Saturday, October 31, 2009

Andrew Gelman's "Applied Statistics"   posted by Razib @ 10/31/2009 05:01:00 PM

Andrew Gelman has started a new blog at ScienceBlogs, Applied Statistics. Someone should design him a header, perhaps a fancified Bayes' theorem?


Social cycles in history due to cognitive differences   posted by Razib @ 10/31/2009 03:11:00 PM

Steve points me to this Jason Richwine piece, Are Liberals Smarter Than Conservatives?. Richwine states:
Religion would seem to be the clear choice of smart people in this hypothetical example, but there would still be a positive correlation between IQ and atheism. The correlation exists not because smart people have necessarily rejected religion, but because religion is the "default" position for most of our society.

This same principle works in places where the default and iconoclastic beliefs are reversed. Japan, for example, has no tradition of monotheistic religion, but the few Japanese Christians tend to be much more educated than non-Christians in Japan. By the logic of someone who wants to read a lot into the Stankov study, Christianity must be the wave of the future, perhaps even the one true faith! But, of course, the vast majority of educated Japanese are not Christians. Just as with atheism in the West, the correctness of Christianity cannot be inferred from the traits of the minority who subscribe to it in Japan.

On the specific issue Richwine is right, Christianity is associated with higher socioeconomic status vis-a-vis non-Christianity across much of East Asia. You can go look in the WVS or Statistics Singapore. Though I do have to note that only in South Korea does there seem to be a positive correlation between theism and socioeconomic status (e.g., in Singapore those with no religion and Christians both have high SES and tend to be concentrated among young professional class Chinese, those with lower SES tend to be Muslims [Malays] and followers of Chinese folk religions). Additionally, in Taiwan, South Korea and Singapore it seems that Buddhism has reworked itself to mimic the aspects of Christianity which made it more appealing to middle-class professionals. This is a classic case of a new equilibrium being attained after the initial outside cultural "shock" of Christianity. Finally, in Japan Christians are basically a rounding error (a few percent at most), so the example of Korea, where they are 1/3 of the population is of more relevance.

But I was struck by a general implication from Richwine's model. Two premises:

1) Elites, cognitive or otherwise, tend to deviate from the "default" norms of society for various reasons (it could be signalling costly behavior to show that they are "above" conventional considerations and such).

2) Eventually, the masses often emulate in the elites in subsequent generations.

The inference would be that cultural cycles should exhibit a pattern where the masses serve as lagging indicators of elite sensibilities. Once the masses start attempting to "catch up," of course the elites have moved on. Empirically implausible? I'll let readers dissect it.


Friday, October 30, 2009

Names frequency changes not always stochastic   posted by Razib @ 10/30/2009 11:15:00 AM

Turns out some names do become popular because of celebrities. Though I guess in the "big picture" the names celebrities have is going to be random. (via Andrew Gelman)

"Ancestral North Indians", Europeans and pigment   posted by Razib @ 10/30/2009 12:15:00 AM

Something that has been nagging me about the recent paper by Reich et al. which models Indian populations as a hybridization event between two ancestral groups, "Ancestral South Indians" (ASI) and "Ancestral North Indians" (ANI). As a reminder, the ANI seem to have been rather like Europeans in their allele frequencies, or at least far closer to Europeans than they were to the ASI (it seems that they compared ANI with Western Europeans). This is interesting. They found in the populations surveyed that the low bound for ANI was 40%, the high ~80% (in the supplements they included some Pathans and Sindhis from the HGDP, and that's where that number comes from). The ~40% low bound for ANI rather surprised me. The populations which they sampled included South Indian tribal groups. In other words, these were the groups arguably least affected by what we term Hinduism and Indian culture (their status as "tribals" as opposed to lower caste or outcaste was generally a function of the fact that they rejected integration and assimilation into mainstream Indian culture and isolated themselves both geographically and in terms of their customs). Just seems weird that these groups would be so ANI.

For a few weeks now Greg Cochran has been asking if I saw something in the paper above about when the admixture between ANI and ASI occurred, or at least if there was a hint about when the authors think it occurred. I said no, there are only hints. I was wrong, I skimmed over the supplement too quickly, they assume 200 generations ago as a parameter in a model they use for simulations. Bingo. Just click the image to the left, and look at the lower right. 200 generations = 5,000 years ago, assuming 25 years for generation time. Let's assume that a South Indian tribal group is a small deme of ASI surrounded by a very large (infinite) deme of ANI for 200 generations. If I assume a constant outmarriage rate of 0.25% per generation (1 out of 400) then at the present time you'd have the tribal group being ~40% ANI.

OK, what about my idea which I presented to John Hawks that Indians "don't really look" like a hybridization between Northern Europeans and the ASI, ASI assumed to be similar to the Andaman Islanders (who I do not believe were necessarily "Negritos," insofar as I suspect their small stature is due to contact with Europeans and Indians, as those who have avoided such contact are seen to be of normal or even above average size for South Asians). Specifically the frequency of light eyes and hair is just way too low among groups which are on the 70-80% ANI range such as Punjabis and Kashmiris, though these groups do tend have more Caucasoid features and lighter (olive) skin. On the other hand, here is something which jumped out at me about the Reich et al. paper: they added two Pakistani populations who fit well in the ANI-ASI cline which most of the Indian groups mapped onto (some groups with "Eastern" origin in both Pakistan and India were discarded from the analysis), and their ANI frequency proportions seemed familiar to me. There are three ANI estimates for both groups:

Sindhi - 78%, 70.7%, 73.7% (78%)
Pathan - 81%, 74.2%, 76.9% (81%)

In the parenthesis is the frequency for the derived (European-like) variant of SLC24A5. The data sets were the same, from the HGDP, though the ancestry estimates used only 10 and 15 of the approximately 50 of each group respectively. There's a suspicious correspondence here. The lowest frequency of the derived variant of SLC24A5 I've seen for a South Asian population is ~30% for Sri Lankan Tamils, with ~50% for Sri Lankan Sinhalese. Remember that a reasonable low bound for ANI for South Asian groups is on the order of 40%.

