Monday, April 30, 2007

Genetics & Health is no more   posted by Razib @ 4/30/2007 03:46:00 PM
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Just a heads up, Genetics & Health has morphed into Eye on DNA. Update your RSS feeds!

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The evolution of gestures   posted by Razib @ 4/30/2007 03:00:00 PM
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Ape gestures and language evolution:
The natural communication of apes may hold clues about language origins, especially because apes frequently gesture with limbs and hands, a mode of communication thought to have been the starting point of human language evolution. The present study aimed to contrast brachiomanual gestures with orofacial movements and vocalizations in the natural communication of our closest primate relatives, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes)...It was found that homologous facial/vocal displays were used very similarly by both ape species, yet the same did not apply to gestures. Both within and between species gesture usage varied enormously. Moreover, bonobos showed greater flexibility in this regard than chimpanzees and were also the only species in which multimodal communication (i.e., combinations of gestures and facial/vocal signals) added to behavioral impact on the recipient.


It is important to remember that phylogeny does not always track morphology or ethology. After all, superficially dolphins and fish exhibit gross morphological similarities, and domestic dogs are the non-human species most sensitive to the cues and messages we send via facial expressions. The power of natural selection can utilize the extant genetic variation within disparate lineages and drive them toward cognate phenotypic conformations. So, I think we should be cautious about the insights that we can glean from studies of our nearest genetic relatives in regards to our own species' evolutionary history. In any case this work might be read with provisional paper on chimpanzee population substructure in mind.


Update: ScienceNow has a good summary.

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Turkey, Islam & the EU   posted by Razib @ 4/30/2007 10:16:00 AM
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A few years ago I pointed out to M. Yglesias that Turkey was more religious than the United States (he emailed me immediately and agreed that that characterization was about right). Less than a year ago I offered that Turkey was a nation with a greater percentage of Creationists than the United States, and so it was not culturally suitable for EU admission. Today M. Yglesias has a post where he suggests that the AKP, the current moderate Islamist party in power in Turkey is basically an analog to the Republican party. There are obviously differences (see Daniel Larison for more exposition), while the AKP has been from its inception (through itself proper or its predecessors) the vehicle for upwardly mobile religious conservatives, the Republican party has been transformed within the past few generations from a party dominated by elite affluent mainline WASPs to one where evangelicals call the shots (notionally at least). Nevertheless, along with Yglesias I tend to think that the rise of groups like the AKP is a good thing, even if they are regressive they accept the democratic principle and so are agents for long term (I mean generations, not years) cultural evolution. The EU agrees. But here is a paradox: I believe that genuine cultural democraticization makes it less plausible that Turkey could be an EU member because at the grassroots it is a far less European nation than its secular elite wants to project.1 And yet the same people who would wink at the idea of dividing North American between Jesusland and the United States of Canada tend to favor admission into the EU of a nation which is still mostly Allahland!

1 - Of course overall the EU been an elite pushed project, and democratic sentiment has tended to give a rubber stamp to something which was already fait accompli. With Turkey though I think this is problematic because the chasm between the alcohol drinking secular elite and Christian missionary throat cutting non-elites is pretty wide.

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Youth is wasted on the young   posted by p-ter @ 4/30/2007 09:54:00 AM
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The New Yorker has an excellent article on geriatrics and the physiology of aging, including a mention of the classic studies in C. elegans. Now I know we have some older readers, and I hope they take no offense, but I have to say, shit, getting old must really suck. And for the younger readers, we are reminded that time is short-- for the love of God, eat, drink, and screw while you still can.



Sunday, April 29, 2007

Improved assessment of national IQ   posted by the @ 4/29/2007 11:49:00 PM
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Heiner Rindermann, Relevance of education and intelligence at the national level for the economic welfare of people, Intelligence, In Press
Cognitive abilities are important for the economic and non-economic success of individuals and societies. For international analyses, the collection of IQ-measures from Lynn and Vanhanen was supplemented and meliorated by data from international student assessment studies (IEA-Reading, TIMSS, PISA, PIRLS). The cognitive level of a nation is highly correlated with its educational level (r = .78, N = 173). In international comparisons, it also shows a high correlation with gross national product (GNP, r = .63, N = 185). However, in cross-sectional studies, the causal relationship between intelligence and national wealth is difficult to determine. In longitudinal analyses with various samples of nations, education and cognitive abilities appear to be more important as developmental factors for GNP than economic freedom. Education and intelligence are also more relevant to economic welfare than vice versa, but at the national level the influence of economic wealth on cognitive development is still substantial.


Combining IQ scores with a variety of other assessments of average cognitive ability at the national level has a lot to recommend it, and I'm glad others have caught on. The conclusions are quite interesting:
The results reported here show that during the last third of the 20th century, education and cognitive abilities were more important for economic wealth than economic wealth was for education and cognitive abilities. This result is stable across the different national samples of education and ability and remains after adding additional factors like economic freedom. Intelligence is even more important for wealth than economic freedom (see also Weede, 2006)! Whereas the importance of intelligence for many personal life outcomes has been recognized for some time (Gottfredson, 2003 and Herrnstein and Murray, 1994), we should realize that intelligence is also an important determinant for the economic and social development of nations (for example the functioning of institutions in the systems of law, economics and politics). The present study shows that a high level of cognitive development can be an antecedent and likely cause for economic growth, but other macro-social outcomes (e.g., democracy, rule of law, national power or health) are likely to be influenced by education and intelligence as well (Rindermann, submitted for publication and Rindermann, submitted for publication). Certainly the positive influence of young people's schooling and intelligence on the level of economic freedom 30 years later (Fig. 4 and Fig. 5) deserves further investigation. Future theoretical and empirical research has to analyze the causal mechanism underlying the effects of ability on development of societies in a more detailed manner. For example, there is a positive relationship with low government spending ratio (r = .47 and rp = .24). Abilities seem to enable a more liberal economic constitution and thriftiness of state interventions. Conversely, a population with low education and intelligence seems to necessitate more state intervention, which tends to widen the influence of powerful special-interest groups.


So higher IQ populations tend to be more libertarian?

A re-colored version of Figure 1 -- a world map -- is below the fold.


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On words   posted by Razib @ 4/29/2007 08:38:00 PM
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Reading The Fall of Rome: And the End of Civilization made me a bit more curious about 'the Dark Ages.' So with that in mind I picked up Europe after Rome: A New Cultural History 500-1000. One page 29:
If we take a long-term perspective, however, it is clear that inherited Roman bureaucracy did not endure. To assert that it decayed would be to adapt and inappropriate narrative of 'decline and fall.' Rather, its constituent elements-documentary forms, legal norms, tax accounting, judicial and archival procedures, and so on-disaggregated and thinned out. In places-but only in some places-fragments of the once-coherent bureaucratic regime then perished. Other fragments took on a new life. Men of property freed slaves, negotiated marriage contracts, endowed churches, and arranged their testamentary bequests in formal documents....


What does decline and fall mean if not the collapse of the social order? Well, it means many things. As Daniel Larison contended in response to my previous post there was a problematic attitude amongst the older generation of classicists to idealize and world of Greece and Rome, as if nothing of greatness occurred between 476 and the Renaissance (an attitude that came to the fore, not surprisingly, during the Renaissance). So you have peculiar situations where authors can report an unending sequence of facts which suggest an epoch of relative material scarcity and decreased social complexity who just won't admit that judged by these metrics there was a downsizing.

Update: Daniel Larison has a response. Let me be clear about one thing: I do not prefer diplomatic or institutional history. Nor do I shun it. But, I am curious as someone who wants to get the richest, most multi-dimensional, perception of the past, how the "small folk" lived.

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The commonness of 40-SD events   posted by agnostic @ 4/29/2007 07:13:00 PM
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How often should we expect to observe events that are 40 standard deviations above the mean? Probably not ever. If we do observe such events more frequently than never, that may be because our initial guess was based on an incorrect model. To pick an example relevant to current events, how many people do you think you're capable of killing in cold blood -- that is, elaborately planning the set-up, commission, and aftermath? Let's assume you're a civilian, not a soldier. I'm guessing most people would say zero, with maybe 1-5% capable of killing in the low single digits, and they'd probably know the victims (e.g., jilted lover). Committing a spree shooting seems so out-there that we ought to observe such things only incredibly rarely (maybe once every 100 years?).

Yet just recently a student at Virginia Tech killed 32, and not long ago the Columbine High School shooters killed 12, and in 1966 the UT-Austin shooter killed 13 (not to mention the dozens of wounded per incident). Such shootings are of course rare, but there's "rare" and then there's rare. This means that we're probably looking at the problem the wrong way: it's likely not true that number of people you could kill is normally distributed about a very low mean (say less than 1). What could make such extreme events so common? The math here will bore those who have studied probability, but hopefully the examples will be worth reading about. And for those who haven't studied probability, this will make a nice "math for the people" intro to different types of distributions.

One easy way for extreme events to be more common than seems plausible is if several variables are involved which interact multiplicatively with each other. To understand some key differences between an additive vs. multiplicative scenario, consider rolling three 6-sided dice, each numbered 0 - 5, with each face equally likely and each die independent of the others. Suppose in Game A we record the "score" as the sum of the numbers showing, while in Game B we record their product.* The probability distributions of scores in the two Games are shown in the pictures linked to below:




We immediately see that the range of possible scores in A is far narrower than in B: 0 - 15 vs. 0 - 125, respectively. Thus, the "extreme score" is much more extreme in the multiplicative case. Importantly, the highest score in A is as likely to happen as its counterpart in B, since there is only 1 outcome out of 216 that will result in a highest score for either Game (all 5s). However, the lowest score in A is less likely to happen than its counterpart in B, since only 1 of 216 outcomes will give it in A (all 0s), but in Game B there are (1 - (5/6)^3) or about 42% of the 216 outcomes -- so, 91 outcomes (in B, just one 0 is needed for the entire score to be 0). We can thus tell that the probability distribution is symmetrical in A (like a bell curve), but highly skewed in B -- in the latter, most of the mass of the curve is concentrated at the lower values (the median is ~5). Still, the expected value is higher in B than in A (15.6 vs 7.5), due to the greater extreme values skewing the distribution in B.

To see how far off-base our thinking can go if we misjudge the way that the variables are related to the score, let's say we observed the equivalent of a score of 125. Had we assumed that the variables were contributing to the score additively, we would then say that this data-point was (125 - 7.5) / 2.96 = 40 SD above the mean! For comparison, this would be like measuring the height of a human being who was 16 feet tall. That's so rare you'd think it was a typo. However, if we paused and thought "y'know, maybe the variables interact with each other," then we might settle on the more realistic idea that such an event had a probability of 1/216 = .005. Converting this into a z-score gives 2.6 SD above the mean, which is still rare in a sense but far more modest and realistic than the erroneous estimate.

Returning to reality, in summarizing the findings of much of the creativity research, I noted that creativity or genius appears to result from the multiplicative interaction between, for instance, high intelligence, together with various personality traits like Psychoticism. This creates a skewed, log-normal distribution whereby most people don't produce anything creative enough to earn the esteem of those who matter, and a tiny handful dominate entire fields. That's why the dice range from 0 to 5 instead of from 1 to 6 in the example above: 0 is special since it indicates lack of some key trait (intelligence, curiosity, persistence, etc.).

It's conceivable that "cold-blooded homicidal output" is also log-normally distributed, with most people not killing anyone in cold blood (or at all), and a tiny few killing lots (e.g., spree shooters, serial killers, etc.). We know from the work on the MAO gene that those with "warrior genes" typically commit violence only when they treated violently during childhood, so that's at least one interaction effect, as well as the sex-by-genotype interaction; presumably there are others (perhaps being taunted frequently at school). Also, researchers in finance talk about how frequently disasterous events occur.

And on the less gruesome side, personal "allure" is probably log-normally distributed, not just because physical attractiveness is probably so distributed, but a person's demeanor animates (interacts with) their plastic form. To make this intuitively clear, model your attraction to someone according to the metaphor "to have a crush" -- consider the average person who embodies your preferences for physical attractiveness (who has traits P), and for intelligence & personality (who has traits I). Let's say that those with traits P make you weak enough to feel like you were burdened by a 10-pound weight, and that those with traits I also made you feel burdened by a 10-pound weight. Now, how much of a sinking feeling would you get if the person had it all in one package? I'd guess that you'd feel weighed down by 100 pounds, not just 20. Ah, romantic love -- one local sickness compounded by many others!

In this way, "freak" occurrences may not be so freaky after all, if the proper relationship holds between the factors that contribute to the event.

* This is not exactly the difference between normal and log-normal distibutions, since each random variable (the outcome of a particular die) isn't normally distributed but uniformly distributed. However, rather than concoct some bizarre game where the outcomes for a die are normal, I've altered some irrelevant details to convey the gist of the difference while keeping the analogy easily accessible.



Saturday, April 28, 2007

The Economist doesn't understand evolution   posted by the @ 4/28/2007 02:54:00 PM
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"Evolution and religion: In the beginning" from The Economist

One time could be an accident:
In the second camp are those, including some high up in the Vatican bureaucracy, who feel that Catholic scientists like Father Coyne have gone too far in accepting the world-view of their secular colleagues. This camp stresses that Darwinian science should not seduce people into believing that man evolved purely as the result of a process of random selection. While rejecting American-style intelligent design, some authoritative Catholic thinkers claim to see God's hand in "convergence": the apparent fact that, as they put it, similar processes and structures are present in organisms that have evolved separately.


Twice is a serious error:
But Benedict XVI apparently wants to lay down an even stronger line on the status of man as a species produced by divine ordinance, not just random selection. "Man is the only creature on earth that God willed for his own sake," says a document issued under Pope John Paul II and approved by the then Cardinal Ratzinger.


Let's be clear, "random selection" is not a short-hand for "random mutation and natural selection". If anything, "random selection" is a description of neutral evolution.

Thus, as written, I have to join the camp that believes "that Darwinian science should not seduce people into believing that man evolved purely as the result of a process of random selection" and that "the status of man as a species [is] produced by ... not just random selection". Amen!

So WTF is wrong with the editorial staff at The Economist? They don't seem to actually understand evolution. You can send them an email and explain it to them.

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Correlation and Aggregation   posted by DavidB @ 4/28/2007 05:25:00 AM
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There are many pitfalls in the interpretation of correlation coefficients. One relatively familiar one is the problem of restriction of range. To use a common illustrative example, if we take a sample of professional basketball players and calculate the correlation between their height and some measure of basketball performance, we will probably find that the correlation is weak. This does not mean that height is not an advantage in basketball: the reason for the weak correlation is that professional basketball players are a group with a restricted range of both height and basketball performance. The influence of height is therefore less conspicuous than if we took a random sample of the general population and tried them out at basketball.

The peril I want to highlight here is less familiar, and, unlike restriction of range, it tends to increase correlations. In general terms the problem arises from the aggregation of data. If data are aggregated and averaged, in some non-random way, the correlation between the resulting average values will often be higher than for the original disaggregated data, and may well increase with the level of aggregation. Suppose we take some trait in which there is a modest correlation at the individual level - say, between education and life expectancy. If now instead of individuals we take the averages for groups of individuals (for example the inhabitants of different towns, or even entire nations), and calculate the correlation between these averages, it is common for the correlation to be higher than for the individuals. It is also likely (though not certain) that as we take the averages of larger or more wide-ranging groups, the correlation will continue to increase. Correlation is essentially a way of measuring the proportion of the variability in a certain trait that can be accounted for by its association with some other trait. If we calculate the average values of the traits for wider and wider groups, the variability (technically, the variance) of the averages themselves will be reduced, because most of the random or localised influences on the data will cancel out as the groups are widened. But as the overall variance decreases, the proportion of the remaining variance explained by more general influences (which do not cancel out) is likely to increase. Technically speaking, the covariance may remain steady while the variance to be explained declines, or the covariance may decline, but the variance declines even faster.

This is all very abstract, so I will give a practical example from George Udny Yule's Introduction to the Theory of Statistics...

Yule notes that in England, according to the official agricultural statistics, there is a modest positive correlation between the yield per acre of wheat and potatoes [Note 1]. Land that is good for growing wheat is also, on average, good for growing potatoes. If we calculate the correlation between wheat and potato yields at a fairly low level of geographical aggregation - the 48 counties of England - the correlation is .2189. If we then group the counties into 24 neighbouring pairs, the correlation increases to .2963. If we further aggregate them into 12 neighbouring groups, the correlation increases dramatically (it nearly doubles) to .5757; for 6 groups the correlation is .7649, and for 3 (which Yule describes as 'the bitter end') it rises to .9902. (Though Yule does not say so, if we actually reduced the number to 2, the correlation would be 1 or -1, as an algebraic identity. Of course in this case calculating the correlation would be pointless). [Note 2]

This does not necessarily mean that other factors correlated with wheat or potato yields are disappearing as the correlation between them increases. It is possible that if we measured, say, the correlation between wheat yield and annual rainfall, the correlation (positive or negative) would similarly increase as wider areas were aggregated. When all random or local factors have been eliminated by averaging, any remaining general factors may be correlated among themselves. For example there will probably be a strong negative correlation between annual rainfall and sunshine.

Unfortunately there seems to be no general rule to predict whether, or by how much, the aggregation of data will affect correlations (except that if groups of data pairs are selected at random from the entire set of data, the correlation between the group means should be approximately the same as between individuals - see Note 3). Yule gives another example of a study where a (negative) correlation increased steadily from -.502 to -.763 when 252 geographical areas were aggregated by stages into 25, but in the same study another correlation changed relatively little, and more erratically, during the same process of aggregation.

I will not attempt to draw any practical conclusions, except to say that it is a problem that deserves to be more widely known and taken into account, especially when we find very high correlations. As Yule advises: 'What explanation we seek in individual cases depends on the individual circumstances. We can only leave the reader with the warning to watch very carefully the possibility of grouping effects, particularly in economic investigations'. Nor is the problem confined to geographical aggregation: it could apply also to grouping by social class, occupation, educational level, or any other criteria. It should not be inferred that that the correlations resulting from grouping are invalid or meaningless, just that the value of a correlation may be relative to the method of grouping. Group correlations derived at different levels of aggregation therefore cannot safely be compared. The problem is presumably well known to statisticians, and has been discussed from time to time since the 1950s, especially in economics and sociology, under the somewhat misleading heading of 'ecological correlation', but it still does not seem to be sufficiently publicised. For example, in psychometrics it could be relevant to the correlation between test results, or between test results and other criteria, such as income. This is mentioned very briefly by J. P. Guilford, Fundamental Statistics in Psychology and Education, 1950, p.355, but on a cursory search I have not found any other reference to the subject in the psychometric literature.

Note 1: examples are taken from G. U. Yule and M. Kendall, Introduction to the Theory of Statistics, 14th edition, 1950, pp.310-315. Yule distinguishes two different but related forms of the problem. In one form, which he calls the 'Modifiable Unit', the items to be correlated are inherently variable in scope, for example because they involve a measurement over a geographical area. In the other form, which he calls the 'Attenuation Effect', the ultimate units of analysis are discrete items, but the problem arises when we choose to average them and then correlate the averages.

Note 2: I assume that correlation is measured by the Pearson product-moment correlation coefficient. The correlation then equals ∑(x - Mx)(y - My)/Nσx.σy, where N is the number of paired values, and Mx and My are the means of the x and y values respectively. If there are only two x values, a and b, and two corresponding y values, c and d, the correlation comes out as (a - b)(c - d)/√(a - b)²√(c - d)². Taking positive values for the two square roots (since they represent standard deviations) the correlation will be either 1 or - 1, depending on whether (a - b)(c - d) has a positive or negative value.

Note 3: This is stated without proof by Guilford, p.216. The explanation for the result is evidently that with purely random grouping, the numerator and denominator of the correlation coefficient are both reduced in the same ratio. Suppose we divide the N individual pairs of correlated data at random into N/n groups of n pairs each. If we designate the deviation values (relative to the population mean) of one variable as a, b, c..., and the corresponding values of the other variable as A, B, C..., then the group means will be of the form (a + b + c...)/n and (A + B + C...)/n. In calculating the correlation between group means, each such pair of means must be multiplied together to give a product of the form (a + b + c...)(A + B + C...)/n². Expanding this gives a sum (aA + bB + cC... + aB + aC... + bA + bC...)/n². But except for the terms aA, bB, cC, etc, which are the products of the individual correlated pairs, the terms in this sum will total approximately to zero, since the factors in each product term are uncorrelated (having been chosen randomly). Since there are N/n groups, the total covariance will be ∑(aA + bB +cC...)/Nn, where (aA + bB + cC...) includes the contribution of all groups. This is 1/n times the covariance of the N individual pairs of data. But by a similar analysis the product of the standard deviations of the group means is 1/n times the product of the standard deviations of the individual values. The numerator and denominator in the correlation coefficient are therefore reduced in the same ratio, and the correlation itself is unaffected. There will of course be some fluctuation due to sampling error.



Friday, April 27, 2007

Intercourse and Intelligence   posted by Jason Malloy @ 4/27/2007 05:19:00 PM
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Tyler Cowen quotes from a new study testing the relationship between grades and delayed sexual activity.

Last December I passed a paper along to Razib showing that high-school age adolescents with higher IQs and extremely low IQs were less likely to have had first intercourse than those with average to below average intelligence. (i.e. for males with IQs under 70, 63.3% were still virgins, for those with IQs between 70-90 only 50.2% were virgin, 58.6% were virgins with IQs between 90-110, and 70.3% with IQs over 110 were virgins)

In fact, a more detailed study from 2000 is devoted strictly to this topic, and finds the same thing: Smart Teens Don't Have Sex (or Kiss Much Either).


The team looked at 1000s of representative teens grades 7-12 in the National Longitudinal Study of Adolescent Health and The Biosocial Factors in Adolescent Development datasets, both of which include an IQ test, and include detailed sexual experience questions ranging from hand-holding to intercourse. As with the other study there was a curvilinear relationship: students with IQs above 100 and below 70 were significantly less likely to have had intercourse than those in between. Also like the other study, they found teens with IQs ranging from 75 to 90 had the lowest probability of virginity (the authors note this is also the same IQ range where propensity towards crime peaks).



Depending on the specific age and gender, an adolescent with an IQ of 100 was 1.5 to 5 times more likely to have had intercourse than a teen with a score of 120 or 130. Each additional point of IQ increased the odds of virginity by 2.7% for males and 1.7% for females. But higher IQ had a similar relationship across the entire range of romantic/sexual interactions, decreasing the odds that teens had ever kissed or even held hands with a member of the opposite sex at each age.

While these authors leave off at grade 12th, it would seem plausible to expect that this relationship extends beyond high school. To explore this, plenty of interesting facts come from a 2001 campus sex survey by the joint MIT/Wellesley college magazine Counterpoint (PDF). Looking within and between colleges, IQ appears to delay sexual activity on into young adulthood.

By the age of 19, 80% of US males and 75% of women have lost their virginity, and 87% of college students have had sex. But this number appears to be much lower at elite (i.e. more intelligent) colleges. According to the article, only 56% of Princeton undergraduates have had intercourse. At Harvard 59% of the undergraduates are non-virgins, and at MIT, only a slight majority, 51%, have had intercourse. Further, only 65% of MIT graduate students have had sex.

The student surveys at MIT and Wellesley also compared virginity by academic major. The chart for Wellesley displayed below shows that 0% of studio art majors were virgins, but 72% of biology majors were virgins, and 83% of biochem and math majors were virgins! Similarly, at MIT 20% of 'humanities' majors were virgins, but 73% of biology majors. (Apparently those most likely to read Darwin are also the least Darwinian!)



Looking at this chart it would strongly appear that higher complexity majors contain more virgins than majors with lower cognitive demand. This paper provides me with GRE scores by academic discipline, and, in fact, the correlation between the percentage of virgins in each Wellesley major and the average 'Analytical' GRE score associated with the discipline is 0.60.

One reason we might guess that smarter people in high school, or in more challenging colleges or majors, delay their sexual debuts is because they are delaying gratification in expectation of future reward. Sexual behavior (or at least the investment needed to procure a partner or sustain one) may compete with time/resources required for other goals, and intelligent people may have more demanding goals. James Watson even hinted at this in a recent Esquire magazine piece:

If I had been married earlier in life, I wouldn't have seen the double helix. I would have been taking care of the kids on Saturday. On the other hand, I was lonely a lot of the time.

While sex may not be marriage, it may still require effort that intelligent people prefer to invest elsewhere. This would fit Aldus Huxley's alleged definition of an intellectual as a person who's found one thing that's more interesting than sex.

Another idea is that smarter people are more risk averse, and delaying these activities is a byproduct of enhanced concerns about unwanted pregnancy and disease. While not avoiding sexual behaviors, per se, they are just less likely to seek it out or consent to it for fear of the potential consequences.

Another idea is that smarter people are more religious or more ethically conservative, and are trying harder to wait for marriage to have sex.

Another idea, consistent with popular media portrayals of geeks and nerds (males at least), is that intelligent people actually want to have sex, but are simply less likely or unable to obtain willing partners because they are disproportionately viewed as unattractive or undesirable as partners.

Another idea is that intelligent people have lower general sex drives. This shouldn't be confused with the first theory, where their sex drives would be normal and they have greater self-restraint.

Some insightful digging by blogger Half Sigma into the General Social Survey, which also includes an abbreviated intelligence test, has turned up a number of associations that speak to these theories. The relationship between sexual activity and intelligence found across adolescence and young adulthood appears to continue on into adulthood proper.

Not only do intelligent people have a delayed onset of sexual behavior, Half Sigma found that they also have a lower number of premarital sex partners throughout adulthood (18-39). While this is consistent with the above theory that high IQ people are more religious and conservative, this is, of course, not true. Religiousness correlates with lower IQ, and as HS shows in the same post, intelligent people were also more likely to say that premarital sex was not immoral. (Leaving those who did think it was immoral to participate in the bulk of it!) Most of the other theories are still consistent with this finding though.

Perhaps more revealing, HS, also showed that intelligence correlates with less sex within marriage for the same age range. While still consistent with pregnancy fears and competing interests, lower sex drive seems like a better fit. In fact another revealing finding from the Counterpoint survey was that while 95% of US men and 70% of women masturbate, this number is only 68% of men and 20% of women at MIT!

Also the idea that more intelligent people are too busy for the opposite sex not just in 7th grade to college, but throughout adulthood and for their own spouse, seems unrealistic. In fact the GSS also shows (PDF) that smarter people spend more time socializing with their friends, indicating their hours aren't spent as uniquely isolated and narrowly channeled as the theory would require.

But lower sex drive and anxiety about sex's consequences can't be the whole story either. Half Sigma also showed that the smartest men in the GSS (approx. IQ >120) were also more likely to visit a prostitute. (Hardly indicative of cautiousness) This may suggest intelligent men are less able to find willing sex partners. Are smart men less attractive to women? Perhaps in some ways. For instance HS found that smart men were less likely to be athletic, and this paper shows, unathletic men and women have fewer sex partners. Athletic men, with more willing sexual partners are also less likely to visit a prostitute. Athletic activity gives men more masculine bodies, which are more attractive to women. A more masculine physique correlates with (PDF) an increased number of sex partners.

So intelligent people have lower libidos and less masculine physiques. What hormone is responsible for both sex drive and masculine builds? That's right: testosterone.

And two new papers suggest that testosterone may depress IQ. One team found that salivary testosterone levels were lower for preadolescent boys with IQs above 130 and below 70. (the same two groups most likely to be virgins in adolescence)

Another paper suggests that a gene responsible for androgen sensitivity and higher sperm counts may also create a tradeoff for intelligence.

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Genetics of speciation   posted by Razib @ 4/27/2007 11:59:00 AM
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RPM points out that the most recent issue of Heredity tackles the issue of the genetics of speciation. Here's an interesting thing I've noted, there are two ways to look at species questions. First, there are the taxonomists, who have been strongly influenced by the cladist revolution. They take a big picture philosophical view, and are obviously greatly concerned with process in terms of classification and demarcation. In contrast, there are the evolutionary geneticists who tend to be less interested in species qua species, as opposed to the process of genetic differentiation. In other words, for the latter camp species discussions are simply an ends toward elucidating the evolutionary dynamics of populations. The taxonomists in contrast are focused on species as the ends for generating their systems of evolutionary relationships. The Neandertal introgression story should make it clear I'm interested in the dynamics of evolutionary processes, not any rigorous species classification.

Addendum: Check out this review of Henry Gee's In Search of Deep Time: Beyond the Fossil Record to a New History of Life, to see what I mean about the taxonomic sensibility. A friend of mine recalls observing a woman in her lab being upbraided by a cladist at an entomological conference for practicing "un-Popperian" science.

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Hitch on Drugs   posted by amnestic @ 4/27/2007 08:19:00 AM
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Via Drug WarRant, Hitchens is playin' my tune lately:
An excerpt from his 21 Solutions to Save the World:
The largest single change for the better in U.S. foreign policy, and one that could be accomplished simply by an act of political will, would be the abandonment of the socalled War on Drugs. This last relic of the Nixon era has long been a laughingstock within the borders of the United States itself (where narcotics are freely available to anybody who wants them and where the only guarantee is that all the money goes straight into criminal hands). But the same diminishing returns are now having a deplorable effect on America's international efforts.

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Thursday, April 26, 2007

The team draft   posted by Razib @ 4/26/2007 11:10:00 PM
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Echoes of Terror Case Haunt California Pakistanis. From the article:
Lodi, a city of 62,000 people 72 miles east of San Francisco, is something of an anomaly among Pakistani immigrants. Most come to the United States to pursue professional careers, to become doctors or academics in large cities. But mainly rural peasants started coming to Lodi around 1920, and residents say 80 percent of the town's 2,500 Muslims are Pakistanis.

They came as agricultural laborers and never really assimilated, preserving their traditional ways by dispatching the young back home for arranged marriages.


I don't really need to offer further comment on this. The culture described in the article seems more reminiscent of European Islam than American Islam, except that the Pakistanis in Lodi seem more gainfully employed. In much of Europe the local Muslim community consists of a monoculture derived from peasant immigrants (e.g., the Turks in German y, the Pakistanis of northern England). In the United States Muslims are ethnically diverse and subject to selective immigration policies which skews the migration stream toward professional elites (PDF). Lodi seems to resemble Europe....

Related: You can watch the Frontline special The Enemy Within on the web. It covers the Lodi case.

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Consciousness Catch-22   posted by amnestic @ 4/26/2007 10:38:00 PM
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I was listening to a lecture by Christof Koch this morning, and I had a thought that I haven't come across before regarding consciousness studies. There may be a very high technical bar for ethical studies into the nature of consciousness, higher than I expected before.My issue may just be the stretchiness of the term 'consciousness', but there might be something of substance in here too. Can we study anything besides humans in order to understand consciousness? If not, then we have to have safe temporary ways to manipulate consciousness in humans, which would mean safe, temporary ways to control neurons in humans. We won't have that for a long time. By the way, I'm not talking about being awake or asleep. I'm talking about a more important type of consciousness. This type:
Are the "pains" that usefully prevent us from allowing our limbs to assume awkward, joint-damaging positions while we sleep experiences that require a "subject" (McGinn, 1995), or might they be properly called unconscious pains? Do they have moral significance in any case? Such body-protecting states of the nervous system might be called "sentient" states without thereby implying that they were the experiences of any self, any ego, any subject. For such states to matter -- whether or not we call them pains or conscious states or experiences -- there must be an enduring, complex subject to whom they matter because they are a source of suffering.

Akbar Ganji says suffering is the source of rights. I think that's simplistic, but it might be some part. My basic point is this: If non-human primates can do consciousness-like things that are worth studying, then wouldn't it be unethical to experiment on them? If consciousness is the substrate for suffering and suffering is the source of rights, wouldn't they have rights like us? I'm not saying that they do have the capacity for suffering, but if they don't, then they might not be worth studying for consciousness anyway.

In other parts of that Dennett essay I quoted above, he notes that outward behavior isn't a good indicator of suffering in the morally meaningful sense. We can see an earthworm writhe and be unconcerned. So if we can't tell if anything is capable of suffering, maybe its not the best line to use for choosing ethically in animal research. A lot of times when I'm thinking about people trying to free chimps or things in that vein I think "That chimp would rip you limb from limb if it got the chance." I really don't think a chimp would have any qualms about drilling a hole in your head and inserting electrodes if it new how. I guess what I'm thinking is that maybe its okay not to show so much consideration because they certainly wouldn't show you any. If we were going to grant chimps human rights, wouldn't they need to take responsibility and act like they deserve it?

Just a couple things I was thinking about. I thought it might be really interesting if a consciousness researcher managed to prove that the research he was doing was unethical.

