Saturday, June 30, 2007

Do phenotypes evolve neutrally?   posted by p-ter @ 6/30/2007 04:02:00 PM
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On the DNA level, most fixations of new alleles are due to genetic drift. But what's the role of neutral processes in phenotypic evolution? I ask because Larry Moran is claiming (in the comments here) thar most phenotypic evolution is also due to drift. I find that hard to believe-- one of his examples, PTC tasting in humans, is certainly not drifting neutrally, and the expression levels of most genes (a "low-level" phenotype one might expect to be allowed to drift) seem to be under strict control (I reviewed some of the evidence for that here).

Good evidence for lack of selective constraint could come from mutation accumulation (MA) lines-- lines bred with a tiny effective population size for a number of generations. The small effective population size allows nearly all alleles (except the most deleterious ones) to drift randomly. One could compare a given phenotype in a number of these lines, then compare to wild isolates-- if the variance in the MA lines is about equal to that in the wild lines, you might conclude that selection is not operating on the phenotype in the wild.

Has this been done? Is anyone aware of experimental evidence for lack of constraint on a phenotype?

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Friday, June 29, 2007

Genome transplantation in bacteria   posted by p-ter @ 6/29/2007 04:08:00 PM
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The folks at the Craig Venter Institute, having patented the technology for creating a synthetic organism, now have at least part of the process working: they report that they can take an entire bacterial genome from one organism and pop it into another, essentially "re-booting" the cell as a new species. The next step, obviously, is to synthesize a custom genome that does something you find worthwhile (digests some nasty chemical, if you're feeling eco-conscious...or produces a nasty chemical, if you're feeling more war-like), and create your own bacteria.

One interesting thing (from a methodological standpoint) about this procudre is that it appears to involve inducing the fusion of the two cells (the researchers don't actually know; they just see the outcome), making it somewhat similar to procedures for creating hybrid cell types in mammals. It's something of an unexpected connection between bacterial transformation and cell fusion.

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Structural variation in humans   posted by p-ter @ 6/29/2007 03:42:00 PM
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Nature Genetics has a free supplement on structural variation, with an emphasis on its role in human disease. Nothing too exciting-- structural variation is simply a type of polymorphism, albeit with some interesting issues regarding detection, but if you're looking for some background and discussion of future directions, it might be of interest.

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Geneographic project in PLOS   posted by Razib @ 6/29/2007 01:03:00 PM
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The Genographic Project Public Participation Mitochondrial DNA Database. This is Spencer Wells' baby. Only mtDNA, and focused more on the methods though they didn't find Neandertal lineages.

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Thursday, June 28, 2007

Genome-wide association study for breast cancer susceptibility   posted by p-ter @ 6/28/2007 08:42:00 PM
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Another genome-wide association study:
Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls [!!!] from 22 studies... SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P < 10-7). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1).
These alleles are of small effect and in areas of the genome about which little is known, again showing that genome-wide association studies are a powerful way of opening up research into novel biology.

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Reanalysing gene expression differences between populations   posted by p-ter @ 6/28/2007 05:59:00 PM
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Early this year, I commented on a paper showing large differences in gene expression between Europeans and Asians. A letter to the editor in this week's Nature Genetics points out a major flaw in part of their analyses.

Expression arrays are tricky tools-- they don't provide a measure of absolute mRNA levels, but rather an output that corresponds to the binding affinities of the mRNA, the ambient conditions, the way the mRNA was handled, and absolute mRNA levels (and a billion and one other things). Study design is extremely important in isolating the effect of the variable you're really interested in (mRNA levels), and it's very difficult, if not impossible, to really compare the raw data from one array experiment with that from another.

The error the authors made is an unfortunate (and pretty elementary) one-- they did the array experiments on the Europeans population in 2003-2004, and the array experiments on the Asian population in 2005-2006 (they actually erroneously claimed the samples were randomized with regard to year in the paper, which would explain why it got past peer review). This means that any variation between the European and Asian populations is perfectly confounded with variation between those two batches. There's no way to correct for this; any difference in mean expression between the two populations is due to a mixture of the "real" effects and the bias from the batch effect. That's a bitch.

Luckily, the authors also did additional analyses (as they point out in their reply)-- they looked at the correlation of expression levels with genotypes. In the figure, you see the population distributions of expression for a given gene on the left, and the within-genotype levels on the right. There doesn't seem to be much of a differences between the two populations within each genotype class, but the population difference is explained almost entirely by the difference in allele frequency between the two populations.

So was their claim of finding nearly 25% of all genes differentially expressed between the two populations likely wrong? Yes. But their conclusion that allele frequency differences play a role in expression differences between populations stands-- it will just take a better-designed study to quantify the effect.

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Coeliac disease - gluten intolerance   posted by Razib @ 6/28/2007 03:04:00 PM
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A comment below about gluten intolerance (which is associated with problems digesting products with wheat) made me curious. In much of Eurasia this would be a serious problem since wheat is the staff of life. Hard numbers are difficult to come by. This is as good as anything else I've seen:
Celiac disease affects as many as 1 in 300 people in Italy and southwestern Ireland, but is extremely rare in Africa, Japan, and China...According to a multicenter study in 2003, there is a 1 in 133 chance that people with no risk factors or family history in the U.S. have celiac disease. Additionally, a person's risk increases to a 1 in 22 chance if they have a first-degree relative with celiac disease and a 1 in 39 chance if they have a second-degree relative...Around 60,000 Americans are diagnosed with celiac disease annually and a total of over 2 million have the disease, making it perhaps the most common genetic disorder in the United States...Celiac disease can occur at any age, and females are more commonly affected than males. Of females presenting during their fertile years, the male to female ratio is almost 3 to 1....


From Wiki:
The vast majority of coeliac patients have one of two types of HLA DQ, a gene that is part of the MHC class II antigen-presenting receptor (also called the human leukocyte antigen) system and distinguishes cells between self and non-self for the purposes of the immune system. There are 7 HLA DQ variants (DQ2 and D4 through 9). Two of these variants-DQ2 and DQ8-are associated with coeliac disease. Every person inherits two copies, one from each parent. The gene is located on the short arm of the sixth chromosome, and as a result of the linkage this locus has been labeled CELIAC1.

Coeliac disease shows incomplete penetrance, as the gene alleles associated with the disease appear in most patients, but are neither present in all cases nor sufficient by themselves cause the disease. Over 95% of coeliac patients have an isoform of DQ2 (DQA1*0501:DQB1*0201 haplotype or more simply DQ2.5) and DQ8 (DQA1*0301:DQB1*0302), which is inherited in families.


Incomplete penetrance might be due to the fact that there are other genetic actors which haven't been elucidated that are necessary for the emergence of this syndrome. Or, there might be environmental or pathogenic triggers which only affect a minority with the necessary genetic predisposition. But in any case, my first thought was gluten intolerance might be the result of an incomplete selection sweep as populations shifted from hunter-gatherer lifestyles to agricultural ones. I'm skeptical of this since populations in Africa and Australia which don't have a history of wheat agriculture don't exhibit this syndrome. Additionally, though wheat agriculture is practiced in north China this was originally a region of millet production. Finally, all the reports suggest massive underestimates of the extent of this condition within the population. Like lactose intolerance this isn't a disease with a clean set of symptoms which are easy to assay quantitatively (is there a way a metric for stool firmness?). The implication of MHC loci as necessary preconditions makes me wonder if gluten intolerance is simply a low frequency condition which is a byproduct of a disease adaptation on the genes in question which was operant in western Eurasia.

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The promise of ES cells   posted by amnestic @ 6/28/2007 11:35:00 AM
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There is a rather salty piece of correspondence in the new Nature Neuroscience from one Maureen Condic regarding Nature's editorial position on the likelihood of development of ES cell-based therapies anytime soon. Apparently, Condic has a skeptical take on the issue and Nature had some disparaging words.

The issues of immune rejection, tumor formation and hESC differentiation raised in my article are not distortions or mere polemic; they are matters of scientific fact. These same concerns have been raised in the scientific literature and voiced by leading scientists in the stem cell field. James Thomson cautioned that "major roadblocks" must be overcome before hESC-derivatives could be safely transplanted into patients, and concluded that surmounting these roadblocks will be "likely to take a long time". Similarly, Robert Lanza noted that immune rejection is a significant problem, and warned that creating hESC lines to match most patients "could require millions of discarded embryos from IVF clinics". Although the editors dismiss as "tenuous" the connection between therapeutic use of hESCs and the genetic/epigenetic abnormalities introduced during cloning, this same concern was raised by Jose Cibelli's recent article in Science.

I think it is important to hear about these obstacles and be realistic about what ES cells could provide. There are other uses of ES cells besides implantation type therapy, of course. For instance, they aid the understanding of basic cell differentiation and cell cycle regulation, topics that are important in cancer research.

The problem for me is that I find the 'moral' objections ridiculous. So if ES cells have any therapeutic or just plain scientific potential at all, then I'm all for it. Am I living in naive bliss thinking that most average people wouldn't give a damn after they really understood what a blastocyst is? Right now, I'm thinking that this is one of a few scientific areas where you could educate the public and actually impact policy in a positive way.

There appears to be a semi-lively debate underway over at the Nature Neuro news blog: Action Potential.

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Sexual dimorphism with no costs takes some time   posted by Razib @ 6/28/2007 12:40:00 AM
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Macho stags have macho sons but daughters are little dears:
The findings show for the first time in animals that some genes are designed to benefit just one gender and can handicap the other sex.

It was found that the female offspring of the biggest and strongest stags were less successful at breeding and had fewer fawns during their lives than daughters of weedy males.


In The Mating Mind Geoff Miller proposed that variance in mutational load could account for the phenotypic variation in traits like intelligence. The brainy and beautiful are simply burdened with fewer deleterious alleles. But the study above suggests another reasons, traits which increase fitness in one sex may decrease it in another. The ideal is for sex dependent gene expression to modulate phenotypic expression so that female offspring of hyper-masculine males are not themselves somewhat masculinized. But the scaffolding of the genes which cause these traits by modifier loci takes time, and perhaps selective pressures are also running ahead so that the variational noise due to differential fitness across sexes is always extant within the population.

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Wednesday, June 27, 2007

Even a caveman could eat it   posted by Razib @ 6/27/2007 10:23:00 AM
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The original human ('Old Stone Age') diet is good for people with diabetes:
In a clinical study in Sweden, the research group has now compared 14 patients who were advised to consume an 'ancient' (Paleolithic, 'Old stone Age') diet for three months with 15 patients who were recommended to follow a Mediterranean-like prudent diet with whole-grain cereals, low-fat dairy products, fruit, vegetables and refined fats generally considered healthy.

All patients had increased blood sugar after carbohydrate intake (glucose intolerance), and most of them had overt diabetes type 2. In addition, all had been diagnosed with coronary heart disease. Patients in the Paleolithic group were recommended to eat lean meat, fish, fruit, vegetables, root vegetables and nuts, and to avoid grains, dairy foods and salt.

The main result was that the blood sugar rise in response to carbohydrate intake was markedly lower after 12 weeks in the Paleolithic group (-26%), while it barely changed in the Mediterranean group (-7%). At the end of the study, all patients in the Paleolithic group had normal blood glucose.


Here's a problem I see: it is a clinical study in Sweden. It stands to reason that Swedes would not be the best test case for a Mediterranean diet. Consider that agriculture became normative in Sweden about 5,000 years ago, 5,000 years after it was the dominant mode of production in the eastern Mediterranean. Note that Sweden is also the epicenter lactose tolerance (thought that seems to have become the norm after agriculture arrived on the scene), suggesting a priori expectation of localized adaptations. In any case, I think one should be cautious about broad generalizations about diet across cultures. Not only jas there been a lot of evolution in regards to the human metabolization of nutritional intakes, we shouldn't be surprised if many of these propensities are local. Selection thinks globally, but acts locally.

Related: All diabetes, all the time.

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Tuesday, June 26, 2007

Against the Ultracalvinists   posted by Razib @ 6/26/2007 10:28:00 PM
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Reguar GNXP reader Mencius has an interesting post titled The ultracalvinist hypothesis: in perspective. Mencius is one of those rare bloggers who focuses on occasional essays where he develops his own ideas as opposed to a barrage of links and responses to the thoughts of others. Here's his introduction:
The "ultracalvinist hypothesis" is the proposition that the present-day belief system commonly called "progressive," "multiculturalist," "universalist," "liberal," "politically correct," etc, is actually best considered as a sect of Christianity.


Update: Cryptocalvinism slight tweaked, follow up post.

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MAOA, alcoholism & abuse   posted by Razib @ 6/26/2007 09:23:00 PM
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Gene Variant Increases Risk For Alcoholism Following Childhood Abuse. We've been following this story for years in various forms. Here's the article in Molecular Psychiatry (a Nature journal). From the abstract:
The MAOA-LPR low activity allele was associated with alcoholism...particularly antisocial alcoholism...only among sexually abused subjects. Sexually abused women who were homozygous for the low activity allele had higher rates of alcoholism and ASPD, and more ASPD symptoms, than abused women homozygous for the high activity allele. Heterozygous women displayed an intermediate risk pattern...The MAOA-LPR low activity allele was found on three different haplotypes. The most abundant MAOA haplotype containing the MAOA-LPR low activity allele was found in excess among alcoholics...and antisocial alcoholics...Finally, a MAOB haplotype, which we termed haplotype C, was significantly associated with alcoholism...and to a lesser extent with antisocial alcoholism....

(the ellipses are p-values)

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The American Scene - part II   posted by Razib @ 6/26/2007 07:23:00 PM
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The American Scene has just premiered as a new group blog with a fresh look & feel. Daniel Larison is a contributor. Now, keeping in mind that many of you use spiffy RSS readers with AJAX functionality which entails a non-trivial client side computational overhead be careful if you're on an older machine. Larison has a tendency to go "machine gun" in regards to post frequency and he might blow up your computer's CPU.

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Monday, June 25, 2007

New York Times on evolution   posted by Razib @ 6/25/2007 11:22:00 PM
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Well, turns out that The New York Times has a whole bundle of articles on evolution up right now (see the links below for some). Carl Zimmer tipped me off to this feature (he did the bug article below).

