atheists are not white & other non-fairy tales.

8 – Which American racial group has the lowest fertility?

7 – No Romans needed to explain Chinese blondes.

6 – To classify humanity is not that hard.

5 – To gain pallor is easier than losing it.

4 – Why Tibetans breathe so easy up high.

3 – Genetics & the Jews.

2 – Verbal vs. mathematical aptitude in academics.

1 – People of class drink alcohol.

The Axial Age & world population

A few days ago Robin Hanson brought this chart of world population to my attention:

On the x-axis you have time, 12,000 years ago to the present. On the y-axis an estimate of the total world population log-transformed. The data is derived from the US Census low estimate. Granting the data’s accuracy for the purposes of reflection, Robin’s question was what could have occurred between 1000 and 500 BC to produce such a rapid population rise?

My immediate response to Robin was that perhaps the transition from widespread utilization of bronze to iron democratized tool use so that more land was brought under cultivation. Bronze tools and weapons were the privileges of the elite because of the high capital investments for the production of the alloy. Stone or copper remained the norm for peasants. With the switch to iron per unit cost of production for metal tools went down. There is a hypothesis for example that only extensive use of iron tools allowed for the clearing of the eastern Gangetic plain and the expansion of Indo-Aryan civilization to the Bay of Bengal.

A second complementary suggestion I made is that biological changes in the horse allowed for the emergence of full-fledged nomadic lifestyles with the development of mounted cavalry. In Empires of the Silk Road the author makes the argument that Inner Asian nomadic groups were much more important in being facilitators for diffusion of ideas, and even the originators of ideas, than we give them credit for. A tentative assertion is made that the Axial Age itself was the work of horse riding nomads! Whatever the reality of that specific claim, one could outline a model where the free flow of ideas accelerated during this period because of the rise of mobile populations such as the Scythians, whose cultural domain spanned the whole Ecumene.

And then there are even stranger ideas, such as Julian Jaynes’ ‘bicameral mind.’


Image Credit: Waldir, Wikimedia Commons

Are Turks acculturated Armenians?

To the left you see a zoom in of a PCA which Dienekes produced for a post, Structure in West Asian Indo-European groups. The focus of the post is the peculiar genetic relationship of Kurds, an Iranian-speaking people, with Iranians proper, as well as Armenians (Indo-European) and Turks (not Indo-European). As you can see in some ways the Kurds seem to be the outgroup population, and the correspondence between linguistic and genetic affinity is difficult to interpret. For those of you interested in historical population genetics this shouldn’t be that surprising. West Asia is characterized by of endogamy, language shift, and a great deal of sub and supra-national communal identity (in fact, national identity is often perceived to be weak here). A paper from the mid-2000s already suggested that western and eastern Iran were genetically very distinctive, perhaps due to the simple fact of geography: central Iran is extremely arid and relatively unpopulated in relation to the peripheries.

But this post isn’t about Kurds, rather, observe the very close relationship between Turks and Armenians on the PCA. The _D denotes Dodecad samples, those which Dienekes himself as collected. This affinity could easily be predicted by the basic parameters of physical geography. Armenians and Anatolian Turks were neighbors for nearly 1,000 years. Below is a map which shows the expanse of the ancient kingdom of Armenia:

Historic Armenia was centered around lake Van in what is today eastern Turkey. The modern Republic of Armenia is very much a rump, and an artifact of the historic expansion of the Russian Empire in the Caucasus at the expense of the Ottomans and Persians. Were it not for the Armenian genocide there may today have been more Armenians resident in Turkey than in the modern nation-state of Armenia,* just as there are more Azeri Turks in Iran than in Azerbaijan. Many areas once occupied by Armenians are now occupied by Kurds and Turks. But a bigger question is the ethnogenesis of the Anatolian Turkish population over the past 1,000 years.

Dienekes has already shed light on this topic earlier, adding the Greek and Cypriot populations to the mix as well as Turks and Armenians. The disjunction between Kurds and the Armenian-Turk clade suggests to us that Turks did not emerge out of the milieu of Iranian tribes in the uplands of southeast Anatolia and western Persia. Like the Armenians the Kurds are an antique population, claiming descent from the Medes, and referred to as Isaurians during the Roman and Byzantine period.

Below is a reformatted K = 15 run of ADMIXTURE with Eurasian population. I’ve removed the labels for the ancestral components, but included in populations which have a high fraction of a given ancestral component. The geographical labels are for obscure populations. I’ve underlined the four populations of interest:

First, let’s get out of the way the fact that Turkish samples have non-trivial, though minor, northeast Asian ancestry. The Yakut themselves are a Turkic group situated to the north of Mongolia. The more southerly and central Asian affinities the nomadic ancestors of the Anatolia Turks may have picked up in their sojourns over the centuries between their original homeland in east-central Siberia and Mongolia and West Asia. The rest of ancestry is rather typical of northern West Asian groups. In particular, Armenians! Here is the ancestral breakdown for the four groups I want to focus on using Dienekes’ labels:

