Open Thread, 6/30/2013

Independence Day is coming up. Very excited to celebrate with my daughter. She may be old enough not to be frightened by the noise. On the other hand I came to the conclusion a few years back that the world might not be a worse off place if the American colonies had remained colonies for a while longer (to be honest my thoughts were triggered over a decade ago when I watched The Patriot and reflected on its misrepresentation of the British armed forces for dramatic effect).

The four million year odyssey of the horse

Credit: Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Credit: Ealgdyth

The horse is a beautiful animal.* That is not a trivial matter, but there is the added fact that historically it is has been of great consequence. Obviously the rise of horses as vehicles of war is preeminent in our minds, but on a more prosaic level draft horses revolutionized many societies via their effect on agricultural productivity. Dogs may be man’s best friend, but horses are arguably** man’s most useful friend. Or at least they were. The critical importance of the horse is probably lost on modern people, but until the rise of the automobile they were ubiquitous in many large cities (this is clear when you ). Today horses are perceived to be luxurious playthings (ergo, the term “horse country”), but during the heyday of the horse-powered world they served the roles of tractors, tanks, automobiles, and telegraphs.

These are just some of the reasons that horse genomics may be of more than passing curiosity for those who are not to the manor born. Horses are part of our history, and as a large charismatic mammal there is a particular interest in the origins of this lineage. This is part of the reason that a new paper in Nature is important, Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. But this is not the only reason that this paper is of worthy note. It extends the time frame of ancient DNA sequencing back by an order of magnitude, from ~50,000 years before the present to ~500,000 years before the present. Obviously that is a big leap, though it is not surprising that these DNA were retrieved from remains in Canada’s Yukon. Often mammalian ancient DNA breakthroughs, which entail the destruction of fossils, presage prehistoric analysis of our own lineage. But I am not quite sure that that will necessarily happen here (with the caveat that there is going to be a lot of ancient human DNA publication of more recent vintage over the next few years), as the expansion of Homo into the far north truly reached an extensive scope only with our particular lineage of sapiens sapiens.*** Nevertheless, this publication no doubt solidifies the new era in phylogenetics, where inferences of trees can be calibrated and checked against long extinct nodes and branches which had heretofore only been posited.

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Mackinder's revenge and the rise of the mongrels

Several years ago I reviewed Christopher Beckwith’s magisterial . In many ways Beckwith’s narrative is a refreshing inversion of the traditional form of macrohistory, whereby charter societies along the Eurasian littoral issue civilizing tendrils toward the heartland, and are met with periodic barbaric eruptions which they then have to assimilate. From what I can gather Beckwith is not a subjectivist. Rather, the inversion of perspective serves to flesh out neglected dynamics at work across history and near prehistory. For example he highlights the reality that core polities of the Eurasian littoral often crystallized on the barbaric marches of established civilization via process of synthesis between the two cultures.  Zoroastrian religion emerged on the northern frontier in Khorasan rather than the southwestern Iranian heartland of Fars. Han China’s predecessor in the form of the Chin dynasty arose from a marcher state in the northwest, and the same was true of the previous ruling house, that of the Zhou. In India classical Hindu civilization first congealed in an elaborated form in Magadha, on the eastern frontiers of Aryavarta. In the West Rome was fundamentally a barbaric and peculiar fringe polity, with only tenuous connections to Magna Graecia, and arguably more influenced by the enigmatic Etruscans.

The last of the World Conquerors?

The vigor of frontiers is such an established historical cliche that I have no great enthusiasm to revisit it in detail. Rather, following Beckwith I believe we need to seriously revisit the proposition that the vast expanses of the Eurasian heartland beyond the civilized frontiers have served as more than just a source of militarized barbarians bent on exploitation. Yes, all that is true, but it seems likely that the cultural and racial melange at the intersection of internal Eurasian trade networks have fundamentally reshaped the contemporary landscapes in ways we are only now beginning to understand. But first, our worldview has to acknowledge that not all peoples and lands have made contributions of equal weight to the shape of the world.

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Yes Virginia, trans-ethnic inferences from GWAS are kosher

Razib’s daughter’s ancestry composition

An F1, r = 0.5 to Razib

Genome-wide associations are rather simple in their methodological philosophy. You take cases (affected) and controls (unaffected) of the same genetic background (i.e. ethnically homogeneous) and look for alleles which diverge greatly between the two pooled populations. Visually the risk alleles, which exhibit higher odds ratios, are represented via Manhattan plots. But please note the clause: ethnically homogeneous study populations. In practice this means white Europeans, and to a lesser extent East Asians and African Americans (the last because of the biomedical industrial complex in the United States performs many GWAS, and the USA is a diverse nation). Looking within ethnic groups eliminates many false positives one might obtain due to population stratification. Basically, alleles which differ between groups because of their history may produce associations when the groups themselves differ in the propensity of the trait of interest (e.g. hypertension in blacks vs. whites).

