Saturday, September 30, 2006

Evolution and God   posted by the @ 9/30/2006 04:20:00 PM

In your opinion, how true is this? ... D. Human beings developed from earlier species of animals.

Frequency Distribution
Cells contain:
-Column percent
-N of cases

Color coding:<-2.0<-1.0<0.0>0.0>1.0>2.0Z
N in each cell:Smaller than expectedLarger than expected

As you would expect, this also holds for BIBLE:

Frequency Distribution
Cells contain:
-Column percent
-N of cases
4: OTHER1.5

The trend holds when you compare across groups by educational attainment. Here is a table of the average response to SCITEST4 (lower = better).

Main Statistics
Cells contain:
-N of cases

Color coding:<-2.0<-1.0<0.0>0.0>1.0>2.0T
Mean in each cell:Smaller than averageLarger than average

God and British Scientists   posted by Razib @ 9/30/2006 03:47:00 PM

From The God Delusion:

1) 1,074 Fellows of the Royal Society were emailed

2) 23 percent responded

3) They were asked various propositions, such as, "I believe in a personal God, that is one who takes an interest in individuals, hears and answers prayers, is concerned with sin and transgressions, and passes judgement."

4) They were invited to choose a number from 1 to 7 indicating strong disagreemant to strong agreemant.

5) 3.3% agreed strongly with the statement that a personal god exists (chose 7), while 78.8% strongly disagreed (chose 1).

In the United States the National Academy of Sciences members exhited theism to the tune of 10%.

Related: God & the scientists, God & the evolutionists.

The rise of welfare?   posted by Razib @ 9/30/2006 10:34:00 AM

Over the past few months I've read Winning the Race by John McWhorter and The Burden of Bad Ideas by Heather Mac Donald. One thing that both books assert is that in the late 1960s and early 1970s there was a proactive campaign by the National Welfare Rights Organization to get as many people on the rolls in places like New York City as possible. McWhorter also notes that there seems to have been a special emphasis on recruiting black Americans to heighten and exacerbate the racialized dimension of the problem. But getting poor people on welfare was only a means to an ends, and that ends was bankrupting the government and overturning the established social order. In other words, to overthrow the Great Society welfare state (and presumably replace with something more politically revolutionary). But in any case, the only reason I bring this up it that as I was reading this I was struck by an analogy to the Starve-the-beast philosophy promoted by Grover Norquist, except in the opposite direction. The key goal in both cases is to "break it" so that you can build it anew....

Friday, September 29, 2006

Skin color and IQ in the GSS   posted by the @ 9/29/2006 11:42:00 AM

A question from Jason Malloy prompted a quick search of the GSS for data on the cause of the Black-White IQ gap. In 1982, the GSS characterized the skin color of Black participants on a 5-point scale (1:very dark brown to 5:very light brown). The very dark/light categories consist of only 50 and 14 individuals, respectively, and so in the following analysis I merged them with the dark/light brown categories, to give three COLOR levels: dark, medium, and light. In the web application, use COLOR(r:1-2;3;4-5) instead of COLOR. The WORDSUM variable is a 10 question vocabulary test, which I'm treating as a proxy for IQ. It is correlated with educational attainment (~.4), and also correlates (~.4-.5) with tests of reasoning and basic knowledge that were given in some years. These other tests are not available for 1982. In the all-subject all-year GSS data set, WORDSUM varies by SEX, and in 1982 COLOR also varies by SEX. Thus, SEX is controlled for in each analysis. WORDSUM is lower in the youngest and oldest age groups, so an AGE(25-65) filter was used.

Table 1. Mean WORDSUM score by COLOR and SEX with ANOVA

Main Statistics
Cells contain:
-Std Devs
-N of cases
COLOR1: Dark4.15
2: Medium5.39
3: Light6.04

color indicates T-statistic, and thus p-value
Color coding:<-2.0<-1.0<0.0>0.0>1.0>2.0T
Mean in each cell:Smaller than averageLarger than average

Analysis of Variance

Main effects89.443.061329.8146.956.0002


We can quantify the effect size of each skin color class using Cohen's d statistic, which measures the mean difference in standard deviation units. In the 1982 dataset, the overall d for the Black-White gap on WORDSUM is -0.63 (among males d=-0.51, among d=-0.74). For comparison, the 1982 male-female gap among Whites is d=-.12, favoring females.

Table 2. Effect size (d) of COLOR on WORDSUM using "light" as a control group


We can also use Whites as the control group.

Table 3. Effect size (d) of COLOR on WORDSUM using Whites as a control group


Thus, there are substantial (moderate to large effect size) differences in WORDSUM scores between the darkest and lightest Blacks in 1982.

As reported by Rushton and Jensen (2005), Shuey (1966) reviewed 18 studies which used skin color as a measure of racial admixture to compare with IQ. Of those 18, 16 found a significant effect of the kind found here, but the overall correlation with IQ was low (r=.1). In this data, the COLOR WORDSUM correlation is r=.31 among males and r=.18 among females, with an overall correlation of r=.23. Off the top of my head, I'm not certain what the expected correlation would be between IQ and skin color among Blacks for a given measure of "between-group heritability" (BGH) as described by Jensen (1998). I'll leave it as an exercise for our mathematically skilled commentators to derive a formula for this relationship and to evaluate the signficance of this finding in explaining the cause of the Black-White IQ gap.

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Fisher and Wright on Population Size   posted by DavidB @ 9/29/2006 02:01:00 AM

As part of background reading for 10 Questions for A. W. F. Edwards I re-read R. A. Fisher's Genetical Theory of Natural Selection, and noted some points of interest. Over the next few weeks I hope to explore these.

The first concerns Fisher's views on the effective population size of species. It is well known that Sewall Wright attached great importance to the internal population structure of species, while Fisher in contrast thought that for most purposes a species could be treated as a single randomly interbreeding population.

This contrast is sometimes posed in stark terms. For example, the historian William B. Provine, in a comment on one of Sewall Wright's papers, says: 'Fisher wrote to Wright to say that he believed effective population size to be a crucial variable, but that he considered most species to be panmictic (random breeding) throughout their ranges, even if their range was the entire world. Wright disagreed strongly'. [4, p. 71]

If this were an accurate representation of Fisher's views, then of course Wright would be right. Most species are obviously not panmictic throughout their ranges. But this in itself should raise suspicions. Scientists seldom espouse views that are obviously absurd. So what did Fisher actually say about population size?

To explore this will take several posts. Here is a first instalment, covering the period before the publication of GTNS in 1930.

Most of Fisher's papers and letters are available online here, but there are a few exceptions. It turns out that some of Fisher's most explicit comments on population size came in a book review in 1921 [1] that is not available online. The Dutch biologists A. L. and A. C. Hagedoorn were early proponents of what is now called genetic drift. In the 1920s and 30s it was often described (by Fisher and Wright among others) as the Hagedoorn Effect. In his review of their book Fisher commented:

The present reviewer has examined this particular point, and finds that in the absence of mutation or crossing [i.e. interbreeding with individuals from outside the group], a perceptible reduction of variability will take place in a number of generations equal to four times the number of the species breeding. In the case of great seasonal fluctuations in number, it is only fair to take the number of interbreeding individuals at its lowest point, but even so the number of interbreeding individuals in any group will seldom be less than five figures...[i.e. less than 10,000].

The number of robins in a county [i.e. an English county, with an area of a few hundred to a few thousand square miles] even in winter must be many thousands, and in a thousand generations interbreeding will have taken place to an extent which will have spread the blood of any local group over the whole country [sic: it is not clear if Fisher meant 'country' or 'county'. Both would make sense in the context].

If a relatively rare animal were taken, such as the badger in this country, and attention were confined to a small isolated district such as the Isle of Man [about 300 square miles, but, alas, without badgers], it might be possible to find a population of not more than 1,000 which had been isolated from other members of the species for several thousand generations; in such a case a reduction of variability might actually be proved to have occurred.

This book review comes nearly 10 years before the publication of GTNS. It also precedes Fisher's own first published calculations on the rate at which random fluctuations would affect genetic diversity. It is however clear that Fisher had already gone far enough into the problem to say that significant loss of diversity would take a number of generations longer than the relevant number of individuals in the population. In saying that 'it is only fair to take the number of interbreeding individuals at its lowest point', Fisher also shows an understanding that the effective population size may well be less than its current size. But Fisher makes no claim that breeding, even within a local area, is literally random (panmictic). The point he makes is that in the absence of geographical barriers (such as in his hypothetical Isle of Man example), the 'blood' of any local group would spread over a much wider area in the course of a thousand generations.

In the following year (1922), Fisher published his first major paper [2] on population genetics. In this paper he considered the rate at which the genetic variance in a population would decline as a result of random processes in the absence of selection, mutation, and migration. Under these conditions each individual gene will have a certain probability of reproducing, or of dying without descendants, in each generation. As each line of descent, once lost, cannot be revived, any original variance of gene types (alleles) will progressively be reduced. In the absence of mutation and migration every gene at a given locus in the population will ultimately be descended from the same ancestral gene, so that all variance will be extinguished. In the paper Fisher shows that the rate of decline of variance depends on the total population size, being slower with larger populations. He calculates that variance will be reduced substantially in 4n generations, where n is the diploid population size. (He later corrected this to 2n, after finding an error in the calculation. Wright, using a different method, had already reached the figure 2n and pointed out the discrepancy to Fisher.) Fisher remarks that:

This is a very slow rate of diminution; a population of n individuals would require 4n generations breeding at random to reduce its variance in the ratio 1 to e, or 2.8n generations to halve it. As few specific groups contain less than 10,000 individuals among whom interbreeding takes place, the period required for the action of the Hagedoorn effect, in the entire absence of mutation, is immense.

I think it is unfortunate that Fisher refers here to 'random breeding', as this may give the impression that the breeding structure of the population affects the outcome. Given Fisher's other assumptions, this is not the case. With the assumptions of zero migration, mutation, and selection, each individual gene can be regarded as one of 2n asexually reproducing entities, with equal reproductive prospects, and this is in fact how Fisher treats it in his calculations. This population of genes can be divided up in any way whatsoever, without affecting the rate of loss of variance in the population of genes as a whole. Imagine that we assign each gene in the original population to a notional 'group' in an entirely arbitrary way, and then trace the descendants of each gene and group through succeeding generations. There will be two simultaneous processes going on: groups will grow, shrink, or become extinct; and within each group the number of descendants of each original gene will increase or decline. Ultimately all the members of the group will be descended from a single gene. Within any group, variance will decline more quickly than in the total population, but in the total population this will be partly offset by increasing variance between groups. Even after each group has become 'fixed' for a particular allele, variance in the overall population will continue to decline due to random-walk fluctuation in the size of the groups, including extinctions. But the original division of the population into groups was imaginary, and the mere act of assigning a gene to an imaginary group cannot influence the course of evolution. The notional division of the population into groups therefore does not affect the outcome. But neither does the existence of real subdivisions such as geographical or breeding groups, provided this does not affect the number of descendants of each individual gene, and by Fisher's assumptions it does not. Random breeding is therefore in this case a red herring.

So far as I am aware, Fisher's next relevant comment on population size came in a letter to Leonard Darwin early in 1929. This was a response by Fisher to a letter from Darwin enclosing an old letter from Francis Galton, discussing the number of ancestors of village-dwellers. Galton noted that in the case of an isolated village the number of ancestors, in any generation far enough back, would hardly exceed the present number of villagers. Fisher expressed interest in Galton's letter, but commented:

It is perfectly true that village communities may be much isolated, but I wonder if Galton ever considered (or people like Fleure, who find 'Neolithic' villages all over the place) how complete the isolation must be to be worth anything genetically.

If only one in 10 filter in from outside in each generation, in seven generations half the population comes from outside and in 70 generations all but 1 in 100. Isolation would be very extreme at this level, in the ordinary course of events, and catastrophic events, war raids, famine, plague, are not so rare as to be ignored in the case of such habitual isolation.

King Solomon lived 100 generations ago, and his line may be extinct; if not, I wager he is in the ancestry of all of us, and in nearly equal proportions, however unequally his wisdom may be distributed.[3, p.95]

This appears to be the first time that Fisher explicitly commented on the effects of migration. The 'King Solomon' example is also interesting. First, there is the claim that if Solomon has any living descendants, he is probably in the ancestry of all of us. Fisher does not explain how he reached this view, but evidently, if all lines of descent do not die out by chance at an early stage, and allowing for an average of around two descendants per generation, the potential number of Solomon's descendants will increase explosively until it is far greater than the actual population of the human species. It does not follow that he is yet in the ancestry of all of us, because even in the absence of geographical barriers, there might not have been time for his 'blood' to have spread throughout the world. If we suppose, for example, that that none of his descendants moved more than 10 miles from their place of conception, then none of his descendants after 100 generations could be more than 1000 miles from Israel. However, recent calculations of the date of the 'Most Recent Common Ancestor' tend to support Fisher's 'wager', with the possible exception of a few isolated tribes like the Andaman Islanders. There might be more dispute about the stronger claim that Solomon would be in the ancestry of all of us 'in nearly equal proportions'. It is not clear how Fisher would have justified it in 1929. But one must remember that he was a physicist by training, and he may have intuitively seen an analogy with physical diffusion processes. If a substance is diffusing through a gas or fluid, in the absence of impermeable barriers, or pumps to reverse the flow, the substance will always flow from areas of greater to lesser concentration (subject to minor stochastic fluctuations), until it is evenly distributed throughout. The 'diffusion' of ancestry would obey the same principle, so it would be reasonable to wager that at some stage Solomon's share in everyone's ancestry would be approximately equal. But the speed with which this outcome was reached would be affected by geographical and behavioural barriers, and it is not obvious whether 100 generations would be long enough to reach an equilibrium state. (To preempt an obvious comment, having Solomon in one's ancestry does not imply having any of his genes. These would be diluted by half at each stage of reproduction, so that after 100 generations most lines of descent would contain none of his genes at all. If he has any living descendants, his average expected share in their genes would only be 1/n, where n is the number of individuals in Solomon's time who have left living descendants.)

Later in the same year (1929) Fisher had a further occasion to discuss the question of migration, as part of a correspondence with Sewall Wright. In 1928 Fisher had begun to expound his theory of the evolution of dominance. Noting that harmful mutations tended to be recessive, Fisher sought to explain this by the selection of modifier genes at other loci tending to suppress the effect of harmful mutations. He recognised that for various reasons this would be a weak form of selection, but considered that if it operated over very long periods of time, in response to recurring mutations, it could have the effect he claimed. Sewall Wright had a number of objections to this. For the present purpose Wright's most important point was as follows :

Selection controls the situation if s [a measure of selective intensity] is larger than 1/2n [where n is effective population size], but is of little importance below this figure. In small inbred populations (1/2n large) even vigorous selection is ineffective in keeping injurious factors from drifting into fixation... In the case of Dr Fisher's modifiers of dominance with selection coefficients at best of the order of mutation rate, the latter must be greater than 1/2n if the gene is not to drift back and forth in the course of geologic time from one state of approximate fixation to the other and practically as freely in the face of the selection pressure as with it.

Unfortunately it is difficult to estimate n in animal and plant populations. In the calculations it [n] refers to a population breeding at random, a condition not realised in natural populations as wholes. In most cases random interbreeding is more or less restricted to small localities. These and other conditions such as violent seasonal oscillation in numbers may well reduce n to moderate size, which for the present purpose [i.e. the effectiveness of very weak selection] may be taken as anything less than a million. If mutation rate is of the order of one in a million per locus, an interbreeding group of less than a million can show little effect of selection of the type which Dr Fisher postulates even though there be no more important selection process [to override the effect of weak selection of modifiers] and time be unlimited.[4, p.75]

In correspondence with Wright Fisher responded to several of Wright's criticisms. On the question of population size he wrote as follows:

I am not sure I agree with you as to the magnitude of the population number n. To reduce it [as Wright had done] to the number in a district requires that there shall be no diffusions even over the number of generations considered. For the relevant purpose I believe n must usually be the total population on the planet, enumerated at sexual maturity, and at the minimum of the annual or other periodic fluctuations. For birds twice the number of nests would be good. I am glad, however, that you stress the importance of this number.[3, p.273]

It is this passage on which William Provine bases his claim that Fisher 'considered most species to be panmictic (random breeding) throughout their ranges, even if their range was the entire world'. It should be evident that Fisher said nothing of the kind. First, as a pedantic point, Fisher did not claim that any species had a range over 'the entire world'. Very few species do, even if we treat land and sea species separately. More important, Fisher did not maintain that species were literally panmictic throughout their range, but only that 'for the relevant purpose' [the relative effects of drift and selection] the appropriate number must 'usually' be the total breeding population of the species, at its periodic minimum size. His reason for this belief was evidently related to the question of 'diffusion', including migration between districts. As he had indicated in his letter to Leonard Darwin, Fisher doubted that isolation of local groups would usually be strict enough, over a period of many generations, to prevent a significant diffusion of genes between localities, which would tend to equalise gene frequencies between them.

