Razib Khan One-stop-shopping for all of my content

December 31, 2010

The union of being brown

Filed under: Brown,Category,Desi,Identity,South Asian — Razib Khan @ 3:56 pm

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!

Filed under: 2010,Blog — Razib Khan @ 3:03 pm

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:

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Mapping the “Green Sahara”

Filed under: geography,Geology,Green Sahara,Human Evolution,Out-of-Africa,Sahara — Razib Khan @ 2:30 pm


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

Filed under: Blog,Friday Fluff — Razib Khan @ 12:00 pm

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 http://tiny.cc/ty6n9 . 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 http://tiny.cc/diffx, 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 http://tiny.cc/cjfpt.

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….

Filed under: Blog — Razib Khan @ 9:01 am

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

Filed under: Blog — Razib Khan @ 8:36 am

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.

’tis the day for last second giving!

Filed under: Culture,Philanthropy — Razib Khan @ 8:17 am

I know many people decide on their yearly charitable giving between Christmas and the New Year. If you’ve waited until now, you might want to take some more time and check out GiveWell’s Top international charities.

December 30, 2010

The Axial Age & world population

Filed under: axial age,Culture,Economics,History,julian jaynes — Razib Khan @ 11:26 pm

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.’

Thoughts?

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

Filed under: Genomics — Razib Khan @ 2:35 am

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.

Are conservatives fatter than liberals?

Filed under: Culture,data,Data Analysis — Razib Khan @ 1:10 am

    The maps above juxtaposes the counties which shifted Republican in the 2008 presidential election vs. 2004 (reddish) and the age-adjusted estimated rates of obesity by county in 2007 (darker blue). One issue which I haven’t seen explored too much are the two faces of Appalachia; the Atlantic facing counties are generally healthier than the lowland countries to their east, even controlling for race. In contrast, the west facing counties have some of the lowest human development indices in the United States. West Virginia is the fattest state. And it seems purely from inspection that the east facing counties of Appalachia which shifted toward the Republicans in 2008 are also amongst the fattest in the nation.


    Rush Limbaugh, fat again

    Is this simply a coincidence? A reader queried me about the relationship between politics and weight, wondering about correlations. I don’t follow politics too closely, but apparently there has been some conflict recently between conservatives who oppose the top-down campaign against obesity spearheaded by our cultural and political elites. My perception, which may be wrong, is that some are portraying this as another liberal culture war. To some extent this is dumb, as it seems that the biggest salient predictor of weight is class. The majority of American adults are overweight according to BMI thresholds, and a significant minority are obese. And yet none of the presidential and vice presidential candidates in 2008, or their spouses, were overweight. Take a look at the candidates during the Democratic and Republican debates in 2008, and you can see that they don’t “look like America.” Despite the efforts of NAAFA this is one way that Americans are not too keen on the candidates reflecting themselves. Rather, it seems that Americans were more accepting of fat heads of state when they were a slimmer folk.

    Looking in the GSS there’s one variable which might shed light on the question of politics and weight, INTRWGHT. This is basically an interviewer assessment of the weight of the respondent. It was collected in 2004. I limited the sample to non-Hispanic whites to eliminate population stratification.


    Liberal Moderate Conservative
    Below Average 7.2 6 6.4
    Average 71.8 73.2 70.9
    Somewhat Above Average 18.3 17.1 18.7
    Considerably Above Average 2.7 3.7 3
    Liberal Moderate Conservative
    Below Average 27.9 32.5 39.5
    Average 24.9 35.7 39.4
    Somewhat Above Average 24.7 32.5 42.7
    Considerably Above Average 21.3 41.1 37.6

    The first set of numbers sums to 100% for the rows, and the second set sums the columns. I don’t see a notable different obetween liberals and conservatives. The only exception might be that liberals are more well represented among those who are below average in weight than those who are considerably above average, but the samples are small enough than I don’t trust that to be anything more than measurement error.