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How the Sabians saved civilization?   posted by Razib @ 4/26/2007 09:17:00 PM
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Reading The Later Roman Empire, 284-602: A Social, Economic, and Administrative Survey I stumbled upon this on page 939:
...In some places paganism survived the Arab conquest. in 830 the people of Carrhae [modern day Harran], a city always notorious for its devotion to the old gods, were threatened with massacre by the Caliph unless they abandoned their religion for Islam or one of the tolerated faiths and only saved themselves by profession themselves to be Sabians. To this day the heretical sect of the Nusairi in the mountains between the upper Ortones and the sea profess doctrines which clearly derive from the Neo-Platonic paganism of the later empire....


The "Nusairi" refers to the Alawites, a heterodox marginally Islamic sect whose claim to fame lay in its control of the modern day state of Syria. I had long known of the late paganism of Carrhae. In other cities where paganism was vital and dominated civic life during the 6th century the Byzantine Emperors employed the force of arms to destroy the temples and crush public sponsorship of non-Christian piety (Gaza, Heliopolis, etc.); the religious life of Carrhae was protected in part by its closeness to the Persian Empire. Some of the philosophers scattered after the closing of the Academy eventually settled in Carrhae, which in some ways resembled a time capsule that had preserved the sensibilities of pagan late antiquity, where the astral cults reigned supreme over a latitudinarian religious culture.


In any case, reading up on the Sabians I am not convinced of a direct connection between this group and the Alawites. Though we must classify and demarcate religious sentiments as if they stand alone, we intuitively understand that a system of beliefs are affected by the Zeitgeist. Carrhae was dominated by Sabians until 1050, when Muslims took over the city (the Sabians were found in nearby areas for several centuries until the Mongol invasions, their folkways are attested by Maimonides). This is approximately the period when many of heterodox Islamic and post-Islamic sects arose, the various Ismaili groups, the Druze and the Alawites & Yezidis. It stands to reason that the Sabians might have influenced the thinking of many of their neighbors because they were a prominent community. Similarly, the Sabians themselves emerged out of the substrate of the northern Levant and upper Mesopotamia, so the similarities between modern groups like the Alawites and the medieval Sabians might simply be due to the fact that they share the same mix of cultural preconditions.1

But my interest in the possibility that the Alawites descend from the last pagan remnants of antiquity in the east disappeared when I read about Thabit ibn Qurra, the most prominent of the Sabians. He was an "Arab" astronomer and mathematician, and one of the heads of the famous House of Wisdom. Some cursory searching on Google Books implies that he was not an anomaly, the Sabians were well represented amongst the translators who mediated aspects of Greek learning and made it accessible to the Arab Islamic world.

Why is this relevant? One of the historical myths of our era is that the Arab Muslim saved the Greek achievement for Western civilization. The argument is that there runs a line of tradition starting during the Greek Classical period down to the modern post-Enlightenment era which was preserved by the efforts of the House of Wisdom. This is false insofar as the Byzantines also transmitted Greek works to the West, and the refugees who washed up on the shores of Italy during the late medieval period as Constantinople fell before the Turks helped spark the Italian Renaissance. But the Byzantine role is not sexy because it doesn't serve a multicultural narrative (before the contemporary period the emphasis placed upon Islamic civilization's role in preserving Greek learning was used as a cudgel against Western Christianity). And yet an important fact about the House of Wisdom is that it was a multicultural affair, and that during the early phases most of the work was in the hands of multilingual dhimmis, who were after all in a position to know Greek and Arabic. Though I had known of the role of Nestorian Christians, the Sabians' part was somewhat of a surprise (I was to understand that some of the translators were pagans, but I had not known that that was a synonym for Sabians from Carrhae). Now, unlike Christians or Muslims, I think one might contend that the Sabians of Carrhae had less ambivalence toward the Greek pagan heritage, after all, their culture was a descendant of one that had sheltered the last of the Neo-Platonic philosophers. I am therefore inclined to wonder if the Sabians in particular were a vector for preserving and promoting the rich intellectual tradition which stretched back to the pre-Socratics? I will have to look into this hypothesis (I'm skeptical actually).

On a broader theoretical level I am curious about the role that small cultures like the Sabians play in the dynamics of cultural and civilizational change. Carrhae remained a pagan stronghold because of an accident of geography, its strategic position near the border with Persia and the protection offered by the Shah resulted in the preservations of its peculiar civic paganism in the face of an aggressively Christianizing empire. Though a man of Carrhae could never hope to be great in imperial service without baptism, if one wanted to be a man of standing and influence within one's own community then pagan profession was necessary so that one could partake of the communal sacraments. The forcible destruction of these sacraments in other pagan cities destabilized this social equilibrium and the result was inevitable Christianization as local elites defected from a religious cult which no longer accrued prestige but was a universal liability.

But though this was the proximate dynamic which led to Carrhae preserving its pagan character, I am offering here the possibility that this might have had a long term ultimate impact of serving as a major conduit for the thought of late antiquity down to the Islamic period. If Carrhae had not preserved its unique culture no doubt the Nestorian scholars of the House of Wisdom would have done their fair bit of translation, but one wonders what the Muslims might have overlooked? This is not to say that Carrhae was a font of rationality and wisdom, many would characterize late Neo-Platonism as a debased supernatural cult with only the faintest philosophical touches. But, just as Hinduism has under its broad umbrella primitive devotionalisms and rarified Avaita Vedanta, so late classical paganism spanned the gamut. In contrast, one might contend that the rise of Christianity and Islam resulted in a constraining of the avowed beliefs of the elite
, a homogenization of the complexities of the late antique intellectual landscape. During the centuries after the rise of Islam perhaps Carrhae served as a reservoir of intellectual diversity? Do microcultures play the same role within the matrix of other homogenizing macrocultures?

1 - This region was the meeting place of Greek, Arab, non-Arab Semite, Armenian, Persian and Kurd, to name a few. There were also variations within this region, Syria had a far stronger Greek presence than northern Mesopotamia, which had an elite Syraic speaking culture. In any case, the presence of deep rooted Astral cults seems universal. I once read that the Ottoman sultan once made progress through a Kurdish town where the residents worshiped the sun. The sultan was angered by this paganism, and eventually the residents were taken under the wing of the local Jacobite bishop. This is very similar to the story of caliph Al-Ma'mum forcing the residents of Carrhae to choose a protected religion, so I am not sure if these incidents are necessarily true, as opposed to repeating a common motif.

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Voles getting around   posted by p-ter @ 4/26/2007 04:38:00 PM
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A follow-up on the vole/monogamy/vasopressin story has just been published in Trends in Genetics. A quick summary of the relevant information:

1. Prarie voles are socially monogomous (note the qualifier "socially". Genetics suggests a certain amount of "infidelity", if one can call it that in voles). Meadow voles are not.

2. There is a regulatory region upstream of the vasopressin receptor that carries a "short" allele in meadow voles and a "long" allele in prarie voles.

3. In vitro, the long and short alleles have higher and lower expression, respectively, of vasopressin.

4. When the prarie vole allele is transformed into meadow voles, there is as marked increase in pair bonding[cite]

5. Within prairie voles, different allele lengths are associated with pair bonding and vasopressin receptor distribution [cite]

This is a fascinating story, and many people, including the authors of the above papers, hypothesized a sort of single "switch" for monogamy in mammals. However,

6. Many non-monogamous species have "long" alleles [cite]

This, then, refutes the possibility of a single genetic switch controlling monogamy in mammals. The response just published in TIG accepts that, but argues against rejecting a role for vasopressin recepter variability in pair-bonding and other social behavior. I agree. The previous studies are quite convincing that such a role does exist (see in particular the experiments in the papers cited in points 4 and 5), and more detailed study of the vasopressin receptor locus is certainly justified.




Epigenetics News on 'epigenetics'   posted by amnestic @ 4/26/2007 03:16:00 PM
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Trevor at Epigenetics News follows up on our recent discussions about the term's increasing popularity. He's cites several good reasons why we might expect to see the term more often, and one reason that may not be all that good:
With all of these high profile and highly funded areas becoming closely associated with epigenetics, is it any surprise that more researchers are finding ways to include their focus as part of "epigenetics"?

If a large enough portion of researchers stretch the word to apply to their topic of interest eventually 'epigenetics' will just mean 'biology'.

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Hitchens on religion   posted by p-ter @ 4/26/2007 07:34:00 AM
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I haven't read any of the books carrying the torch for the "New Atheism", but I dig Christopher Hitchens's style, maybe I'll make an exception. Slate has published an excerpt from his forthcoming book, God is Not Great.

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Why is so much biological research centered on genes and DNA?   posted by the @ 4/26/2007 01:00:00 AM
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You'll find one professional's answer below the fold. What's missing is a discussion of genes as replicators.


from the SEP - Molecular genetics:

In official and public contexts, scientists appeal to the fundamental theory associated with molecular genetics to justify centering research on genes and DNA (e.g., see the websites of funding agencies such as National Center for Biotechnology Information). Genes are typically referred to as “the fundamental units” that are responsible for guiding all basic life processes. Usually a combination of causal and information metaphors are invoked to explain the role of genes. Genes are said to produce RNA and polypeptides, to provide instructions, or direct processes. But philosophical investigation has shown that these kind of sweeping claims cannot withstand careful scrutiny. Why, then, is so much research centered on genes and DNA? One answer to this question is that biologists are blinded by an ideology of genetic determinism. But Wagner's defense of gene centrism suggests another answer, an answer that resonates with Keller's explanation (2000) of why gene talk is useful.

It has been proposed that the real reason biologists center attention on genes and DNA is that genes are difference makers that can be used to trace and manipulate a broad range of biological processes (Waters 2004a and 2006). This scientific practice makes sense independently of any fundamental theory associated with molecular genetics. In the case of molecular genetics, it is investigative pragmatics, not fundamental theorizing, that drives scientific research. The basic theory suffices to explain the investigative utility and results of gene-centered approaches. The fundamental theory is, in an important sense, epiphenomenal with respect to the design and implementation of gene-centered research. On this view, the role of the fundamental theory should be understood in Latourian terms (1987, 1988), as a platform for rallying the troops and bringing resources to research endeavors. The design of the laboratory experiments and the reason why the experiments work, can be explained in terms of broad investigative strategies, the basic causal theory of molecular genetics, and the details of the experimental contexts.

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Earwax and breast milk   posted by the @ 4/26/2007 12:57:00 AM
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Miura, Yoshiura, Miura, Shimada, Yamasaki, Yoshida, et al. A strong association between human earwax-type and apocrine colostrum secretion from the mammary gland. Human Genetics.

Here we provided the first genetic evidence for an association between the degree of apocrine colostrum secretion and human earwax type. Genotyping at the earwax-type locus, rs17822931 within the ABCC11 gene, revealed that 155 of 225 Japanese women were dry-type and 70 wet-type. Frequency of women without colostrum among dry-type women was significantly higher than that among wet-type women (P < 0.0002), and the measurable colostrum volume in dry-type women was significantly smaller than in wet-type women (P = 0.0341).


Related from Razib: Here are two posts from me on earwax distributions worldwide.

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Wednesday, April 25, 2007

A good heart of ren   posted by Razib @ 4/25/2007 10:58:00 PM
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GNXP commenter Mencius has a blog. As you might expect, more think than link!

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PKM Zeta on This American Life   posted by amnestic @ 4/25/2007 12:57:00 PM
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The new Showtime version of This American Life has a segment featuring Todd Sacktor and Andre Fenton. They published a remarkable paper (discussed on gnxp) last year showing that specific inhibition of PKM Zeta (a consitutively active version of protein kinase C) can erase memories. This is all in rats of course. So if you have Showtime, it'll air tomorrow night, Thursday the 26th.

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ScienceBlogger threatend with legal action   posted by Razib @ 4/25/2007 11:17:00 AM
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Final Update: Victory Day! In response to Shelley's request I've removed the text of the original email.


A fellow ScienceBlogger has been threatened with legal action for reproduction of figures. Obviously we post figures here on this weblog pretty frequently. It isn't to screw over the companies doing the publishing from making profits, we just want to talk science. We don't repost whole papers. It seems highly likely no one who sees the figures on our weblog is going be disinclined then to buy the article if it piques their interest (more likely they'll go to the local university library). Instead, we're giving free publicity to the journal in question. So is what was done fair use or not? Honestly, I don't care too much, it seems that they just wanted the bad publicity/review to go away. So I say give them more! Here is the text of the email:

[removed]

Addendum: Thinking about it more, I wonder what percentage of sales massive academic publishers make via the "buy this article" option which pops up when your institution doesn't have access? My own hunch is that very few people go this route, but rather will simply ask the researcher in question for a reprint/PDF if it is of particular academic interest. From a sales perspective I can't believe that reproduction of figures would in any way diminish the interest of an individual in a paper or article. Rather, it is more likely to increase interest (i.e., whetting appetite). So even assuming that the email Lisa Richards sent was defensible on legal grounds it doesn't seem to make much business sense to take up time doing something like this. Unless of course, as I noted above, the main motive was just to squelch some negative publicity.

Finally, I don't want to give the impression that bloggers have a carte blanche to say or do whatever they want to on the web. But, that being said, when someone to whips out the law as a cudgel against discussion of a topic, they should know that if the cause is unjust they'll be blog-mobbed.

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Breaking: People are different   posted by p-ter @ 4/25/2007 10:10:00 AM
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Heredity has a summary of a study on the genetics of gene expression differences between European and Asian populations (which I summarized here). The opening lines are a striking glimpse into the academic world:
It has often been observed that people are different. Indeed, some observers have gone further to suggest that this diversity exists between people from different parts of the world, or of different ethnic groups, and it is hereditary. This latter observation has led to a certain amount of contention over time. As a result, many geneticists have been wary about asserting that such differences exist.
That's right, it's contentious to say that the "diversity" we are all so fond of might have some relation to genetic diversity, something that is patently obvious given a basic knowledge of evolutionary processes and a pair of eyes.

But whatever, it's a good summary of the research, though I must take issue with the argument that gene expression variation between individuals may have no effect on phenotype:
[W]hile the exact numbers of differences could be debated, the data at least suggest that there should be considerable variation in actual humans. But, does this matter? One problem with establishing the importance of microarray results is that they only tell about gene expression, not about the physiological effects of the gene. Earlier studies on the dynamics of metabolic pathways have shown that fluxes through the pathways may be relatively insensitive to changes in the concentration of many of the enzymes in a pathway
...
Overall, it is not clear how the variation in gene expression relates to phenotype, and fitness
This shows a striking lack of familiarity with studies on the evolution of gene expression. Where it has been well-studied, it's clear that gene expression levels are under strict control-- they are under strong negative selection and do not vary neutrally[1]. This implies, of course, that changes in gene expression have an effect on fitness (though it's true the precise effects of individual genes are mainly unknown). Changes in gene expression levels are very likely to have some sort of phenotypic consequence.

[1] Citations: For a meta-analysis of gene expression evolution in a number of organisms, see this paper, which concludes "Our analyses used a number of metrics to show that most mRNA levels are evolutionary stable, changing little across the range of taxonomic distances compared. This implies that, overall, widespread stabilizing selection on transcription levels has prevented greater evolutionary changes in mRNA levels."

A more rigorous look at changes in gene expression in Drosophila concludes, "Although spontaneous mutations have the potential to generate abundant variation in gene expression, natural variation is relatively constrained". In C. elegans, as well, a similar study to that done in Drosophila concludes, "We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences."

These studies have all looked at broad evolutionary patterns; some researchers are now able to look at the evolution of gene expression globally while making inferences about individual genes. For example, this study in humans identifies a number of genes whose expression has evolved rapidly in humans, as well as a number whose expression levels appear to be stable.

Overall, to imply that genetic differences between populations, which then translate into gene expression differences between populations, have no effect on phenotype or fitness is naive at best.

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Small planet!   posted by Razib @ 4/25/2007 09:21:00 AM
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Check out these two posts on the extrasolar planet. I remember reading as a kid a short Poul Anderson essay on "how to design a habitable planet" (for a science fiction story).

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My Wikiddiction   posted by Razib @ 4/25/2007 02:07:00 AM
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Of late I have been leaving my laptop behind and taking my books to coffee shops to get my reading done. The reason is simple, I have a compulsive tendency to look up data on references made within the text of any book. For example, if there is an offhand reference to the Dual Monarchy of Austria-Hungary, I have to look it up so I know more about it. I probably do this sort of thing around two times per page, and the discontinuity it generates is a real bother. When reading material on the internet, in particular Wikipedia entries, I have to make an effort not to click illuminating links precisely because I know that within a few minutes I'll have become snared in a whole new tangle of facts. I assume I'm not the only one....

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Tuesday, April 24, 2007

Population genetics of a deletion   posted by p-ter @ 4/24/2007 09:41:00 PM
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When we talk about genetic variation between populations, most of the time we're referring to SNPs or other "simple" polymorphisms, mostly because that's what we have data on. Detailed population genetics studies of copy number variants are just starting to appear; this paper is one of them. It's an anlysis of the frequency of a deletion of the gene APOBEC3B, involved in immunity to retroviral infection. As you can see in the map below, the gene is present in most people of European and African descent, but is missing in a significant fraction of Asian and Native American populations. Nothing revolutionary here, but expect more studies of this sort in the future.

ADDENDUM: I hasten to add, lest RPM read this post, that when I say these studies are starting to appear, I'm speaking about these sorts of studies in humans. In Drosophila, large deletions and inversions are the classic genetic polymorphisms used in population genetic analyses (due to their easy visibility in polytene chromosomes).

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Against Evo Devo?   posted by Razib @ 4/24/2007 11:58:00 AM
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A new paper in Evolution, THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION.
An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes...Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.


One of the coauthors, Jerry Coyne, has taken aim at evo devo before.

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Monday, April 23, 2007

The adaptiveness of religion   posted by Razib @ 4/23/2007 11:27:00 PM
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I have a long post on my other blog about the reality that in I believe religion must be analyzed at different levels of organization. On the one hand, religious beliefs must be "fit" in the context of what representations our minds can accept, find plausible and memorable. But higher up the chain of organization religion can play a utilitarian role in demarcating and differentiating social groups. The relationship between these two levels is fleshed out in more detail in the post. Below the fold I've placed a list of my main posts on religion over the past year....



The nature of religion and Breaking the Spell
Modes of religion
Who Dan Dennett think he be foolin'?
An evolutionary anthropology of religion
God lives, deal with it!
Belief & belief in belief
Logical consistency is irreligious
God & morality
Are people naturally religious? Yes....
The round-eyed Buddha
Nerds are nuts
Atheism, Heresy and Hesychasm
The God Delusion - Amongst the unbelievers
Innate atheism & variation across societies
"Hard-wired" for God
Buddhism, a religion or not?
Why do people believe in God?
Is religion an adaptation?
Theological incorrectness - when people behave how they shouldn't....sort of
The gods of the cognitive scientists

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Religion-normed   posted by Razib @ 4/23/2007 11:20:00 PM
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I have said many times that phrases like "moderate Muslim" must be normed to the distribution of attitudes amongst Muslims. To be in the moderate/median central region of the distribution of Islamic beliefs is not the same as being in the moderate/median central region of the distribution of Christian beliefs. I have made it pretty obvious that over the years I have come to the conclusion that selection, so to speak, will probably eventually shift the Muslim median religio-phenotype closer to the Christian one. That being said, Ali Eteraz pointed me to an interesting site, Apostasy and Islam - 100+ Notable Islamic Voices affirming the Freedom of Faith. On the one hand, it is a good thing that there notable Muslims who agree that it is not acceptable that those who disavow the Islamic religion are subject to the death penalty, at least de jure, in much of world. But, the fact that 100 scholars need to be firm and vocal on this issue tells you about the "state of Islam".

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Darwinism & conservatism   posted by Razib @ 4/23/2007 10:56:00 PM
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An AEI event, Darwinism & Conservatism, May 3rd in Washington DC. John Derbyshire will be there.

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Conservation of expression in human and mouse brains   posted by p-ter @ 4/23/2007 05:01:00 PM
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Speaking of human brain evolution, PLoS Genetics gives us this, "Conservation of Regional Gene Expression in Mouse and Human Brain":
Here we compare gene expression profiles of human motor cortex, caudate nucleus, and cerebellum to one another and identify genes that are more highly expressed in one region relative to another. We separately perform identical analysis on corresponding brain regions from mice. Within each species, we find that the different brain regions have distinctly different expression profiles. Contrasting between the two species shows that regionally enriched genes in one species are generally regionally enriched genes in the other species. Thus, even when considering thousands of genes, the expression ratios in two regions from one species are significantly correlated with expression ratios in the other species. Finally, genes whose expression is higher in one area of the brain relative to the other areas, in other words genes with patterned expression, tend to have greater conservation of nucleotide sequence than more widely expressed genes. Together these observations suggest that region-specific genes have been conserved in the mammalian brain at both the sequence and gene expression levels. Given the general similarity between patterns of gene expression in healthy human and mouse brains, we believe it is reasonable to expect a high degree of concordance between microarray phenotypes of human neurodegenerative diseases and their mouse models. Finally, these data on very divergent species provide context for studies in more closely related species that address questions such as the origins of cognitive differences.
Long story short-- the human brain is not some freak/miracle; studying mouse brains will be worthwhile as a tool for understanding human brains in general. This is also a step towards understanding what exactly it is that makes a human brain so different genetically from a mouse brain-- which developmental pathways have been altered, which parts of the brain most diverged? Previous studies of gene expression evolution have treated the "brain" as a single organ; now we can get in at its finer details.

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Human Brain Evolving   posted by Razib @ 4/23/2007 04:03:00 PM
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For anyone around Bloomington, there's a symposium Human Brain Evolving, this Friday and Saturday. You can see the abstracts online. Looks like Bruce Lahn will be there. If anyone wants to send me a "report" after attending just use the contact drop down to the right and I might post it.

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Sunday, April 22, 2007

Homo urbanis   posted by Razib @ 4/22/2007 11:33:00 PM
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PNAS has a paper titled Growth, innovation, scaling, and the pace of life in cities, which notes that a majority of humans now live in cities. I know that historically cities were a population sink (and only a small minority ever did live in cities), but, I have to wonder what evolutionary implications the normativeness of city life will have on our species over the next few hundred years (assuming some sort of collapse or explosion doesn't make the idea of humanity irrelevant)? I say this because I suspect that the transition from hunter-gatherer to "dense" village living was highly significant (as illustrated by the mass disease die off in the New World when exposed to the Eurasian pathogen pool). Robin Dunbar's work suggests that our cognitive social intelligence doesn't scale up much past around 200 individuals. Villages aren't necessarily that much more populous than this, but cities are.

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Against Universal Grammar   posted by Razib @ 4/22/2007 04:46:00 PM
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To all those with some familiarity with psycholinguistics, what do you think about The New Yorker by John Colapinto, The puzzling language of an Amazon tribe? What are the best commentaries on this thesis? My interest has been piqued, but I'd like to know more (here's an article on the tribe in question, and check out the wiki entries).

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Validity of national skin color-IQ   posted by the @ 4/22/2007 10:36:00 AM
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We previously reported that a measure of school achievement built from national test scores has a nearly perfect correlation with national IQ (at least in the range of scores tested). Subsequently, Lynn et al. (in press) published a very similar analysis:
This paper examines the relationship of the national IQs reported by Lynn & Vanhanen (2002, 2006) to national achievement in mathematics and science among 8th graders in 67 countries. The correlation between the two is 0.92 and is interpreted as establishing the validity of the national IQs. The correlation is so high that national IQs and educational achievement appear to be measures of the same construct. National differences in educational achievement are greater than differences in IQ, suggesting an amplifier effect such that national differences in IQs amplify differences in educational achievement. Controlling for national differences in IQ, slight inverse relationships of educational achievement are observed with political freedom, subjective well-being, income inequality, and GDP. However, public expenditure on education (as % of GDP) was not a significant predictor of differences in educational achievement.


The IQ's Corner blog has an interesting note about forthcoming commentary.

On a related note, recall that Templer & Arikawa (2006) reported a near perfect environmental correlation between national skin color and national IQ for old-world countries. An unfortunately confused commentary by Hunt & Sternberg accompanied the publication. They wrote: "We argue that the report by Templer and Arikawa contains misleading conclusions and is based upon faulty collection and analysis of data. The report fails to hold up for quality of data, statistical analysis, and the logic of science." The criticisms by Hunt & Sternberg are based largely on a misreading of Templer & Arikawa's methods, particularly the method for deriving national skin color values.

A paper published in 2000 by Jablonski & Chaplin ("The evolution of human skin coloration") can more directly address these criticisms. Jablonski & Chaplin published a table of skin color reflectance values from many old world populations (Table 6, also see the appendix). I very crudely averaged values from the same country to make a new measure of national skin color. This measure of national skin color correlates with the skin color index of Templer & Arikawa at r=-.91 (the negative is not important here). The reflectance measure of skin color correlates with national IQ at r=.87. The school achievement measure of Lynn et al. correlates r=-.79 with the skin color index of Templer & Arikawa and r=.75 with the skin color reflectance values crudely averaged from Jablonski & Chaplin. Thus, the skin color values derived by Templer & Arikawa are well validated by an external data source and the national IQ-skin color relationship is found to be robust across two measures of national IQ and two measures of national skin color.

Note that there are substantially more missing values in the school achievement and skin reflectance data sets (no imputation of missing values) with missing values skewed towards lower values of national IQ/school achievement and darker skin colors. Also note that the blind averaging use on the skin reflectance data most likely attenuates the correlations.

Templer & Arikawa had two abstracts at the 2006 ISIR conference, which provide additional support for the validity of the measures and their relationships:

source

Correlations of Skin Color and Continent with IQ
Donald I. Templer & Hiroko Arikawa

The present study determined (1) the correlations between skin color and IQ across the countries of three different continents; and (2) the correlations of both skin color and continent in the three pair combinations with the three continents. The product-moment correlations between IQ and skin color were -.86 across the 48 African countries, -.55 across the 48 Asian countries, and -.63 across the European countries. When the 96 countries of Africa and Asia were combined skin color correlated -.86 and continent correlated .75 with IQ. The respective correlations were -.97 and .89 across the 81 countries of Asia and Europe, and -.71 and .54 across the 81 countries of Europe and Asia. In multiple regression continent yielded minimal increment to skin color in predicting IQ. In an earlier study (Templer & Arikawa, 2006a) skin color correlated more highly with IQ than racial category, but racial category yielded greater increments in multiple regression than did continent in the present study. The present findings, combined with previous research relating skin color and IQ (Templer &amp;amp;amp;amp;amp;amp; Arikawa, 2006a; 2006b), indicate that skin color is a robust correlate of IQ in an international perspective.


Empirical Support for Rushton's K Differential Theory
Donald I. Templer & Hiroko Arikawa

The purpose of the present study was to empirically substantiate Rushton's Differential K Theory that purports that groups of persons with K (in contrast to r) characteristics have a life history and reproductive strategy that includes higher intelligence, less reproduction, less sexual activity, better care of offspring, lower birth rates, greater life expectancy, better impulse control, and greater social organization. The present research intercorrelated national mean IQ, infant mortality, HIV/AIDS rates, birth rates, prevalence rates, and life expectancy in 129 countries in Africa, Asia and Europe. All of the correlations were substantial and in the expected direction. Also supportive of Rushton's theory is that there was only one factor which accounted for 75% of the variance and was labeled "K-r continuum." All five variables were correlated with an economic variable (per capita income) and a biological variable (skin color, which correlated highly with intelligence in previous research). Skin color correlated more highly with all five variables than per capita income so as to support the contention of Rushton that this continuum is biologically based. Factor analysis with all seven variables yielded one factor that accounted for 73% of the variance.

Jason Malloy adds: Templer & Arikawa's research follows Lynn and Rushton in arguing that cold temperatures were a significant force in the evolution of human race differences in intelligence. I have stated some problems I find with this hypothesis here, although it is also largely consistent with the geographic distribution of global populations by IQ. A recent analysis by blogger Audacious Epigone adds yet another revealing data point to this association.

Latitude (and hence colder climate) is associated with IQ not only cross-nationally (.67) but within the US as well. AE found a correlation of .70 between his measure of state IQ and the latitude of the most populous city in each of the 50 states. Furthermore intelligence is associated with latitude equally for both US whites and blacks (.52 and .51).

It's not immediately apparent if and how this association is genetic or environmental. Either way it seems fair to seriously consider that global warming will provide yet another detrimental negative pressure on the intelligence of human populations in the coming decades.

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Saturday, April 21, 2007

HIV in Africa   posted by Razib @ 4/21/2007 01:29:00 PM
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Recently I stumbled upon this story, Speeding HIV's Deadly Spread: Multiple, Concurrent Partners Drive Disease in Southern Africa, via Radio Open Source. The important point is that one of the major variables in the spread of HIV in Sub-Saharan Africa is the nature of sexual networks (it shouldn't be too hard to imagine that social network theory models this well). From the article:
Researchers increasingly attribute the resilience of HIV in Botswana -- and in southern Africa generally -- to the high incidence of multiple sexual relationships. Europeans and Americans often have more partners over their lives, studies show, but sub-Saharan Africans average more at the same time.
...
...Husbands spent months herding cattle while their wives, staying elsewhere, tended crops, Mosojane said. On his return, a husband was not to be quizzed about his activities while he was away. He also was supposed to spend his first night back in an uncle's house, giving his wife time to send off boyfriends.


Steve Sailer has long been emphasizing the low paternal investment that African males engage in as part of the problem. Without a consistent and reliable single male to supplement her own economic productivity (in much of Africa women were the primary agricultural producers) it seems that it would be rational to "diversify" one's portfolio. This is obviously not the only issue, the variation in HIV infection rates across the continent which track circumcision rates show that the dense sexual networks facilitate the spread of the virus at different rates depending upon the nature of the "choke points" (so to speak).

Note: The report suggests that circumcision was discouraged by European colonial missionaries in southern Africa. I'm skeptical of this for several reasons. First, during much of the colonial period circumcision was the norm in England, which was the dominant power in this region. Second, colonial influence seemed to be irrelevant in most of east & west Africa, where the rates of the practice follow traditional patterns. There is one group in Kenya that does not practice circumcision (unless, I assume, they are culturally Muslim, such as Barak Obama's father), the Luo. Is it because they were less colonized than other ethnic groups? I doubt it. Finally, I am to understand that Zulus circumcision specifically ended due to the command of the warlord Shaka. This predated colonization or missionaries. So, I think it is important not to take all the contentions in the article without a grain of salt since the reporter is obviously dependent on sources who will tell him whatever they want (i.e., I think the idea that circumcision was discouraged by whites is probably plausible because of the dominance of Post-Colonial theory which makes Europeans gods who have ultimate power over the direction of all the world's cultures).

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Information-rich podcasts   posted by amnestic @ 4/21/2007 12:25:00 PM
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Doing dissections is boring. Learning about international politics while doing dissections is less boring. Hence, I recommend checking about the Carnegie Council for Ethics in International Affairs podcast. Here's a list of more educational podcasts from Big Monkey, Helpy Chalk, including a conference on Neural Correlates of Consciousness.

On a less nerdy tip, these mixes by siik are dope. And the Mixtape Show... Wack Shit - Not Allowed. Ever.




Refugia & demographic history   posted by Razib @ 4/21/2007 12:10:00 PM
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John Hawks has a long interesting post on the possible phylogeographic impact of Ice Ages and Interglacials upon Neandertal demographics. I believe John had earlier posited that worldwide variations in long effective population size might generate the differences in genetic diversity across modern human populations.

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Journal questions   posted by Razib @ 4/21/2007 02:26:00 AM
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If I were to add 5 cognitive science journals and 5 history journals to my RSS/reading list, which ones would they be? The only cognitive science journal I'm familiar with is Cognition.

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Alleles on the move?   posted by Razib @ 4/21/2007 01:03:00 AM
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Hsien Hsien Lei reports on an interview in the May/June issue of Stanford Magazine with L.L. Cavalli-Sforza:
...A major genetic change which started already some centuries ago, with the navigation of the oceans, and is becoming faster now, is globalization. This is having major genetic consequences. It will bring back greater unity of the species, by diluting and eventually canceling differences among ethnic groups existing today, that are largely if not exclusively the consequence of adaptation to environments that differ most climatically to which modern humans spread in the last 50,000 years....


