Archive for July, 2008

Breeding the future

By Razib Khan | July 30, 2008 7:37 pm

Some results from the GSS on what people perceive the ideal number of children is based on social variables. Additionally, the realized number of children the respondent has. I limited the sample to whites who were 40 or older (there are people who have children past 40, but I assume that most of the discrepancy, or not, between ideal and realized will be evident by that age).

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No one knows nothing about The Foundation

By Razib Khan | July 30, 2008 4:17 pm

Chris Orr at The Plank reports that Isaac Asimov’s Foundation series is going to be given the film treatment. Orr is skeptical, and so am I. As far as space opera goes the Foundation universe was a cerebral and sedate treatment; they’ll have to rewrite a lot of it to get some action to spice up the story. David Brin’s Uplift based novels read much more like the outlines of scripts; but after The Postman they probably won’t want to risk that. Even if there’s a lot going on space opera doesn’t always translate well. Remember David Lynch’s take on Dune? Because of the success of Peter Jackson’s Lord of the Rings trilogy I suppose the film industry will go on this turn-novel-series-into-film-series kick for a while. I think after the disappointment of The Golden Compass one has to admit that Jackson ended up making good films, and you can’t just assume that the “based on” formula is going to make an endeavor a success.


Denomination is rather heritable; socioeconomic status less so….

By Razib Khan | July 29, 2008 8:07 pm

I was curious about a few social variables which often associate across generations, and also within families. So I looked in the General Social Survey for denomination, highest degree and socioeconomic index, which I knew were surveyed for the individual (respondent), their parents and their spouse. Below the fold are the correlation matrices generated. Remember that if you assume a linear dependency you square the correlation (e.g., 0.50 → 0.25) to find out how much of the variation in X can be accounted for by variation in Y.

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No Polynesian origin for pre-Columbian chickens???

By Razib Khan | July 29, 2008 5:51 pm

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA:

European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl…The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin. A published, apparently pre-Columbian, Chilean specimen and six pre-European Polynesian specimens also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing no support for a Polynesian introduction of chickens to South America….


Theological beliefs by denomination

By Razib Khan | July 28, 2008 6:08 pm

One of the problems with intellectual conversations is that they are generally restricted to intellectuals. By their nature intellectuals tend to value reflection and some semblance of comprehension and consistency. This is a “curved” scale; I’m not contending here that intellectuals really attain a very high absolute level of analytic clarity or coherency, but, the process itself tends result in a minimal baseline of plausibility to a propositional sequence.
I’ve pretty much come to the conclusion that the problem with attempting to understand human cognition as a sequence of inferences generated from propositions is that most people don’t even make the nominal attempt to engage in the act of deep reflection. The heuristics and biases which shape modal psychology are determined by a combination of intuition, custom and conformity. Paradoxes of inconsistency are no great issue when ideas and propositions have only a minimal level of contingency. Arguments are ad hoc and operationally instrumental. The aforementioned guides of intuition, custom and conformity hone mental reflexes which can be accessed rapidly and with reasonable surety, despite the lack of deep comprehension.
In most cases I don’t believe that the disjunction between the preferred ideal way that intellectuals reflect and the modal operation of human cognition is much of an issue. Intellectuals, or those who fancy themselves as such, might struggle with issues of ontology. But I do not believe that this is particularly on the radar of the typical individual whose concerns are more prosaic, the basic material and emotional comforts and securities of life. Confusions only emerge when institutions and systems aim to span the full gamut of conventional cognition. For example, in politics or religion, where intellectuals build systems which are very relevant to the lives of most humans. Because of the general obscurity of intellectual constructs to the “average Joe” there is a large body of literature which exists to make abstruse concepts “relevant” in everyday terms to everyday people (e.g., instead of “soteriology,” what is “God’s plan for you”).
Because of the chasm between those inclined to think, write and expound, and the typical human, I believe it is critical that we inspect the shape of what people actually believe, as opposed to what one might expect if they were idealized inferential machines. So with that, I will reproduce below the fold a selection of religious data from the Barna Group:

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Humanities "vs." science

By Razib Khan | July 27, 2008 4:52 pm

Chad has a post up The Innumeracy of Intellectuals, where he goes on a rant against humanities academics and their blithe complacency in relation to their ignorance of science & mathematics. Two points….
1) One of the major issues with humanistically oriented intellectuals, I believe, is a lack of anthropological fluency with the culture of science. As a case in point, a contributor to the literary weblog The Valve dismissed my assertion that scholars who study science should have some immersion in scientific education at some point with the quip that experience with multiple choice tests wouldn’t add anything to their comprehension. The reduction and dismissal of even an undergraduate science education to multiple choice tests bespeaks a lack of awareness of what science coursework for those majoring in the sciences often consists of (i.e., solving problem sets, laboratories and undergraduate research).
2) One of the major issues with scientifically oriented intellectuals is that they attempt to translate scientific methods into humanistic domains where there just isn’t the proven return on investment at this point. Some forms of Marxism were an attempt to reduce history into a deterministic process controlled by a few parameters; I suspect that explains the attraction Marxism, and socialism more broadly, had for scientific intellectuals early in the 20th century. The hypoethico-deductive methodology which the scientifically educated are habituated to engaging in must be used very judiciously when examining humanistic questions. What exactly do general axiomatic theories have to tell us about the influence of Hellenistic motifs on early Umayyad art? How exactly has Theory really worked out for the humanities so far? Certainly an appreciation of art can be reduced ontologically to neuroscience, but the outcome of the Superbowl can also be reduced to quantum level dynamics. So?
Finally, I also don’t think that the attitude of humanists toward science is really one of superiority. I think it is pretty clear that today science is the queen of the intellectual enterprise, and within science physics is the gold standard by which other disciplines judge themselves. I think most of the bluster by non-scientists about their ignorance is rooted in some embarrassment, just as I think most non-physicists (this is mostly aimed toward biologists) know that they wish their own field had attained even a fraction of the power of physics in modeling the world around us.
Janet touches upon most of the hypotheses re: science vs. humanities….


Are liberals against nuclear power more than conservatives? Yes

By Razib Khan | July 25, 2008 6:11 pm

Because of the increased prices in gasoline and the perception of scarcity in terms of power, there has been a lot of talk about nuclear. There have been many comments of late from the Right that the Left is opposed to the utilization of nuclear power, and often gleeful the observation that many European countries such as France and Sweden are highly reliant on this technology. But is it true that liberals are more averse to nuclear than conservatives? I checked the GSS for the following questions:
– Nuclear power dangerous to the environment?
– Likelihood of nuclear meltdown in 5 years?
– Nuclear power a danger to my family?
The tables below show the proportion of various ideologies in terms of responses to these questions. The responses to the left are more nuclear skeptical than those to the right.

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Style is timeless

By Razib Khan | July 25, 2008 5:05 pm

I’ve been reading Critique of Pure Reason and An Enquiry Concerning Human Understanding in the evenings. It should be no surprise that the former is a more tedious read than the latter, David Hume being the better stylist than Immanuel Kant. In faireness, one presumes that translation from the German might add some overhead in terms of obscurity (though I’ve heard that the German isn’t the model of clarity either). Nevertheless, I’m struck by the fact that Kant’s prose reminds me a great deal of Stephen Jay Gould. I think this is interesting because Gould drew so much inspiration from out of favor Germanic conceptions of biological processes and paradigms, in particular the importance of bauplan. An analog to Hume might be Richard Dawkins’, who if excessively simple in his formulation nevertheless gains in economy as a result.
P.S.: I haven’t read Hume since college, and I have to say I’m a lot less impressed than I once was. Dude was wrong a lot!