    There is another variable in regards to weight which I think is interesting: GENENVO1. The respondents were given this scenario: “Carol is a substantially overweight White woman. She has lost weight in the past but always gains it back again.” Then they were asked to rate the proportion of the outcome which could be attributed to genes. The means were as follows:

    Liberals, 54% environmental
    Moderates: 56% environmental
    Conservatives: 61% environmental

    I was a little dubious about this result, since it goes against stereotype. So I checked the other similar questions.

    “George is a Black man who’s a good all-around athlete. He was on the high school varsity swim team and still works out five times a week.”

    Liberals, 54% environmental
    Moderates: 54% environmental
    Conservatives: 59% environmental

    “Felicia is a very kind Hispanic woman. She never has anything bad to say about anybody, and can be counted on to help others.”

    Liberals, 54% environmental
    Moderates: 58% environmental
    Conservatives: 60% environmental

    “David is an Asian man who drinks enough alcohol to become drunk several times a week. Often he can’t remember what happened during these drinking episodes.”

    Liberals, 55% environmental
    Moderates: 56% environmental
    Conservatives: 58% environmental

    The differences are small, but consistent. It could be incorrect coding, and I don’t know how it relates to the current perceived polarization on the issue of weight. My own suspicion is that this is more a creation of the media than anything else, but I am going to look at correlations on the county level data next. But at this point I doubt there’s a culture war around fat. Being fat may not be immoral, but most people would rather be slim. Though how we get there is a matter of some contention naturally.

December 29, 2010

An appropriate name

Filed under: Admin,Introduction — Razib Khan @ 10:07 pm

Brown:

Brown is sometimes used to refer to brown people in general or sometimes more specifically to the darker skinned Indo-Aryan and Dravidian of South Asia.

Pundit:

The term originates from the Hindi term pandit, which in turn originates from the Sanskrit (a language from ancient India) term paṇḍitá, meaning “learned” (see also Pandit). It refers to someone who is erudite in various subjects and who conducts religious ceremonies and offers counsel to the king.

My friend Dr. Daniel MacArthur thinks I’m quite erudite.

Why the “brown pundits”

Filed under: Admin,Introduction — Razib Khan @ 9:35 pm

Zach introduced us pretty well earlier. I’m Razib Khan, I generally cover science and history. I am also known as “razib the atheist” on the Sepia Mutiny weblog. I am brown. All four of my grandparents were born in the eastern part of Bengal, what became Bangladesh. Some of my great-grandparents were born outside of Bengal, from Delhi to Assam. But to my knowledge all my recent forebears are of South Asian provenance, though I suspect Burmese heritage as well.

I have known Zach Latif since 2002. We disagree on many issues, but we are united by a deep interest in history, the superstructure of culture, and the broader patterns of society. Additionally, we are both atypical as South Asians go. Zach, a Baha’i of Pakistani background and recent Persian ancestry. Myself, an atheist American of Bengali ethnicity and originally Bangladeshi nationality. I should also add that I have a deeply skeptical, and moderately unsympathetic stance, toward Islamic civilization, and general lack of comprehension of the abstruse biases of South Asian philosophy and religion. My own personal orientation is in sympathy with the Cārvāka.

Please also follow our twitter account: http://twitter.com/#!/brownpundits. Also, “like” our Facebook page.

December 28, 2010

Beware of British newspapers: fossils edition

Filed under: Human Evolution — Razib Khan @ 10:32 pm

Several readers have pointed me to a headline in a British newspaper, Did first humans come out of Middle East and not Africa? Israeli discovery forces scientists to re-examine evolution of modern man:

Scientists could be forced to re-write the history of the evolution of modern man after the discovery of 400,000-year-old human remains.

Until now, researchers believed that homo sapiens, the direct descendants of modern man, evolved in Africa about 200,000 years ago and gradually migrated north, through the Middle East, to Europe and Asia. Recently, discoveries of early human remains in China and Spain have cast doubt on the ‘Out of Africa’ theory, but no-one was certain.

Professor Avi Gopher, a researcher from Tel Aviv University’s Institute of Archaeology, holds a pre-historic tooth at Qesem cave, an excavation site near the town of Rosh Ha’ayin
The new discovery of pre-historic human remains by Israeli university explorers in a cave near Ben-Gurion airport could force scientists to re-think earlier theories.