Population Greek Cypriots Turks Armenians
West Asian 37.6 54.1 47.2 56.3
Central-South Asian 5.3 8.6 18.2 18.4
North European 25.1 5.6 12 12.3
South European 27.4 20.8 9.4 8.4
Arabian 3.4 8 4.3 3.4
Altaic 0.3 0 2.6 0.1
East Asian 0.3 0.2 2.2 0
Central Siberian 0.1 0.2 1.4 0.2
Chukchi 0 0 1.1 0.2
South Indian 0 0.1 0.8 0.3
Nganasan 0.1 0 0.4 0.2
Koryak 0.1 0 0.2 0.1
East African 0 0.4 0.1 0
West African 0 0 0.1 0
Northwest African 0.3 1.9 0.1 0

And now the correlations between the populations by ancestral components:

Greek Cypriots Turks Armenians
Greek * 0.863 0.823 0.813
Cypriots * * 0.941 0.946
Turks * * * 0.997
Armenians * * * *

Let’s remove the East Eurasian and African components, and recalculate the proportions by taking what remains as the denominator:

Population Greek Cypriots Turks Armenians
West Asian 38.1 55.7 51.8 57.0
Central-South Asian 5.4 8.9 20.0 18.6
North European 25.4 5.8 13.2 12.4
South European 27.7 21.4 10.3 8.5
Arabian 3.4 8.2 4.7 3.4

And the recomputed  correlations:

Greek Cypriots Turks Armenians
Greek * 0.747 0.640 0.647
Cypriots * * 0.901 0.908
Turks * * * 0.999
Armenians * * * *

With all the ~0 ancestral components which were common across these four populations removed the correlations have gone down. Except in the case of the Armenian-Turk pair, because I’ve removed the ancestries which differentiate them.

So what’s a plausible interpretation? A straightforward one would be that the Muslim Turk population of Anatolia has a strong bias toward having been assimilated Armenians, rather than Greeks. The cultural plasticity of Armenians in late antiquity and the early medieval period was clear: individuals of ethnic Armenian to origin rose the pinnacles of the status hierarchy of the Orthodox Christian Greek Byzantine Empire. The Macedonian dynasty of the Byzantines under which the civilization reached its mature peak were descended from Armenians who had resettled in Macedonia. Just as plausible to me is that eastern Anatolia as a whole exhibited little genetic difference between Greeks and Armenians, and the former were wholly assimilated or migrated, while the Armenians remained. One way to test this thesis would be type the descendants of Greeks who left eastern Anatolia during the population exchange between Greece and Turkey in the 1920s. But the difference between Greeks and Cypriots also points us to another possibility: perhaps the Greeks of Greece proper (as opposed to Anatolia) were much more strongly impacted by the arrival of Slavs? One need not necessarily rely solely on the Scalveni migrations either, water tends to be a major dampener to conventional isolation-by-distance gene flow, so the Greek mainland may always have been subject to more influence from the lands to the north.

Whatever the details of ethnogenesis may be, it will be interesting to see how things shake out as we increase sample sizes and get better population coverage. These results may be due to regional selection bias. One might expect that the descendants of Rumelian Turks be more “European” than Anatolian Turks. But, these data do seem to suggest on face value that Armenians are the population which Anatolian Turks have the most genetic affinity with.

* My main hesitation would be that Armenians are a very mobile population, and their numbers within a modern Turkey may have declined simply through emigration, just as those of Christian Arabs have over the 20th century.

Technology & genetics in the 21st century

I assume there will be more stories like this in the next year, Gene Machine:

The machine that could change your life is a compact device, only 24 inches wide, 20 inches deep and 21 inches high. At a glance you might mistake it for a Playskool toy–or, better yet, the Apple II computer, which sparked a revolution. Indeed, this gizmo, developed in a drab office park overlooking a duck pond in Guilford, Conn., could have as dramatic an impact as any technology since the personal computer and help kick off a market that one day could be worth perhaps as much as $100 billion.

Take a closer look. On the right side is an 8-inch touchscreen, on the left a dock that allows data to be downloaded to an iPhone. Below that is a row of four test tubes, marked with a circle, an X, a square and a plus sign. These symbols represent the four basic chemical letters, or bases, the body uses to form DNA–guanine, cytosine, adenine and thymine.

Audaciously named the Personal Genome Machine (PGM), the silicon-based device is the smallest and cheapest DNA decoder ever to hit the market. It can read 10 million letters of genetic code, with a high degree of accuracy, in just two hours. Unlike existing DNA scanners the size of mainframes and servers, it fits on a tabletop and sells for only $50,000, one-tenth the price of machines already out there. For the first time every scientist, local hospital and college will be able to afford one. If the PGM takes off and regulators let him, your family doctor could buy one–and so could you, if, say, you wanted to see how fast that thing growing in your fridge is mutating.

Rothberg faces three formidable hurdles. First, the market for sequencing is dominated by Illumina of San Diego, whose big machines have helped make most of the major discoveries so far–and competing won’t be easy. Next, a novel (and faster) approach could leapfrog the Ion Torrent device. Finally, sequencing could ultimately be a bust if it proves tough to find genes linked to disease, or improved cancer diagnoses and hoped-for improvements in manufacturing drugs.

This seems a case where the technological innovation has raced ahead of the science which could leverage the new possibilities. Then again, it might also be a chicken & egg issue. If firms such as 23andMe get enough customers they might be able to drive the research themselves and therefore create their own demand.