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Gould, part deux?   posted by Razib @ 6/25/2007 10:41:00 PM
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The New York Times has a piece, Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift, which alludes to rumblings under the foundations of the Modern Neo-Darwinian Synthesis. The standard allusions to evo-devo are in there, but this stuff struck me as kind of bizarre:
Transitions between species documented by the fossil record seemed to be abrupt, perhaps too abrupt to be explained by the modern synthesis. If this were generally true, it could render irrelevant much of natural selection occurring within species, because just as mutations are produced randomly with respect to the needs of a species, with selection shaping these into new adaptations, new species might evolve randomly with species selection shaping them into evolutionary trends. This challenge was greeted with less than fulsome praise by evolutionary biologists studying changes within species. The resulting hubbub has yet to fully die down. But the newer work cuts closer to the core of the modern synthesis, and is potentially more revolutionary, because it addresses the fundamental question of how really new things happen in the history of life. What brought about the origin of animals, or the invasion of land?


The bolded part, "perhaps" transforms into talk about species level selection. Frankly that strikes me as a bit much. Additionally, I think the "orthodox" view can handle rapid evolutionary changes followed by periods of stasis. Giving it a new name or added emphasis ("punctuated equilibria") does not a paradigm shift make. Evolutionary science as crystallized in the 1950s is not a canon. New findings will add nuance and insight to the pervasiveness of constraint & contingency, or the possibility of functional evolution being driven random walk processes. Perhaps you can call that a paradigm shift (i.e., it's something called science, not the the quarrel of the ancients and the moderns). But the allusive and indirect dance of the prose gets a bit tiresome. Give a paleontologist a pen and watch the erudition bleed out and obscure the potential clarity?

In other news, The New York Times has a piece about the study of evolutionary processes via microbial models. The very microevolutionary processes which the above article seems to imply might be a dead end.

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Nick Wade on recent evolution human   posted by Razib @ 6/25/2007 08:43:00 PM
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Humans Have Spread Globally, and Evolved Locally:
No one yet knows to what extent natural selection for local conditions may have forced the populations on each continent down different evolutionary tracks. But those tracks could turn out to be somewhat parallel. At least some of the evolutionary changes now emerging have clearly been convergent, meaning that natural selection has made use of the different mutations available in each population to accomplish the same adaptation.

This is the case with lactose tolerance in European and African peoples and with pale skin in East Asians and Europeans.


Nothing new to readers of this weblog, but Wade does a good job surveying the various angles.


Related articles on recent human evolution.

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Brains are plastic! Brain are hard-wired!   posted by p-ter @ 6/25/2007 08:29:00 PM
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When talking about the genetics of intelligence, it's inevitable that some people feel a sense of moral outrage and grasp at any argument they can find to soothe it. Case in point:
[W]hile many behavioral traits have a heritable component, it's not anything like what the naive extremists among the cognitive science crowd think. There are no genes that specify what you will name your dog [WTF? -ed]- in fact, most of the genes associated with the brain have very wide patterns of expression and functions that are not neatly tied to behaviors: how does an allele of an adhesion factor map to your performance on a math test? It doesn't, not directly.
And how does an allele in a transcription factor map to your susceptibility to diabetes? Or how does an allele in some unknown gene map to your weight? Or how does an allele in a fatty acid gene map to Alzheimer's disease? They don't, not directly. Luckily, people are working on figuring out how that mapping function works.

This inanity was inspired by agreement with this post where some crazy...oh...wait:
So you're perfectly happy to agree that there is genetic variation in the human population which affects the facility with which various cognitive skills are learned, and so mental ability?

A: Sure.




Treat the stranger as you would be treated   posted by Razib @ 6/25/2007 02:40:00 PM
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Spontaneous Altruism by Chimpanzees and Young Children:
Debates about altruism are often based on the assumption that it is either unique to humans or else the human version differs from that of other animals in important ways. Thus, only humans are supposed to act on behalf of others, even toward genetically unrelated individuals, without personal gain, at a cost to themselves. Studies investigating such behaviors in nonhuman primates, especially our close relative the chimpanzee, form an important contribution to this debate. Here we present experimental evidence that chimpanzees act altruistically toward genetically unrelated conspecifics. In addition, in two comparative experiments, we found that both chimpanzees and human infants helped altruistically, regardless of any expectation of reward, even when some effort was required, and even when the recipient was an unfamiliar individual-all features previously thought to be unique to humans. The evolutionary roots of human altruism may thus go deeper than previously thought, reaching as far back as the last common ancestor of humans and chimpanzees.


The roots of altruism may go back quite far indeed; the elaboration and extension, not so much. After all, pigeons and rats have numeracy. Only humans have math. This might be the case where it is not the sufficiency of one necessary condition but the necessity of multiple conditions. Science Now has a summary.

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Writing and how we think   posted by Razib @ 6/25/2007 09:51:00 AM
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There have long been scholars who try to show that writing systems have been important players in world history (e.g., the Chinese system vs. the alphabetic ones). Chris of Mixing Memory reports some interesting data which suggests that these sort of conjectures need not just be hypotheses, at least on the first order level of effect:
However, recent evidence argues against this explanation. Several studies have shown that adults who learned to write in a right-to-left writing system (as in Hebrew), as opposed to left-to-right (as in English), tend to put agents on the right and patients on the left, with actions tending to be represented as moving from right to left. In other words, the inherent spatial aspect of action representations could be a product of the writing system we use, rather than the wiring of our brain....

...The fact that the children who couldn't write didn't show the bias, while adults educated in left-to-right and right-to-left writing systems showed opposite, language-consistent biases in agent placement strongly suggests that it is the writing system, and not the innate wiring of the brain, that our action representations are inherently spatial.

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Martin Nowak interview (translated)   posted by agnostic @ 6/25/2007 12:11:00 AM
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Martin Nowak, whose new book Evolutionary Dynamics is a must-read, recently gave an interview (PDF) for the Italian magazine Panorama. Unfortunately, it is only in Italian, so to put my break time to good use, I've translated it below. I'm fairly certain that everything is correct, but any errors are due only to me. See here for Razib's posts on Nowak's book.
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[Headline]: Give, and ye shall receive: it's not the Gospel but Darwin
According to the American biologist and mathematician Martin Nowak, the motor of evolution and of survival of the species is altruism.
--by Chiara Palmerini

[Photo caption]: Equations of generosity. Martin Nowak. Below, the Amish, a community founded on mutual aid.

There was a pest that tormented biologists as early as Darwin: how is it that humans, and sometimes animals too, sacrifice themselves for others in a world that evolved according to the law of survival of the fittest? His successors have found some solutions. Richard Dawkins, for example, has maintained that the true selfish agents are genes, willing to do anything -- including to sacrifice an individual, for example the mother, to perpetuate themselves within the child. The problem is that altruism and generosity are not observed only among relatives. What next, then? In a singular reversal of perspective, the biologist and mathematician Martin Nowak maintains that cooperation, far from being a problem for evolution, is one of the laws that propels it, on a par with random mutation of DNA and natural selection. At Harvard, Nowak directs the program for evolutionary dynamics, in which mathematics is applied to the study of evolution. While passing through Varenna, Italy, for the conference Evolvability: the evolution of evolution, organized by the "Piero Caldirola" International Centre for the Promotion of Science, he responds to Panorama.

Why is cooperation a law of evolution?

Because it permits the construction of complexity. For example, it's cooperation between cells that leads to multicellular organisms. Without cooperation, the evolutionary process will not reach the highest levels.

Are cooperation and altruism the same thing?

According to most evolutionists, yes. But I think that the motivation should be important if it's altruism: the true altruist helps without selfish motives.

In your recent work in Science, you describe five mechanisms for the evolution of cooperation. What are they?

The first is cooperation among relatives, summed up by the motto of John B.S. Haldane: "I'd lay down my life for two brothers or eight cousins." But cooperation is also observed between people not related by blood. The rule that matters here is: "I scratch your back, you scratch mine," which still leaves out many aspects of cooperation among humans -- we help even those who will not be able to return the favor.

So then?

Then the rule of indirect reciprocity comes into play, which is typical of human societies. "You scratch my back, I'll scratch the back of someone else." Here reputation counts: helping someone serves to establish a good self-image, which will be rewarded by others. Even though some forms of indirect reciprocity are found among animals, only among humans does it develop fully. It's no accident that as a species we are very interested in gossip. Language could have evolved for acquiring information and spreading gossip, in tandem with indirect reciprocity.

Is not Darwinian generosity an oxymoron?

No, even in a situation where all compete against all, forgiveness and generosity can be a winning strategy.

You cite the Gospel as an example of indirect reciprocity: give, and ye shall receive. Evolution and religion, however, do not agree so much.

If you ask me, it's incorrect to interpret the theory of evolution as though it led necessarily to atheism.

Are you a believer?

Yes.
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Sunday, June 24, 2007

Sperm competition and pornography   posted by agnostic @ 6/24/2007 09:08:00 PM
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Recently Razib posted on a review of sperm competition (PDF), part of which claims:

Kilgallon & Simmons [(2005)] documented that men produce a higher percentage of motile sperm in their ejaculates after viewing sexually explicit images of two men and one woman (sperm competition images) than after viewing sexually explicit images of three women.

Motile sperm are the kind that are capable of moving themselves by swimming. The idea is that if a guy watches a video with two guys and one girl, he'll try to leave more swimming sperm since they now have to compete with those of the other man (so his mind thinks). Now, the proper reaction is to think that two guys going at one girl simultaneously was probably as rare, or even more rare, in our evolutionary past than it is today, so how would we show an adaptation to it? Fortunately the study in question is available online for free -- here -- and it's only two pages long, so read it. Let's review the key findings.

In the Results, we read:

Subjects viewing images of sperm competition had a greater proportion of motile sperm in their ejaculates than those viewing images of females (52.1 +/- 7.3% versus 49.3 +/- 8.0%; F1,23=5.08, p=0.034).

That 3% difference in means is swamped by the standard-error bars of 7% - 8%, and the p-value, while under the 0.05 threshold, is uncomfortably close to it, considering the margin of error and the smallish sample size. So this result could easily be a fluke -- or not, but it warrants no confident statement that the study "documented" a pattern. "Somewhat suggested," perhaps, but gimme a break.

This equivocal data aside, it gets worse when the authors looked at the concentration of sperm per volume:

Men viewing images depicting sperm competition had fewer sperm in their ejaculate than those viewing images of females (61.35 +/- 1.27 versus 76.64 +/- 1.26 * 10^6 sperm ml^-1; F1,36=8.48, p=0.0061). [my emphasis]

Now the effect is clear, but it contradicts the hypothesis that men's bodies will make more of an effort to defeat the other male's sperm when watching "sperm competition" images. In fact, given these two findings, maybe "two guys on one girl" ought to be called "sperm anti-competition" images.

The strongest finding (read the paper for the data) was that men who thought the pornography was "more explicit" than what they'd seen previously had a much higher percentage of motile sperm and much higher concentration of sperm per volume. The authors suggest that men for whom this sort of pornography was old news had become habituated to it. That rings true anecdotally: I'm sure most guys recall how loudly their heart was pounding when they watched their first adult film.

This raises an interesting possibility: if it's largely the novelty factor that's causing men to produce more sperm, and more motile sperm, would this carry over into the case where novelty was based on the ethnicity of the girl? The study design would be pretty simple: recruit a bunch of Latino-American and Anglo-American men, and randomly assign them to two groups, one that watches a scene featuring one man and one woman of the same ethnicity as the viewer, and another that watches a scene featuring one man of the same ethnicity as the viewer and one woman of the opposite ethnicity (Latin or Anglo). Then see if "jungle fever" played any role in how much sperm the men produce. I'm assuming the actresses in all scenes would be rated beforehand to ensure that any guy would find them very attractive. That's why it has to be Latinos and Anglos -- Blacks and Anglos might not work simply because too many White men don't find Black women as attractive as women of other groups, and that could be a problem.

The other reason you might expect guys to produce more sperm when viewing a different-ethnicity girl is that throughout most of human history, including today in most parts of the world, it was incredibly rare to see someone from a noticeably different ethnic group. Even in the few cases where it happened, one of them would have been "just passing through" the other's region. Thus, the male would not know anything about her mating habits, and would have to assume the worst -- that she had a mate already. And if such encounters were fleeting, "strangers in the night" situations, then he would stand to gain everything by impregnating her. He'd never see her again, after all, so why not go the extra mile sperm-wise to make sure? Then he'd have another man raising his child: all benefit and little cost.

You could also look at sperm content from real-life interracial couples, but there could be confounding factors. Maybe if you conducted the research where there were hordes of youngsters who were more-or-less open to mating with anyone -- say, Cancun during Spring Break -- you might be able to collect enough subjects to randomly assign them to the real-life versions of the video study suggested above. "Y'know, as long as you're mating with any old person, why not take part in our study?"

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Oh to be a tuna baron   posted by p-ter @ 6/24/2007 12:05:00 PM
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I enjoyed this review of The Sushi Economy, mainly because I was fully unaware of the fact that there are people referred to as "tuna barons". Apparently they're Australian aquaculturists that have made a killing on the rising popularity of sushi. It doesn't have quite the ring of "oil baron", but hey, you take what you can get.

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Saturday, June 23, 2007

Immigration bill   posted by Razib @ 6/23/2007 10:30:00 PM
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An FOB (friend of the blog) has a prescription for how you can be proactive if you are a restrictionist and want to affect the pending senatorial proceedings.

According to Krikorian and Kaus, these are the 12 Senators on the fence (there may be more). Perhaps you could post this list with the following directions. It took me all of 10 minutes to do this.

1) open up each link in a new tab in Firefox

2) prepare a message in a text editor, such as the following:

"Dear Senator,

Please vote AGAINST cloture on the upcoming immigration bill. It is a
disaster and would be ruinous for this country if passed. Thank you.

Sincerely,

XXX

[Signature with affiliations, etc. may also be useful to include]"

3) paste it into each text field, update the contact info, and hit send.
It's ok if you're out of state, the Senate in particular is a national
organ.