Archeologists from Tel Aviv University say eight human-like teeth found in the Qesem cave near Rosh Ha’Ayin – 10 miles from Israel’s international airport – are 400,000 years old, from the Middle Pleistocene Age, making them the earliest remains of homo sapiens yet discovered anywhere in the world.

The “hook” as far as the tabloid is concerned is implicit but straightforward: humans arose in the Holy Land! More broadly I think the recent changes in our understanding of human origins over the past year have unsettled the field enough that sensationalists have an excellent opportunity to populate the landscape with ludicrous claims. One of the beauties of Out of Africa was its elegant parsimony; extraordinary claims were easily dismissed and ignored. But now assertions once viewed as tendentious have to be addressed and examined. There is no single paradigm which so powerfully dominates our conception of reality that deviations from expectation can be ignored without even a superficial glance. This requires greater diligence on our part.

Thankfully Brian Switek has reviewed the original paper on which the media accounts are based. A Fistful of Teeth – Do the Qesem Cave Fossils Really Change Our Understanding of Human Evolution?:

As the authors themselves state, “Resolution of these alternative scenarios must await further discoveries of additional and more complete Middle Pleistocene remains from southwest Asia.” The identity of the Qesem Cave humans remains unclear, as do their origins. Even if they turn out to be early members ofHomo sapiens, this does not automatically mean that our species evolved in Israel first. Instead, such a conclusion would raise several alternative scenarios, including the possibility that there are as-yet-undiscovered deposits of early Homo sapiens fossils in Africa which document an earlier dispersal from Africa distinct from the one around 70,000 years ago. For now, though, the identity of the Qesem Cave humans cannot be conclusively determined. All the grandiose statements about their relevance to the origin of our species reach beyond what the actual fossil material will allow.

Carl Zimmer also observes the disjunction between substance and hype:

Nowhere in this conclusion do the authors say that these teeth belong to Homo sapiens. Nowhere do they say they have just doubled the age of our species. Nowhere do they say that our species evolved in the Near East, not in Africa. There are only some vague hints that the teeth might be “Skhul/Qafzeh-like.” Or they might be something else.

While the paper itself is non-commital in its conclusions, it contains lots of good detail about the teeth, which is why it probably got accepted at the American Journal of Anthropology. Who knows how some reporter got the idea that scientists had discovered the oldest fossils of Homo sapiens. It does seem that one of the authors has played footsie with reporters, offering some tasty quote-bait.

The rise of the skulls!

Filed under: Anthroplogy,Human Evolution,Paleoanthropology — Razib Khan @ 1:55 pm


Neanderthal, La Chapelle-aux-Saints

Fossils matter. Fossils are evidence. That was Milford Wolpoff’s refrain in the 1987 NOVA documentary which heralded the long cresting of mitochondrial Eve and Out of Africa. Fossils remain highly relevant and important when it comes to deeper time phylogenetic relationships, but it does seem that they have only served to supplement the genetic data when it comes to recent human origins (e.g., calibrate and fine-tune molecular clocks). The paleoanthropologist Tim White, whose own position on human origins is at some contradiction from Milford Wolpoff’s, nevertheless felt the need to reiterate the relevance of fossils at a conference several years ago where most of the participants were geneticists (we received a preview of Ardi). Chris Stringer, who advocated for an Out of Africa model before Allan Wilson and his students roiled the academic waters often seems to have been relegated to nothing more than an adjunct to the molecular biologists in the public mind despite his priority. I think we are a turning point, and must acknowledge that recent human origins can no longer remain a one horse buggy. Genetics itself in the form of ancient DNA research, as well as more powerful analytic techniques utilizing larger autosomal data sets, have overturned and challenged the old conventional wisdom gleaned from trusting inferences derived from the patterns of variation of extant populations.


Consider two books from the early 2000s, The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry, and The Real Eve: Modern Man’s Journey Out of Africa. Both were ambitious works drawing bold lines between the patterns of history and genes, disproportionately maternally transmitted mtDNA (ergo, the references to Eve). Even at the time they were works of hubris, mtDNA is one locus, tracing one long uninterrupted line of foremothers. But it misses the total genome variance, and may be subject to various biases. A decade on though we now have grounds to suspect that much of the story told in both works is false. Europeans may have a more complicated history than we could have imagined. Some of the assumptions behind the second book, that most of today’s genetic variation crystallized during the Last Glacial Maximum ~20,000 years ago, also seems likely to be false.