Fisher's letter prompted Wright himself to think about the effects of migration (apparently for the first time), and he replied to Fisher as follows:

I was much interested in your comment on the population number... Since I wrote, I have been trying to get a clearer idea of the effect of diffusion, and I see, at least, that isolation in districts must be much more nearly complete than I realized at first, to permit random fixation of strains.[5, p.256]

Wright then discussed the effect of migration into a district at random from the entire population, and concluded:

I must admit that rather strict isolation is necessary on this basis to maintain appreciable variation of q, and I recognise of course that variation in q does not interfere much with selection unless it is so great as to bring about a U-shaped piling up close to q = 0 and q = 1. I am not entirely clear as to the effects of interchange between adjacent districts with similar q's. Presumably there could be considerably more such interchange without preventing a drifting apart of the q's for more remote districts. However, it seems clear that N must be based on the entire species, unless isolation is substantially complete, in considering the interference with selection.[5, p.256]

Thus, we reach the remarkable result that far from 'disagreeing strongly' with Fisher's position on the point at issue in the correspondence, Wright explicitly agreed with him!

In the same letter Wright asked Fisher whether he had published anything on the 'diffusion problem', and Fisher replied:

I have so far published nothing on the 'diffusion problem', but have in the press a book on 'The Genetic [sic] Theory of Natural Selection', which has part of a chapter on the cohesion of species in relation to the problem of their fission. I think it must be generally true that the ancestry of all individuals of a species is practically the same except for the last 100 or perhaps 10,000 generations, and that a gene frequency gradient is maintained by selection between different parts of a species' range. So that well-marked local variations may or may not be incipient species, according as real fission, cessation of diffusion, ultimately supervenes.[5, p.258]

This appears to be Fisher's last comment on the subject before the publication of GTNS in 1930, to which I will turn in a further post.

[1] R. A. Fisher: Eugenics Review, 13, 1921, 467-70, review of A. L. and A. C. Hagedoorn, The Relative Value of the Processes Causing Evolution.
[2] R. A. Fisher: On the Dominance Ratio, 1922 (online)
[3] J. H. Bennett (ed.): Natural Selection, Heredity and Eugenics, Including selected correspondence of R. A. Fisher with Leonard Darwin and others. 1983.
[4] Sewall Wright, Evolution: Selected Papers, ed. William B. Provine, 1986.
[5] William B. Provine: Sewall Wright and Evolutionary Biology, 1986.

Thursday, September 28, 2006

Moral sentiments and Material Interests   posted by John Emerson @ 9/28/2006 03:19:00 PM

Not by Genes Alone, Peter Richerson and Robert Boyd, eds., Chicago, 2005.
Moral sentiments and Material Interests, Herbert Gintis, Samuel Bowles, Robert Boyd, and Ernst Fehr, eds., MIT, 2005.

Moral sentiments and Material Interests is, from my point of view, an enormous advance on all the orthodox economics I've ever read. My primary complaint is "What took so long?" For decades now economics has been spreading disinformation, and it's about time that they started looking at reality. (The ev psych ideas found in the Gintis book are more fully developed in Not by Genes Alone. I should note that both books include a lot of technical argument which I haven't even touched upon. What I've written here is only a summary of the conclusions, written from the point of view of a non-biologist and a non-economist).

The book's starting point is an empirical look at the actual economic behavior of individuals, in order to see whether it matches the rational-self-interest assumed by economic theory. It is found that it doesn't, and the actual behavior observed is next interpreted in terms of evolutionary psychology. Finally, the political and social significance of these new observations is sketched.

The empirical studies are standard cash-incentive psych lab tests designed to find out where people actually stand on the altruism / self-interest scale. In general, the tests find that people behave more altruistically than they would if they decided according to rational self-interest. (The tests also find that the degree of altruism varies according to culture, and is not a universal).

The results of these experiments square with my own convictions, but I've always felt that this kind of artificial, low-payoff game-playing is of only moderate scientific value -- there's even some evidence that the authors themselves think this way. To me the real story is that there's never been any evidence at all that economics' assumption of individual economic rationality is valid, and a lot of evidence that it isn't. The rationalizations found in Friedman's Positive Economics have allowed economists to rely thoughtlessly on these unproven assumptions for about five decades, and if a few little experiments are required to convince them to drop this inaccurate and unproven default, that's cool with me. But it's a little like someone cherry-picking Bible verses to make their point to the Vatican.

The authors define three mechanisms leading to altruism and social cohesion: strong reciprocity, conformity, and "costly signaling". These are made possible by innate dispositions evolved in two steps -- simple reciprocity first at the early primate small group level, and the more complex behaviors next at the early human. Altogether they make possible genetic selection for altruism, via net fertility advantages for all members of organized social groups (not simply biological groups or kinship groups) which are successful because their members behave altruistically. Biological competition within the group is suppressed by non-innate social and cultural mechanisms, giving an advantage to members of the group on the average, but not to every individual. This way, with gene-culture coevolution and mutualism, there can be genetic selection for a degree of innate altruism in a way that there could not be without culture and society, which form a kind of artificial environment.

"Strong reciprocity" is what replaces "rational self-interest". It consists of the weak reciprocity described by Axelrod (initial cooperation, continued until the partner defects) plus an additional altruistic propensity to punish defectors even if there's no personal advantage in doing so. In a society of strong reciprocators (altruists both in giving and in punishment), defectors do not have an advantage, whereas in a society of non-punishing altruists, the defectors have an advantage which causes the defector gene to drive out the altruist gene.

Two other behaviors are mentioned. "Conformity" is a weaker principle explaining social uniformity in the absence of the threat of punishment, and mostly applies to cases in which there is no clearly-perceptible advantage or disadvantage for the individual, so he just does what everyone else does. "Costly signaling" only appears in one chapter, which uses the biological concept to explain generosity of the potlatch / largesse / big man type. To me these are less immediately interesting than strong reciprocity, though "costly signaling" is a step on the way toward defining a more complex heirarchal society extending beyond the face-to-face level.

A significant advantage of this book is that it describes a social world which, like the world observed and described by historians, has "multiple equilibria and tipping points" and is thus less stable and less predictable than the imaginary world of equilibrium economics.

In the final chapter Bowles and Gintis point out that local community is always grounded on a fundamental ethic of strong reciprocity. They describe it as a positive force which is usually wrongly maligned by the partisans of the market, the state, and elite culture. This brings them close to the communitarians, for whom the local community is a valid and necessary third leg of society, distinguishable (and sometimes at odds with) both pure market behavior and the state. (A lot of liberationist and libertarian ideology is hostile to the naive sorts of strong retribution that make small-group community possible).

The three innate principles described by these authors can be thought of as a ground for ethics, and the authors speak openly of "trust" and "fairness". However, all actual ethics involves further cultural processing, beyond the innate foundation. For one example, one of the great advances making civilization possible was the suppression of vendetta and feud, which are completely natural developments of "strong reciprocity". For another, the mechanisms of natural ethics described here work best at the face-to-face level. The description, much less the attainment, of fairness (the goal of strong reciprocity) within a large, complex, multi-level society is an extremely tricky and difficult task indeed. (The authors do touch on these questions, and they cite Fried's Evolution of Political Society, which sketches a general view of the move toward complex society).

Anyway, after about fifty years, economics seems to be returning to the real world.

(Slightly revised Sept 29)


My post got a bit of attention from Donald Luskin:
If the nature of selfishness is more complicated that economics typically assumes, if it is indeed tied up in considerations of family, friends, nation, species -- whatever -- then let the science of economics try to adopt itself to those complexities.
I have trouble thinking of this as a useful addition to the theory of rationality. It reminds me of the Chinese philosopher Chuang Tzu's humorous mysticism: "Yes, I'm selfish! But I'm selfish for the whole universe, not just for me!"

I also have a new piece up at

Wednesday, September 27, 2006

Far Left sociobiology   posted by Razib @ 9/27/2006 11:51:00 PM

The frogs at AlphaPsy point me to this article, Anarchism and Social Nature, in a Left-anarchist publication. The focus of the piece is a review of The Blank Slate by Steven Pinker, and here is the punchline:
We, along with most other ideologies on the Left, have based our theory on a mistaken concept of human nature. We have learned over the years to distrust words like sociobiology, evolutionary psychology, cognitive science, and above all that dreaded buzzword, 'hard-wired' - yet we can no longer ignore the fact that these sciences are probably right about human nature.

AlphaPsy has a detailed analysis, so I'll hand it off to them.

Related: The Conflict Within - The Left's Version of Creationism, The Turning of the Tide.

Digit ratio predicts sport performance in female twins   posted by the @ 9/27/2006 10:14:00 PM

From the BBC:

A King's College London team found women whose ring finger is longer than their index finger are more likely to achieve higher levels in sport. The ratio between the fingers has already been linked to traits in men like cognitive ability and sperm count. The study appears online in the British Journal of Sports Medicine. The researchers, from King's Twin Research Unit, examined hand X-ray images of 607 female twins aged 25-79 from the UK. In each case they measured the lengths of the second and fourth fingers of each hand. The volunteers also ranked their highest level of achievement in a list of 12 sports on a questionnaire. The researchers found women with longer fourth fingers were significantly more likely to be among the top achievers in all the sports listed.

I can't find the paper online, but I'd like to see it because the news report hints at that the result has a more fascinating twist.

Lead researcher Professor Tim Spector said: "The reasons for these findings are unclear. "Previous studies have suggested the change in finger length was due to changes in testosterone levels in the womb but we also found that finger length was 70% heritable with little influence of the womb environment. "This suggests that genes are the main factor and that finger length is a marker of your genes." The ratio between the two fingers is fixed before birth and remains constant during life. As this is the case, the researchers suggest that examining finger length may help to identify talented individuals at an early, pre-competitive stage. No specific genes have yet been identified that control finger length. Experts believe it is likely that multiple genes are responsible.

So perhaps the digit ratio is also largely heritable. Can anyone find the study?

Quad-hybridity   posted by Razib @ 9/27/2006 08:01:00 PM

I was doing a "literature survey" and I stumbled upon Daniella Alonso, the product of a marriage between a Japanese Peruvian father as a Puerto Rican mother (European + African + Amerindian). I am haunted by dreams of synergistic epistasis and Übermensch....

Married to the sea   posted by Coffee Mug @ 9/27/2006 07:39:00 PM

In case you're not enjoying it already, allow me to bring your attention to Married to the Sea. I find the more juvenile stuff the funniest, but here's some science/evolution related to justify the post. Personal favorite.

The god of death   posted by Razib @ 9/27/2006 07:30:00 PM

One of the common ideas for why religion appeared is that it is a way of assauging fear of death. Chris of Mixing Memory reports on research which tests this hypothesis. Here is Chris' summary:

In summary, then, when fundamentalists had their beliefs in Biblical inerrancy successfully challenged (i.e., they were presented with Biblical contradictions, and thus changed their minds about the existence of such contradictions), thoughts of death became more salient for them. So it does appear that religious beliefs, for fundamentalists at least, serve to minimize existential anxiety.

But this science, so not everything follows our intuition:

Strangely, the participants who were least likely to complete the stems with death-related words were the low fundamentalist participants who had read the passage about Biblical contradictions.

So for some religionists death and faith seem closely coupled, but not all religionists. At least if psychological experiments give us any window into the soul.

Brown gaucho & Tangled Bank #63   posted by Razib @ 9/27/2006 06:36:00 PM

Our old friend Brown Gaucho is hosting Tangled Bank #63. I enjoyed his post, The importance of evolution in medicine. BG is a primatologist-turned-med student, so he knows of what he speaks. But, I do have to take some issue with this contention:

Anatomically and genetically, humans haven't changed all that much in the past 100,000 years.

Yes, anatomically modern humans emerged over 100,000 years ago, but, that does not suffice to allow us to assume that genetically humans haven't changed "all that much." Of course, that depends on how you define "all that much," but a supercharged immune system forged in the fires of the Eurasian pathogen pool & lactose tolerance don't show up in the fossil record....

Stabilized, not activated   posted by Coffee Mug @ 9/27/2006 06:01:00 AM

The Daily Transcript reports on a PNAS study showing that transcription occurs in bursts. Transcription factors (regulators of when a gene is "on" or "off") are often characterized as 'activators' or repressors. The paper suggests activators may instead be stabilizers. Genes are always flipping back and forth between different levels of on and off states and when transcription factors bind they can hold one state steady. When upregulation happens a gene isn't 'turned on', it is just kept on. He's got a nice little def. of transcription on the left there. You are eventually gonna need to know what transcription and translation are. Might as well be now.

Epistasis correlates with genomic complexity   posted by Razib @ 9/27/2006 01:07:00 AM

From PNAS:
Simpler genomes, such as those of RNA viruses, display antagonistic epistasis (mutations have smaller effects together than expected); bacterial microorganisms do not apparently deviate from independent effects, whereas in multicellular eukaryotes, a transition toward synergistic epistasis occurs (mutations have larger effects together than expected). We propose that antagonistic epistasis might be a property of compact genomes with few nonpleiotropic biological functions, whereas in complex genomes, synergism might emerge from mutational robustness.

Some have argued that synergistic epistasis is the way that "sex pays off" for complex organisms. Sexual reproduction tends to break apart superfit correlations of alleles, but synergistic epistasis is a way to recoup this loss (and evade Muller's Ratchet). A figure below the fold....

Related: Through the rugged roads of gene land.

AlphaPsy   posted by Razib @ 9/27/2006 12:57:00 AM

Just a heads up, a new blog which addresses culture via a naturalistic lens is now up and running, AlphaPsy. In the Cavalli-Sforza 10 Q's he stated that cultural anthropology just isn't scientific, and is positively hostile to science. This is a different direction, and very much a minority take, but good things start small.

Tuesday, September 26, 2006

GSS - POLIDEOFULL   posted by the @ 9/26/2006 05:19:00 PM

From the GSS, POLIDEOFULL combines two markers (political affiation and self-description along a liberal-moderate-conservative axis) to form 21 categories. Here are the average WORDSUM scores for each group. The liberal-conservative axis has been color-coded from dark blue to dark red for each of Democrats, Independents, and Republicans. Restricted to whites only. Here's the data:

Obviously people who self-identify as extremely conservative Democrats or extremely liberal Republicans score poorly on WORDSUM. Liberal Dems, Liberal Indepedents, and Conservative Republicans socre better than average. Interestingly, Conservative Indepdents score lower.

Main Statistics
Cells contain:
POLIDEOFULL1: Extreme Lib Dem4.336.895.838.778.867.15
2: Lib Dem4.736.467.448.078.816.88
3: Moderate Lib Dem4.686.486.888.058.616.57
4: Moderate Dem4.905.896.387.337.835.82
5: Moderate Con Dem4.776.165.747.608.106.02
6: Con Dem4.695.746.707.317.275.57
7: Extreme Con Dem3.824.867.
8: Extreme Lib Ind4.396.106.678.479.296.50
9: Lib Ind4.326.306.248.018.436.52
10: Moderate Lib Ind4.366.527.158.048.696.73
11: Moderate Ind4.876.026.487.498.156.05
12: Moderate Con Ind5.036.436.367.468.386.58
13: Con Ind4.595.966.527.657.896.02
14: Extreme Con Ind4.225.746.677.547.675.50
15: Extreme Lib Rep3.584.00---
16: Lib Rep4.445.906.336.776.605.64
17: Moderate Lib Rep4.516.356.077.608.006.34
18: Moderate Rep4.976.086.417.447.426.13
19: Moderate Con Rep5.206.396.797.698.086.79
20: Con Rep5.016.476.827.548.066.73
21: Extreme Con Rep4.726.576.397.399.136.58
COL TOTAL4.776.176.597.678.276.28

Data access to the GSS   posted by the @ 9/26/2006 10:20:00 AM

Half Sigma made a series of interesting posts about the General Social Survey. I recently noticed that GSS data are available thru a very useful web application. Click that link to a go at it. Below the fold is a brief primer on what I've learned from playing around with it.

If you want to jump right in, get started with Row=WORDSUM, Column=GOD.
Also fun: Row=POLVIEWS, Column=CHILDS

Getting started help page

useful "Analysis" options:
* Frequencies or crosstabulation - produces heat-map tables like Half Sigma's posts
* Comparison of means - useful to compare WORDSUM scores between groups
* Correlation matrix - useful for "pairwise" correlation matrix
* Comparison of correlations - compare correlations when controlling for another variable
* Multiple regression - multiple R

The lower left panel is a topic-sorted index of variables. Pick a variable from the list and click "view" to get a description. Use this panel to build your queries, or type in variables yourself.

useful variables:
* SEX (1=male, 2=female)
* RACE RACECOMB (1=white,2=black,3=other)
* WORDSUM - a 10 Q vocabulary test
* EDUC and DEGREE - measures of education
* INCOME - family income

filtering: to limit an analysis to a subset of the total population
* example: "age(18-50), racecomb(1)" = Whites age 18-50

How the other half of differential psychology lives, Part 1   posted by agnostic @ 9/26/2006 10:03:00 AM

When we talk about individual differences in psychology here at GNXP, they are almost always differences in some form of intelligence -- the real-world consequences of these differences, what inter-group variation there is in the trait, the lower-level biological correlates of such differences, and so on. This is all well and good, but we shouldn't forget the other half of differential psychology: personality. Unfortunately, more of the history of personality theory has been plagued by cultish trends and airy-fairyness compared to the history of intelligence investigation -- probably the first names that come to your mind are Freud, Jung, and so on; whereas the first names that come to mind for intelligence researchers would be bona fide scientists like Spearman, Jensen, and so on. I've put together a little whirlwind tour of personality theory because of its inherent importance to those interested in: 1) what dimensions we differ on from one person to another; 2) what the lower-level biological correlates are of such differences, including what alleles of which genes are involved; 3) what inter-group variation there is in such traits; and 4) how personality traits relate to the study of human evolution, especially by the force of selection. Now, each of these topics could easily fill a journal issue or two, so I emphasize that this will be a whirwind tour. This first Part looks at the first two questions; the second will look at the latter two. For those interested in greater exposition and references, the best textbook on the topic is Personality Traits by Matthews, Deary, & Whiteman, which covers the first two topics I'm addressing, though not the second two topics.

