Why white men get testicular cancer more than black men

Likely an individual with derived allele on KITL locus (Credit: David Shankbone)
An individual polymorphic on the KITL locus? (Credit: David Shankbone)
Pigmentation is one of the few complex traits in the post-genomic era which has been amenable to nearly total characterization. The reason for this is clear in hindsight. As far back as the 1950s (see The Genetics of Human Populations) there were inferences made using human pedigrees which suggested that normal human variation on this trait was controlled by fewer than ten genes of large effect. In other words, it was a polygenic character, but not highly so. This means that the alleles which control the variation are going to have reasonably large response, and be well within the power of statistical genetic techniques to capture their effect.

I should be careful about being flip on this issue. As recently as the mid aughts (see Mutants) the details of this trait were not entirely understood. Today the nature of inheritance in various populations is well understood, and a substantial proportion of the evolutionary history is also known to a reasonable clarity as far as these things go. The 50,000 foot perspective is this: we lost our fur millions of years ago, and developed dark skin, and many of us lost our pigmentation after we left Africa ~50,000 years ago (in fact, it seems likely that hominins in the northern latitudes were always diverse in their pigmentation)

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The age of the sword

Credit: Aviok
“Think not that I am come to send peace on earth: I came not to send peace, but a sword.” -Matthew 10:34

“There were giants in the earth in those days…when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.” -Genesis 6:4

Seven years ago I wrote a short post, Why patriarchy?, which attempted to present a concise explanation for the ubiquity of what we might term patriarchy in complex societies (i.e., not “small-scale societies”). Broadly speaking my conjecture is that social and political dominance of small groups of males (proportionally) over the past several thousand years is an example of “evoked culture”. The higher population densities in agricultural societies produced a relative surfeit of accessible marginal surplus, which could be given over to supporting non-peasant classes who specialized in trade, religion, and war, all of which were connected. This new economic  and cultural context served to trigger a reorganization the typical distribution of power relations of human societies because of the responses of the basic cognitive architecture of our species inherited from Paleolithic humans. Agon, or intra-specific competition, has always been part of the game on human socialization. The scaling up and channeling of this instinct in bands of males totally transformed human societies (another dynamic is elaboration of cooperative structures, though this often manifests as agonistic competition between coalitions of humans).

To get a sense of what I mean when I say transforming, consider this section of an article in The Wall Street Journal which profiles the wife of one of the 2012 New Delhi gang rape:

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Open Thread, 10/13/2013

Six months back there was a lot of discussion of Y haplogroup A00, An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. Now there’s an attempt by some of the researchers on that paper to raise money to collect more samples. Which of Cameroon’s peoples have members of haplogroup A00?:

This is Round Two of our fundraising for our groundbreaking research on the world’s earliest-branching Y-chromosome lineage, A00. Its origins lie in the earliest days of humanity’s emergence, the exact time very much in debate, but almost surely over 200,000 years ago. We first discovered it in early 2012, when the results of the Perrys’ Y-DNA tests were unlike anything seen before. We learned that they have matches among some of the diverse peoples of Southwest Cameroon. The new samples to be collected by Matthew in his homeland will allow us to learn much more about A00.

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And truth shall come out of the mists of legend

And he will be a wild man; his hand will be against every man, and every man’s hand against him; and he shall dwell in the presence of all his brethren.

– Genesis 16:12

By now you may have seen or read two important papers which just came out in Science, 2000 Years of Parallel Societies in Stone Age Central Europe, and Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. The details have been extensively explored elsewhere. If you don’t have academic access I highly recommend the supplement of the second paper. It’s also very illuminating if you don’t have a good grasp of the nuts and bolts of archaeology (I do not). I can’t, for example, confirm whether the merging strategies of different archaeological cultures were appropriate or not, because I’m not totally clear in my own head about the nature of these distinct archaeological ‘cultures’ (quotations due to the fact that archaeologists infer culture from material remains, and so they may not be cultures in the sense we understand culture). But the overall finding is clear, in ancient Europe thousands of years ago there were multiple demographic replacements and amalgamations. The post-World War II thesis in archaeology that one could not infer changes in the demographic character from material remains (because the latter can diffuse purely through memetic means) seems to be false. The correspondence is surprisingly tight.

