So that reader survey that I mentioned last week is done. I’m mostly interested in seeing the changes since I’ve moved to Discover from ScienceBlogs. I assume that the standard 85% male readership has shifted somewhat toward more balance, but I don’t know. Many of the basic demographic questions (sex, race, age, etc.) are the same, but I swapped out ones I usually ask with others. At this point I’m rather sure that a huge proportion of the readers of this weblog are introverted nerds, so I’m not going to ask about personality type and what not. I took some reader suggestions, so there are questions about what you read, as well what your somatotype is. I converted the political question to a 0 to 10 scale that I wouldn’t have to recode if I did a scatter plot, and also so that it’s a little more fine-grained.

As usual all questions are optional. I timed it and should take you 5 minutes max, though I guess I can’t account for lack of clarity in prose. If you don’t see your exact response, but want to respond, I think it is totally fine to give the closest equivalent.

To take the survey, click here. After you’re done it’ll bring you back to this website. You can review results here.

Below are percentage breakdowns of last winter’s survey by sex.

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Most of you in the science blogosphere have probably come across Razib’s recent post on linguistic diversity and poverty. The basic argument being that linguistic homogeneity is good for economic development and general prosperity. I was quite happy to let the debate unfold and limit my stance on the subject to the following few sentences I posted previously:

From the perspective of a linguist, however, I do like the idea of really obscure linguistic communities, ready and waiting to be discovered and documented. On the flip side, it is selfish of me to want these small communities to remain in a bubble, free from the very same benefits I enjoy in belonging to a modern, post-industrialised society. Our goal, then, should probably be more focused on documenting, as opposed to saving, these languages.

Since then, the debate has become a lot more heated, with Neuroanthropology wading in against Razib, which, in the second-half of the post at least, is worth reading just to get the general flavour of the other side in this debate. Having said that, I wasn’t convinced by the evidence Greg Downey used to dismiss Razib’s hypothesis, so I decided to actually look at the literature on the subject. The first paper I found upon searching was one by Nettle et al, in which they examine the relationship between cultural diversity and societal instability using a large cross-national data set of 212 nations. Importantly, they look at cultural diversity in the context of three areas: linguistically, ethnically and religious affiliation. Also, they draw a distinction between within-nation (alpha) diversity and between-nation (beta) diversity. Lastly, unlike other studies on the subject, where simple regression or correlation methods are used, the current study employs structural equation modelling (SEM):

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About six months ago I did a survey of the readership of my two Gene Expression blogs (before moving to Discover). The N was around 600. You can view the raw frequency results here. One of the issues which I was curious about: did the disciplinary background of readers have any major correlates with responses? So I created three categories from the data on disciplines:

-Science
-Social Science
-Not Science

Social science had its own section, but for science I amalgamated those who studies Math, Engineering, Natural Science and Medicine. The balance were under “Not science.”

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Readers might find these responses of interest. Mostly I just laughed, though some of you may be a bit more serious than I, so if anthro-gibberish drives you crazy, don’t follow the links. As I told “ana” below a lot of the discussion we had was basically just talking past each other. I kept telling her she was vacuous because she was assuming presuppositions which I simply did not share as empirical background descriptions of the world (e.g., a strong form of linguistic relativism where the specific nature of a language shapes cognition). Though at least she was concise. On the other hand, see this small section of Creighton’s response:

I think this is what bothered me the most about Khan’s piece. No discussion of what poverty means, what it is, how it’s defined. I could be completely wrong, but that led me to feel that there was a high degree of Eurocentric neo-colonialism behind Khan’s proposition. Who is saying to who what “median human utility” means? Are we assuming that homeownership, vehicle ownership, and other tangible measures of economic prosperity are involved? Is access to fresh food and water part of this measurement? Khan didn’t discuss poverty at all and he didn’t acknowledge that the neo-colonial policies of certain nations are at least partially responsible for the long-term economic suffering of many of the people he is referring to. I just got the feeling that he was telling the people who belong to small language communities to accept defeat and learn English. It incited me even more that his justification for making this decision was in purely economic terms. Abandoning your heritage will pay out in the end. But will it?

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Mexico: Ancient woman suggests diverse migration:

A scientific reconstruction of one of the oldest sets of human remains found in the Americas appears to support theories that the first people who came to the hemisphere migrated from a broader area than once thought, researchers say.
Mexico’s National Institute of Anthropology and History on Thursday released photos of the reconstructed image of a woman who probably lived on Mexico’s Caribbean coast 10,000 to 12,000 years ago. She peeks out of the picture as a short, spry-looking woman with slightly graying hair.

Anthropologists had long believed humans migrated to the Americas in a relatively short period from a limited area in northeast Asia across a temporary land corridor that opened across the Bering Strait during an ice age.

But government archaeologist Alejandro Terrazas says the picture has now become more complicated, because the reconstruction more resembles people from southeastern Asian areas like Indonesia.

I think this gets at the fallacy:

But Gillespie cautioned against comparing a reconstructed face from 10,000 years ago to modern populations in places like Indonesia, which have also probably changed over 10 millennia.

“You have to find skeletons of the same time period in Asia, or use genetic reconstructions, to make a strong connection, and cannot rely on modern populations,” she wrote. “Do we have any empirical data on what Southeast Asian women looked like … 10,000 years ago?”

A few years ago some scholars asserted that Kennewick Man resembled “South Asians.” I’m open to the possibility of a more complex peopling of the Americas, but until we get ancient DNA (something that is very difficult in the USA), it seems rather strange to make assessments of phylogenetic descent based on phenotypic similarities between one ancient specimen and modern populations.