-------------

Bond (R-Mo.)

http://bond.senate.gov/contact/contactme.cfm

Bingaman (D-N.M.)

senator_bingaman@bingaman.senate.gov

Burr (R-N.C.)

http://burr.senate.gov/index.cfm?FuseAction=Contact.Home

Boxer (D-Calif.)

http://boxer.senate.gov/contact/email/policy.cfm

Cochran (R-Miss.)

http://cochran.senate.gov/contact.htm

Conrad (D-N.D.)

http://conrad.senate.gov/webform.html

Ensign (R-Nev.)

http://ensign.senate.gov/forms/email_form.cfm

Levin (D-Mich.)

http://levin.senate.gov/contact/index.cfm

Gregg (R-N.H.)

http://gregg.senate.gov/sitepages/contact.cfm

Nelson (D-Neb.)

http://bennelson.senate.gov/contact/email.cfm

Hatch (R-Utah)

http://hatch.senate.gov/index.cfm?Fuseaction=Offices.Contact

Webb (D-Va.).

http://webb.senate.gov/contact/

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To go where the gods go   posted by Razib @ 6/23/2007 01:33:00 PM
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I was having a discussion with a friend last month about the effect of religious belief on morality. My own hunch was that all things controlled religion makes a minimal impact upon average life time behavior. Rather, I suspected that religious beliefs tended to increase the amplitude of fluctuation between being "good" and "bad." Religion tends to motivate humans toward intense and acute enthusiasm. From the outside on occasion we can judge those enthusiasms to be abominable (Holy Wars, witch hunts and inquisitions), and on other occasions they are admirable (charitable activities, the drive for social justice underpinned by divine certitude, etc.). Additionally, on a personal level the immoral often use religious casuistry to absolve themselves of guilt, blame or shame at the same time that the moral are driven toward ever more incredible acts of compassion, humanity and selflessness. In other words, religion may act as a dispersive parameter on the distribution of human behaviors. A Humean skepticism and moderation may lead to a life of relative tranquility and stability, but it may also be perceived by some as pedestrian, without the element of high art that comes with extreme variations in one's character and station in life. To some extent these thoughts strangely meandered over into my reflections on this essay: Don't become a Scientist! by physicist Jonathan Katz:
Typical postdoctoral salaries begin at $27,000 annually in the biological sciences and about $35,000 in the physical sciences (graduate student stipends are less than half these figures). Can you support a family on that income? It suffices for a young couple in a small apartment, though I know of one physicist whose wife left him because she was tired of repeatedly moving with little prospect of settling down. When you are in your thirties you will need more: a house in a good school district and all the other necessities of ordinary middle class life. Science is a profession, not a religious vocation, and does not justify an oath of poverty or celibacy.


Not a religious vocation, yes. And yet why is it that so many very bright men and women go into a field notorious for the lack of remuneration? The fact is that 99.99% of scientists will turn to dust, their names forgotten to generations of the future, their theses left to rot in the back rooms or in degrading digital archives. Their toil ultimately in vain. Of course there is the flip side, the prestige (if you get a tenure track slot at a decent institution), and on very rare occasions the fame of equivalent to being a rock star (though rarely do the greatest researchers overlap with the greatest scientific rock stars). Our very civilization is dependent and contingent upon the findings of science, and yet the reality is that most scientists will never achieve fame or fortune. But the hope and the dream is what drives men and women of ostensibly high intellectual aptitude.

Aristotle Onassis once said that without women what would be the point of wealth? I have joked that civilization is what men invented to impress women. The point is that rationality, the ground of our being, is ultimately a bit ludicrous if we engage in excessive cogitation and seek out its roots and fundamentals. During the 18th and 19th centuries scientific discoveries were made by gentlemen who wished to one-up each other and make their mark on the world. Their wealth was expended in the acquisition of knowledge to increase their reputation and status in the proximate, and to assure their everlasting fame and glory in the ultimate. Human behavior varies; for every Charles Darwin there were no doubt thousands of gentlemen of leisure who wiled away their time with the hunt and the drink. But the key point is that there was a Charles Darwin. History and the advance of our species is driven by the irrational dreams of the few. A history of Human moderation would likely have been far less traumatic and uneventful, but would history have ratcheted up toward the modern world that we see around us? I have spoken with some admiration of the stability and continuity of the Imperial Chinese civilization, which maintained its basic shape for 2,000 years, from the age of the Hellenistic empires in the wake of Alexander all the way down to the 20th century. But many of have adduced that this very stability was the reason that the Middle Kingdom never gave birth to modernity. The dampening powers of the Chinese system, its careful repeated evasions of cultural collapse, might have been the very cause for its inability to soar into the heavens like the phoenix exploding from its own ashes.

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Dangerous ideas - the book   posted by Razib @ 6/23/2007 01:15:00 PM
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John Brockman is repackaging his "What is your dangerous idea?" question from 2006 into a book. Steven Pinker and Richard Dawkins, probably the two brightest lights in the firmament of Brockman's stable, have written a preface and afterward for the book. You can read them online. Dawkins in particular touched on a subject which might interest readers:
Are there any dangerous ideas that are conspicuously under-represented in this book? I have two suggestions, both of which can be spun into either the 'is' or the 'ought' box. First, I noticed only fleeting references to eugenics, and they were disparaging. In the 1920s and 30s, scientists from the political left as well as right would not have found the idea of designer babies particularly dangerous - though of course they would not have used that phrase. Today, I suspect that the idea is too dangerous for comfortable discussion, even under the license granted by a book like this, and my conjecture is that Adolf Hitler is responsible for the change. Nobody wants to be caught agreeing with that monster, even in a single particular. The spectre of Hitler has led some scientists to stray from 'ought' to 'is' and deny that breeding for human qualities is even possible. But if you can breed cattle for milk yield, horses for running speed and dogs for herding skill, why on earth should it be impossible to breed humans for mathematical, musical or athletic ability? Objections such as 'These are not one-dimentional abilities' apply equally to cows, horses and dogs, and never stopped anybody in practice.

I wonder whether, sixty years after Hitler's death, we might at least venture to ask what is the moral difference between breeding for musical ability, and forcing a child to take music lessons. Or, why is it acceptable to train fast runners and high jumpers, but not breed them? I can think of some answers, and they are good ones which would probably end up persuading me. But hasn't the time come when we should stop being frightened even to put the question?


Dawkins' intellectual hero W.D. Hamilton was one of the last open and vocal eugenicists within the biological community (though if you read some of the introductions to his collected papers his own views changed over time and became more nuanced). The school of evolutionary biology which Dawkins in his own body of work elucidates is derived in a direct line from R.A. Fisher. One of the fathers of modern statistics and evolutionary genetics, Fisher was as a noted eugenicist whose own prolific brood were a testament to his beliefs that the phenotypically fit (by whatever metric he defined "fit") should translate that into reproductive fitness. Another of Brockman's intellectuals, Armand Leroi, has taken a more direct tack. Dawkins must know that we are on the precipice of the eugenic era, whether we call it that or not. While the first era of eugenical enthusiasm was characterized by top-down central planning and a rather gross understanding of the elements of human heredity (it was pre-DNA after all), the second will be a bottom-up affair generated by the mass action of small effects derived from millions of individual choices by parents. One assumes that somewhere R.A. Fisher is smiling.

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Writing to Science : Commenting on a blog :: Apple : X?   posted by p-ter @ 6/23/2007 08:01:00 AM
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In Feburary, a little "Education Forum" article in Science analysed quite a bit of data to come to the conclusion that standardized test scores are a good predictor of a number of measures of success in graduate school. Check the article for the actual numbers-- there are quite high (~0.4) correlations between various test scores and things like faculty reviews, publication record, GPA, and graduation. This is wholly unsurprising.

This week's issue carries a number of responses. One is seriously on par with comments we get on posts about standardized tests on this blog (I don't mean to offend regular commenters, but that's not a compliment). And it's from a professor at MIT:
The Education Forum by N. R. Kuncel and S. A. Hezlett is scientifically unsound and socially reprehensible. The authors, editors, and approving reviewers must all bear responsibility for publication of a report that is fundamentally flawed, but that, if unchallenged, could set back hard-won progress toward reducing unfair discrimination in graduate school admissions by decades. Members of admissions committees who are prone to unfairly discriminate against underrepresented graduate school applicants may use Kuncel and Hezlett's work to justify excluding students solely on the basis of the authors' erroneous assertion that test scores commonly evaluated for graduate school admission predict future graduate and postgraduate performance. Kuncel and Hezlett write, "Accurately predicting which students are best suited for postbaccalaureate graduate school programs benefits the programs, the students, and society at large, because it allows education to be concentrated on those most likely to profit." Even if standardized testing could identify students who were "most likely to profit" from a graduate education, only a crude, backward society would actively seek to limit opportunity in this manner. However, standardized testing cannot do this. Kuncel and Hezlett make the elementary error of equating aggregate correlations with predictive power. Nothing in their analysis permits an admissions committee to look at an applicant's test scores and validly predict what that student would accomplish in the graduate program or their career thereafter. In fact, even their misrepresented correlation analysis has obvious flaws. No attention is given to the likelihood that the specific test score distributions of unfairly discriminated groups will differ substantially from that of the larger majority group whose distributions predominate in the correlation data [note that this point was explcitly considered in the original paper, and the correlations hold *within* groups]. Finally, the misrepresented correlations are themselves over-stated by the authors. More than half of the variance in "later performances" cannot be attributed to the observed variance in standardized test scores.
You can walk through all the internal inconsistencies and irrationalities yourself (or read the response), but it's a little frightening to think someone wanted to sign their name to this and send it for publication.



Friday, June 22, 2007

"Lap"land   posted by Razib @ 6/22/2007 06:18:00 PM
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Pamela Anderson To Open A Chain Of Strip Clubs?:
She writes on her website: "I thought of a great way to celebrate my Finnish heritage at home. I'm going to look into opening a chain of strip clubs and I'll call them Lapland!"

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Wednesday, June 20, 2007

The biology of homosexuality   posted by p-ter @ 6/20/2007 05:40:00 PM
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Appropriately enough, considering some recent conversations here, AlDaily links to an interesting article in New York Magazine on the biology of human sexuality. The concept of natural variation was apparently quite the shock to the field:
"The brain was considered pretty hardwired," says Roger Gorski, a neurobiologist at UCLA who researches sexual differentiation. "It was male or female, period. Then Simon's study shows that there could be intermediates. That wasn't just a watershed-it pushed the water over the waterfall."
The study being alluded to in the quote apparently showed that the size of a particular part of the brain in gay men tends to be smaller-- closer to the female mode than that of the heterosexual male.

One interesting tidbit:
A large-scale study within the next year is expected to determine more conclusively if a gene (or genes) is linked to sexual orientation. Alan R. Sanders, a psychiatrist from Northwestern University, is enrolling 1,000 pairs of gay brothers in one of the largest sexual-orientation studies ever undertaken. With the experiment, funded by an NIH grant of over $1 million, Sanders will attempt to map genes that influence sexual orientation.
Sexual orientation is obviously "genetic", in the sense that without brains (constructed by genetically controlled developmental pathways) it wouldn't exist. But if there is genetic variation that predisposes one to homosexuality, it would likely be eliminated fairly quickly from the population (assuming this variation has no effects on any other phenotype, a likely false assumption). However, if the mutational target size is large enough (ie. if slight alterations in any of 100 different pathways could lead to slights shifts in preference), mutation-selection balance might lead to a much higher rate than what one might expect.

Then again, the MZ twin concordance rate is about 50% (according to this article), which mean both environmental (probably intra-uterine) and stochastic forces are also rather important. I find the association between hair whorls/handedness and homosexuality interesting; both those traits are hypothesized to be influenced by developmental stochasticity.

FYI, here's one current model (likely wrong or a major simplification, but as they say: all models are wrong, but some are useful) for the genetics of handedness:
On the basis of these findings, combined with other results (KLAR 1996), I hypothesized that a single dominant gene, RGHT1 (for right-handedness), causes the development of both RH preference and clockwise hair whorls and that both traits are randomly distributed to the left and the right side in individuals homozygous for the nonfunctional, recessive r (for random-handedness) allele. Handedness discordance of monozygotic twins was also attributed to randomness resulting from the deduced r/r genotype. Thus, genetic etiology for handedness was supported for the unselected human population by results of both hair-whorl correlation and familial inheritance of the handedness trait.

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Tuesday, June 19, 2007

Winged insects and degree of civilization   posted by agnostic @ 6/19/2007 10:30:00 PM
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A recent article in Nature, which we blogged about here, reviewed the consequences of agriculture on the nature and prevalence of pathogens that have plagued human beings. One key datum that Wolfe et al. (2007) discuss is the difference between the vectors (or transmitters) of infectious disease in the tropical vs. non-tropical regions, where agriculture has flourished the longest: almost all of the nasty infectious diseases in the tropics are spread by winged insects [1], whereas most of those in the more advanced areas are spread by human-to-human contact, polluted water, or parasites of small animals (such as the fleas that spread the Bubonic Plague). One consequence of this is that, as the authors note, infectious diseases in the tropics tend to be chronic rather than acute -- in crowded populations that characterize agricultural societies, it won't take long for you to pass your germs to someone nearby, after which point you've served your purpose and can be left alone for the time being (if you aren't shortly killed). If there aren't many people nearby to infect, you're going to have to serve as the host for much longer.

The authors do not note, however, an important evolutionary reason for why the geography of tropical regions causes them to be more plagued by insect-transmitted disease. This shortcoming is odd considering that one of the authors, Jared Diamond, has written best-selling books on human evolution (The Third Chimpanzee) and geography and civilization (Guns, Germs, and Steel). I haven't read either of these in full, so to be sure he didn't cover this issue in GGS, I searched it at Amazon and found no discussion of the prevalence of wingedness among insects. In any case, the key pattern is that the proportion of insects that are winged increases as both latitude and altitude decrease. At a more fine-grained level, wingedness is more common in habitats that are in some sense temporary or unstable, while flightlessness is more common in more permanent, stable habitats [2].

The basic insight comes from life history theory: in unstable habitats, an individual may be born into awful conditions due to temporal and/or spatial hetereogeneity. Here, it will pay to have a means of migrating to a more hospitable area, while in less volatile habitats an individual probably won't get caught with their pants down, and so flightlessness would increase. Just think of the energy a bug would save by not growing and maintaining their wings if it didn't need them. Most tropical areas have all three features: low in elevation, close to the equator, and more unstable habitat-wise [3]. It's no surprise, then, that such areas are more wracked by insect-borne infectious diseases. There are simply far more winged bugs that can travel far distances transmitting pathogens to humans.