One of the novel insights of the field of human genomics is that universal selection pressures have resulted in alternative genetic responses to converge upon the same phenotype. For example, the light skin of East Asians & Europeans are independent derivations from the darker skinned ancestral type, and the genetic architecture of the trait attests to this. Now, the extent of intergroup admixture today is actually very modest, after all, very little European specific genetic material is entering the populations of China or South Korea! Nevertheless, in places like the United States widespread admixture between Europeans & East Asians is occurring, so you have the confluence (collision?) of genetic architectures which emerged in parallel meeting their "other half" for the first time. Since East Asians and Europeans have already been subject to sweeps which moved them (presumably) to their phenotypic optimum the selective value of the introduced alleles is probably not that high. On the other hand, pleiotropy implies that many loci have myriad side effects, and one never knows what can happen when you jump from one genetic background to another (good or bad). Since many of the alleles which differentiate East Asians from Europeans that evolved in parallel are the result of relatively recent sweeps I doubt they're embedded in essential contingent coadapted gene complexes, so I would be surprised by widespread negative or positive fitness effects because of statistical epistasis.

The reason I'm focusing on alleles with selective value is that moments like the settlement of the Americas by a small group of Iberian men and the generation of a mestizo population within a century through hybridization are rare events. If random-mating forces are what we depend on to eliminate between group variation I think we'll be waiting a long, long, time, because people tend combine in pairs of likes. It might only take one migrant per generation between demes to keep them from wandering off into alternative genetic directions (the larger the population the smaller the between generation sampling variance, while the smaller the population the bigger impact that one migrant can have on the gene pool), but many demes haven't had that much migration for a long, long, time. In contrast to a focus on neutral loci and total genome content, Loren Rieseberg's work has suggested that the spread of high advantageous alleles can maintain species continuity and coherency.

Related: 10 questiosn for L.L. Cavalli-Sforza.

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Friday, April 20, 2007

God, the theory and the practice....   posted by Razib @ 4/20/2007 11:52:00 PM
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In the comments the unicorn-riding TGGP says:
When I was religious I didn't have a problem with evolution, because my idea of God was omniscient enough to arrange a deterministic universe in such a manner so as to produce the results He wanted without having to get up off His Holy Couch very often to get stuff done. I suppose it doesn't make much sense for an omnipotent God to be so lazy, but that's just what I figured I would do in His position.

Though theists in the Abrahamic tradition do generally avow a belief in god who is omniscient & omnipotent (among other characteristics), outside of the constraints of time & space, psychological & anthropological research tends to converge upon the consensus that the human working cognitive conceptualization of "god" doesn't include these traits. Unscripted narrations where god is integrated into human affairs always imply a model of the deity bounded by time & space & partaking of the same banal universe as believers, though exhibiting powers and perceptions of far greater magnitude than that of mortals.1 This makes sense when one considers that the human mind itself has constraints in terms of how it can model the universe, and a god which transcends the universe is simply beyond gestalt comprehension. An analogy might be that one can believe in higher spatial dimensions than the three we perceive as a matter of logic, but a intuitive conceptualization of higher dimensionality spaces is beyond the grasp of the human mind.2

In any case, the cognitive reality that humans have in their mind the concept of a limited god, despite their sincere professions of belief in a transcendent one, seems to make theistic evolution somewhat more understandable as a natural response to the facts of the universe.3 If the implicit internal models of gods have within them constraints imposed by natural processes then a deity who utilizes such processes easily drops out of the chain of inferences. This does not speak to the theological plausibility of such a god (i.e., working from first principles in regards to the nature of god as a being with traits x, y, z, etc.), but human beliefs and thoughts are not internally consistent.

1 - Participants in the studies of which I'm referring to are prompted to generate novel stories where the gods in which they believe in operate upon the universe over which they have dominion. Working backward from the characteristics of these stories, that is, working up the chain of implied inferences invariably leads researchers to conclude that the conceptualization of the god within these narrations contradicts an omniscient & omnipotent being outside of the universe. This model is consistent to the cross-cultural universality of particular times, places and objects being propitious and sacred to the gods, even though said gods are often notionally unbounded from time & space.

2 -To be clear, the anthropomorphic gods of yore remain ascendant within the human cognitive substrate, no matter the historical fact of their intellectual defeat at the hands of philosophical theism. Humans now believe in the god of the philosophers, but they imagine the god of the ancestors. I contend that many of the "paradoxical" behaviors of theists in response to tragedies or successes and the character of their relationship with the gods whom they avow to believe in can be explained by this "double truth," the disjunction between the philosophical & the cognitive deity.

3 - This does not speak to the validity of theological arguments for theistic evolution, rather, it only suggests that the reason the concept might "make sense" to a large number of theists is because follows from their implicit god-concept.

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Localizing recent adaptive evolution in the human genome   posted by Razib @ 4/20/2007 03:52:00 PM
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Just out in PLOS Genetics, Localizing recent adaptive evolution in the human genome. This has been accepted, but not reedited. Here's part of the abstract:
Within these regions, genes of biological interest include genes in pigmentation pathways, components of the dystrophin protein complex, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep.


If you read the paper you'll note that they claim to be able to detect sweeps near fixation.

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Chimps more evolved? - part III   posted by Razib @ 4/20/2007 03:38:00 PM
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More genes underwent positive selection in chimpanzee evolution than in human evolution
is on PNAS' site now....

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Democracy now!   posted by Razib @ 4/20/2007 12:26:00 PM
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The Economist has a long piece (it seems free) about Creationism around the world. What strikes me is how nutty the most "grass roots" religions are in comparison to "top down" ones (the latter are more opaque and obscure when they want to sidestep the absurdity of their religious claims). For example,, in the Muslim world Turkey in particular cranks out Creationist crap now just like American fundamentalist Protestants do (they used to just import and translate, but now they are apparently translating from Turkish into European languages). In Africa and Brazil it seems grassroots/Protestant churches are more vigorous about promoting anti-science than established Catholic ones. Why? One answer could be that the sola scriptura results in a natural Biblical literalism. I doubt it, and the reason is that many of these groups are not modeled upon Calvinist churches which emphasize scholarly and close scripture reading, they're Pentecostal, (in Brazil and Latin America the overwhelming majority of Protestants are Pentecostal) groups whose "ministers" are loose in their mastery of literacy (because the Holy Ghost speaks to them). One could make the sola scriptura argument for Muslims as well. Again, I think similar objections hold: Muslims, like many fundamentalist Protestants, aren't big readers of their canonical texts. They repeat sound bites drilled into them on high. There are plenty of anecdotal examples to suggest that this might not be a bad thing, insofar as literalism often collapses after a close reading of the text (since many people living in the Third World are illiterate, or functionally so, close reading isn't really possible).


So what's going on? I suspect that the difference here is organization. Protestant groups are highly fissionable. When American denominations have gone in a liberal direction (Methodists, Presbyterians, etc.) conservative factions have broken away (e.g., the Free Methodists). Similarly, just as the Southern Baptists have become ever more conservative more liberal congregations have created dissident umbrella organizations. The point is that the relatively loose organizational structure of Protestantism in many nations results in an increased variance in the modal belief set of denominations. Extremely "modernist" Christian (and post-Christian) movements have come out of Protestantism, but so have extremely fundamentalist "reactionary" movements. Catholicism has within it a range of opinions, but its institutional superstructure tends to constrain the manifestation of this at the elite levels. Sunni Islam is far more like Protestantism in its looseness of organization, and so grass roots organizations will express the full range of beliefs. But, while Protestantism might have the same variance as Sunni Islam, I don't think its mean is the same. That is, while liberal Protestant groups are legion (in the USA they collect together in The National Council of Churches), the cognates are thinner on the ground in Islam.

Ultimately, I think the world wide dynamism of Creationism is simply an outgrowth of the power of mass culture, and the democratic impulse. If the voice of the people is the voice of God, you will see on exhibit a rather low g product that conforms to the tastes and aptitudes of the conventional consumers of ideas. Paul Bloom argued in Wired for Creationism that there are strong psychological impulses in regards to theorizing about categories which tilts the playing field in favor of Creationism, until social and cultural conditioning wean many off their intuitions. Fundamentalist Protestantism and modal Islam are simply natural expressions of these cognitive intuitions. This trend is not limited to these two traditions, in In Spite of the Gods Edward Luce recounts the surreal experience of visiting a "research" institute in central India devoted to exploring all the salubrious byproducts of the cow. Some of the work seemed worthwhile, but Luce was a bit taken aback when asked to remove his shoes (out of respect) and walk through the feces and urine of the cows under study. The guide explained that the healing properties of these bovine byproducts were well attested and that Luce had nothing to fear. Clearly the attempt by some Hindu "fundamentalists" map their religious ideas onto the modern world resemble the quixotic intellectual endeavors of Muslim and Christian fundamentalists (a minority of Hindus have created their own form of Creationism as well). The cognitive and sociocultural processes are the same here, the rise of mass culture not only results in the transformation of science into magic, but also implies the attempt to convert emotionally salient magic into science.

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Karl Marx was wrong, and it is just happened that he had the right species!   posted by Razib @ 4/20/2007 11:17:00 AM
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Ron Bailey in Reason has a piece which summarizes some recent work suggesting that humans are "innately" egalitarian. Unfortunately, it is titled Natural Born Communism. There is a robust and consistent finding that humans tend to often behave in a manner which suggests that they are not Homo economicus. Psychologists have long reported that humans can exhibit inexplicable altruistic tendencies (that is, impose punishment on others at costs to themselves without any future possibility of payoff), and those with an evolutionary bent have often hypothesized that this is due to "misfiring" of cognitive modules maladapted to mass society. Kin selection, reciprocal altruism and group selection have all appeared as models in part to explain deviations from Homo economicus. But, there is an important point which I think suggesting a Communist inclination elides: humans tend to dislike inequality (or, on the whole will tend to minimize it when possible when they are the not the "winners," which is most of the time by the nature of the game), but that does not mean that they wish to live in system where private property is abolished and production is directed from on high. In other words, I think there is something to be said for making a distinction between the "Commanding Heights" philosophy (implemented in the Post-War Era in Britain by Labor), where major industries were nationalized and put under state control, and the Nordic model of high taxation and redistribution in concert with private control of property and assets. Ron concludes:
...It's hard to see how an inborn drive could arise in Pleistocene hunter gatherers such that people spend their scarce resources to reduce other people's resources promotes either individual or group survival. Or is enforcing equality really all that different an activity from punishing non-cooperating cheaters? Perhaps early in human evolution, large differences in income actually correlated with cheating and thus automatically merited punishment. Another puzzle is if humans are instinctively egalitarian, how did early hierarchical civilizations in which the incomes of priests and kings were significantly higher than those of peasants come about at all? Finally, finding that humans have an innate tendency toward enforcing a norm of income equality would explain the persistent attraction of communism, progressive tax rates, the demand for universal government-supplied health care, minimum wage laws and other such destructive modern leveling ideologies and policies.


I think one overarching issue is that evolutionary advantage is often a matter of relative fitness (and happiness is also likely relative). In societies which over the long term are not characterized by open-ended economic growth or great natural increase in effective population it stands to reason that many would perceive the world as zero sum (certainly in their lifetimes). If a man in your tribe was a superior hunter his generosity may increase the fullness of your belly on several occasions, but what genetic solace would that give if his virtuosity in the games men play allows him to become the alpha who monopolizes the attentions of all the females in your small tribe? How long would your woman be yours if a greater part of her protein intake was due to the efforts of another man? Perhaps better to kill the showoff and maintain a mediocre equilibrium with your fellow non-alphas! Finally, Ron asks how and why hierarchical civilizations arose if we are naturally egalitarian. The easy, and uninformative, answer is that humans are complex with many evolutionary tensions girding us, and at any given time we can place a particular emphasis a subset of our drives and impulses shaped by social context and personal interests. But, I would offer that perhaps the reality that Neolithic populations seem to have expanded greatly in numbers over several thousands of years allowed for a moment in the sun for a succession of alpha males. In larger population agglomerations human anonymity allowed alphas to appeal to counterforces to the jealous rivals nearby, the enemy of the enemy afar is my friend. But the life of men like Julius Caesar shows that the counteracting vector remains operative at particular moments to offer correctives, even if Rome was on an inevitable path toward the Dominate, the republican illusion remained powerful enough to stay the hand of the logic of naked explicit autocracy.1

Addendum: The title is a reference to E.O. Wilson's contention that "Karl Marx was right, it is just that he had the wrong species" (i.e., eusocial insects). I am implying that clearly Communist economics doesn't work, but, the mental biases of humans renders us vulnerable to its messages. Though as I note, the main attraction is probably redistribution, not a more abstract abolition of selfish human action.

Related: Why patriarchy? Galor and Moav: Property rights as an evolutionary force.

1 - Let me elaborate. The first emperor, Augustus Caesar, was notorious for maintaining the illusion of republican continuity. He was the first citizen, nothing more (well, until he started accepting the titles that the sycophantic Senate gifted him). It was with the transition to the Flavian Dynasty that the hereditary principle became explicit and without concealing artifice, the founder Vespasian stated that if his sons did not succeed him to the purple no one would. In the early 3rd century the emperor Septimius Severus dispensed with the illusion that the law had any independence from his will, having his decrees read out in the Senate without consultation. Now, he was Rome. Finally, by the 4th century oriental despotism became normative as all pretense that Rome was not a monarchy ruled by kings was stripped away. The models now were not their republican forebears, but the glittering Sassanid court. Julian the Apostate was mocked in part by contemporaries for his traditionalist sympathies toward returning to a simpler time, where the emperor was lacking in divine glamor and oriental opulence. Instead of accepting this as a Roman virtue, Julian's abstemious nature was taken as projecting a mean and unbecoming image for the emperor.

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Thursday, April 19, 2007

How to find the important SNP   posted by amnestic @ 4/19/2007 08:48:00 PM
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There is a gene I care about carrying a SNP associated with a phenotype I care about. Unfortunately, that SNP is intronic, and if it has an effect the prediction isn't obvious. I would like very much to find a list of SNPs in significant LD with this one, but I am finding the HapMap/Mart impenetrable. In this article, Navigating the HapMap, I got a hint of hope:
Alternatively, one might use the SNP filter function to highlight other SNPs that are in LD with a specific list of SNPs of interest (e.g. SNPs associated in a study). This enables the user to identify all SNPs in LD with an associated SNP to allow functional analysis to identify putative causal SNPs for further analysis in the lab.

I can't find this option. Any helpful hints?




The case for selection at ASPM   posted by p-ter @ 4/19/2007 04:46:00 PM
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We've folowed much of the story of the gene ASPM here, largely because of the evidence that it has been under selection both along the lineage leading to humans and up to the current day. Evidence for the former has been provided by a number of studies, while evidence for the latter largely from a paper out of Bruce Lahn's lab. The conclusion that the locus is currently under selection was challenged (poorly) in a technical comment in Science last year, and now another technical comment challenges the conclusion for selection again.

This challenge, unlike the last one, cannot be lightly dismissed. A group led by David Reich, prior to the publication of the Lahn paper, had sequenced select parts of the ASPM gene and begun their own analyses of the gene. As they reported last year at a conference, they find no evidence for selection at the locus.

How could these two groups come to such different conclusions? It's perhaps worthwhile to highlight the major difference in the two methodologies-- Lahn's group determined the statistical significance of their data using coalescent simulations (that is, they simulated data under a number of different models and see if their actual data is an "outlier" when compared to the simulations), while Reich et al. prefer to compare their data to an empirical distribution (that is, they see if the area in question is an "outlier" compared to other genomic regions). Both of these methods have their problems, something worthwhile to keep in mind the next time you see a small p-value on a statistic. In particular, if one is unable to simulate the precise demographic history of a population, simulation will give biased p-values. Tests based on the empirical distribution generally don't have this issue, but instead assume that only a small proportion of the genome is under selection and that selected loci will be outliers. These are not just questionable assumptions; they have indeed been questioned, and the conclusions are not heartening.

The figure on the right is from a paper published in Genome Research that asks, appropriately enough, "How reliable are empirical genomic scans for selective sweeps?". It shows a color coded landscape for the false negative rate (the percentage of selected loci that will be missed in an empirical genome scan) for a population that has experienced a bottleneck (like Europeans) for different statistics and different assumptions about significance thresholds and the precentage of the genome under selection. Red areas are where the false negative rate is near 100%, fading to green at about 50% and finally blue (of which there isn't much in this figure) at 0%. As the authors conclude, "Our simulations suggest that while empirical approaches will identify several interesting candidates, they will also miss many--in some cases, most--loci of interest".

So it's certainly possible that this is a case study in the lack of power of empirical distributions to detect selected loci. Of course, maybe not. This analysis certainly does not lend support to the contention that ASPM is under selection, but nor does it eliminate it. It's clear that better tests for selection are needed. Lahn et al. have apparently decided not to respond to Reich et al.; they're likely thinking that this debate will not be resolved until those better tests are devised.

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Evolution on high   posted by Razib @ 4/19/2007 04:09:00 PM
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Ann Gibbons reports on the evolution of high altitude tolerance among Tibetans presented at The American Association of Physical Anthropologists meeting last March:
Beall reported at the meeting that women with high levels of oxygen in their blood had more than twice as many surviving babies as had those with low oxygen levels--a ratio of 1:0.44. This is a startlingly strong selection pressure, she says--even stronger than that on the sickle cell gene, which protects against malaria and has a fitness ratio of 1:0.66.
...
But exactly how do these women manage to carry extra oxygen in their blood? They do not produce more hemoglobin the way Andeans living at high altitude do. One possibility is that the women with high oxygen have an adaptation that Beall is exploring independently in these same Tibetan villagers. She found that some villagers exhale extra nitric oxide in their breath, a sign of additional amounts of the gas in their blood. In those Tibetans, nitric oxide dilates the blood vessels so they can pump more blood and oxygen to organs and tissues, as measured by images of heart and lung blood vessels. The Tibetans can boost their blood volume--and so pump more oxygen to their tissues--without producing more hemoglobin or raising the blood pressure in their lungs.


From talking to Greg Cochran I am to understand that the Tibetan adaptations result in greater physiological fitness than the strategies in the New World. Certainly it seems that the Andeans utilize a "brute force" technique, just crank out more hemoglobin. The evolutionary context would be that highlands of Peru have been populated by humans influenced by natural selection for only the past few tens of thousands of years (likely closer to the low end), while Eurasia has likely had high altitude living hominids for eons, so the wisdom of selection has had a far longer time to crank out alleles. It is interesting to me that Gibbons uses the sickle cell trait as a point of comparison: this is a recent evolutionary response to a powerful selective pressure, and, a classic case of heterozygote advantage where the population's mean fitness is dragged down by the clumsy and brute force method of this "fix" because of the generation of sicke cell homozygotes. The fact that such genetic variation exists within the Tibetan villages surveyed is somewhat surprising to me insofar as the fitness implications seem so strong that I can not understand why the alleles would have not fixed by now. If it is an overdominant trait, where the heterozygote has greater fitness than the homozygotes, then the variation will be preserved at an equilibrium conditioned by the fitness of the homozygotes. On the other hand, recent migration might have introduced "lowland" alleles into the population. Here is a snip from the author's abstract:
...This paper presents a case study illustrating the human adaptability and quantitative genetic approaches to explaining the unique biological characteristics of Tibetan highlanders that are thought to be adaptations offsetting high altitude hypoxia. There is evidence of strong directional natural selection operating on a major gene for oxygen saturation of hemoglobin in this population, although the genetic locus is not known....


Use of the term "quantitative genetic" implies, to me, a trait with a continuous range. But the impression I got from the quotations above is that the researchers divided women into a few discrete categories (i.e., did they simply compare the fertility of women in category "high oxygen" vs. "low oxygen" or did they did track correlation between oxygen levels and fertility and do a regression to predict the latter from the former?). Finally, reference to a "major gene" means that even if it is a quantitative trait with multiple loci contributing to the total effect there is obviously one locus of large effect. Beall suggests that directional selection is occurring upon this locus, so perhaps the Tibetans are relatively newcomers to their locale if selection is still working to optimize their fitness?

Long time readers of this weblog will know that Cynthia Beall has done work in the past which suggests that different highland populations have developed different adaptations to the same problems. With the recent data that is coming out in regards to skin color this should not surprise. In any case, I notice that the NAS has a interview with Dr. Beall, so check it out if you curious.

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Gene Genie   posted by Razib @ 4/19/2007 10:12:00 AM
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There's a new gene related carnival, Gene Genie, currently at Neurophilosophy. Also, the next Mendel's Garden is at Epigenetics News.

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UK "Social Trends" 2007   posted by DavidB @ 4/19/2007 02:02:00 AM
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Readers with an interest in UK affairs may like to know that the annual statistical survey Social Trends has recently been published. Go here for a free download (click on the link "Full Report" for a 3Mb pdf file).

GNXP readers may find the chapter on population (migration, birth rates, etc) the most interesting.



Wednesday, April 18, 2007

French science   posted by p-ter @ 4/18/2007 10:26:00 PM
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While we here in the US go on about "framing" in the 2008 election (or whatever the hell that uproar was about), France is preparing for the first round of their presidential election on Sunday. The major candidates (Sego, Sarko, and the farmer dude) all answered some questions for Nature, which were published this week. Check the promises made in the answer to this question; I'm actually curious about the chances of real reform getting pushed through:
How would you modernize France's universities?

M. Sarkozy: As of the day after the elections, I will be ready to launch a major reform of French universities designed to give them much more autonomy. This will include powers to recruit, to fix salaries, to decide how they organize themselves, to build endowments and to diversify their funding sources. I will also rebuild the way that they are governed, restructuring their executive boards and the ways they choose their presidents.

M. Bayrou: After a massive increase in student numbers over the past two decades, enrolment has now stabilized, and this makes it possible to envisage a new phase of long-term development. The universities suffer three ills: the absence of recognition of the PhD, lack of funding and a poorly adapted governance structure. We need to reach spending-per-student levels equal to or more than the average of OECD countries, continue the rapprochement with the Grandes Ecoles that has now begun, and make changes in the ways the universities are run.

Mme Royal: I favour a rational, optimal use of resources based on evaluation; this means we must provide favourable working conditions for all researchers. If we supported only a small proportion of researchers it would mean that we would be paying the others without benefiting from their potential. That would be absurd.
I also find it striking how easily one can classify the candidates into their respective places on the political spectrum based on a single question.




Genetics and the Flynn effect   posted by the @ 4/18/2007 07:47:00 PM
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Follow up to IQ, height & Crooked Timber: John Quiggin @ Crooked Timber wrote "I'd be interested to read a GNXP view of the main developments in recent decades, taking account of the Flynn effect." I don't know that a "GNXP view" exists on this subject aside from what appears to be the scholarly consensus where such a consensus exists. However, as a down payment on a response, I've gathered several sources which should help to inform the interested reader about modern views on the genetics of IQ and the Flynn effect.

For a general background on IQ and intelligence, two publications in response to The Bell Curve:
* "Intelligence: Knowns and Unknowns", the APA task force report (1995)
* "Mainstream Science on Intelligence", signed by 52 professors (1994)

For a quick technical review of the genetics of g, see the review by Plomin (2003), which I pasted below the fold. (Lest you think there's nothing new, note the distribution of publication dates among the references.)

For a bleeding-edge discussion of the Flynn effect, I can recommend two sources. A draft of a new book by Flynn and a book review by Lynn (pasted below the fold).

Regulars may want to begin by reading below the fold.


Guest Editorial
Genetics, genes, genomics and g
Robert Plomin1

1Social, Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, London SE5 8AF, UK. Email: r.plomin@iop.kcl.ac.uk
Abstract

Molecular Psychiatry (2003) 8, 1-5. doi:10.1038/sj.mp.4001249

This issue includes three papers1,2,3 on a topic of increasing interest to molecular psychiatrists: the genetics of intelligence. There was also a related article in a previous issue of Molecular Psychiatry.4 These four papers represent the range of research on genetics (quantitative genetic twin studies), genes (molecular genetic attempts to identify genes) and genomics (understanding the function of genes). The goal of this editorial is to put these papers in perspective.

Intelligence is the most complex¾and most controversial¾of all complex traits. So why study the genetics of such a complex and controversial trait? The word 'intelligence' has so many connotations that the symbol 'g' was proposed nearly a century ago to denote the operational definition of intelligence as a 'general cognitive ability' representing the substantial covariance among diverse tests of cognitive abilities such as abstract reasoning, spatial, verbal and memory abilities.5 In a meta-analysis of 322 studies, the average correlation among such diverse tests is about 0.306 and a general factor (first unrotated principal component) typically accounts for about 40% of the tests' total variance.7 As discussed below, multivariate genetic analysis shows that the genetic overlap among cognitive tests is twice as great as the phenotypic overlap, suggesting that g is where the genetic action is. Although g is not the whole story, trying to tell the story of cognitive abilities without g loses the plot entirely.

This strong genetic g factor running through diverse cognitive processes has important implications for genetic research in neuroscience since g is molar and flies in the face of the widespread assumption in cognitive neuroscience that the brain functions in a modular manner.8 In addition, the long-term stability of g after childhood is greater than for any other behavioral trait,9 it predicts important social outcomes such as educational and occupational levels far better than any other trait,10 and it is a key factor in cognitive aging.11 g is specifically relevant to molecular psychiatry because, as discussed below, mild mental retardation appears to be the low extreme of the normal distribution of g. Moreover, at least 200 single-gene disorders include mental retardation among their symptoms.12

Quantitative genetics

Quantitative genetic research¾twin and adoption studies¾estimates the net effect of genetic variation on phenotypic variation regardless of the number of genes involved or the complexity of their interactions. Such research charts the course for molecular genetic studies by identifying the most heritable components and constellations of phenotypes. The first twin and adoption studies were conducted in the 1920s on g and suggested substantial genetic influence.13,14,15 Since then, with the exception of personality assessed by self-report questionnaires, more research has addressed the genetics of g than any other human characteristic. Dozens of studies including more than 10 000 twin pairs and hundreds of adoptive families as well as more than 8000 parent-offspring pairs and 25 000 sibling pairs consistently indicate substantial heritability.16 Heritability estimates vary from 40 to 80% but meta-analyses based on the entire body of data yield estimates of about 50%,17,18 with increasing heritability from infancy (20%) to childhood (40%) to adulthood (60%).19 Most of the genetic variance for g is additive, which facilitates attempts to identify genes responsible for its heritability.20

Since the substantial heritability of g is better documented than for any other biological or behavioral dimension or disorder, quantitative genetic research has moved beyond heritability to ask more refined questions about development, about the interface between nature and nurture, and about multivariate issues.21 A finding of great significance for molecular psychiatry and neuroscience has emerged from multivariate genetic research that analyzes the covariance among cognitive tests rather than the variance of each test considered separately.20 As noted earlier, the average phenotypic correlation among diverse cognitive tests is about 0.30. In contrast, multivariate genetic research indicates that genetic correlations among such tests are at least 0.80 on average.22 (A genetic correlation indexes the extent to which genetic effects on one trait correlate with genetic effects on another trait independent of the heritability of the two traits.) The extremely high genetic correlation among diverse cognitive tests means that genes associated with one cognitive ability are highly likely to be associated with all other cognitive abilities. This evidence for 'genetic g' means that g is an excellent target for molecular genetic research in the cognitive domain.

It should be noted that genetic g does not necessarily imply that there is a single fundamental brain process that permeates all other brain processing, such as a 'speedy brain',8 neural plasticity,23 or the quality and quantity of neurons.24 It has been proposed that g exists in the brain in the sense that diverse brain processes are genetically correlated.25 For example, gray and white matter densities in diverse brain regions are highly heritable, substantially intercorrelated across brain regions, and correlated genetically with g.26,27

One of the papers in this issue provides a good example and description of multivariate genetic analysis.3 Rather than analyzing the covariance between cognitive tests, the study investigated the genetic and environmental origins of the covariance between normal variation in behavior problems and g in children. For 376 pairs of twins from 6 to 17 years of age, nearly all of the modest phenotypic correlation (-0.19) between behavior problems and g could be accounted for by genetic covariation. Similar results were obtained in another study of 4000 pairs of young twins assessed at 2, 3 and 4 years; the large sample made it possible to show that phenotypic and genetic links may be stronger at the extremes of behavior problems and cognitive problems.28

Another multivariate genetic finding of great importance concerns genetic links between common disorders and dimensions of normal variation. This research suggests that common disorders (but not rare disorders) are merely the quantitative extreme of the same genetic and environmental influences that operate throughout the normal distribution. For example, a sibling study of mental retardation found that the average IQ of siblings of severely retarded probands was normal, 103, which implies that severe mental retardation shows no familial links with normal variation in g.29 This finding makes sense in relation to the rare single-gene12 and chromosomal causes30 of severe retardation that are not usually inherited because they occur spontaneously. In contrast, siblings of mildly retarded probands showed a substantially lower mean IQ score of 85.29 In other words, mild mental retardation but not severe retardation shows familial (presumably genetic) links with normal g variation. The first twin study of mild mental retardation confirms that mild mental retardation is strongly linked genetically to normal variation in g.31 This evidence for strong genetic links between disorders and dimensions¾evidence that is typical of common disorders such as hyperactivity, depression and alcoholism¾provides support for the quantitative trait locus approach to molecular genetics, discussed later.

Identifying genes

There is a lot of life left in the old workhorse of quantitative genetics, especially in investigating developmental, multivariate and environmental issues that go beyond merely estimating heritability. However, the most exciting direction for research on intelligence and cognition is to move beyond genetics to genes, that is, to identify some of the genes responsible for the substantial heritability of g and other cognitive abilities and disabilities. In contrast to the slow progress in identifying genes for schizophrenia and manic-depression, greater progress has been made in the cognitive domain, most notably the well-documented association between apolipoprotein E gene and dementia32 and a solid 6p21 linkage with reading disability that is beginning to be narrowed down in association studies.33

The quantitative trait locus (QTL) perspective has come to dominate molecular genetic research on complex quantitative traits such as g as well as common disorders such as dementia and reading disability. The QTL perspective is the molecular genetic extension of quantitative genetics whereby multiple genes are assumed to be responsible for heritability, implying that genetic variation is distributed quantitatively.34 For this reason, a QTL perspective on g naturally leads to molecular genetic research on normal variation, as is also the case for personality research.35 Two papers on molecular genetics in this issue are distinctive in that they focus on normal variation in g using large unselected samples.1,4 They report positive associations between normal variation in g and two candidate genes: Cathepsin D (CTSD; 4) and cholinergic muscarinic 2 receptor (CHRM2; 1). The effect sizes are small (heritabilities of 3 and 1%, respectively) as expected for QTLs, but are easily detected as significant with the large sample sizes of these studies (767 and 828, respectively). Research on complex traits should be aiming to break the 1% QTL barrier, that is, 80% power to detect QTLs when they account for as little as 1% of the total variance (1% heritability), which requires an unselected sample of about 800 individuals when a single marker is studied (P = 0.05, two-tailed; 36).

The CTSD paper4 is especially interesting in relation to the extensive molecular genetic research on dementia, which will be the source of much more molecular genetic research on g. Beginning with individuals at least 50 years old, g was assessed during a 15-year period in order to investigate the cognitive decline indicative of dementia. As in other studies, initial g scores are correlated negatively with decline across the 15 years, supporting the brain reserve capacity theory of dementia, as explained in the paper. However, CTSD is not associated with cognitive decline, which confirms the results of several other studies that found no association between CTSD and dementia. The exciting finding is that CTSD is associated with g at the first test session. Longitudinal quantitative genetic research on g indicates that age-to-age stability is largely mediated genetically whereas change is largely environmental in origin.21 This suggests that the heritability of dementia defined as decline might be modest in contrast to the heritability of g. We do not yet know how heritable dementia is because only a few small twin studies have been reported and their results are mixed.37 What is needed is a multivariate genetic analysis of g and dementia in order to investigate the extent of their genetic overlap.

Other reports are beginning to emerge of candidate gene associations with g. Most notably, a functional polymorphism (VAL158MET) in the enzyme catechol O-methyltransferase (COMT) has been reported to be associated with g-related cognitive functioning in two studies.38,39 An association with g has also been reported for a gene involved in controlling homocystein/folate metabolism.40 Because research on dementia will be the immediate source of more molecular genetic research on g as in the CTSD study in this issue,4 it is worth noting that the apolipoprotein gene, which shows a strong association with dementia, shows no association with g in childhood41,42 or in adults.43

Despite the power of the two studies in this issue to detect QTL associations, replication will be crucial because the track record for replicating candidate gene associations is not good.44 This is of particular concern with studies using unselected samples because it is tempting to study many measures as well as many candidate genes thus increasing vulnerability to false positives. As a chastening confession to underline the need for replication, both papers cite our report of an association between IGF2R and g in two samples,45 but our new independent sample as large as the previous two samples combined has not replicated the association.46

Other molecular genetic issues relevant to these CTSD and CHRM2 reports are generic issues involved in any attempt to find QTLs for complex traits whether assessed as disorders or dimensions. One such issue is the use of functional polymorphisms. In the CTSD study,4 the candidate gene polymorphism is functional (C>T, Ala>Val); in the CHRM2 study,1 the single nucleotide polymorphism (SNP) is in the 3' untranslated region of the gene. The use of functional polymorphisms involves direct association that greatly increases power because it tests the hypothesis that the polymorphism is the QTL rather than relying on the marker being in linkage disequilibrium with the QTL associated with the trait (indirect association). Another advantage of using functional polymorphisms is that when associations are found, the usual house-to-house search for the culprit gene is circumvented, although it is always difficult to identify beyond reasonable doubt the QTL suspect from a line-up of genes in the neighborhood.