The genetic data no longer cohere together in a plausible integrated whole. And that is of course the beauty of science, that it is subject to revision and revolution, that it eats away at its own foundations on occasion when those foundations are wanting. The very tools of modern genetics have undercut the confidence in genetics as a whole to answer broad expansive historical questions on its own. This is not a flaw in genetic science, it is the strength of science generally. Unlike some systems of thought science does not rest upon timeless creeds and formulas.

So where now? We need to do more than give lip service to a multidisciplinary perspective. We need to embrace it. This means a new relevance and importance to those who know and can interpret the fossil record. It also means more attention to anthropological and historical patterns, which may indicate the probable sample space of genetic outcomes. It will be harder and more uncertain work than what has come before, but the results will hopefully exhibit closer fidelity to the reality that was. False certainty is worse than an admission of ignorance

Image Credit: Wikimedia Commons

December 27, 2010

Denis Dutton, 1944-2010

Filed under: Uncategorized — Razib Khan @ 11:59 pm

Professor, web entrepreneur Denis Dutton dies. Readers of this weblog probably know him for Arts & Letters Daily and The Art Instinct. I never knew the man personally, but he made an impact on me through his website and articles. We shared friends, and I was proud when Arts & Letters Daily put this website on its blogroll, and sent us the occasional link. For me blogging is about ideas, not people, but when someone passes on those ideas are made flesh.

Out of Africa: mend it, don’t end it!

Filed under: Culture,Genetics,Genomics,Multiregionalism,Out-of-Africa — Razib Khan @ 11:51 pm

Dilettante human genetics blogger Dienekes Pontikos has a post up with a somewhat oblique title, Is multi-regional evolution dead? I say oblique because a straightforward title would be “Multi-regionalism lives!” He posted a chart from a 2008 paper which outlines various models of human origins, and their relationship to molecular data at the time. I have also posted the chart, but with a little creative editing on the “assimilation” scenario to reflect the possible Neandertal and Denisovan admixture events. Of these models the “candelabra” can be rejected as highly implausible. It posits very deep roots in a given region for distinct human populations. Unless you accept some sort of hominin population structure in Africa which were maintained by distinctive migrations out of Africa then the “replacement” model can be discarded (since the classic replacement model did not posit ancient African population structure being of any relevance outside of Africa you’d have to salvage it with a modification in light of new results).

So the two primary disputants are a resurrected multi-regional model, and the assimilation model. But these two are really endpoints on a spectrum of models. What you need to do is vary the number of discrete populations and the rate of migration between the populations over time. The beauty of the replacement model was its parsimony: as far as recent human origins were concerned past gene flow via migration was a relatively academic concern. It was an exceedingly simple narrative framework. Consider this first episode of a 2009 British documentary, The Incredible Human Journey:

In the first episode, Roberts introduces the notion that genetic analysis suggests that all modern humans are descended from Africans. She visits the site of the Omo remains in Ethiopia, which are the earliest known anatomically modern humans, and visits the San people of Namibia to demonstrate the hunter-gatherer lifestyle. In South Africa, she visits Pinnacle Point, to see the cave in which very early humans lived. She then explains that genetics suggests that all non-Africans may descend from a single, small group of Africans who left the continent tens of thousands of years ago. She explores various theories as to the route they took. She describes the Jebel Qafzeh remains in Israel as a likely dead end of a traverse across Suez, and sees a route across the Red Sea and the around the Arabian coast as the likelier route for modern human ancestors, especially given the lower sea levels in the past.

A neat and tidy story. But reality is getting a lot less tidy & neat. Personally, the assimilation model as we understand it now seems to be the most plausible model. It remains more parsimonious than the alternatives: ancient population structure and complex patterns of gene flow and hybridization. But parsimony has misled us toward undo confidence in the recent past, so we should not weight this as strongly at this point. Where would we be without ancient DNA extraction? Some researchers have long claimed a more complex model than Out of Africa, but as long we relied in inferences from extant populations theses result were ignored or dismissed (notably, ancient DNA extraction is also unsettling our understanding of the very recent human past).