One consequence of all this chronic disease must surely be increased difficulty in founding, let alone maintaining, a great human civilization. Chronic diseases which begin to strike early on in life are likely one reason that mean sub-Saharan African IQ is about 70, while mean African-American IQ is about 85, a full standard-deviation above. Possible mechanisms are not difficult to think of: the parasite that causes Sleeping Sickness get into your brain and slowly destroys it, your body may divert resources to disease defense and repair rather than on "luxury" items like higher IQ, and so on.

Even controlling for IQ, being afflicted with chronic disease must sap one's ability to doggedly pursue long-term projects, whether artistic or scientific, that foster civilization. Probably the best shot sub-Saharan Africa has is south of the Zambezi River, which doesn't suffer from a tropical hellhole climate. At best they could reach the level of African-Americans, who don't dominate Silicon Valley, but who have contributed scores more to the world's culture than Africans in sub-Saharan Africa. [4] Even in the US, most high African-American culture has largely sprung from cities outside of the dreadful "humid subtropical" climate of the Southeastern states (for example, New York and Chicago).

That pattern is also evident among American Whites, by the way: at the most northern fringe of the Southeastern US there are first-rate research universities (Duke and UNC - Chapel Hill, both in North Carolina), but the region is largely bereft of civilization-propelling institutions. In fact, blogger Inductivist has shown, using General Social Survey data on Whites, that it is a larger source of and magnet for duller Whites, compared to other regions (see here and here). Now, clearly I'm not proposing that epidemic Sleeping Sickness, malaria, etc. are causing the problem in the US. But whatever the more numerous bugs in the Southeast are transmitting to humans, it could partially account for the discrepancy between its level of culture and that of the Northeast. Indeed, from Inductivist's reckoning, it appears that most intelligent people with any sense from that region decide to haul ass to the Mid-Atlantic and New England states.

[1] From p. 280 of Wolfe et al:

A higher proportion of the diseases is transmitted by insect vectors in the tropics (8/10) than in the temperate zones (2/15) (P less than 0.005, chi-square test, degrees of freedom, d.f. = 51). This difference may be partly related to the seasonal cessations or declines of temperate insect activity.

[2] For a brief overview, see pp. 349-56 of Roff (2002). For extensive literature reviews, simulations, and so on, see Roff (1990) and Roff (1994).

[3] As for the non-obvious claim of greater temporal variation as you move toward tropical areas, see Roff (1990: 405):

I tested the hypothesis that habitat persistence varies with latitude with data on the rates of succession on abandoned farmland. In the northerly states of the United States (Wisconsin, New Jersey, Illinois, and New York) shrubs appear only 10-20 yr after abandonment, and even after 40 yr succession does not proceed beyond a very open woodland/parkland condition (Thomson 1943, Bard 1952, Bazzaz 1968,1975, Mellinger and McNaughton 1975, Pickett 1982), while in the more southerly states of North Carolina, Tennessee, and Georgia a closed canopy is formed within 15-30 yr (Billings 1938, Oosting 1942, Quarterman 1957, Nicholson and Monk 1974, 1975, Lindsay and Bratton 1980). In the Mexican tropics invasion by trees occurs within the first 2 yr, and these may reach a height of 10 m within 5 yr (Purata 1986): in the upper Rio Negro region of the Amazon Basin a loose canopy of Cecropia spp. 5 m high was formed within 22 mo (Uhl et al. 1981).

Sidebar: Detroit is fortunate to be situated as far north as it is, or else the reclamation of the city by the wild would have wholly swallowed up most of the area long ago (see here too).

[4] Alternatively, they could follow the lead of the elite strata of South Asia, who have managed to build a civilization despite vying with tropical Africa for status as the world's chamberpot of infectious disease. There, though, the elites have striven for centuries to isolate themselves genetically from those in lower castes, as well as to minimize their physical contact with the even more bug-bitten lower classes.

References

Roff, D. (1990). The evolution of flightlessness in insects. Ecological Monographs, 60(4), 389-421.

-------- (1994). Habitat persistence and the evolution of wing dimorphism in insects. The American Naturalist, 144(5), 772-98.

-------- (2002). Life History Evolution. Sinauer Associates: Sunderland, MA.

Wolfe, N., C. Dunavan, & J. Diamond (2007). Origins of major human infectious diseases. Nature, 447, 279-83.

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Paternity test without DNA   posted by p-ter @ 6/19/2007 09:02:00 PM
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Eye on DNA links to this online paternity calculator, which takes into account blood group, eye color, and earlobe type to determine whether a guy's traits are consistent with paternity. Kind of cool. Someone actually asked me whether this was possible the other day, and the earlobes thing was the only one I could come up with. Eye, skin, and hair color are all kind of tricky; I doubt they get much precision from their eye color measure.

Any trait with fairly simple inheritance should do the trick; the problem is that most aren't easily visible. Ability to roll your tongue could be a marker, for example. Anyone else got thoughts?

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A mechanism for miRNA-mediated repression   posted by amnestic @ 6/19/2007 07:13:00 PM
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RNA interference is a process by which small (20-22 nt) RNAs bind to a fully or partially complementary messenger RNA and reduce the amount of protein product from that mRNA. The general rule is that if the match is perfect (full complementarity) then the target mRNA is cut into two pieces and destroyed forthwith. If the match is imperfect such that there are bulges in the double stranded RNA that forms between the interfering RNA and the target, then the target is sequestered to a newly discovered cellular entity called a Processing Body (P Bodies, PBs). There are enzymes in PBs capable of degrading mRNAs, but sometimes the mRNAs can be released and become translationally competent again.

New research from Kiriakidou et al in Cell provides a mechanism for this translational repression sans degradation. The effects of small interfering RNAs (siRNAs) are mediated by the Argonaute family of proteins (Ago1, Ago2, etc). This family can be subdivided depending on the proteins' ability to cleave RNA and thus carry out the "perfect-match" type of translational repression, but even non-cleaving Agos can do the sequestration route for repression. The latest news is that this can be achieved by blocking interactions between the cap-binding translation initiation factor eIF4E and the 5' cap of mRNAs.

Let me unpack. For efficient initiation of protein synthesis from an mRNA, several proteins must assemble into complexes centered around the mRNA. There are several proteins that bind near the other end of the mRNA where there is a cap. A cap is a modified guanine nucleotide flipped around backward and stuck on the head-end of the mRNA early in its life. One protein in particular, eIF4E recognizes the cap structure and binds to it, recruiting other initiation factors and eventually the small ribosomal subunit. This is an important and highly regulated step in protein synthesis. For instance, there is a family of proteins (4E-BPs) whose sole function is to bind eIF4E and get in the way of cap-binding. If they become highly phosphorylated because of this signaling pathway or that, they let go and translation proceeds. Ago proteins can do the same thing, but on the cap side and without the phosphorylation business.

They showed the effect by first purifying an Ago protein with and without important amino acids for cap-interaction and testing for binding with caps immobilized on a column. Only Ago proteins with the two important (phenylalanine) amino acids could bind. Further assays in vivo showed that the mutant Agos couldn't mediate translational repression.

There are a couple predictions to make based on these findings.

1) Organisms with Agos that lack this domain should be bad at this process.
This domain is not found in Ago proteins of plants, archaea, or fission yeast, in Drosophila AGO2 and in most members of the C. elegans Ago protein family, with the exception of ALG-1 and ALG-2. In addition, the MC domain is absent from proteins of the PIWI family.
I can't recall if any of there is anything already contradictory in that list. I think there is definitely something weird about the way plants handle siRNAs, but the details escape me.

2) RNAs that are capable of cap-independent translation should not be regulated by this process. There is debate about the degree to which mRNAs can undergo cap-independent translation, but the field is moving along as though internal ribosomal entry sites are an important cellular tool, so these RNAs should escape translational repression via this process.

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Japanese Learning RPG   posted by amnestic @ 6/19/2007 02:08:00 PM
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I know this isn't the Learn Japanese forum, but when I have time for playing around I've been enjoying this Final Fantasy / Zelda takeoff that helps you with katakana, hiragana, and some kanji. It is called Slime Forest. The slimes attack and yell characters at you to which you must respond appropriately. Save the princess!



Monday, June 18, 2007

The genetics of racial differences in hypertension susceptibility   posted by p-ter @ 6/18/2007 04:47:00 PM
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Part three of the "genetics and race" debate in the pages of The New Republic is up. One point the debaters seem to have oddly fixated on is the racial disparity in the prevalence of hypertension-- for those of you unaware, African-Americans have higher rates and more extreme forms of the disease.

The debaters at TNR seem to be aware of two hypotheses for why this disparity could exist: first, the "slavery hypothesis", according to which the slaves that survived the long trip from West Africa in sub-human conditions were those that were able to retain sodium and resist dehydration (sweating causes the loss of salt, which must then be replaced), leading to a massive selective event for improved salt retention that today manifests itself as hypertension. The alternative, they seem to think, is that discrimination and an abundance of unhealthy fast food restaurants in African-American neighborhoods in conjunction lead to the differential susceptibility.

There's no doubt that environmental factors play a role in hypertension, and it's likely that differential exposures to those factors play a role in this phenomenon. But in terms of genetics, it's certainly not the slavery hypothesis or nothing. I actually see no reason to invoke it-- the key observation (perhaps not a groundbreaking one) is that African slaves came from Africa, which is quite different from North America. One obvious difference between the two continents is climate. Is it possible that West African populations were adapted to an West African climate; perhaps in such a way that increases hypertension susceptibility in the US today? Absolutely.

I present as evidence this (open access) paper, which states (in the title) that "Differential Susceptibility to Hypertension is Due to Selection during the Out-of-Africa Expansion". I strongly recommend at least the introduction for anyone interested in this topic.

The authors look at a number of alleles involved in salt retention and blood pressure, and perform analyses simlar to those done in the paper on tonal languages and two brain-expressed genes-- they examine the correlations of the allele frequencies with distance from the equator. When they compare these correlations with those from randomly chosen loci, they find the salt-retention alleles are outliers, suggesting they've undergone selection in reponse to latitude (which they interpret as a proxy for climate). While in the tonal languages case I urged skepticism about causation, these alleles are already known to be involved in hypertension. This just presents evidence that the differences in allele frequencies between populations is due to natural selection, as opposed to some neutral process.

So African populations (and thus, African-American populations as well) have different allele frequencies of at genes known to be involved in hypertension. There is no doubt that this divergence plays a role in the different susceptibilities of African-American and European-American populations to this disease.

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More detecting natural selection   posted by Razib @ 6/18/2007 04:03:00 PM
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A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
The evolution of new functions and adaptation to new environments occurs by positive selection, whereby beneficial mutations increase in frequency and eventually become fixed in a population. Detecting such selection in humans is crucial for understanding the importance of past genetic adaptations and their role in contemporary common diseases. Methods have already been developed for detecting the signature of positive selection in large, genome-scale datasets (such as the “HapMap”). Positive selection is expected to more rapidly increase the frequency of an allele, and hence, the length of the haplotype (extent of DNA segment) associated with the selected allele, relative to those that are not under selection. Such methods compare haplotype lengths within a single population. Here, we introduce a new method that compares the lengths of haplotypes associated with the same allele in different populations. We demonstrate that our method has greater power to detect selective sweeps that are fixed or nearly so, and we construct a statistical framework that shows that our method reliably detects positive selection. We applied our method to the HapMap data and identified approximately 500 candidate regions in the human genome that show a signature of recent positive selection. Further targeted studies of these regions should reveal important genetic adaptations in our past.


I'm in a hurry/busy, so no real comment. It's PLOS, so it's free. Read it.

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Etruscans - don't know nothing about DNA   posted by Razib @ 6/18/2007 12:00:00 PM
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The Etruscan origin story is now in the news again after the lead researcher presented his findings that these ancient people show strong evidence of a genetic affinity with Anatolians at a conference. I put a quick round up over at ScienceBlogs, but this piece in the LA Times is a bit disconcerting. Here are some archaeologists:
"I guess I would have to say that I am unconvinced at this stage," said archeologist Anthony Tuck of the University of Massachusetts at Amherst, who is excavating an Etruscan site in Italy. "It is premature to declare the issue resolved on our current understanding of this genetic evidence."

Archeologist Jean Macintosh Turfa of the University of Pennsylvania's Museum of Archeology and Anthropology was more dismissive. "There is really no sound archeological evidence that shows the influx of a big migration, or any kind of influx, from Asia Minor," she said. "There is never a sharp break in cultures, no destroyed villages, etcetera."

Turfa and Tuck hold to the view that the Etruscans evolved from the Villanovan culture, which emerged in central Italy. But the genetic findings will force a harder look at the evidence about their origins.


I really hope that the reporter didn't go quote mining until he found someone with a "dissenting" view, that's just bad journalism. Let's review the lines of evidence:

1) Y chromosomal lineages suggest a link with Anatolians.

2) mtDNA, both ancient and modern, suggest a link with Anatolians. The ancient mtDNA results (from 2004) was argued by some to have been possible contamination, etc., but I think that the findings from modern mtDNA (combined with other data) should force us to reorient our priors in evaluating that previous finding.

3) mtDNA from cattle suggests a parallel phylogenetic relationship between Anatolian and Tuscan populations.

These genetic arrows are now converging upon one conclusion: that there was some link between ancient Anatolians and Etruscans beyond what we would expect. One could dismiss one or two findings, but the alignment here should be worth noting. But that's not all. The island of Lemnos yields evidence that a language closely related to Etruscan before the Athenian conquest of the 6th century BCE was in use. Lemnos is the north Aegean. One plausible explanation is that an Etruscan trading colony was long resident here. Another explanation is that the inhabitants of Lemnos are part of the same "Lydian" Diaspora as the Etruscans. The Etruscans-are-native-to-Italy hypothesis would imply that the former explanation is what we should accept, but in light of the new data the Lemnos records should, I think, be taken as evidence of the latter scenario. The ancient scholars who addressed the origin of the Etruscans offered three alternative scenarios, that they were indigenous to Italy, that they were from Anatolia, or that they were from northern Europe. What is the likelihood that out of the sample space of possibilities Anatolia (as opposed to Greece, Libya, Egypt, etc.) would be selected as a possible point of origin? Prior to the emergence of these strong genetic data I do think one could imagine it was a flight of fantasy, but now it seems likely that its selection was not arbitrary.