Another generic issue is that more systematic approaches to candidate genes are needed because any of the tens of thousands of genes expressed in the brain could be proposed as candidate genes for g.47 One early association study of g examined 100 candidate genes (not including CTSD or CHRM2) but found no more replicated associations than expected by chance, although the design only provided power to detect QTLs of about 2% heritability.48 A more systematic strategy is to investigate all polymorphisms in particular gene systems.49

Another strategy is to conduct genome-wide scans for association analogous to genome scans for linkage except that many thousands of markers are needed in the case of association. The first genome-wide search for association with g has been reported using 1842 simple sequence repeat (SSR) markers using DNA pooling and groups selected for high g and controls.50 Despite a highly conservative replication procedure designed to avoid false positives, two SSRs replicated cleanly in two independent case-control samples but neither SSR association was replicated in a transmission disequilibrium test using parent-offspring trios. Genomic control analyses showed that the failure to replicate using the parent-offspring trios was not due to population stratification. Since SSR markers are unlikely to be functional, they rely on indirect association for which power falls off quickly as a function of the linkage disequilibrium distance between the marker and the QTL.51,52 Using indirect association, tens or hundreds of thousands of markers are needed for genome scans in order to exclude QTLs of 1% heritability, although haplotype maps can reduce the required number of markers.53,54

Ultimately what is needed for genome-wide association scans is to genotype every functional polymorphism in the genome. As a step in this direction, we are currently using DNA pooling to conduct a genome-wide g scan of all brain-expressed nonsynonymous SNPs in coding regions that are currently available in public databases with allele frequencies greater than 10% in Caucasian samples.55 Polymorphisms in promoters and other gene regulatory coding regions seem even better candidates for QTLs but they are much more difficult to identify and to demonstrate their functionality. Moreover, coding DNA does not have a monopoly on QTLs¾noncoding RNA is likely to be a source of QTLs too,56 although determining functionality of polymorphisms in noncoding RNA will be even more difficult.

It remains to be seen whether increasing power using large samples and direct association will yield replicable QTLs. DNA pooling will be useful in this context because it costs no more to genotype 1000 individuals than 100 individuals.57 Pessimists can reasonably worry about the gloomy prospect that the culprit genes will never be caught because the heritability of g might be caused by many genes with miniscule heritabilities. Some might hope that such research is never successful because of the ethical issues that would be raised if genes for g were found.21 Interesting discussions of these issues are available specifically in relation to genes and g58 and more generally in relation to behavioral genetic research.59

Behavioral genomics

Quantitative genetics assesses the net effect of genes on behavior without knowing anything about which genes are involved. Molecular genetics identifies genes associated with behavior without knowing anything about the mechanisms responsible for the association. As we approach the postgenomic era in which the complete human genome sequence and all functional variations in the genome sequence are identified, the future of behavioral genetics is functional genomics, that is, understanding how genes affect behavior.60

Functional genomics usually refers to the bottom-up agenda of molecular biology such as gene expression profiling and proteomics. However, there are higher levels of analysis for understanding how genes function which need not wait until the bottom-up approach reaches them. At the other end of the continuum is the top-down approach that investigates the function of genes in relation to behavior of the whole organism. For example, the issues about multivariate relationships of heterogeneity and comorbidity, developmental change and continuity, and the interface between genes and environment can be addressed with much greater precision once genes are identified. The term behavioral genomics has been proposed to emphasize the value of this top-down level of analysis.61

Rodent models will be valuable for functional genomic research because of their ability to manipulate both genes and environment and the power they offer for investigating brain processes such as single cell recordings, micro-stimulation, targeted gene mutations, antisense DNA that disrupts gene transcription, and DNA expression. The value of rodent models rests with understanding genetically driven brain processes, not with phenotypic validity. For example, mouse models have made the greatest progress in understanding the psychopharmacogenetics of alcohol-related processes even though mice do not become drunk of their own volition.62 In this sense, although it sounds absurd, mouse models of reading disability will be valuable for understanding the brain processes underlying the genetics of reading disability. The ultimate test is whether the same genes affect the same brain processes in mouse and man.

In terms of rodent models of g, clearly there are major differences in brain and mind between the human species and other animals, most notably in the use of language and the highly developed prefrontal cortex in the human species. However, g in man does not depend on the use of language¾a strong g factor emerges from a battery of completely nonverbal tests.7 Moreover, low-level tasks¾for example, information-processing tasks assessed by reaction time¾contribute to g.63 Indeed, g can be used as a criterion to identify animal models of individual differences in cognitive processes. If g represents the way in which genetically driven components of the brain work together to solve problems, it would not be unreasonable to hypothesize that g exists in all animals.64 Although much less well documented than g in humans, increasing evidence exists for a g factor in mice across diverse tasks of learning, memory and problem solving.65 A large-scale integrative program of research called genes-to-cognition is under way that uses mouse models for functional genomic research in the cognitive domain.66

One of the papers in this issue serves as an example of the value of rodent models for functional research.2 The research brings together neurotransmitter assays, brain anatomy, a broad battery of behavioral measures, a development approach from infancy to adolescence to adulthood, and pharmacology in an experimental study in which epidermal growth factor (EGF) was administered to neonatal rats. Although a test of learning ability did not appear to be affected by the neonatal treatment, other abnormalities were observed in adults but not in adolescents such as sensorimotor gating, motor activity and social interaction in a pattern reminiscent of schizophrenic symptoms and which were ameliorated by clozapine. This research covers a wide range of functional approaches, but the missing link from a functional genomics perspective is genetics. Although transgenic studies indicate the important role of the EGF gene family on brain structures and monoamine pharmacology, there is as yet no evidence that polymorphisms in genes related to EGF are involved in schizophrenia or other cognitive disabilities or abilities. This program of research showing the importance of EGF is likely to stimulate genetic research using EGF candidate genes.

In our age of increasing specialization, the most exciting prospect for functional genomic research in the postgenomic era is that DNA will integrate research in the life sciences from cells to societies and that bottom-up approaches will meet top-down approaches in the brain. g is an excellent target for such integrative research because an exciting synergy will quickly emerge simply by connecting the dots of knowledge already available, for example, in gene targeting studies of learning and memory in mice, brain imaging studies of cognitive processes in the human species, and extensive quantitative genetic research.
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--------------------

Book review
J.R. Flynn, What is intelligence? Beyond the Flynn Effect, Cambridge University Press (2007).
doi:10.1016/j.intell.2007.03.003 How to Cite or Link Using DOI (Opens New Window)
Copyright © 2007 Elsevier B.V. All rights reserved.

Richard Lynna, E-mail The Corresponding Author
a4 Longwood House, Bristol BS8 3TL, UK
Received 2 March 2007; accepted 13 March 2007. Available online 17 April 2007.

A warm welcome must be extended to this book in which the author discusses the issues raised by the Flynn Effect. There are two major problems. First, what are the factors responsible for the increase of intelligence that has been observed in a number of countries during the last 80 years or so? Second, why has this increase been so much greater in reasoning ability/fluid intelligence, as measured by the Wechsler similarities and non-verbal tests where it has averaged around 3.6 IQ points a decade, and the Progressive Matrices, where in some samples it has averaged around 7 IQ points a decade, than in tests that measure acquired knowledge/crystallized intelligence (vocabulary, information and arithmetic), where it has averaged only around 0.5 IQ points a decade.

Flynn's answer to the problem of the cause of the Flynn Effect is that increases in education have led the people thinking more scientifically and logically (“science has engendered a sea change … formal education played a proximate role”). He uses Piaget's concepts of concrete and formal thought processes to explicate this. Previous generations were as good as later generations at concrete thinking, but more recent generations have advanced to the formal stage where they analyse problems in terms of abstract concepts. But he does not mention that this theory has been disconfirmed by Fleiller, Jautz, and Kop (1989) who demonstrated that concrete thinking has improved at the same rate as formal thinking.

Flynn is by no means the first to attribute the Flynn Effect to improvements in education. Many others have done the same, including several of the early observers of the Flynn Effect such as Cattell (1973, p. 275): “the inter-generational changes … probably represent the unquestionably marked improvement in schooling”.

The theory that improvements in education can explain the Flynn Effect encounters two problems. The first is that the cognitive abilities that are learned in schools (arithmetic, information, vocabulary, and math, science and reading tested in the American NAEP) have shown very little increase; it is the cognitive skills that are not learned in schools that have shown the large increases. This is the opposite of what would be expected if better or more education has enhanced cognitive abilities. A second problem is that the Flynn Effect has been found in 4–6 year olds who have had very little education, and even in infants (e.g. Hanson, Smith, & Hume, 1985). This suggests that an important contributor to the Effect lies in improvements in pre-natal and early post-natal nutrition, as argued in detail in Lynn, 1990 and Lynn, 1998. It may be, however, that some of the large gains in fluid intelligence found in military conscripts are attributable to later cohorts having had more education than earlier.

Flynn attempts to refute the nutrition theory of the Flynn Effect by asserting that there is no evidence that nutrition has improved in the second half of the twentieth century. He asserts that there have been no increases in height (improvements in nutrition are indexed by increases in height) in the United States in children born after about 1952, although intelligence has continued to increase. Contrary to this contention (1) the data compiled by Komlos and Lauderdale (in press) show that height in the United States increased in those born from 1955 to 1975 (white men from 177.8 to 179.5; white women from 164.1 to 164.9); (2) height stabilised after 1975 and Flynn's own data show that intelligence gains decelerated after 1985 and turned negative in children from 1989 to 1995. In Europe also heights increased from 1960 to 1990 (Larnkjaer, Schroder et al., 2006); from around 1990 heights and intelligence have both stabilized in Denmark and Norway. The case for improvements in height running parallel with increases in intelligence, as predicted by the nutrition theory, is much stronger that Flynn allows.

Furthermore, the nutrition theory of the Flynn Effect explains why fluid intelligence has increased so much more than crystallized intelligence. Several studies have shown that sub-optimal nutrition impairs fluid intelligence more than crystallized intelligence. Hence as nutrition has improved over time, fluid intelligence has increased more. It has even been shown that the Wechsler subtests that are most impaired by sub-optimal nutrition and improve most with nutritional supplements are those for which the Flynn Effects have been the greatest (e.g. arithmetic, similarities and block design) (Botez, Botez, & Maag, 1984).

Flynn proposes that the effect of better education on the increase in intelligence is enhanced by the “individual multiplier” and the “social multiplier”. The concept of the “individual multiplier” is that the intelligent have a thirst for cognitive stimulation and this increases their intelligence. This again encounters the problem that the Flynn Effect is present in infants. The “social multiplier” posits “that other people are the most important feature of our cognitive development and that the mean IQ of our social environs is a potent influence on our own IQ”. If this were so, the IQs of adopted children should be associated with the IQs of their adoptive parents, and there should also be a strong correlation between the IQs of unrelated children reared in the same adoptive families. Both these predictions have been disconfirmed. Scarr and Weinberg's (1978) study found that the correlation between the IQs of adopted children aged 18 and the IQs of their adoptive parents was .14 (i.e. zero), while the correlation between the IQs of unrelated children reared in the same adoptive families was − .03. The effectively zero correlation between the IQs of unrelated children reared in the same adoptive families has been confirmed in a study of 52 pairs aged 13 (r = − .16) (Plomin, 1986, p. 237).

Although I have not been persuaded by Flynn's arguments on the causes of the Flynn Effect, and I could not find an answer to the question “What is Intelligence?” beyond what is already widely accepted, I found his book to contain many interesting ideas and observations and I recommend it in the confident expectation that many potential readers will find the same.

References
Botez, M. I., Botez, T., & Maag, U. (1984). The Wechsler subtests in
mind organic brain damage associated with folate deficiency.
Psychological Medicine, 14, 431−437.
Cattell, R. B. (1973). Abilities: Their structure, growth and action.
Boston: Houghton Mifflin.
Fleiller, A., Jautz, M., & Kop, J. -L. (1989). Les reponses au test
mosaique a quarante ans d'intervalle. Enfance, 42, 7−22.
Hanson, R., Smith, J. A., & Hume,W. (1985). Achievements of infants
on items of the Griffiths scales: 1980 compared with 1950. Child:
Care, Health and Development, 11, 91−104.
Komlos, J. and Lauderdale, B. E. (in press). The mysterious trend in
American heights in the 20 century. Annals of Human Biology.
Larnkjaer,A., Schroder, S.A., et al. (2006). Secular change in adult stature
has come to a halt in northern Europe and Italy. Acta Paediatrica, 95,
754−755.
Lynn, R. (1990). The role of nutrition in secular increases of
intelligence. Personality and Individual Differences, 11, 273−285.
Lynn, R. (1998). In support of the nutrition theory. In U. Neisser (Ed.),
The rising curve: Long term gains in IQ and related matters
Washington, D.C.: American Psychological Association.
Plomin, R. (1986). Development, Genetics and Psychology. Hillsdale,
New Jersey: Lawrence Erlbaum.
Scarr, S., & Weinberg, R. A. (1978). The influence of family
background on intellectual attainment. American Sociological
Review, 43, 674−692.

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Do no stupidity....   posted by Razib @ 4/18/2007 03:09:00 PM
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I am interested in evolution. As you know, I have "evolution" and "genetics & evolution" queries on my RSS from google news. Over the past few weeks nearly every day The Conservative Voice has been peppering my feed with Creationist apologia, sometimes, it is the majority of new articles google is bringing back! Some idiot named Babu Ranganathan is especially prominent in the production of this garbage (sometimes I get his columns from both the The Conservative Voice and other publications where he is syndicated, how the hell do you get a syndicated column when your homepage is hosted on geocities for god's sake!). In any case, a few weeks ago (about a month ago) Google News picked up my ScienceBlogs blog. For a lot of the genetics and evolution related queries a cute little cat is now staring back at me! But today, after deleting another retarded Creationist comment, I realized that I can date a spike in the number of these operational spams (often clearly cut & pasted from Creationist websites) precisely from the time when Google News picked up my weblog. So it seems I'm not the only one searching for and retrieving queries on evolution all the time. Months ago "amnestic" offered that all the talk about evolution on blogs was about dinosaurs and Creationism, and I chided him by pointing out that there was a lot of discussion of evolution in a substantive manner. I encouraged him to read The Genetical Theory of Natural Selection. But today I'm wondering if I was too quick and harsh...it seems that most people care about evolution only as it relates to "Culture Wars," while the "scientific press" is content to show how 21st century genomics "refutes" 19th century hypotheses about orthogenesis or a chain of being....

Related: You might want to check out my review of Evolution for Everyone.

Update: Babu is not syndicated, rather, his columns get picked up now and then (e.g., he is a "special contributor." Yes, he is special)....

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Tuesday, April 17, 2007

When Rome fell   posted by Razib @ 4/17/2007 07:19:00 PM
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Update: Daniel Larison, a Byzantine history graduate student, responds.

The past is the undiscovered country. I have argued before that ignorance of the past makes for good contemporary myth-making, and in fact, it might aid in the process. After all, facts tend to introduce ambiguity and muddiness into an elegant and forceful narrative. Over the years I've come to understand, and even respect, some "Post Modernist" critiques of grand historical narratives precisely because the naked influence of social parameters is so clear in the sample biasing of a few factual points to support tenuous conjectures. This tendency doesn't always fall in the direction that you might think, in From Plato to NATO the conservative historian David Gress makes the argument the the liberal post-War consensus, typified by Will Durant, reshaped the idea of the West toward a minimalist conception which leapfrogged the over 2,000 years between Classical Athens and Enlightenment (with a possible exception for the Renaissance), stripping away the detritus of the Middle Ages and its incontrovertibly Christian character as well as the authoritarianism of the Roman Empire. Gress argues that this elides the reality of the complex organic emergence of the Western identity as a compound of Classical, Christian and Germanic elements which developed between the fall of Rome and the breaking apart of Christendom during the Reformation. The Fall of Rome: And the End of Civilization by Bryan Ward-Perkins advances a different critique of a different dominant narrative, that Rome did not decline and fall, it simply evolved into something different. The author is an archaeologist, so the argument is heavily biased toward material remains. His basic thesis is that there was a marked drop off in social complexity and economic output during the transition between the Empire and the Germanic successor states, and that this can fairly be termed "decline." Additionally, there was also a definite change in the culture of the ruling caste, ergo, the "fall" of the Roman autocratic system.


Several lines of evidence are used to draw up the material case. First, Imperial Roman pottery exhibited aesthetic virtuosity, diversity of motif, quantity and standardization. Also, one can trace widespread trade routes because of the style and nature of pottery produced at a particular location. The author makes the last point compelling by explaining that archaeologists are confident that a given pottery shard found in 6th century Iona, in Scotland, is derived from a site in modern day Tunisia. Maps clearly illustrate that pottery derived from one production center (e.g., in southern France) can be found on sites across the Roman Empire (though with increased density as one nears the point of production). The emphasis on manufacturing continues when the author observes that tiling on roofs was common in much of Italy during the Roman period. Though this seems a banal fact, the tiles required some native industry and their later disappearance is a testament to the decline in local economic capacity. Additionally, wheel driven pottery production disappeared from most of the Western provinces of the Empire (and so the pottery was invariably of inferior quality and style), while in Italy where this process continued a diverse and wide randing suite of pottery styles and aesthetics were sharply truncated down to one dominant type. Of course, accepting these talking points means accepting the archaeologist's expertise and notorious bias toward writing history via pottery and other material goods. But here is a point which I think is less parochial:
There is also some fascinating recent evidence from the ice cap of Greenland, that seems to confirm, for metalworking, the general picture from pottery, that manufacturing in the Roman period was on a grand scale. Snow, as it descends to earth, collects and traps atmospheric pollution; in the Arctic it then forms a distinct annual layer, distinguishable from that of other years by a partial thaw in the summer and a subsequent refreezing. By coring into the ice cap and analyzing the samples, it is therefore possible to reconstruct the history of atmospheric pollution through the ages. This research has shown that lead and copper pollution-produced by the smelting of lead, copper, and silver-were both very high during the Roman period, falling back in the post-Roman centuries to levels t hat are much closer to those of prehistoric times. Only in around the sixteenth and seventeenth centuries did levels of pollution again attain those of Roman times....


This, I think a rough gauge of the nature of industry in western Europe in regards to its quantitative scope which nicely supplements the author's qualitative sense.

There is one way that one can uncontroversially assert that Rome did not fall: it continued in the east and morphed into the Byzantine Empire. Wards-Perkins does not deny that while the western provinces of the Empire fell the east remained vital. In fact, he shows that the material remains in Anatolia, the Levant and Egypt attest to a vibrancy through the 5th and 6th centuries. But these same data are also important in highlighting the universal trends which were brought to bear locally at particular times and places. For instance, coinage disappeared, or became rare, throughout much of western Europe just as the Roman provinces fell under Germanic rule. Graphs which record the quantities retrieved at a specific archaeological site as a function of time illustrate this neatly. At each site sharp drops in coin production can be correlated with historical dynamics. For example, the Balkan cities of the Empire exhibited a sharp decrease late in the 6th century, while Anatolia and the Levant only dropped off in the first half of the 7th. Some of the eastern cities did not bounce back to 6th century levels until the 10th century. Finally, the cities of Egypt and the Levant in particular showed the least variation over time as they maintained robust coin production through the 7th and 8th centuries. What's going on here? You can open up an encyclopedia (or, go to Wikipedia), and easily establish probable cause. During the last decades of the 6th century Avars and their Slavic vassals flooded the Balkan provinces of the Eastern Roman Empire, and imperial writ did not extend much further than Constantinople, Thessalonika and a few other fortified citadels in mainland Greece. During the first decades of the 7th century Persia and Byzantium were engaged in a "World War," during which Avars and Slavs from the north besieged Constantinople and Persian armies pushed through the Levant into Syria in the south and north through the heart of Anatolia to the shores across from the capital city (the Empire was only saved by a sweep around Anatolia by sea which enabled deep penetration into the Persian heartland). The 10th century was a Byzantine renaissance, whereas prior to this period the emperors at Constantinople were at a disadvantage to Muslim caliphs based out of Damascus or Baghdad, now they were expanding deep into the Levant (reconquering Antioch), pushing into Armenia and even claiming suzerainty over Mesopotamian emirs. Finally, why were sites in the Levant and Egypt so robust in their coin production through the 7th and 8th centuries? Simple, these were the heartlands of Umayyad Caliphate, the cities of the Levant and Egypt were buoyed by the expansion and preeminence of the greatest power of the day. This is not to write history-by-coins, but rather to show that material metrics can be mapped onto our intuitive gestalt sense of social complexity & economic productivity.

There is much more to The Fall of Rome than a tally of pots, pans and coins. The first third of the book breezily touches upon the conventional narratives of institutional, political and military decay that occurred during the 5th century within the Western Roman Empire. In short, the author concedes that the older models which posit a night and day transition between Romanitas and the barbarism of Germanic warlords were too glib and simplistic. Even in what became England, where a Roman province was culturally assimilated by a Germanic folk movement in contradiction to the other canonical cases (e.g., France, Spain and Italy) the local indigenous population was not exterminated. Written records during the 7th and 8th centuries imply that Anglo-Saxon lords had British speaking vassals. We know from genetic data that this is not unfounded. But, we also know that it is precisely in England that a substantial genetic impact was achieved by Germanic peoples overlain upon the indigenous substrate. In contrast, the signal is weak, if discernible at all, in the provinces of the Roman Empire which preserved post-Latin speech and culturally absorbed the newcomers. Nevertheless, in England the "blood price" for British vassals of the Anglo-Saxon lords was substantially less than that upon similar status members of the ruling race. Though German chiefs and warlords might have been patrons of classical culture (e.g., Theodoric), it is notable that they also clung to their heretical Arian faith (taking centuries to convert), sported mustaches and maintained their own hairstyles, enforced legal inequalities between German and Roman, and even encouraged the implementation of statutes to prevent intermarriage between the peoples. Though many elite families of Roman origin flourished under the new dispensation, it is clear that dispossession also occurred as the German ruling caste expropriated properties for its own maintenance and enrichment. The specific dynamics were local, and varied over both space and time. Romans were not summarily massacred so long as they were useful or necessary, but neither was it a condominium of equals.

Much of this must seem rather obvious to most of you. For the widely read public the idea of the decline and fall of Rome has never been denied, and it remains the consensus view. But, this not true within the academy. In fact, I had dinner with a recent graduate of Columbia University's classics program who disputed that there ever was a decline based precisely upon what he had learned at this institution. If not decline and fall, what? There seem two broad counter-arguments. First, there is the position that the Germanization of the Western Roman Empire was voluntary, insofar as Germanic federate allies of the Empire were invited in and over time simply took over the temporal reigns from the Roman bureaucratic class. In other words, business as usual, the names simply changed. Another tack seems to be to deemphasize material remains and cultural complexity, and suggest that the energies of the post-Roman Western world were funneled into Christianity. Ward-Perkins notes that encyclopedias of Late Antiquity are heavily tilted toward coverage of religious arguments, schisms and transformations, with relatively little space given to architecture, secular learning or politics. In other words, though Late Antiquity might be materially poorer than the Classical Imperial period, at least in the west, it was spiritually superior. Frankly, to me this is reminiscent of Communist era attempts to dismiss the consumer cornucopia of the capitalist world by suggesting that socialist man was spiritually richer if materially poorer. Ward-Perkins does not deny that the Roman empire's plentitude might be perceived as somewhat vulgar, and he makes the argument that the relative commonality of casually obscene and frivolous graffiti before the Empire fell and its near total absence after is another testament to the relative sophistication of the masses during the Pax Romana in comparison to the successor states: a large minority of the population could read and write (he gives 10-30 percent as ballpark figures). Interestingly, of all the Roman Emperors, Justin I in the early 6th century was the first illiterate to ascend to the purple! (see the full list of emperors) Of course we know that amongst the Germanic kings who ruled after Rome illiteracy was no shame or out of the ordinary.

As the book nears its conclusion I was wondering we were going to be asked, "Who is the Proust of the Papuans?" The author makes the case that the average Roman was materially richer and more likely to be literate than the average post-Roman, and he believes that this matters. Ward-Perkins is adamant that the revision to the field of Late Antiquity was necessary, the orthodoxy of the previous era was too reductive and value-laden, but, in the end history is not flat and differences do matter and count. Words like "Civilization" and "Barbarian" have gone into disrepute, but the author clearly believes that they have some substance and utility. Civilization declined in the Italian peninsula during the period between 400 and 600. It continued in Anatolia during the same period. What is civilization? Ward-Perkins does not give a simple definition, but rather suggests that the sum totality of economic productivity and societal complexity of a particular culture at a particular time allow one to slot it into a continuum populate by peoples across time and space. Repeatedly within The Fall of Rome the argument is made that material culture reverted back to an almost prehistoric state. Repeatedly the contention is made that material culture in many locales did not bounce back to Roman standards for centuries or even a millennium. Whether this is good or bad, this is a reality. I think that reading the evidence presented one can make the case that social complexity in many parts of western Europe reverted to Bronze Age analogs, a small warrior elite served by a scribal caste (in this case, often tied to the church) which extracted goods and services in kind from a peasant population which was predominantly engaged in year to year subsistence. In places like England, what was Britannia, literacy disappeared, just as it did in Greece after the fall of the Mycenaeans.

In the book's final chapter the author names names, so to speak, as to the factors behind the current consensus. He notes that in southern Europe, for example Italy, the old fashioned conception of a decline and fall hold true in all their glory and simplicity. The civilized Romans fell to the savage barbarian hordes who brought down all that was good and grand in the world. In contrast, he notes that the scholars who are foremost in pushing for a model of Late Antiquity which emphasizes continuity are northern European and North American. The author observes that research funded by the European Union to explore the past of the continent is ostensibly discussed in English and French, but often the debates switch into German because of the ethnic makeup of the scholars involved. In short, the revision of Late Antiquity and the rehabilitation of the Germanic successor states is in large part a product of the work of German scholars. It is clear that some of what they argue has validity to it, but The Fall of Rome makes the case that it has gone too far. The author recounts that during the period before and just after World War II the pendulum had swung the other way, and French historians accused the Germans of "assassinating" Rome and therefore civilization (making a partial exception for, of course, the Franks). With the integration of Germany into Europe and its central role in the EU this irrational hostility abated. But now the scales have titled in the other direction. Ward-Perkins is at a loss to explain exactly why North American scholars tend to favor the hypothesis of continuity and evolution as opposed to a decline and fall of one civilization and the transition toward a different cultural matrix. He hypothesizes that perhaps the emphasis on Christianity is more congenial in the United States, but the concentration of Late Antiquity scholars in "Blue America" seems make this less plausible (the exception to this is Rodney Stark, who in his recent spate of books does explicitly draw upon revisionist scholars to support his case that all that is good in the West is attributable to the Christian religion). I think that part of the congeniality is the Proust of the Papuans factor, all cultures are created equal and we must not speak of civilization. The hyper-skeptical sensibility which emerged from the Post Modern movement that fleshed out all the contradictions and false constructions within the older historical paradigms has birthed its own solid orthodoxy. All things are equal. Difference does not exist because everything is so different, who are we to judge? Just not, lest ye be judged.

Complexity does not mean description and characterization are beyond our reach. A stance of scholarly epoche as an instrument toward understanding does not entail universal Pyrrhonism. An acknowledgment of the failings of positivism removed from skepticism does not mean that fictions are our only salvation against ignorance. History is not physics, bias exists, subjectivity is the condition of our humanity, but that does not mean that striving is without meaning, that we can not move toward a closer approximation of reality as it was. The imprecision of verbal description, its inability to capture the moments about a given distribution, does not mean that misunderstandings should plant the seeds for perpetual future discord buffeted by the winds of social faction. Julius Caesar was a literate man of some cultural sensitivity, but he was also a megalomaniac for whom genocide was a tool of his own personal advancement. We can understand that individuals are complex entities, with various facets and perspectives, that Caesar could act with generosity and brutality. But this complexity does not imply that we can not place him within his proper social context, the universal richness of individual humans does not render them beyond specific characterization and contextualization in the range of the species. It is clear that Rome was a squalid slave state. It is also clear that the Germanic successor states were not without positive qualities. But just because someone received an A+ mark does not mean they are necessarily a stellar student, and one C- does not imply mediocrity.

Addendum:
The Fall of Rome makes a few attempts to explain how and why Rome fell (and how and why Byzantium did not), but the book is mostly about the aftermath, not the process itself. For that, I highly recommend Peter Heather's The Fall of the Roman Empire: A New History of Rome and the Barbarians.

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The wild man of the forest   posted by Razib @ 4/17/2007 10:26:00 AM
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Since we're talking about chimps, check out this long story about the species which surveys the opinions and research of a range of primatologists.

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Chimps more evolved? - part II   posted by Razib @ 4/17/2007 09:19:00 AM
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The Scientist has some good quotes in a article on the chimp positive selection story from yesterday:
The screen failed to find evidence for positive selection of two genes involved in brain development and cognition - ASPMM and Foxp2 - that studies have previously identified as positively selected genes in the human lineage. Zhang and Lahn agreed that the discrepancy likely results from differences in statistical power between the methods used in the current study and those used in previous work, which also incorporated polymorphism data.


Update: MIT Technology Review has more:
To Zhang's surprise and disappointment, the positively selected genes were not related to brain or cognitive function but to more mundane cellular housekeeping duties. "One explanation might be that the number of genes responsible for evolution of the human brain may be very small," Zhang speculates.
...
"It is very rare that there will be enough changes in such a short lineage to tell us there is positive selection," says Lahn. "I'm very surprised that they claim these are positively selected genes. I would guess if they tried to publish each of these genes as an example of positive selection, there wouldn't be enough supporting data for the majority of them."

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Macaques are not human   posted by p-ter @ 4/17/2007 07:11:00 AM
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One of the more interesting parts of the paper reporting the sequencing of the rhesus macaque (also noted by Carl Zimmer) is that a number of mutations that cause Mendelian disease in humans are actually ancestral. That is, people with the disease have mutated to a sequence that's the same as the macaque one. Perhaps most notable are mutations in genes important in amino acid synthesis; one might expect these pathways to be well conserved. As the authors write:
In humans, these mutations greatly perturb the normal serum amino acid levels. Direct examination of macaque blood revealed lower concentrations of cystine and cysteine than in the human and slightly higher concentrations of glycine than in the human, but no increase in phenylalanine or ammonia, which might have been a predicted result of these changes. Although the effect of the observed alleles might be greatly influenced by compensatory mutations or other environmental factors, it remains a possibility that the basic metabolic machinery of the macaque may exhibit functionally important differences with respect to our own.
1. This is a strong argument for studying rare Mendelian diseases in humans. People sometimes bitch, "Who cares? Disease X affects 5 people in the entire world, why bother?". The answer, of course, is that those people are the human equivalents of knockout mice (to be horribly cold about it)-- people carrying rare recessive mutations are an important source of information about how those genes work in humans (see also this example), especially if those same genes are involved in different pathways in model organisms like the macaque or the mouse.

2. The ancestral disease alleles are also of prime interest for more detailed studies of selection. Deleterious mutations, of course, always have a probability of becoming fixed in a population; it takes more to show selection. But it's interesting ot note that the authors find a number of the mutations lead to mental retardation in humans. Could some of these genes be involved in human brain expansion and cognitive capabilities?

