Archive for July, 2009

Richard Dawkins, The Economist & bylines

By Razib Khan | July 23, 2009 12:17 pm

The Economist has a review up of a book about Richard Dawkins’ influence, The Selfish Genius: How Richard Dawkins Rewrote Darwin’s Legacy. But it would really be nice to know who wrote something like this:

Her argument that the selfish-gene model is being superseded by other forms of evolutionary explanation relies on an overinterpretation of those alternatives.

In disputed areas of science perspective matters, and who someone is is a critical part of the information in judging their argument. I’m assuming this book review was written by someone who knows some evolutionary biology, in fact, someone with a familiarity with the Oxford zoology department where Dawkins has spent most of his career (In a hard-to-find-online piece about The Economist in The New Republic from about 10 years ago Andrew Sullivan claimed that most of the writers at The Economist hailed from one college at Oxford). I’m less hostile to Dawkins (on the science) than someone like Larry Moran, but it would be nice to know who is writing defenses of him nonetheless.

CATEGORIZED UNDER: Culture, Evolution

Genetically profiling the brain: it all ends with dopamine

By Razib Khan | July 23, 2009 9:35 am

Earlier today I linked to a Jonah Leher post on food that hooks into the role that dopamine plays in our decision making. Dopamine looms in the neuroscience angle of Jonah’s book How We Decide because the chemical’s role in cognition is established. Dopamine related genes are often fingered in behavior genetic studies as the causal root of some observed psychological variation. So a new paper in Nature Neuroscience is in perfect position to stand astride the literal slush pile of this research, Prefrontal and striatal dopaminergic genes predict individual differences in exploration and exploitation:

The basal ganglia support learning to exploit decisions that have yielded positive outcomes in the past. In contrast, limited evidence implicates the prefrontal cortex in the process of making strategic exploratory decisions when the magnitude of potential outcomes is unknown. Here we examine neurogenetic contributions to individual differences in these distinct aspects of motivated human behavior, using a temporal decision-making task and computational analysis. We show that two genes controlling striatal dopamine function, DARPP-32(also called PPP1R1B) and DRD2, are associated with exploitative learning to adjust response times incrementally as a function of positive and negative decision outcomes. In contrast, a gene primarily controlling prefrontal dopamine function (COMT) is associated with a particular type of ‘directed exploration’, in which exploratory decisions are made in proportion to Bayesian uncertainty about whether other choices might produce outcomes that are better than the status quo. Quantitative model fits reveal that genetic factors modulate independent parameters of a reinforcement learning system.

There are many moving parts here. A lot of the neuroscience-speak is way over my head, so I won’t pretend to reprocess what I had to hum through. First the authors review some general psychological & behavioral economic tendencies in terms of how individuals vary in decision making. In plain language it seems that some people have a strong aversion to negative inputs, others tend to focus on positive outcomes, and finally there is the variance in risk aversion (same expected value, but different deviations around that expectation). For example, there is the old behavioral economic chestnut that individuals tend to be risk averse on average, and prefer smaller guaranteed returns over gambling on getting more at the cost of a high risk of gaining nothing. Of course this does not take into account human variation in these dispositions. Using an experimental procedure whereby subjects were rewarded based on increased or decreased reaction times, risk aversion and reinforcement biases were probed. In this paper these psychological phenotypes are simply a preamble, as there is a nearly immediate attempt to relate these behaviors to the specific architecture of the brain, along with its neurochemistry. In particular the interactive role of dopamine, the one neurotransmitter to bind them all. Dopamine is then connected to the genes noted above, which seem to have roles in dopamine related pathways so as to up or down regulate production. Finally the paper also has an abstract computational model of decision making which allows them to associate variation on the specific locus to a particular parameter.
Figure 5 illustrates the whole package:

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Basketball in China

By Razib Khan | July 23, 2009 3:57 am

In China, a Rocky Ascent for Basketball. I love this quote:

Chinese players like Wang Yong of the Dongguan Leopards support the increased participation of foreign players. “Chinese and foreign players are a harmonious blend,” he said. “I’ve learned a lot from them this season and feel I am a better player.”