There is though the pattern of greater African genetic diversity. Dienekes observes that a recent paper reports that some Indian populations may be more diverse genetically than HapMap Africans. I’m not too keen on overturning a generation of consensus yet in regards to this question based on one deeply sequenced region on one chromosome comparing some Indian tribal groups to two HapMap African populations (Yoruba, and a Kenyan Bantu group). So I accept the pattern of greater diversity until further research brings it more into doubt. Now the question is to explain the pattern. The most plausible explanation would naturally be the one outlined above in the 2009 documentary: non-Africans are the descendants by and large of a small number of Africans who left ~100,000 years B.P. They went through a population bottleneck which reduced genetic diversity sharply. Their genetic variance was a subset of that of Africans (with some admixture from other human lineages outside of Africa, as it now happens).

But, there are other possibilities. One option sounds rather bizarre to me on first blush:

With respect to the reduced genetic diversity, one idea is that it is the result of genetic drift following a bottleneck in a small African population. But, the data can just as well be explained by species-wide selection which culled genetic variation.

Presumably selection would operate outside of Africa and homogenize non-Africans through a series of sweeps. Remember that selection and stochastic population events can sometimes be hard to differentiate, because both expunge variation from long swaths of the genome, resulting in long linkage disequilibrium blocks. This seems rather incredible as a proposition to me. Could selection operate all across Eurasia in such a fashion? From what I can tell in relation to more recent signatures of natural selection that does not tend to occur. The pattern for skin color for example is convergent phenotypes through different genetic architectures. How could gene flow tie together ancient human lineages and not H. sapiens sapiens? On the other hand, this could be an explanation for the consistent and taxon wide pattern of encephalization (though I believe this occurred in Africa as well).

A second alternative would be that Africa’s greater genetic diversity is simply a function of a much longer term effective population. In this model the climatic fluctuations of the Pleistocene periodically reduced non-African population to such an extent that these groups became a very minor proportion of the total census size of humans, and were so were swamped out by gene flow with the more numerous African humans. It seems to me that an extreme case of this model really verges into the same territory as the assimilation model. So I see this as more of a difference of degree than kind.

Dienekes points to Y chromosomal markers which suggest “back-migration” to Africa. I don’t totally discount this, but looking at the enormous diversity in groups like the Bushmen, I don’t think we can attribute that to back-migration from Eurasia. It is notable that the Bushmen are basal to the rest of humanity, including the Yoruba + (Eurasicans + Australasians). Also, the genetic divergence between the Denisovan/Neandertal clade and modern humans is only ~33% greater than between Bushmen and Papuans. Speaking of differences of degree, that is becoming more and more the case when it comes to the so-called “dead ends” of human evolution and ourselves.

Finally, there’s the issue of non-neo-African admixture. Reich et al. give a figure of ~7.5% in Melanesians, and ~2.5% in Eurasicans. It is valid I think to point out that though others have offered figures in the literature before only with the reference sequences of ancient DNA are these widely accepted values. Perhaps they would be revised upward with other sequences. But two cautions:

- There are only so many hominins to go around. Australia and the New World were only settled by modern humans. So how many were there running around in Eurasia? I think perhaps there may have been something different in South Asia, but that’s just a very uninformed guess.

- On the margin it seems clear that the autosomal DNA has enough fudge that interpretation meant that the archaic admixture signal could be dismissed. But the upper bound can’t be that high, or the Fst values would be more extreme than they currently are. Modern humans do seem to share a great deal of “shallow” common ancestry.

At the end of the day I am going to put my money on the assimilationist model because I believe in diminishing marginal returns. The Out of Africa replacement model was maximalist. Some tweaking on the margin is not very surprising, at least in hindsight, but more baroque forms of multi-regionalism have far too many moving parts. Newtonian mechanics may have been superseded in some domains by Einstein’s theories and Quantum Mechanics, but for many purposes it does very well at predicting phenomena and modeling the world. I have full expectation of further refinements in the assimilation model, but I would bet that the age of revolutions is over for a long time. Then again, my confidence is modest at best. This is no time for certitudes.