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Monday, April 16, 2007

Heights of daredevils: shorties get the girls   posted by agnostic @ 4/16/2007 08:46:00 PM
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To expand on the findings of a previous post on shorter guys dominating the pretty boy and hip hop niches, itself inspired by a discussion at Steve Sailer's blog on short guys dominating the rockstar niche, let's now consider the average height of males who specialize in another show-off niche: daredevils. Since performing physically dangerous stunts must require a certain degree of athleticism, you might think that daredevils would tend to be taller than average, as in basketball, football, and other popular sports. On the other hand, perhaps what counts more than height or dominance are nimbleness, ability to maintain one's balance, and being a smaller target (e.g., when being charged by a bull or having darts thrown at one's body). To investigate, let's have a look at the heights of the main cast of the popular MTV daredevil show Jackass. [1] Examining just the hardcore, professional members:

Jason Acuña - 4'7
Bam Margera - 5'8
Chris Pontius - 5'8
Preston Lacy - 5'8
Ryan Dunn - 5'9
Brandon Dicamillo - 5'9
Steve-O - 5'10
Dave England - 5'10
Johnny Knoxville - 6'0.5
Ehren McGhehey - 6'1

Using the data at the excellent celebheights.com website, I could only verify the heights of Knoxville, Margera, and Steve-O (in the thread on Knoxville). The other heights are from their imdb.com entries, and so are probably exaggerated by 1 inch or so (this is clear from comparing cast members when they stand side-by-side in stunts). Making no adjustments, and leaving aside the outlier of Jason "Wee Man" Acuña (a "little person"), the mean here is 5'9.7; while reducing the unverifiable heights each by 1 inch gives a mean of 5'9.1. For American males age 20-39 (see the PDF here, p.10), mean height is 5'9.6, based on a sample of 1441. I assume the SD for height of the general population is 3 in., though the test is not affected by any reasonable choice. We accept the null hypothesis of no difference in means between daredevils and a random sample of males, regardless of whether we use the unadjusted or adjusted data (both p greater than 0.6 using a two-tailed t-test). Even norming to non-Hispanic White height does not make the results significant (p ~ 0.3). Admittedly the n is small, and perhaps a larger dataset on professional daredevils would resolve the issue of whether there truly is no difference or whether the non-significant trend toward shorter stature here is actually significant.

Looking at a related group of elite athletes in "extreme sports" such as skateboarding and BMX (rather than the all-purpose daredevils of Jackass), I found this handy webpage for a star-studded event that includes height info. NB: Tony Hawk is actually ~6'2, not 6'3 as reported at the above website (let alone the claim of 6'4 at imdb.com), according to several profiles (e.g., this one and this one), and by comparing him and Johnny Knoxville when they stand side-by-side in a stunt for Jackass Number Two. It's always safer to round down when we're talking about self-reported male height. Comparing the mean of these 15 males -- 5'9.3 -- with that of the aforementioned representative sample of American males, we again accept the null hypothesis of no difference in means (p greater than 0.7 using a two-tailed t-test). As with the stunts of "well-rounded" daredevils, those of the specialists too do not appear to demand taller or shorter than average height.

So, if daredevils tend to be of average height, why the insinuation in the title of the post that they qualify as "shorties?" In the mating arena, the minimum height for an American male to qualify as a "good blind date" is probably 6' or 6'1, so that men who are shorter than this must make up for it somehow. For example, a study of online dating outcomes (PDF) suggested that a 5'10 male would have to earn $32,000 more than a man of 6' in order to receive the same amount of attention from women. The idea is that females are more concerned with quality than quantity of mates, so that they focus on traits as proxies for quality. Since it's rare to find a male who scores highly on all desirable traits, most women face a trade-off between competing "almost dream guys."

Being a professional daredevil is a pretty easy way to signal your genetic quality -- only the truly blessed can perform one dangerous stunt after another without being disfigured, mamed, paralyzed, or killed (watch the bloopers reel for amateur daredevils and see). You need at least general intelligence, boldness and risk-taking, and physical deftness / coordination. So, this could be another instance of the Handicap Principle. Once the first few daredevils in history figured out that they could impress girls as sex symbols, they would have had more children than the population average, increasing the frequency of alleles implicated in the relevant traits. This logistic growth would have continued until their niche became saturated (i.e., when it would pay off more to specialize in some other niche than join the daredevils). Again, it's hard to attention-whore when everyone is exhibitionistic in the same way. [2] This show-off quality is what distinguishes the daredevil niche from others that might also preserve variation in daredevil-ish traits, such as that of young soldiers (cannon fodder). By hypothesis, daredevils are more narcissistic than soldiers.

These processes will maintain genetic variation in traits such as excitement-seeking and height when other pressures might want to erode such variation; e.g., females might in general want a 6' partner or a cautious father of her children. In the comments of a related post on the heights of female sex symbols, Jason asked whether the trend toward shorter male height was an effect of production companies wanting to minimize the height difference between male and female stars, preventing awkward shots. The data on daredevils suggests that this is not a reason, as they rarely appear kissing females on film, and the same is true of rockstars.

And returning to another post on the role of technology in preserving variation, new technology will help people to identify who is cut out to be a daredevil since most stunts involve taking punishment from some product of human artifice, taunting but escaping from a deadly predator using technology, and in general using technology to push the limits of human performance. Now, this is not to say that pre-industrial individuals were jumping off cliffs with a parachute, but the Spanish matador requires only a sword (and really a stick with a large, sharp arrowhead might do). Also, Jackass members Chris Pontius and Steve-O developed their own daredevil show, Wildboyz, in which they often don't use technology at all, but rely on withstanding assults from wild animals (e.g., having their buttocks stung repeatedly by scorpions or surviving a swim with killer sharks). So, there's no reason this dynamic could not have started tens of thousands of years ago, although surely recent history, during which human beings have radiated into a myriad of diverse physical and social environments, will have created different frequencies of such traits between populations. [3]

We now turn to the question of whether daredevils actually do manage to mate with top-choice females, since status per se isn't attractive (as Half-Sigma likes to point out w.r.t. World of Warcraft nerds). Here are some photos of the girlfriends / wives of the sub-6' daredevils:

Bam Margera's wife
Bam Margera's former fiance
Chris Pontius' wife
One of Steve-O's girlfriends (others)
Best example: Wee Man's girlfriend (see pics "w/ Trisha")
Dave England's wife
Dave Mirra's wife (in the middle)
Carey Hart's wife is singer Pink
Bucky Lasek's wife

Perhaps more important than quality is quantity of mates, since the latter is more of a limiting factor on male reproductive success. Steve-O says here that he often sleeps with groupies, and judging from the friends on the MySpace pages of the Jackass members, their groupies are plenty -- and plenty attractive. On a final note, the shorter male readers should take this into account when encouraging your sons to take up one activity or another: if you want them to be successful with females, they'd better train hard to enter a niche that's tailored to short or average-height guys.

[1] No student of human biodiversity can forever avoid pop culture icons, filled as their ranks are with freaks and deviants of all kinds. The only DVD I've ever bought is Jackass Number Two, which I highly recommend to all the young male readers, if you haven't seen it already. The DVD contains lots of bonus footage, too. It is easily one of the most hilarious movies I've ever seen. For those who are unfamiliar with the material, here are a few illustrative examples from YouTube (both NSFW): here and here.

[2] Another clear example of the exhibitionistic appeal of the Jackass members is that they frequently engage in very homoerotic behavior, although none are gay. This is like the increasingly large group of straight girls in college (and, I hate to think, high school) who conspicuously make out with each other at parties (leks) in order to monopolize the attention of the alpha males.

[3] One puzzle is why sub-Saharan Africans are not only underrepresented among daredevils, but are positively freaked out as a group by the idea. (Watch any black stand-up comic show long enough, and soon you'll learn that they love to joke about how insanely death-defying White people can be, in contrast to the sensible Blacks. Another frequent topic is that White people stick around to find out what's going on in a calamitous situation, whereas Blacks immediately get the hell out of there.) This is a puzzle because they are well represented in most other show-off niches such as dancers, singers, athletes, models, and so on. Two possible reasons for this are the aforementioned aversion to "danger in nature," as well as their group's mean IQ of 85. Again, part of the daredevil appeal is that you rely on smarts to avoid accidents. Linda Gottfredson recently argued that avoidance of accidents was part of the reason why human beings became more intelligent (her first paper under 2007). The Jackass members are smart enough to pass high school-level classes at least (though Chris Pontius dropped out); Steve-O attended the University of Miami for a time, and his father is a high-ranking business executive.

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Salaam   posted by Razib @ 4/16/2007 07:51:00 PM
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So I was at Starbucks the other day, and there was this swarthy dude hanging around (OK, my thought was, "dude looks like a terrorist?!?"). Anyway, these two women, one 60ish and another 40ish were staring at him, and finally the older one was like, "Where are from???" Swarthy-man responded, "I'm from Sawoooodi Arabia" (phonetic for Saudi Arabia). The older woman then asked, "What do they speak where you are from???" The Saudi man responded, "Arabic." There was then a long conversation which I didn't follow closely, until the two women got up to leave. The younger one then turned out, clasped her hands together in the Namaste gesture and bowed ever so slightly and said, "Salaam!" The Saudi guy seemed a bit confused but he smiled and responded with a "Salaam."

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Neuroscience Basics II: Dendrites, Axons and Action Potentials   posted by Matt McIntosh @ 4/16/2007 06:56:00 PM
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There are four kinds of ions involved in the intricate feedback system described in Part I: calcium (Ca2+), potassium (K+), sodium (Na+), and chloride (Cl-). They all serve different functions, but for now all you need to know is that first three carry a positive charge while last is negative, and that "at rest" the interior of the neuron caries a negative charge relative to its surrounding environment. With me so far? Onward.

Each type of ion exists in different concentrations within the the neuron when it's "at rest", and this concentration is governed by how permeable the cell membrane is under conditions of inactivity. In this state, K+ flows pretty freely in and out of the membrane and is close to equlibrium, but the others are all restricted (and thus out of chemical equilibrium) to varying degrees: Na+, Cl-, and Ca2+ are all banging at the gates to get inside. Also, each type of ion channel permits flow at different rates, K+ being the slowest of the four. I mention this now because it becomes important later on.

So let's say that while a neuron is just minding its own business, some meddling neuroscientist comes along and injects a bunch of Na+ ions into it. Since sodium ions carry a positive charge, this would make the voltage across the cell membrane tend to become less negative—i.e. it would move the neuron closer to electrical equilibrium with its environment (known as "depolarization"). If it had been Cl- ions instead, the opposite would occur: the voltage would become more negative, moving the system further from equilibrium (known as "hyperpolarization"). Or suppose instead that some K+ ions were sucked out; hyperpolarization would tend to occur in this case too. But in each case, the excess ions would gradually be pumped out by the cell's regulatory system (or more ions allowed to flow in, in the K+ example), bringing it back to the initial set point.

This is exactly what happens in normal neural activity, except instead of a meddling neuroscientist it's mediated by ion channels. When the synaptic endpoints of the neuron's dendrites (which I'll talk more about in a later post) recieve a particular neurotransmitter, their ion channels for Na+ or Cl- will open depending on which neurotransmitter it is. We'll get into neurotransmitters more later, but for now I'll just introduce two of them: GABA and glutamate.

To simplify it in very crude terms for now, GABA is the signal for "open some Cl- channels" and glutamate is the signal for "open some Na+ channels", which will cause an influx of these respective ions into the cell, lowering or raising the voltage accordingly. Glutamatergic transmissions from other neurons are considered "exicitory modulation" because they tend to encourage the neuron to fire, while GABAergic transmissions are considered "inhibitory modulation" because they tend to discourage it.

Whether or not a neuron "fires" depends on whether the summed ionic charges inside it cause the neuron to depolarize below a certain threshold: in the short run, if there's an equal influx of Cl- ions and Na+ ions then the effects will be a wash—the overall voltage doesn't change and nothing happens. Once the dust clears, the sodium and chloride ions get pumped out and the cell goes back to waiting for the next round of stimulus.

But if the influx of Na+ outweighs the influx of Cl- by a certain threshold (i.e. the excitory stimulus outweighs the inhibitory stimulus), it sets off a chain reaction which I'll now describe. Remember that I said in Part I that some (but not all) of the ion channels in the cell were voltage-senstive (or "voltage-gated"); now two of these become important.

First, there are voltage-gated Na+ channels that start to open up when the cell depolarizes, allowing more sodium ions in and depolarizing it further in a wave of positive feedback that starts in the dendritic region and spreads along the cell body toward the axon. (When Cl- ions are predominant, they act to cut this process off at its starting point by overpowering the positive charge and keeping the downstream sodium gates from opening, halting the chain reaction before it really takes off.) Once the cell depolarizes past a certain point, these gates close again and the Na+ stops flowing in.

As the influx of Na+ spreads through the cell, it triggers the opening of a special set of K+ channels that are normally closed, but open up when the cell depolarizes past a certain threshold, allowing K+ ions to flow out of the neuron and causing the cell's voltage to start going negative again. As I mentioned a few paragraphs ago, the action of these K+ gates is slower than those for Na+, so you end up with a second wave of re-polarization lagging behind the initial wave of depolarization.

Once the depolarizing wave reaches the axon, the real action begins. Most axons in mammals are coated with a sheath of myelin (basically a special extra-thick layer of phospholipids), which acts as an insulator preventing any ion transfer across the cell membrane and makes the axon the most highly conductive region of the neuron. If it isn't obvious why, you can think of an unmeylinated axon as a leaky pipe: when a pipe is full of holes, it takes a lot of force to push water all the way through it because the water keeps diffusing outward. Myelin effectively "plugs the holes", which means it requires less force to push "water" (charge) through the "pipe" (axon) at a faster rate. So myelin speeds up transmission along the length of the axon by easing propagation of electrical charge.[1]

However, there are still only so many ions, so in order to keep the charge from dimnishing as it travels the length of the axon, fresh influxes of Na+ are necessary. For this purpose, there are periodic breaks in the myelin sheath about a micron wide, known as nodes of Ranvier.[2] These nodes are each loaded with a whole bunch of hair-trigger Na+ channels that will open up under conditions of depolarization, and their combined effect is to make the current move along the axon in a series of fast hops, basically acting as voltage repeaters.

The K+ channels continue to play catch-up, bringing the charge back to normal negative polarity in the wake of the wave of positive charge. Eventually the ion pumps in the cell will clean everything up and bring all the ion levels back to baseline, but right now the cell is busy just trying to normalize its voltage. This entire process is called an "action potential", or simply a "spike" because of the spike that appears on a voltmeter monitoring the neuron during an action potential. One important feature of an action potential is that "a spike is a spike is a spike"—the amplitude of the wave is always the same for every single action potential. This is the only part of the neuron that can be considered "digital": either it fires or it doesn't, with no grey area. (What can change is the number and frequency of spikes, but that's for later posts.)

Once the wave of positive charge reaches the endpoints of the axons ("axon terminals"), sodium's job is done and voltage-gated calcium channels are waiting to pick up the ball. When the voltage at the axon terminal goes positive, there's a flood of Ca2+ into the axon terminal, which triggers . . . well, we'll get into that later after we cover synapses in the next post.

Addendum: There are, of course, many more ways of modulating neural activity than I've presented here, but when writing an introduction to the workings of any complex system you have to balance the need for thoroughness against the need to avoid overwhelming the reader with too much at once. For instance, there's almost no such thing as a neurotransmitter or ion that just does one thing in the brain, but the goal for now is to get the gist across so everyone has a working mental model of neural processes and then build up the complexities from there.

Notes:

[1] Those of you with an interest in Ashkenazi intelligence & diseases will rightly perk up here. Some of recessive diseases they're prone to like Niemann-Pick screw up the myelin sheath in ways that likely result in faster signal propagation in a heterozygote.

[2] How these guys got a piece of neuroanatamy named after them, I'll never know.

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Chimps more evolved?   posted by Razib @ 4/16/2007 03:00:00 PM
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The times has a mildly stupid article up, Chimps are ahead of humans in the great evolutionary race, which just goes to show that the people writing the headlines often have no comprehension skills, or just don't bother reading more than the first paragraph of a story. As confused as the article is it contradicts such a stark assertion. Here's the important point:
They found 154 human genes that showed evidence of the rapid positive selection that marks out adaptive traits, but 233 chimp genes with the same qualities.


Read the article with great caution, some of the sentences are very confused. That being said, I'm less interested in the raw count of differences in regards to evidence of positive selection (which can be sensitive to the test you're using, for example), then what differences exist between the loci in question. If the authors had found something suggestive I'm assuming they would have trumpeted it. Here's the journal reference: Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.0701705104, so keep an eye out for it (the lab's website gives the title as More genes underwent positive selection in chimpanzee evolution than in human evolution). I'm assuming that this will be the link: http://www.pnas.org/cgi/doi/10.1073/pnas.0701705104. Also, here's something that caught my attention:
It is also possible that there are more adaptive genes in the human genome that have been positively selected, but that these emerged too recently to have been detected by the study.


Hmm....

Update: Much more intelligible article in ScienceNow. More details about the paper:
...the fast-evolving genes in humans and chimpanzees do not readily account for the obvious physical differences between the two species, Zhang points out. In the chimp, genes that have outpaced those in humans include ones involved in protein metabolism, gene transcription, and stress response. "You wouldn't immediately notice if the chimpanzee has a better stress response than a human," says Zhang. In the human, too, the differences appear to be subtle, with selection working rapidly on genes concerned with fatty acid metabolism and phosphate transport.
...
But that's not the whole story, argues Ajit Varki, a physician-scientist at the University of California, San Diego. "It's a terrific paper, but they're only looking at one mechanism, the changing amino acids in proteins. Other mechanisms in gene evolution--such as gene expression, duplication, conversion, and inactivation--are likely to be equally important." Further, Varki adds, these types of genomewide analyses are limited, because they do not address the issue of gene function. "It could be that the deletion of a specific gene or a single amino acid change could have more biological significance than a large number of genes that seem to have undergone many changes." And that means we're still a long way from explaining what makes us human--or them chimpanzee, he says.


Regular readers will know that exploring differential gene expression and copy number are hot fields that are coming to the fore. I assume that the paper itself will be a little less annoying than these overwrought popular press articles.

(yes, I'm not even addressing the orthogenetic or chain of being talking points, who cares? That's for the general public)

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I don't like Mondays?   posted by the @ 4/16/2007 02:42:00 PM
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Everybody okay?



Sunday, April 15, 2007

On the use of the word 'epigenetic'   posted by amnestic @ 4/15/2007 10:27:00 PM
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It appears that I'm not the only one musing on the meaning of 'epigenetic'. This timely essay from Mark Ptashne in Current Biology, takes a hard line, even calling into question the connection between histone modifications and epigenetics.
As a glance at the literature will reveal, however, histone modifications - acetylation, phosphorylation, methylation, and so on - are now often explicitly called 'epigenetic modifications'. This despite the fact that, so far as I am aware, no histone modification has been shown to be heritable.

This section might be relevant if you are looking to 'epigenetic mechanisms' for the stability and persistence necessary for a long-term memory mechanism:
Why might one be pre-disposed to misuse the term epigenetic? The term is sometimes used in the context of "maintaining stable states of gene expression", as though some 'locked in' mechanism, involving histone and/or DNA modifications, were required for stable states of gene expression in eukaryotes. But, in the first instance, there would seem to be no such special requirement: lambda lysogens are essentially infinitely stable in the absence of the specific signal that inactivates the repressor, and this system - of course - involves no histones.

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Female sex symbols: somewhat taller than average   posted by agnostic @ 4/15/2007 05:48:00 PM
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A recent John Tierney blog entry cited a much discussed study of online dating behavior (PDF), which suggests that shorter than average women have it easier in the online dating market, with the ideal height being about 5'2 - 5'3, and taller heights incurring increasingly greater costs. [1] However, women clearly vary in height well outside this range, so something is responsible for so much variation in height being maintained. Here I examine a fairly obvious, partial reason: being somewhat taller than average pays off if a woman is specializing in a niche that depends on sex appeal, in particular sex appeal that incorporates a fair amount of moxie / aggressiveness.

To test this hypothesis, I used celebheights.com to determine the heights of the women listed in the Maxim 2006 Hot 100 ranking. It's somewhat of a "sample of convenience," but it's hard to argue that the women there aren't sex symbols or that Maxim has an irrational bias toward women of a certain height. I could only find data for 77 of them [2], which you can see below the fold. [3]


The above frequency distribution by two-inch blocks (up to and including the right endpoint) shows that the heights of sex symbols are approximately normal (skewness = 0.07, or essentially symmetrical), with mean = 65.6 in. and SD = 2.8 in. A representative sample (PDF p.10) of 1,371 US women aged 20-39 showed that their mean height is 64.1 in., making sex symbols on average 1.5 in. taller than the average American woman. Using any reasonable estimate of variance in the general female population, a two-tailed t test shows that this difference in means is significant (t = 4.5, p less than .0001 -- perhaps lower; my calculator cut it off there). Clearly, being a bit taller than average helps in becoming a sex symbol. But does it matter even within the sex symbol set? Not really. Here is rank in the list as a function of height:


The Spearman rank correlation coefficient between height and rank in the list is 0.14 but is not significant (p greater than 0.2). So, being a bit taller than average probably helps you get noticed, but it is not of central importance. Note, though, that the non-significant relationship is not due simply to a restricted range for height in this sample -- the SD of 2.8 in. is close enough to the commonly used estimate of 3 in. for the general population.

Having established the greater average height of such women, what accounts for this pattern? This tends to be the most bullshitty part of a report, so I'll just throw out some guesses, and readers can add their own two cents in the comments. (Apologies for not researching / citing this section, but my hunch is that it'd be easy to dig up a few references for and against each of the guesses, as the "why" is always harder to pin down.)

Conjectures that assume there's something sexy about tallness per se:

- Longer legs. My eyes feast upon other parts, so perhaps in the comments the leg men can explain the appeal of long legs.

- Greater height tricks the eye into seeing a thinner figure. Fatter is usually not sexier (unless it's fatter than Kate Moss), since it reflects poorer health.

Conjectures that assume height isn't sexy per se, but that it covaries with some sexy other traits:

- Greater height could reflect a higher degree of male-typical hormones, which would aid the female in projecting the less passive / "take what she wants" attitude that characterizes sex symbols.

- Greater height could reflect better nutrition and healthy development in general -- think of all those Midwestern model types who grew up away from pathogen- and- toxin-infested urban areas. Good health is sexy per se.

A conjecture that assumes height isn't related to sexiness at all:

- Greater height is necessary to stand out from the crowd and intimidate other women in the entertainment industry. Maybe the average guy couldn't care less about a woman's height, but to break through and survive in a cut-throat industry, sheer height helps.

Whatever the reasons turn out to be, it's clear that there are reproductively prosperous niches that taller than average women are suited to, so that some genetic variation in height will be preserved despite males' apparent greater interest in females who are 5'2 - 5'3. Presumably the same is true in the other direction: former rockstar Shakira says here that being petite (she is ~5'1) causes men to act protective around her. Petite women might have a more sprightly, giggly appeal; so, alleles for shorter height could be preserved either due to the sexiness of girly girls or due to their receiving more protection and investment from others because of their pedomorphic stature.

[1] Oddly, the authors phrase this as a trade-off of height vs. income -- i.e., how much more income would a 5'10 woman have to earn compared to a 5'4 woman in order to garner the same amount of male attention? This makes sense when looking at female preferences since most female online daters are concerned principally with the guy's height and income, and thus face a trade-off should a particular guy not excel at both traits. It makes zero sense to look at male preferences this way, though, since most men are interested in many other physical traits before height even enters their mind, and income and power are not sexy to most men.

[2] I coded the women by rank only, so if a reader wants to know which data are missing, I'll upload the Excel sheet, and they can see for themselves. Almost all of the missing data are from the bottom of the ranking anyway, so the more important points are accounted for.

[3] I took the cited height for granted if it was an integer; otherwise I browsed through the text of the entry and discussion to decide which number was most accurate, sometimes rounding up, sometimes down, and sometimes keeping it as is. (19 of 77 data-points are non-integers, so I didn't round indiscriminately.)

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Data visualization sites   posted by the @ 4/15/2007 01:38:00 AM
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In the spirit of Gapminder, I've noticed three data visualization sites which present user-generated content:
* Many Eyes (does maps!!!)
* Swivel
* Data360

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Saturday, April 14, 2007

IQ, height & Crooked Timber   posted by Razib @ 4/14/2007 08:08:00 PM
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John Quiggin @ Crooked Timber has a post where he moots ideas re: IQ & height. If you're inclined to give dkane a helping hand, swing on over! Just remember, the gang @ CT are much, much, smarter than you, so tread lightly....

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Friday, April 13, 2007

Macaque genome   posted by p-ter @ 4/13/2007 07:56:00 AM
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No time to comment extensively, but I thought I'd point out this collection of (open access) papers associated with the publication of a draft version of the rhesus macque genome. Of partcular interest is this paper on human-specific changes in genomic structure:
Knowledge of the rhesus macaque genome sequence enables reconstruction of the ancestral state of the human genome before the divergence of chimpanzees. However, the draft quality of nonhuman primate genome assemblies challenges the ability of current methods to detect insertions, deletions, and copy-number variations between humans, chimpanzees, and rhesus macaques and hinders the identification of evolutionary changes between these species. Because of the abundance of segmental duplications, genome comparisons require the integration of genomic assemblies and data from large-insert clones, linkage maps, and radiation hybrid maps. With genomic triangulation, an integrative method that reconstructs ancestral states and the structural evolution of genomes, we identified 130 human-specific breakpoints in genome structure due to rearrangements at an intermediate scale (10 kilobases to 4 megabases), including 64 insertions affecting 58 genes. Comparison with a human structural polymorphism database indicates that many of the rearrangements are polymorphic.




Dinosaur proteins???   posted by Razib @ 4/13/2007 12:06:00 AM
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This extraction seems whack. Did people know this was going to come out?

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Thursday, April 12, 2007

Fragile X protein as an mRNA stabilizer   posted by amnestic @ 4/12/2007 09:33:00 PM
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Fragile X mental retardation is a very common mental disability resulting from reduced expression of a protein called fragile X mental retardation protein (FMRP). The most obvious difference in Fragile X brains is that the receiving end of most excitatory synaptic input, dendritic spines, are misshapen. They look thin and immature rather than mushroom-y or stubby. FMRP has been shown in recent times to regulate the expression of other proteins at the translational level. It can bind different mRNAs and interfere with their ability to be translated into proteins.

PSD-95 (Post-Synaptic Density-95) is a central organizing protein in the architecture of synapses. It contains several protein-protein interaction domains, allowing it to serve as a scaffold in dendritic spines. Of particular interest is its ability to regulate a dendritic spine's excitability by clustering glutamate receptors in the post-synaptic density. Check the figure below. It can hook up the major excitatory neurotransmitter receptors to the NMDA receptor (heavily implicated in learning), and it can hook these both up to the actin cytoskeleton which determines the whole shape of the spine/synapse.
There is a new paper in Nature Neuroscience showing that FMRP binds to PSD-95 mRNA and that binding increases the stability of PSD-95 mRNA. The first reason this is novel is because normally FMRP regulates RNAs by keeping them away from the protein synthesis machinery, but in this case it is keeping the RNA away form degradation. Another novel aspect is that FMRP appears to bind in between to AU-rich elements (AREs) in the PSD-95 mRNA, connecting it to a larger literature regarding AREs and mRNA degradation. This paper does not show experiments showing that these AREs target PSD-95 mRNA for decay, but it leaves open the possibility. The idea would be then that FMRP binds the mRNA and blocks binding of proteins that would like to grab the RNA and drag it off to be degraded.

I have only read the paper once, but here is a figure that is bothering me:

They are showing that PSD-95 protein levels are reduced in FMRP knockout mice, ostensibly because FMRP is no longer stabilizing the mRNA so we get less protein. It appears from looking at the graph and the western blot that they are using eIF4E as a loading control (i.e. they are normalizing the PSD-95 protein levels to the eIF4E levels), but as far as I know this is very unconventional. Conventionally, something like tubulin or actin would be used as a loading control. I'm sure some reviewer wiser than me got a reasonable explanation, but I'd be willing to believe that eIF4E levels could be affected by loss of FMRP. Look at the cerebellum data. It looks weird, right?

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Who's your daddy???   posted by Razib @ 4/12/2007 02:05:00 AM
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Via Genetics and Health I came across this story:
But modern-day science often unearths secrets long buried. When the DNA results landed on Isaac Owusu's dinner table here last year, they showed that only one of the four boys - the oldest - was his biological child....


I'm not interested in the details of the story (immigrants who find out their putative children aren't their biological issue). Rather, whenever I bring up paternity I do note angry comments seem to emerge unbidden from regular readers who ordinarily seem placid. Why? The reality in the United States is that it is in the "child's best interest" to have a father, and whoever gets "tagged" with fatherhood has a lifetime's worth of bills. But I'm interested in some more "deep time" questions, because the issue of paternity is important to two threads we've discussed on this weblog of late: facultative homosexuality and selection in pre and post Neolithic societies.


Why is female virginity and fidelity so prized, so honored, unto death, in some societies? Simple: in those societies property is passed down through patrilineages. If the "stranger" happens to be the eldest male in his lineage in a given generation someone who is not of that lineage genetically can have total control over a whole family. In contrast, in many small scale societies which are not necessarily patrilocal (women do not move to the man's house upon marriage) or patrilineal infidelities are of lesser concern because frankly there isn't that much at stake. Males do not control the means of product, nor are they expected to fully support one woman and all her offspring. This is not limited to small scale societies, consider Sambandham, a form of "casual marriage" (rough translation) amongst the matrilineal Nairs of southern India. In contrast in north India Hindus practice strict exogamy and patrlineal descent, as well as thorough patriarchy, enforced by the culture. There is no casual element to marriage, and new brides are assumed to be under the dictatorial and tyrannical rule of their mothers-in-law. In Arab societies the importance of male lines of descent is so important that women are sequestered and protected as pure resources, bearers of the next generation of males to lead the clan. Non-marital sex can have dire functional consequences for dozens or hundreds of people, so it "makes sense" that the harsh regimes we see imposed on young women are operative amongst Arabs. Most societies do not lay at either extreme, consider that Genghis Khan's main wife was kidnapped and raped early on in their marriage, and so the paternity of his eldest "son," Jochi, was always in doubt. Though he acknowledged Jochi as his son the uncertainty about his paternity led to him being passed over for the preeminent position amongst his brothers and was the root of tensions which resulted in a rift with his "father."

What does this mean for the evolution of human societies? We've alluded to the power of reproductive skew and within group variance being heightened after the transition to mass societies because of the spread of agriculture. We've also alluded to the possibility of metapopulation dynamics and within group dampening of status & reproductive variance in hunter-gatherer conditions. Though it is a rare individual who takes no interest in the fidelity of his putative mate, the study of small scale societies seems to suggest that the extreme tendencies of Arab cultures are not manifest within them. Rather, infidelity generates discord, irritation or anger, but there are no great material or status inheritances at stake. But once super-males arose with mass societies and the emergence of "men in groups" then the stakes were raised. Harems guarded by eunuchs are the logical end stage of the development of the super-male optimal strategy, but there are many small steps along the way. Pre-Neolithic societies were never "matriarchal" and "peaceful," and I suspect that Marijas Gimbutus' Old Europe was no such culture. But, Old, Old Europe might have been a bit less fixated on sexual paternity because the stakes across the generations were just not as large.

Related: How Well Does Paternity Confidence Match Actual Paternity?

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Don't call it science fiction!   posted by Razib @ 4/12/2007 01:39:00 AM
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Wired has a funny story about the terror that marketers have about pushing anything as "science fiction" or "sci-fi." This is very relevant today, as Kurt Vonnegut has just passed away, and he is one of many writers (e.g., Phillip K. Dick) who left the science fiction ghetto. What makes science fiction so horrifying? I hold that it is a demographic issue: the core readership of science fiction consists of ugly young adult males. Once I was in Montpelier, VT, in a used book store. I was curious where the science fiction section was so I just scanned the aisles, and sure enough there was a slightly overweight, greasy haired and pasty faced male around the age of 25 rooting through copies of E.E. Smith. I knew I'd hit pay dirt. In any case, as Isaac Asimov once observed, all great fiction is to some extent science fiction and fantasy. If someone in the 1930s read contemporary fiction they might perceive it as near future sf with a character based focus. Epic poems like the Iliad and Odyssey are really little different than a lot of "high fantasy" except in their quality. Speaking of which, anyone read good science fiction or fantasy of late? And is there any good site that reviews? SF Site seems to like everything (the last SF and/or fantasy that I read was The Thousandfold Thought).

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Wednesday, April 11, 2007

High Sensitivity Test   posted by Razib @ 4/11/2007 10:38:00 PM
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Take the test here to see if you are highly sensitive. You probably know if you are, but let's see how many GNXP readers score 14 or more. Probably more than 15-20%. I scored a 2 FYI.

(post your score in the comments)

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South Park + 300 => genius!!!!   posted by Razib @ 4/11/2007 09:30:00 PM
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If you've watched 300 and are a fan of South Park, you have to watch the most recent episode.

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Pope on evolution   posted by the @ 4/11/2007 06:48:00 PM
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AP and others have the story.

Benedict added that the immense time span that evolution covers made it impossible to conduct experiments in a controlled environment to finally verify or disprove the theory.

"We cannot haul 10,000 generations into the laboratory," he said.


Setting aside the inappropriately narrow view of how science is done, this is factually incorrect. 10k E. coli generations take ~1 year. 10k yeast generations is <2 years. There are yeast strains that have been evolving in wine for hundreds of years.

