2011, onward, ho!

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

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

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Mapping the "Green Sahara"


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

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

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

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On to 2011….

Predictions, expectations, etc.

More use of the term “polytypic”.

Ötzi turns out to have Near Eastern affinities.

The Hobbits finally have some genetic material successfully analyzed.

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

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Top 10 Gene Expression posts of the year

According to Google Analytics, they are:

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

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

8 – Which American racial group has the lowest fertility?

7 – No Romans needed to explain Chinese blondes.

6 – To classify humanity is not that hard.

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The Axial Age & world population

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

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

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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:

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Technology & genetics in the 21st century

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

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

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

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

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

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

Are conservatives fatter than liberals?

    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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