History in the genes

By Razib Khan | July 24, 2008 3:28 pm

I’ve posted a fair amount about the new field of historical population genetics. Some of the most popular mass-market books in genetics deal with this field, for example Spencer Wells’ Journey of Man. On the other hand, there’s a lot of sloppy overreach on the part of some practitioners, especially due to the excessive reliance on uniparental lineages; the unbroken female and male lineages (mtDNA and NRY). Nevertheless, in specific narrow cases where hypotheses are being tested they can be very illuminating.
For example, here is a question: do the mixed-race populations of the Caribbean exhibit any evidence of descent from the indigenous pre-Columbian populations? This is an open question because it was in the Caribbean that the first and most extreme die-offs of native populations occurred when exposed to Eurasian pathogens. The short answer seems to be yes, some indigenous ancestry does persist into the present.
This was first confirmed in Puerto Rico, Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis:

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The evolution of language and biology

By Razib Khan | July 24, 2008 12:18 am

Sandman has a post up, Can There Be A Synthesis Between Cultural And Biological Evolution?, taking off on the PLoS Biology article, Across the Curious Parallel of Language and Species Evolution. Read both. I would add one important point though: linguistic and biological evolution are simply subsets of evolutionary dynamics. That is why Martin Nowak’s book of that name, Evolutionary Dynamics, naturally has a section on the evolution of language. Several evolutionarily oriented thinkers have attempted to translate models originally developed for biology into the domain of culture. Cultural Transmission and Evolution and Culture and the Evolutionary Process are two works which I think are good introductions to the field.

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Drugs & science & insight

By Razib Khan | July 23, 2008 2:06 pm

I posted before on Why scientists should do drugs (if they choose), via Tyler Cowen, a Jonah Lehrer article in The New Yorker:

Many stimulants, like caffeine, Adderall, and Ritalin, are taken to increase focus — one recent poll found that nearly twenty percent of scientists and researchers regularly took prescription drugs to “enhance concentration” — but, accordingly to Jung-Beeman and Kounios, drugs may actually make insights less like, by sharpening the spotlight of attention and discouraging mental rambles. Concentration, it seems, comes with the hidden cost of diminished creativity. “There’s a good reason Google puts Ping-Pong tables in their headquarters,” Kounios said. “I you want to encourage insights, then you’ve got to also encourage people to relax.” Jung-Beeman’s latest paper investigates why people who are in a good mood are so much better at solving insight puzzles. (On average, they solve nearly twenty percent more C.R.A. problems.)

In other words, what may make a more efficient engineer may also dampen creativity in a theoretical physicist….


Populism & public religion

By Razib Khan | July 23, 2008 12:37 am

Half Sigma points me to The Legend of a Heretic, which chronicles the close relationship between Robert G. Ingersoll, a prominent American agnostic of the 19th century, and the Republican Party elite of that time. It seems ironic that though we are a nation which explicitly bans formal religious tests, we live at a time where an implicit religious test exists. This despite the fact that Andrew Jackson was probably the first of our presidents who would be considered an orthodox Christian. But even as late as 1908 a Unitarian, William Howard Taft, was president (despite some grumblings about his unorthodox Christianity).

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The Dark Knight

By Razib Khan | July 21, 2008 5:51 am

I didn’t watch The Dark Knight this weekend. Anyone else out there?


John Hawks gets tenure!

By Razib Khan | July 21, 2008 4:10 am

How to blog, get tenure and prosper: Starting the blog. ‘nuf said.


Why does race matter for women?

By Razib Khan | July 20, 2008 3:50 pm

One social science finding which I’ve wondered about over the past few years is the result that women care much more about the race of a potential mate than men do. The fact that individuals tend to want to mate assortatively with those who share their characteristics is no surprise. Rather, what does surprise are a series of papers that show a very strong asymmetry in strength of preference between males and females. To be crass about it, an attractive warm body will do for a man, but women strongly prefer a body with the packaging of their own race!
First, let’s keep this in perspective, here are the correlations from the GSS for married individuals for several variables of note (I’ve filtered for whites here):
Ethnicity – 0.40
Highest Degree – 0.55
Socioeconomic index – 0.32
I think it’s interesting to note that the variable which reveals meritocratic achievement has the highest correlation. Ethnicity is something you’re born into, and socioeconomic index is a metric which derives from the milieu in which you were raised.
This post is going to review some findings in a paper which attempts to both describe the differences in race preference for dating by race and across genders, and, why those differences might emerge the way that they do. The paper is Racial Preferences in Dating, Review of Economic Studies (click the link to download and read the whole thing yourself!). Here’s the abstract:

We examine racial preferences in dating. We employ a Speed Dating experiment that allows us to directly observe individual decisions and thus infer whose preferences lead to racial segregation in romantic relationships. Females exhibit stronger racial preferences than males. The richness of our data further allows us to identify many determinants of same-race preferences. Subjects’ backgrounds, including the racial composition of the ZIP code where a subject grew up and the prevailing racial attitudes in a subject’s state or country of origin, strongly influence same-race preferences. Older subjects and more physically attractive subjects exhibit weaker same-race preferences.

A few points need to be made clear: males do not exhibit statistically significant racial preferences by and large. That’s somewhat shocking to me. I’m not surprised that older subjects have weaker biases, I suspect frankly they’re more realistic and don’t want to narrow their options anymore than they have to. Finally, I’m totally confused as to why hotties would be less race conscious; you would figure if hybrid vigor is real that the marginal returns would be greatest for the fuglies (specifically, assuming that fugitude correlates with individual mutational load and hybridization would be better at masking that load). But the most relevant demographic point is that these are Columbia University graduate students. In other words, a cognitively & socially elite sample.

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HIV may not be associated to Duffy!?!?!

By Razib Khan | July 20, 2008 2:38 am

Over the past few days I’ve blogged a bit about the story about an HIV susceptibility allele; Evolution, a reason for the African HIV epidemic?, Overplaying “AIDS genes” and HIV susceptibility, a “black” thing, not a Duffy thing?. But there’s an important post Genetic Future, Duffy-HIV association: an odd choice of ancestry markers:

In the Duffy study the authors attempt to perform this type of correction using a set of just 11 markers they describe as “differentially distributed between European and African populations”. p-ter notes that several of these markers are not particularly ancestry-informative, and indeed on closer inspection it’s clear why this is: these genes weren’t originally selected on the basis of ancestry informativeness, but rather because they are associated with HIV biology. Every single one of the 11 markers has some association with HIV: three of them have previously been associated with HIV infection, progression, or response to treatment (CCR5 delta32, APOBEC3G H186R, GNB3 C825T); most of the remaining markers are in genes that are known binding targets or modulators of HIV (CCR5, CXCR4, PD1, TRIM5, IL-2, IL-4).

If that’s true – and it’s difficult to see any other rationale for using these HIV markers rather than a set of validated AIMs – this is poor form for at least two reasons. Firstly, it’s unlikely that using such a weak set of ancestry-informative markers provides an effective correction for a marker with as strong a correlation with ancestry as Duffy (as p-ter notes, all of the supposed ancestry markers are far weaker predictors of ancestry than the Duffy variant). Secondly, testing several different variants for an association with HIV and then only reporting the one that achieved significance creates the perfect conditions for a false positive due to multiple comparisons – it’s entirely possible that the Duffy association would not have survived correction for multiple testing. It’s difficult to assess this fully because the manuscript doesn’t seem to report a single P value (!), although I note that the lower edge of the 95% confidence interval of the odds ratio in Figure 2C is perilously close to 1 following their ancestry “correction”.

Read the whole thing…but something is starting to smell fishy. Hey Dave Appell, blogs rock and peer review sucks! (sometimes)


Viability selection and genetic screening

By Razib Khan | July 19, 2008 10:05 pm

sherilyn009.jpgJust a quick follow up to my post about genetic screening of embryos and subsequent implantation. The spontaneous abortion rate for humans is very high. Probably on the order of 50% of fertilized ova implant and complete to term. I’ve seen numbers all over the place. In any case, I assume many of these are chromosomal abnormalities. But I’ve also posted to data which strongly suggests that immunological incompatibilities between mother & fetus also play a role in spontaneous abortions and may result in natural selection which we’re not too well aware of. In The Cooperative Gene the evolutionary biologist Mark Ridley suggests that because of spontaneous abortion we should be less than worried about reduced efficacy of natural selection in purging deleterious alleles from the gene pool; as the genetically unfit reach viability and reproduce their alleles will be culled at the stage of of the embryo and fetus.