Let's begin with the psychometric basics. Unlike intelligence, where there emerges a single general factor (g) among factor analyses of performance on intelligence tests, there is no such thing in the domain of personality. The two personality questionairres most researched, validated, and used by researchers are the Eysenck Personality Questionnaire (EPQ) and that developed by the Big Five researchers, the NEO-PI. Factor analysis is performed on the responses to reveal what higher-level dimensions of personality exist. Though the EPQ nominally measures three traits, while the NEO-PI measures five, they actually measure quite similar traits. The two factors Extraversion and Neuroticism are common to both questionairres, and arguably go back to Galen's typology of the four temperaments. The third trait measured by the EPQ, Psychoticism, appears to be a higher-level combination of the two orthogonal NEO-PI factors Agreeableness and Conscientiousness -- that is, someone who scores high on P would score low on both A and C. Eysenck's P factor shows a skewed distribution in the population, whereas the others show more normal distributions, suggesting that it is the A x C interaction that is measured by P. Big Five researchers also measure Openness to Experience, but this is the most open to question of the five -- it is non-trivially correlated with intelligence and may or may not appear in other cultures -- so I'll mostly look at the other four on the NEO-PI, which allows me to talk separately about A and C instead of just P. (Another popular questionairre, Cattell's 16PF, shows significant intercorrelations among some of the factors, and grouping them into higher-level factors leads to something like the Big Five factor structure.)

Aside from the vague connotations the names carry, what do they actually measure? See here for the description of what the NEO-PI measures at the factor and facet levels. The one caveat in trying to keep straight what these measure is that Neuroticism measures one's emotional stability vs instability -- it does not necessarily reflect "Woody Allen" neuroticism. Just as P is the likely A x C interaction, so this Woody Allenesque neuroticism is the result of low-E x high-N interaction ("melancholics" in Galen's typology). Also bear in mind that one's experience of positive vs negative emotion are the result of the two orthogonal factors E and N -- higher E goes along with greater frequency of positive emotions, while higher N goes along with greater frequency of negative emotions. So, it is possible to experience a heightened frequency of both positive and negative emotions if one is both highly extraverted and highly emotionally unstable ("cholerics" in Galen's typology). Or put another way, scoring low on N doesn't make one happy but simply calm, and likewise for scoring low on E. Such a greater tendency toward equanimity is what characterizes Galen's "phlegmatics." The common assumption that higher E protects one from negative emotions is confusing higher E with the high-E x low-N interaction ("sanguines" in Galen's typology).

I've mentioned Galen's typology of the four temperaments because it was the first model that sought to combat two typical objections to psychometric measurement: 1) that the tests measure what the tests measure, i.e., have little real-world relevance; and 2) that the traits measured are either fleeting non-traits or that they're mere social constructs (though I doubt the latter was bandied about much in his time!). Now, Galen was completely wrong about what the underlying biological causes of personality differences were (who even knows what the "black bile" is which he thought melancholics had an excess of?), but then most medical investigation until roughly the 19th C was a mishmash of unfounded conjecture and quasi-religious superstition. He was correct, however, to look for enduring biological differences that could account for the stable trait differences in personality. Let's look at the answers to these two objections in more detail.

First, though we're most familiar with the real-world consequences of intelligence differences -- most on display in outcomes of academic and job performance -- personality differences also predict real-world outcomes. Extraversion predicts how socially engaging one is in social settings (for example, how long one talks to others). Neuroticism predicts susceptibility to anxiety or depression, as well as marital satisfaction. Agreeableness also predicts marital satisfaction (not surprising, as this measures how trusting, caring, and cooperative one is). Conscientiousness predicts job performance, especially the non-intellectual aspects of it -- punctuality, for example. As mentioned before, Openness seems to measure aspects of intelligence, so it's a predictor of intelligence differences.

As I assume most reading this are interested in what the typical personality profile looks like for top scientists, either to alter their personality in the desired direction (not easy, but not impossible, especially by taking mind-altering substances like caffeine), or to evaluate how promising an applicant for a science position is. The major study on point was Cattell's 1965 survey of living eminent scientists, using his 16PF questionairre. They showed clear deviation from average toward the following poles: unsociable, intelligent, emotionally stable, dominant, brooding (or serious, introspective), undependable (not rule-following), bold (or venturesome), sensitive (as in Openness to Feelings or Aesthetics -- not necessarily as in tender & caring), trusting, guilt rejecting (or self-assured), radical (not conventional: like high-O), self-sufficient (not group-oriented), and self-disciplined. They scored average on the traits imaginative vs practical, forthrightness vs diplomatic, and tense vs relaxed. These were "eminent researchers," so there is undoubtedly variation -- presumably at the lower level of "lab monkey," dependability would matter much more, while at the more pioneering level it may be detrimental (the absent-minded professor too engrossed in his work to care about protocol and decorum). I looked at one real-world consequence of differences in such traits in my post on sex differences in scientific eminence.

Turning now to the search for lower-level biological causes of these traits, let's start with a few simpler observations. The first is that these traits are that -- stable traits. For some odd reason, a camp of social psychologists wanted to wish personality traits away by noting that scores on such traits did not predict all that well an individual's behavior in a particular situation. The situation was therefore thought to mold behavior. What these psychologists failed to pick up in their intro statistics class is that one data point will give you a garbage estimate of how well the independent variable predicts the dependent variable. It turns out that when you examine a person's behavior over a wide range of situations numerous times, their personality traits do predict what you'd expect -- e.g., that the introverts tend to be less socially engaging, although they might be more sociable among their close relatives over Christmas dinner. Clearly traits are situation-sensitive -- a disagreeable person is not constantly on the warpath, and neurotics are not forever freaking out -- but they still represent biases in how the individual will behave. For example, two individuals get an F on a test -- to a low-N person, this might be a cause for re-evaluating what objective measures can be taken to get a better grade on the next test; while a high-N person might overreact and turn their frustration inward, focusing on their negative emotions. Same situation, different "coping styles."

Not only are these traits stable across situations, they are pretty stable across the lifespan, at least after about age 30, both on a population aggregate level (50 y.o.s are not pronouncedly different in aggregate personality measures than 30 y.o.s) and throughout an individual's course. Even the decade from age 20-29 seems not to involve much change. Real personality changes occur mostly during adolescence, with maybe / maybe not some additional tweaks during the third decade of life, and little change after 30. Such persistence suggests a genetic component, and indeed twin and adoption studies give heritability estimates about equal to what you'd find for intelligence -- roughly, narrow-sense ~ 0.35 and broad-sense ~ 0.5, with the environmental variance representing non-shared as opposed to shared factors. Interestingly, a recent study found a positive correlation between prevalence of the pathogen Toxoplasma Gondii and aggregate level of Neuroticism at a national level (more on national differences in Part 2). Whether or not one becomes infected, or whether or not an infected person sees an increase in Neuroticism, is largely a stochastic affair -- presumably this sort of developmental noise accounts for most of the non-shared environmental variance.

As for the supra-gene / sub-psychometric level, the literature is pretty ambiguous. This may not be as bad as it may seem -- whereas with intelligence, we're talking about raw horsepower or ability, with personality traits we're talking about context-sensitive behavioral strategies. We know that genes and non-genetic biological causes (like germs) serve to build something which results in stable biases across situations (but sensitive to them), but for all we know, this may be instantiated in an If/Then program that's impossible to pin down on a given number of gross properties of the brain, like brain size, glucose metabolization rate, and so on, for intelligence. So, unlike intelligence research which focuses on combinations of these lower-level gross properties, the personality research seems to be moving more toward the cognitive level, while still acknowledging that this cognitive architecture must have a neural substrate, but not necessarily an easily observable property like volume of white matter in some brain region.

To return to the example of differing level of Neuroticism influencing response to a failure on a test, we might imagine a simple toy model of Neuroticism where environmental inputs are analyzed and coded, and these analyses then pass into a mechanism for determining reponse (remain calm, freak out, etc.). Individual differences in Neuroticism could be re-stated as differences in how high or low of a threshold the box has for outputting the "freak-out" response -- let's say stimuli are coded from 1 to 9 in increasing order of threatening potential. Stimuli coded as 9 would manage to freak out anyone -- say, a rabid animal charging toward you -- while stimuli coded as 1 would only manage to freak out Woody Allen -- say, you stub your toe first thing in the morning. Thus, a high-N individual would have a low threshold (anything 1-9) for responding in a freak-out way, while a low-N individual would only lose their cool if they'd processed a level 9 stimulus. This is a cognitive model . Other cognitive models have the coding mechanism do most of the work in explaining differences in N -- high-N people are biased to code stimuli as threatening and lock attention onto them, which low-N people would regard as non-threatening. Eysenck's sub-cognitive view was that higher-N people had more easily excitable sympathetic nervous systems -- the involuntary fear/fight/flight/sex system.

Having said this, there is extensive (though again, muddy) data on the biological correlates of E in particular. The original idea (well, after the four humors, that is) is due to Eysenck, who thought that extraverts had lower basal levels of cortical arousal, while introverts had higher levels. Appealing to the Yerkes-Dodson Law, he hypothesized that there was an optimal level of cortical arousal for performance in life's tasks. Thus, those low in arousal (extraverts) would seek to artificially boost their arousal in order to function more comfortably -- namely, by engaging in social stimulation, living a fast-paced life, and so on. Introverts, by contrast, would tend to avoid such stimulation, since their arousal levels are thought to be high enough already, at or above the optimal level. One prediction is that extraverts should tend to respond in a less extreme manner than introverts to increased levels of stimulation. Extraverts are better at performing tasks when there is background noise, they are less startled by abrupt loud noises, and they salivate less profusely when lemon juice is squeezed into their mouths. However, some of these results -- especially measures of cortical arousal such as EEG measures -- are not always replicated, or, worse, show the opposite of the predicted pattern. As with research into the biological causes of intelligence differences, some of these meager results are likely due in part to the non-representative samples used in studies -- namely, squeeze 100 college students from Psych101 into the lab over the weekend, and get your results instantly.

In Part 2, I'll look more at genes, since that will provide a nice transition to discussion of inter-group differences, as well as the significance of personality research to human evolutionary biology.

Monday, September 25, 2006

"The Student"   posted by Darth Quixote @ 9/25/2006 08:58:00 PM

The release of Richard Dawkins' new book The God Delusion (of which I have only read the first few pages) has returned my thoughts to the issue of what stance atheistic futurists such as myself should take toward the religious beliefs of our family members, friends, and fellow citizens between now and whatever singularities lie on the horizon. I have reached no definite conclusion on this point. I am torn between, on the one hand, (1) my devotion to the seeking of truth, and my revulsion toward the stupidities and barbarisms daily committed in the name of religion; and, on the other hand, (2) the innumerable small and quiet (and occasionally large and dramatic) ways in which faith is a force for good in the lives of people that I know. Perhaps this is all an illusion, but it seems to me that for many people religion is an irreplaceable inspiration to virtue, means of community, and source of solace in the face of barely endurable afflictions. When I read Dawkins on religion, no matter how right he is, no matter how devastating his blows, I get the sense of someone with a callous lack of understanding and sympathy for simple human frailty.

I thought this was an appropriate occassion to recall Anton Chekhov's classic short story "The Student." Perhaps I am wrong to see in it an acknowledgement of the importance of religious tradition (by an avowed atheist and anti-clericalist no less); to say what a Chekhov story is "about" is often to diminish it. But no matter. It is a wonderful story and worth reading in any case. The translation below is by Constance Garnett:

At first the weather was fine and still. The thrushes were calling, and in the swamps close by something alive droned pitifully with a sound like blowing into an empty bottle. A snipe flew by, and the shot aimed at it rang out with a gay, resounding note in the spring air. But when it began to get dark in the forest a cold, penetrating wind blew inappropriately from the east, and everything sank into silence. Needles of ice stretched across the pools, and it felt cheerless, remote, and lonely in the forest. There was a whiff of winter.

Ivan Velikopolsky, the son of a sacristan, and a student of the clerical academy, returning home from shooting, kept walking on the path by the water-logged meadows. His fingers were numb and his face was burning with the wind. It seemed to him that the cold that had suddenly come on had destroyed the order and harmony of things, that nature itself felt ill at ease, and that was why the evening darkness was falling more rapidly than usual. All around it was deserted and peculiarly gloomy. The only light was one gleaming in the widows' gardens near the river; the village, over three miles away, and everything in the distance all round was plunged in the cold evening mist. The student remembered that, as he had left the house, his mother was sitting barefoot on the floor in the entryway, cleaning the samovar, while his father lay on the stove coughing; as it was Good Friday nothing had been cooked, and the student was terribly hungry. And now, shrinking from the cold, he thought that just such a wind had blown in the days of Rurik and in the time of Ivan the Terrible and Peter, and in their time there had been just the same desperate poverty and hunger, the same thatched roofs with holes in them, ignorance, misery, the same desolation around, the same darkness, the same feeling of oppression--all these had existed, did exist, and would exist, and the lapse of a thousand years would make life no better. And he did not want to go home.

The gardens were called the widows' because they were kept by two widows, mother and daughter. A campfire was burning brightly with a crackling sound, throwing out light far around on the ploughed earth. The widow Vasilisa, a tall, fat old woman in a man's coat, was standing by and looking thoughtfully into the fire; her daughter Lukerya, a little pockmarked woman with a stupid-looking face, was sitting on the ground, washing a cauldron and spoons. Apparently they had just had supper. There was a sound of men's voices; it was the laborers watering their horses at the river.

"Here you have winter back again," said the student, going up to the campfire. "Good evening."

Vasilisa started, but at once recognized him and smiled cordially.

"I did not know you; God bless you," she said. "You'll be rich."

They talked. Vasilisa, a woman of experience who had been in service with the gentry, first as a wet-nurse, afterwards as a children's nurse expressed herself with refinement, and a soft, sedate smile never left her face; her daughter Lukerya, a village peasant woman who had been beaten by her husband, simply screwed up her eyes at the student and said nothing, and she had a strange expression like that of a deaf-mute.

"At just such a fire the Apostle Peter warmed himself," said the student, stretching out his hands to the fire, "so it must have been cold then, too. Ah, what a terrible night it must have been, granny! An utterly dismal long night!"

He looked round at the darkness, shook his head abruptly and asked:

"No doubt you have heard the reading of the Twelve Apostles?"

"Yes, I have," answered Vasilisa.

"If you remember, at the Last Supper Peter said to Jesus, 'I am ready to go with Thee into darkness and unto death.' And our Lord answered him thus: 'I say unto thee, Peter, before the cock croweth thou wilt have denied Me thrice.' After the supper Jesus went through the agony of death in the garden and prayed, and poor Peter was weary in spirit and faint, his eyelids were heavy and he could not struggle against sleep. He fell asleep. Then you heard how Judas the same night kissed Jesus and betrayed Him to His tormentors. They took Him bound to the high priest and beat Him, while Peter, exhausted, worn out with misery and alarm, hardly awake, you know, feeling that something awful was just going to happen on earth, followed behind. . .. He loved Jesus passionately, intensely, and now he saw from far off how He was beaten. . . . "

Lukerya left the spoons and fixed an immovable stare upon the student.

"They came to the high priest's," he went on; "they began to question Jesus, and meantime the laborers made a fire in the yard as it was cold, and warmed themselves. Peter, too, stood with them near the fire and warmed himself as I am doing. A woman, seeing him, said: 'He was with Jesus, too'--that is as much as to say that he, too, should be taken to be questioned. And all the laborers that were standing near the fire must have looked sourly and suspiciously at him, because he was confused and said: 'I don't know Him.' A little while after again someone recognized him as one of Jesus' disciples and said: 'Thou, too, art one of them,' but again he denied it. And for the third time someone turned to him: 'Why, did I not see thee with Him in the garden today?' For the third time he denied it. And immediately after that time the cock crowed, and Peter, looking from afar off at Jesus, remembered the words He had said to him in the evening. . . . He remembered, he came to himself, went out of the yard and wept bitterly--bitterly. In the Gospel it is written: 'He went out and wept bitterly.' I imagine it: the still, still, dark, dark garden, and in the stillness, faintly audible, smothered sobbing.. . . ."

The student sighed and sank into thought. Still smiling, Vasilisa suddenly gave a gulp, big tears flowed freely down her cheeks, and she screened her face from the fire with her sleeve as though ashamed of her tears, and Lukerya, staring immovably at the student, flushed crimson, and her expression became strained and heavy like that of someone enduring intense pain.

The laborers came back from the river, and one of them riding a horse was quite near, and the light from the fire quivered upon him. The student said good-night to the widows and went on. And again the darkness was about him and his fingers began to be numb. A cruel wind was blowing, winter really had come back and it did not feel as though Easter would be the day after tomorrow.

Now the student was thinking about Vasilisa: since she had shed tears all that had happened to Peter the night before the Crucifixion must have some relation to her. . . .

He looked round. The solitary light was still gleaming in the darkness and no figures could be seen near it now. The student thought again that if Vasilisa had shed tears, and her daughter had been troubled, it was evident that what he had just been telling them about, which had happened nineteen centuries ago, had a relation to the present--to both women, to the desolate village, to himself, to all people. The old woman had wept, not because he could tell the story touchingly, but because Peter was near to her, because her whole being was interested in what was passing in Peter's soul.