But what about my contention that other European-like pigmentation alleles don't fit because the phenotype isn't what you'd expect. You can look at a blue vs. brown eye variant of OCA2 in the HGDP. Another eye color variant, HERC2. And here is a variant of TYR which causes light skin. The interesting point would be to look at the Indian samples, but I don't have really good proxies for that (in one paper which surveyed Indian Americans various language groups ranged from 70-100% in derived SLC24A5 frequency, but it is very difficult to imagine that these correspond well to many groups in the Reich paper. Specifically, it's biased toward higher status/caste groups). I might have spoken too soon, though it still seems to me that something is off. Perhaps Europeans changed after ANI left. Or perhaps ANI changed when it arrived in India. One recent data point which I find curious is that a paper just came out which suggests that populations of the Andronovo culture in Trans-Siberia, which is assumed to be the precursor to the Indo-Iranians, seem to resemble modern day Russians in pigment phenotype. At least judging from the genes extracted and sequenced.

More later when my thoughts become more settled.

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Thursday, October 29, 2009

Center-Right world?   posted by Razib @ 10/29/2009 03:49:00 PM

One of the persistent structural issues with American politics is that a greater number of Americans self-identity as conservative than liberal, so the Republican party can be dominated by conservatives in a manner in which the Democratic party can not. This is not to speak to whether people are in substance more conservative or not, rather, I'm still addressing self-perception. You can see the trend over the past 30 years from the GSS in the United States:

I was curious as to whether this bias is an international phenomenon. There is a question in the WVS which asks: 'In political matters, people talk of "the left" and "the right." How would you place your views on this scale, generally speaking?' The scale goes from 1, which is furthest Left, to 10, which is furthest Right. I looked at the WVS 3, 4 and 5 (a span from the mid-1990s to the late 2000s). Here is a histogram generated from the median values of all the nations (some replicated across waves):

As you can see, the central tendency just a bit to the Center-Right. The median value in the data set is 5.6 (standard deviation 0.68). No idea if this means anything, but I did wonder if sometimes there's a human cognitive bias to perceive oneself as "conservative" because of risk-aversion, but these results don't seem to be very strong (I'm sure some of the results, such as Vietnam, are due some strange quirks of phrasing which didn't translate well). Here's a table of the data points....

Country Mean Political 
Zimbabwe 3.7
India 4.4
Egypt 4.5
Spain 4.6
Andorra 4.6
Burkina Faso 4.7
Germany 4.7
Spain 4.7
France 4.8
Bulgaria 4.8
Iran (Islamic Republic of) 4.8
Germany 4.8
Spain 4.8
Serbia and Montenegro 4.8
Iraq 4.9
France 4.9
Russian Federation 4.9
Russian Federation 4.9
Slovenia 5
Republic of Moldova 5
Italy 5.1
Bosnia and Herzegovina 5.1
Greece 5.1
Hungary 5.1
Israel 5.1
Netherlands 5.1
Slovakia 5.1
Great Britain 5.1
Albania 5.1
Bosnia and Herzegovina 5.1
Hungary 5.1
Macedonia, Republic of 5.1
Netherlands 5.2
Switzerland 5.2
Uruguay 5.2
Chile 5.2
Germany 5.2
Macedonia, Republic of 5.2
Serbia and Montenegro 5.2
Croatia 5.2
Republic of Korea 5.2
Slovenia 5.2
South Africa 5.2
Great Britain 5.3
Slovenia 5.3
Cyprus 5.3
Albania 5.3
Belgium 5.3
Croatia 5.3
Portugal 5.3
Sweden 5.3
Australia 5.3
Belarus 5.3
Romania 5.3
Slovakia 5.3
Sweden 5.3
Switzerland 5.3
Ukraine 5.3
Brazil 5.4
Chile 5.4
Mali 5.4
Austria 5.4
Italy 5.4
Republic of Korea 5.4
Lithuania 5.4
Luxembourg 5.4
Poland 5.4
Armenia 5.4
Chile 5.4
Estonia 5.4
Latvia 5.4
Canada 5.5
Japan 5.5
Canada 5.5
Denmark 5.5
Nigeria 5.5
Uganda 5.5
Ukraine 5.5
Azerbaijan 5.5
Australia 5.6
Norway 5.6
Sweden 5.6
Finland 5.6
Ukraine 5.6
Rwanda 5.6
Ireland 5.6
Republic of Moldova 5.6
Northern Ireland 5.6
Finland 5.6
Nigeria 5.6
Norway 5.6
United States 5.7
Argentina 5.7
Peru 5.7
New Zealand 5.7
Morocco 5.7
Jordan 5.7
Belarus 5.7
India 5.7
Japan 5.7
Peru 5.7
South Africa 5.7
Argentina 5.7
Mexico 5.7
Poland 5.7
Uruguay 5.7
South Korea 5.8
Bulgaria 5.8
Finland 5.8
Iceland 5.8
Latvia 5.8
Malta 5.8
Romania 5.8
Turkey 5.8
United States 5.8
Bulgaria 5.8
Lithuania 5.8
New Zealand 5.8
Peru 5.8
United States 5.8
Poland 5.9
Serbia 5.9
Guatemala 5.9
Estonia 5.9
Jordan 5.9
Morocco 5.9
Pakistan 5.9
Brazil 5.9
Czech Republic 5.9
Georgia 5.9
Japan 5.9
Romania 6
Taiwan 6
Moldova 6
Georgia 6
Argentina 6
Czech Republic 6
Trinidad and Tobago 6.1
Philippines 6.1
Turkey 6.1
Mexico 6.2
Turkey 6.2
Thailand 6.2
Algeria 6.2
Kyrgyzstan 6.2
Venezuela 6.3
El Salvador 6.3
Hong Kong 6.4
Philippines 6.4
Ghana 6.5
Indonesia 6.6
Ethiopia 6.6
Indonesia 6.6
Puerto Rico 6.6
Taiwan Province of China 6.6
Colombia 6.6
Dominican Republic 6.6
India 6.6
South Africa 6.7
Zambia 6.7
Mexico 6.7
Puerto Rico 6.7
Venezuela 6.7
Colombia 6.8
Tanzania, United Republic Of 6.8
Bangladesh 7
Bangladesh 7.6
Viet Nam 9
Viet Nam 9.1

Note: The scale on the question is 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10. So 1-5 would be on the Left side, and 6-10 on the Right.