See also chemostat

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Darwinian reductionism   posted by p-ter @ 4/11/2007 04:32:00 PM
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As a general rule, I find most philosophy of science unbearable, mostly for the reason that the amount of factual error made by these philosophers is impressive. I find it analogous to many conversations I've had outside the US about the US political system-- people maybe get the general outline, but often make confident and utterly wrong assertions about the details. So when I read this review of Darwinian Reductionism, I was fairly unsurprised to see that the reviwer pointed out factual errors. But still, this is pretty impressive:
The lack of concern with the genome is highlighted, for example, when in the course of a single paragraph he says that sculpting of the genome by natural selection has resulted in "a division mainly into genes" and refers to 95 percent of the human DNA sequence appearing to be "mere junk" (another hypothesis that has been widely rejected). It is conceivable that Rosenberg means to define genome so as to exclude the junk, although I have never encountered such a usage before
...
More striking is his remark that alternative splicing is "uncommon but not unknown," whereas it is actually widely accepted that such splicing occurs in more than 70 percent of human genes. Although Rosenberg has researched some biological topics in detail, the book contains other lapses as well. He appears to be unaware, for instance, that methylation occurs in contexts other than sexual imprinting. And I was struck by his remark that the world is now mainly populated by sexual species; in fact, the overwhelming majority of organisms now, as ever, are prokaryotes and (relatively) simple asexual eukaryotes




The quest for equality   posted by Razib @ 4/11/2007 03:34:00 PM
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Rooting Out the Robin Hood Effect:
After several rounds, a noticeable pattern emerged: The rich suffered, and the poor got a helping hand. Over 70% of the money spent to drain another player's purse was directed at richer players, while around 60% of income-boosting spending went to poorer players, the team reports tomorrow in Nature. What's more, the poorest participants spent almost twice as much money draining incomes than top earners did, and the top earners spent 77% more than the poorest players to boost lower incomes.


Now, from page 156 of Evolution for Everyone:
...Lee's informant [amongst the Bushmen] was perfectly aware of the purpose of all this jesting: "When a young man kills much meat, he comes to think of himself as a chief or a big man, and he thinks the rest of us as his servants or inferiors. We can't accept this. We refuse one who boasts, for someday his pride will make him kill somebody. So we always speak of his meat as worthless. In this way we cool his heart and make him gentle.


The author's point is to the illustrate the emergence of groups amongst humans, and how they dampen within group differences. He uses the literature to show that our closest relatives, the chimpanzees, tend to be less egalitarian in this manner than small scale societies. Amongst our cousins to the alpha males go all the spoils. This is interesting especially in light of Herrick's earlier post about the possibility that post-Neolithic populations shifted from one of predominant between group (band) selection (i.e., the importance of metapopulation dynamics) to within group selection (i.e., the rise of the super alpha male). One consequence of mass societies is that concerns like the one above seem old-fashioned, and certainly the scope of human "groups" today on the level of nationalities is simply too large to constrain the ego driven quest for status of superior individuals. Between group selection needs groups of small size, and many of them. One may posit a two-step process that led to the crystallization of modern human society as we know it. First we made the transition from individuals competing within a loose social matrix to that of the tightly bound small groups which acted in concert against each other, then again at the rise of mass societies spurred by agriculture individuals and smaller groups (families, guilds, etc.) operated in a much more complex and multi-faceted conditonal manner to maximize their fitness.

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"High Sensitivity" folk   posted by Razib @ 4/11/2007 02:52:00 PM
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A few days ago I blogged about David S. Wilson's new book, Evolution for Everyone, without having read it (there was an extract in The New York Times). Well, I just read it. As I noted Wilson is a thinker with whom I have strong disagreements, but his interdisciplinary vision results in some good food for thought. Look closely at his bibliographies! I will post a review at my other weblog when I have some distance, but I thought I'd jot down a few thoughts/notes which might be of interest to readers. For example:
Highly sensitive people (or animals) are likely to be slow in a novel situation for the simple reason that they are processing new information. They are "stopping to check it out" rather than "forging ahead." Given too much sensory input, highly sensitive people tend to become overwhelmed and withdraw from the situation. This is a form of shyness, but highly sensitive people are not intrinsically shy. After all, the purpose of processing all of that information is to arrive at new solutions to life's problems. A highly sensitive person who succeeds at doing this can become as outgoing and gregarious as someone who is merely "forging ahead." Some individual differences (such as sociability) are not innate but are manifestations of other individual differences (such as information processing) that are....

...

In plain language that anyone can understand, she explains that the trait is normal, is present in about 15 to 20 percent of the population, and exists in about the same proportion in other species. It is a great gift that can also be a liability in some situations. It is especially misunderstood in our own culture, which values toughness and regards extreme sensitivity as abnormal (it's easier to be a highly sensitive person in Asia)....


First, it is probably obvious to regular readers that I am not a highly sensitive person. Second, I have been guilty of characterizing the highly sensitive as abnormal or pathological. Third, if 15-20% is a good estimate of their population level proportion (at least in the USA) I tend to associate in my own life disproportionately with highly sensitive individuals. I will hazard to guess that this psychological morph is an evolutionarily stable strategy amongst humans in part because of the synergistic possibilities of small groups consisting of personalities of various shades which bring their own special talents and propensities to the table.

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Teams of rivals   posted by Razib @ 4/11/2007 08:47:00 AM
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Rereading some chapters of Sewall Wright & Evolutionary Biology I was struck by the author's contention that Sewall Wright's relatively close relationship with Theodosius Dobzhansky was spurred on by the collaboration between R.A. Fisher & E.B. Ford. What theory Fisher propounded, Ford was reliably keen to find data for. With the rift and rivalry between Wright & Fisher in the early 1930s, Dobzhanksy emerged as an empirically minded confederate who Wright viewed as a possible source of data which would confirm his own hypotheses. The reality (to me) seems that both Wright and Fisher were making grand theoretical assertions beyond the discriminating power of the empirical tests of the time, but it is interesting to human nature playing within science, even as the scientists (Fisher in particular) in question were keen theorists of just that nature.

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Tuesday, April 10, 2007

Say what?   posted by Razib @ 4/10/2007 10:02:00 PM
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So I saw this entry over at the Superficial about Kate Moss running around with fat chicks...and it took me to this Wikipedia entry about one of the women in the photo:
The magazine cited her 'non-conformity'...as the reason for her selection - she is a lesbian, an outspoken advocate of gay rights, weighs around 15 stone (about 225 lbs.)...and is also in a relationship with a transgendered individual who was born a woman but identifies as a man....
...
...Ditto posed nude for On Our Backs, a women-run lesbian erotica magazine. "It was a big moment in my life," she told Curve magazine. "It was kind of a radical thing to do. I got my period just 10 minutes before we got there, and I was totally bleeding. I was doing it with my tranny boyfriend, who I'm in love with, and I was totally bleeding - how radical is that? - and I'm a fat person, and I'm a femme. It felt really good."


? Say what? Someone has to make a South Park episode about this.

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Culture & (co)evolution   posted by Razib @ 4/10/2007 02:54:00 PM
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I want to clarify a few points that I alluded to below. The fact that lactase persistence is nearly fixed in northern Europe can be used to make obvious inferences about the culture of this region. Cultural traditions clearly shaped via direct selection the gene frequencies and therefore the expressed phenotype. But most gene-trait relations that we are interested in are more complex, and the selection regime is less cut & dried. When it comes to "culture," broadly speaking (as opposed to something very precise such as the utilization of dairy in the daily diet), it is hard to make generalizations which yield us more information than we started with. One of the problems that crops up is that written texts, and avowed norms, can give a skewed perspective of the reality in the past and present.


If aliens looked at the preserved letters of Roman nobility such as Symmachus as the models for the nature of ancient Latin, they would likely be very mistaken. The likely reality is that modal Latin spoken by the masses was very different from elite Latin preserved in the extant literature, and can be gauged by the fact that Christian church made a proactive effort to recruit more of the elite into the priesthood because of the awkwardness that occurred when common preachers addressed upper class parishioners in "rough" dialect. There is also the issue that avowed norms are not always practiced widely. In Mother Nature Sarah Blaffer Hrdy observes that the lower caste vassals of the Masai espouse the same preference for sons that their overlords do, but mysteriously their mortality rates are inverted from that the Masai so that female children seem to do better than male children. The functional explanation is pretty obvious, female children can "marry up" into the Masai, while male children have far less chance of social mobility. This Trivers-Willard effect has been discerned in other situations, but, the fact that extant documentary evidence tends to skew toward the upper classes often masks the extent of daughter-preference among the lower orders (e.g., a survey of cemeteries of peasants in medieval Europe showed a bias toward youg male offspring). Additionally, modernization tends to result in the inevitable percolation of elite norms down to the masses, in India this can be seen in the spread of dowry during the early 20th century downward from the upper castes and the extinction of the practice of brideprice (where the family of the bride receives payment). But sometimes even in these societies modernization does only so much, ethnographic studies of the Khasi (a matrilineal society) and neighboring Bengalis (a patrilineal society) showed that both societies exhibited the maternal "grandmother effect" insofar as grandmothers favored the offspring of their daughters more than their sons. This should not surprise in regards to the Khasi, who are matrilineal, and where men and women are relatively equal in their relationship, but Bengalis notionally base their society around male descent groups. Like most north Indian societies women are strangers in their husband's houses (patrifocality is the norm, in contrast again to the Khasi), and their children are members of their husband's family. But the reality is often far different, in my own family my mother would wryly observe that it is somewhat indecent that her children have a closer relationship to her brothers (our maternal uncles) than to my father's brothers and sisters. Though this is not "decent," it is an ancient pattern attested within Indo-European societies. Anthropologically the explanation is often that maternal uncles can be assured of relation to their nieces and nephews by their sister to a greater extent than paternal uncles can be to their nieces and nephews by their brother. This is not a line of thinking which would be greeted positively by traditional Bengalis of course.

In any case, a few months ago I thought about the possible shallowness (or recency) of such avowed social norms when an acquaintance of mine told me the following story: basically, he had left a non-profit in Afghanistan. The reason was that his boss was having an affair with a woman who was also employed by this NGO. My acquaintance's boss was married to a close friend of his, and the "other woman" was engaged to a fellow Pashtun in Kabul. The short of it is that everyone knew of the affair in the organization, and some of them who were posted in Kabul were not happy with the possibility that a family tragedy might arise out of this, especially with the woman's impending marriage. Now, I bring this up because Pashtuns are pretty freaky about how much they control their womenfolk. When my father was a student in Pakistan the locals explained that whenever you saw one man chasing after another with a scythe or any other such dangerous implement it was likely to be a Pashtun. The locals thought it was great fun and seemed to act as if this was normal (this was Islamabad in the late 1960s). It was simply the "Pashtun way." And yet was this always the Pashtun way? The woman who I allude to above seemed to have sexual feelings which allowed her to indulge in very dangerous activities (in the context of Pashtun culture). For gene-culture coevolution to work the selection must either be persistent or powerful. Because of the variation of cultures over time in regards to particular traits persistence is often difficult. As to the strength or power of selection, I suspect that though it can be powerful in a small segment of the population, for most of history formalized norms codified in the texts which we analyze to make sense of the past were relevant for the elites. This means that the majority of the population lived "pre-civilized" lives as producers of surplus for the elites, who were the engines and consumers of civilization.

Addendum: I've re-edited the part about the NGO & Afghanistan to be more general so that individuals can't figure out who I was talking about (in case you saw version 1). I myself don't know.

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Mutations in superorganisms   posted by p-ter @ 4/10/2007 02:45:00 PM
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Symbiosis, as we all know, is that lovely relationship where two organisms mutually benefit from a dependent relationship. Aphids, for example, feed entirely on plant phloem, which is lacking certain amino acids. Their bacterial symbiont synthesizes these amino acids, while getting other necessary nutrients from the aphids. The bacterial genome shows the signs of this remarkable relationship, having a much reduced size with only certain necessary genes.

But the fact that the aphids and bacteria both need each other to reproduce means that mutations in the bacteria may have a phenotype in the aphid, and vice versa. This has been elegantly demonstrated in a new paper, Aphid thermal tolerance is governed by a point mutation in bacterial symbionts. The title pretty much says it all, but I'll quote a bit from the abstract:
A model of obligate symbiosis is that between aphids and the bacterium Buchnera aphidicola, which supplies essential nutrients. We report a mutation in Buchnera of the aphid Acyrthosiphon pisum that recurs in laboratory lines and occurs in field populations. This single nucleotide deletion affects a homopolymeric run within the heat-shock transcriptional promoter for ibpA, encoding a small heat-shock protein. This Buchnera mutation virtually eliminates the transcriptional response of ibpA to heat stress and lowers its expression even at cool or moderate temperatures. Furthermore, this symbiont mutation dramatically affects host fitness in a manner dependent on thermal environment. Following a short heat exposure as juveniles, aphids bearing short-allele symbionts produced few or no progeny and contained almost no Buchnera, in contrast to aphids bearing symbionts without the deletion. Conversely, under constant cool conditions, aphids containing symbionts with the short allele reproduced earlier and maintained higher reproductive rates.
Humans, of course, are superorganisms, in that we're infested with billions and billions of microorganisms. We could reproduce without them, I imagine (though it would be pretty tough to test that hypothesis), but there's much evidence that the genotypes of out residents plays a role in all manners of phenotype. In this aphid case, ths role is particularly striking-- do aphids have one genome, or two? Perhaps it's best to think of this as a mitochondrial DNA-like mutation.



Monday, April 09, 2007

Sex in The New York Times   posted by Razib @ 4/09/2007 09:45:00 PM
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There are two articles of note in The New York Times up about about human sexuality, one by Nick Wade, and another by Natalie Angier. I found the Angier article too verbose, and Wade's was a bit simplistic, but reading them both emphasizes some insights from sex research. First, men and women are different, and in particular males seem to be more exclusively hetero or homosexual. No surprise to anyone. Additionally, there is within population variation in sexual response and attitudes. Some of this, I suspect, is due to the prevalence of mixed-strategies within the human population. In other words, negative frequency dependent selection maintains some behavioral tendencies within the population at low proportions. But I was especially interested in this:
Romantic love, which in its intense early stage "can last 12-18 months," is a universal human phenomenon, Dr. Fisher wrote last year in The Proceedings of the Royal Society, and is likely to be a built-in feature of the brain. Brain imaging studies show that a particular area of the brain, one associated with the reward system, is activated when subjects contemplate a photo of their lover.


I read a fair amount of history, and historians often say things like "love was invented by the troubadours in the 14th century in the Provence." But what does "love" mean? Clearly not all cultures lionize romantic love to the same extent, but, the idea of the love ballad or stories of tragic love seem universal. Some of you may know that I've been interested in the levels of selection debate: to me the universality of the psychological propensity toward love is a strong argument for the power of within group selection as opposed to between group selection. As the story of Romeo and Juliet illustrates romantic love across group boundaries can cause serious problems. The most extreme form of arranged marriages are normative in many "advanced traditional" societies (e.g., parts of Eurasia with a long history of complex civilization), and especially prevalent amongst elites for whom marriage ties serve as bounds which cement between family alliances. And the norms of society can make many individuals comfortable with the idea of arranged marriage, but it seems that it is rather easy to change these attitudes in the offspring of immigrants who come from cultures where arranged marriage is the norm. Parents may attempt to inculcate the importance of arranged marriage in their children, but unlike say nominal religious affiliation, this is one case where parent-child transmission exhibits a great deal of erosion.

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Gayrabia - full article   posted by Razib @ 4/09/2007 06:58:00 PM
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You can read full article about being gay in Saudi Arabia here (thanks to Diana). This was the funniest part:
...Few people in the kingdom, other than the mutawwa'in, seem to take the process seriously. When the mutawwa'in busted the party that led to Marcos's deportation, they separated the "showgirls" wearing drag from the rest of the partygoers, and then asked everyone but the drag queens to line up against the wall for the dawn prayer. At the first of the three ensuing trials, Marcos and the 23 other Filipinos who'd been detained were confronted with the evidence from the party: plastic bags full of makeup, shoes, wigs, and pictures of the defendants dressed like women. When the Filipinos were returned to their cells, they began arguing about who had looked the hottest in the photos. And even after his punishment and deportation, Marcos was unfazed; when he returned to Jeddah, it was under the same name.


I am struck that the author of the article notes a shortage of "bottoms" in Saudi Arabia. The main reason from the evidence presented within seems to be the preponderance of facultative homosexual behavior among straight males who don't have sexual outlets (e.g., not married, or their wife is not available). In contrast, I am to understand that in the US gay culture there is a shortage of "tops" and "straight acting men." In a way it seems that Saudi Arabia (and other such cultures, of which there are many, if not to the same extent) presents an opportunity for the obligate homosexual.

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Population genetics to the rescue!   posted by p-ter @ 4/09/2007 04:59:00 PM
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I've worried before about the evolution of antibiotic resistance and its potential impact on human health. In that post, I noted that
The one thing we have going for us is that we understand the basics of evolution-- that is, we can predict how a population of bacteria will respond to the next antibiotic, and we have an idea of the population dynamics at work as resistance spreads. I have the feeling that somehow this information could be used to defuse the "arms race", but I'm not sure how...

It turns out other people have better imaginations than I; check out this paper, Antibiotic interactions that select against resistance. From the abstract:
Normally, the presence of a drug confers an advantage on its resistant mutants in competition with the sensitive wild-type population1. Here we show, by using a direct competition assay between doxycycline-resistant and doxycycline-sensitive Escherichia coli, that this differential selection can be inverted in a hyper-antagonistic class of drug combinations. Used in such a combination, a drug can render the combined treatment selective against the drug's own resistance allele...Our findings demonstrate a previously unappreciated feature of the fitness landscape for the evolution of resistance and point to a trade-off between the effect of drug interactions on absolute potency and the relative competitive selection that they impose on emerging resistant populations.

The idea is simple: imagine a combination of antibiotics in which the combined effect is weaker than that of one of the drugs alone (the curve labeled "suppression" in the figure). You might normally want to avoid this situation. But if the combined effect is weaker than the effect of a single drug alone, a resistant bacteria might only see the effect of one of the drugs, which, in this case, is stronger than the combination. Thus, selection against resistance. It's quite clever.

Of course, it's far from being implemented-- in their toy situation, only resistance against one of the drugs is being selected against, so resistance against the other drug is a possibility. A detailed analysis of the paramter space for multi-drug combinations, plue empirical measurements of multiple drug interactions, would go a long way. Also, these experiments were done with sublethal concentrations of the drugs in a pretty contrived situation. Nonetheless, this is really cool. Could "applied population genetics" become a real field?

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The Value of Being Naive   posted by Matt McIntosh @ 4/09/2007 01:44:00 PM
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Go read Hawks on Nisbet & Mooney:

This kind of cynical strategy is the province of used car salesmen and other charlatans. And it's easily exposed by any clever critic who happens to be watching . . .

My point isn't that these critics are right, but that such criticisms pretty much write themselves! A scientist trying to "frame" in this way is going to end up discredited unless they retreat to the facts anyway. This is, after all, why scientists are typically so cautious in print -- because they work in a field where bad arguments are quickly torn apart by their critics. Why in the world would anyone think politics would be any easier?


This is pretty much right, and I just want to add that this is especially bad advice to give to scientists, because scientists wouldn't be scientists if they were really good salespeople. Spinning is not their comparative advantage, and "fight the enemy on his own turf" is awful tactical advice. Scientists owe whatever respect and deference they're given to the fact that they're percieved as being interested primarily in the truth: their reputation for earnestness and lack of guile is a big part of their cred. The best way to get people to regard you as honest is to really be naively honest.

People may be dumb in a lot of ways, but they generally know how to spot when someone's trying to sell them something, and telling scientists that they should behave more like salespeople will result in them being regarded in much the same way—and they are never going to be better salespeople than professional demagogues. I can think of no better way to erode whatever benefit of the doubt that scientists currently enjoy in our culture. If scientists try to play the political game, they're going to lose. Better to try to stay above the fray than get dragged in and trampled for sure.

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Nature's Oracle: A Life of W. D. Hamilton   posted by Razib @ 4/09/2007 02:01:00 AM
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I just noticed that Nature's Oracle: A Life of W. D. Hamilton by Ullica Segerstrale is finally on Amazon's website for pre-orders (expect it sometime in 2008). You can view the table of contents online. Seeing as how R.A. Fisher's biography (written by his daughter!) made the man seem something of an ass I'm a bit trepidatious about biographies of men of science, but Defender's of the Truth treated Hamilton with some sensitivity, so I'm not that worried.

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Sunday, April 08, 2007

Americo-Browns & sex   posted by Razib @ 4/08/2007 09:50:00 PM
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Abhi @ Sepia Mutiny points me to this study, "Sexual Decision-Making of Immigrant East Indians: Risky or Not?". You can see the data in the chart to the left. The sample size was hella small, and possible bias in their subjects is a pretty clear critique. That being said, this study illustrates a general trend, and that is the assimilation of 2nd gen browns into American culture despite the wishes of their parents, who often came here for economic opportunities denied them in brownland, but were intent on preserving 1972 brown values in the USA (haircuts and all). As I've pointed out before, a very significant minority of American browns are already marrying outside of their putative ethno-racial community (higher for 2nd gen as opposed to 1.5ers, the data in that table doesn't distinguish). One must also remember also that from the perspective of parents marrying across intra-brown ethnic/caste lines is also not endogamy, but those numbers will be masked in the data cited (endogamy being a metric which measures the influence on parental instruction of the values of children). The number of browns is far higher today than when I was a child, so one might assume that the outmarriage rates would be lower in the future as the pool of potential spouses born in the USA increases. Interestingly, the authors cite research from Canada which indicate that browns born in the cold north are more traditionalist than other Canadians, suggesting preservation of "values" across generations from their parents. But the dynamic might be different because of the Canadian policy of multiculturalism and the larger number of individuals from South Asia in relation to the overall population has allowed for the emergence of brown peer groups. These peer groups could serve as enforcers of "traditional" values derived from their parents. Of course parent-child values transmission does occur in some ways in the USA, for example, the nominal religion of brown Americans is generally not Christianity (and a likely majority of Christians are from families in Kerala which were Christian to begin with). To compare the impact of peer groups and parental values one must look at the overall context.

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To get gas is glorious!   posted by Razib @ 4/08/2007 08:49:00 PM
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A friend pointed to this article in The Economist, China's dairy industry, which chronicles the recent problem of oversupply. Apparently, due to a recent fad amongst the urban middle class to drink milk & milk products many Chinese farmers began to buy cows to produce milk. The problem is that supply quickly outstripped the demand, which you can see is leveling off.

Does this surprise? It shouldn't. The Chinese are notoriously lactose intolerant. This doesn't mean that they explode when drinking milk, rather, large quantities of lactose in the digestive systems of those without the functioning lactose enzyme are undigested, and, can result in the emergence of a set of intestinal flora which result in gas, irritable bowel syndrome and at the extreme, diarrhea. Though none of these are life threatening in a modern context, they are not the recipe which suggests possible repeat customers. I was especially struck by this statement: "Officials are not giving up. To the industry's delight, the prime minister, Wen Jiabao, visited a dairy farm last year and said his dream was that all Chinese drink half a litre of milk a day, especially schoolchildren." Now, one study reported that 20% of Japanese adults exhibited physiological response of lactose intolerance when about 7 ounces of milk were ingested. Half a liter is closer to 17 ounces (yes, I know that Japanese and Chinese are different, but not on this phenotype).

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Churchill's Jewish Ancestry - Not!   posted by DavidB @ 4/08/2007 04:17:00 AM
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This post has only a marginal relevance to gnxp, but for those who may be interested I am putting it below the fold.

In the British Press there has recently been some controversy about Winston Churchill and alleged anti-semitism. An unpublished magazine article of 1938, not written by Churchill but allegedly approved for publication in his name, contains references to Jews which would get him into trouble today, though at the time they would have seemed relatively innocuous.


But what I want to discuss is a claim that Churchill himself had Jewish ancestry on his mother's side. According to a letter by Mark Corby in the London Times on 22 March, 'his mother Jenny Jacobson/Jerome was a New York Jew, as was pointed out by Moshe Kohn in an article in the Jerusalem Post of January 18, 1993'. But a letter on 26 March from David Watson denied this, claiming that Churchill's American ancestry could be traced back to the early 18th century, without a sign of any 'Jacobson'.

Now I don't personally care much whether Churchill had Jewish ancestry or not, but I see from the internet that this claim (specifically, that his maternal grandfather changed his name from Jacobson to Jerome) is popular in certain circles. Why did Churchill hate that nice Mr Hitler? Why did he betray the Aryan race? Why, it's obvious, isn't it - he was one of those!


So I wanted to see whether there is any basis for the claim. I began with an internet search, but found nothing to support the claim other than repeated references to the article by Moshe Kohn. Since a newspaper article is hardly a good primary source, this does not inspire confidence. My next step was to visit a library with excellent biographical collections. There are countless biographies of Churchill, a few of his mother Jenny, and one of his mother's father, Leonard Jerome. On browsing relevant parts of these, I found them unanimous in tracing Churchill's Jerome ancestry back to Timothy Jerome, of Huguenot descent, who migrated to America around 1717. Of course, this might all be an elaborate cover story, but if so it is one that could easily be refuted. The biographies contain references to public figures, such as Leonard Jerome's uncle Judge Hiram Jerome, and records in public archives which could be checked by anyone suspicious of a cover-up. The only serious gap in the official records of Churchill's ancestry is a long way back in the female line, which cannot be traced beyond his great-great-grandmother, Anna Baker. According to family legend, she was part-Iroquois Indian, which the family believed accounted for the prevalence of dark eyes or complexion in the family. This does have a certain whiff of cover-up, but if so the cover-up may be of something other than Jewish blood. According to one account, Churchill himself believed there was a drop of black somewhere in his ancestry (see Elisabeth Kehoe, Fortune's Daughters: The Extravagant Lives of the Jerome Sisters (2004), p.4). In any case, the usual claims of Jewish ancestry concern Churchill's mother's father, Leonard Jerome, and not the female line leading back to Anna Baker.

Nevertheless, to be sure that I had not missed anything, I searched the internet again, and found two pieces of 'evidence' occasionally cited in support of the story. One is a claim that Churchill's cousin, the Irish writer and politician Shane Leslie, wrote a biography of Churchill which was left unpublished at Churchill's insistence, allegedly because it let the cat out of the bag concerning the Jeromes' Jewish ancestry. But Shane Leslie also wrote his own autobiography, Long Shadows, published after Churchill's death, in which he described his Jerome ancestors. Leslie passed on his researches into the family history to his daughter, Anita Leslie, who wrote biographies of both Leonard and Jenny Jerome, and to Ralph Martin, biographer of Jenny (Ralph G. Martin, Lady Randolph Churchill: A Biography (1969).) None of these books mentions any Jewish ancestry. If Shane Leslie had discovered a secret which he was persuaded not to publish during Churchill's lifetime, why would he continue to suppress it after Churchill's death?

The other piece of 'evidence' is a claim that the historian David Irving had proved Churchill's Jewish ancestry in his book Churchill's War. If David Irving told me the time, I would check five different clocks before I accepted it, but he does admittedly have a reputation for finding new documentary evidence (usually provided by elderly Nazis), so I naturally went back to the library to look at Churchill's War. In volume 1, published in 1987, I find nothing to suggest any Jewish ancestry for Churchill. But in volume 2, published in 2001, at last we find a reference - in a real, published book - to Churchill being 'born of partly Jewish blood' and having a 'part-Jewish mother' (page xii). So I turned with trembling hands to the end-notes (page 855) to find the documentary basis for these assertions - only to find nothing but a reference to Moshe Kohn's article of 18 January 1993!

So it seems that all roads lead to Kohn. I therefore decided I must track down his article in the Jerusalem Post. I did not expect this to be easy, but I found that the JP has searchable online archives going back at least to 1993. On searching for articles by Moshe Kohn referring to Churchill I got a surprise. There is indeed a relevant article, but its date is not 18 January, as stated by Irving and all the others, but 15 January. This has two fairly obvious implications: first, those repeating the incorrect date are copying directly or indirectly from David Irving, and second, they have not read the article for themselves. If they had, they might be less confident in their assertions.

The article itself is clearly aimed at an Israeli audience with Israeli preoccupations. It begins with a passage of heavy sarcasm:


THANK God - at last we know the truth about Winston Churchill: he was a psychopathic revanchist, obsessed with defeating Germany in World War II, thus preventing Adolf Hitler from saving civilization from the Red menace. Several rational British historical revisionists have just revealed this, half a century after Churchill inflicted all that pain and grief on those poor Germans.


These 'revisionists' are not named, but David Irving himself (at that time still not entirely discredited) is one obvious target. Another possibility is John Charmley, whose book Churchill: A Political Biography, appeared around the beginning of 1993.

But Kohn continues:


Or is it a related idiosyncrasy that bothers those revisionists? I mean the streak that caused Churchill to draw on Jewish - particularly biblical - modes and language, especially regarding the treatment of enemies like Hitler and Mussolini. Are they particularly galled by his penchant for calling on God, despite his rejection of "the Christian or any other form of religious belief" (as he wrote to his mother in 1898)? And with typical Churchillian cunning, he did all that in the name of "Christian civilization"... (That cunning no doubt came to Churchill in the Jewish genes transmitted by his mother, Lady Randolph Churchill, nee Jenny Jacobson/Jerome. )


And that's it. That is the entirety of Kohn's discussion of Churchill's alleged Jewish ancestry. It is not even clear that it is intended seriously. (Kohn died in 2005, so we cannot ask him.) The whole of Kohn's first paragraph, directed at the 'revisionists', is written in a mode of sarcasm. (The rest of the article is a defence of Churchill, who is presented as a model for hard-line Israeli politicians.) Kohn evidently suspected that the revisionists had an underlying anti-semitic motive, and his reference to Churchill's Jewish ancestry may be nothing more than an allusion to some pre-existing anti-semitic rumour or fantasy. On the assumption that Moshe Kohn himself was Jewish - which seems a fair guess - he would hardly have seriously referred to 'cunning... in the Jewish genes': a stereotypical piece of anti-semitic nonsense. But even if Kohn's reference to Churchill's Jewish ancestry was intended seriously, it is of no value as historical evidence, and no competent historian would rely on it without supporting documentation.

I conclude that there is no worthwhile evidence to support the claim of Jewish ancestry, and there seems to be strong documentary evidence against it. I say seems, because I have not examined the archival sources for myself. But the burden of proof is on those who wish to show that the official account is false.

PS: to avoid confusion, I should make it clear that I am not David Boxenhorn, who occasionally contributes to this site. David is an Israeli, and therefore might be thought to have a personal interest in the issue. I do not.

PPS: While on Churchillian themes, I take the opportunity to recommend the HBO/BBC drama The Gathering Storm. I was impressed by this when it was first screened, and I watched it again recently on DVD. It has a superb cast, including Albert Finney, Vanessa Redgrave, Jim Broadbent, Derek Jacobi, Tom Wilkinson, Linus Roache, Lena Headey, Celia Imrie, Hugh Bonneville, and a host of familiar character actors in minor roles. Indeed, this got a bit distracting: I kept expecting Hugh Laurie to pop up playing Bertie Wooster. Also, the background music was sometimes intrusive. And the script (like Churchill's memoirs on which it was based) was probably unfair to Stanley Baldwin. But all quibbles apart, it was a fine drama, above all for Albert Finney's performance as Churchill.





Why people believe in weird things....   posted by Razib @ 4/08/2007 12:01:00 AM
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1 in 5 Americans believe in reincarnation, the same numbers as in Europe. One can ascribe this to the influence of Indian religion, but recall that reincarnation has ancient roots within Europe. My own suspicion is that reincarnation is an "evoked" belief which many humans find plausible. Like the existence of gods it doesn't have to be "invented" by a genius, cognates naturally emerge in a parallel manner across human societies due to the universal mix of psychology & environment. I have made no secret of the fact that my own position is that modal human theism likely emerges from conventional and prosaic human cognitive processes (e.g., agency detection), but what about supernatural ideas like reincarnation? A new paper, The false fame illusion in people with memories about a previous life (popular press summary), sheds some light on the modal cognitive processes which might account for belief in past lives which seem to be a recurring phenomenon in human culture. Researchers found that those who claimed to have past life memories made consistent and systematic errors in a particular psychological task. In short, it seems that these individuals tended to be more suggestible and prone to allowing mistakes in associational memory creep into their recollections. It seems possible then that cognitive "misfiring" opens up an avenue whereby these strange mental concepts can easily slip into the domain of plausibility (innate mind-body duality already seems to convince us about the permanence of the soul). The control group was less likely to make these mistakes, and were also less likely to believe in reincarnation, but this does not negate the general relationship and the likelihood that similar (if attenuated) cognitive processes are at work on a broad scale across human societies.