The genetic data seems strong to me. That being said, the archaeologists have long noted continuities between the Villanovan Culture and the Etruscans. What gives? I think the solution is simple: the Etruscans had a non-trivial (genetically detectable to the present) exogenous element, but it also drew upon the local substrate. Taking a step outside of this particular issue that should be pretty clear & obvious. The Greeks show this hybrid tendency, a large proportion of words in their language show no Indo-European cognates. There are legends of Pelasgians, a confused term which might have referred to unassimilated elements amongst the non-Greek speaking inhabitants of the peninsula. The same dynamic can be seen in north India, where a hybrid culture arose which exhibited both pre-Aryan and Aryan elements. The archaeological continuity might very well be a reality in Tuscany simply because that the Etruscans did not exterminate the local peasantry, but rather, entered into a relationship of overlordship and subsequent cultural absorption. The continuity of material culture might be due to the fact that the folkways of Anatolia (housing structure and material, field arrangments, crops, etc.) were not applicable to the ecological needs of north-central Italy, or that the original settler Etruscans were a particular occupational slice of their peoples, perhaps a mercantile elite who were oriented toward the sea (they were well known traders) as opposed to agriculture. Just as Christian peasants and landlords in Anatolia were absorbed into the culture and identity of their Turkic rulers after 1100 over a period of time, so it seems that a possible model is one where Etruscan elite culture had this pull upon locals whom they ruled. Subjects of the Roman Empire absorbed some elements of Romanitas from their culture elites (language and religion), but they did not all become the villagers of Latium in replica form simply due to the local ecological constraints (dwelling architecture and farming techniques suitable for the Mediterranean don't transplant that well to northern Gaul). New data forces us to construct amenable hypotheses, not simply dismiss it.

Note: I put Lydian in quotes because it is likely an anachronism. The Etruscans were as Lydian as the tribes who resided on the north shore of lake Superior in 1500 were "Canadian."

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Sunday, June 17, 2007

Math texts as piano recitals (a rant)   posted by agnostic @ 6/17/2007 08:04:00 AM
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Math textbooks should teach the student the material, and how to think mathematically, as soon as possible and with the least amount of work as possible. If we view learning math as learning classical piano, we'd want a tutorial that clearly walked us through the basics and showed us the guts of a piece of music rather than force us to figure most of it out on our own. It would be arrogant for the tutorial to consist of: "You want to learn classical piano? All right then, listen to this virtuosic recital and repeat it." *

In particular, I'm griping about Rudin's Principles of Mathematical Analysis, apparently "the Bible" of introductory analysis textbooks. I stopped reading after I finished the second chapter, which is a primer on topology -- containing exactly one diagram. I guess all those figures I had to draw for high school geometry class were just to help the stupids grasp what must actually be a verbal enterprise. What a joke. I don't know if this is due to a puerile belief that grown-up books contain no pictures, a puritanically Platonic hatred of the sense of sight as opposed to reason, or simply a misguided belief that students should expend their mental energy in visualizing what the author is explaining. The author should just show the student what the basic picture is, and direct their mental energy toward hard work for advanced problems.

With no guide, the student is left to conjure up his own mneumonic devices, which is bad since he may not be very imaginative but may still want to grok the material; and even the more imaginative students would be better served by using their imagination for complicated problems. It's like having first-graders make up their own alphabet for a creative writing class -- just teach them the damn alphabet, and focus their energy on the creative composition part.

Several complaints at the Amazon entry for PMA mention its lack of motivation, and this is very true: Rudin gives the impression that the ideas sprang, Athena-like, fully formed from the head of their discoverer. The other principal complaint is that the proofs are too terse, requiring the reader to fill in lots of gaps -- this isn't so bad, although again it does waste the reader's limited time and resources. But the former flaw is even worse because it conveys no sense of discovery: some guy had a hunch, used his visual intuition (or something similar) in order to conceive the idea, which he then fleshed out in more detail, assuming it was on the right track. To quote from George Simmons' introductory calculus text, presentations like those of Rudin "produce belief without insight, and are therefore fundamentally unsatisfying. It is important to know that a mathematical theorem is true, but it is often more important to understand why it is true" (p.852 with original italics; he is discussing a weakness of using mathematical induction in explaining a theorem).

For instance, almost every introduction to induction that I've seen uses the example of the sum of the first n natural numbers, 1 + 2 + 3 + ... + n. The formula is given -- it is n(n + 1) / 2 -- and the author walks through the proof himself or asks the reader to do so. In either case, the formula materializes ex nihilo, as though this configuration of symbols just appeared to someone in a dream. In fact, it it easy to provide a visually intuitive reason that this formula is correct; a well known example is shown below:


We start with 1 block at the bottom, then 2 in the row above, each successive row containing 1 block more. Adding up the blocks from the n rows tells us what the sum of the first n natural numbers is. Now, if we make a copy of the array and flip it, it interlocks nicely with the original array to form a rectangle whose width is n and whose length is (n + 1). Since the sum only comes from the blocks in the original array, it must be half the area of this rectangle -- that is, n(n + 1) / 2. Anyone who has passed algebra and geometry can see that this is true, so the fact that this insight -- or indeed any insight into the formula -- is left out of most introductions to inductive proofs just shows how committed many writers are to producing "belief without insight." This is a serious error because, in the words of the great Henri Poincare, "It is by logic that we prove, but by intuition that we discover."

As an example of a book that strikes more of a balance between the two, Pugh's Real Mathematical Analysis works well (I found out about the book by reading through some disgruntled reviews of PMA at Amazon). Another good example is Artin's Algebra, also considered a Bible of its field, but whose author isn't primarily concerned with showing off his virtuosity. Ironically, Artin's book on abstract algebra has more diagrams and pictures than Rudin's book on real analysis! I'm sorry, but I just can't get over that. It's even more bizarre that Rudin was awarded a Steele Prize for mathematical exposition, since he's (in)famous for barely expounding at all on the ideas in his books. In fairness, I haven't read "Big Rudin," and I hear it is better.

To sum up, textbooks are meant to instruct, not necessarily to awe. Euclid's Elements is one of the most impressive feats of human reasoning, but without pictures or sense of purpose it stinks as a textbook on geometry. A confused review (PDF) of the matter apologizes for textbooks written a la Euclid since they are more terse, elegant, and cleansed of temporal impurities like images, "behind the scenes" motivation, and applications. At least the writer of the Elements was also the creator of many of the ideas presented therein, similar to a Bach fugue if it were performed by Bach himself, who was a keyboard virtuoso as well as a first-rate composer. But in the context of training new students, marveling at the beautiful should take a back seat to cultivating their ability to create original ideas, which is obviously not to say it should be jettisoned altogether.

* On a related note, reading through the reviews at Amazon and elsewhere, it seems that the mathematics community currently suffers from a sickness similar to that of the classical music community, whereby a non-trivial portion of the group focuses on and argues over the merits of the interpreters of great ideas, more so than on the great ideas and their creators themselves. Perhaps this is just a sociological way to signal in-group status: any boob may like this or that piece by immortal composers like Bach and Beethoven, but only the initiated have a preference for Rubinstein or Horowitz. Grow up and focus on what's important.



Saturday, June 16, 2007

Diversity & trust   posted by Razib @ 6/16/2007 08:47:00 PM
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The New York Times Magazine has a piece up about Robert Putnam's work which shows that ethnic & racial diversity decreases trust, not just between groups but between and individual and society as a whole.

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Fear of a genetic planet   posted by Razib @ 6/16/2007 07:45:00 PM
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Gene bashing - dilemma of black geneticists working on the National Institute of Health's Human Genome Project:
"I don't fear science. The [development of the] wheel, fire and aircraft have done a considerable amount of harm...far more than genetic research is likely to do," Bowman says.

Anyway, he adds, "we are already in a eugenic society. "We can collect an ovum from a prospective mother and sperm from a prospective father, allow them to develop to the eight-cell stage, test one cell...and make a diagnosis for pre-symptom colon cancer or breast cancer," says Bowman.

Still, he says, "I'm willing to take my chances with the bad parts. The fears are misplaced."


Life comes at you fast. I don't deny that it is important to reflect upon the implications of science, but substance free hand wringing is time wasted on the tracks as the train is speeding in your direction.

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Dissecting the regulatory differences between human and chimp   posted by p-ter @ 6/16/2007 04:08:00 PM
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Many evolutionary biologists are content to focus on large-scale trends in evolution-- they debate whether protein-coding or regulatory changes are more important in adaptive evolution, or look to compare the numbers of genes undergoing selection in different lineages. To each their own, of course, but I find those sorts of questions unsatisfying (for the moment), because ultimately, they cannot be answered without a molecular, reductionist approach. That is, the major breakthroughs in evolutionary biology will be in identifying specific molecular changes that have occurred during evolution and characterizing their phenotypic effects.

Case in point: the study of gene expression differences between humans and chimps. There have been a number of studies on the general trends in gene expression evolution between the two species. Some tissues are more constrained, some tissues less so. This is of interest, of course, but what we (I?) really want to know is: which specific genes are differentially regulated in humans as compared to chimps, in which tissues, when in development, and what specific genetic changes cause this differentil expression? The large-scale evolutionary trends will become apparent once this (extremely difficult) question is answered.

It's because of the apparent intractability of this question that people tend to shy away from it. However, that's starting to change. Last year, using a painstakingly constructed multi-species microarray (as opposed to the human specific one used-- to study both humans and chimps-- in previous studies), Yoav Gilad identified specific genes in the liver (chosen because of its relative homogeneity) that have undergone human specific regulatory changes.

Now, he's looking for the specific polymorphisms underlying these changes. A recently published pilot study explains the approach:
Most phenotypic differences between human and chimpanzee are likely to result from differences in gene regulation, rather than changes to protein coding regions. To date, however, only a handful of human-chimpanzee nucleotide differences leading to changes in gene regulation are known. In order to identify differences in regulatory elements between human and chimpanzee, we focused on ten genes that were previously found to be differentially expressed between the two species. We then designed reporter gene assays for the putative human and chimpanzee promoters of the ten genes. Of seven promoters that we found to be active in human liver cell lines, human and chimpanzee promoters had significantly different activity in four cases, three of which recapitulated the gene expression difference seen in the microarray experiment. For these three genes, we were therefore able to demonstrate that a change in cis influences expression differences between humans and chimpanzees. Moreover, using site directed mutagenesis on one construct, the promoter for the DDA3 gene, we were able to identify three nucleotides that together lead to a cis regulatory difference between the species. High-throughput application of this approach will provide a map of regulatory element differences between humans and our close evolutionary relatives.
Something to look forward to...

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Recent human evolution in Evolution   posted by Razib @ 6/16/2007 02:11:00 PM
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Evolutionary geneticist Alan Templeton has an article in Evolution, GENETICS AND RECENT HUMAN EVOLUTION:
Starting with "mitochondrial Eve" in 1987, genetics has played an increasingly important role in studies of the last two million years of human evolution. It initially appeared that genetic data resolved the basic models of recent human evolution in favor of the "out-of-Africa replacement" hypothesis in which anatomically modern humans evolved in Africa about 150,000 years ago, started to spread throughout the world about 100,000 years ago, and subsequently drove to complete genetic extinction (replacement) all other human populations in Eurasia. Unfortunately, many of the genetic studies on recent human evolution have suffered from scientific flaws, including misrepresenting the models of recent human evolution, focusing upon hypothesis compatibility rather than hypothesis testing, committing the ecological fallacy, and failing to consider a broader array of alternative hypotheses. Once these flaws are corrected, there is actually little genetic support for the out-of-Africa replacement hypothesis. Indeed, when genetic data are used in a hypothesis-testing framework, the out-of-Africa replacement hypothesis is strongly rejected. The model of recent human evolution that emerges from a statistical hypothesis-testing framework does not correspond to any of the traditional models of human evolution, but it is compatible with fossil and archaeological data. These studies also reveal that any one gene or DNA region captures only a small part of human evolutionary history, so multilocus studies are essential. As more and more loci became available, genetics will undoubtedly offer additional insights and resolutions of human evolution.


Here is a summary of Templeton's offering, "Out of Africa again and again."

Related: Neandertal introgression.

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Personal Libraries   posted by Razib @ 6/16/2007 11:59:00 AM
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Darwin Catholic has a post about his growing family library. Over the past 5 years the number of books in my "library" has been growing a steady but constant rate. But there are definite patterns in terms of how my collection has been piling up. I tend to keep technical books, but trade in non-technical books after one or two readings. Initially this meant I had a lot of programming related books (still have 'em), but over the past few years I've been depending on online supplements like Safari Library. Now my technical books tend to be more oriented toward science, the collected papers of Motoo Kimura or W.D. Hamilton, or D.S. Falconer's Introduction of Quantitative Genetics. My non-technical books I often take to the used book store and try to trade them in for more technical books. For example, recently I exchanged Future of Freedom & Lust in Translation for Scientific Reasoning: The Bayesian Approach. The result is over time my small library has a larger and larger proportion of books on genetics & mathematics and a constantly changing cast of works of history, sociology, psychology, etc. The rule of thumb that works for me is that I tend to retain books with a high load of contingent theoretical information, and am casual about trading in those works which are dense on loosely related fact. Across the sample space of facts I have rather good recall and I don't usually refer back to the original works from which I derived those facts because it is usually quicker to go to the internet and look up an isolated datum for confirmation then to rummage through the index of a book where it might be found. In contrast, theoretical constructs are harder to retrieve on the web in a fully fleshed out form without a lot of effort,1 and quite often without regular usage I forget how to implement the detail of technical methods. I still remember the general outline of my course on the Peasants' War of 1525 as well as my linear algebra classes, but in the former case individual errors in recall don't result in the collapse of the whole structure of knowledge. In the latter case I've had to revisit linear algebra texts for details because small errors compound so as to make my recall close in worthless in many cases in implementation.

1 - A lot of the introductions to models on Wikipedia & elsewhere seem a bit simple. Then, when you go to papers there is the implicit assumption of a lot of background detail. So it seems to me that there is a space on the web for mid-level formalism and theory which is often missing, and can be most easily found in textbooks which you wouldn't normally find in your local public library.

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The Starbucks effect?   posted by Razib @ 6/16/2007 11:54:00 AM
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As Some Grow Weary of Web, Online Sales Lag:
...Nancy F. Koehn, a professor at Harvard Business School who studies retailing and consumer habits, said that the leveling off of e-commerce reflected the practical and psychological limitations of shopping online. She said that as physical stores have made the in-person buying experience more pleasurable, online stores have continued to give shoppers a blase experience. In addition, online shopping, because it involves a computer, feels like work.