And joy suddenly stirred in his soul, and he even stopped for a minute to take breath. "The past," he thought, "is linked with the present by an unbroken chain of events flowing one out of another." And it seemed to him that he had just seen both ends of that chain; that when he touched one end the other quivered.

When he crossed the river by the ferryboat and afterwards, mounting the hill, looked at his village and towards the west where the cold crimson sunset lay a narrow streak of light, he thought that truth and beauty which had guided human life there in the garden and in the yard of the high priest had continued without interruption to this day, and had evidently always been the chief thing in human life and in all earthly life, indeed; and the feeling of youth, health, vigor--he was only twenty-two--and the inexpressible sweet expectation of happiness, of unknown mysterious happiness, took possession of him little by little, and life seemed to him enchanting, marvellous, and full of lofty meaning.

Sunday, September 24, 2006

Speaking of...   posted by Coffee Mug @ 9/24/2006 11:10:00 PM

...epigenetics[1] and non-coding RNAs. I encourage everyone to check out the new Cell and find "the first genome-wide high-resolution mapping of DNA methylation and the first systematic analysis of the role of DNA methylation in regulating gene expression for any organism" and a new microRNA target prediction method (rna22) that makes big (perhaps too radical?) predictions about the percentage of mRNAs regulated by this pathway.

I haven't even had time to read the methylation paper yet, it looks like tiling arrays are used and this will be the third instance of that technique I've come across in the past week. Basically, this is an array that contains little chunks of sequence making up all of the non-repetitive parts of the genome. You can then wash some sample over it and see which chunks of sequence on the array get sample stuck to them through hybridization. Looks like in this paper they pulled out all the methylated vs. unmethylated DNA and hybridized that to the tiling array. Scanning the paper I note that when methylation occurs within the coding portion of a gene it is likely to be expressed whereas when methylation occurs in the promoter region it is likely to be controlled in a tissue-specific manner. Also, they present some evidence downplaying the role of microRNAs in transcriptional regulation through guided methylation, which was getting some buzz a couple or three months ago. BTW, this study was performed in a plant genome; Arabidopsis thaliana to be exact.

On the other hand, microRNAs in translational regulation are still getting played up as a major force. I won't pretend to understand all of the pros and cons of rna22's algorithm, but they do some false positive and sensitivity analysis and predict that it will find 1 false-positive binding site per 10,000 nucleotides and will discover 83% of real binding sites. With those rates in mind, consider the number of binding sites their algorithm predicts in the human genome. Conventional wisdom is that microRNAs are most likely to bind to the 3' untranslated region of mRNAs, so that is where you should look for binding sites. 92.3% of 3' UTRs in the human genome contain one or more "target islands" according to rna22. Even better, 99% of coding sequences are in the human genome do the same. That result almost seems outlandish to me, but I really have no expertise to evaluate it from.

Whenever the Schratt et al. paper came out earlier this year I was totally hyped on it. One microRNA (miR-134) was found to control LIMK-1 expression and thus dendritic spine morphogenesis. The translational repression of LIMK-1 was released in response to brain-derived neurotrophic factor (BDNF, associated with LTP and memory and all that jazz). I thought, "Maybe miR-134 has multiple synapse-related targets that are co-upregulated by release from microRNA inhibition in the face of synaptic activity." I was thinking in the 50-100 range. This paper predicts 2318 targets for miR-134. There are not that many dendritically localized RNAs, so my little theory is at best incomplete.

Finally, everything you knew about microRNA-target hybridization is wrong. Many heuristic-based approaches have focused on the "seed region" of miRNAs for target recognition. The idea is that it is particularly important for the first 7 or so nucleotides of a miRNA to match its target sequence and bind effectively. This paper says good seed-binding can still lead to crappy translational repression, and poor seed-binding (weird base-pairs or nucleotides with no binding partner at all) can still lead to strong repression. So everything right is wrong again and we can all go back to the drawing board, but at least now we have IBM on our side.

[1]I'm a little concerned that people won't understand the connection between epigenetics and DNA methylation. It seems like lately when I see the term it refers to any sort of heritability that can't be directly attributed to DNA sequence. When I first learned the term it was primarily in relation to the molecular modifications that can occur around the DNA. For instance, DNA can be methylated and histones (the proteins that DNA wraps around to condense) can be acetylated or methylated or phosphorylated. People were very concerned with the methylation states of chromosomes and how they were modified by paternal and maternal imprinting. Of late, it seems that there is increasing focus on potential environmental effects on germline genome which are epigenetic in the broad sense, but may or may not be in the DNA methylation sense. Maybe I'm the only one who finds this distinction necessary/troublesome.

Epigenetics is the new genetics   posted by JP @ 9/24/2006 09:04:00 PM

A couple new papers review the factors that play a role in determining an individual's epigenotype and the role of said epigenotype in the aetiology of autism spectrum disorders.

We still do not understand the rules governing the establishment and maintenance of the epigenotype at any particular locus. The underlying DNA sequence itself and the sequence at unlinked loci (modifier loci) are certainly involved. Recent support for the existence of transgenerational epigenetic inheritance in mammals suggests that the epigenetic state of the locus in the previous generation may also play a role. Over the next decade, many of these processes will be better understood, heralding a greater capacity for us to correlate measurable molecular marks with phenotype and providing the opportunity for improved diagnosis and presymptomatic healthcare.

Here's a question that's been bothering me: how could one demonstrate the extent of epigenetic inheritance in humans? Any "easy" look at heritability is confounded by genetic effects. Here's my experiment: I'd need a number of genetically identical sperm with different epigenetic profiles and a number of genetically identical eggs with different epigenetic profiles (and assume I know these genome-wide profiles). I make me a bunch of twins, and determine their genome-wide epigenetic profile at some stage of development. Any correlation between the epigenetics of the children and the epigenetics of the parents would be most parsimoniously explained by epigenetic inheritance. This is probably both technically and ethically impossible, so is there any other way?

Saturday, September 23, 2006

Another genetics of skin color review...   posted by JP @ 9/23/2006 08:03:00 PM
Share/Bookmark Like the study Razib linked to a couple days ago, this one looks for signatures of selection in a number of genes suspected to play a role in the generation of natural human skin color variation. And also like the previous study, they find that different genes are implicated in derived light skin color of east asians and northern europeans (see the figure on the left for a crude representation of this).

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Friday, September 22, 2006

There is nothing like data......   posted by Alex B. @ 9/22/2006 06:47:00 PM
Share/Bookmark ruin a perfectly good theory. So says Beth Visser and colleagues in the latest edition of Intelligence. She tested Gardner's theory of Multiple Intelligences (MI), gasp!, empirically. What did she find?

Our analyses of tests measuring the "intelligences" of Gardner's MI theory revealed that many of those tests were substantially intercorrelated, despite representing different domains of Gardner's framework, and also showed strong loadings on a g factor and strong correlations with an external test of general intelligence. These results are difficult to reconcile with the core aspects of MI theory.

More specifically, the researchers combed over quite a few tests to find two or three that match Gardner's own explication of his intelligences. When they gave them to a group of college students, (surprise surprise) they all had a strong correlation with each other, except the tests that measured Bodily-Kinesthetic, Intrapersonal, and Musical "intelligence." I don't think anyone outside of Gardner and his sycophants think that tests that measure Bodily-Kinesthetic skills are actually a subset under intelligence. Likewise, Intrapersonal intelligence is little more than self-esteem/self-concept, which we know doesn't really predict anything; the low musical correlations, however, were a bit of surprise (esp. given Carroll's opus), but in all likelihood, this a solely a function of the tests horrible reliability.

What can we conclude? (a) sans physical ability and self-esteem, Gardner's intelligence domains can best be thought of as second-stratum factors of Carroll's hierarchy, (b) that being said, before any more time, effort, and energy is exerted in MI, Gardner or his colleagues need to provide "falsifiable, testable, MI-based hypotheses that would predict results different from those predicted by existing models of the structure of mental abilities," and (c) any educational curriculum based on MI theory is, currently, a waste of teacher time and student energy.

And you're surprised?   posted by Razib @ 9/22/2006 05:38:00 PM

I haven't watched football in years. But I'm still a Steelers fan. When I see a Steelers game when I'm in the bar it recaptures a special something from my teenage years...that passionate, unthinking, unreflective, pure partisanship. But why? The team isn't what it once was, I barely recognize most of the players. The style of play changes from year to year on contingencies having to do with coaching, rosters and the newest fad in the NFL (remember "Run & Shoot"?). But team loyalty is real. Of course some teams do have some stability, as the Rooney family in Pittsburgh has been a fixture for decades, and teams usually are geographically stable for long periods of time. But the dispersion of Yankees, RedSox and Cubs fans show that national brands aren't hard to develop, you have to capture a mystique. In case of the Yankees, it was one of victory, in the case of the RedSox and Cubs, it was one of tragic defeat.

Spectator sports seem trivial, and yet they trigger strong psychological tendencies toward group affiliation among humans. The substance of spectator sports, the narratives, are not really filled with genuine gravity, but fans imbue them with significance. In The Nurture Assumption and Not by Genes Alone there is ample reporting of social psychological evidence which suggests that the nominal assignment of group affiliation to subjects can induce heightened altruism toward individuals you have never met, and never will. Labels matter, even if the substance is imaginary.

I only bring this all up because of the common refrain I hear, "But you can't even tell the groups apart," or, "They've been neighbors for so long," or, "We worship the same God, let us make peace." These sort of statements are predicated on the logic that substantive cultural/genetic/social distance is the root of group violence or conflict, but the reality is that ingroup-outgroup barriers are often notional (superficial, simply markers) and hard & sharp. Even if neigbhoring groups are physically similar, the tatoos they wear can exhibit almost no intragroup variance, and are perfectly distinctive characters between the groups.

There are substantive issues which drive groups to conflict. The poor resent the rich, there are issues of public monies to divide, or, there is a conflict in how to use a communal resource, etc. Nevertheless, a great deal of the time & passion derives from, at least the outside, superficial differences. Cries from the "inside" that the differences are superificial go unheeded, because difference doesn't matter, as long as you can recognize your own group, you behave as any human would, you look for tatoos, not "rational" self-interest.

Harvard superstition   posted by Razib @ 9/22/2006 09:52:00 AM

Jonah Lehrer on the origins of magical thinking:

What's the moral? Magical thinking is built into our brain at a pretty basic level. Although these Harvard students don't really believe in Voodoo, a few experimental tricks can seduce them into delusion. A similar psychology probably explains why the vast majority of Americans (between 70 and 85 percent) believe that their prayers are being answered. Reality has a way of tricking the mind.

Harvard students all have IQs above 130. Most Americans do not.

Thursday, September 21, 2006

Illegal Immigration - The Hard (and Cold) Way   posted by TangoMan @ 9/21/2006 10:50:00 PM

If you're a Romanian who wants to get into Canada, but you're already on their watch lists because they've deported you before and intercepted you on your other attempts to enter the country illegally, what to do? Why that's simple, flank the enemy and make your run for the weakest border front, so buy an airline ticket to Greenland, buy an 18 ft. fiberglass boat and cross the daunting sea to make landfall on the frozen tundra of the Canadian High North:

It's hard to slip under the radar in a tightly-knit community of less than 200, and as the Romanian emerged from a thick fog onto the shores of Grise Fiord, he was met by a welcoming party of curious Inuit. Wet from the journey, with no food and only 20 litres of fuel remaining, the Romanian was nonetheless freshly shaved and eager to sell his boat to raise money for his airfare south.

Those who met him offered to take the man, whose name has not been released, to the local Co-op store to buy food.

On the way, they happened to run into RCMP Const. Ian Johnson, and the Romanian's scheme crumbled.

Ah, the Mounties get their man, even in the desolate frozen tundra. See maps here.

Tripoli (Benghazi) Six   posted by Razib @ 9/21/2006 10:07:00 PM

Declan Butler is urging everyone to get the word out about the Bulgarian and Palestinian medics falsely accused of infecting children with AIDS. I've known about this story for a while, and like a lot of tragedies it has bubbled in the background. The reality is that even doing good in a nation like Libya can get you trapped in the capricious net of dictactorial fiat, and how they maybe be facing execution. Get the word out! Not only are six innocent lives hanging in the balance, but what sort of chilling message will this send to professionals out to do some good in the world where they are most needed?

Other ScienceBloggers make their case. Mike Dunford has the low down on how to help by doing something. If you have a blog, consider linking and bringing attention to this matter. Mass action is crucial!

Is intergenic expression functional?   posted by JP @ 9/21/2006 06:42:00 PM

Both Coffee Mug and I have made a big deal out of the fact that a large percentage of the genome in eukaryotes is transcribed into RNA. In the comments, however, gc has been skeptical of inferring much from this fact, noting that the transcription machinery of the cell is inherently "leaky". A new paper adds some fresh data to the mix.

Here's what they did: in five chimps and five humans, the researchers isolated four different tissues and measured the expression levels (using a tiling array) of a number of overlapping 25-bp segments in the ENCODE regions. These segments could then be divided into genic (i.e. protein coding) and intergenic regions.

There are a number of ways these data can be looked at to determine whether the expression of different classes of sequence is functional. First, for a given tissue, one can determine the overlap between the probes expressed in chimpanzees and humans. If the percentage overlap in genic and intergenic regions is the same, that would support the hypothesis that the intergenic regions are acting similarly, in an evolutionary sense, to genic regions, and are possibly functional.

Further, previous studies have shown that gene expression in the brain is highly conserved between humans and chimps, implying negative selection, while gene expression in the testis is highly diverged, implying positive selection. If intergenic probes show the same pattern, it would suggest that the same forces are acting on intergenic transcription. And as natural selection is not expected to play a role in determining the expression of non-functional transcripts, this would then suggest the intergenic transcription is functional.

On doing both of these tests, the authors found that intergenic transcription does indeed behave like genic transcription, giving strong support for the functionality of these transcripts. Previously, gc has raised the point that expression is a continuous, rather then a binary, variable, and indeed, among the top 5% of expressed probes, there are many more genic regions, but apart from that, the raw number of genic and non-genic probes expressed at a given intensity seem pretty similar (leading to an overrepresentation of genic regions, but still...). In my opinion, this paper gives hope to those who think that the "dark matter" of the genome plays an important role in phenotypes and that leaky transcription isn't going to be the dominant story coming out of the ENCODE data.

Selection in humans, a follow-up   posted by JP @ 9/21/2006 10:21:00 AM

To follow up on a previous post on determining the fraction of the human genome under selection (as well as Coffee Mug's post on non-coding RNAs), here's a paper which claims that, in raw numbers, more non-coding DNA has been under selection in humans than coding DNA. But still, using their method, based on the distribution of insertions and deletions in the genome, there's not a whole lot of the genome under selection-- something like 0.3%. However:
For four reasons, [this estimate] may be a considerable under-estimate. First, the method necessarily only exploits orthologous regions that retain sufficient resemblance to allow their accurate alignment. Lineage-specific or orthologous segments whose sequences have diverged greatly as a consequence of positive selection are thus not able to be aligned and are not counted towards the genomic total. For example, it has been shown that sequences unalignable between human and mouse often contain structural RNA elements. Secondly, sequences are often not included if they have recently gained function, owing to their sequence divergence being intermediate between those of neutral and constrained sequences. Thirdly, the method misses adaptive sequence within which selection has not acted heterogeneously, but instead has driven both beneficial indels and substitutions to fixation. Finally, it also overlooks positively selected sites, or short regions, that are scattered among a majority of constrained bases.

This is also interesting, given results from Bruce Lahn's lab showing accelerated evolution of nervous system genes in humans:
More recently, we exploited this signature of selection upon indels to conduct a genome-wide scan for positive selection on small functional intronic elements. We find such elements to be especially abundant in the introns of genes that are expressed in the brain (Lunter and Ponting, submitted for publication)

Skin color genes in different populations   posted by Razib @ 9/21/2006 02:15:00 AM

Identifying genes underlying skin pigmentation differences among human populations:

...we measured allele frequency differentiation among Europeans, Chinese and Africans for 24 human pigmentation genes from 2 publicly available, large scale SNP data sets. Several skin pigmentation genes show unusually large allele frequency differences among these populations. To determine whether these allele frequency differences might be due to selection, we employed a within-population test based on long-range haplotype structure and identified several outliers that have not been previously identified as putatively adaptive. Most notably, we identify the DCT gene as a candidate for recent positive selection in the Chinese. Moreover, our analyses suggest that it is likely that different genes are responsible for the lighter skin pigmentation found in different non-African populations.

There are many posts about skin color in the GNXP archives. This should not surprise. The fact that SLC24A5 was positively selected for in Europeans and correlates with light skin, but remains ancestral in both Africans and East Asians, while the Arg163Gln variant of MC1R seems under selection in East Asians, but under relaxed selection or possibly diversifying selection in Europeans suggests that different genetic strategies are scaling the same phenotypic fitness landscape. Additionally, two different strategies suggests to me that gene flow has been low enough so that one best case strategy (i.e., the highest fitness peak in a large admixing population) isn't automatically selected across Eurasia across the common genetic background. You know what they say, selection is stochastic....