Image Credit: AP Photo/ Mexico’s National Institute of Anthropology and History

I was travelling on Monday so couldn’t post the open thread and then forgot. But now that I think about I think Friday would be better in any case, because I don’t post much on the weekends. So again, questions, links, what you’re reading. You know my motto, “Don’t be stupid” (fwiw, posting links to flickr photos of your cats is not stupid).

Have a good weekend.

Ancestry-Shift Refinement Mapping of the C6orf97-ESR1 Breast Cancer Susceptibility Locus. Many single nucelotide polymorphisms associated with a risk factor may actually not be the causal agent in a mechanistic sense. It’s just very close to and tightly associated with the real genetic cause. If the tightness of that association varies by population, then the utility of that marker varies between populations as a predictor. This is why us colored folk should be wary of risk alleles discovered in studies of European populations insofar as we apply those results to ourselves.

Will Your Children Grow Up To Be Servants And Nannies? In the period between 1800 and 1970 the wage gap between unskilled and skilled workers closed, the wage premium on education and specialized skills decreased. Since 1970 in the developed world the gap has started to grow again (see Farewell to Alms). I won’t explore in depth the long term implications of assortative mating, heritability of psychological and behavioral traits, and a genuine meritocracy which rewards skill, diligence and intelligence fairly. Think on it though if you have the brains and the knowledge base, and feel compassion unless you’re a psychopath.

Adaptive Evolution of Genes Duplicated from the Drosophila pseudoobscura neo-X Chromosome. The target of selection is more than just SNPs. The unit of selection may be more than just the individual.

Anguish of Romantic Rejection May Be Linked to Stimulation of Areas of Brain Related to Motivation, Reward and Addiction. I’ve never been addicted to a drug, have no fixation on shopping, and such. But now I guess I can imagine what that feels like, and I feel really sorry for people who are addicted in any way.

Ford Makes Money Again. But What About That Debt? I really hope Ford does well. They’re in a bind because they didn’t fail and get bailed out by the government. The world turned upside down.

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Dr. Daniel MacAthur & Dan Vorhaus offer their takes on the recent hearings in Congress on the direct-to-consumer genomics industry, A sad day for personal genomics & “From Gulf Oil to Snake Oil”: Congress Takes Aim at DTC Genetic Testing. I guess I lean toward light regulation. I don’t think that DTC personal genomics will result in systemic decrease in human happiness, and tight regulation will increase the costs of innovation and constrain access and reduce affordability. Though I guess that for some that’s a feature, not a bug.

My main point, which I think I got across on the Genomes Unzipped comments is that fraud, error and misrepresentation are rife across many health-related sectors in American society. The nutrition and diet industry are prime examples. Bad journalism on the health beat causes way more suffering than DTC genomics kits ever will, as people who are not intelligent make precipitous decisions based on the latest result which managed to slip through the p-value gauntlet and are sexy enough to be written up in USA Today. And, there are widespread distortions within our health care sector which really need to be addressed (I’m thinking in particular of frank talk about end of life palliative care). With that as the basis for judgement I don’t think that the fraud and misrepresentation one can find in DTC personal genomics is exceptionally worrisome or notable to warrant such attention or focus. This is an inefficient allocation of concern and regulatory resources, driven more by the industry’s puffed up claims and the apocalyptic projections of the skeptics.

Despite the reality that I’ve cautioned against taking PCA plots too literally as Truth, unvarnished and without any interpretive juice needed, papers which rely on them are almost magnetically attractive to me. They transform complex patterns of variation which you are not privy to via your gestalt psychology into a two or at most three dimensional representation which can you can grok immediately. That is why History and Geography of Genes was so engrossing. You recognize patterns which were otherwise unrecognizable. But how you interpret those patterns, that’s a wholly different matter. And how those patterns arise is also not something one can ignore.

First, let’s start with an easy case. To the left is a PCA plot with four populations. Nigerians, East Asians (Chinese + Japanese), Europeans (whites from Utah), and finally, African Americans. The x-axis is the first principal component of variation, and the y-axis the second. That means that the x-axis is the independent dimension of variation within the patterns of genetic data which explains the largest fraction of the total amount of genetic variation. The sum totality of the variation can be decomposed into an large set of independent dimensions which can be rank ordered from the largest explanatory components to the smaller ones, successively by number. In a human genetic context the first principal component invariably separates Africans from non-Africans, and the second principal component often maps onto a west-east axis from Europe to the New World. Subsequent principal components can often be useful in smoking out fine scale distinctions, or relationships which are confused by the existence of similar but different signals in admixed populations.

The interpretation of this plot is rather easy. You see that African Americans lay along a continuum between Nigerians and Europeans, skewed toward Nigerians, with some outliers toward East Asians. We know from other genetic findings that ~20% of the African American ancestral quanta is European, but, that quanta is not equally distributed across the population. ~10% of the African American population is more than 50% European in ancestry, while 90% is less than 50% European. And so you have a distribution which reflects this variation. As for the outliers, I will speculate and suggest that these are indications of Native American ancestry among some African Americans.

The story I presented above is probably plausible as an explanation of the visual because we have a wealth of historical data to corroborate the plausibility of that narrative. The fit between the results from the technique of analysis of genetic variation and what scholars have long inferred from textual sources is relatively easy. It is far more difficult to look at a PCA plot, and generate a plausible narrative that you yourself accept with a high degree of confidence with little external support. It is with that caveat in mind that I present Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping:

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