Targaryen genetic load

I have to point you to this post on royal inbreeding in A Song of Ice and Fire. They reference my post on the Habsburgs. Well done! In any case, one possibility is that the Targaryen lineage may have purged their genetic load through inbreeding. The basic logic is that all the recessive traits are going to be “exposed” every generation, resulting in a far stronger selection coefficient against those alleles than would be the case in a outbreed population (where most deleterious variants with recessive expression are masked by being present heterozygote genotypes).

How income, class, religion, etc. relate to political party

Update: There was a major coding error. I’ve rerun the analysis. No qualitative change.

As is often the case a 10 minute post using the General Social Survey is getting a lot of attention. Apparently circa 1997 web interfaces are so intimidating to people that extracting a little data goes a long way. Instead of talking and commenting I thought as an exercise I would go further, and also be precise about my methodology so that people could replicate it (hint: this is a chance for readers to follow up and figure something out on their own, instead of tossing out an opinion I don’t care about).


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The evolution of the human face

The face is an important aspect of our phenotype. So important that facial recognition is one of many innate reflexive cognitive competencies. By this, I mean that you can recognize a face in a gestalt manner, just like you can recognize a set of three marbles. You don’t have to think about it in a step-by-step fashion. Particular types of brain injuries can actually result in disablement of this faculty, and a minority of humans seem to lack it altogether at birth (prosopagnosia). That’s why I’ve long been interested in the genetic architecture and evolution of craniofacial traits. I long ago knew the potential range of pigmentation phenotypes for my daughter because both her parents have been genotyped, but when it comes to facial features we’re stuck with the old ‘blending inheritance’ heuristic. The most obvious importance of teasing apart the genetic architecture of craniofacial traits is forensics. It might not put the sketch artist out of a job, but it would be an excellent supplement to problematic eye witness reports.

But it isn’t just forensics. The issue has evolutionary relevance. It looks like that in terms of morphology our own lineage has had a lot of diversity up until recently. I’m thinking in particular of the ‘archaic’ looking humans recently discovered in China and Nigeria, who seem to have persisted down into the Holocene. More generally, humans as a whole have become more gracile over the last 10,000 years. Why? There are two extreme answers we can look to. First, gracile humans have replaced robust humans. Second, natural selection for gracility has resulted in the in situ evolution of many populations over the last ~10,000 years. An interesting aspect of this is that it looks as if many salient traits have been targets of selection, and therefore evolution and population differentiation.

Here the top 10 SNPs which deviate from the overall phylogenetic tree of population relationships in the HGDP data set:


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The agricultural "express train"

One model for the spread of the agricultural way of life into Europe is of inexorable “demic diffusion” via a “wave of advance” of farming populations met by a land surplus. Conceptually and analytically it’s an elegant model. It’s also fundamentally methodologically individualistic, and so in keeping with the spirit of the age. There’s no need to appeal to higher order social structure or organization, farmers who have a specific cultural toolkit drive the dynamic through endogenous growth in pre-state cultures through the production of large families. This growth washes over the frontier of the advance, and the original locus of the demographic pulse synthesizes across a transect with the indigenous substrate. In the early aughts historical geneticists Bryan Sykes and L. L. Cavalli-Sforza sparred over whether demic diffusion was useful or not as a conceptual framework. Sykes reported chromosomal results which implied that 75 percent of the ancestry of Europeans derives from Pleistocene hunter-gatherers. Cavalli-Sforza’s riposte was that the original model did not specify a particular Paleolithic-Neolithic ratio, but rather characterized a dynamic which emphasized the necessity of migration as a mediator for cultural changes (the two perspectives are outlined in and ).


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The upper class is more Republican

A few months ago I listened to Frank Newport of Gallup tell Kai Ryssdal of Marketplace that upper class Americans tend to be Democrats. Ryssdal was skeptical, but Newport reiterated himself, and explained that’s just how the numbers shook out. This is important because Newport shows up every now and then to offer up numbers from Gallup to get a pulse of the American nation.

Frankly, Newport was just full of crap. I understand that Thomas Frank wrote an impressionistic book which is highly influential, , while more recently Charles Murray has come out with the argument in that the elites tend toward social liberalism. I’m of the opinion that Frank is just wrong on the face of it, but that’s OK because he’s an impressionistic journalist, and I don’t expect much from that set beyond what I might expect from a sports columnist for ESPN. Murray presents a somewhat different case, as outlined by Andrew Gelman, in that his “upper class” is modulated in a particular manner so as to fall within the purview of his framework. Neither of these qualifications apply to Frank Newport, who is purportedly presenting straightforward unadorned data.

When the “average person on the street” thinks upper class they think first and foremost money. This is not all they think about, but in the rank order of criteria this is certainly first on the list. We can argue till the cows come home as to whether a wealthy small business owner in Iowa who is a college drop out is more or less elite than a college professor in New York City who is bringing home a modest upper middle class income (very modest adjusting for cost of living). But to a first approximation when we look at aggregates we had better look at the bottom line of money. After that we can talk details. And the first approximation is incredibly easy to ascertain. Below is a table and chart which illustrate the proportion of non-Hispanic whites after 2000 who align with a particular party as a function of family income, with family income being indexed to a 1986 value (so presumably $80,000 hear means what $80,000 would buy in 1986, not the aughts).