Note: A illustration of models:

Around the Web – December 27th, 2010

Filed under: Blog,Daily Data Dump — Razib Khan @ 12:12 pm

Hope Christmas went well for everyone. No complaints about mine.

Pinboard. Thanks for the Delicious replacement recommendations. I know that Delicious is going to be sold and not shutdown, but confidence is lost. Pinboard seems to work well, and you can import all your Delicious bookmarks. Additionally, there’s a serviceable Chrome extension so that I can easily add bookmarks. Already have the new RSS up: http://feeds.pinboard.in/rss/u:gnxp/.

HTC Evo 4G. I’m not an early adopter of hardware, but I have no big complaints about the HTC Evo 4G. It’s lame that they call it 4G when Sprint’s 4G coverage is so sparse (no coverage in San Francisco, but coverage in Merced and Stockton!). But their version of Android is reasonably user friendly, though not as much as the iPhone (or at least what I could gather from playing around with the iPhones of others). Though I already ran into one app which made the phone crash and reboot. It was an online banking app, distributed by that specific bank.

The genome of woodland strawberry (Fragaria vesca). It’s in Nature, but open access!

Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. This paper has gotten a lot of coverage. I didn’t hit it mostly because of the time investment I made in the Denisovan paper, but I do think it is interesting. The deep separation of African forest and savanna elephant populations may be interesting because of the sort of analogies one can make about the gross evolutionary pressures on mammalian lineages due to ecological and geological parameters. I’m thinking in particular of apes, the bonobo-chimpanzee and hominin vs. ‘great ape’ divisions.


Peretz in Exile. The future of Israel seems to be that of a more conventional Middle Eastern state. The ultra-Orthodox are reproducing at a fast rate, and currently their labor force participation is low. This is not sustainable. I suspect once they are forced to enter the labor market en masse they will be much more assertive than they are now in the domain of politics. Producers can call the shots more than consumers.

Person of the Year 2010. Mark Zuckerburg. Nothing too original in the piece, though it’s well written. I would also add that it’s a pretty good sign that Facebook’s phase as an “It” company is nearing an end as it starts to saturate the mainstream media chatter. It’s profitable, and it will get bigger, but the rate of growth is already decreasing (second derivative is negative). Amazon, Microsoft and Google make bank, so it isn’t as if Facebook is going away. But soon there’ll be someone else on the horizon (I’m skeptical of the sustainability of Groupon in some of the areas where it is popular, such as restaurants).

Conflict Over Squatters Divides Argentina. Peronism has always been a contradiction in so many ways.

Tallinn-Evans $125,000 Singularity Challenge. ” Jaan Tallinn, a founder of Skype and Ambient Sound Investments, and Edwin Evans, CEO of the mobile applications startup Quinly, every contribution to the Singularity Institute up until January 20, 2011 will be matched dollar-for-dollar, up to a total of $125,000.”

Thiel Fellowship. Deadline December 31st.

Grown-Up Startups. “Why old people make better entrepreneurs than young ones.” I’m interested in the academic literature on this. I believe it is better for society to produce more failed entrepreneurs than successful financial engineers. A few Fritz Haber’s per generation will do.

The Priorities of the Left. Kevin Drum explains why the nature of the Left and Right coalitions in the USA over the past two generations have resulted in more economic and social liberalism. That is, less regulation and welfare state, more individual personal liberty. See The Age of Abundance for a positive take on this.

Necessity Pushes Pakistani Women Into Jobs and Peril. “Then he confiscated her uniform, slapped her across the face and threatened to break her legs if he saw her outside the home….Her family may be outraged, but they are also in need. Ms. Sultana donates her $100 monthly salary to supplement the household budget for expenses that the men in her family can no longer pay for….” Men during the Victorian era regularly visited brothels. There is a level of sexual “traditionalism” which turns men into habitual perverts and male relatives of women into de facto chattel slave owners. This is relatively common in the Muslim world and much of South Asia. I think most people lead more balanced lives somewhere between this sort of barbarism and the “no rules” sexual liberation experiments which have caused such havoc in communes since the 19th century.

