A few months ago I had a post up about Game of Thrones, where I argued that to a great extent the book and the world that George R. R. Martin created was racist because that’s true to how pre-modern worlds generally are constructed structurally. When fantasists create a ‘secondary world’ they are almost always using our own universe as a prototype, often shading or refashioning some aspect here and there to taste. A true fantasy which is totally counter-intuitive and lacks familiar coherency is without any anchor for a reader, and so lacks narrative power. Fantasy stripped away of injustice or oppression would be without dramatic tension. Utopia does not sell. Additionally, the speculative element in this literature is sharply bounded by precedent. Modern fantasy in its origins is simply an elaboration of the epic literature which is often at the root of contemporary civilizations. J. R. R. Tolkien attempted to create in his own works a simulacrum of a rich epic folk past for the Anglo-Saxon peoples analogous to what the Scandinavians had thanks to Snorri Sturluson’s efforts.

My post on Martin’s work was prompted by the ruminations of one Saladin Ahmed, whose piece in Salon manifested all the stale standard post-colonial inflected drivel which riddles much of popular literary criticism. Ahmed popped up in the thread of my post, but actually misunderstood the intent! The reason is pretty straightforward I think: our “paradigms” are so different that he had a hard time hearing me correctly initially. I responded to Ahmed, but weirdly enough though he hung around the comment thread he never really engaged with me after I made my own stance clearer to him. Whether it disturbed him, or did not interest him, I will never know.

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Apparently Mayim Bialik, Ph.D. neuroscience, is skeptical of vaccination. This just goes to show you that “science education” itself is no guarantee of immunity against acceptance of false propositions. Rather than reason from one proposition to another independently humans operate in an ecology of ideas. Bialik’s general suite of beliefs about mothering and her social milieu make her stance on vaccination rather unsurprising, notwithstanding that she has a doctorate in neuroscience.

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A correspondent emailed me to tell me that Linda Chavez, whose father was a New Mexican Hispano, was found to have Sephardic Jewish ancestry in Henry Louise Gates Jr’s Finding your Roots series. This brings me to point to a recent paper, The impact of Converso Jews on the genomes of modern Latin Americans:

Modern day Latin America resulted from the encounter of Europeans with the indigenous peoples of the Americas in 1492, followed by waves of migration from Europe and Africa. As a result, the genomic structure of present day Latin Americans was determined both by the genetic structure of the founding populations and the numbers of migrants from these different populations. Here, we analyzed DNA collected from two well-established communities in Colorado (33 unrelated individuals) and Ecuador (20 unrelated individuals) with a measurable prevalence of the BRCA1 c.185delAG and the GHR c.E180 mutations, respectively, using Affymetrix Genome-wide Human SNP 6.0 arrays to identify their ancestry. These mutations are thought to have been brought to these communities by Sephardic Jewish progenitors. Principal component analysis and clustering methods were employed to determine the genome-wide patterns of continental ancestry within both populations using single nucleotide polymorphisms, complemented by determination of Y-chromosomal and mitochondrial DNA haplotypes. When examining the presumed European component of these two communities, we demonstrate enrichment for Sephardic Jewish ancestry not only for these mutations, but also for other segments as well. Although comparison of both groups to a reference Hispanic/Latino population of Mexicans demonstrated proximity and similarity to other modern day communities derived from a European and Native American two-way admixture, identity-by-descent and Y-chromosome mapping demonstrated signatures of Sephardim in both communities. These findings are consistent with historical accounts of Jewish migration from the realms that comprise modern Spain and Portugal during the Age of Discovery. More importantly, they provide a rationale for the occurrence of mutations typically associated with the Jewish Diaspora in Latin American communities.

The evidence for the Lojano community is stronger in the paper than the Hispano samples. Nevertheless, it is interesting to view this in light of the 2000 piece in The Atlantic, Mistaken Identity? The Case of New Mexico’s Hidden Jews”. Long story short, cultural anthropologists posited in the late 1990s that the Jewish cultural features of Hispanos were distortions of the beliefs of Protestant missionaries. Thank god for genetics.