Wednesday, October 28, 2009

Germs, collectivism and serotonin   posted by Razib @ 10/28/2009 01:38:00 PM

Culture-gene coevolution of individualism-collectivism and the serotonin transporter gene:
Culture-gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism-collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture-gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism–collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture-gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism-collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture-gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed.

Here's what I see going on:

High pre-modern pathogen load → collectivist values → S allele & dampening of psychological responses associated with S allele in populations where it is extant at lower frequencies.

It's Open Access so you can look at their regressions yourself. The association with pre-modern levels of pathogens is a strong point for me, these sorts of biological factors would result in a consistent "push" over long periods of times which culture itself might not have. The agricultural civilizations of Asia were always going to be rich ecologies for infectious diseases. So it would be interesting to look at the frequencies of the S & L alleles on a finer scale; for example, in the islands of Japan. Though that case I suspect that lower-density areas would have had so much migration that selection wouldn't have time to maintain different allele frequencies.


Many nations are getting more religious, but young people are still less religious   posted by Razib @ 10/28/2009 12:13:00 AM

One thing that has bothered me, or at least piqued my interest, are two seemingly contradictory facts:

1) Many regions & nations have seen a resurgence of religion in the past generation (i.e., 1980s to 2010). The post-Communist and Islamic world most prominently. There is quantitative data for the post-Communist world, while for the Islamic world it is more impressionistic (e.g., the shift toward more stark outward "conservatism" in dress among the young).

2) But The World Values Survey does not show a skew toward religiosity among the young for most nations. Very few in fact. This is a bit curious in light of some plausible background assumptions. For example, religious people have more children the world over within each nation (though religiosity at the national level may have a more unpredictable relationship to fertility, as evident in Western Europe).

I decided to present the data which I'm basing the second assertion on. The WVS has several "waves." I decided to look at wave 5, wave 4 and wave 2, which were done during the mid to late 2000s, around 2000 and 1990 respectively. I also looked at the question:
How important is God in your life? Please use this scale to indicate- 10 means very important and 1 means not at all important.

The WVS interface outputs mean values (as well as standard deviations). You can then drill-down and cross with age of the respondents in 3 classes:, 15-29, 30-49, and 50+. I was curious as to age related changes, so I simply put the mean values of the importance of God by age class into the linest function. So, if the mean values were 7, 8 and 9 for the age classes from youngest to oldest, the linest would output a slope of 1 as I omitted x values (so the classes would be recoded implicitly as 1, 2, 3, etc. for x's). If you reversed it, it would output -1. So, negative values indicate that the younger are more religious than the old. Here are some trends in the data.....

Here are some charts ordered by the values generated by linest by wave. The countries at the top exhibit larger differences between the young and old. Observe the large asymmetry in the number with positive vs. negative values (that is, many more nations have more secular young than old). You need to click to see the larger version.

Some of the nations span the waves (many do not). 30 nations span wave 5 and wave 4. Here are the correlations between the same columns across waves:

Mean religiosity = 0.98
Trend of religiosity by age = 0.84

I don't know if the samples are representative (though the developed world ones do seem to be, I've checked with independent surveys and they often match up well), but the two waves seem consistent with each other here.

Now let's compare wave 2 and wave 5. So from from ~1990- to ~2005.

Mean religiosity = 0.92
Trend of religiosity by age = 0.77

How about differences in mean religiosity from wave 2 to wave 5? Here we see a bias toward greater religiosity in the 26 countries found in both waves.

The results match expectation. The nations to the right, those which have seen the most increase in religiosity are post-Communist ones. No surprise there. The nation furthest to the left is Spain, it's gone through the most striking shift toward secularism since 1990. That is in line with what the news reports, the position of the Catholic Church at the center of Spanish life has been collapsing since the 1980s (more accurately, since the end of the Franco regime).

One assumes that the difference in religiosity by age cohort is a feature of less religious societies. If everyone is religious, as is the case in some Muslim and African countries, then there can't be any variance. Merging all 3 waves together, here's a scatter plot which shows the trend:

Now a labelled plot of wave 5.

An interesting point of contrast is China and Spain. In the 1970s Spain was still a pro-clerical right-wing authoritarian regime, while China was an atheist left-wing regime. Political pressures toward conforming to a particular attitude toward religion have abated in both nations over the past generation, and while Spain has become much more secular, China seems to more religious. The mean value of the importance of God in one's life in China is 3.7 in the youngest age group, and 3.5 in the oldest (survey taken in 2007). In 1990 it was 1.5 and 1.8 respectively.

The big test would be to see how the 15-29 compared to 30-49 between wave 2 and wave 5. I'm a little worn out by this right now, so I'll look at that systematically tomorrow (or the next day), but spot checking Russia seems to show that the rank-order holds, but all age cohorts became more religious (not relevant for the youngest cohort in wave 5 because they weren't surveyed in 1990). In Spain the 15-29 year olds in wave 2 who became 30-49 year olds in wave 5 are invariant. If you want to get a jump ahead of me, here are some raw data file (excel):




Here are two preliminary comments:

* All the post-Communist nations have seen a resurgence in religion (perhaps with the exception of the Czech Republic). But this is a phenomenon which has "lifted all boats," older people who were militant atheists who went on anti-religious rampages in their youth have been swept along, just as generations who barely remember Communism exhibit the nominal culturally grounded religious sensibilities normal in many societies. I've read a fair number of news stories over the years about the generational "God-gap" in the post-Communist states, but I suspect that it makes a punchier story-line than to suggest that there's been a broader societal shift. That it isn't a case of atheistic pensioners vs. youthful churchgoers.