Fears Growing of Mugabe’s Iron Grip Over Zimbabwe. The difference between Zimababwe and Bostwana show to some extent the importance of contingency. It is arguable that the rational thing for an autocrat to do is behave like Robert Mugabe, squeeze as much out of the orange as possible and leave it dry. But the cost in aggregate misery is high. I think this might give us an insight into the problems Western nations are starting to have due to problems of coordination for the greater good.

Female Bomber Kills Dozens in Pakistan, Official Says. Never underestimate the pragmatism of “principled” radicals. Here you have a case of reactionaries who would prevent women from becoming literate using a woman as a weapon of war; a highly transgressive act which even most Western nations avoid except in circumstances of extreme need.

Chip To Sequence Genome In Minutes? Someday. Though let’s wait a bit, because the hype is getting to become a bidding war in this area.

What is a human? Mulling the implications of the Denisova admixture paper.

Too Big To Bail. “Is Japan the next major world economy to tank?”At ~120 million people Japan has a population greater than the “PIIGS” combined. I do think either innovation will save them/us, or, they/we’ll have to get used to a reduction in nominal per capita wealth.

Self-organising principles in the nervous system.

Neandertal band of brothers. John Hawks on the Neandertal cannibal story, and its implication of patrilocality. Only ~70% of human societies are patrilocal, so I wouldn’t be surprised if our own lineage doesn’t exhibit the extreme obligate social patterns of bonobos, elephants and chimpanzees.

Genetic evidence for patrilocal mating behavior among Neandertal groups. The paper is open access. Social evolution and cannibalism all in one!

The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations. “Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (~10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study.” First, I suspect that the dating here is wrong. Second, I don’t think that southern Indian populations by and large have such deep roots, because there are strong pointers from the autosomal data that they don’t, and, the nature of farmer & hunter-gatherer interaction make it implausible, though not impossible.

Jon Tester draws ire of liberals. This is a bad thing in Montana? Avowed liberals are only ~20-25% of the American electorate, vs. ~30-40% who are avowed conservatives. This means that liberals can mobilize and impact successfully when the public is on their side (e.g., “Don’t ask, don’t tell”). But when it come to policies where there is less unanimity locale matters.

Slouching toward idiocracy?

Filed under: Brain,Cranial Capacity,Evolution,Human Evolution — Razib Khan @ 1:32 am

The September issue of Discover Magazine had an interesting piece, If Modern Humans Are So Smart, Why Are Our Brains Shrinking? It’s now online, though to read the full article you’ll have to have a print subscription, or, pay 99 cents to get a digital copy of that issue. John Hawks is described as “a bearish man with rounded features and a jovial disposition.”

The background to this phenomenon is rather simple. For several millions years up to ~200,000 years ago there was a study increase in hominin cranial capacities. I say hominin because it seems that this increase was evident in all branches of the human lineage. Neandertals were increasing in cranial capacity, just as African humans were. Then there was a leveling off and stabilization. Finally, over the past 15,000 years or so there has been a decline, from a median of 1,500 cubic centimeters (cc) to 1,350 cc.

You can read the article for an elaboration on the various hypotheses. But roughly, some think we’re getting less intelligent, while others believe that the brain is reorganizing its structure and development. Remember that the brain uses about ~20% of our caloric intake. It’s a metabolically expensive organ.

I would like to add that even if the median human intelligence is decreasing, the current generation has the largest absolute number of very bright people alive at any given time. This is a natural function of the large human population. If the stability of civilization rests not on the median human, but the coordination and mobilization of large numbers of cognitively gifted humans, then perhaps we should not worry too much in the short to medium term. Even with stabilizing world populations we’ll have a generation or two of large numbers of brights before differential fitness of the smart and dull really start eroding the numbers of the former.