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The twilight of Lady Gaga

The other day my office mate wondered “what ever happened to Lady Gaga?” Obviously Lady Gaga is still around and making plenty of money, it doesn’t seem like she’s the pop culture phenomenon she once was. Of course you can live for decades off your early notorious culture changing explosion onto the scene. Madonna is proof of that. But it’s still of interest to know when someone is, or isn’t, the “It” thing. I don’t follow pop culture that closely, but I can say that I remember Gaga before she was Gaga. I was hanging out on the Lower East Side in January of 2006, and there were Gaga posters announcing her opening a show somewhere nearby. One of my friends was freaking out, because she was apparently a big deal. A few years later she did become just that. But somewhere along the way it seems that Lady Gaga has gone from the foreground to the background.

As is my wont I wanted to quantify this. I pulled Google Trends data for Lady Gaga, Katy Perry, Taylor Swift, and Adele from July 2008 to January 2013. I then plotted them with a loess smoothing function. You can see the results below. Nothing that surprising (though if you limit the search results to the United State Taylor Swift becomes a much bigger deal):

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The beloved brontosaurus and other tales

Classic 1897 painting of Diplodocus

Contemporary depiction of Diplodocus
Credit: Nobu Tamura

A few weeks ago I happened to listen to a fascinating interview on NPR with Brian Switek, the blogger behind Laelaps, and author of . Switek was discussing his newest book, . To be frank I was captivated by the discussion, and immediately purchased a copy of the book. The reason is simple: despite our current divergent interests Brian Switek began at the same place I did, with dinosaurs. Though after reading I can’t assert that my dinomania matched Switek’s, it was of the same quality. The difference is that while Switek remained true to dinosaurs, my own interests wandered into other domains. Today I am focused more upon evolutionary forces operating on the scale of thousands of years within a species, rather than geological scale transmogrifications. But every now and then I wonder about dinosaurs, and whatever happened to them over the past 20 years after my “dinosaurs years” faded into the distance.

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Sexual selection: ignore the blonde?

Frank analytic clarity?

Sexual selection is a big deal. A few years ago Geoffrey Miller wrote , which seemed to herald a renaissance of the public awareness of this evolutionary phenomenon, triggered in part by debates over Amotz Zahavi’s in the 1970s. Of course Charles Darwin discussed the process in the 19th century, and it has always been part of the arsenal of the evolutionary biologist (I first encountered it in Jared Diamond’s , where he lent some credence to Darwin’s supposition that human racial differences may be a consequence of sexual selection). But this bump in recognition for sexual selection seems to be accompanied by its co-option as a deus ex machina for all sorts of unexplained events. And yet as they say, that which explains everything explains nothing.

To get a better sense of the current scientific  literature I consulted A Guide to Sexual Selection Theory in the Annual Review of Ecology, Evolution, and Systematics. The image above is from an actual box in this review! Normally technical boxes illuminate with an air of superior authority (e.g. “it therefore follows from eq. 1…/”), but it seems to me that the admission that a parameter can be represented by the verbal assertion that it’s complicated tells us something about the state of sexual selection theory. In short: its formal basis is baroque because the dynamic itself is not amenable to easy decomposition.

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Gorging Gudea style

He liked a good brew!
recently made me aware of this fascinating piece in The New York Times, For Its Latest Beer, a Craft Brewer Chooses an Unlikely Pairing: Archaeology. Here’s the catchiest aspect: a microbrewery is attempting to recreate the taste of ancient Sumerian beer! Why? Though it’s purportedly educational, obviously it’s also the “cool” factor which is at the root of this enterprise. The brewery doesn’t aim to sell this. I say why not!

A few years ago Paul Boom wrote the book . This may seem like a trivial exploration of a topic, after all, who doesn’t know how pleasure works? But when you plumb the depths of genuine hedonism there are often rapid diminishing marginal returns when you simply apply a robotic calculus of more sensory vividness. Rather than a stronger chocolate, sometimes you want a finer chocolate. But what does that even mean? One thing that a standard hedonistic account of pleasure often underplays is that it is not a simple toting of sensory qualities. Rather, it is the essence of the thing that matters.

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