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People probably came with pots

Update: Just watch this movie.

No time to write about it now, but check Science Magazine this afternoon (in a few hours from this posting) for a major paper on ancient mtDNA, and the striking correlation between changes in lineage frequencies and cultures that they discovered. Turns out that when you peel back the palimpsest it is much more complicated and surprising than we’d have thought. National Geographic, which funded the project, already has a post out on it:

What they found was that the shift in the frequency of DNA lineages closely matched the changes and appearances of new Central European cultures across time. In other words, the people who lived in Central Europe 7,000 years ago had different DNA lineages than those that lived there 5,000 years ago, and again different to those that lived 3,500 years ago. Central Europe was dynamic place during the Bronze age, and the genetic composition of the people that lived there demonstrates that there was nothing static about European prehistory.

Genographic Project Director and National Geographic Explorer-in-Residence, Spencer Wells expounds: “spanning a period from the dawn of farming during the Neolithic period through to the Bronze Age, the [genetic] data from the archaeological remains reveals successive waves of migration and population replacement- genetic ‘revolutions’ that combined to create the genetic patterns we see today.”

I hope this doesn’t lead to a new simplicity to replace the old one of no migration.

Anagram edition: "Ice Genus"

This isn’t the face of the future

I was in the audience when Anne Morris, co-founder of GenePeeks, gave a presentation to outline the services that they are aiming to provide at the Consumer Genetics Conference. Honestly my biggest reaction was, “Oh, this is 2013, I suppose. And boy, Lee Silver has a lot of energy” (he kept bouncing around the back of the conference room). From what I can tell the “technology” is the sort of brute-force “subtlty” only feasible in our era because of the intersection of sequencing and computation. After the presentation it looks like GenePeeks is revving up its marketing engine (as promised). From a lengthy BBC story which reads more like a press release with caveats:

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Why I love genetics

Gregor Mendel
A few years ago I had a discussion with a friend about our academic backgrounds. She is a neurobiologist by training, so I remarked in an offhand manner that I’d had an interest in neuroscience years ago. In fact, I admitted that I had even dabbled with the idea of pursuing graduate work in that discipline. More specifically cognitive neuroscience. Stanislas Dehaene’s work, detailed in The Number Sense and Reading in the Brain, was of great fascination for me (cognitive and evolutionary psychology, of the sort outlined in Steven Pinker’s The Language Instinct, has also been something of a personal obsession).

I didn’t go that route…I’ve been writing for 10+ years now, and long time readers can probably attest to the fact that I’ve become more and more focused on genetics as time goes by. This is due to the reality that I really like genetics. Really. The friend with whom I was having the conversation about our various interests admitted she couldn’t even imagine an alternative universe version of me who would nerd out on neuroscience. That would be a bizarro-world Razib.

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Along the edge of the Ecumene

Citation: Turchin, Peter, et al. “War, space, and the evolution of Old World complex societies.” Proceedings of the National Academy of Sciences (2013): 201308825.

A few weeks ago, Peter Turchin, who runs the excellent Social Evolution Forum, published a paper in PNAS, War, space, and the evolution of Old World complex societies. It is open access, so you can read it yourself. And Turchin himself has responded to questions at length. You might also check out my reviews of two of his books, as well as my interview with him. From all that it should be clear that broadly speaking I am enthusiastic about Turchin’s project, Cliodynamics. Historical details matter, but Turchin’s aim is to establish a broad brush framework of the coarse dynamics which shape the scaffold for specific aspects of historical process. Without this background all we have are cluttered details.

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How normal is the two child norm?

Less than even two! Image credit: Yoshi Canopus

A few years ago Greg Cochran mentioned to me how he perceives the two child family to be the new bourgeois normal, enforced by the professional class and blue-haired ladies alike (this impression is informed by the fact that he has more than two children). This seems to align with my own general sense, but then again how normal is my socioeconomic milieu? So I decided to look at the General Social Survey. I limited the sample to non-Hispanics whites age 45 and over, constrained to the interval 2000-2012,* and broke the data into male and female classes. I crossed the number of children, binned 0, 1, 2, 3, 4, and 5+, with the highest educational attainment of the individual.** In other words I limited the data set, and looked at how the number of children of individuals varied as a function of education.

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