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HIV susceptibility, a "black" thing, not a Duffy thing?

By Razib Khan | July 19, 2008 2:20 pm

DARC and HIV: a false positive due to population structure?:

The authors are aware of this potential confounder, and develop a measure of admixture based on 11 SNPs to include as a covariate in their regression. However, this measure is kind of weak, which I imagine in the sticking point for the skeptics in the Times article. If you have access to the supplemental information, take a look at it–several of these 11 SNPs are in the same gene, which means they’re not independent, and several don’t even have big frequency differences between African and European samples (if you’re trying to judge via SNPs whether someone is more African or European, those SNPs better have a big frequency difference between Africa and Europe). This is probably not a precise measure of ancestry. In fact, the Duffy null allele they claim as associated is a better predictor of ancestry than any of these SNPs.
So it’s quite possible that the authors have simply shown a correlation between level of African ancestry and susceptibility to HIV (which could be due to any number of sociological, demographic, or genetic factors), rather than an association between Duffy null and susceptibility to HIV. Here’s a relatively simple test of this possibility: genotype rs1426654 (the nonsynonymous SNP in SLC24A5) in their sample and perform exactly the same test as performed with Duffy. The motivation for this is that this SNP shares the property of Duffy null of being highly informative about ancestry, while being in a gene that presumably plays no role in HIV infection. If you get an association there, it seriously calls the Duffy result into question; if not, you feel a bit more comfortable.

This is why mapping human variation is so important. Note that the genetic variation itself might not even be responsible for greater susceptibility to HIV in a causal sense; if circumcision does have a role in reducing the spread of HIV then cultural practices which correlate with genetic variation can also produce spurious correlations. As an illustrative example in South Africa there is a correlation between HIV infection rates and decreased Khoisan ancestry. I say this because the Zulus have higher infection rates than the Xhosa, and the latter have a great deal more Khoisan ancestry than the former. The differences have been attributed to the fact that the Xhosa practice circumcision and the Zulu do not, so the differences in genes is just coincidental.


The Perfect BabyTM

By Razib Khan | July 18, 2008 8:12 pm

Genetic Future points me to a Nature News story, Making babies: the next 30 years. He highlights this section:

There’s speculation that people will have designer babies, but I don’t think the data are there to support that. The spectre of people wanting the perfect child is based on a false premise. No single gene predicts blondness or thinness or height or whatever the ‘perfect baby’ looks like. You might find genetic contributors but there are so many environmental factors too.

The details are important here. Height is a tough cookie; it seems like there are going to at least hundreds of loci which control most of the normal human variation (if not thousands). But blondness is a bad example; pigmentation is only controlled by a few loci. Getting a fix on OCA2, SLC45A2, SLC24A5 and KITLG will get you what you want. That doesn’t mean the parents don’t have to have the variation necessary, they do, but they can probably guarantee a little blonde beast if they have the potentiality. And it seems that this really isn’t a function of the genetic future, the number of embryos parents would need to guarantee a little Aryan baby if they both have Aryan blood isn’t that high (probably 10-100 embryos depending on the purity of Aryan blood of the parents).
In any case, read the Genetic Future post for the bigger picture.


R. A. Fisher and Epistasis

By Razib Khan | July 18, 2008 1:34 pm

David takes a slight detour in this Sewall Wright, series, R. A. Fisher and Epistasis:

My next note on Sewall Wright will cover the exciting subject of the adaptive landscape. As every schoolboy knows, Wright considered epistatic gene interactions very important in determining the ‘peaks’ of the landscape. A sharp contrast is sometimes drawn between Wright and R. A. Fisher in this respect….

This is a preamble to a very long and dense post. If it interests you in the subject, I’d also recommend Epistasis and the Evolutionary Process. You might also check out this older post of mine on evolutionary epistasis.
Related: Notes on Sewall Wright: Population Size, Notes on Sewall Wright: the Measurement of Kinship, Notes on Sewall Wright: Path Analysis, On Reading Wright and Notes on Sewall Wright: Migration.


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