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Wednesday, September 20, 2006

Hope for red-headed stepchildren the world over   posted by JP @ 9/20/2006 03:11:00 PM

Expose a person to sunlight, and odds are the UV rays will jump-start a pathway leading to an increase in skin pigmentation, i.e. tanning. However, some people simply don't tan. These people often, one may have noticed, have red hair. It's no coincidence-- there's a well-known association between fair skin, red hair, and a defective version of a gene called MC1R. Homozygotes for the defective allele don't tan, thus leading to a greater chance of UV damage and skin cancer.

Red-headed mice, it turns out, have similar problems with tanning (on their ears, which are apparently a great model for human skin). In a new paper, researchers have demonstrated the role of MC1R is the tanning pathway, and have also reinstated the tanning pathway to MC1R-deficient mice using a topical application of a drug. This is cool stuff, and implies that one day it could be possible for redheads to simply put on a cream before heading to, say, Florida. The researchers obviously thought the same thing:
To test whether forskolin treatment might protect against UV carcinogenesis, xeroderma-pigmentosum-complementation-group-C-deficient mice (Xpc-/-) were crossed to the fair-skinned Mc1re/e; K14-Scf (C57BL/6 background) mice and subjected to either forskolin-containing or vehicle-control topical treatments for four weeks, before daily exposure to 250 mJ cm-2 UV-B (along with continued topical treatments) for 20 weeks-a UV dose approximating 1-2 h of ambient midday sun exposure at sea level in Florida, during July.
That cosmetic companies will now come up with creams that allow you to tan more at a given UV dose seems a given.

Tuesday, September 19, 2006

More on non-coding RNAs   posted by Coffee Mug @ 9/19/2006 10:02:00 PM

If the 24-hour science news cycle hasn't knocked it out of the banks yet, recall that there was some hub-bub about a non-coding RNA (ncRNA) being a candidate for the fastest-evolving human gene. There was some discussion about whether ncRNAs might be something to keep an eye on and why RNAs might be particularly good at evolving quickly. This review from March had some factoids worth mulling.

There are more ncRNAs than you thought:

  • Half of the "full-length long Japan" library of human cDNA clones appear to be non-coding. Anti-jargon: cDNA (complementary DNA) is sequence read off of RNA backwards. This group tried to take a very large scale unbiased picture of the RNAs floating around in human cells and did bioinformatics to guess whether they coded for protein or not.
  • The FANTOM 3 consortium sez that 62% of the mouse genome is transcribed. Half of these transcripts are non-coding.
  • MicroRNAs are a subset of ncRNAs that regulate other RNAs. 70% of microRNAs can be found in the brain. There's a big section in the review on particular brain-specific miRNAs and potential roles in development.
  • There are seven brain-specific small nucleolar RNAs (snoRNAs). These are RNAs that act as enzymes to chemically modify nucleotides in other RNAs. There is a particularly provocative connection between snoRNAs and serotonin receptor subtype processing in Prader-Willi Syndrome, a form of mental retardation arising from deletion of a chunk of chromosome 15.
  • LINE-1 retrotransposons make up 17% of the human genome. These are the so-called "jumping genes". They code for the proteins to reverse transcribe them back into the genome. So it's relatively easy for them to proliferate. Technically they aren't non-coding, but the RNA is used in a nontraditional way in that it serves as a template for reading the gene back into the genome at some point. There is some evidence for a role for active LINE-1s in neural differentiation.
The authors say ncRNAs might evolve more quickly because they can be duplicated with less probability of harm than coding RNAs. I'm not so sure about their argument. I'll buy the first point, that ncRNAs are generally smaller and can be duplicated with greater fidelity. They then state that their small size also decreases their likelihood of disrupting existing genes. It seems to me that size wouldn't matter. If a chunk of DNA gets copied into the middle of some gene, the gene should be disrupted. Maybe the consequences could be worse in the specific case where the duplication occurs between regulatory elements and the transcription start site, so that the gene's regulation is more disrupted the further the promoter is pushed from the gene, but this seems like it would be uncommon.

I stated a while back that one reason for expecting a lot from RNAs over protein is that RNAs used to do the whole job back in the good ole days of the RNA World. Surprisingly, I was not the first brilliant, original thinker to arrive at this conclusion. In fact, these folks end by referencing Sean Eddy, who wrote a whole review about the importance of ncRNAs and how the RNA World isn't over. From his review:

The discovery of RNA catalysis and the "RNA world" hypothesis for the origin of life provide a seductive explanation for why rRNA and tRNA are at the core of the translation machinery: perhaps they are the frozen evolutionary relic of the invention of the ribosome by an RNA-based 'riboorganism'. Other known ncRNAs have also been proposed to be ancient relics of the last riboorganisms123-125. The romantic idea of uncovering molecular fossils of a lost RNA world has motivated searches for new ncRNAs. However, as these searches start to succeed, more and more ncRNAs are being found to have apparently well-adapted, specialized biological roles. The idea that ncRNAs are a small and ragged band of relics looks increasingly untenable. The tiny stRNAs and miRNAs, for example, seem to be highly adapted for a world in which RNAi processing and developmentally regulated mRNA targets exist.

Therefore, consider an alternative idea - the "modern RNA world". Many of the ncRNAs we see in fact have roles in which RNA is a more optimal material than protein. Non-coding RNAs are often (though not always) found to have roles that involve sequence- specific recognition of another nucleic acid. (The choice of examples in Figs 1, 2 and 4 is deliberate, showing how snoRNAs, miRNAs and E. coli riboregulatory RNAs all function by sequence-specific base complementarity.) RNA, by its very nature, is an ideal material for this role. Base complementarity allows a very small RNA to be exquisitely sequence specific. Evolution of a small, specific complementary RNA can be achieved in a single step, just by a partial duplication of a fragment of the target gene into an appropriate context for expression of the new ncRNA.

Buddha-fro   posted by Razib @ 9/19/2006 09:50:00 PM

Ruchira Paul points me to an interesting fact which I had always noticed, but never noted, and that is that many Japanese Buddhas have curly hair. Can anyone tell me why this is? I am struck by the fact that depictions of Buddha by Greco-Bacterians was often Apollonian in character, and I am to understand that this culture was prominent in depicting the Buddha at an early time period. Is this a Greco-Bacterian influence, or something else?

Women in science again   posted by the @ 9/19/2006 01:18:00 AM

Broad National Effort Urgently Needed To Maximize Potential of Women Scientists and Engineers in Academia
Studies have not found any significant biological differences between men and women in performing science and mathematics that can account for the lower representation of women in academic faculty and leadership positions in S&T fields.

Authors: 17 women (e.g. Elizabeth Spelke), 1 man

Their explanation:
a pattern of unconscious but pervasive bias, "arbitrary and subjective" evaluation processes and a work environment in which "anyone lacking the work and family support traditionally provided by a 'wife' is at a serious disadvantage."

That must explain why bachelor scientists are less productive than their married counterparts, no? Oh, wait...

Bias must also explain why the same systematic differences in male : female ratios by discipline is found in Asian : White comparisons:
The ratio of Asian to White in 45 academic disciplines correlated .09 with mean Verbal GRE of discipline, .79 with Quantitative GRE, .58 with Analytical GRE, .62 with Verbal + Quantitative + Analytical GRE, and .75 with Quantitative − Verbal GRE. The respective correlations of ratio of males to females in discipline were .12, .83, .61, .66, and .77. The rho between the two sets of correlations is 1.00 (p < .01.) The rank order Asian/White and male/female correlation with GRE mean were also similar, and the rho between these sets of correlations is .90 (p < .05). This correlation is congruent with the contention of Lynn (1987) that the structure of Mongoloid intelligence is to the structure of Caucasoid intelligence as the structure of male intelligence is to the structure of female intelligence.

Pope   posted by Razib @ 9/19/2006 01:18:00 AM

Aziz & Randall on the the Pope affair. Though I'd say both of them would broadly fit into the center-Left or center-Right coalitions, I'd also say that both tend to read the facts first before drawing conclusions....

Update: Ed Brayton has more. As does our Catholic brother in Darwin.

Monday, September 18, 2006

Nicholas Wade in Current Biology   posted by Coffee Mug @ 9/18/2006 10:59:00 PM

Hit it up if you have access. For the less fortunate:

Were you surprised at the reaction to the book? Yes. The human past is a touchy subject because many people use it - quite misguidedly in my view - to reason from what was to what ought to be. You mustn't say people practised cannibalism in the past because that would justify cannibalism today. Despite its absurdity, this argument makes almost every attempt to reconstruct the past controversial.

In my book I tried to let the facts speak for themselves, a somewhat more original idea than it may sound because some writers about the deep past, like the otherwise very readable Jared Diamond, start with explicitly political premises and adduce facts to support them. I cannot see that this is a justifiable scientific procedure, the popularity of Guns, Germs and Steel notwithstanding. Having compiled my apolitical account, I figured the conclusions that had emerged would be about equally vexatious to the right and the left. But so far, which I hadn't expected, the book has had more attacks from the left, particularly for the lese-majeste (accents removed by CM, cos i dunno the codes for'em) of saying our recent ancestors, far from being noble savages, were a lot more savage than we are.

What has been the reaction of the scientific community? Many people have been kind enough to tell me they liked the book, though I wasn't sure how to interpret the comment of one biologist who said he read it on nights when he couldn't get to sleep. I've been a little disappointed it hasn't received more reviews from scientific journals because it has enough references for scientists to follow the technical background. Both Nature and Science assigned the book for review, but to dreary ideologues who assailed my failure to discover that political correctness has been evolution's guiding principle all along, though fortunately they managed to find no other errors. I think these journals would have served their readers better with apolitical reviews.

Sunday, September 17, 2006

The wit and wisdom of Shaquille O'Neal   posted by Darth Quixote @ 9/17/2006 11:49:00 PM

Classic Shaq quotes in no particular order, except that the leadoff quote is HBD-related ... just to make this a true GNXP post ...

Nobody wants to get dunked on by a white guy.

Tell Yao Ming I said this: "Ching-chong-yah-wah ... ah-soooo ..."
Yao Ming's response:
Chinese is a hard language.

Some things you just can't question. Like you can't question why two plus two is four. So don't question it, don't try to look it up. I don't know who made it, all I know is it was put in my head that two plus two is four. So certain things happen. Why does it rain? Why am I so sexy? I don't know.

After winning the state high school basketball championship:
REPORTER: Shaquille, what do you attribute your team's success to?
SHAQ: I attribute it to me.

I'm like the Pythagorean Theorem. Not too many people know the answer to my game.

One time I put up 40, 50 points dunking on Shawn Bradley. After the game he brought his family over. He was like, "This is my wife. She wants to take a picture." I'm like, "Nice to meet you." I smile into the camera, take the picture, and then feel guilty about dunking on him so many times.

I knew I was dog meat. Luckily, I'm the high-priced dog meat that everybody wants. I'm the good-quality dog meat.

Pat Riley is a good-looking man. It's my job to keep him looking good.

Rolling down the window of his SUV while driving through South Central and shouting at the top of his lungs:

The Spurs? They're a good WNBA team.

I am Superman. And the only thing that can kill Superman is Kryptonite. And Kryptonite doesn't exist.

Y'all reporters like my quotes, don't you? Yeah. My quotes are Shaqalicious.

Me shooting 40% at the foul line is just God's way to say nobody's perfect.

After a 25-point comeback victory against the Boston Celtics:
They shot the ball well early. What comes out of the microwave hot doesn't always stay hot. I know, because I eat bagels in the morning.

I had an awful first quarter but I picked it up. To all you single guys out there, it's not how you start the date, it's how you finish it, sir. A lot of people can, you know, start the date with flowers and candy, but if you don't finish the date ... you know what I mean?

When asked how he would defend himself:
I wouldn't. I would just go home. I'd fake an injury or something.

When describing his MBA classmates' reaction to him:
"They would all say, 'You're not like we thought you would be. You're not as smart as we thought that you would be.'"

When asked to compare Penny Hardaway, Kobe Bryant, and Dwayne Wade:
The difference between those three is the Godfather trilogy. One is Fredo, who was never ready for me to hand it over to him. One is Sonny, who will do whatever it takes to be the man, and one is Michael, who if you watch the trilogy, the Godfather hands it over to Michael. So I have no problem handing it over to Dwyane.

I'm like Pampers, toothpaste, and toilet paper. I'm proven. To be good. And useful.

On returning from a trip to Europe:
REPORTER: Shaq, did you visit the Parthenon?
SHAQ: I don't know. I can't really remember the names of the clubs that we went to.

They call me the Big Sewer because I have a lot of shit in my game.

When asked whether the Sacramento Kings might dethrone the Lakers:
I'm not too worried about the Sacramento Queens.

I'm tired of hearing about money, money, money, money, money. I just want to play the game, drink Pepsi, wear Reebok.

Utah had beaten us in the playoffs the year before, and my knee was screwed up, so Greg Ostertag was scoring, blocking a couple of my shots. I guess it gave him confidence. Lord knows, after seeing his game, he needs it. I went to talk to him after a practice and let him know he needs to just play and not talk. I said, "Man, you need to watch what you say," And he was like, "Fuck you, watch what you say." So I was like, "Oh, you bad now?" I wasn't even mad, it was like a reflex. My openhanded right came up and smacked him upside his crewcut head. He went down, fetal position, whining, "My contact lenses, my contact lenses!" If Ostertag had known I'd taken Tae-Bo with Billy Blanks, he wouldn't have said that.

On why Phil Jackson assigned him to read Thus Spake Zarathustra:
Nietzsche was a difficult book to read. Nietzsche was so unique, they thought he was crazy. I guess Phil thinks I'm very unique to a point where I may be crazy.

When asked about his relationship with Kobe Bryant:
I'm a married man. A married man doesn't want to have a relationship with another man. So stop asking me about it ... OKAY?

On his physical conditioning:
My weight numbers, sometimes it's going to be a higher number, and you mere Earthlings, when you hear a high number, you're automatically going to think it's fat because you're only of this planet. But no, I'm just a big, sexy, beautiful man that's up in the 340s, 350s.

Neuronal taxonomy based on expression profiles   posted by Coffee Mug @ 9/17/2006 10:50:00 PM

Techniques like this on a larger-scale might help get a handle on nervous system evolution. They took several mouse lines expressing fluorescent proteins under the control of different promoters and isolated individual cells from brain regions like the cingulate cortex, somatosensory cortex, hippocampus, and amygdala. They then used a microarray to look at the level of ~13,000 mRNAs within each cell type and measured the distance between the expression profiles to generate a tree. The major distinction between excitatory and inhibitory neurons (glutamatergic vs. GABAergic) was the first split. Cortical pyramidal neurons (the bulk of cortical neurons) were the most closely related by this measure. There are pyramidal neurons in the hippocampus as well and these weren't too far from the cortical version. Interesting to see how closely the neocortex stuck to the template of allocortex cell-types as it evolved. Lots of interesting tidbits. The genes that are expressed at different levels in different cell-types tend to be part of gene families. The authors claim this provides support for the notion of gene duplication loosening the clamp of selection a little bit. I've been curious about how much one can generalize experimental results from hippocampal to neocortical pyramidal cells and vice versa. I'll tell you why if I ever find time to discuss these papers.

Neuronal cell-type dendrogram below the fold:

funtwo on youtube   posted by the @ 9/17/2006 06:10:00 PM

Humans: nothin' special?   posted by JP @ 9/17/2006 05:49:00 PM

The abstract for this article by Adam Eyre-Walker (whose work I've quibbled with before) caught my eye:
The role of positive darwinian selection in evolution at the molecular level has been keenly debated for many years, with little resolution. However, a recent increase in DNA sequence data and the development of new methods of analysis have finally made this question tractable. Here, I review the current state-of-play of the field. Initial estimates in Drosophila suggest that about 50% of all amino acid substitutions, and a substantial fraction of substitutions in non-coding DNA, have been fixed as a consequence of adaptive evolution. Estimates in microorganisms are even higher. By contrast, there is little evidence of widespread adaptive evolution in our own species.
...[double take]...huh?

Or how about this:
A few years ago, there was great optimism that, by looking for the signature of selective sweeps, it might be possible to use genomic scans of DNA diversity to identify regions of the genome that had recently undergone adaptive evolution. Unfortunately, this program of research has not proved as fruitful as had been hoped.
The Voight et al. paper familiar to most readers does get a mention, but Wang et al. doesn't. These two results, along with an excess of linkage disequilibrium in genes in human compared to non-genic regions, certainly suggests widespread selection, though perhaps this selction is not detected using traditional methods.

Of course, it's not the size of the selection coefficient that matters, rather how you use it, but still, it seems to me to be a bizarre claim that human have not been under widespread selection. Perhaps compared to Drosophila?

Mendel's Garden #6   posted by Razib @ 9/17/2006 04:47:00 PM

Mendel's Garden #6, bitch.

Rushton   posted by Alex B. @ 9/17/2006 04:34:00 PM

J. Philippe Rushton has two new things of interest:

1) A new homepage with his full vita--with many of the newer articles being downloadable.