* The Muslim countries are really weird. On most of the religious data in the WVS the only nations which approach or surpass them consistently are the African ones, and these do not exhibit the uniformity of outlook of the Muslim ones, especially the "core" Muslim nations of the Middle East. In some of the surveys for Pakistan no Pakistanis in a sample of 2,000 will admit to not believing in God, and in one survey all the respondents gave the highest value for the importance of God in their life on a 1 to 10 scale. By all, I mean all 2,000. It isn't implausible to me that somehow someone who was really religious just recoded the survey data to make Pakistan seem more religious than it was, but if so that bespeaks a zealous conformity of outlook in the society. But overall many of the Muslim nations are so religious that there isn't variation in belief by age group because there isn't variation much of belief, period. Everyone's on the same page. When you see women donning the hijab or men growing beards I think perhaps we should reconceptualize what's going on, as it isn't renewed orthodoxy (belief) as opposed to a change in orthopraxy. Of course it may be that Muslim nations do exhibit variation in religiosity, but they're just off the scale here. I suspect of the funniest shock-documentary projects would be to have someone run into a public square in the Muslim world screaming that God is dead. Of course, it might be a suicide mission!

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Tuesday, October 27, 2009

What Darwin Said: Part 7 - Levels of Selection   posted by DavidB @ 10/27/2009 05:43:00 AM

This is the seventh and last in a series of posts about Charles Darwin's view of evolution. Previous posts were:

1: The Pattern of Evolution.
2: Mechanisms of Evolution.
3: Heredity.
4: Speciation
5. Gradualism (A) , which dealt with Darwin's views on gradualism in the rate of evolutionary change.
6. Gradualism (B), about the size of the mutations adopted by natural selection.

This final post deals with Darwin's views on the levels of selection in evolution. Does selection occur mainly between genes, individuals, families, groups, species, or what? In the modern debate on levels of selection, Darwin has been quoted in support by both sides: those who accept, and those who reject, a major role for selection above the level of the individual organism.

Unless otherwise stated, all page references are to Charles Darwin: The Origin of Species: a Variorum Text, edited by Morse Peckham, 1959, reprinted 2006.

This post will be (relatively) brief, because there is already an excellent detailed study [Ruse] which I have little to add to.

Darwin's position on levels of selection can be summarised in four points:

1. His formulation of the process of natural selection is expressed almost entirely in terms of selection among individuals, based on what he calls 'individual differences'. In this respect he differs from Wallace, who referred mainly to selection between 'varieties'. It has recently been argued that Wallace (in 1858) did not quite 'get' the idea of natural selection after all. Be that as it may, Wallace was always more welcoming than Darwin to what we would now call group selection.

2. Darwin gave no autonomous role to selection between species or varieties. In so far as he did mention selection at these levels, it was as a by-product of selection at lower levels. For example, if a newly introduced species displaces an indigenous one, it is because the individual organisms of the first species are competitively superior to those of the second.

3. Darwin recognised the possibility that selection might operate on individuals indirectly, via the individual's relatives, as in the case of neuter insects. Thus he had the germ of the modern ideas of kin selection and inclusive fitness, but these were not fully developed until much later.

4. At a level between the family and the species, Darwin recognised a role for selection between social communities, notably among social insects and human 'tribes'. Most of the recent debate about Darwin's views on levels of selection has concerned the interpretation of this 'community selection'.

Darwin's most explicit statement on the issue in the Origin says in the first edition (with italics added):

Natural selection will modify the structure of the young in relation to the parent, and of the parent in relation to the young. In social animals it will adapt the structure of each individual for the benefit of the community; if each in consequence profits by the selected change [172]

In the fifth edition the word each is revised to this and in the sixth to the community. It has been suggested [Richards p.217] that these changes involve an important shift towards group selectionism. In the first edition, traits benefiting the community are only selected if they are also beneficial to the individual, but in the fifth and sixth editions such a trait can be selected if even if it is harmful to the individual. I agree that this is an important revision, but I think it is only stating as a general principle something that Darwin had already accepted in individual cases. He believed that the sterility of neuter insects had been selected for the good of the community [417]. Likewise, the sting of bees is useful to the community, and is selected for that reason, even though it kills the individual bee when it is used [374]. Since dying, or becoming sterile, are clearly against the interests of the individual, these examples were inconsistent with Darwin's original formulation, and his revisions may just have been a belated recognition of this.

If a trait is beneficial to the community, but harmful to the individual who possesses the trait (like the bee's sting), the question arises how such a trait can increase in frequency. In the case of the sterile classes of social insects Darwin saw fairly clearly that the solution was in the relatedness of the members of the colony:

This difficulty, though appearing insuperable, is lessened or, as I believe, disappears, when it is remembered that selection may be applied to the family, as well as to the individual, and may thus gain the desired end... Thus I believe it has been with social insects: a slight modification of structure, or instinct, correlated with the sterile condition of certain members of the community, has been advantageous to the community: consequently the fertile males and females of the same community flourished, and transmitted to their fertile offspring a tendency to produce sterile members having the same modification [416-17].

The same mechanism does not apply where individuals are not genetically related. In the fifth edition Darwin discussed the problem in the context of the sterility of hybrids:

With sterile insects we have reason to believe that modifications in their structure and fertility have been slowly accumulated by natural selection, from an advantage having been thus indirectly given to the community to which they belonged over other communities of the same species; but an individual animal not belonging to a social community, if rendered slightly sterile when crossed with some other variety, would not thus itself gain any advantage or indirectly give any advantage to the other individuals of the same variety, thus leading to their preservation [445]

Darwin concluded (contrary to the position of Wallace) that the sterility of hybrids, and the inter-sterility of different species, had not evolved directly by natural selection but as a by-product of other changes. Unfortunately in the sixth edition the quoted passage was omitted, as Darwin believed he had more convincing new evidence that the sterility had not been selected.