Where do these psychological limitations come from? I think some if it is pretty obviously specified on the innate level. We're a social species. The great evolutionary biologist William D. Hamilton famously did his pioneering work on kin selection in London train stations because of his loneliness. It is one thing to worry about the de-humanizing effect of modern technology, but it is important to remember at the end of the day we do remain human.

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This just in....   posted by Razib @ 6/16/2007 12:01:00 AM
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I just looked at the google analytics data for this website for the first time in about 6 months. Sitemeter is great, but google analytics allows for a fine grained analysis of the data. Looking at the top key word search queries and the highest ranked landing pages, I conclude that people really like porn. Especially Arab porn.

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Friday, June 15, 2007

Darwin pedantry   posted by Razib @ 6/15/2007 07:11:00 PM
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So, I saw this article about a Charles Darwin exhibit at a museum, and this quote irritated me:
"A lot of people don't know his mother was heir to the Wedgwood ceramics fortune or that Darwin married his first cousin," Skwerski [the curator in charge of the exhibit] says. "For a man who essentially studied genetics, you better believe he worried about what damage he might be doing by intermarrying."


Darwin didn't know about genetics. The term "genetics" itself was coined by the Mendelian William Bateson in 1905 after the rediscovery of Mendel's work. Darwin studied inheritance, of which Mendelian genetics is a model and system. To say Darwin studied genetics is like saying that Moses' religious thinking was rooted in Christology.

(I'm open to being corrected on the details here!)

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If it ain't pathological, it's crap!   posted by p-ter @ 6/15/2007 05:04:00 PM
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A recent paper on the genetics of attention deficit and hyperactivity disorder (ADHD) notes that the some of the genetic variants predisposing to disease are fixed or at high frequency in some populations, suggesting the work of natural selection (see here for molecular evidence and review). The authors note that "it is unclear if ADHD should be considered as a nosological entity or as a common variant of human behavior".

Of course, if it were just a common variant of human behavior, no one would get money to study it. This encourages the pharmaceutical company approach to an area of interest-- instead of studying the variation is social aptitude, people study "social anxiety disorder". Instead of behavioral morphs, "attention deficit disorder". This is problematic, because pathology is largely an extreme on a continuous spectrum-- in that spectrum lies the bulk of the information.




Race, TNR debate   posted by Razib @ 6/15/2007 01:12:00 PM
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TNR is continuing the debate on race. Not much to read really, but this caught my attention:
I found your characterization of race as a "cluster concept" provocative and intellectually honest, since you admit its imprecision....


Imprecision? Really? Well:
Of 3,636 subjects of varying race/ethnicity, only 5 (0.14%) showed genetic cluster membership different from their self-identified race/ethnicity.


So let's be precise about the term "imprecision." No doubt Plato would sniff at mistyping rate of 0.14%. Also, since we're talking science here one should be familiar with the distinction between accuracy and precision. I think in fact that as the number of informative loci increase an inference of ancestry is rather precise (reproducible). But perhaps the author of the above piece finds the precision of genetic science wanting? That being said, I am a bit confused as to why then his academic interests lay in history, an even more imprecise field, than in physics or mathematics where his passion for precision might be suitably sated.

Race is a social construction. But it is not one constructed purely from human ideology. That many perceive Greeks as white and Turks as non-white is a reflection of social axioms (Christians are white, Muslims are brown). That may perceive Greeks as white and Thai as non-white is not a reflection of social axioms (Greeks exhibit physical characteristics of the white race, Thais do not). Humanists are well schooled in the interplay between ideology and facts in generating a narrative of the world. To pretend as if there is no factual basis in the outlines of an ideology is a denial of reality, which would less concerning if not for the fact that most Americans parrot this very line about race as if it was universally accepted.

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Russia's army majority Muslim in 2015?   posted by Razib @ 6/15/2007 11:44:00 AM
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I am a bit tardy with my second part of my review of God's Contintent, Christianity, Islam and Europe's Religious Crisis. There are some other things I have to take care of, and the previous post, though fruitful, took a lot of my time in terms of moderation (once the post went off the front page I didn't keep track of it and it seems more ignorant and/or low IQ people started commenting). But, yesterday someone made the comment that they'd read that the Russian army was going to be majority Muslim by 2015. I deleted the comment since it seemed such an implausible assertion and it really served no use to me. That being said, I decided to google this assertion and came up with Daniel Pipes' post. Now, I don't know about you, but a lot of the "data" seems to be basically hand waving. For example, compare & contrast:
Plus, Russians of Orthodox background are converting to Islam. (For one important case, see the story of Viacheslav Sergeevich Polosin.)
...
Another indication of Islam's progress among Russians concerns former-Russian-spy-turned-dissident Alexander Litvinenko, who died of Polonium-210 poisoning in London on November 23. He converted to Islam on his deathbed...
(vs.)
Silantyev also dismisses as myth the idea of mass conversions of ethnic Russian to Islam. "Less than 3,000 ethnic Russian have converted to Islam" during the past fifteen years, he says. In contrast, over that same period, almost 2 million ethic Muslims have become Orthodox Christians. In 70 percent of marriages between a Muslim and a Christian, for example, the Muslim spouse converts to Christianity.


One would have to look up the source of these data in the last case, but at least there are some numerical figures here as opposed isolated cases which are held up as exemplars. Additionally, one might be a bit skeptical about mass conversions to Islam by Russians when one considers that half of Russian men are dying from alcohol related causes. I am pretty sure that most readers of these alarmist headlines are also unaware that the vast majority of Russian Muslims are native born and indigenous, part of the absorption of Muslim peoples which occurred during the 18th century expansion (that most Russian Muslims are part of native ethnic minorities is implicit in Pipes' data, but I suspect that most readers won't connect the dots and will project Western European realities of foreign migrants and their offspring). This is the reason that Islam is one of Russia's historical religions. Though like most Russian monarchs Catherine the Great encouraged and facilitated the conversion of Muslims to Orthodoxy, she also sponsored religious notables within the Islamic establishment who argued for the acceptability of subordination of Muslims to a non-Muslim potentate (though who did not accept this emigrated to the Ottoman Empire). Of course cultures change and Russian Islam is now being influenced by Saudi backed ideologues, but the point is that a little historical context is necessary to really understand what it means when one say that "10-20% of 'Russians' are Muslim."

Now, of course the demographic profile of Russia's ethnic majority is pretty dire. That being said, please because cautious of translating "if current trends hold" to "current trends predict the inevitable." After all, before the fall of Communism ethnic Russian fertility was higher than in most of the West, but today it is lower. Much has changed in 15 years demographically, so predicting the current moribund state 30 years into the future seems a bit much.

P.S. Small historical footnote some might find amusing. Click here to read about a prominent European general and strongman who won battles with the help of at least 40,000 Muslim soldiers on European soil in the 20th century.

Note: Again, I'm going to be deleting comments of no use to me. Use to me = offer up more data, generate an insightful analysis, cite some good sources, etc. Sincerity without knowledge is best not seen or heard.

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Trial By Jury: Not Black and White?   posted by DavidB @ 6/15/2007 04:32:00 AM
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There have been reports in the British Press this week about the influence of ethnicity on the decisions of juries. This is based on a study published by the newly formed Ministry of Justice (formerly part of the Home Office).

The press reports have generally been along the lines that 'juries are not affected by ethnic bias'. The truth, as usual, is more complicated. The research itself is available here (2Mb pdf file) The key part of the report for the present purpose is Chapter 6, on Jury Decision-Making.

Those who read the report will be able to make up their own minds, but I will offer a few comments below the fold.


It is important to understand the methods of the study. It is based on 27 simulated jury deliberations on a single case. The facts and evidence in the case were identical except that in 10 simulations the 'defendant' was white, in 9 he was Asian (which in Britain usually means South Asian), and in 8 he was Black (page 162). (There is also variation in the 'victim' of the crime.)

The 'jurors' themselves were taken from people summoned for jury service at Blackfriars Crown Court in London. The jurors watched the evidence on videotape then, without discussion, individually recorded their provisional verdict. The jury then discussed the case and recorded their final verdicts (individually and collectively). The 'pool' of potential jurors is ethnically mixed, and except for one (all-white) jury, the juries contained a mixture of white and non-white participants, but always with whites in a majority. As the authors stress, it would be hazardous to extend the findings to other parts of Britain or to unmixed juries.

Despite the optimistic headline reporting of the findings, there is in fact evidence of substantial ethnic or racial bias on the part of some jurors. As the authors put it (page 164), 'jurors of different ethnic backgrounds reached significantly different verdicts depending on the race of the defendant. BME [black and minority ethnic] defendants were less likely to be found guilty than white defendants, while the White defendant was much more likely to be found guilty by BME jurors than White jurors.'

The best quantitative indicator of the extent of juror bias is probably the table on page 180, which gives a breakdown of 'guilty' votes by the ethnicity of jurors and defendants. Since the facts of the case were the same, if jurors were unbiased we would expect the distribution of guilty votes with respect to the ethnicity of defendants simply to reflect the proportions of Whites, Blacks and Asians among them, which it will be recalled were 10: 8: 9, or in percentages 37: 30: 33. If then we express the figures in the table as percentages of all guilty verdicts by the jurors in question (using the 'first vote' figures), we get the following:

................................White defendant.....Black defendant....Asian defendant
Unbiased expectation.......37................................30..........................33
White jurors....................45.................................21..........................33
Black jurors.....................55.................................18..........................26
Asian jurors.....................72...................................0..........................28

It will be seen that both Black and Asian jurors appear more lenient towards Black defendants, and more severe towards White defendants, than would be expected by chance. There is a slight indication of leniency towards Asian defendants by Black and Asian jurors, but this may not be statistically significant in view of the small numbers of jurors involved. White jurors seem slightly biased in favour of Black defendants and against White defendants.

These figures cannot simply be explained by jurors being biased in favour of their own group, since Asians are more lenient towards Blacks than towards Asians, and Whites are more lenient towards both Black and Asians than towards Whites. (I do not understand the assertion at the bottom of page 180 that White jurors show some leniency towards Whites in comparison to all non-whites. The authors seem to have forgotten that non-whites make up a substantial majority of defendants in the simulations, so that the combined numbers of 'guilty' votes for non-white defendants from White jurors are still less than would be expected. If anyone thinks I have misunderstood this, please comment.)

The relative percentages of guilty votes might reflect either leniency towards blacks, severity towards whites, or both. It is difficult to disentangle these motives, but this may be partly remedied by looking again at Figure 6.12. If a particular group of jurors were severe towards one group of defendants, without being lenient to others, this would show up in a higher overall conviction rate. There is in fact some indication in the table that Black, and especially Asian, jurors are positively severe towards Whites, as well as lenient towards Blacks. The authors recognise the leniency towards Blacks, which they attribute to a perception by jurors that the justice system itself is biased against Blacks, and a consequent need to compensate for the bias. They do not (I think) recognise any bias of jurors against Whites, and therefore do not seek to explain it.

In view of all these findings the generally optimistic tone of the press reports (and the conclusions of the research report itself) may be surprising. The optimism is based on the fact that the overall final verdicts of the juries do not seem to have been affected by the ethnic composition of the jurors. The authors appear to take the view that the jury system is robust enough to cope with a bit of bias. Perhaps it is, but I suggest two reasons for caution. First, I suspect that the tone of the conclusions would have been less optimistic if the bias of jurors had been against non-whites. Much wailing, gnashing of teeth, and ritual self-flagellation would have ensued. Second, and more important, the lack of practical impact of the jurors' bias on the verdicts of juries may be largely due to the particular features of the real-life case on which all the simulations were based. Although few details were given, it seems to have been a case where there was a serious conflict of evidence and any reasonable jury would have been unlikely to reach a guilty verdict. In the real-life case there was a hung jury (page 164), while in the simulations only one of the 27 juries reached a guilty verdict, and a majority were 'hung'. It is impossible to say, based only on this case, whether the bias of some jurors would have a serious impact on other cases. It only takes 3 jurors to block a guilty verdict in English Courts (see note 257 of the report for details), so there is a serious possibility that in some cases a bias in favour of Black and Asian defendants would lead to people who would otherwise be properly convicted going free.



Thursday, June 14, 2007

European fertility   posted by Razib @ 6/14/2007 05:33:00 PM
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Article in The Economist.

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Wednesday, June 13, 2007

Neandertals - "human" or not?   posted by Razib @ 6/13/2007 06:08:00 PM
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New Scientist has an article about Neandertals being human. Kambiz has an extensive comment, but this is important:
Another hotly debated piece of Neandertal humanity, is the burial at Shanidar Cave, where archaeologists found pollen from flowers on and around the Neandertal individual. They interpreted it as a form or mourning, or paying respects, like we do too but others contest that it's just flowers or pollen that blew over the bodies.


Clearly, the Shanidar Cave example is not just a cause of inference, but an effect based on one's priors. That is, the likelihood that the flowers are evidence of burial rites are conditioned on all the other pieces of data which we have on had about Neandertals. This sort of thing is why I punt to John Hawks so often, I simply don't know all the constellation of the data in paleoanthropology with enough confidence that I'm comfortable with the filters I'm employing.

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17th century open borders?   posted by Razib @ 6/13/2007 02:45:00 PM
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Andrew Sullivan says:
And lepers everywhere! I tell you: the nineteenth century was one frigging amnesty after another. And the seventeenth century! We had no control of the borders whatsoever.


This is a common perception that comes up over and over again. From Albion's Seed:
...The founders of Massachusetts, unlike rulers of other European colonies, deliberately excluded an aristocracy from their ranking system.

At the same time, the leaders of Massachussets also made a concerted and highly successful effort to discourage immigration from the bottom of English society. They prohibited entry of convincted felons (many of whom ahd been punished for crimes of poverty) and place heavy impediments on the path of the migrant poor. A series of poor laws were enacted in Massachusetts, which rules of settlement and "warning out" that were even more strict than in England.


The author, David Hackett Fisher, argues that the character of various American regions, in particular New England, the Mid-Atlantic, and the lowland and upland South, was shaped in large part by the character of the British immigrant streams to each region. Whether you quibble with the details of his thesis, the general picture seems to be one where the initial parameters had a strong influence on the future course of events for centuries. In any case, the American colonies were not really characterized by "open borders" by any stretch of the imagination.