Around ScienceBlogs

By Razib Khan | July 22, 2009 11:27 pm

Rocket Science
Irreplaceable data
The Neuroscience of McGriddles
Very off topic: Why I won’t be at my high school reunion
The Best Eclipse of the Century is Tomorrow!


The digital future, freedom & control

By Razib Khan | July 22, 2009 6:07 pm

Why 2024 Will Be Like Nineteen Eighty-Four:

The power to delete your books, movies, and music remotely is a power no one should have. Here’s one way around this: Don’t buy a Kindle until Amazon updates its terms of service to prohibit remote deletions. Even better, the company ought to remove the technical capability to do so, making such a mass evisceration impossible in the event that a government compels it. (Sony and Interead–makers of rival e-book readers–didn’t immediately respond to my inquiries about whether their devices allow the same functions. As far as I can tell, their terms of service don’t give the companies the same blanket right to modify their services at will, though.)

Robert Heinlein’s Friday wasn’t one of his better works, but, I still remember the argument that one of the protagonists made in favor of a library of paper books: roughly, they’re off the grid and robust enough to survive a collapse of technological civilization. I have nothing against e-books, and plan to invest in an e-book reader when the technology gets its kinks worked out. But various information technologies do have trade offs. I recall that a shift in the type of paper used for books means that works published today are going to disintegrate much faster that those published hundreds of years in the past. But, it also means that books are very cheap and widely available. The column above takes a glass half-empty worst-case scenario attitude, but it’s worth examining.


Australian Aborigines arrived via South Asia

By Razib Khan | July 22, 2009 11:01 am

xo-map.pngBMC Evolutionary Biology has a new paper which will be up soon (not on site), Reconstructing Indian-Australian phylogenetic link. ScienceDaily has a preview:

Dr Raghavendra Rao worked with a team of researchers from the Anthropological Survey of India to sequence 966 complete mitochondrial DNA genomes from Indian ‘relic populations’. He said, “Mitochondrial DNA is inherited only from the mother and so allows us to accurately trace ancestry. We found certain mutations in the DNA sequences of the Indian tribes we sampled that are specific to Australian Aborigines. This shared ancestry suggests that the Aborigine population migrated to Australia via the so-called ‘Southern Route'”.

Remember that the mtDNA of South Asians tends to be related to the populations to their east far more than Y lineages, or the total genome content. In other words, the genetic variation of the whole genome tends to put South Asians closer to West Eurasians, while the mtDNA passed only through mothers offers a more mixed picture, with many clustering with East Eurasians. So naturally mtDNA is where you go to find deep connections to the peoples of Australasia (there are some anthropological models which suggest that female lineages may serve more as a deep substratum than male lineages, which have more long distance network connections). In The Journey of Man Spencer Wells was also able to find a link to Australian Aborigines in at least one South Indian man in the Y chromosome.
Australian publications naturally have a bit more detail:

The scientists carried out genetic tests on 966 individuals from 26 of India’s “relic populations” and identified seven people from central Dravidian and Austro-Asiatic tribes who shared genetic traits only found in Aborigines.

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CATEGORIZED UNDER: Anthroplogy, Evolution, Genetics

Comments might not work

By Razib Khan | July 21, 2009 5:39 pm

After 4 PM/7 PM PDT/EDT. Movable Type upgrade.



By Razib Khan | July 21, 2009 4:59 pm

Is an awesome weblog. You should read it.


Babies can understand meaning behind dog barks?

By Razib Khan | July 21, 2009 3:01 pm

We know that dogs can read human faces, it turns out that babies can infer the meaning of different dog barks:

New research shows babies have a handle on the meaning of different dog barks – despite little or no previous exposure to dogs.
Infants just 6 months old can match the sounds of an angry snarl and a friendly yap to photos of dogs displaying threatening and welcoming body language.

CATEGORIZED UNDER: Cognitive Science

Who supports the space program?