In the Descent of Man, Darwin returned to the issue in the context of the evolution of human morality. He believed that tribes containing 'a greater number of courageous, sympathetic, and faithful members' [Descent of Man, 1871, p.162] would succeed in competition against other tribes, but he saw a problem in explaining how such virtues could evolve within a tribe: 'But it may be asked, how within the limits of the same tribe did a large number of members first become endowed with these social and moral qualities, and how was the standard of excellence raised?' [163] He thought it was very unlikely that these qualities could be directly favoured by natural selection within a tribe. As a 'probable' solution, he suggested two important factors. One was what we now call 'reciprocal altruism', i.e. that a benefit might be provided in the expectation of a return benefit [163]. To complicate matters, Darwin believed that habitual behaviour, once acquired, could be transmitted by 'Lamarckian' inheritance [163-4]. The second, and more important, factor was 'the praise and blame of our fellow-men' [164]: 'it is hardly possible to exaggerate the importance during rude times of the love of praise and the dread of blame' [165]. Darwin does not explain how praise and blame are converted into individual fitness, but modern theorists have devised game theoretical models to handle these issues, which tend to confirm the importance of reputation. An individual who gains a reputation as a cheat or shirker will be excluded from the benefits of social life, with adverse effects on fitness.

Finally, Darwin returns to the point that tribes with many individuals possessing traits of courage, etc, 'would be victorious over most other tribes; and this would be natural selection' [166]. This passage is the main basis for the claim that Darwin became a 'group selectionist'. In a sense this is true, since it does give selection between groups (tribes) a role in promoting the spread of a trait. However, I do not think Darwin intends it as part of the solution to the question 'how within the limits of the same tribe did a large number of members first become endowed with these social and moral qualities'. If he did, the solution would clearly be invalid. The process of group selection envisaged by Darwin presupposes that some tribes already have 'many individuals' possessing the qualities in question. At best group selection has a role in reinforcing and extending the prevalence of altruistic traits which have first emerged within the tribes for other reasons.

The crucial problem for group selectionists has always been to explain how altruistic traits can become common within a group despite harming individual fitness. Darwin sidesteps the problem in this form, since his two suggested mechanisms (reciprocal altruism and 'praise and blame') in fact raise individual fitness, perhaps sufficiently to offset the loss of fitness. The problem of altruism still remains for those theories in which altruists suffer a net loss of individual fitness. If 'genes for altruism' are randomly distributed, and the benefits of altruism are simply proportional to the number of altruists in the group, then altruism will always be eliminated (apart from recurrent mutations) [Maynard Smith p.166]. A solution is however possible if either (a) genes for altruism are concentrated in some groups above chance levels, for example because close relatives tend to live near each other; or (b) the benefits of altruism are not simply proportional to the number of altruists. If chance concentrations of altruists gain disproportionate benefits, altruism can be selected despite its fitness detriment to those altruists who fall outside such concentrations. 'Synergistic' effects of this kind are quite plausible [Maynard Smith p.167], yet this solution to the problem has been strangely neglected.

Group selection of some kind is therefore possible, and it is an empirical matter to determine its prevalence and the mechanisms responsible in any particular case. Darwin did not solve the problem, but at least it may be said that he recognised it more clearly than any evolutionist before R. A. Fisher, and that he sketched out most of the possible solutions to the problem that have been explored more fully by his successors.

This post brings to an end my series of posts on 'What Darwin Said', which I regard as my contribution to 'Darwin Year'. I have not aimed to cover every aspect of Darwin's work, even in evolutionary theory - notably, I have not discussed sexual selection. I hope however that I have clarified Darwin's views on most of the issues that are still under serious debate. I have also tried to evaluate how far Darwin's views have stood the test of time. Overall, I think the answer is 'remarkably well', considering the extent of ignorance and false beliefs in Darwin's time on many key issues such as the nature of inheritance. But Darwin was not infallible, even with the evidence available to him, and it would be short-sighted to defend evolutionism in general by pretending (in the manner of diehard Marxists) that the Master was always right.

John Maynard Smith, Evolutionary Genetics, 1989.
Robert J. Richards, Darwin and the Emergence of Evolutionary Theories of Mind and Behavior, 1987.
Michael Ruse: 'Charles Darwin and Group Selection', Annals of Science, 37, 1980, 615-30, repr. in The Darwinian Paradigm, 1989.

Monday, October 26, 2009

The slob factor   posted by Razib @ 10/26/2009 11:01:00 PM

FuturePundit observes a phenomenon which might open up a possible avenue for nudge:
Clean rooms also increased willingness to volunteer and donate to charity.

That's just the sense of smell. We have other senses. What does room color do to us? Which color makes us most unfair? Red? Yellow? Is it the same color that makes us most cynical or most haughty? And what does the feeling of slime on one's hands do to one's disposition? Probably something similar to nasty smells is my guess.


Better genetics for living   posted by Razib @ 10/26/2009 10:29:00 PM

I'm really happy that Tomorrow's Table joined ScienceBlogs. 1) the blog has science, 2) its intersection with policy (food production) is pretty important.


The means of taxation   posted by Razib @ 10/26/2009 04:25:00 PM

Over at New Majority David Frum has a review up of Chris Wickham's The Inheritance of Rome: Illuminating the Dark Ages, 400-1000. Frum elaborates on one of Wickham's central theses about the nature of the fall of the Roman Empire, the shift from direct taxation to assignments of land (what eventually evolved into what we term 'feudalism'). Wickham's book has been discussed in detail on this weblog before, he works within a Marxist framework whereby impersonal social and economic forces loom large, so you won't get too much on battles as opposed to tax receipts.