2) A new article(co-authored with the late Douglas Jackson), showing pre-collegiate males are smarter ("have higher g"), at least as measured by the SAT, than females across ethnic groups and SES. This seems to hold for both SAT-Math and SAT-Verbal. Of note: a) the sample size is huge: 100,000 people; 2) males were "overrepresented" at the higher tails of the SAT/IQ distribution, females were "overrepresented" at the lower tails---but, of course, folks with Mental Retardation and Borderline Cognitive Functioning do not, in general, take the SAT, and since the sample used was the 1991 SAT "validity" folks, the lower tails of the SAT distribution should be around 90ish in a regular IQ distribution. Thus, what we have here, is some more evidence that males are more likely to be in the upper tails of the IQ distribution, while females are more likely to be in the center. This, then, averages to about a 3 IQ points advantage for males---a trend that others have also found (e.g.,)

Saturday, September 16, 2006

Gods of the sword   posted by Razib @ 9/16/2006 03:15:00 PM

Over at my other blog I have a long post Spread by the sword, which analyzes the perception that Islam is a religion of the sword. I was influenced by some of Robert Pape's insights to offer two parameters which I think are important

1) The spread of Islam was often accompained by herrenvolk. In the early centuries Islam and Arab rule were coterminus. The Ummayyads were the "Arab Kingdom." Later the Turks took up Islam as their national ideology, and in places like the Balkans and India to be Turkic and Islamic was synonymous (many South Asian Muslims are "Khans" after all). In contrast, both Buddhism and Christianity tended to spread via elite co-option. Kings and nobles converted to the new religion and over time. This leads me to my suggestion that one reason the historical memory of Islam as a religion of the sword is going to be inevitable when the herrenvolk are expelled, in places like the Balkans, Spain and India non-Muslim elites returned to power and of course the memory of Islamic rule grates. In contrast in places like Japan or England the fall of the Christianizing dynasty was irrelevant because the whole elite had converted (I did think of a major example of where Buddhism was more like Islam in the way it spread, see the other post for details).

2) Which brings me to a second important point: Christianity & Buddhism spread into "pagan space" on the western and eastern edges of Eurasia. Interestingly World War II was an example where the pre-Christian and pre-Buddhist aspects of nations converted in the second half of the 1st millenium drifted toward a more "pagan" sensibility (e.g., Himmler's neo-Paganism and State Shinto). But by and large the pagan response was attenuated, and, to some extent both Buddhism and Christianity integrated with their pagan substratum and absorbed it (more with Buddhism I would argue, as pagan religious traditions like Bon, Shinto and Taoism all exist in ostensibly Buddhist cultural contexts, while explicit non-Christian traditions except for Judaism disappeared in the West). The contrast with Islam is clear, Islam spread into Zoroastrian, Christian, Jewish and Hindu lands. I think that Manuel Paleologus's question as to what Islam brought that was new is actually not inaccurate: both Buddhism and Christianity introduced wholly new lexicons and acted as civilizational mediators. In contrast, Islam was civilized, both by Greek Byzantine and Sassanid models. In short, the fact that Islam has bloody borders is a natural consequence of its expansion into cultures which need no civilizing and have religious ideologies which are naturally resistent to marginalization and offer compelling narratives to elites. The best analogy for the spread of Islam is that of Protestantism, not Christianity or Buddhism (interestingly, if you look at the works of may Byzantine thinkers [e.g., John of Damascus] there is a tendency to via Islam as simply a heresy that is wholly derivative of Christianity, which I think is one reason that Paleologus was so dismissive).

These aren't the only parameters, but I think they are not irrelevant.

Friday, September 15, 2006

The devo book I want   posted by Coffee Mug @ 9/15/2006 02:17:00 PM

I read Endless Forms, and I read Coming to Life by Christ. But I still don't feel like I've got anything like a grip on development. Endless Forms avoided specific terminology too much IMHO. I don't think it necessarily helps anyone's understanding to make up a new term like "tool-kit genes" in place of "transcription factor." So I didn't learn all that much from Mr. Carroll. Coming to Life was a little less lay-book-ey, but still left out the details and (I felt) that there wasn't an overarching theme. It felt like a list of facts, a description, at a somewhat general level of what happens during development.

I think Dr. Davidson's new book, The Regulatory Genome: Gene Regulatory Networks In Development And Evolution, might be the solution I'm looking for. But since it is more like a textbook it comes at more of a textbook price: $70 new, ~$60 on Amazon. Dunno how quick I can get it at a library. Anyway, here is some from the book review in Nature Genetics:

The book begins with an introduction of his idea of the regulatory genome or the regulatory apparatus encoded in the genome. In the second chapter, he explains in detail cis-regulatory modules and the structural and functional basis of regulatory logic. Here the author emphasizes that comparison of genome sequences of different animals (or species) is helpful to identify highly conserved cis-regulatory modules. After a brief explanation in chapter 3 of animal development as a process of regulatory state specification, Davidson argues persuasively that cis-regulatory modules act as networks and that the gene regulatory networks are the key to understanding embryonic development (chapter 4) and evolutionary construction of various animal forms (chapter 5). It is also emphasized that computational and systems biological approaches are essential to create the networks. Every step of his logic is presented with examples to explain his idea, with beautiful, well-designed color figures. His concept of the significant roles of gene regulatory networks in development and evolution can be clearly understood using the aforementioned key terms. Namely, animal embryogenesis seems to be established by a complex combination of input and output linkages, plug-ins and differentiation gene regulatory batteries, usually in this order. The diversity of animal forms may be explained in terms of core kernels, alteration in deployment of plug-ins, input and output linkages and differentiation gene regulatory batteries. This order is important for understanding animal evolution at the level of phylum, class, order and family, respectively.

Thursday, September 14, 2006

10 Questions gets you interviewed elsewhere!   posted by Razib @ 9/14/2006 11:04:00 PM

Just a note, a few weeks ago Australian Radio emailed me about Matthew Stewart's contact information since they couldn't find him anywhere else. I passed it along, and now Matthew will be doing an interview for them Saturday morning (the archive should show up in a few days).

The Pope's address   posted by Razib @ 9/14/2006 10:56:00 PM

Read the Pope's address the University of Regensburg. His erudition and precision of speech leaves me pleasantly disposed toward him despite the many intellectual bones I have to pick with his argument. Living in the United States religious leaders are generally rather "populist" in their speech and habits, a nice change.

Adapting Minds, David J. Buller   posted by Razib @ 9/14/2006 08:56:00 PM

Chris of Mixing Memory points me to this very interesting review [PDF] (demolition to be honest) of David J. Buller's Adapting Minds, a critique of Evolutionary Psychology which made some waves last year. Even if you haven't read Buller's book, the review will be of interest as it covers a lot of ground.

Paternity & all that   posted by Razib @ 9/14/2006 06:57:00 PM

Here is a nice little essay on issues surrounding paternity certainty. But this is the real interesting part:

Several studies have shown that a mother's relatives pay much more attention to her children than the father's relatives do. One proposed explanation is subconscious suspicions of paternity uncertainty. In 1997, Steven Gaulin, Donald McBurney, and Stephanie Brakeman-Wartell, at the time all affiliated with the psychology department at the University of Pittsburgh, asked 278 college students to rate on a scale from 1 to 7 how much their aunts and uncles seemed to care about their welfare. The students reported that the relatives on the mother's side of the family paid ``significantly more" attention to them.

The degree of reduced interest from the father's relatives was what you would expect, if those relatives were assuming a 13 to 20 percent chance the child wasn't related to them. Similar studies--including one published as recently as this May in Evolution and Human Behavior--have found that maternal grandparents pay significantly more attention to children than paternal grandparents, and have offered similar explanations.

The maternal grandmother effect seems real. I did a lit search on this last year, and I found ethnographies in which surveyed the Khasis of northeast India, and their Bengali neighbors to the south. The Khasis are matrilineal, while the Bengalis are most definitely not, and yet in both groups the maternal grandmother effect was noticeable. It is in the Bengalis that I found it most interesting, because I obviously know a little bit about this culture and it is very patrlineal.

Heritable epimutation plays a role in colorectal cancer   posted by JP @ 9/14/2006 05:58:00 PM

Recently, there has been great interest in the role of epigenetics in the generation of phenotypes. One major question is whether epigenetic mutations can be passed through the germline, as the genome is demethylated, then remethylated, during development. A new paper provides evidence one example of an inherited epimutation, plus an association with the development of cancer. It's still possible, of course, that the epigenetic mutation is caused by a genetic mutation, giving the illusion of epigenetic inheritance. But the evidence is growing that epigenetic inheritance is a widespread and important phenomenon...

Nerdcore Hip-Hop   posted by Coffee Mug @ 9/14/2006 07:19:00 AM

Here is a repository of links to nerdy nerdy rapping. Seems like most of the expert nerdiness is computer-related. MC++ and Frontalot are probably the best known. Frontalot has a recent incredibly nerdy take on Wagner in collaboration with Baddd Spellah (I suppose the track is attributed vice versa.)

Wednesday, September 13, 2006

Atheism, Heresy and Hesychasm   posted by Razib @ 9/13/2006 07:43:00 PM

I have a long post, Atheism, Heresy and Hesychasm, on my other blog. It is basically about how unbelievers might relate to the society around them.

GNXP Wiki   posted by the @ 9/13/2006 07:17:00 PM

Update:GNXP Wiki wants you!

We have setup a wiki to accompany the GNXP blog. The site is, and you'll find a link in the sidebar. The utility and wisdom of this decision is not yet clear to us, but it does seem like a worthwhile experiment.

Several overlapping functions have been envisioned for the wiki site, and perhaps you'll come up with more.
  • An encyclopedia of human biodiversity topics, without the edit wars

  • A repository/summary of GNXP blog content in topical rather than chronological form--to keep older material from being forgotten

  • An outlet for intellectual collaboration with more permanence than the comment threads; perhaps an incubator for new blog content

Anyone who has used Wikipedia should be familiar with the Mediawiki software we're using. Editing is open to anyone who registers for an account. (New account registration is currently open.) Like the comments threads, we're retaining broad editorial control. But because this is a wiki, that control also lies with you (alert us/me of problems). An initial period of experimentation is expected.

Update from Razib: In spring of 2004 I deleted the category template for Movable Type in a panic as I was trying to reduce overhead due to a webhost breathing down my neck. Since then many readers have asked for category pages. Well, here is your chance, add to the GNXP reading list.

Fun with zip codes   posted by JP @ 9/13/2006 05:29:00 PM
Share/Bookmark The title says it all.

Pharmacogenetics for every nation   posted by JP @ 9/13/2006 03:25:00 PM

One of the recurring themes on this blog is that different populations differ genetically, and that these differences have major importance in public policy and health. Jason Malloy has passed on a link to one project that aims to inject genetic information into public health decisions: the PharmacoGenetics for Every Nation Initiative (PGENI).

Under the banner of pharmacogenetics, researchers complile data on how individual sequence variants affect pharmacological traits like drug metabolism. Further, on determining the worldwide distribution of these variants, it is possible to better predict those traits based on ethnic group. And if it turns out that certain drugs work better in people of chinese ancestry than in those of european ancestry, that information might be of great importance to public health officials in china and in europe. An example:

Han Chinese, for example, are more than four times as likely as white Americans to have a variant of a gene called TYMS that makes the drug methotrexate less effective at treating rheumatoid arthritis. US doctors prescribing this drug often initially hold back from also prescribing corticosteroids, which can help ease arthritis symptoms, because of the risk of side effects. For China, however, PGENI suggests combining methotrexate with corticosteroids right from the start.

This information is of particular value in countries that can't afford to test directly for pharmacologically relevant alleles in individual patients, and which thus must rely entirely on ethnicity to make prescriptions. PGENI has four goals:

1. Enhance the understanding of pharmacogenetics in the developing world

2. Help build local infrastructure for future pharmacgenetic research studies

3. Provide guidelines for medical prioritization for individual countries using pharmacogenetic information

4. Promote the integration of genetic information into public health decision making process

Definitely a project to watch, and a great example of the immediate clinical worth of this kind of research.

Hi   posted by John Emerson @ 9/13/2006 03:12:00 PM

The regulars here know me pretty well by now, but I'll introduce myself anyway. My name is John Emerson, and I've been a commenter here for some time. Over the last few months I've made some long comments which really should have been posts, and finally I asked Razib for posting privileges. My own site is Idiocentrism; the most interesting page there for most people here would be my archive of writings on Eurasian history, especially those dealing with the Mongols, the nomads, and the steppe.

Why Religion?   posted by John Emerson @ 9/13/2006 03:00:00 PM

Like Razib, I'm secular and an atheist, and this forces me to ask myself, "Why religion?" If religion is as false as it seems to be, why does it exist?

I have three answers. These are not exclusive but overlapping, and the fact that two of them are more or less mutually incompatible often leads to apparently paradoxical developments.

Religious belief can be either functional or dysfunctional, either from the social or from the individual point of view. The falsehood of a religion does not entail its harmfulness, and in fact the robustness of religious belief suggests that religion must be in some way, at least socially, more functional than not.

In different ways my three explanations of religious belief all center on "long shot" situations, where the chances of success by routine means are low or doubtful. (This squares with Malinowski: where routine non-magical methods work most of the time, the most superstitious tribesman will use them). In all cases they also involve choices which are probably not rational from the individual's point of view, but are rational from the point of view of the species.

Thus, these forms of religion can be called altruistic. I'm not up to date on the evolutionary debate on innate altruism -- innate dispositions which lead the organism to behave in a way which reduces his or her own personal evolutionary success, while enhancing the evolutionary success of the group (species or kingroup) to which he or she belongs. As I understand that's been a hard case to make even with the help of kin altruism.

Perhaps the innate trait leading to altruistic behavior is not intrinsically altruistic, but is exapted for altruism within a learned, conventional, non-innate social context such as religion. Candidates for such innate dispositions might be those toward male bonding, submissiveness, and anger against outsiders.

My first two explanations of religion are familiar and have been given by Marx, Nietzsche, and many others. First, religion gives comfort to people whose actual situation in life is unendurable, or almost. Hope for an imaginary and unreal future paradoxically makes the painful present more bearable. This is the "opiate of the people" explanation, and is associated with exploitation, heirarchy, and domination.

Second, religion can motivate self-sacrifice, for example in war. In some sense this might be thought of as a version of the first, but the behaviors of the submissive peasant and the soldier are so different that I thought I'd list them separately. Just like the first case, this involves some degree of altruism: Religion tends to use promises about the afterlife to sugarcoat an earthly life which is hard to face rationally and is, in fact, a very bad deal.

My third point is by far the most interesting. New religions, crazy as they usually are, can be compared to mutations in biology. Even if most of them are harmful, some of them successfully move into new niches in the historical landscape. Thus, even though most new religions, like most new genes, are destructive or neutral, whatever bold, successful social innovations there are have often been religious in motivation. For most people conventional behavior and the status quo are the robust default choices except in the very worst situations, and in fact many people will follow the rules even if it literally kills them.

My favorite example of this is from Polynesia. Polynesia was settled during the Christian era by shiploads of families migrating with their pigs and their tools. Polynesians were great navigators, but the big discoveries -- of New Zealand from Hawaii, for example -- were made by people jumping off into the void, who could not know where they would land or whether there was any land there at all. The evidence I've seen suggests that these voyages were motivated by religious visions of an apocalyptic sort. Most such expeditions must have died miserably, but the ones who didn't succeeded gloriously (settling Samoa, Hawaii, New Zealand, and so on.)

Thus new religions, like mutations, are high-risk high-stakes gambles.

My premise is that serious religious belief is never individually rational, leading as it does to self-sacrifice, submission to exploitation, and crazy gambles. I've thought of trying to describe the circumstances in which new religious beliefs are successful and socially rational (after the fact), but that isn't at all easy.

The three variables I've figured out are: 1.) the worse-adapted conventional practice becomes, the more likely it is that a new religion will be an improvement. 2.) The more successful a conventional practice is, the more likely it is that people will be able to experiment, since they have more leisure and more surplus. 3.) If there's a significantly more favorable niche accessible from the conventional niche, whichever innovator gets there first will have an advantage. (#1, #2, and #3 are completely independent, and #1 and #2 or more or less incompatible. I suspect that evolutionists have worked this kind of question out more systematically.)

I should also point out that religions of submission (#1) readily morph into religions of rebellion (for example, by promoting a minor deity or by revising the theogony.) This is historically observable and shouldn't be thought of as problematic. In terms of my argument, anyone in condition #1 has no good choices: both submission or rebellion can lead to extreme misery, and seldom does either lead to happiness or success. For someone in these circumstances to flip from one desperate solution to the other is nothing strange.

In my opinion, the payoff of this piece is the suggestion that new religions, while irrational, are like mutations. Few of them succeed, but they are part of the cruel and bloody process of proliferation and decimation (variation and selective retention) which constitutes both evolution and history.

M.D. Ph.D. but can't use Pubmed?   posted by the @ 9/13/2006 09:52:00 AM

"What is needed is a healthy donor," said Dr. Jamie Grifo, director of reproductive endocrinology at New York University Medical Center. "There's no evidence that because some guy made it through college that his offspring will." [link]

Really? Let's check Pubmed:

PMID 11523706
A high heritability was found for body height (h2 = 0.78 in men and h2 = 0.75 in women), and a moderate heritability for education (h2 = 0.47 and h2 = 0.43, respectively).

PMID 8639155
In a "psychometric" model of twin resemblance, based on separate self-reports in 1981 and 1989, genetic factors explained 57% of the stable variance in educational achievement, while environmental factors shared by twins accounted for 24% of the variance. Corrections for phenotypic assortative mating for educational level, however, suggested that estimated common-environmental effects could be entirely explained by the correlation between additive genetic values for mates. Taking this into account, heritability "true" educational attainment in Australia may be as high as 82% with the remaining variation being due to individual environments or experiences. Unlike previous studies in Scandinavian countries, results in Australia suggest that factors influencing educational success are comparable between women and men and for individuals born at different points during this century.