December 26, 2010

Patterns of human height & lifestyle

Filed under: Culture,Genetics,Height — Razib Khan @ 3:02 pm

Steve Hsu, The mystery of height:

I was looking at The Formosan Encounter: Notes on Formosa’s Aboriginal Society, A Selection of Documents from Dutch Archival Sources. The Dutch came to Taiwan (then called Formosa) in the early 17th century and these translated documents record their impressions of the Austronesian natives. (Both the Dutch and Chinese settlers traded with the natives during this period.)

One report states that the aboriginal men were taller by a head and neck, on average, than the Dutch. (The average Dutchman came only to the shoulder of the average native?) Another report describes the aborigines as tall and sturdily built, like semi-giants. This paper on historical Dutch height suggests that 17th century Dutchmen were about 170 cm or so on average. Holland was the richest country in Europe at the time, but nutritional conditions for average people were still not good by modern standards. So how tall were the aborigines? Presumably well above 180cm since “a head and neck” would be at least 20cm! (Some Native Americans were also very tall when the Europeans first encountered them.)

But, strangely, the descendants of these aborigines are not known for being particularly tall. This paper reports that modern day aboriginal children in Taiwan are shorter than their Han counterparts. On the other hand, the Dutch are now the tallest people in the world, with average male height exceeding 6 feet (183 cm). This kind of reversal makes one wonder whether, indeed, most groups of humans have similar potential for height under ideal conditions, as claimed here. (Note the epigenetic effects — several generations of good nutrition might be required for a group to reach its full height.)

And now from the The Economist:

About 12,000 years ago people embarked on an experiment called agriculture and some say that they, and their planet, have never recovered. Farming brought a population explosion, protein and vitamin deficiency, new diseases and deforestation. Human height actually shrank by nearly six inches after the first adoption of crops in the Near East….

Here is one model which I am in some sympathy with:

Constant warfare was necessary to keep population density down to one person per square mile. Farmers can live at 100 times that density. Hunter-gatherers may have been so lithe and healthy because the weak were dead. The invention of agriculture and the advent of settled society merely swapped high mortality for high morbidity, allowing people some relief from chronic warfare so they could at least grind out an existence, rather than being ground out of existence altogether.

The indigenous people of the Andaman Islanders in the Bay of Bengal are often classed as “Negritos.” This is in part a reference to their small size. But here is a description of the only population which has refused outside contact, the Sentinelese:

From the boat one could not made out their facial features but they appeared to be of a fairly good height. As our landing parties approached the beach the Sentinelese disappeared into the forest….

Here’s a video of a later contact with the Sentinelese. They seem to be a trim and normally proportioned people, though I can’t judge their heights too well.

In developed nations height is about ~80-90% heritable. That means that most of the population variance in height can be attributed to variance in genes. The distribution of heights of children are well predicted by the heights of parents. But what about between population differences? A great deal of this is obviously due to different environmental inputs. And yet some differences do seem to remain on the margin. Then there is the strange fact that American whites are now shorter than population-controlled Europeans, an inversion of the 19th century pattern.

A combination of epigenetics, genetic variation, and the balance of nutritional inputs, explain much of the world wide variation. Ten years ago I probably would have weighted #2 more than I do now. I suspect that the balance of nutrients, and not just the amount of calories, matters more than we might have thought. This may explain much, though not all, of the decrease in height with the shift from hunter-gatherer lifestyle to farming. Farming can extract an order of magnitude more calories per unit of land, but at the cost of nutritional diversity. Also, in regards to short hunter-gatherer populations such as the Bushmen, Pygmies, and many of the Negritos, their social and cultural marginalization has a lot of complex downstream effects (though please note black Americans have about the same mean height as white Americans, so we need to be careful here). Australian Aborigines are not particularly short, suggesting that long term co-existence with agriculturalists may have had an impact on other hunter-gatherer groups, as they were pushed into marginal lands, and exposed to the density dependent diseases of farmers. It is the last element which I believe explains some of the size difference of the Sentinelese from other Andaman Islanders. It may be that the common microbial flora of Eurasians has a deleterious impact on isolated populations, and results in low grade morbidity which shifts the development of these groups. When a group of Andamanese were separated from Indians in the 1960s they recovered much of their health, and the population began to grow again.

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