But jumping forward in history 1,500 years I am struck by some of the same issues which crop up in the 18th century with the rise of the British Empire, and its ascendancy over continental powers such a France despite its smaller population (on the order of 1/3 France's population in the early 18th century I believe). The argument roughly runs that Britain constructed a military-financial complex, whereby it could utilize debt to finance its wars, while France was dependent on more conventional forms of direction taxation. This is a classic case of using leverage to beat an opponent which by all rights should have you outgunned on paper. The early American republic saw conflicts between those who wished to emulate the British state (Alexander Hamilton) and those who did not (Thomas Jefferson). We know who won that debate. In any case, it is important to remember that before 1800, and in particular before 1500, differences in per capita wealth between regions were trivial compared to what we see today. The most extreme differences in per capita wealth might be 50%, while something closer to 10-25% were much more typical. This is why Greg Clark asserts blithely that for almost all of human history per capita wealth remained approximately what it was when our species were all hunter-gatherers in Farewell to Alms. No, what was different between Rome and the "barbarian" lands beyond the limes had less to do with median differences in wealth, and more to do with how the wealth was allocated and leveraged. This is why, I think, nomad elites invariably invaded civilized states despite the likelihood that the average nomad was likely more affluent than the average peasant; civilized super-elites could extract much more surplus from their subjects than nomadic warlords could from their inferiors.

Addendum: One thing want to add, structural and institutional innovations often only result in a transient advantage. For example, both Tim Blanning and Peter Turchin point out that the most consistent predictive variable for victories during the wars which erupted in Europe after the French Revolution was the size of armies. The initial victories of the French were simply a function of the revolutionary state's putting many more men under arms, while most of the European monarchies stuck longer with smaller professional armies. Once other states caught up the French advantage disappeared. But despite the fact that the equilibrium was restored after a generation, I think we can admit that the transient was very important as a "hinge of history."

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Svante Paabo believes modern humans & Neandertals interbred   posted by Razib @ 10/26/2009 02:20:00 PM

Neanderthals 'had sex' with modern man:
Professor Svante Paabo, director of genetics at the renowned Max Planck Institute for Evolutionary Anthropology in Leipzig, will shortly publish his analysis of the entire Neanderthal genome, using DNA retrieved from fossils. He aims to compare it with the genomes of modern humans and chimpanzees to work out the ancestry of all three species.
Paabo recently told a conference at the Cold Spring Harbor Laboratory near New York that he was now sure the two species had had sex - but a question remained about how "productive" it had been.

"What I'm really interested in is, did we have children back then and did those children contribute to our variation today?" he said. "I'm sure that they had sex, but did it give offspring that contributed to us? We will be able to answer quite rigorously with the new [Neanderthal genome] sequence."

The way Paabo is couching it, what he has found then seems likely to be evidence that humans who had just expanded Out of Africa contributed to the genomes of Neandertals. In other words, modern human introgression into Neandertals. Of course if the gene flow was from modern human to Neandertals exclusively, then it would be an evolutionary dead end since that lineage went extinct.


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Saturday, October 24, 2009

When you can meet online, will colloquia disappear?   posted by agnostic @ 10/24/2009 07:08:00 PM

The other day I saw a flier for a colloquium in my department that sounded kind of interesting, but I thought "It probably won't be worth it," and I ended up not going. After all, anyone with an internet connection can find a cyber-colloquium to participate in -- and drawn from a much wider range of topics (and so, one that's more likely to really grab your interest), whose participants are drawn from a much wider range of people (and so, where you're more likely to find experts on the topic -- although also more know-nothings who follow crowds for the attention), and whose lines of thought can extend for much longer than an hour or so without fatiguing the participants.

So, this is something like the Pavarotti Effect of greater global connectedness: local opera singers are going to go out of business because consumers would rather listen to a CD of Pavarotti. It's only after it becomes cheap to find the Pavarottis and distribute their work on a global scale that this type of "creative destruction" will happen. Similarly, if in order to get whatever colloquia gave them, academics migrated to email discussion groups or -- god help you -- even a blog, a far smaller number of speakers will be in demand. Why spend an hour of your time reading and commenting on the ideas of someone you see as a mediocre thinker when you could read and comment on someone you see as a superstar?

Sure, perceptions differ among the audience, so you could find two sustained online discussions that stood at opposite ends of an ideological spectrum -- say, biologists who want to see much more vs. much less fancy math enter the field. That will prevent one speaker from getting all the attention. But even here, there would be a small number of superstars within each camp, and most of the little guys who could've given a talk here or there before would not get their voices heard on the global stage. Just like the lousy local coffee shops that get displaced by Starbucks -- unlike the good locals that are robust to invasion -- they'd have to cater to a niche audience that preferred quirkiness over quality.

So the big losers would be the producers of lower-quality ideas, and the winners would be the producers of higher-quality ideas as well as just about all consumers. Academics wear both of these hats, but many online discussion participants might only sit in and comment rather than give talks themselves. It seems more or less like a no-brainer, but will things actually unfold as above? I still have some doubts.

The main assumption behind Schumpeter's notion of creative destruction is that the firms are competing and can either profit or get wiped out. If you find some fundamentally new and better way of doing something, you'll replace the old way, just as the car replaced the horse and buggy. If academic departments faced these pressures, the ones who made better decisions about whether to host colloquia or not would grow, while those who made poorer decisions would go under. But in general departments aren't going to go out of business -- no matter how low they may fall in prestige or intellectual output, relative to other departments, they'll still get funded by their university and other private and public sources. They have little incentive to ask whether it's a good use of money, time, and effort to host colloquia in general or even particular talks, and so these mostly pointless things can continue indefinitely.

Do the people involved with colloquia already realize how mostly pointless they are? I think so. If the department leaders perceived an expected net benefit, then attendance would be mandatory -- at least partial attendance, like attending a certain percent of all hosted during a semester. You'd be free to allocate your partial attendance however you wanted, just like you're free to choose your elective courses when you're getting your degrees -- but you'd still have to take something. The way things are now, it's as though the department head told its students, "We have several of these things called elective classes, and you're encouraged to take as few or as many as you want, but you don't actually have to." Not exactly a ringing endorsement.

You might counter that the department heads simply value making these choices entirely voluntary, rather than browbeat students and professors into attending. But again, mandatory courses and course loads contradict this in the case of students, and all manner of mandatory career enhancement activities contradict this in the case of professors (strangely, "faculty meetings" are rarely voluntary). Since they happily issue requirements elsewhere, it's hard to avoid the conclusion that even they don't see much point in sitting in on a colloquium. As they must know from first-hand experience, it's a better use of your time to join a discussion online or through email.

