Archive for December, 2010

2011, onward, ho!

By Razib Khan | December 31, 2010 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.

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CATEGORIZED UNDER: Blog
MORE ABOUT: 2010

Mapping the "Green Sahara"

By Razib Khan | December 31, 2010 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:

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CATEGORIZED UNDER: Geography, Human Evolution

Friday Fluff – December 31st, 2010

By Razib Khan | December 31, 2010 12:00 pm

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

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CATEGORIZED UNDER: Blog
MORE ABOUT: Blog, Friday Fluff

On to 2011….

By Razib Khan | December 31, 2010 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.”

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Top 10 Gene Expression posts of the year

By Razib Khan | December 31, 2010 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.

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'tis the day for last second giving!

By Razib Khan | December 31, 2010 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.

CATEGORIZED UNDER: Culture
MORE ABOUT: Philanthropy

The Axial Age & world population

By Razib Khan | December 30, 2010 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?

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CATEGORIZED UNDER: Culture, Economics, History

Are Turks acculturated Armenians?

By Razib Khan | December 30, 2010 1:25 pm

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:

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CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics

Technology & genetics in the 21st century

By Razib Khan | December 30, 2010 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.

CATEGORIZED UNDER: Genomics
MORE ABOUT: Genomics

Are conservatives fatter than liberals?

By Razib Khan | December 30, 2010 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.

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CATEGORIZED UNDER: Culture, Data Analysis
MORE ABOUT: Culture, Data

Beware of British newspapers: fossils edition

By Razib Khan | December 28, 2010 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.

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CATEGORIZED UNDER: Human Evolution
MORE ABOUT: Human Evolution

The rise of the skulls!

By Razib Khan | December 28, 2010 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.

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CATEGORIZED UNDER: Anthroplogy, Human Evolution

Out of Africa: mend it, don't end it!

By Razib Khan | December 27, 2010 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:

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CATEGORIZED UNDER: Culture, Genetics, Genomics, Uncategorized

Around the Web – December 27th, 2010

By Razib Khan | December 27, 2010 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.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Blog, Daily Data Dump

Slouching toward idiocracy?

By Razib Khan | December 27, 2010 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.

http://www.youtube.com/watch?v=L0yQunhOaU0

CATEGORIZED UNDER: Evolution, Human Evolution

Patterns of human height & lifestyle

By Razib Khan | December 26, 2010 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:

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CATEGORIZED UNDER: Culture, Genetics
MORE ABOUT: Height

Open Thread – December 25th, 2010

By Razib Khan | December 25, 2010 12:03 pm

This is a scheduled post (As many of my posts are by the way. Shout out to the stupid readers who occasionally wonder why I’m not partying when a post goes live on Friday night!). Merry Christmas! I’m probably playing around with my HTC Evo 4G if you’re reading this on Saturday, or eating, etc.

What do you think of Christmas? A friend pointed out that Christmas’ religious origins may be clear in the name (Christ’s mass), but the world holiday itself originally meant holy day, and had clear religious connotations. Christmas seems an appropriate holiday for the de facto post-Christian pagan environment of the modern USA. Elements of most European Christmas celebrations draw rather obviously from pre-Christian mythos, customs, and tradition, though because of the nature of human cognition many of them are not too difficult to reinterpret in a Christian manner. That’s obviously what happened. And in turn the specific and distinctive Christian coloring of the holiday has become attenuated in much of the West. The secular and commercialized version of Christmas has even spread to Japan.

CATEGORIZED UNDER: Blog
MORE ABOUT: Blog, Open Thread

Friday Fluff – December 24th, 2010

By Razib Khan | December 24, 2010 4:15 pm

FF3 1. First, a post from the past: Lions, and tigers, and snow leopards! Oh, my!.

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MORE ABOUT: Friday Fluff

Reminder, 23andMe sale through Christmas

By Razib Khan | December 23, 2010 9:50 am

A reminder that 23andMe’s sale is valid until Christmas. Including the mandatory yearly subscription to their “Personal Genome Service”, that’s $160 (though you only get charged $99 + shipping initially, the subscription is $5/month). I didn’t quite go up to the 10 kits per person, but I did come close. There will likely be new amateur and/or open source genome projects in 2011, so if you’re from an underrepresented community this might be useful as a public good. It is true that the probability of finding actionable medical information is low, but you can do whatever you want with your ~1 million SNPs indefinitely. Channeling Sally Struthers, can’t you afford the purchase of ~1 million SNPs for the cost of 10% of a cup of expensive Starbucks coffee drinks per day for a year? That’s 1/60th of a penny per SNP!

(and for the record, I am not getting a cut)

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: 23andMe

The paradigm is dead, long live the paradigm!

By Razib Khan | December 23, 2010 3:24 am

Mitochondrial DNA and human evolution:

Mitochondrial DNA from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DMAs stem from one woman who is postulated to have lived ab7out 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly

And so was published in the year 1987 the paper which established in the public’s mind the idea of mitochondrial Eve, which gave rise to a famous cover photo in Newsweek. This also led to the Children of Eve episode on the PBS documentary NOVA. Here is the summary:

NOVA examines a controversial theory that traces our ancestry to a small group of women living in Africa 300,000 years ago.


As Milford Wolpoff has complained it is probably accurate to characterize the documentary as not particularly “fair & balanced.” Mitochondrial Eve may have been controversial, and subsequently plagued by issues of molecular clock calibration as well as spurious interpretations of the cladograms, but the tide of history was on its side, and PBS was telling that story. And the story was not just the primary science, rather, one had to understand the controversy in light of the debates among paleontologists and between paleontologists and molecular biologists. A group of researchers, spearheaded by Chris Stringer argued for the recent origin of modern humans from Africa on the basis of fossils alone. They were challenged by an established school of multiregionalists who argued for deeper roots of modern human populations, which derived from local hominins which diversified after the the migration of H. erectus out of Africa. The argument of the multiregionalists was that selective sweeps across the full range of the human populations gave rise gradually to modern humanity as we know it, a compound of specific ancient local features and trans-population characters which unified us into a broader whole. Stringer and company presented a simpler model where anatomically modern human being arose ~200,000 years ago in Africa, and subsequently expanded to other parts of the world, by and large replacing the local hominin populations. In the multiregionalist telling Neandertals became human beings, while Out of Africa would imply that Neandertals were replaced by human beings.

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