PMID 2392892

The broad heritability of SES, educational attainment, fecundity, and risk for divorce ranges from 0.30 to 0.50

PMID 2719624
Typical heritability values in the three youngest groups (weighted means) were .43, .51, and .66 for occupation, education, and IQ, respectively. ... Genetic variance influencing educational attainment also contributed approximately one-fourth of the genetic variance for occupational status and nearly half the genetic variance for IQ. The values for the between-families variances (reflecting family environment and assortative mating) varied from 2 to 35% in the three youngest groups... All the between-families variance was common to all three variables. For educational attainment and IQ, the bulk of this between-families variance is probably genetic variance due to assortative mating. The common-factor environmental within-family variances were generally small, and the specific estimates seemed to contain mainly measurement error.

PMID 4039415
For females born after 1940 and before 1961, the relative importance of genetic (38-45%) and familial environmental (41-50%) differences changes very little. For males born during the same period, the broad heritability of educational attainment has increased substantially (67-74%), and the environmental impact of family background has correspondingly decreased (8-10%). For males, at least, having well-educated parents no longer predicts educational success, as measured by duration of education, independent of the individual's own innate abilities.

Tuesday, September 12, 2006

Why are people Creationists?   posted by Razib @ 9/12/2006 06:22:00 PM

John Wilkins has a two part series up about why people are Creationists. He plans to continue it. John starts within the bounded rationality paradigm, which has a lot going for it. The only thing, which John might get to, is that rationality is not just bounded, it is strong biased toward particular conceptual structures. Children are not just indoctrinated into a Creationist narrative, they tend to prefer it when they are not taught otherwise. Psychologists like Paul Bloom have found that children are generally intuitive Creationists when young, but those raised by non-Creationist parents shed these beliefs, while those raised by Creationists do not.

Update: Part 3 is up. John hints at cognitive parameters. Part 4 is coming up.

Addendum: I will offer my own personal childhood experience with evolution. My parents never talked about this issue, and I didn't know that my father was a Creationist until I was a teenager (yes, I'm not close to my parents obviously). When I was 8 I checked out a book from the library about the "origin of humans" (I was into paleontology so I assumed it was about human evolution). That book turned out to be a Creationist book all about Ham, Shem and Japeth as the founders of the human race, and I was enraged and bitched out the librarian when I returned it as I believed there was some intellectual fraud going on here (I didn't say it in those words). I can't really recall the first time I read about evolution, probably when I was 7 as that was age that I had an avid interest in dinosaurs. I personally never found it peculiar, as I don't even recall being surprised or confused by the concept. It was as natural an idea for me as a God in heaven is for many children. Only in my teenage years did I comprehend that other humans might not find evolution such an "obvious" idea.

Update II: Part 4.

The main issue I would have with John's model is that I am personally skeptical of the reasoning powers of most of the human race. Nations with higher rates of acceptance of evolution are not necessarily ones where the populace is more well educated, rather, they are simply ones where organized higher institutions tend to accept evolution as a given, and so people avow the belief which is socially accepted. The US, and many Muslim nations (for example) have powerful elite counter-evolutionary movements in the form of religious literalism.

Genius: Quest for Extreme Brain Power   posted by Razib @ 9/12/2006 12:26:00 AM

Genius: Quest for Extreme Brain Power. The documentary (Sunday, 10 PM EDT, CNN) seems like it will attempt to hit upon the neurological correlates of IQ. Neurometrics, not psychometrics?

Sunday, September 10, 2006

Multiculturalism in Europe   posted by Razib @ 9/10/2006 08:37:00 PM

Frontpage Magazine has an interesting symposium titled The Death of Multiculturalism (part II here). Long time readers of this blog know that my own views about Islam have shifted somewhat over the past 4 years in that I am not so terrified of Muslims ruling over dhimmis in Europe within a generation or two. But, that does not mean that issues do not need to addressed. Some of the analogies used by the FP contributors are ridiculous, but they and their fellow travellers address a serious and important question: the integration (or lack of) non-Western peoples into Western republics and constitutional monarchies. Over the past 4 years, especially since Pim Fortuyn's assassination, the rate of increase of multiculturalist hegemony seems to be decreasing (though my understanding is that the Labor party will likely win the next election in The Netherlands). In 2002 Jean-Marie Le Pen won nearly 20% of the vote in the presidential election, and right-wing populist parties have been on the march throughout much of Europe. European Muslims are by and large not part of the societies in which they reside, and to a large extent are recipients of massive government subsidies. It seems inevitable that resentments and tensions will come to a head, the question is not will the Muslim Question be addressed, but how. This means that the discussion needs to spread more equitably across the political spectrum, and the sooner the better.

More positive selection....   posted by Razib @ 9/10/2006 12:56:00 AM

Another paper with HapMap data, Allele Frequency Matching Between SNPs Reveals an Excess of Linkage Disequilibrium in Genic Regions of the Human Genome in PLOS Genetics (so totally open access). The synopsis is clear, so no need to quote. Two points

1) This is a methodological attempt to attain more precision in ascertaining linkage disequilibrium within the genome in regards to SNPs by comparing those variants where frequencies matched.

2) The empirical results are the same as previous papers. a) Evidence of massive selection via "haplotype blocks," basically signatures of selective sweeps through human populations, and, b) more of these in Europeans and East Asians than Africans.

If you get confused when we talk about LD, read the paper. It isn't all that exciting, but I think the repetition and banality of the exposition would be beneficial if you're unclear in regards to the concept.

Update by Darth Quixote: The PLoS site has an Excel file listing the genes contributing most to the excess LD in the respective samples. Perhaps our genomicist friends will get something of it.

Saturday, September 09, 2006

Israeli fertility: The importance of culture   posted by David Boxenhorn @ 9/09/2006 01:12:00 PM

Israel is the only country I know of where fertility increases as income goes up, among "normally" wealthy. (The super-rich might be another story, but they don't have much of a statistical presence). From here:

In virtually the entire modern world, increased wealth and education are linked with plummeting birthrates. The New York Times reported this week that Europe is "wrestling" with birthrates which have "reached a historic and prolonged low... straining pension plans and depleting the work force across the continent." The EU projects a shortfall of 20 million workers by 2030. In 1990, no European country had a fertility rate of less than 1.3 children per woman; by 2002, 15 countries did. The "birth dearth" has become a political issue in Germany, Russia and the Czech Republic. "Almost all countries are increasing baby bonuses," the article reports. While the US fertility rate currently hovers around the replacement level of 2.1, the rate among American Jews is considerably lower: 1.86.

Israel is almost another world. The average fertility rate is 2.7 children per woman - by far the highest of any modern democracy in the world. Moreover, the average size of families with a high monthly income - above NIS 50,000 - is 4.3 people, compared to 3.7 for families with more modest salaries.

What's going on here?

ACCORDING TO demographer Sergio DellaPergola, we are different than Europe and America in our attitudes toward family size. "Here, people would like to have three children at least." If they don't, it is generally because of economic restraints, as demonstrated by the fact that, in Israel, the upper-middle class is associated with more children, not fewer.

Vivien Leigh: Case Solved?   posted by DavidB @ 9/09/2006 02:31:00 AM

In my last piece on Vivien Leigh (a few entries below) I suggested that the key to the mystery of her ancestry might be the odd name Yackjee: the family name of her mother and maternal grandfather.

In comments on my post there were some genealogy links, and in one of these I noticed the variant spelling Yackchee. That led me to this entry for a wedding in Bengal in 1911:

COOK - YACKCHEE, March 22nd 1911, at St Thomas Church Middleton R W., by the Rev Fr Van-de-Murgal S.J., Henry Mitton Cook, of Mitcham, Surrey, England to Ellen Maude, youngest daughter of J.P. Yakchee, late Registrar, Board of Revenue, L.P. 32 Theatre Road, Calcutta.

But I noticed that in this entry the name was also spelled Yakchee, so I Googled on that spelling and immediately got numerous results.

The key discovery is that there is a town in Afghanistan called Dah Yakchee Khana . So if a man from Dah Yakchee Khana moved to Bengal at some time in the early 19th century (at which time Britain had a quasi-imperial role in Afghanistan, with disastrous results), he and his descendants might well use the name Yakchee in some form - the spelling of Afghan and Indian names in the Latin alphabet would of course be variable. This would explain the connection of the name Yackjee with Bengal and its extreme rarity even there.

So the exotic element in Vivien's ancestry may not be Indian, or Armenian, but Afghan. Though of course between the original migration from Afghanistan and the birth of her mother's father, Michael John Yackjee, the Yackjee line may have mixed with other elements.

Added: Well, I gave it my best shot. The Afghan connection is not conclusive, but until anyone comes up with a better explanation for the origins of the name Yackjee/Yackje/Yackchee/Yakchee/Yakchi... I will stick to this hypothesis.

Of course, the name of the town Dah Yakchee Khana itself presumably means something in an Afghan language (Pushtu?) The word khana means 'house' in Hindi, and probably something similar in cognate languages, so I wondered if Dah Yakchee Khana means something like 'the home of Yakchee' - in which case Yakchee might be a common Afghan name. But it is not on this list.

Friday, September 08, 2006

Standardized test score distributions-what are they measuring?   posted by rosko @ 9/08/2006 11:58:00 PM

I know this has nothing intrinsically to do with genetics, but it has something to do with cognitive ability testing, which I know is a favorite topic of discussion on GNXP. I was inspired to write a post on this since I am in the process of preparing for the GRE. Among the preparation materials that ETS provides are the distributions of verbal and quantitative test scores by graduate field of study.

Out of curiosity I looked through these, and found some interesting results. In particular, the shape of the distribution of quantitative test scores varies drastically by intended field of study. It is approximately normal for the humanities and some of the biological sciences, but is extremely left-skewed for physics, math and engineering majors, having a peak at around 700 but rising again near a perfect score of 800. In some cases this ceiling effect in quantitative scores is so severe that it's impossible to score above the 90th percentile!

The verbal scores show a very different pattern. The humanities and social sciences mostly show normal distributions, whereas the hard sciences typically show a bimodal distribution but with a similar mean. There is no evidence, though, in any major for a ceiling effect even remotely resembling that for the quantitative scores. The difference is such that, even though I scored a full 80 points lower on the verbal section than the quantitative section of a practice test, I didn't see a single major where I would have been at a higher quantitative than verbal percentile. This raises the question of what the verbal test is actually measuring, and why its mean seems to vary so much less by major. One explanation I came up with is that verbal tests measure mostly how much education you have had, and how much reading you have done, rather than intellectual aptitude. This is because they ask you for things like antonyms of quite uncommon words. In any case, I doubt that it measures the type of verbal ability factor that has been shown to trade off with visuospatial ability in many studies, including those assessing gender differences. If it were so, I would expect the scores to vary more, with the less spatially-oriented fields showing more left-skewed distributions. Also, I have always done well on verbal tests although I am predominantly a visuospatial thinker, and have always found analyzing literature to be one of the most difficult tasks. Any thoughts?

Admin & GUI thread   posted by Razib @ 9/08/2006 10:54:00 PM

I have decided to switch sort order on Haloscan comments so that new comments come first now. Also, I have decided to start the "open thread" again and place it to the right (your right). Same as usual, post whatever related to this blog. I'm also getting a few requests for some GUI streamlining and what not. I'm open to suggestions, though I think David did most of the important stuff which his Haloscan hacks. A minor note: for those who comment, if you have a consistent and regular handle you are not treated like the next random turd that wanders in. In contrast, please don't post "I think x" with no supporting justification if you are not a known quantity, who the fuck cares what you (whoever you are) think? If Steve C. asserts something about physics without much citation, I'll listen, and the same with David K. if he says something about the financial industry. But if "anon" posts something I'll be likely to tell you to STFU if you don't feel like taking the time to provide some cites.

Update: Due to immediate protest I made the sort order as it was.

Mexican Americans are not mostly Amerindian   posted by Razib @ 9/08/2006 10:15:00 PM

I was talking to a friend of mine the other day and he mentioned Mexican Latinos being Amerindian. I have looked up data on this before and I recalled Mexican Americans being about 50/50 in most of the surveys (averaged out). The genetical data and historical literature seems to imply male Iberian ancestors and female Amerindian ancestors. I pointed out to my friend that there is a problematic bias in who he classifies as "Latino" as he walks down the street: white Latinos are not Latino until you know their name, while more Amerindian looking Latinos are Latinos simply via visual inspection. In other words, there is a bias among Latinos you don't know to simply pick out the more Amerindian ones within a given family, so Latinos are naturally more Amerindian looking to most people. I myself noticed this when I observed that some family members within a group of related Latinos I would have assumed were white if I had not seen them in the context of their near kin (some of whom looked Amerindian, and most who looked mixed). An idiotic brown reader (a Kashmiri pandit who fancied himself white despite his no doubt sand niggerish Persian appearance) offered that of course Mexican Americans were mostly Amerindian, look at Cheech Marin. Now, this goes to show that not only white people are guilty of not being able to tell different peoples apart, Cheech Marin has a prominent mustache in many photos. No matter what you assess in regard to his overall phenotype, when was the last time you saw a mustache in a fully unadmixed Amerindian??? The reader was clearly an unreflective moron, but then, so are many GNXP readers as over the years (I'm talking over all 4 years of this blog) individuals have claimed over & over that American Latinos are mostly Amerindian. At which point I double-check PUBMED, make a cite, and that's that (taking all of 30 seconds). But I'm tired of this.

Before one can have a discussion one must have some familiarity with the facts. Steve points me to these two neat charts (cite):

Here are the individual data points....

My hunch is that the Colorado sample of Mexican Americans is a little whiter than average, but, that still doesn't mean that I believe American Latinos (Mexican Americans) are predominantly Amerindian. The reality is that a disproportionate number are from the northern, more European, states of Mexico. So on a priori grounds we would expect that Mexican Americans would be whiter than the average Mexican, and the large indigenous minority has begun to emigrate only within the last few decades to this country.

Why is this important? Because people keep saying on the comment boards that Mexican Americans are predominantly Amerindian, and that doesn't seem to be true. They are a hybrid population. Houses collapse on a foundation of lies.

We tell ourselves stories   posted by Coffee Mug @ 9/08/2006 09:14:00 AM

The September issue of Hippocampus is a special on Hippocampal Place Fields and Episodic Memory. Episodic memory is the type of memory that you immediately think of if you are not a memory researcher. It is what Proust is doing while Remembrancing (which is part of why he is such a favorite quotee among the memory community). EM is supposed to have key elements that distinguish it from other memory types, one of which is this experience of "mental time travel". This is an idea almost entirely based in introspection. It is not clear how to ascertain if a patient is replaying the experience subjectively or merely retrieving facts without the VR-like aspect. The subjective nature of this type of memory retrieval makes it well-nigh impossible to study in rodents. But it may be that people who are mostly concerned with the mental time travel issue are hardly interested in memory, per se, but are rather interested in our ability to "fill in the gaps" and create continuous narratives. From the second article of the issue by Ferbinteanu et al.:
Furthermore, though intuition also suggests that our memories are veridical-an accurate reproduction of past events-empirical data indicate that autobiographical memories are in fact reconstructed by active processes sensitive to systematic errors based upon inattention, suggestion, expectancy, and familiar cognitive scripts (Schacter, 1999; e.g., Conway, 2001b). Even completely false memories are acquired easily (Loftus, 1997, 2004) and activate the same neural network involved in true memories (Okado and Stark, 2005). These memory distortions show that rather than "traveling down the memory lane" to re-experience past events, memories for episodes are reconstructed representations based on fragmentary data fit together using heuristics (Schacter, 1999; Conway and Pleydell-Pearce, 2000).
So, you don't really remember. You confabulate based on the information you have at hand, the "fragmentary data". I have gotten so paranoid about confabulation that I will hardly ever state one of my memories of a past event as fact. I would be a horrible murder-trial witness. I notice errors all the time among friends of mine that are better story-tellers. We will be reminiscing about some event 4 or 5 years ago and place some individual there that we didn't even know yet. Everyone knows we have memory errors. I wonder if better story-tellers are better at "smoothing the curve". We have a bunch of data points stored up, but it may take our narrative-building ability (which may be uniquely human) to experience "mental time travel".

This habit humans have of telling ourselves stories seems pervasive. I am reminded of the hyperactive agency detection device, proposed as an explanation for our need to make gods. Also, Gazzaniga's experiments with split-brain patients:
Studies on split-brain patients have dominated Dr. Gazzaniga's work ever since. In the 1970's, he and his colleagues reported that the left hemisphere acts as an interpreter, creating theories to makes sense of a person's experiences.

Their first clue came from an experiment Dr. Gazzaniga carried out with Dr. Joseph LeDoux, now at New York University. A patient called P.S. was shown a picture, and was then asked to choose a related image from a set of other pictures. What P.S. didn't know was that he was being shown a different image in each eye.

Dr. Gazzaniga and Dr. LeDoux showed P.S. a picture of a chicken claw in his right eye and a snow-covered house in the left eye. P.S. pointed to a chicken with his right hand and a snow shovel with his left.

''I'll never forget the day we got around to asking P.S., 'Why did you do that?''' said Dr. Gazzaniga. ''He said, 'The chicken claw goes with the chicken.' That's all the left hemisphere saw. And then he looks at the shovel and said, 'The reason you need a shovel is to clean out the chicken shed.'''

Dr. Gazzaniga hypothesized that P.S.'s left hemisphere made up a story to explain his actions, based on the limited information it received. Dr. Gazzaniga and his colleagues have carried out the same experiment hundreds of times since, and the left hemisphere has consistently acted this way.