By Razib Khan | July 21, 2009 12:25 pm

I just listened to a radio segment on public sentiments toward the Apollo space program expenditures in hindsight. The polling had a small N, 3 people in Los Angeles on the street. But it got me wondering: who supports the space program? There is a variable in the GSS, NATSPAC, with a large sample size, which states:

We are faced with many problems in this country, none of which can be solved easily or inexpensively. I’m going to name some of these problems, and for each one I’d like you to tell me whether you think we’re spending too much money on it, too little money, or about the right amount.

I limited the results to between 1998-2008. Below are the demographic trends.

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Darwin is a white thing

By Razib Khan | July 21, 2009 9:09 am

charlesdarwin.pngI was mentioning to a friend that Whoopi Goldberg is apparently a semi-moon landing denialist. At least Goldberg isn’t a Creationist like fellow View co-host Sherri Shepard. In fact Goldberg took issue with Shepard’s stance when it came up. Rather disappointing when it comes to the moon landings then, though of course attitudes toward evolution for most people are cultural markers, not genuine assessments of the scientific consensus. It is interesting that both Shepard and Goldberg are black. The black community is more Creationist than the American popualtion as a whole, and have less general knowledge of science. My friend asked: is black opposition to evolution a function of their greater religious conservatism, as is the case with their attitudes toward homosexuality?
The General Social Survey question in regards to evolution which has the largest N is EVOLVED. N = 2,256 for whites and 368 for blacks. I cross-referenced several variables with race. Results below.

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C.S.I. 50,000 years B.C.

By Razib Khan | July 21, 2009 2:27 am

Shanidar 3 Neandertal rib puncture wound and paleolithic weaponry:

Since its discovery and initial description in the 1960s, the penetrating lesion to the left ninth rib of the Shanidar 3 Neandertal has been a focus for discussion about interpersonal violence and weapon technology in the Middle Paleolithic. Recent experimental studies using lithic points on animal targets suggest that aspects of weapon system dynamics can be inferred from the form of the bony lesions they produce. Thus, to better understand the circumstances surrounding the traumatic injury suffered by Shanidar 3, we conducted controlled stabbing experiments with replicas of Mousterian and Levallois points directed against the thoraces of pig carcasses. Stabs were conducted under both high and low kinetic energy conditions, in an effort to replicate the usual impact forces associated with thrusting spear vs. long-range projectile weapon systems, respectively.
Analysis of the lesions produced in the pig ribs, along with examination of goat ribs subjected primarily to high kinetic energy stabs from an independent experiment, revealed consistent differences in damage patterns between the two conditions. In the case of Shanidar 3, the lack of major involvement of more than one rib, the lack of fracturing of the affected and adjacent ribs, and the lack of bony defects associated with the lesion (such as wastage, hinging, and radiating fracture lines) suggests that the weapon that wounded him was carrying relatively low kinetic energy.
While accidental injury or attack with a thrusting spear or knife cannot absolutely be ruled out, the position, angulation, and morphology of the lesion is most consistent with injury by a low-mass, low-kinetic energy projectile weapon. Given the potential temporal overlap of Shanidar 3 with early modern humans in western Asia, and the possibility that the latter were armed with projectile weapon systems, this case carries more than simple paleoforensic interest.

The last paragraph is elliptical, but the circumstantial evidence seems to be that this Neandertal male was injured by an anatomically modern human with weapons. No one tell R. Brian Ferguson! In any case, ScienceDaily has more more direct exposition:

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Why we're fat

By Razib Khan | July 20, 2009 10:06 pm

Derek Thompson at The Atlantic passes on this awesome chart:
OK, OK, obesity is more complex than that. But check out The Big Max:
Using New York’s calorie-disclosure regulation to get the most for your money


The modifier on innovation

By Razib Khan | July 20, 2009 3:12 pm

Felix Salmon has been at the center of a discussion on the merits and value-add of financial innovation. He notes:

Then there’s the more purely financial innovation. There are good things here too — fractional reserve banking, factoring, common-stock limited-liability companies, tradable fungible bonds, stock-market index funds, that sort of thing. But on this front I think the low-hanging fruit was plucked decades if not centuries ago, and that we’ve long since entered a world of diminishing returns when it comes to the positive developments. Meanwhile, the negative developments, from portfolio insurance to CDO-squareds, have been arriving at an ever-accelerating pace.