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The revival of the American city?

I’ve never watched Mad Men, but I really can’t help but hear all about the show. One thing that has struck me about the change from then, ~1960, to now, ~2010, is the alignment of quantitative demographic trends with impressionistic cultural ones. The 1970s were a disaster for the old urban order. Below are the top 10 cities by population in 1960 and 2010.

Rank 1960 2010
1 New York New York
2 Chicago Los Angeles
3 Los Angeles Chicago
4 Philadelphia Houston
5 Detroit Philadelphia
6 Baltimore Phoenix
7 Houston San Antonio
8 Cleveland San Diego
9 Washington Dallas
10 St. Louis San Jose

The rise of the “Sun Belt”, housing bubble notwithstanding, is a real and awesome phenomenon. Below the fold I’ve taken some demographic trend data for the top 10 cities of 1960. The first two panels show raw population data. The second two panels show the decade-to-decade change in population in terms of multiples (i.e., 1.2 for 2010 means that the population in 2010 was 1.2 times that in 2000).


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No comments please, we've made it through peer review (?)

Recently pointed to the vibrant discussion over at Genomes Unzipped on a moderately infamous paper from Science last year, Widespread RNA and DNA Sequence Differences in the Human Transcriptome, asserting that it is “exactly what open peer review should be like.”  This made me wonder, it’s been over five years since Chris Surridge asked why there was so much more commentary on a PLoS ONE paper, By Hook or by Crook? Morphometry, Competition and Cooperation in Rodent Sperm, on blogs than on the paper itself. Has anything changed? The most viewed paper on PLoS Biology, How Many Species Are There on Earth and in the Ocean?, has 9 comments for 45,000 article views. In contrast, Genomes Unzipped has 14 comments for likely far fewer page views. Additionally, if you find the post on the weblog the comments automatically load. Not so with the PLoS Biology paper, you have to click through (yes, I see how this can be a feature, not a bug, but in that case why even bother with comments if you provide an email address for correspondence?)

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Neanderthals came in all colors

There’s a report in Science about a new short paper about Neandertal pigmentation genetics. The context is this. First, in 2007 an ingenuous paper was published which inferred that it may be that Neandertals had red hair, at least based on an N = 2 from two divergent locations. The new study looks at three Croation samples, and reports genotypes which are correlated with a swarthier phenotype in modern populations. But the results are neither here nor there: everyone interviewed in the paper assumes that like modern Europeans Neandertals were a polymorphic set of populations when it comes to pigmentation. There are lots of reasons for this agreement, despite issues one might take with this paper.

The report on the paper in Science has two sections which I want to zoom in on. First, “Nearly 60% of the formula’s predictions matched the subjects’ actual physical appearance, the authors say. The team considers that accuracy rate satisfactory, given the complexity of the genetics behind skin color and other physical traits.” Do you consider 60 percent satisfactory? What curve are you grading on? I’m willing to bet that the reporter didn’t consider 60 percent satisfactory, and neither do I. If you look in the paper you’ll see that their method predicts that a Yoruba in the HGDP sample has blue eyes and red hair. Several of the Papuans are predicted to have blue eyes.

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The collapse of logic & human culture

Slavery’s last stronghold:

Moulkheir Mint Yarba returned from a day of tending her master’s goats out on the Sahara Desert to find something unimaginable: Her baby girl, barely old enough to crawl, had been left outdoors to die.

The usually stoic mother — whose jet-black eyes and cardboard hands carry decades of sadness — wept when she saw her child’s lifeless face, eyes open and covered in ants, resting in the orange sands of the Mauritanian desert. The master who raped Moulkheir to produce the child wanted to punish his slave. He told her she would work faster without the child on her back.

Trying to pull herself together, Moulkheir asked if she could take a break to give her daughter a proper burial. Her master’s reply: Get back to work.

“Her soul is a dog’s soul,” she recalls him saying.

Consider this. A father in a biological sense leaves his daughter out to die of exposure so as to increase the economic production of the mother of his daughter! Not only that, he obviously considers his daughter an animal. The full article is about slavery in Mauretania, a nation which maintains the practice in de facto form. Because this slavery clearly has a racial character, with a light-skinned population of North African origin enslaving a dark-skinned population of Sub-Saharan origin, there is an obvious “hook” for a Western, and particularly American, audience. But to be fair, if I can use that term, de facto slavery exists in organized form in other parts of the Sahel and Sahara (e.g., among the Tuareg), though the practice is far less pervasive in magnitude.

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When independent thought flourishes

One of the things I instinctively hated about my “ancestral culture,” that of Bangladesh, is that there wasn’t that great of an emphasis on individual independent thought. Why, for example, was it important never to drink water while you were eating, as opposed to after you were done? The response was simple: that’s the rule. Even if there was a functional rationale, there wasn’t even any pretense at offering a reasoned explanation for why a custom was a custom. It’s just how it was.

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