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Universal Grammar - follow up   posted by Razib @ 6/13/2007 12:30:00 PM
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Edge has a transcript of a talk by Dan Everett, the heterodox linguist who was the subject of a profile in The New Yorker. Video coming soon.

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Darwin (Catholic) becomes Mexican   posted by Razib @ 6/13/2007 12:12:00 PM
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Darwin Catholic has an interest post about work Americans won't do. Darwin & his wife believe in doing their own yard work (I believe they live in Texas, so is probably pretty transgressive). So check this:
I was pounding away with a short-handled mattock when one of a group of teenagers slouching by shouts in my general direction, "Stupid wetback! What ya doin?"

Now, I'm half-Mexican in ancestry, but no one ever guesses it. My hair isn't that dark, and although I take a tan if I get around to going outside enough, I'm not really olive at all. But apparently if I'm wearing workboots, jeans and a white t-shirt and covered in sweat and dirt while working in the yard -- it is actually possible for people to recognize my Mexican background. Perhaps I was even doing some of that famous work that Americans won't do.


A few months ago I was at a fancy restaurant that was going through some renovation, and I overheard one of the diners chatting up one of the owners. They were discussing how nice the new facade was turning out, and the diner blurted out, "Is the man working on this Latin American?" Turns out he wasn't (at least that's what the owner said). Anyway, here is a map of the density of illegal immigrants across the United States. In most of America there is a lot of work that Americans won't do.

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Why genes don't determine race?   posted by Razib @ 6/13/2007 10:59:00 AM
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TNR, the journal of the center-left, just published an article titled Why genes don't determine race. The article doesn't merit much of a response aside from "Why Platonism is wrong on race." The article makes it implicitly clear that the new racial genetics is often one of conditional probabilities, not fixed determinism, but the strawman of "genetic determinism" shines brightly in the rhetoric. In any case, there are good points made in the piece, the obesity epidemic that is rampant in the black American population isn't going to be solved by declarations that it is "in their genes." But, an understanding of the genetic background adds non-trivial utility to formulating a proper public policy response, because there are likely some issues of norm of reaction lurking in the background. As documented in Some Like it Hot: Food, Genes and Cultural Diversity, varied populations often exhibit different nutritional responses.

Addendum: In the annals of race, Slow Wave Activity During Sleep Is Lower In African-Americans Than Caucasians.

Related: Race the current consensus. The Platonic Ideal and the Empirical Reality. Race is obsolete...? Reality of race is one place. Race.

Update: This response very good.

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Tuesday, June 12, 2007

Parents matter...and they don't   posted by Razib @ 6/12/2007 10:02:00 PM
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First, Daddies' girls choose men just like their fathers:
Women who enjoy good childhood relationships with their fathers are more likely to select partners who resemble their dads research suggests. In contrast, the team of psychologists from Durham University and two Polish institutions revealed that women who have negative or less positive relationships were not attracted to men who looked like their male parents.

Due to be published in the July issue of Evolution and Human Behaviour, the study investigated evidence of parental sexual imprinting, the sexual preference for individuals possessing parental characteristics, in women. The team used facial measurements to give a clear view of how fathers' facial features relate directly to the features of faces their daughters find attractive.


This comes very close in my book to "they had to do a study on that???" That being said, it is somewhat interesting in light of the finding that daughters prefer men who smell like dad (MHC).

In other news, Male Depression Is Linked to Poor Sibling Relations, not the parent-child relationship.

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Tufte   posted by p-ter @ 6/12/2007 04:07:00 PM
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Via ALDaily comes this profile of Edward Tufte, described in the article as "the world's only graphic designer with roadies".

The guy has a huge following in the scientific community--The Visual Display of Quantitative Information is proudly displayed on many a bookshelf. I've only browsed through it, but even that has been enough to make me cringe every time I see the lines and colors of the default Excel graph.



Monday, June 11, 2007

You decide   posted by Razib @ 6/11/2007 09:31:00 PM
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Melissa Theuriau, is she all that?


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The Tao of sperm competition   posted by Razib @ 6/11/2007 08:32:00 PM
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I found this amusing paper, Adaptation to Sperm Competition in Humans, via google scholar. The topic itself isn't necessarily amusing, but the description of how a human penis is engineered to scoop out the sperm from another male can't help but induce some smirks. In any case, most of the time we've discussed sperm competition it has been in an explicitly physiological & anatomical context. How viscous is the sperm? How quickly does it dry up and serve as a "plug"? How large are the testicles of various primate species? This paper examines possible "psychological adaptations," and tries to offer an explanatory model for proximate phenomena. For example, why do males tend to ejaculate larger volumes after viewing pornography which involves group sex between two males and one female than between three females? Of course, being evolutionary psychology in the classic mode there really isn't examination or entertainment of human differences, which might open up the possibility of a multiplicity of conditional strategies varying in terms of utilization across individuals.

Related: Our sperm competition posts.

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Mitochondrial genetics   posted by p-ter @ 6/11/2007 06:58:00 PM
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Most studies of the genetics of human traits focus on a specific disease phenotype, or some extreme of phenotypic variation that a clinician can call "pathological". Because of this disease-centric approach, the genetics of basic cellular processes often go unstudied in humans (I'm not kidding when I say some medical doctors and clinicians were resistant to the idea of looking at the genetics of gene expression, one of the most logical places to start understanding the cell). However, complex diseases are, as the name implies, complex; it's certainly of interest to study the various pathways involved in their aetiology in isolation.

It might not be the "sexiest" phenotype to look at, but this new paper, on the genetics of mitochondrial genome number, is an excellent example of such a "reductionist" approach. Variation in mitochondrial genome number and integrity is important in a number of human diseases, including common and expensive ones like Type II diabetes-- finding the genes involved in this phenotype will be an important part of any systems-level model of such diseases.




HS talks: calcium, calmodulin, and calcineurin   posted by amnestic @ 6/11/2007 05:32:00 PM
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A recent paper issue of Cell came with an ad for the Calcium Signalling series from Henry Stewart Talks. These are apparently nicely produced lecture-format videos from experts reviewing diverse areas of biology. I'm not willing to shell out the $690 it would take to view the whole thing, but they have a free talk of the month: Calcium, Calmodulin, and Calcineurin by Stephen Bolsover that you might want to kick back with a glass of red and consume.

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Sunday, June 10, 2007

Bound to repeat   posted by Razib @ 6/10/2007 10:30:00 PM
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Xun Zi, the least idealistic of the great Confucian sages stated, "Mozi was blinded by utility and did not understand culture." Blinded by the utility, it seems a problem which intellectuals are still plagued by, until they realize they are bounded by the culture....

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Saturday, June 09, 2007

NAS audio interviews   posted by Razib @ 6/09/2007 11:25:00 PM
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The National Academy of Sciences has a small archive of interviews with prominent members.

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Safari Library   posted by Razib @ 6/09/2007 10:27:00 PM
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Recently I resubscribed to the Safari online tech library (a lot of O'Reilly titles, but not exclusively) after a hiatus of a few years. Previously their system was basically like Netflix, you could put some items on your bookshelf contingent upon your subscription level. Now they have a $40/month level where you have full access to their whole library! Of course, there's really nothing in there that you couldn't find through clever google searches, but if time is $ it really does make it a lot simpler to have it all in one place.

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Friday, June 08, 2007

Genome-wide association for heart disease   posted by p-ter @ 6/08/2007 03:20:00 PM
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Following on the heels of the results of the Welcome Trust Case-Control Consortium are two papers reporting associations between risk of coronary heart disease/heart attack and an allele on chromosome 9. Like many of the signals coming out of these recent genome-wide studies, the polymorphism implicated is not in a gene, and no functional effect is immediately obvious; this will take a while to sort out.

This is another promising result, though. The nay-sayers who argued against the HapMap and whole-genome association are finding themselves proved very wrong. As is often the case in science, the Luddite position was not tenable-- technology opens all sorts of doors for biology, and a paper from 1996 (which was for essentially science fiction at the time) has proved quite prescient.

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Synthetic biology   posted by p-ter @ 6/08/2007 08:55:00 AM
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Carl Zimmer has an interesting post on Craig Venter's goal of making a synthetic organism. Apparently, Venter has filed for a patent on the process (essentially, synthesizing a minimum number of genes necessary for life, and transforming it into a cell).



Thursday, June 07, 2007

I see sea shells   posted by Razib @ 6/07/2007 02:36:00 PM
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By now some of you have heard about the possibility of symbolism via sea shells 82,000 years ago (give or take 10,000 or so) on the Moroccan coast. This is important because it is another data point which precedes The Great Leap Forward around 40,000 years ago. In The Dawn of Human Culture Richard Klein argued that a biological rewiring of our brains resulted in the explosion of human creativity initiated during the Great Leap Forward. This is important, because anatomically modern humans preceded the cultural explosion by over a hundred thousand years (this includes the attainment of brain sizes in the range of the modern). These ancient finds in Africa prior to the Great Leap Forward imply that the basic raw material might have long been bubbling in the background before the take off. I don't know what to make of this really as I am not particularly "up to speed" on the enormous sample space of findings and the nuances of the extant fossil data. But this caught my eye from the story in The Economist:
Even more intriguingly, although the beads from Grotte des Pigeons are not from precisely the same species used at Blombos, the two are indistinguishable to the untrained eye. Stone-age South Africans, like their northern cousins, could have chosen any one of hundreds of shell shapes to make into beads, yet they adopted essentially the same fashion. The immense distance between the two ends of the continent makes an ancient African exchange system appear improbable. Then again, a chance predilection for the same beads is unlikely as well.


From what I recall the Olduwan toolkit persisted roughly the same form over millions of years and on a transcontinental scale. Is this because a world wide system of trade and cultural exchange existed to stabilize the motifs and techniques? I doubt it, rather, it seems plausible that there was a biological origin for this "cultural complex". It seems possible that our erectine predecessors flaked away stones to produce hand-axes just as the bower bird instinctively constructs its nests or the beaver their dams? The Great Leap Forward is different perhaps not because of the evidence of symbolism or creativity, but the rate of change of that creativity and its exuberant diversity, which resembles modern humans in their variation. Of course, own species has seen a ramp up in the rate of acceleration of cultural evolution. Consider that Egyptian culture maintained its basic outline for nearly 2,000 years, the same period which separates us from Classical Rome!

Related: John Hawks has more.

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Wednesday, June 06, 2007

Genome-wide association studies in the UK   posted by p-ter @ 6/06/2007 05:59:00 PM
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Results from the most ambitious (and expensive) set of genome-wide association studies for common diseases were published today in Nature (open access! You can read it for free!). Funded by the Welcome Trust in the UK, a "dream team" of clinical geneticists and statisticians assembled a common set of 3000 controls to compare genetically to around 2000 cases each of Type I diabetes, Type II diabetes, arthritis, cardiovascular disease, Crohn's disease, bipolar disorder, and hypertension.

This study is being trumpeted as a major success, and to some extent, it is-- for all diseases except hypertension, at least one strong signal and many weaker signals were identified. As correlational studies are largely hypothesis-generating, some of these will lead to major discoveries about the pathology of disease. In Crohn's disease, for example, the consortium has found a couple loci involved in autophagy and the elimination of intracellular bacteria. They also confirm the association of another locus involved in autophagy. It's easier for people working on a disease to focus on pathways that are already known to be involved in the disease (for example, there's a known autoimmune component to Crohn's disease); it often takes this kind of top-down study to jolt people out of complacency.

The consortium has also make publicly available an impressive suite of software, along with new algorithms for genotype calling and mutlti-locus association, incorporating information from the HapMap. These tools are certainly at the cutting edge, and represent major advances in their own right.

On the other hand, one can't help but notice that the loci identify contribute only a fraction of the known genetic component of these diseases. This is a proof of principle-- the base has been laid; it's now feasable to scale these sorts of case-control studies up to tens of thousands of individuals. But is that really the most effective way at getting at the genetic basis of these diseases? Perhaps not.

A final comment-- I noted in the comments of a previous post that the big data sets used for population genetics these days are generated for medical reasons. There's a ton of population genetic information here, which the authors are likely going to make more use of the future. They do give us a glimpse, though-- they note a number of genomic regions that show marked geographic variability within the UK (and note they limit themselves to self-identified "white Europeans"):
Thirteen genomic regions showing strong geographical variation are listed in Table 1, and Supplementary Fig. 7 shows the way in which their allele frequencies vary geographically. The predominant pattern is variation along a NW/SE axis. The most likely cause for these marked geographical differences is natural selection, most plausibly in populations ancestral to those now in the UK. Variation due to selection has previously been implicated at LCT (lactase) and major histocompatibility complex (MHC), and within-UK differentiation at 4p14 has been found independently, but others seem to be new findings. All but three of the regions contain known genes. Aside from evolutionary interest, genes showing evidence of natural selection are particularly interesting for the biology of traits such as infectious diseases; possible targets for selection include NADSYN1 (NAD synthetase 1) at 11q13, which could have a role in prevention of pellagra, as well as TLR1 (toll-like receptor 1) at 4p14, for which a role in the biology of tuberculosis and leprosy has been suggested.

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What does Mark Thoma mean?   posted by TangoMan @ 6/06/2007 03:14:00 PM
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I'm having some trouble deciphering the economic principles underlying the following argument that Mark Thoma made regarding economic inequality:
As for inflation, in general, if wage growth equals inflation plus productivity growth, there is no inflation pressure.


Now I understand an argument which allocates to wages the productivity growth derived from more efficient workplace practices but my understanding of labor market economics is that the majority of productivity gains result from capital investment, so if all, which Thoma seems to imply, or even most, productivity growth is allocated to labor then none, or only some, of the gain will be allocated to capital. Yet, we know that capital will not invested in an environment of substandard, or non-existent, returns, so when labor is awarded a benefit that results from capital investment how does this not lead to inflationary pressure?




On Confucian Human Nature   posted by Razib @ 6/06/2007 01:17:00 PM
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I was reading The Chinese Experience, a cultural history, when I was struck by something in the chapter on Confucianism:
...The belief that all men are born equal and are infinitely perfectible is a basic and profoundly humanistic Confucian doctrine, which is not paralleled in the main Christian tradition, which holds that all men are of equal value, rather than that they are born with similar characteristics. The belief goes back to the Analetcs, which includes the saying, 'By nature men are close to each other; through experience they become remote from each other'....