I often hear in the media that Hispanics are “socially conservative.” For that sort of thing you do need “quick & dirty” rules-of-thumb, and the assertion seems broadly plausible. On the other hand, the Hispanic attitude toward gay marriage isn’t really that different from non-Hispanic white (see GSS MARHOMO variable). So I decided to query non-Hispanic white and Hispanic attitudes to a range of “hot-button” social issues in the GSS. I also broke it down by college vs. non-college educated cohorts. All results are from the year 2000 and later.

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Of all the taxonomic ranks species is the most clear, distinct, and concrete. More practically, it is the level which most naturally falls out of the patterns of life’s tree. Or does it? If the term “species concept” does not ring a bell, please see this entry. If it does, how do you define species in a non-arbitrary manner?

To my surprise there is apparently a move on the part of the Republicans in the House of Representatives to curtail funding for The American Community Survey. I am not too excited by the idea that you could get fined for not filling out a government survey form, but neither do I think that abolishing social statistics is the correct solution to this problem. Rather, better surveys which compensate for biases in response rates are the direction we need to go. The reality is that a government of our scope and continuing responsibilities needs the best social statistics that money can buy. I understand that many believe that some of the functions of our government are illegitimate or unwarranted, but destroying the government’s general ability to function is counter-productive unless you want to total social collapse to trigger a revolution.

Second, government data collection is a public good with positive externalities. If we abolish endeavors such as the American Community Survey than social data will be the domain only of corporations, who are not always keen on sharing that data.

For genetic genealogy buffs, I highly recommend Gedmatch. It’s been rolling out a lot of new features, including ancestry inference tools from the major genome bloggers. Here is my “chromosome paining” using Zack Ajmal’s reference populations:

Foer Returns to New Republic as Editor:

Two months after buying a majority stake in The New Republic, the technology entrepreneur Chris Hughes has lured one of its former stars, Franklin Foer, back to the magazine as its editor.

…

The print magazine and Web site will be redesigned and the page count of the print edition will be expanded, Mr. Hughes said. He added that when he was researching whether to buy the New Republic, he had to read through old editions on microfilm in the archives at the New York Public Library.

Mr. Hughes’s goal is to guide The New Republic out of the category he called “little magazines” in Washington like The National Review and into a category that includes magazines he sees as more natural competitors, like The New Yorker, the Economist and New York Magazine.

I don’t add much value in a lot of areas, so I don’t say much. But this piece seems to make a major omission: the analogous model to what Chris Hughes is aiming to do with The New Republic is what David Bradley did with The Atlantic, down to the robust web strategy. The New Yorker, the Economist, and New York are all really different beasts, aside from being relatively prominent.

It is sometimes fashionable to assert that higher socioeconomic status whites are the sort who will impose integration on lower socioeconomic status whites, all the while sequestering themselves away. I assumed this was a rough reflection of reality. But after looking at the General Social Survey I am not sure that this chestnut of cynical wisdom has a basis in fact. Below are the proportions of non-Hispanic whites who have had a black friend or acquaintance over for dinner recently by educational attainment:

35% – Less than high school
36% – High school
47% – Junior College
45% – Bachelor
59% – Graduate

I thought this might have been a fluke, so I played around with the GSS’s multiple regression feature, using a logistic model. To my surprise socioeconomic status was positively associated with having a black person over for dinner, and age negatively associated. These two variables in fact tended to exhibit equal magnitude values in opposition, and always remained statistically significant. Just to clear, I created a variable Non-South vs. South below (being Southern increases likelihood of having had a black person over for dinner). All the individuals surveyed are non-Hispanic whites for the year 2000 and later. You can add and remove variables, but SEI and age tend to be rather stable, and statistically significant, throughout.

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I highly recommend Åse Fixes Science, in light of our recent conversations about psychology. It’s a fascinating and important discipline, but it is hard to make heads or tails of it all.