The fact that colloquia are voluntary gives hope that, even though many may persist in wasting their time, others will be freed up to more effectively communicate on some topic. Think of how dismal the intellectual output was before the printing press made setting down and ingesting ideas cheaper, and before strong modern states made postage routes safer and thus cheaper to transmit ideas. You could only feed at the idea-trough of whoever happened to be physically near you, and you could only get feedback on your own ideas from whoever was nearby. Even if you were at a "good school" for what you did, that couldn't have substituted for interacting with the cream of the crop from across the globe. Now, you're easily able to break free from local mediocrity -- hey, they probably see you the same way! -- and find much better relationships online.

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Friday, October 23, 2009

EDAR & lubrication   posted by Razib @ 10/23/2009 11:18:00 PM

Enhanced Edar Signalling Has Pleiotropic Effects on Craniofacial and Cutaneous Glands:
The skin carries a number of appendages, including hair follicles and a range of glands, which develop under the influence of EDAR signalling. A gain of function allele of EDAR is found at high frequency in human populations of East Asia, with genetic evidence suggesting recent positive selection at this locus. The derived EDAR allele, estimated to have reached fixation more than 10,000 years ago, causes thickening of hair fibres, but the full spectrum of phenotypic changes induced by this allele is unknown. We have examined the changes in glandular structure caused by elevation of Edar signalling in a transgenic mouse model. We find that sebaceous and Meibomian glands are enlarged and that salivary and mammary glands are more elaborately branched with increased Edar activity, while the morphology of eccrine sweat and tracheal submucosal glands appears to be unaffected. Similar changes to gland sizes and structures may occur in human populations carrying the derived East Asian EDAR allele. As this allele attained high frequency in an environment that was notably cold and dry, increased glandular secretions could represent a trait that was positively selected to achieve increased lubrication and reduced evaporation from exposed facial structures and upper airways.

Every explanation for the "classic Mongoloid" phenotype seems to go back to "cold and dry." Some things never change.


What's going on at ASHG 2009?   posted by Razib @ 10/23/2009 10:11:00 PM

If you haven't been following the goings-on via Twitter, Luke Jostins has been posting some tidbits on his blog, Genetic Inference. If you get interested in something, remember you can search abstracts.

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Inferring demographic history   posted by Razib @ 10/23/2009 12:52:00 PM

Very interesting paper in PLoS Genetics, Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data. Here's the author summary:
The demographic history of our species is reflected in patterns of genetic variation within and among populations. We developed an efficient method for calculating the expected distribution of genetic variation, given a demographic model including such events as population size changes, population splits and joins, and migration. We applied our approach to publicly available human sequencing data, searching for models that best reproduce the observed patterns. Our joint analysis of data from African, European, and Asian populations yielded new dates for when these populations diverged. In particular, we found that African and Eurasian populations diverged around 100,000 years ago. This is earlier than other genetic studies suggest, because our model includes the effects of migration, which we found to be important for reproducing observed patterns of variation in the data. We also analyzed data from European, Asian, and Mexican populations to model the peopling of the Americas. Here, we find no evidence for recurrent migration after East Asian and Native American populations diverged. Our methods are not limited to studying humans, and we hope that future sequencing projects will offer more insights into the history of both our own species and others.

And from the abstract:
We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40-270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17-43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3-26.9 kya), and our analysis yields no evidence for subsequent migration.

I would keep in mind these 95% confidence intervals, but I immediately wondered about this European-East Asian divergence time just like Dienekes.

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Thursday, October 22, 2009

Welcoming Nicolae Carpathia   posted by Razib @ 10/22/2009 08:00:00 PM

After I hit "post" for the entry below, cheering linguistic uniformity, I realized that perhaps a word should be said about the obvious downsides. Large populations are probably a spur to innovation as the raw number of individuals of the smart fraction reaches critical mass. But denser populations also gave rise to numerous infectious diseases. Travel is a boon to communication, but it also spreads disease. The larger the population, and the more interconnected the populations, the more opportunities open up for pathogens. Similarly, despite the gains from global trade and common capital markets it also generates synchronous business cycles (and, perhaps exacerbates volatility). Good things usually have downsides. And so it would be with the rise of linguistic uniformity: a demagogue who could communicate with clarity, and subtle allusive power, to billions, would be enabled.


From Cantonese to Mandarin   posted by Razib @ 10/22/2009 07:00:00 PM

In Chinatown, Sound of the Future Is Mandarin:
He grew up playing in the narrow, crowded streets of Manhattan's Chinatown. He has lived and worked there for all his 61 years. But as Wee Wong walks the neighborhood these days, he cannot understand half the Chinese conversations he hears.

Cantonese, a dialect from southern China that has dominated the Chinatowns of North America for decades, is being rapidly swept aside by Mandarin, the national language of China and the lingua franca of most of the latest Chinese immigrants.

It's more complicated than that, as the article notes that Cantonese replaced the closely related dialect of Taishanese. Another interesting twist is that the new wave of migrants are themselves not necessarily native speakers of a Mandarin dialect as they are generally from Fujian. Rather, Standard Mandarin is a lingua franca among common people in the Chinese world now in a manner it may not have been when the earlier waves of South Chinese arrived in the United States. In Singapore and Taiwan the Chinese also derive from various regions of Fujian, but Mandarin is an official language, and the monolingualism in dialects is only common among the old.

This is just a specific case of a general dynamic; French, German and Italian all replaced numerous regional dialects, some of which still retain local vitality. Just as Taiwan's predominantly Fujianese population accepts Standard Mandarin, so Switzerland's dialect speaking population accepts Standard German as the official public face of the language (no matter that privately they may converse in Swiss German).

Though linguists and anthropologists bemoan the decline of diversity and local flavor, when it comes to communication this is probably a good thing for the individuals and the societies in which they live. Not only is language often a divisive fault line, but it serves as a barrier to the exchange of ideas and socialization. Whatever marginal cognitive benefits are accrued to individuals who learn multiple languages, on the balance uniformity of speech opens up many possibilities of coordinated action. Even the ancients knew that.