The generality of this is not surprising to me. If you read histories of the intellectual ferment in early 20th century China you note that it was the conservative and reactionary Mandarin class who argued most vociferously against the European ideas regarding the racial chain of being and eugenics. Instead, liberal progressives were open to Western science, which implied innate between group and within group differences, while the Confucians were immovable form their time tested tabula rasa dogma.

Of course, to some extent both groups were guilty of overreach, the Confucians rejected the new science which did point to heritable aspects of human nature and reality of individual differences (though to be fair, their moral-political system was the most robust our species has seen, persisting across 2,000 years). As for the racial science of the early 20th century, it was a coarse and clumsy beast which was vulnerable to the rise of the the tabula rasa methodologies in the human sciences, from behaviorism to Boasian cultural anthropology. But I do think it is important to note that in Geography of Thought Richard Nisbett reports that East Asians are still far more likely to attribute individual performance to context, circumstance and effort than innate aptitudes when compared to Westerners. My comment a few weeks ago on Confucianism in China was predicated in part on hints like this that the pre-Communist cultural sensibilities have persisted down to the present day. Many scholars argue that the ostensibly revolutionary Cultural Revolution was at the heart Confucian, placing emphasis on moral worth & will as opposed to technical efficiency & pragmatism. Sometimes you really have to look between the pages of the book to see that the title is deceptive.

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Tuesday, June 05, 2007

Mark Chu-Carroll on Edge of Evolution   posted by Razib @ 6/05/2007 10:56:00 AM
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I'm not normally a big fan of fisking anti-evolutionists (the rotten fruit hands too low), but Mark Chu-Carroll of Good Math, Bad Math has a very funny (and obviously enraged) response to Michael Behe's newest piece of work, The Edge of Evolution: The Search for the Limits of Darwinism. Readers of this blog might find Carroll's analysis of Behe's misuse of the idea of fitness landscapes very informative. I find fitness landscapes fascinating myself, but if your reading of them is telling you that evolution can't happen, then I think the logical thing would be to look at the problems with landscapes. They aren't exactly rock-hard formal systems at this point. Until recently they weren't really formal at all, and Will Provine has made the case that for two scientific generations everyone used them in an incoherent fashion (including their originator, Sewall Wright).

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Monday, June 04, 2007

Pre-Columbian Polynesian contacts?   posted by Razib @ 6/04/2007 09:42:00 PM
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John Hawks points me to this story in The New York Times about research to be published in PNAS. Basically the researchers found that chickens buried in south-central Chile about a century before the Spanish contact with the New World were genetically most similar to those from Polynesia. This is a pretty obvious case for pre-European contact between Old and New World peoples. Frankly, on a priori grounds this is a no brainer, if Polynesians could make to Easter Island it seems implausible that continental South America would be too far. Also, there is historical documentation which suggests that the Incas used chickens in their religious rituals when the Spanish first entered their territory. One could hypothesize that the chickens had spread via cultural diffusion from the region of first contact in the Caribbean, but these genetic data puts that theory to rest (another case where genetic data clarifies a historical question). There is no real data which suggests that Polynesians had any demographic impact upon the New World. This makes sense, the effective population of th sources of colonization would have been relatively small compared to target population, so the expeditions would have been tiny. Genetic drift over the past few centuries might have inundated the small signal of intermarriage on the neutral markers which have been assayed in this region, but I wouldn't be surprised if meta-population dynamics are at work in explaining why we might not detect a signature of admixture (south-central Chile might have been subject to pre-state social processes which involved more deme vs. deme competition and extinction). Imagine that the Polynesians intermarried with a particular tribe, it maybe that that tribe was exterminated in internecine warfare rather soon after the initial hybridization event, though the utilization of chickens had already spread to hostile neighbors via furtive contacts. Finally, the spread of chickens seems to be pretty analogous to the introgression story. Chickens jumped the population barrier because they were a positively selected cultural character.

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Recent human evolution   posted by p-ter @ 6/04/2007 08:34:00 AM
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The major genome scans for selection in humans (e.g. Voight et al. 2006 and Wang et al. 2006) have all been focused on incomplete selective sweeps-- alleles that are on their way to fixation in a given population, but haven't quite made it. A new paper in PLoS Genetics takes a look at those alleles that have already made it in one population or another, developing a robust test to find fixed population differences.

This is a magnificent paper, and should be required reading for anyone interested in the field of human evolutionary genetics. There's a ton of information condensed into this article; I'll run down some of the most important points:

1. The major problem people have with some genome scans is that, while they generate a number of candidate loci for selection, there's no real way to separate out those likely most fruitful for follow-up. These authors use a statistic that is robust to many demographic situations, recombination rate heterogeneity, and just about anything else you can throw at it. The loci they identify are not just enriched for true selective events; the majority are worth following up.

2. They find selected loci in pathways for skin color (including SLC24A5) and hair morphology in Europeans. It's always seemed somewhat obvious that the major visible differences between population groups should be selected for, but this provides important evidence in favor of that. Various genes involved in nervous system development (including genes known to be involved in Alzheimer's) have also been under selection in various populations. Finally, they note an abundance of heat shock proteins under selection, which seems surprising. I really have no explanation for that.

3. Centromeric regions of many chromosomes have been under selection. I find this fascinating, as the most likely hypothesis for the reason why is meiotic drive. This force could turn out to be a major player in evolution.

4. We've mentioned hemochromatosis here before, essentially it's a hereditary genetic disorder that appears at a particularly high frequency in Europeans, which seems to be the result of selection. The authors here do indeed find the signature of selection at this locus, but the signal is centered at a cluster of histone genes 150kb away. So maybe hemochromatosis has "hitch-hiked" its way to high frequency.

5. They find fewer signals of selection in the African-American sample than in the other samples. I'm generally skepical of claims like this, and they note that they indeed had less power to detect sweeps in the African-Americans (since they're looking at fixed differences, European admixture into the sample should reduce power). It's nice that they look at this; I recall another paper that made claims about absolute frequencies of selection along different lineages without considering power at all.

6. There seems to be much evidence for selection making populations different, less so for selection affecting all populations equally. Human evolution is continuing, and making us genetically different.

For those who want to browse, here's a link to a table with the 101 regions with the strongest evidence for selective sweeps.

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Sunday, June 03, 2007

Genetics carnivals   posted by Razib @ 6/03/2007 02:10:00 PM
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Gene Genie hosted by Hsien at Eye on DNA. Mendel's Garden, over at The Daily Transcript (via evolgen).

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Genetic correctness?   posted by p-ter @ 6/03/2007 08:28:00 AM
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A rather confused essay by Kurt Jacobsen, published in Logos, has been making the rounds recently. It's about eugenics and what he calls "genetic correctness", apparently his term for the belief in a "correct" genome. It begins:
The advent of Dolly the cloned sheep in 1996 - RIP in 2003 - left many an onlooker feeling both celebrative and uneasy. With irrepressibly manic ingenuity the biological sciences are dissolving our supposedly fuddy-duddy moral boundaries so that many scientists find themselves in debates they really would rather avoid as to the wisdom of playing cavalierly with recombinant DNA.
It's an unfortunate start-- I'm not sure if there's supposed to be a relationship between those two sentences. Cloning (the subject of the first) does not, of course, make use of recombinant DNA (the subject of the second). Read the wikipedia article on recombinant DNA (noting the alternative definition of the word "cloning"), then compare to the technique used for mammalian cloning. They're simply two separate things.

This is perhaps a technical issue, but relevant to his ultimate point. Yes, scientists would rather avoid ethical discussion about recombinant DNA, but one could argue from the other perspective as well-- many ethicists (and really, we're all amateur ethicists) are finding themselves in positions of trying to judge technologies they really don't understand. They can't be bothered to learn all the silly details, so they make an argument from ignorance. This is a case in point.

Much of the essay is an interesting history of the eugenics movement, demonstrating the role of scientists, sensationalist media, and popular hysteria in the forced sterilizations and political movements of the time. Yes, many scientists and pseudo-scientists lent their names to questionable treatments for "feeble-mindedness", and yes, some praised the Nazi eugenics regime. There is much to be learned from such history. But I doubt the role of scientific results themselves in shaping people's political beliefs. I could be wrong, but I find it difficult to believe that many "social Darwinists" were all gung-ho about social programs and helping the poor before reading about the "survival of the fittest", nor do I think many people decided supporting social programs was a great thing after reading about the naturalistic fallacy. It's much easier to search out arguments to support your world-view than to change said world-view in response to facts.


After recounting the rather sordid history of state-sponsored eugenucs, Jacobsen is clearly uncomfortable about modern "eugenics", as the underlying scientific principles are the same. But those underjlying principles are, in fact, correct. Jacobsen writes:
Scientists already found that a stable genotype can correspond to a continuous variations in phenotype, that "many symptoms regarded as pathological might only arise from interaction of genotype with surrounding conditions" and that "a genotype cannot always be derived from phenotype" - findings which should have extinguished the theoretical basis of eugenics.
This is obviously wrong. The entire basis of livestock breeding is based on selection on "quantiative traits" -- traits that show such a "continuous variation in phenotype". The theory is sound -- there's no doubt that, should humanity want to be a little taller, forced sterilization of short people would, over the course of a couple hundred years, get us there.

Jacobsen wants to have it both ways here-- first, he denies that genetics plays a role in disease:
In the 1990s "psychiatric geneticists began to propose genetic anticipation, the tendency of some illness-causing genes to expand in size when passed from generation to generation, as the mechanism behind the increasing severity of schizophrenia or manic-depressive illness as handed down by a family tree." Hence, the problem cannot be family conflict or lousy schools (both rooted in bad social conditions), the child instead is blamed - with the very best intentions - as carrier of disease or a misshapen gene, which supports the biopsychiatric inclination to "reduce human conduct and social conflict to grossly sluggish neurotransmitters in a particular type of nerve cell." It's not begging the question, you see, it's genetic.
Then (after puzzlingly dismissing genetic anticipation. Is it really so much more compassionate to blame a family for causing the increased severity of a disease when it actually is genetic?), he laments the possibility of an increasing role for prenatal genetic testing (which, if he's right and things are just too complicated to understand, shouldn't be able to properly test for anything).
The future holds out the spectacle not of coercive control but of a "eugenics of the free market." Andrews relates a case of an HMO instructing a couple, who found through amniocentesis that their child-to-be possessed a gene for cystic fibrosis, that it would not pay for the child's care if the pregnancy came to term.
It's interesting that Jacobsen wants to make us feel uncomfortable about genetic testing with this anecdote; if anything, it makes me question the insurance system. (and indeed, I've argued before that genomics should provide a push for socialized health care).

I could go on, but this essay is simply a hodge-podge of all the different things that make people uncomfortable about genetics-- designer babies, gene patents, the word "eugenics", something about "reductionism". Oh, and didn't the Nazis like genetics? All the arguments are there, even the contradictory ones and the ones that say more about how some of our infrastucture (the patent system, the insurance system) is unprepared to deal with genetic information than about the genetic information itself.


Related: Notes on eugenics, To breed a better human-we have the technology

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Friday, June 01, 2007

Tonal languages, ASPM, and MCPH   posted by p-ter @ 6/01/2007 06:26:00 PM
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The article Razib mentioned earlier on the correlation between genetics and language type has been published. Effectively, the results of the paper are in their one figure (right), which shows population frequency of the two alleles on the x and y axes. The filled squares represent non-tonal languages, and the empty squares tonal languages. There's an association between allele frequencies and language type, and the magnitude of the association is an oulier when considering other loci in the genome, suggesting that it is not simply due to population migration and history. My comments:

1. I have never seen an article so apologetic about its conclusions. About every other sentence explains what they have not shown-- a gene for "speaking Chinese", a proof of causality of the alleles, any sort of racial anything. Probably the result of unsympathetic reviewers.

2. The approach they take is one that's likely to be widely employed as more world-wide genotype data become available-- make a hypothesis that there should be a correlation between allele x and world-wide variable y, then test the correlation for a number of loci. If your allele x is an outlier, you've found something interesting. I'm not sure of the best way to analyse this data, nor am I sure the outlier approach is really effective. Some sort of statistical framework would be nice here, as a way of truly assessing the significance of a result like this.

3. As both ASPM and MCPH are polymorphic within populations, the best way to test the authors' hypothesis (as I'm sure they're well aware) is to do an association study on any of the variables they mention as being involved in slight biases towards a given language type. This would be interesting. But the authors also claim that the lingistic bias towards a language type is small, but amplified by cultural transmission, so possibly undetectable on an individual level. So can this hypothesis be falsified?

4. I'm trying to figure out the logic behind the placement of the dotted lines in the figure. It's not halfway between to min and max allele frequencies. It's not computed in any manner. Yet they make claims about the relative frequencies of each type of language in each quadrant. This seems highly questionable-- the human mind is highly capable of detecting patterns and forming groups, even when data are random. I'm not claiming the data points here are random, simply that the positioning of the lines in the figure serves to bias our thinking (note that a slight move to the right of the vertical line, or a move up to 50% on the horizontal line, would put a population in a quadrant they don't think it should belong in).

Overall, the paper is suggestive. Maybe highly suggestive? But I'd wait for a bit more data before coming to any conclusions.

UPDATE: Mark Lieberman at Language Log posts on the study, explaining more concretely the difficulties of the outlier approach. Bob Ladd, one of the authors of the study, then responds in a guest post:
Consequently, we've gone about as far as we can go with statistics; the only real confirmation that we are onto something will now come from experimental work demonstrating the existence of the hypothesized genetically-induced "cognitive bias" in individuals, followed by studies clarifying the neurological basis of the bias. As Daniel Nettle says in his Commentary on the print version of our paper (appearing soon), our work is really hypothesis-generating rather than hypothesis-testing.
We are now generating precise hypotheses about the nature of the bias, and hope to start testing them soon.
...
Now, it's certainly true, as Mark says, that our geographical correlations would mean more if they had proceeded from some experimental demonstration of some sort of genetically linked, language-related, cognitive/behavioral/perceptual difference. But given the widespread assumption (rooted in the Boasian tradition, but with a significant contemporary boost from Chomsky) that the human language faculty is absolutely uniform across the species, it's very unlikely that we would have been able to get funding to look for such a difference first. So we started by doing something we could do on our own without such support, namely testing the apparent correlation. Having done that, we hope we are now in a better position to apply for funding for the expensive part of the research

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