When intermediation related operations go north of 1/3 of your economy something is out of whack. In Knowledge and the Wealth of Nations David Warsh points out that economists have had great difficulties in explaining economic growth and rising productivity from the beginning of the profession with Adam Smith. Innovation is an exogenous parameter outside of their models. Societies such as the Syracuse of Archimedes or Song China may have had the engines of technological innovation ready to go, that critical bridge between science and engineering, but the cultural matrix was not going to facilitate any mass revolution catalyzed by gains from productivity due to technology. Utopia in the pre-modern age was egalitarian primary production, not mass affluence and endless horizons of innovation and increased material wealth. Double-entry bookkeeping, the printing press and a shift toward rule of law and representative government may have allowed for technologically driven economic lift-off which reshaped our perceptions of the possible, and generated a virtuous feedback loop. It seems though today that the legal, financial and institutional scaffolding around the engine of technological innovation is possibly growing so thickly that we are in jeopardy of reverting back to the state of pre-modern economic stasis.
Addendum: Also, it seems to me that most contemporary financial “innovation” is actually just trying to extract more juice out of the orange; gains of efficiency, as opposed to ground-breaking game changers (such as double-entry bookkeeping or the joint-stock corporation). At some point when there’s no juice to be extracted you’re going to just end up redistributing the juice to the benefit of the “innovators,” if you know what I mean….


Japanese are brown-eyed a bit differently

By Razib Khan | July 20, 2009 2:52 pm

Genotyping of five single nucleotide polymorphisms in the OCA2 and HERC2 genes associated with blue-brown eye color in the Japanese population:

Human eye color is a polymorphic phenotype influenced by multiple genes. It has recently been reported that three single nucleotide polymorphisms (SNPs) within intron 1 of the OCA2 gene (rs7495174, rs4778241, rs4778138) and two SNPs in intron 86 (rs12913832) and the 3 UTR region (rs1129038) of the HERC2 gene – located in the upstream of the OCA2 locus – have a high statistical association with human eye color. The present study is the first to examine in detail the genotype and haplotype frequencies for these five SNPs in an Asian (Japanese) population (n = 523) comprising solely brown-eyed individuals. Comparison of the genotype and haplotype distributions in Japanese with those in African and European subjects revealed significant differences between Japanese and other populations. Analysis of haplotypes consisting of four SNPs at the HERC2-OCA2 locus (rs12913832/rs7495174/rs4778241/rs4778138) showed that the most frequent haplotype in the Japanese population is A-GAG (0.568), while the frequency of this haplotype is rather low in the European population, even in the brown-eyed group (0.167). The haplotype distribution in the Japanese population was significantly different from that in the brown-eyed European group (FST = 0.18915).

OCA2 & HERC2 are the loci where variation seem to be able to account for 3/4 of the variation between those with blue and brown eyes in Europe. This is obviously important for forensic anthropology. But how well do the phenotypes map back onto genotypes? It depends. With skin color various light-skinned populations have different genetic architectures. There are many ways to do the same thing, in particular if it is simply loss of function. Similarly, as per neutral theory many mutations will not have any functional effect, and rather are simply a record of population history via random genetic drift. The sequence of SNPs, genetic variants, which make out these particular haplotypes illustrate this, as brown-eyed Europeans and brown-eyed Japanese have different genetic architectures. Since the region around OCA2 & HERC2 seems to have a generalized effect on pigmentation it may not be that the differences are even neutral. Below the fold are worldwide frequencies of the different SNPs above (from HGDP selection browser):

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Genetics of taste: umami & polymorphisms on TAS1R

By Razib Khan | July 20, 2009 2:18 pm

Perceptual variation in umami taste and polymorphisms in TAS1R taste receptor genes:

A subset of subjects displays extremes of sensitivity, and a battery of different psychophysical tests validated this observation. Statistical analysis showed that the rare T allele of single nucleotide polymorphism (SNP) R757C in TAS1R3 led to a doubling of umami ratings of 25 mmol MPG/L. Other suggestive SNPs of TAS1R3 include the A allele of A5T and the A allele of R247H, which both resulted in an approximate doubling of umami ratings of 200 mmol MPG/L. We confirmed the potential role of the human TAS1R1-TAS1R3 heteromer receptor in umami taste by recording responses, specifically to L-glutamate and inosine 5′-monophosphate (IMP) mixtures in a heterologous expression assay in HEK (human embryonic kidney) T cells.

ScienceDaily has more details:

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Red Planet

By Razib Khan | July 20, 2009 3:10 am

Moon astronauts urge Mars mission:

At a rare public reunion of the Apollo 11 crew, Buzz Aldrin and Michael Collins said Mars instead of the Moon should be the focus of exploration.
Neil Armstrong, the first man on the Moon, said the race to get to the Moon had been the ultimate peaceful contest.
He said it was an “exceptional national investment” for the US and ex-USSR.
The trio spoke at an event at Washington’s National Air and Space Museum to mark the 40th anniversary of their mission.
Mr Armstrong told the audience: “It was the ultimate peaceful competition: USA vs USSR.

Apparently 4 out of 5 people alive today were not alive when the first moon landings occurred in 1969!


Your religion is false on MR

By Razib Khan | July 19, 2009 2:08 pm

Tyler Cowen gives a positive review of Your Religion is False:

In addition to its humor, I prefer the content of this book to the better-known “new atheist” tracts. Grus yields many of the strongest arguments. For instance the biographical and sociological correlates with belief (most people choose the religion they grew up with, or encountered through a friend, etc.) suggest that, in this area, intuitions which feel “certain” simply cannot be trusted.

Also see associated weblog.


Go to church & be faithful!

By Razib Khan | July 18, 2009 5:02 pm

Tom Rees has a blog post, Religion and marital infidelity, which shows that religious attendance, but not belief, correlate with a tendency to not have affairs. I think the critical point here is that religion is a complex phenomenon, and we condense many separate dimensions or parameters into one term. For example, there seems to be a tendency with higher socioeconomic status to be positively associated with religious attendance and affiliation, but negatively associated with religious beliefs.


The biological bases of behavioral variation

By Razib Khan | July 18, 2009 4:27 pm

Alex Tabarrok points me to a new paper on the effects of Toxoplasma gondii, Increased incidence of traffic accidents in Toxoplasma-infected military drivers and protective effect RhD molecule revealed by a large-scale prospective cohort study:

We confirmed, using for the first time a prospective cohort study design, increased risk of traffic accidents in Toxoplasma-infected subjects and demonstrated a strong protective effect of RhD positivity against the risk of traffic accidents posed by latent toxoplasmosis. Our results show that RhD-negative subjects with high titers of anti-Toxoplasma antibodies had a probability of a traffic accident of about 16.7%, i.e. a more than six times higher rate than Toxoplasma-free or RhD-positive subjects.

The idea of an infection resulting in behavioral changes shouldn’t be that surprising, as children we are all told about the dangers of rabies. These sorts of phenomena, whereby microorganisms hijack the behavioral phenotype of hosts shouldn’t be that surprising to anyone familiar with the manner of thinking introduced in The Selfish Gene. But there’s a difference from an idea in theory and a concrete and prevalent instantiation of that idea. Infection by Toxoplasma gondii is relatively common, but it also varies a great deal by region. The idea that some human cultural variation might be due to infection by a pathogen is likely shocking to many, but this may well be the tip of the iceberg, the effect of infection by Toxoplasma gondii seems easily measurable via reaction time.
But it also seems in relation to reaction time the effect of Toxoplasma has an interaction with Rh phenotype and varies as a function of time. The relationships are illustrated by Figure 1:

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