A few weeks ago I met Chris Mooney for some drinks & snacks, and we talked about his new book, The Republican Brain: The Science of Why They Deny Science–and Reality. It was an interesting conversation. We have a long history, so it wasn’t as if we were strangers. I recall Chris from the late 1990s when we were both involved in the college “freethought” movement, and later when I followed his political journalism at The American Prospect. On the whole we’re on different political “teams,” though neither of us seems particularly enthusiastic “players,” so to speak (I think at this point I can disclose that when I emailed Chris a few times when he worked at TAP to object to items in a particular piece, I often found that he concurred with my specific objections). I assume that to push copies Chris had to make sure that the emphasis was on Republican and not conservative in the title for his new book (and also, it exhibits nice parallel to The Republican War on Science). For me this is unfortunate because I have a lot more sympathy for conservatism, than I do for Republicans. Of course that’s a trite thing to say. And bemoaning the state of party politics in the United States is as old as the origination of political coalitions over 200 years ago (remember, many of the Founders, including George Washington, opposed a party system, which they believed would produce unnecessary faction). But I am of the opinion that due to its sheer scale and diversity the United States of America may be poised for an age of sectional discord. A throwback to the first half of the 19th century in the first decades of the 21st. Sometimes “this time” is different.

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In the comments below Nathaniel Comfort asks:

What I do, as a historian, is take something apparently simple and make it more complicated. I wonder about how your curves, e.g., would be applied in real life. *Specific* couples, *particular* children–individuals, cases, persons, context.

I’m asking things like:

-What would your hypothetical psychopathic lovebirds do with that information?

Comfort is referring to this figure I generated, which shows the potential distribution of outcomes for two individuals who tend toward more psychopathy than the general population. It seems to me that this question is easily answered if simply replace “psychopathy” with “odds for heart disease.” Endophenotypes aren’t magical, they’re just sometimes hard to characterize. But once you get a good grip on them you can make standard quantitative genetic predictions. One of the points I wasn’t clear about in the chart is that I assume that the “trait” being measured is the tendency toward psychopathy as measured by a paper & pencil test in one’s youth. This does not entail that an individual in fact behaves like a psychopath. Rather, it simply implies that they’re odds of behaving like a psychopath as an adult are highly elevated. I can’t find the link, but there was a story (which I blogged) a few years ago about a scientist who was studying the peculiarities of psychopath brain structure…and found out that he himself exhibited the same morphology typical of a psychopath. The point is that changing the odds or loading the die does not entail that an outcome is determined.

For example, imagine that you have a long family history of alcoholism. You marry another person with the same history. This sort of thing is heritable, and you’ve just loaded the die for your children. How can you try and compensate? I can think of one simple strategy: convert to a cohesive religious group which bans alcohol consumption, such as Mormons or Salafi Islam. The key here is that the social group is the environment. One can’t likely change that given any environment one’s children are more likely to be alcoholics, but the basal odds are shifted a great deal if you go from being a Catholic to a Mormon.

Also, as a new parent, one thing that I have realized is that behavior genetic understanding of human nature is very useful, it tells us that “attachment parenting” is pretty much crazy. Really more of costly signalling for upper middle class couples than anything else (though less crazy than the 18th century French middle class craze for country wet-nurses which resulted in incredibly high infant mortality rates). Being raised in a Romanian orphanage fucks you up. Your parents, not so much. The “nature vs. nurture” debates are going to continue indefinitely. But parents are will continue to matter less on a day to day level than they think in relation to the outcomes of their children. You can get to set the ground-rules, but there’s no way you will dictate the game.

The special “Human Conflict” issue of Science seems free if you register. No time to read it now, but there’s a lot of interesting looking articles. (via Dienekes)

John Hawks already discussed the Keinan and Clark paper in Science, Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants. To borrow a critique, much of human genomics up to this point has been WEIRD. A reanalysis of the same finite population sets, over and over. No longer. Soon thousands upon thousands of whole genomes will come online, and innumerable rare alleles will start filling the background in. The ultimate end point of this will be when whole families have 100X coverage, and a set of unique mutational variants to each individual within the family unit will become known.

Ed Yong has a piece in Nature on the problems of confirmation bias and replication in psychology. Yong notes that “It has become common practice, for example, to tweak experimental designs in ways that practically guarantee positive results.” The way this has been explained to me is that you perform an experiment, get a p-value of > 0.05 (significance). You know that your hunch is warranted, so just modulate the experiment, and hope that the p-value comes in at < 0.05, and you have publishable results! Obviously this is not just a problem in psychology; John Ioannidis has famously focused on medicine. But here’s a chart which shows that positive results are particular prevalent in psychology:

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