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Saturday, April 07, 2007

Just don't use the word 'race'   posted by the @ 4/07/2007 03:35:00 PM
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That seems to be the conclusion of a recent review of Nick Wade's Before the Dawn published in Nature Genetics:
My reluctance to recommend the book stems also from Wade's discussions of 'race' and biology. I agree with Wade that there is something biological about racial categories. In my opinion, although racial identity is socially negotiated, people use physical traits as cues when 'assigning' a racial identity to themselves or another individual. Racial categorization isn't blind to biology. ... Although one might detect biological differences between races, any highlighting of the racial categories (just a subset of groups with biological correlates) has social costs, according to recent social science research. On the other hand, Neil Risch, cited often in the book, has argued that there are significant (medical) costs of ignoring the relationship between racial categories and biology. I suggest that these different costs be weighed in each circumstance where one might link 'race' and genetics. Wade's broad description of races as clearly delineated biological entities is unjustified in the context of a book about human history intended for a general audience. Why use the term 'race', when 'geographic ancestry' or 'continental origin' are more accurate and less costly in social terms, especially since Wade's definition of 'race' is "continent of origin"? I suggest acknowledging the correlation between racial labels and continents of origin, and saving the term 'race' for contexts in which social costs are outweighed by other costs.


This is not the argument I expected to follow the sentence "My reluctance to recommend the book stems also from Wade's discussions of 'race' and biology." In this case, the author isn't being snide by putting race in quotes, as she really means the word race rather than its referent. How often do scholars write that consternation over race is largely related to extra-scientific concerns?

However, I have to criticize this argument, at least to the extent that I'm able to examine the evidence presented. A footnote to the "recent social science research" showing that using the word 'race' is harmful (but that cryptic synonyms are OK) would be appreciated, as this forms the basis of the argument against discussing 'race'. Is it only harmful to discuss 'race' and 'genetics' or 'biology'? Is the attribution of racial differences to environmental/cultural causes not similarly harmful? Is it really true, as is implied, that Wade is morally obliged to substitute most instances of "race" in his text with "continent of origin"?

There's a lot to commend in this review, largely stemming from the reviewers' honesty and directness, and especially in contrast with this hatchet job published in the sister journal Nature.

Update - full text:
Given the rich content of Nicholas Wade's latest book, Before the Dawn, I wish I could simply recommend the book, describe its highlights and stop there. Wade provides a valuable overview of the last ten years of scientific literature on genetic insights into the history of our species. He is an excellent storyteller, weaving the scientific results into a thrilling tale of human migration and settlement, competition and warfare, cultural and linguistic evolution and environmental challenges. The history of our species is a fascinating one, and Wade brings it to life.

I congratulate Wade for taking great pains to qualify many of his statements with terms such as "seems" and "appears to." In an important, related vein, early in the book he notes that any "intent" suggested in biologists' statements about evolution reflects shorthand communication and is not meant to imply that evolution has any particular goal "in mind." Evolutionary biologists will certainly appreciate that note. Furthermore, given that few readers will be specialists in all the fields represented in the book (paleoanthropology, archaeology, linguistics, genetics and more), many will appreciate Wade's practice of defining terms.

Despite the book's many strengths, I am reluctant to recommend the book unconditionally. I found some sections of the book challenging to read, as I looked for supporting evidence for various claims. For example, Wade suggests that the San, peoples in southern Africa who subsist via foraging, are the "closest living approximation to the ancestral human population." Behaviorally, this might be true. However, Wade goes on to suggest that the San may not have evolved genetically, as "foragers have presumably had much the same environment for the last 50,000 years." Wade appears to be unaware of the diverse environments even today within sub-Saharan Africa; furthermore, the changing global climate over the past 50,000 years has often had dramatic impacts on humans living in Africa.

Although at many points in the book Wade notes the speculative nature of conclusions from genetic, archaeological or geographic data, he occasionally treats those conclusions as fact elsewhere. For example, he writes, "There is no way to know for certain the nature of the interaction between the two human species [anatomically modern humans and Neanderthals]." Yet elsewhere he writes, "...[the Neanderthals] crushed the attempt by anatomically modern humans to penetrate the Levant." The reader is at risk of being lulled by numerous "maybes," "seems" and "appears" into trusting unsupported but confidently stated comments elsewhere in the book.

My reluctance to recommend the book stems also from Wade's discussions of 'race' and biology. I agree with Wade that there is something biological about racial categories. In my opinion, although racial identity is socially negotiated, people use physical traits as cues when 'assigning' a racial identity to themselves or another individual. Racial categorization isn't blind to biology. Yet Wade puts words in the mouths of the American Anthropological Association (AAA) when he states that the AAA "dismisses the idea that biological differences can be recognized between races." He backs up his statement with an AAA quote that makes a different point: "any attempt to establish lines of division among biological populations [is] both arbitrary and subjective." Although one might detect biological differences between races, any highlighting of the racial categories (just a subset of groups with biological correlates) has social costs, according to recent social science research. On the other hand, Neil Risch, cited often in the book, has argued that there are significant (medical) costs of ignoring the relationship between racial categories and biology. I suggest that these different costs be weighed in each circumstance where one might link 'race' and genetics. Wade's broad description of races as clearly delineated biological entities is unjustified in the context of a book about human history intended for a general audience. Why use the term 'race', when 'geographic ancestry' or 'continental origin' are more accurate and less costly in social terms, especially since Wade's definition of 'race' is "continent of origin"? I suggest acknowledging the correlation between racial labels and continents of origin, and saving the term 'race' for contexts in which social costs are outweighed by other costs.

Wade's chapter on language is replete with details of relationships among languages, methodology for reconstructing those relationships and arguments in support of methods that are purported to give ages of languages. Although much of this discussion will undoubtedly provoke many linguists, the most provocative element in this chapter is a more general statement: "The mutability of language reflects the dark truth that humans evolved in a savage and dangerous world in which the deadliest threat came from other human groups." I see little support for this conjecture. Language, at least a language rich in elements, cannot come into being without being mutable. And as Wade notes earlier in the book, "Language would have made small groups more cohesive, enabled long-range planning and fostered the transmission of local knowledge and learned skills." Mutability may reflect these advantages rather than a "savage and dangerous world."

Where I am familiar with the relevant scientific literature, I see the details that Wade includes in this, his latest book, as accurately representing scientific findings. Wade often wraps these scientific details in dramatic stories, thereby creating a book both informative and entertaining. However, some of Wade's general themes, such as his claim of a very high level of aggressiveness of prehistoric hunter-gatherers, are just that—dramatic stories. Readers will benefit most by considering each such claim as one among several plausible interpretations of the data.

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Neuroscience Basics I: Electricity and Equilibrium   posted by Matt McIntosh @ 4/07/2007 11:40:00 AM
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One of the awkward things about GNXP is that we've got an audience that's very mixed in terms of knowledge, so it's hard to know just how much background information you should assume when writing posts. In the archives we've got "basic concepts" posts on population genetics and psychometrics that hopefully help lay-readers follow the more technical posts on these subjects, but so far we don't have too much "neuroscience 101" stuff. With that in mind, this is going to be the first in a series of posts that try to give the uninitated reader an adequate background to follow the more advanced posts by Amnestic.

Most people are familiar with terms like "neuron", "synapse", and "neurotransmitter" and have a vague notion that the brain operates with electrical impulses and chemical messenger molecules like serotonin and dopamine, but don't have a clear idea of how these things all fit together—much the same way that I know that there are things called an "alternator" and "transmission" under the hood of a car but don't really know how these things work together to make the car go. But the basic idea of how neurons work is pretty easy to understand.

Neurons are fundamentally devices for transmitting and storing small amounts of information in an analog format. Most of you have probably seen diagrams of what neurons look like: a fat cell body called the "soma" with a lot of branches radiating from it called "dendrites", and a big fat tube extending from it called the "axon" which also has a bunch of braches sprouting from it. The dendrites are the input sites, the axon is the output, and synapses are the sites where the endpoints of dendrites and axons meet. A synapse is where the actual communication between two neurons occurs, but before we get to that it'd be better to understand what decides whether they even communicate at all.

Neurons, like all animal cells, have a membrane "skin" composed of two layers of phospholipids (fatty acids attached to a phosphate group). This is what keeps the cell's insides inside and everything else outside, and it works in a rather ingenious way: the phospholipids are polar molecules which at one end are attracted to fats and at the other end attracted to water. The reason why oil and water don't mix is the same reason your cells stay cohesive: the lipid molecules cling together and form a collective barrier that most molecules won't pass through. In the case of a cell membrane, instead of just forming round globules they form a uniform wall.

Of course this membrane isn't totally impermeable, since a cell needs to allow certain chemicals to enter and exit, just as complex living organisms do. There are a variety of different doors embedded within the wall—specialized channels that permit this or that kind of atom or molecule to bypass the membrane based on their electrical charges and/or shape, like bouncers at a nightclub. This selective permeability is central to cell function in general, and in neurons the most important purpose it serves is to control the difference in electric charge between the inside and outside of the cell via different concentrations of ions.

If you recall your chemistry classes, ions are atoms that have had one or more electrons either removed or added to their outermost electron shell, giving them either a positive or negative charge. Ions are the basis of bioelectricity—the bridge between biochemistry and electricity. When people talk about electrical impulses in your nervous system, they're talking about changes in the proportions of various ions.

In accordance with the second law of thermodynamics, ions (like everything else) tend to spread out evenly unless impeded. That's where the cell membrane comes in: by selectively channeling ions in and out of the cell while maintaining a barrier, it can control the difference in concentrations of ions inside and outside the cell. Because of the electric charge of ions, this creates a difference in charge, AKA "potential [electrical] difference"—in a word, voltage. (Voltage is defined as the difference in electrical charge between two points with a resistive barrier between them.) So cells in general and neurons in particular are always operating out of equilibrium with their environments, chemically and electrically.

The neuron has a negative feedback system that works to maintain a voltage "set point", just as your thermostat works to keep your house's atmosphere at a temperature set point. Just what that set point is will vary from neuron to neuron for reasons I'll explain in later posts; for now all you need to know is what role that system plays in neural activity—arguably, this feedback system is the foundation of all neural function.

Many of the ion channels embedded within the cell membrane are voltage-senstive and will alter their shape if the voltage gets "too high" or "too low", thereby closing or opening those channels to the free flow of particular kinds of ions (there are different channels for potassium ions, calcium ions, etc). You can probably see how this works now: when the voltage drops or rises beyond a certain point, some of the gates will open and permit ions to go the way they want to—toward equilibrium, which could be into or out of the cell depending on the charge of the ions and the voltage across the membrane. This will tend to bring the neuron back to its voltage set point.

Ohm's law governs the relationship between current, voltage and resistance in a conductive medium: voltage equals current multiplied by resistance. In the cell, the impermeability of the membrane corresponds to resistance and ion flow corresponds to current. Holding voltage constant (the set point), changing the resistance (permeability) necessarily means a corresponding change in the current (ion flow). I highlight this because this simple relationship is a helpful way to summarise the whole process I've just described, and is easier to remember than the details about the biochemical specifics.

So now that we've got the basic mechanism down, next up I'll discuss the exogenous causes of changes in voltage, which is where dendrites and axons come in.

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Gayrabia   posted by Razib @ 4/07/2007 10:54:00 AM
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The Atlantic has a story in the May issue on homosexuality in Saudi Arabia. Like many things in the Arab world there is the de jure and de facto. Since this is only available in full in print I'll have to wait to read the whole thing, but I wonder how much they emphasize the difference between facultative homosexuality and obligate homosexuality? After all, many men in prison have sex with other men, but they aren't homosexual by choice, they are sexual with a strong preference for females and so they select the most feminine males and turn them into "bitches" to generate an illusion. For non-upper class young males (those with money can travel abroad) it seems that Saudi Arabia might exhibit some of the characteristics of a prison, and so sexual urges are "released" upon other males (or, unfortunately the domestic help). I also wonder as to the role of single-sex socialization in priming these tendencies. I am often struck by the fact that in societies where males generally form close friendships only with other males there is quite a bit more physical and emotional affection between the same gender than is acceptable (and not deemed "gay") in the United States, where sexes socialize freely and straight males are generally averse to non-violent physical contact with each other. In fact, it seems to me that when sex relations in the United States were more distinct insofar as the genders inhabited disjoint social domains there was less fear of being perceived as homosexual if you were physically close with another man. One can find analogs of this situation in single-sex education as well. In any case, my only point is that articles like this might be a bit less shocking if Americans weren't such a peculiar bunch, and the patently homophobic citizens of 1900 might be able to intuitively understand the social dynamics here more than moderns.

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Look, it's a tree!   posted by Razib @ 4/07/2007 02:46:00 AM
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A new PLOS paper, free for your perusal, Generalized Analysis of Molecular Variance. If AMOVA is your thing, read closely, but I thought I would highlight a figure of interest. We can rattle on all we want about correlation structure...but a picture is worth a thousand posts. OK, a neighbor-joining tree:

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Bible Guy   posted by Razib @ 4/07/2007 12:59:00 AM
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I really messed up a lot of The New Testament....
You know the Bible 86%!

Wow! You are awesome! You are a true Biblical scholar, not just a hearer but a personal reader! The books, the characters, the events, the verses - you know it all! You are fantastic!

Ultimate Bible Quiz
Create MySpace Quizzes

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Evolution's Empire   posted by Razib @ 4/07/2007 12:44:00 AM
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David Sloan Wilson, the doyen of Multilevel Selection theorists, has a new book out, Evolution for Everyone: How Darwin's Theory Can Change the Way We Think About Our Lives. It seems pretty clear to me that Wilson is trying to "do a Dennett" here. But unlike Dennett, who was not a scientist himself and so operated within standard evolutionary science by regurgitating Richard Dawkins' work (who was himself simply a channel for W.D. Hamilton and John Maynard Smith), Wilson is known to be something of a heterodox figure because of his emphasis upon higher levels of selection than the individual. Via these models of interdemic (group) selection Wilson has attempted to revive functionalism within anthropology (see Darwin's Cathedral). An extract of his book up over at the The New York Times:
If our own species can be included in this grand synthesis, there is every reason to do so. It would be like a strange figure emerging from the shadows to enjoy the warmth of a campfire with good company. My own career shows that this is possible. Just like Darwin-not because I share his personal attributes but because I share his theory-I have seamlessly added humans to the bestiary of animals that I study, on topics as diverse as altruism, beauty, decision making, gossip, personality, and religion. I publish in anthropology, economic, philosophy, and psychology journals in addition to my biological research....


Having reread Unto Others: The Evolution and Psychology of Unselfish Behavior, which Wilson co-wrote with Elliott Sober, I am not surprised at the boasting above. Unlike Darwin or E.O. Wilson, David Sloan Wilson doesn't mask his ego under a self-deprecating exterior, he makes it clear that other scientists just lack his subtle perspective, his Olympian breadth of knowledge. Other scientists find math hard, are cowed by Political Correctness and swept along with the latest scientific fashions. They can't see what's right before their noses, mere mortals that they are. Wilson's ego is big enough to venture boldly into some pretty treacherous waters, recall that several years ago he wrote to defend Kevin Mac Donald against charges of anti-Semitism (Mac Donald works within a group selectionist framework). Unlike some of the cheerleaders for group selection theory he notes in Unto Others that shifting the level of selection up the hierarchy simply moves the conflict to that level (i.e., from inter-individual to inter-group). At the end of the day I often find Wilson's work just a bit too clever by a half, but I'll pick up this book for laughs and the bibliography. Even if Wilson's ideas are crap because all sorts of stuff have been blended together to produce a confused mush, the raw material of his sources are often quite illuminating.

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Friday, April 06, 2007

French demographics   posted by Razib @ 4/06/2007 06:52:00 PM
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I found some interesting fertility data for France in Wikipedia. I've converted them into Excel charts for easier viewing. A note for those who are interested in this topic, a January poll suggests that 3% of French identify as Muslims. This is probably due in part to the fact that a majority of individuals whose ancestry traces to historically Muslim regions are secularized (an individual in the GNXP chat suggested that they suspect that 25% of French are Muslim because the government doesn't take surveys. Remember, google is your friend!).







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Thursday, April 05, 2007

Mendelian variation in dog size   posted by Razib @ 4/05/2007 10:50:00 PM
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DNA study sheds light on dog size:
The new research suggests that a mutation in this gene [IGF-1] led to the appearance of small dogs more than 10,000 years ago.


I say that we should research a way to resurrect sub-fossilized humans so that the individual who let this mutant "tiny dog" survive can be killed. I mean, how many time have you been walking down the street and a midget dog is barking their head off in your direction? Perhaps there is pleiotropy so that small size is inversely proportional to obnoxiousness? I mean, if you're that unpleasant in regards to personality you better look like a mushed up furry ass baby!

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300 culture watch   posted by Razib @ 4/05/2007 10:44:00 PM
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Just noticed that the 'art house' movie theater downtown started showing 300 today. That is, on a Thursday!

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Wednesday, April 04, 2007

New GRE cancelled - the cost of attempted gap-reduction?   posted by agnostic @ 4/04/2007 11:38:00 PM
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The NYT reports that a completely revised GRE has been deep sixed, not merely delayed (read the ETS press release here). The official story is that there is some insurmountable problem with providing access to all test-takers, an issue apparently too complicated for ETS to bother trying to explain it to us. You figure, since this was such a huge project that was suddenly halted, they'd want to clearly spell out why they dumped it -- unless that's the point. Although I'm no mind-reader, the true reason is pretty obvious: the made-over test was designed to narrow the male-female gap at the elite score level, but this diluted its g-loadedness such that it couldn't reliably distinguish between someone with, say, a 125 IQ and a 145+ IQ, which is what graduate departments who rely on super-smart students worry about. Rather than admit that this psychometric magic trick went awry and lopped off a few limbs of g-loadedness, they spun a yarn about access to the test. [1]

To put this in perspective, for those who took the SAT before spring 2005 -- which is everyone here, I assume -- the New SAT now includes a Writing test with both multiple choice grammar questions and a 25-minute persuasive essay. No admissions committee is paying serious attention to this silly addition, although high schoolers obsess over it. The real changes are that the Math test no longer includes the "quantitative comparison" questions (column A, B, equal, can't tell?), and the flavor of the questions is a bit more "book smarts"-based than before. Also, the Verbal test (now called Critical Reading) has zero analogies, fewer sentence completions, and much more passage-based reading. The gutted portions are those that are more highly g-loaded, for sure in the Verbal test, and most likely in the Math test as well. [2]

We now ask why ETS intentionally stripped the SAT of some of its g-loadedness? Certainly not because they discovered IQ had little value in predicting academic performance, or that some items tap g more directly than others -- so why re-invent the wheel? Since scores on various verbal tasks highly correlate, this change cannot have affected much the mean of any group of test-takers. But if getting a perfect score required scoring correctly on, say, 10 easy questions, 5 medium, and 5 difficult (across 3 sections), a greater number of above-average students can come within striking distance of a perfect score if the new requirement were 10 easy, 9 medium, and 1 hard. I don't know exactly how they screwed around with the numbers, but that's what they pay their psychometricians big bucks to do. Now, reducing the difficulty of attaining elite scores, without also raising mean scores (as with the 1994 recentering), can only have had the goal of reducing a gap that exists at the level of variance, not a gap between means. This, then, cannot be a racial gap but the male-female gap, since here the difference in means is probably 0-2 IQ points, although male variance is consistently greater.

Certainly this reduces the power of the SAT to detect very brainy people -- those with an IQ of 145 or 160 or whatever big number you want -- but I can easily imagine that both ETS and elite universities such as Harvard were willing to trade off a bit of g-loadedness in order to close the male-female gap at the elite level. Harvard students wouldn't look stupider, of course: their prestige is based on their mean SAT score compared to those of others. And they probably have other ways of figuring out who is very brainy vs. fairly smart. (As an aside, this also explains why lots more high-scoring applicants will be rejected by top schools, another paradox that is easily, even if only partially, resolved by clear thinking.) Moreover, attending Harvard isn't all about having a 145 IQ -- a non-trivial number of their graduates will join professions that don't require eigth-grade algebra or sophisticated analysis (say, political office). So that, too, may lessen their concern over the SAT becoming somewhat less g-loaded.

Not so with the GRE -- those who score at the elite level here are hardcore nerds who are planning to do serious intellectual work, and elite graduate departments pay attention mostly to the applicant's intellectual promise. MIT's math department probably doesn't care that an applicant scored 650 on the Math portion but showed singular potential for leadership roles. So, I imagine something similar to the SAT make-over happened, only this time the professors and/or ETS' psychometricians discovered that it would make a joke of a test used to detect the very brainy in search of elite graduate work.

To make this concrete, let's assume that, among applicants to graduate school in the arts and sciences (i.e., future scholars, not professionals), males enjoy only a 0.1 SD advantage in mean IQ (or 1.5 IQ points), as well as a 0.05 SD advantage in their standard deviation. Then a test that is reliable up to 3 SD above the female mean will have 30% of those above this threshold being female. (For comparison with the real world, grad students at CalTech are 30% female.) Almost 10 percentage points can be gained by dumbing the test down so that it's only reliable up to about 2 SD, in which case 39% at the top will be female. Dumbing it down further so that it can only detect those 1 SD above the female mean just adds about 5 further percentage points; females will make up 45%. My guess is that they weren't foolish enough to toy around with a GRE that only tested up to an IQ of 115, but that they took a risk on some version that tested up to about an IQ of 130. Though that's just about enough to get you into MENSA, the real hullabaloo over sex disparities has raged within the halls of the uber-elite: Harvard (Larry Summers), MIT (Nancy Hopkins), Stanford (Ben Barres), and so on. At such an elite level, an applicant with an IQ of 130 would be like a 6'3 guy trying out for the NBA (whose mean height is 6'7). Although the NBA doesn't automatically weed out those 6'3 and under, surely the recruiters would protest to the manufacturers if their new-fangled measuring sticks only measured up to 6'3!

Pursuing this hunch, I picked up my Kaplan GRE self-study book and found out that they knew at least roughly what the new GRE was going to look like. Here were the proposed new question types for Verbal and Math:

Verbal
Reading Comprehension (4 types)
Sentence Completion (2 types)

Math
Word Problems (4 types)
Data Interpretation (2 types)
Quantitative Comparison (1 type, as before)

Notice the huge change in the Verbal test, which parallels the change in the SAT Verbal test: analogies are gone, and most of the test is reading comprehension. As for Math, they did keep the Quant Comps, but most of the new question types thereof sound too touchy-feely to be of good use: Word Problems include old-fashioned ones, plus "Free Response," "All That Apply," and "Conditional Table" (Kaplan admits they didn't know the exact names -- maybe the last was a contingency table type?). "Free Response" sounds like it would be more g-loaded since you can't rely on answer choices, but it definitely isn't, at least not if this type was to resemble its counterpart on the SAT. Here, you grid in your own answer, but only non-negative rational numbers can be gridded, precluding the use of any questions whose answer had a root or exponent or absolute value, whose trick hinged on the properties of positives vs negatives vs 0, whose answer was an equation or inequality, and most importantly whose point was abstract symbol manipulation (such as "solve for V in terms of p, q, and r"). Since females are better than males at calculation, and worse than males on more abstract math problems, "Free Response" is an easy way to obscure the male advantage at "thinking" math.

Not knowing much about what the other two new types of Word Problems are, I think it's still safe to say they were just as vacuous. In fact, the Data Interpretation problems were to come in 2 types: the old-fashioned one, and a new one called -- don't laugh -- "Sentence Completion"! For christ's sake, why not just turn some of the harder ones into Writing problems in disguise, where the test-taker corrects the grammar of a word problem rather than actually solve it! This psychometric flimflam is ultimately what all would-be gap-reducers must reduce themselves to, at least when the concern is the sex gap at uber-elite levels where those who matter will brook no nonsense over the basic tests being dumbed down.

[1] Since I'm pretty tired by now of writing about the "women in science" topic, for background info I'll just link to a very lengthy post of mine on point, plus Steven Pinker's debate with Elizabeth Spelke.

[2] See p.2 of the full PDF linked to in this post from the GNXP archives. It contains a graphic showing the g-loadedness of various cognitive tasks. Analogies are the most highly g-loaded verbal tasks, reading comprehension one of the least so (though still enough to validate its use on tests).

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Language families in maps & trees   posted by Razib @ 4/04/2007 07:58:00 PM
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This page has a bunch of language maps and phylogenies. Nothing you couldn't find in Wikipedia, but, all in one spot.

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Men on the move   posted by Razib @ 4/04/2007 07:13:00 PM
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Kings 2:24:
[14] And he carried away all Jerusalem, and all the princes, and all the mighty men of valour, even ten thousand captives, and all the craftsmen and smiths: none remained, save the poorest sort of the people of the land.

[15] And he carried away Jehoiachin to Babylon, and the king's mother, and the king's wives, and his officers, and the mighty of the land, those carried he into captivity from Jerusalem to Babylon.

[16] And all the men of might, even seven thousand, and craftsmen and smiths a thousand, all that were strong and apt for war, even them the king of Babylon brought captive to Babylon.


This refers to the Babylonian Captivity of the Judaean elite. I have alluded to the possibility of a male bias in the settlement of ancient Greek colonies, but if this passage is to be believed the skilled elite that the Babylonians removed from Judah was overwhelmingly male, and they did not return to their "homeland" for nearly 2 generations. Historically the most well documented instance of male mediated gene flow is the emergence of a mestizo population in the New World, where Iberian males entered into polygynous relations with many indigenous females. The outcome was a total phylogeographic disjunction between male and female lineages across large swaths of Latin America (that is, Y chromosomes suggest a West European origin, mtDNA suggest an Amerindian origin). One can see an echo of this in India as well, where Y lineages (e.g., R1a) are more likely West Eurasian than female lineages, or in England, where male lineages are more likely to imply Anglo-Saxon ancestry than female ones. A primary reason that I was willing to credit the likelihood of a mass migration in the case of the Etruscans is that female lineages also implied exogenous origin! In general the genetic data suggests that on average females were more likely to move because of patrilocality, but, it seems likely that long range dispersions would be mediated by male migration.

In any case, we have discussed the admixture of European Jews with local female lineages before. In the Commentary article Charles Murray mentions the possibility of truncation selection event being a causative factor in the creativity of the Babylonian Captivity. But if you want to go down that route, one might also suggest the possibility of assortative mating by the Judaean gentry with Mesopotamian women.

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Amber & Teak   posted by Razib @ 4/04/2007 05:43:00 PM
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The Himalayas as a Directional Barrier to Gene Flow:
...Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.

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Ancient Etruscans too were Monica Belluccis   posted by agnostic @ 4/04/2007 10:46:00 AM
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Nick Wade has a good article in the NYT on the origins of the Etruscans, which if you've been following Razib's coverage of the topic (here, here, and here) will sound pretty familiar. However, the following ancient account of their women caught my eye:
"Sharing wives is an established Etruscan custom," wrote the Greek historian Theopompos of Chios in the fourth century B.C. "Etruscan women take particular care of their bodies and exercise often. It is not a disgrace for them to be seen naked. Further, they dine not with their own husbands, but with any men who happen to be present."

He added that Etruscan women "are also expert drinkers and are very good looking."

Judging physical attractiveness is pretty easy -- you don't need to subject the person to a gauntlet of cognitive tasks like you do to gauge their intelligence, or see them behave in diverse situations to discern their level of extraversion. It's also a quality that males are apt to pay particular attention to, especially if it is so pop-out-of-the-background that a person emphasizes that a woman is very good looking. So, I think it's safe to say this ancient historian's remark is at least in the ballpark.

Moreover, it's hard to believe that within the past two or three thousand years the selective advantage for good looks would have diminished within an environment that's pretty pathogen-infested -- while Italy is no Nigeria, it's bad enough to have spawned local responses to malaria. We must also bear in mind that, compared to 21st-century Italy, environmental conditions back then were surely much less favorable to developing good looks, so that judging the appearance of Etruscan females from statues and frescoes from our modern lens might be a bit unfair.

Bearing that in mind, who among the moderns can we look to in order to investigate whether Etruscan women tend to be good-looking? My first thought was my third-year Italian professor, who hailed from Perugia and was still quite fetching even in her 50's (and I may have been deceiving myself; my female classmates said she was probably 60). After searching around for more well known individuals, I couldn't believe the felicitous end-result: Monica Bellucci herself comes from an Umbrian town of under 40,000 people (and that's as of 2001, not 1964 when she was born). What better proof do you need? Etruscan women were, and are, hotties.




Statistics blog   posted by p-ter @ 4/04/2007 09:26:00 AM
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For those of you into the whole statistics thing, Andrew Gelman (whose book Bayesian Data Analysis I just bought) and company have been churning out some interesting posts over at Statistical Modeling, Causal Inference, and Social Science. Check it out.

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Nerds are nuts   posted by Razib @ 4/04/2007 04:59:00 AM
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Reading In Spite of the Gods: The Strange Rise of Modern India, I stumbled upon this passage on page 151:
...Whereas the Congress Party was dominated by lawyers and journalists, the RSS was dominated by people from a scientific background. Both groups were almost exclusively Brahmin in their formative years...three out of four of Hedegwar's [the founder, who was a doctor -Razib] successors were also from scientific backgrounds: M.S. Golwalker...was a zoologist...Rajendra Singh was a physicist; and K.S. Sudarshan...is an engineer....



Some quick "background." The RSS is a prominent member of the Hindutva movement, roughly, Hindu nationalism. Some people have termed them "Hindu fundamentalists," suggesting an equivalence with reactionary religious movements the world over. There is a problem with such a broad brush term: some proponents and adherents of Hindutva are not themselves particularly religious and make no effort to pretend that they are. Rather, they are individuals who are attracted to the movement for racial-nationalist reasons, they view "Hindus" as a people as much, or more than, a religion. One could make an argument that the "Christian Right" or "Islamism" are not at the root concerned or driven by religious motives, but, members of both these movements would assert at least a pretense toward religiosity almost universally.

With that preamble out of the way, I was not surprised that the RSS had a core cadre of scientifically oriented leaders. This is a common tendency amongst faux reactionary movements with a religious element. I say faux because these movements tend to be extremely innovative and progressive in the process of attempting to recreate a mythic golden past. The militancy of some of the organizations in the Hindutva movement, like the VHP and RSS, has been asserted by some Hindu intellectuals as being...un-Hindu. Some of the early intellectuals in the movement admitted that they were attempting to fight back against Islam and Christianity by co-opting some of the modalities of these two religions. The question becomes at what point does pragmatic methodology suborn the ultimate ends? I won't offer an answer because I have little interest in that topic, at least in this post. Rather, I want to move back to the point about scientists and their involvement in "fundamentalist" religious movements. Scientifically trained individuals are over represented within Islam in the Salafist Terror Network. As a child the fundamentalist engineer was a cut-out stereotype amongst the circle of graduate students in the natural sciences from Muslim backgrounds that my parents socialized amongst. Ethnological research confirms that Islamist movements are highly concentrated within departments of engineering at universities. Engineers are also very prominent in the Creationist movement in the United States. If civilizations can be analogized to organisms, then a particular subset of technically minded folk get very strange when interfacing with the world around us...and turn into fundamentalists.


So why the tendency for technical people to be so prominent in these groups? First, let me clarify that just because technical folk are heavily over represented amongst religious radicals does not mean that religious radicals are necessarily a large demographic among technical folk. Rather, amongst the set of religious radicals the technicians seem to rise up to positions of power and provide excellent recruits.

There is I think a socioeconomic angle on this. Years back I was curious as to the class origin of different scientific professions. I didn't find much, but the data I did gather implied that engineers are generally more likely to be from less affluent backgrounds than more abstract and less practical fields like botany or astronomy. This makes sense, engineering is one of the best tickets to a middle class livelihood, and it might necessitate fewer social graces (acquired through "breeding") than medicine or law. As it happens, oftentimes fundamentalist movements draw much of their strength from upwardly mobile groups who are striving to ascend up from lower to lower-middle-class status. Though the Hindutva movement in India is mostly upper caste, it is not concentrated amongst the English speaking super elite who are quite Westernized, but rather its strength lay amongst the non-Western sub-elites (e.g., merchants in small to mid-sized cities) or the petite bourgeois. Islamism in much of the world can be traced to the anomie generated by the transformation of "traditional" societies through urbanization and other assorted dislocations, and as peasants enter the modern world Islamic orthodoxy is a way to moor themselves within the new urban matrix and the world of wage labor. Similarly, the rise of the Christian Right can be tied in part to the entrance of evangelicals into the broad middle class as the Old South became the New South and air conditioning led to the blossoming of the Sun Belt.