''The interpreter tells the story line of a person,'' Dr. Gazzaniga said. ''It's collecting all the information that is in all these separate systems that are distributed through the brain.'' While the story feels like an unfiltered picture of reality, it's just a quickly-thrown-together narrative.
The point of the Hippocampus article is that we can ignore this business for now, while we study how the hippocampus brings together the information that we actually have remembered rather than confabluated. This process is amenable to animal studies, which is great because we are getting really good at multi-electrode recording in the rat hippocampus and gaining lots of insight into place cells, which may provide the spatial context for remembered events to happen in. Which brings up an interesting question: Do you ever remember an event without remembering where you were during that event? Or does the term "event" imply a spatial setting?

Vivien Leigh Again   posted by DavidB @ 9/08/2006 04:59:00 AM

There are more interesting things about Vivien Leigh than whether or not she was Anglo-Indian [see Note on terminology], but I have now consulted a few biographies, so I will summarise the evidence.

The biographies I have seen are by Anne Edwards (1977), Alexander Walker (1987), and Hugo Vickers (1988).

First, it should be explained that Vivien's original name was Vivian [sic] Hartley. Her father was an Englishman named Ernest Hartley, of well-documented Yorkshire stock.

The uncertainty is on the maternal side. Vivien's mother's Christian names were Gertrude Mary, but this is about the only undisputed thing about her. Her family name is given variously as Yackjee, Yackje, and Yackje with an acute accent on the 'e'. There are also three versions of her birthplace. According to Anne Edwards, she was born in Ireland (version 1) and educated in an Irish convent school. According to Hugo Vickers 'it has been invariably stated that Ernest's wife, Gertrude Yackjee, was also born in Yorkshire' (version 2). Vickers's term 'invariably' is incorrect, because we have just seen that an earlier biographer (Edwards) gives a different version. In any event, Vickers goes on to say that the 'Yorkshire' version is also false, because 'Gertrude's passport reveals that she was born in Darjeeling (version 3) on 5 December 1888'.

Where Gertrude's ancestry is concerned, the 'official' claim of part-French ancestry appears to be fictitious. Vickers says:

Due to the mythomania of Hollywood producers and others, a number of conflicting stories have grown up about the origins of Vivien's parents. Just before the shooting of Gone with the Wind, for example, David O. Selznick informed Ed Sullivan: 'Scarlett O'Hara's parents were French and Irish. Identically, Miss Leigh's parents are French and Irish'.

In fact, there is no evidence of any French ancestry. Gertrude did however probably have some Irish ancestry. Anne Edwards claimed that Gertrude was wholly Irish - born and raised in Ireland. This is probably false, but the fact that her family was Roman Catholic, and their choice of Christian names like Gertrude and Mary, does suggest an Irish connection. According to Vickers, there is a story in the family that Gertrude's maternal grandparents, named Robinson, came from Ireland to India to avoid social disapproval of their mixed marriage (one was Catholic and the other Protestant), but they were killed in the Indian Mutiny of 1857. Their daughter (Gertrude's mother) was left in an orphanage and cared for by nuns. While she was in the orphanage she was seen by Michael John Yackjee, 'a man of independent means', who 'decided to make her his bride', married her, and had a large family. This all has a fairy-tale ring to it, but stranger things have happened. Gertrude is described as having auburn hair and blue eyes, so she must at least have had a substantial proportion of European ancestry.

There have however been persistent rumours of something more exotic. According to Alexander Walker, 'some of the close friends Vivian made in her schooldays felt that the child's great beauty confirmed what they had heard about her mother being part-Indian by birth'. On the other hand, Vickers says that 'most who recall the Hartleys in India remember that Mrs Hartley had Armenian blood, believing that this explained Vivien's dark Eastern beauty'.

Vickers goes on to record an interesting discussion with the writer Xan (Alexander) Fielding. Fielding is the grandson of Mary Yackjee, Gertrude's sister, who married an Englishman named Percival Fielmann (later changed to Fielding). According to Vickers,

To this day he [Xan Fielding] is uncertain of his grandmother's origins, but he believes they might have been half-caste Parsi Indian. One of his aunts, Orlene, was very dark, and both Gertrude and Vivien had tight hair which crinkled easily. If the half-caste theory is true, it explains why so little information has been forthcoming. Both the pure Indians and the British in India looked down on the half-castes. Thus, such origins were invariably disguised. The name Yackjee was sometimes changed to Yackje [with an accent], or they used the inherited maternal name of Robinson, though this does not appear on Gertrude's marriage certificate.

The claim of social prejudice is borne out by anecdotes about Ernest Hartley's relationship with Gertrude. At one point when a friend asked him who was the girl (Gertrude) in the front seat of his car, he replied evasively 'It's the chauffeur's sister'. (But perhaps she really was?) When Ernest announced that he wanted to marry Gertrude his friends told him he must expect social ostracism in the British community of Calcutta, and he was required to resign from his exclusive clubs, though he and the charming Gertrude later regained social acceptance. The reaction of the British community does at least suggest that Gertrude was suspected of being 'half-caste'. (It is interesting, by the way, that Hugo Vickers could use the now-verboten term 'half-caste' as late as 1988.)

None of this is conclusive evidence. The book by Vickers is by far the most thorough and well-researched, and has an impressive list of sources, including close family members. But even Vickers does not seem to have explored the family background in India; quite reasonably, as it was only peripheral to his subject. From internet sources it appears that a more recent author (Gloria Moore) claims to have definite knowledge of Vivien's part-Indian ancestry, but I do not know whether this would stand up to investigation. The biggest puzzle is the origins of Michael John Yackjee. The name, in any of its versions, is not British or Irish - at least, I did not find a single Yackjee in online British telephone directories. In a general internet search for the name Yackjee, the only examples are from Bengal, but it must be uncommon even there. Nor does it look Armenian, as most echt-Armenian names end in -ian or -yan (e.g. Gulbenkian, Petrosian, Egoyan). I leave the puzzle for our intrepid and cosmopolitan readers to solve.

Note on terminology
The term 'Anglo-Indian' usually refers to someone from a community of mixed British or Irish and Indian ancestry. In the 19th century it was common for the lower ranks of the British military and commercial classes in India to marry Indian women, who would convert to Christianity (Catholic or Protestant). Their offspring could not easily marry either British or Indian partners, and therefore became a distinct endogamous community, with occupations mainly in the railways and public services. Anglo-Indians in this sense should be distinguished from the offspring of mixed Anglo-Indian marriages in Britain today. There is also an older usage of 'Anglo-Indian', used to describe the higher levels of British society in India under the Raj. In this sense the term is analogous to 'Anglo-Irish', and does not imply any Indian ancestry. Intermarriage at the higher levels of society was rare after the 18th century. This old usage can cause misunderstanding when people like Rudyard Kipling or Augustus De Morgan, whose ancestry was entirely European, are described as 'Anglo-Indian'. There are also people of mixed Indian-European ancestry where the European side is not predominantly British or Irish - e.g. French, Portuguese, or Dutch. Intermarriage would produce all kinds of complicated mixtures. 'Eurasian' would be a better term than Anglo-Indian in these cases.

Visitor loyalty   posted by Razib @ 9/08/2006 12:32:00 AM

Despite what sitemeter says I have always held that the genuine/core audience of GNXP is around 300-500 individuals. I judge from poll responses, which always seem to peak around 300. But check this graph out from GOOGLE ANALYTICS, which I've had on this site since late March....

Thursday, September 07, 2006

The game   posted by Razib @ 9/07/2006 10:16:00 PM

Ed Brayton points me to this summation by Jonothan Rowe of the position that America the nation was not founded as a "Christian nation" as understood by many evangelicals. Rowe links to this article in a Christian magazine which makes that case Thomas Jefferson was not an "orthodox" Christian as conservative Protestants would understand the term. I am not an expert in this area, but I have read enough of Jefferson's correspondence and biographies to be skeptical that the man would have affirmed the Nicene Creed, which seems a necessary condition for claiming him as an orthodox Christian, but I have seen fundamentalists assert exactly this. Of course, there is a flip side, I have met atheists who deny that Constantine was genuinely a Christian, after all, he sanctioned the depiction of Sol Invictus on coins after his reputed conversion and held pagan priestly offices. The argument is that Constantine was an opportunist who never believed in Christianity, and the faith's rise was simply a Machiavellian ploy. But the sum totality of the historical record would seem to suggest that Constantine did believe himself to be a Christian, and would be recognized as such by Christians today (with allowances made for the fact that the Nicene Creed was obviously not formulated until near the end of his life and that deathbed baptism was not uncommon during this period).

The point is that the furthering of knowledge is a hard slog, a noisy process which takes 9 steps back for every 10 steps forward. One of the the main issues is to guard against the creeping advance of error in the service of ideology. Creationism is one such error. The leap from Athenian Greece to modern democracy, and glossing over republican & imperial Rome, Christianity and the medieval period, is another such error. Natural science has the world around us to keep us honest, but the human sciences relies upon our own good will, sincerity and due diligence. Let's not be stupid.

Foxp2 and genomic imprinting   posted by Razib @ 9/07/2006 01:04:00 AM

The American Journal of Human Genetics has a new preprint up that tentatively suggests that there is a parental specific genomic imprinting associated with FOXP2. I've put up the PDF as "foxp2.pdf" in the GNXP Forum. In short, it seems that the paternal copy might be overexpressed relative to the maternal copy. Anyone care to offer an explanation for why the male copy (which would presumably be less genetically close to the other male copies in a sib-cohort) might want FOXP2 overexpressed relative to the female copy?

Wednesday, September 06, 2006

Brown or not?   posted by Razib @ 9/06/2006 08:20:00 PM

Was Vivien Leigh brown? Below David B., our resident Briton, claimed that Ms. Leigh was a product of miscegenation. After cursory examination of the various facts I would bet she was not of mixed ancestry, though I suspect that the data here will always be thin on the ground (I think it best to judge that her character was white, so to speak, on this issue and allow that her claims about her ancestry were the naked and plain truth). Below the fold are some images and a poll, you vote, you decide, Europa's own raven beauty or seed of cross-color copulation? (Leigh was born in the darkest heathen India in the age before cosmetic surgery, low mutational load I do believe I spy in that face....)

Hot, yes, but brown or not?
Vivien Leigh has a touch of brown
No brown is she
Free polls from

...on a related matter,

Lower mutational load than Keira Knightley?
Hell yes! That bitch made it through the pathogenic bath of India!
Hell no! Knightley's stomach is quite fit.
Free polls from

Fisher-Wright controversy   posted by Razib @ 9/06/2006 07:38:00 PM

Rob Skipper has completed his 3 part series on the Newton-Leibniz controversy (with a bit less acrimony I would think) of evolutionary genetics in the mid-20th century, Whatever Happened to the Fisher-Wright Controversy?, Whatever Happened to the Fisher-Wright Controversy? Redux and Whatever Happened to the Fisher-Wright Controversy? Final (with footnotes).

Interracial Beauties   posted by DavidB @ 9/06/2006 12:34:00 AM

I see that Gone With the Wind actress Vivien Leigh has been voted Britain's most beautiful woman of all time.

I don't put much trust in these absurd polls (who voted? how were they chosen? were they given a list of candidates?), but just to annoy certain people I will point out that Vivien Leigh (born in Darjeeling) is generally reputed to have been Anglo-Indian - that is, of mixed British-Irish and Indian ancestry. It should be mentioned that she always denied this, attributing her dark looks to some improbable European source on her mother's side, but in those days such cover-ups were routine.

Added: I said above that Vivien is 'generally reputed' to have been Anglo-Indian. This was evidently overstating the matter. She is included on some lists of prominent Anglo-Indians, but such lists may tend to claim people as Anglo-Indian on slender or unreliable evidence. The 'official' version of Vivien's ancestry, as recorded for example on IMDB and Wiki, is that her maternal ancestry was French and Irish, and many of her admirers (fan clubs, etc) accept this as true. Her mother's family name - spelled variously as Yackje or Yackjee - does not appear to be either French or Irish, but it may well be a corrruption of some more common name. I apologise for using the word 'cover-up' in such a way as to imply that Vivien's own account was false. I was just trying to make the point that, at that time, there was strong prejudice against mixed race people, and that 'cover stories' were in fact common. They might even be insisted on by the movie studios. Reflect for the moment on the likelihood that an openly Anglo-Indian actress would have got the role of Scarlett O'Hara.

I do not claim to know the truth of the matter. I will probably look up a few biographies and see what they say.

Monday, September 04, 2006

Mendel's Garden #5   posted by Razib @ 9/04/2006 11:41:00 PM

Mendel's Garden #5 hosted by RPM of Evolgen.

Nanotechnology   posted by Fly @ 9/04/2006 10:17:00 AM

Productive Nanosystems

First molecular biology and now nanotechnology.

Stereotype Fret   posted by agnostic @ 9/04/2006 09:49:00 AM

There's something of a buzz in the blogosphere (and probably more so if you give it a few days) about an article in the September issue of Science which purports to show that a social psychological intervention narrowed the Black-White race gap in academic performance. Specifically, the authors claim that having Black students write a brief (15-minute) essay on which values matter to them and why (e.g., friends and family because they provide support in hard times) can counteract Stereotype Threat (ST), thereby boosting their academic performance compared to Black students who are not so shielded. Before getting into the nitty-gritty of the article, though, a few words are in order on ST. First, psychologists have already pointed out that it is a non-starter for explaining the Black-White IQ gap: while being told that a task is an IQ test lowers performance among Black subjects on average (by hypothesis, because it induces greater stress), absence of this threat does not eliminate the Black-White IQ gap, which remains the same. Think of the effect of anti-depressant drugs -- to the extent that they work at all, they bring the person to their "true" happiness level, rather than transform them into sprightly, sanguine souls.

Sunday, September 03, 2006

Hypocrisy   posted by Razib @ 9/03/2006 12:42:00 AM

Like many people I'm not a big fan of hypocrites. Why should you believe in what someone says if they don't practice what they preach? Yet the other day I had a passing thought.

Assume you have a person who

a) has a "must eat" module which is always in hyperdrive
b) but also knows rationally that overeating is bad

On the one hand, the reflective & rational conscious mind knows quite well that gorging is bad, but other mental processes don't get the picture. If one takes a unitary view of the mind one would say that someone who says eating too much is bad and perhaps even supports legislation which would discourage overeating, and yet ate a great deal all the same, is a hypocrite. Perhaps they're trying o display their virtue, or monopolize all the food for themselves. Who knows? There has to be a rational reason why they engage in contradictory speech, belief and behavior.

And yet if we accept a modular mind we see that the reasons might not be that rational at all. Certainly nothing is black and white, modularity can have different levels of encapsulation, and if you plan ahead you can make sure you are out of the choice "danger zone." But, I suppose from now on I'll be willing to give hypocrites a bit more slack, or at least not dismiss their arguments prima facie, their conscious mind might be on the right track even if their credibility is undermined by their lack of impulse control in other contexts.

One Arab contribution   posted by Razib @ 9/03/2006 12:17:00 AM

In What Went Wrong?, Bernard Lewis muses over the shocking lack of cultural productivity of the Arab world of late. Below the fold, one undisputed example of Arab cultural productivy....

Shakira is a bad influence on brown chix.

Saturday, September 02, 2006

Animation for biology education   posted by Fly @ 9/02/2006 01:51:00 PM

Cellular Visions: The Inner Life of a Cell

This animation demo shows how biology may be taught in the near future.


"In some instances, that meant sacrificing literal accuracy for visual effect. What we did in some cases, with the full support of the Harvard team, was subtly change the way things work," Liebler says. "The reality is that all that stuff that's going on in each cell is so tightly packed together that if we were to put every detail into every shot, you wouldn't be able to see the forest for the trees or know what you were even looking at. One of the most common things we did, then, was to strip it apart and add space where there isn't really that much space."

There isn't a soundtrack to explain what you are seeing and the animation sequences jump too much for teaching. However, if you know some microbiology you can recognize much of what is being shown.

Obesity & IVF   posted by Razib @ 9/02/2006 11:22:00 AM

Shellee of Retrospectacle has a long post on the obesity & IVF issue. A point that we should all keep in mind:

While it may be discrimination in a pay-for-treatment health care system, socialized health care has not only the right but (I believe) the mandate to administer that care in a financially- and health-conscious way.

Admin question   posted by Razib @ 9/02/2006 10:03:00 AM

Anyone find this blog through ScienceBlogs? Post in comments.


Finland & Himmler's scholars   posted by Razib @ 9/02/2006 01:06:00 AM

In The Master Plan: Himmler's Scholars and the Holocaust the author claims that:

  • The attempts by a Finnish anthropologist to assert that the Finns were an "Aryan" people was greeted with some hostility from his colleagues. There was a reference to Finns having their own ideas, but the footnote wasn't clear and I don't have time to track it down (and the cite is clear a German language publication). But, I wonder if part of the issue might be what Jaakkeli has spoken of in regards to Finnish ideas of hybrid vigor

  • He filmed Karelian illiterate magicians and witches and recorded their "spells." It would be interesting to see this footage as the-European-as-primitive-savage would be a novelty.

  • One argument for the Finns' Mongoloid/Asian origins was that their reserved and taciturn character was more Asiatic than European.

Friday, September 01, 2006

Race & conservatism   posted by Razib @ 9/01/2006 08:17:00 PM

John Derbyshire has a new piece, Race & conservatism, in the New English Review. You can comment here. Also, check out Derb's Montana diary.