But there are likely other factors at play which are not sociological or cultural, but individual. Fundamentalists tend to be "literalists," and have a tendency to look at their religious texts as divine manuals which describe and prescribe every aspect of the world. In some ways this is a new tendency in our species, at least as a mass movement. One can definitely trace scriptural fundamentalism to the Protestant Reformation with the call to sola scriptura, but in the West its contemporary origin can be found in the reaction in the late 19th century and early 20th century to textual analysis of the Bible by modernists. The assault on the historicity of the Bible, combined with both mass literacy and a democratic culture in the United States, led inevitably to a crass literalism that birthed the peculiarities which we see before us in the form of Creationism and its sisters. A literal reading of the Bible leads to ludicrous conclusions, but if one perceives that the game is all or nothing, then perhaps one must assert the truth value of Genesis as if it was a scientific treatise. Religious professionals have often been skeptical of literalism because a deep knowledge of languages and the translation process highlights various ambiguities and gray shades, but for those whom the text is plain and unadorned by deeper knowledge its meaning is "clear" and must be take at its word. Scientists and engineers live in a world of axioms, laws and theories, which though rough and ready, must be taken as truths for predictions and models to be valid. You make assumptions, you construct a model, and you project a range of values bounded by errors. Once science is established you take it is as a given and don't engage in excessive philosophical reflection. This is "normal science." The axioms are validated by their utility in an instrumental fashion in engineering and model building. Obviously religious truths are different. Plainly, the direct material benefits of religion, magic, is easily falsifiable. The indirect benefits, the afterlife, etc., are often beyond verification. A critical examination of the Hebrew Bible shows all sorts of fallacious assumptions. For example, there is an implication that the world is flat and that the sun revolves around the earth. Though these contentions are not defensible, there are a host of other assertions which are less plainly incorrect, or at least seem to be refuted only by a more complex suite of contingent facts (e.g., the historical sciences in the form of geology and evolutionary biology falsify the creation account, but these are complex stories which require acceptance of a chain of inferences). Obviously many religious people have a deep emotional attachment to their faith. If one is told that one's religion is based on a book, and that book plainly seems to imply ludicrous assertions, how to square this circle? Many a scientific mind simply accepts the ludicrous axioms and starts to generate inferences. Consider the Water Canopy Theory. Or, the Hindutva ideology that Aryans originated in India, spread to the rest of the world, and so brought civilization (the gift of the Indians). Or that Hindu mythology records the ancient use of nuclear weapons and spaceships. There are even books like Human Devolution: a Vedic alternative to Darwin's theory. Strictly speaking much of this work is not irrational, insofar as it exhibits internal logical coherency. The axioms are simply ludicrous.

Which gets me back to the way scientists think: though some scientists are very philosophical, the way in which science is taught is often not particularly focused on the nature and reasoning beyond the axioms given. PV = nRT. Why? There are quick primers in regards to the root of the Ideal Gas Law, but the key is to take this law and utilize it to solve problems. But what if PV = nRT is subjective, a misinterpretation. Perhaps a cultural mix-up resulted in a transcription error which introduced the gas constant, R. This is an idiotic question to ask in science. If you're taking a course on the kinetics of gases you don't have long discussions lingering upon the nature of motion and gas particles, those are assumed. In contrast in softer disciplines the very concept of "motion" an "particles" are subject to critique because the objects of study are far more slippery. Is it the "Red Sea" or "Sea of Reeds"? Does the Bible refer to Mary as a virgin or an unmarried woman? Does the color coding of the Aryans and Dasas in the Vedas refer to literal differences in complexion, or are they narrative conventions? Language lacks the interpersonal precision of mathematics, and while uniformitarianism has served us admirably in the natural sciences, the dynamic nature of idiom, phrase and speech within shifting context means that teasing apart meaning from the records of the past can be a difficult feat which requires care, erudition and common sense.

Up until this point I have focused on the way scientists work, and the necessity of background assumptions, and the relative short shrift they often give to the "meta" analysis of background concepts. Though I don't want to push this line of thought too far, I will offer the following illustrations of behaviors which I think are not totally unlike the manner in which some fundamentalists behave. Someone tells a child to "pull the door behind" them. He proceeds to unscrew the hinges and drag the front door across to the street to his house. Siblings are told that there is life after death by their parent. They proceed to plan the death of one so that some confirmation of this possibility can be ascertained. These two instances are real examples of individuals who exhibit Autism/Asperger's Syndrome. Anyone who would behave in this way lacks common social sense. I believe that a disproportionate number of those who are attracted to fundamentalism tend to lack the same perspective and contextualizing capacity in regards to their religious beliefs. If they can do some matrix algebra too, they're nerds. On a mass scale, consider that both Salafis among Muslims and Puritans among Calvinists debated whether all that was not mentioned within their Holy Texts as permissible were therefore impermissible. I suspect that for most people common sense might persuade one to the conclusion that these sort of debates imply a lack of a sense of proportion, frankly, of normalcy.

In sum:
  • Hard core religious fundamentalists are somewhat atypical psychologically
  • Scientists and engineers are also atypical psychologically
  • Some of the traits modal within these two sets intersect
  • Resulting in a disproportionate number of scientists amongst fundamentalists
  • Science converges upon rock solid truths, which become the axioms for the next set of projections and investigations. Fundamentalism presents itself as axioms and clear and distinct inferences from those axioms. Both are fundamentally elegant and simple cognitive processes, but, the content is so radically different that the outcomes in regards to truth value are very different
  • Mass literacy and mass society, as well as the decentralization of authority and power, likely made fundamentalism inevitable as the basal level of individuals with susceptible psychological profiles could now have direct access to the axioms in question (texts)
  • Just as some scientists tend to take ideas to their "logical extremes" (e.g., the "paradoxes" of physics) no matter the dictates of common sense, so some fundamentalists take the logical conclusion of their religious texts to extremes
  • No matter the religion it seems that modernity will produce faux reactionary fundamentalism because of the nature of normal human variation combined with universal inputs (e.g., the rise of normative consumerism, urbanization, etc.).


Note: Much of what I said above applies to non-religious domains. After all, many scientists were once Communists and Nazis.

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Sewall Wright Again   posted by DavidB @ 4/04/2007 01:31:00 AM
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In a recent post on Sewall Wright I discussed some of the difficulties of Wright's work and mentioned that I had been unable to find a derivation of a certain formula in his paper Systems of Mating Part 1. On the remote chance that someone somewhere is tearing their hair out over the same problem, I should mention that I have now found a derivation and will include it in a subsequent post.

Meanwhile, as often happens, I have been sidetracked by related issues: in this case, the so-called debate between Mendelians and Biometricians in the early years of the 20th century, and the work of Pearson, Yule, Fisher and others on the genetic correlation between relatives. (See also Razib's very interesting post here.) As this is relevant to Wright's early work, I may write a post on it before I come back to Wright.

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Tuesday, April 03, 2007

Cultural evolution causes biological evolution   posted by agnostic @ 4/03/2007 07:13:00 PM
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Returning to a favorite theme here -- debunking the balderdash that recent human evolution is cultural rather than biological -- consider how simple technological changes can influence human biological evolution. Take musical instruments: in an environment with no musical instruments, and thus essentially no music, you'd never know who were the rockstars (if male) or the dancing queens (if female). With no way to detect these sexy phenotypes, natural selection could not change the frequencies of alleles that contributed to them. But once the presence of musical instruments becomes a predictable feature of the environment, suddenly there's a pressure to be a good performer, and so traits both physical (dexterity, agility) and psychological (extraversion, emotional volatility) will increase, at least up to a point where any further increase would be a bad bet for newcomers as they crowd an already saturated niche. It's hard to show off when everyone else shows off in the same way.

Now, we commonly urge youngsters to "find their niche," yet many people ignore the obvious corollary of this ecological phrase, namely that whatever cultural processes spawn new niches will also result in a change in frequency of alleles implicated in the traits needed to thrive therein. Unlike Darwin's finches, humans don't need to expand into an unsettled archipelago to undergo adaptive radiation -- we can stay fixed geographically but broaden the range of niches in our "social-cultural space."

At my personal blog, I sketched out a reason for why technological progress tends to be more bustling than progress in more abstract disciplines like geometry, where progress appears to stagnate for quite awhile until "the next big thing" comes along. Basically, the purer arts and sciences are the hobbies of weirdos, whereas technology is usually a matter of life and death: i.e., outperforming the technology of your adversaries. This literal arms race keeps the pace of technological progress much more frenzied than in other cultural areas. The key is that new shields, spears, guns, and ships don't affect the fitness of just soldiers, because most of this new stuff will be ripped off by others to innovate civilian life.

For instance, there would be no common cars if militaries had not pioneered the technology of interchangeable parts and mass assembly-line production for ships and firearms. Nor could their interiors and exteriors be held together were it not for the common use of steel, an alloy whose first modern production method -- the Bessemer Process -- resulted from its inventor's efforts to more efficiently produce firearms for the Crimean War, and whose Captain of Industry (Andrew Carnegie) made his fortune through contracts to build warships for the US Navy. And since the widespread availability of the automobile, many males have carved out a niche whose appeal to females centers around owning a car when other males don't (the guy in 10th grade with his own car) or using their car to signal machismo (drag racers). So, to paraphrase a related slogan on technological changes fueling biological changes: howitzers hatched heart-throbs in hot rods.

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Note to self: avoid vinclozolin   posted by p-ter @ 4/03/2007 06:04:00 PM
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Speaking of epigenetics, here's a rather interesting phenomenon:
Environmental contamination by endocrine-disrupting chemicals (EDC) can have epigenetic effects (by DNA methylation) on the germ line and promote disease across subsequent generations. In natural populations, both sexes may encounter affected as well as unaffected individuals during the breeding season, and any diminution in attractiveness could compromise reproductive success. Here we examine mate preference in male and female rats whose progenitors had been treated with the antiandrogenic fungicide vinclozolin. This effect is sex-specific, and we demonstrate that females three generations removed from the exposure discriminate and prefer males who do not have a history of exposure, whereas similarly epigenetically imprinted males do not exhibit such a preference. The observations suggest that the consequences of EDCs are not just transgenerational but can be "transpopulational", because in many mammalian species, males are the dispersing sex. This result indicates that epigenetic transgenerational inheritance of EDC action represents an unappreciated force in sexual selection. Our observations provide direct experimental evidence for a role of epigenetics as a determinant factor in evolution.

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A note on '2s'   posted by p-ter @ 4/03/2007 03:39:00 PM
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On this site, given our interest in the research by Hawks and Cochran, most people are familiar with Haldane's result that the fixation probability for an advantageous allele is about 2s. According to the paramaterization of most modern population genetics texts, this is somewhat confusing-- normally, the fitnesses of different genotypes (call then AA, Aa, and aa) are noted as 1, 1+sh and 1+s. s is then the advantage to one homozygote and h is a parameter that takes into account dominance. Simple acceptance of Haldane's result would lead one to think that the most important parameter in determining the fixation probability is s. This is counterintuitive, given that any new allele exists for a while almost exclusively in heterozygotes.

Indeed, as noted by Hawks and Cochran, the original derivation of Haldane's result ( note the use of generating function methods in a branching process, very similar to an epidemiological model I've outlined before) considers only a dominant allele, in which case h=1 and 1+sh = 1+s. For an allele of arbitrary dominance, however, the fate of the new allele is almost completely determined by its effect in the heterozygote, in which case the probability of fixation is better noted as about 2hs, rather than 2s.




A fitness floor?   posted by Razib @ 4/03/2007 12:29:00 AM
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PLOS Biology has an interesting new paper out, Understanding the Evolutionary Fate of Finite Populations: The Dynamics of Mutational Effects:
In any population, two factors determine whether the average fitness of individuals will increase...or decrease: the size of the population and the distribution of mutational effects...Although it is relatively simple to get quantitative information on population size, it is much harder to gain insight into the distribution of mutational effects...Here, we use laboratory evolution of a bacterial virus to quantify the distribution of mutational effects. Our results reveal that the average impact of a mutation is approximately constant with respect to fitness, that most mutations have small effects, and that the rate of beneficial mutation depends on the fitness of the organism. Our study demonstrates the simple, but perhaps underappreciated fact that mutational effects are dynamic. It also proposes and tests an explicit model of adaptation in which organismal fitness specifies both the rate and distribution of deleterious and beneficial mutations, and it presents specific and testable predictions of the circumstances under which populations will adapt.


From the abstract: "The most consistent result in more than two decades of experimental evolution is that the fitness of populations adapting to a constant environment does not increase indefinitely, but reaches a plateau. Using experimental evolution with bacteriophage, we show here that the converse is also true. In populations small enough such that drift overwhelms selection and causes fitness to decrease, fitness declines down to a plateau." In regards to fitness reaching a plateau, this is intelligible via R.A. Fisher's argument that mutations of large effect will tend to overshoot the fitness optimum. The "plateau" occurs simply because a population is presumably converging upon the local fitness optimum, and as it approaches that optimum mutations which increment it toward that state must by the nature of the landscape be of small enough effect so as not to overshoot the peak. Conversely, the authors of this paper argue that the fitness floor which occurs when a population size is small and random genetic drift overwhelms the purifying power of selection (so that deleterious mutations may fix in the genetic background) may be generated by the emergence of compensatory epistasis which acts as a break upon further accumulation of "deleterious" alleles. By this, they mean that alleles at loci which in the "normal" genetic background (i.e., closer to the fitness optimum) would be detrimental toward fitness may now actually favorable because of interactions with other normally "deleterious" alleles at other loci.

Consider a set of loci, numbered from 1 to 10. Assume that they are fixed for a range of alleles in the normal genetic background. If loci 1 mutated from a to b in the normal genetic background it might be deleterious. But, if loci 3 were mutated from a to b then one might imagine that the interaction between two b alleles across the loci might result in a less deleterious outcome than either one in the conventional genetic background. Any thoughts on the relevance of this to the mutational meltdown hypothesis?

Related: Rugged Roads of Gene Land.

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Monday, April 02, 2007

Epigenetics in Memory, II   posted by amnestic @ 4/02/2007 09:09:00 PM
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Epigenetics. What is it? Let's ask some reputable sources.

From the glossary of a review in the current Nature Reviews Genetics:

Epigenetic - Refers to mitotically or meiotically heritable changes in gene expression that do not involve a change in DNA sequence.


From the Cell epigenetics review issue a month and a half ago:

Epigenetics, in a broad sense, is a bridge between genotype and phenotype-a phenomenon that changes the final outcome of a locus or chromosome without changing the underlying DNA sequence. ... More specifically, epigenetics may be defined as the study of any potentially stable and, ideally, heritable change in gene expression or cellular phenotype that occurs without changes in Watson-Crick base-pairing of DNA.


Both definitions suggest that, to be epigenetic, something must 1) be heritable and 2) not be attributable to DNA sequence. Imagine if you took that "ideally" very liberally and dropped the heritability requirement. Now a change in gene function must be attributable to something besides DNA sequence. At that point epigenetics becomes gene regulation. Living cells are constantly performing gene regulation in myriad ways. If we loosen the definition enough, epigenetic could mean signal transduction, regulation of protein synthesis and degradation, and any and all transcriptional modulation. Definitions can and do change. One thing I'd like to do in this post is generate discussion as to the most useful way to use the term epigenetics, so that we can communicate most efficiently about the various biological topics now gathering under its umbrella.

Here is a third definition from David Sweatt and Jonathan Levenson:

A third definition posits that epigenetics is the mechanism for the stable maintenance of gene expression that involves physically 'marking' DNA or its associated proteins. This allows genotypically identical cells (such as all cells in an individual human) to be phenotypically distinct (for example, a neuron is phenotypically distinct from a liver cell). The molecular and physical basis for this type of change in DNA or chromatin structure is the focus of this review. By this definition, the regulation of chromatin structure is equivalent to epigenetics.


In this definition, they are equating a mechanism for epigenetics with epigenetics. Now we have the same term at two levels of analysis. If you're a Hofstadter fan you can probably think of a lot of mischief to stir up when you run into this situation, but that's not the real problem. The problem stems from the fact that we already know that epigenetics isn't restricted to the regulation of chromatin structure, so in simplifying the term to one set of mechanisms we are discarding information and excluding mechanisms that we may not have even discovered yet. A lot of the time, Sweatt and Levenson use the term 'epigenetic mechanisms' to mean regulation of histone modification and DNA methylation. If we mean chromatin structure, why not say that? Why do Sweatt and company trade in 'chromatin modification' for 'epigenetics'? It's not an entirely arbitrary thing to do. The best understood mechanisms for epigenetic phenomena are DNA methylation and histone modification, hands down, and if you search Pubmed for epigenetics you will have a very difficult time finding an article that doesn't involve some combination of these chromatin 'marks'.

The most-studied instance of epigenetics is probably imprinting. It has something for everyone, from an exciting battle-of-the-sexes evolutionary explanation to a cellular mechanism veiled in mystery. Very briefly, imprinting occurs when, for instance, you get the exact same DNA sequence for Gene A from mom and dad (you get two of each gene in case you forgot), but only the Dad copy of Gene A is active. The Mom copy is imprinted and thus silenced. Some percentage of human genes are imprinted. I think it's less than ten percent, can't remember. How is the gene expressed differently if the DNA sequence is the same? Well, during egg-ogenesis Mom added a methyl group (CH3, not a very reactive group, just makes the molecule bulkier) to a bunch of the cytosines in and around Gene A, thus changing them to 5-methyl-cytosines. This is called DNA methylation. In this example the gene is maternally imprinted, but don't get it twisted. Dads can imprint too. DNA methylation can affect gene expression directly by hiding sequences that would normally be recognized by regulatory proteins or indirectly as there are proteins that recognize methylated DNA and can recruit chromatin modification complexes to that locus. By the way, if any of this is terribly interesting to you please go check out one or two of the billion reviews on this stuff as I am not an expert in this area and I'd hate to lead you astray.

DNA is often packed up by wrapping it around proteins called histones like you wrap the string around your yo-yo before you put it in the drawer. Unwrapping DNA from the histones allows other proteins (like RNA polymerase) access to the DNA and generally means an upregulation of that gene's activity. You can attach or detach acetyl groups or methyl groups (or phosphate groups or ubiquitin groups or SUMO groups, histones must look like Katamari Damacy) to the histones to make them more or less attracted to the DNA. Histone acetylation (by HATs) and deacetylation (HDACs, histone deacetylases) are core mechanisms for switching a section of chromosome between transcriptionally active and inactive states. There is a complex relationship between DNA methylation and histone modifications. As a basic scheme, DNA methylation is more often associated with silent genes wrapped tightly around deacetylated histones. The two occur independently though. Many transcriptional activators play their part by dragging some histone modification machinery to the gene they are interested in, so histones are dynamically modified in many cases of transcriptional regulation, whereas DNA methylation has been thought to be a more stable, long-lasting modification.

So, yes. Very often 'epigenetic mechanism' refers to DNA or histone modification, but there are other ways of passing information between generations of organisms or cells without touching the DNA sequence. Yeast can transmit information across generations in the form of prions, infectious protein conformations. Think of Ice-9 in Cat's Cradle. When prions touch other normally folded proteins of the same type, they can transfom the normal protein. So a protein with the exact same amino acid sequence can fold up two different ways, one of which (the prion form) can be passed on to the offspring of the prion-infected yeast. Thus, a phenotypic determinant is passed across generations with no help from the DNA sequence. Also, last year a French group reported an instance of epigenetics in which accumulation of some abnormal RNA molecules in mouse sperm is responsible for inheritance of a specific coat pattern. All that is to say is that there are lots of ways to transmit information across generations and cell divisions.

I think the thing about chromatin modification that was initially appealing to Sweatt and colleagues in terms of memory was its apparent stability. Research into cell differentiation, the process by which your basic stem cell produces the diverse array of cell-types required, has implicated chromatin modification as a strong influence. The idea is that to make, for instance, a neuron, you have to permanently set up a certain transcriptional program to make things like neurotransmitter receptors, so you go ahead and permanently turn on those genes. In some sense you could extend cell differentiation to a highly refined level so that the cell types aren't broad classes like neuron and skin cell, but rather 'neurons storing memory A' and 'neurons storing memory B'. Following this train of thought or something like it, they began to look for signs of chromatin modification in response to learning. They discovered that after a hippocampus-dependent form of fear conditioning, histones in the hippocampus are modified. Acetylation and phosphorylation are high one hour after training, but return to baseline by 24 hours. Given that we know that many genes are upregulated in response to fear conditioning and that transcription factors that activate genes have a history of modifying histones it would have been quite a surprise if we hadn't seen any changes. At this point, I began to get a little unhappy with the papers coming out of the Sweatt lab because I felt like the histone-modification story wasn't telling us much that we didn't know.

So far, the epigenetics in memory story has been presented in a theoretical framework emphasizing the stability of chromatin modifications and the persistence of long-term memories. Just so I don't mischaracterize, here is a quote from 2006:

One question that has eluded neuroscientists is, How can the brain store information over the lifetime of an organism in the face of molecular turnover? This question is especially relevant for understanding a complex process such as cognition, which relies heavily on the ability to store and recall information for periods longer than the half-lives of most of the molecules utilized in these processes. Chromatin is the one structure that remains relatively constant in almost every cell of a metazoan. It is not surprising that many recent studies in the nervous system indicate that from invertebrates to mammals, chromatin is a dynamic structure that integrates potentially hundreds of signals from the cell surface and effects a coordinated and appropriate transcriptional response. More important, chromatin is perhaps the only structure in a neuron capable of such higher-level signal integration and information storage that is not continually turned over.


To rephrase: Memories are persistent. Therefore the molecular mechanisms for memory are persistent. Most molecules don't last, so they can't do the job. Chromatin structure lasts, so it is a good candidate for long-term memory storage.

Here are my various criticisms of this line of thinking:

1) You can't have your cake and eat it too. Is chromatin a dynamic structure changing in the face of new stimuli or is it a solid, stable basis for long-term information storage? Once a cell's epigenome has been modified to store a memory does it somehow get write-protected? It seems to me that there are some chromatin modifications that are highly stable (i.e. the ones that control cell differentiation) that should be very unresponsive to the day-to-day vagaries of cell signaling, otherwise you would have neurons de-differentiating all willy-nilly. Another separate set of chromatin modifications must respond to cellular stimuli and allow dynamic gene expression to fit the needs of the cell in the current situation.

2) A cell only has one epigenome, but encodes more than one memory. That's the wonderful thing about synapses; they allow multiple excitability configurations. An average neuron has thousands of synapses. Memory 1 can light up synapses X, Y, and Z and cause the cell to fire a burst of action potentials whereas Memory 2 lights up a different set of synapses causing the cell to fire at a slower, more consistent rate. Maybe when synapse X loses its ability to excite the cell you forget a little bit and the burst of action potentials is weaker. That's one scenario. The point is illustrated empirically in studies like Vazdarjanova and Guzowski, (2004), which shows that 35% of cells in the CA1 region of the hippocampus light up in response to a single experience, and there is some 15% overlap between cell populations responding to two different contexts. The point of that report is actually to show that representations are relatively non-overlapping, but they aren't so sparse that you can afford a cell per experience. Is there some way to propose chromatin modification as a long-term memory mechanism that doesn't make this sparsity requirement?

3) The molecular turnover problem was never a problem. Sure molecules turnover, so the memory can't be housed in a single individual molecule. Dendritic spines (structures forming excitatory synapses), on the other hand, can remain stable for as long as we can record them. All of the molecular constituents of the spine turn over, but the structure remains. All of your skin cells die and are replaced, but your body remains intact. It's not an issue. The only way that molecular turnover would be an issue is some critical mass of the molecules in a structure turned over at once. I can imagine some mechanisms involving the post-synaptic scaffolding and structurally induced biochemical states, but the mechanism doesn't matter for putting the molecular turnover issue to bed. We have observed neuronal structures remaining intact for long periods of time. Apparently there are parts of the cell that are stable besides the chromatin.

I can maybe think of a way out of #2, but #3 seems very clear and very much in conflict with the theoretical framework for this work. So when the new Miller and Sweatt came out I was thinking, "This is just the histone papers again with DNA methylation." I skimmed it, saw some of the experiments I expected, and gave it a general thumbs down. Now that I've given it a few reads I think the paper has some relevant and really novel findings, a major one being that DNA methylation is regulatable in nondividing cells.

The enzymes that methylate DNA are called DNA methyltransferases (DNMTs). They most commonly add the methyl group to the C in the sequence, CG. Remember that DNA is double-stranded so you get a CG - GC quartet of nucleotides at these preferential methylation sites. There are two major classes of DNMT in mammals: de novo and maintenance. Maintenance DNMTs make sure that if a portion of the genome was methylated in a dividing cell, say a neuronal precursor cell, then that portion will be methylated in the daughter cells produced by the division. During DNA replication just prior to cell division you have double stranded DNA containing one of the original strands (with methylated CGs) and one newly synthesized strand. A maintenance DNMT recognizes the dsDNA with only a methylated CG facing an unmethylated GC and makes them match. De novo DNMTs can make new methylation sites where there was no indication of methylation to begin with. Their major role is during the 'reset' of methylation states that occurs during gametogenesis and in the preimplantation embryo, and they have been considered relatively quiet in the fully developed adult.

The first thing Miller and Sweatt did was to show that the level of de novo DNMT mRNA is increased after fear conditioning. They then injected DNMT inhibitors into the hippocampus after fear conditioning and blocked long-term memory consolidation. I initially thought this experiment was suspect because I didn't understand that DNA methylation is not expected to be part of a cell's normal function. I associated DNA methylation with histone deacetylation and my understanding is that histone acetylation states are very commonly altered to tweak this or that gene's level up or down. In reality, people have hardly tested the effects of DNMT inhibitors in non-dividing cells. The literature is full of attempts to selectively target cancer cells with DNMT inhibitors because they have a habit of dividing too much. You would still like a more specific manipulation, a way of inhibiting DNMTs at specific genomic loci would be nice, but the behavioral control experiments in this paper go a long way toward showing that the drugs are not simply killing off neurons. The inhibitors are only effective at a time point shortly after training, defining a maximum window of some 6 hours in which relevant genes are demethylated and remethylated or vice versa in response to behavioral training.

They next showed regulation of methylation at genes that are positively and negatively associated with memory formation. Protein phosphatase 1, a 'molecular constraint on learning and memory', is transiently methylated leading to reduced levels, whereas reelin, which has been associated with synaptic plasticity shows reduced methylation levels and increased mRNA expression. This second finding is pretty important. The identity of the mammalian demethylating enzyme is unclear leading some to question if an active demethylase exists at all. Demethylation in dividing cells can be achieved by simply being lazy about methylating new DNA. According to Hermann et al. in 2004, the 'best evidence so far for active demethylation in vivo" was the rapidity of sperm chromatin demethylation after fertilization. I'd say reduced methylation at the reelin locus in non-dividing cells within an hour after behavioral training is quite strong evidence. In fact, this window of very rapid demethylation at a specific locus suggests a strategy for investigating the biochemistry of mammalian demethylation. It should be possible to trap any proteins that are associated with the reelin promoter in the hour or so after training using techniques like chromatin immunoprecipitation.

Finally, they emphasize that the methylation changes are transient. Everything returns to baseline by 24 hours after conditioning. This very obviously contradicts the idea of DNA methylation as a memory storage tool. For some reason, the discussion section still won't let it go though. Look at this:

This attribute is, however, consistent with the role of the hippocampus as a structure contributing to memory consolidation but not memory storage. It will be interesting to determine if the Crick/Holliday mechanism plays a role in perpetuating long-term changes in adult neurons in the cortex, at known sites of long-term memory storage.


The hippocampus' role in various types of memory may or may not be temporary. This is a broadly debated issue and in my humble opinion, the folks making the case for a long-term role for the hippocampus are doing a fine job. Regardless, no one suggests that the hippocampus is only involved for less than a day. So there must at the very least be a mechanism besides DNA methylation that helps maintain the memory for a week or so.

I spent a lot of time looking into ways to specifically affect DNA methylation at certain loci. I found a paper where they made chimeric DNMTs with a custom DNA-binding domain and inserted the recognition sequence for that domain into the area to be methylated. To achieve this in vivo with any sort of temporal specificity would require the combination of at least three transgenes either through traditional methods or injection of viral vectors. The temporal specificity (within 6 hours) would still not really be on point, so I guess this isn't the solution.

So now we know that some genes are regulated by methylation state in response to learning. The obvious next question is which genes. How does the cell decide which genes to turn up and which ones to turn down? Is there a signature pattern of CGs that indicates memory repressor vs memory enhancer genes? Do transcription factors that are already implicated in memory-related gene expression recruit DNA demethylase activity?

A broader question remains. Why should mRNAs get expressed in response to learning anyway? Why involve the nucleus when the action is out at the synapses? I'm convinced that its important, but for my money, local protein synthesis from pre-existing RNAs seems a more specific response to changes in input patterns. Does anyone reading have an explanation for the need to produce new RNAs so far from the locus of plasticity?

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Mendel's Garden #13   posted by Razib @ 4/02/2007 07:13:00 PM
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Over at my fellow ScienceBlogger Alex Palazzo's palace.

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Modern humans in China - they did exist!   posted by Razib @ 4/02/2007 05:59:00 PM
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There's a new article that's going to come out in PNAS which reports the discovery of a find which exhibits predominantly modern human morphology with some archaic features, and those archaic features seem to be derived from local hominid populations. They've dated it to around ~40,000 years ago, which is important since East Asia is something of a black hole in regards to archaic H. sapiens (i.e., there's some very ancient erectus finds like Peking Man from millions of years in the past, and recent human reminds from the past 10,000 years, but little which sketches out the past few hundred thousand years). The BBC has the best write up so far. Don't believe the stuff about "debunking Out of Africa," one fossil does not a paradigm shatter. Rather, I think these finds are pretty good evidence for genetic assimilation of archaic substratum into the expanding wave of Africans. An important background fact to keep in mind: H. erectus and direct descendants of the original erectine populations were resident in East Asia until a rather recent period. One line of thought connects the extinction of erectus populations explicitly with the Out of Africa burst presumed to have occurred around 50,000 years ago.

Update: Science has a nice summary.

Related: Of lice & men. Erectine harems.

Update: John Hawks weighs in.

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Sunday, April 01, 2007

Nothing in the pipeline but posts?   posted by Razib @ 4/01/2007 10:33:00 PM
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If you haven't, you might be interested in checking out In the Pipeline. Derek Lowe has been "in transition" between jobs for a month or so and has been taking the down time to crank out good quality posts everyday. It's a joy. No doubt he'll have a job soon, so check it out while it's still happening....

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HDTV, passing me by....   posted by Razib @ 4/01/2007 10:23:00 PM
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Regular readers of this weblog know that I haven't had regular access to a television for several years. I haven't had cable since the middle of 2004. One thing that I've been struck by lately is how cultural waves are passing me by...I was having some wine at a local bar the other day and was dazzled by the crispness of the picture. I then realized, this was HDTV. It seems likely that while I will be without television, the rest of the society will switch to HDTV in the next few years. Strange days. The main problem I have with this is my enjoyment of South Park is being compromised by my lack of cultural fluency. YouTube helps...but it can't replace the importance of immersion in trash-TV. There will come a day that my South Park laughs may come from gutter humor which needs not support from common pop-culture currency.

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Homo floresiensis from Sulawesi?   posted by Razib @ 4/01/2007 08:46:00 PM
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I just finished reading a review copy of A New Human: The Startling Discovery and Strange Story of the "Hobbits" of Flores, Indonesia. The title says it all, and one of the authors is Michael Morwood, one of the lead researchers of the group which published the initial papers. Definitely not a "fair & balanced" work,1 though reasonably interesting (I found the ethnology and evolution more interesting than the stratigraphy and tephrochronology, but that's just me). One of the surprising assertions that Morwood makes (foreshadowed early on) is that the H. floresiensis was derived from a popuation which likely came from the north, in particular the island of Sulawesi. Morwood's argument derives from reading the ocean currents (north to south) in the region, and the nature of the local island biogeography. He also suggests that it is likely that the first modern humans arrived on Flores with the Papuan expansion less than 10,000 years ago (due to the emergence of the garden-culture complex based around yams, taro, etc.). An implication of Morwood's reading of the nature of the spread of mammals in east-central Indonesia is that the initial colonization of Australiasia might have occurred via a "northern" route, from Sulawesi to the east, rather than stepping from Java, to Bali, to Lombok, and so forth.

I'll probably have more comment later.

1 - John Hawks is noted as one of the individuals at "one end of the spectrum" in regards to asserting that the LB1 fossil was pathological.

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NOVA, online   posted by Razib @ 4/01/2007 07:06:00 PM
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Looks like NOVA, the PBS science program, has finally put a bunch of shows online.

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