Note: Of course with the dying of a language with a large body of literature some aspect of immediate comprehension and memory of the past vanishes. When it comes to dialect traditions I obviously weight the loss of collective memory less because I tend to perceive oral cultures as encoding cross-cultural values by and large. There may be a thousand twists on the tale of the "Trickster god," but moral of the story is rather the same. In any case, when the last native speaker of Sumerian died no doubt there was a subtle shift in perceptions of the story of Gilgamesh, but I think such losses are a small cost to pay for mutual intelligibility.

Addendum: According to Peter Brown in The Rise of Western Christendom the shift from Syraic dialects to Arabic among the Christian populations of the Levant and Mesopotamia was the tipping point in terms of conversion to Islam. So from some perspectives unintelligibility and separation of language are beneficial. Consider Hasidic Jews and Amish who have long been resident in the United States but continue to speak dialects of German amongst themselves (in my experience the Amish speak English without any accent except for a somewhat quaint aspect, but I have read and heard Hasidic Jews who speak English with a very strong accent which indicates they learned the language in their later teens at the earliest).

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Wednesday, October 21, 2009

People can't judge their own political ideology   posted by Razib @ 10/21/2009 07:17:00 PM

Or, perhaps they're norming to their local context. In any case, Andrew Gelman pointed to Boris Shor's site, who then linked to his research on ideology, which led me this working paper, All Together Now: Putting Congress, State Legislatures, and Individuals in a Common Ideological Space. Here's what jumped out at me:
I have also found that the common space scores perform exceedingly well as a predictor of individual vote choice compared with even a non-naive three item composite ideology. The common space scores even do as well or better than party identi cation in predicting both presidential and congressional voting. In fact, conventional de nitions of ideology, predicated on self-reporting, show themselves to be completely inadequate.

The "common space scores" is derived from Project Vote Smart's NPAT.


The Marxist Mesticos   posted by Razib @ 10/21/2009 05:00:00 PM

Today I listened to a Planet Money podcast about Angola's oil economy, which is an extreme manifestation of the typical dysfunctions which occur due to the presence of black gold. But it got me to thinking about a book I read recently, Africa: Altered States, Ordinary Miracles. Though the author is a journalist and not a scholar there is a good balance between historical and economic framing and the expected travelogue. Most of the chapters can be read a la carte, and are geographically or topically constrained. For instance, one of the last chapters is about the arrival of Chinese to Africa. Some estimates suggest that at any given time there are 5 million Chinese workers on the continent!

For me the most interesting chapter was on Angola. I would be interested in what a scholar of the history of this nation would say about the historical sketch presented. Like many Portuguese possessions Angola has a mixed-race population, mesticos. They are predominantly European in culture and outlook, and according to the author they generally played the role of middlemen minority in this region between Europeans and native Africans. For most of the colonial period the mesticos engaged in arbitrage activity involving human capital. They were slavers. The 20th century brought unexpected, and unwanted changes, for the mesticos. The Salazar dictatorship encouraged a mass migration of white Portuguese, particularly of working or lower classes, to Angola in an effort to relieve population pressures. The mesticos then found their indispensable role as middlemen irrelevant, and in fact the new immigrants received preference in a host of jobs which had traditionally been in the purview of the mesticos. While in other colonial possessions mixed-race minorities tended to identify with the mother country, the mesticos did not, because the mother country was destroying their niche within Angola.

From what I can tell the mesticos are only a few percent of the population. Angola, like most African nations, is ethnically diverse. According to the author of Africa: Altered States, Ordinary Miracles most of the nationalist movements were taking an Africanist position, and de facto aligned with particular ethnic groups. The mesticos lacked the numbers to be of importance within these ethnic coalitions. Additionally, they could not align themselves with the colonialist position because 20th century Portuguese colonialism was qualitatively different from what had come before and was leading to their dispossession.

There was one political grouping, which had a presence in Portugal, which was open to them. And that was the Communist party. The Communist party spoke in terms of class, and not nationalism or ethnic loyalties, and so mesticos were accepted within its apparatus. An argument therefore emerges that Angola's Marxist-Leninist political movement was in fact a vehicle for the empowerment of a mercantile middleman minority! Though the bete noire of the Marxists, Jonas Savimbi, wore many ideological hats, his movement to a first approximation a reassertion of the indigenous African groups of the interior in opposition to the coastal mesticos and the arriviste Portuguese. By the 1990s Communism was spent as an international force, and the Popular Movement for the Liberation of Angola rapidly transformed into an officially socialist party, but its commitment to socialism is notional. Rather, Angola operates in a fashion similar to most one-party petro-states.

Note: The current President of Angola is not a mestico, but the child of immigrants from Sao Tome and Principe.


Live tweeting ASHG 2009   posted by Razib @ 10/21/2009 02:59:00 PM

Dr. Daniel MacArthur and Luke Jostins. Also see the #asgh2009 hash-tag.


Tuesday, October 20, 2009

Being Michael Behe   posted by Razib @ 10/20/2009 11:25:00 PM

Reading Joe Thornton's response to Michael Behe, I'm struck by the de ja vu that the exchange induces. I remember reading Darwin's Black Box when it came out, and being confused as to why this was such an awesome challenge to evolution, and following the debates in its wake. Behe seems to think he's pwning everyone, when his arguments from outside of his charmed circle seem a bit flimsy and amateurish.

But let's assume that Behe doesn't have any screws loose. There have to be presuppositions which allow for his arguments to seem rock-solid and irrefutable in his own cognitive universe. I know that some readers of this weblog have ID sympathies. Normally I just delete those sorts of comments because I'm an intolerant evolutionist/intolerant of idiocy (your selection of the two options obviously depends on your starting point). But I'm genuinely curious from an anthropological perspective, why does Behe think his arguments are not being refuted over and over? I could go read the ID & Creationist weblogs, but the quality of the comments are low, and individuals like William Dembski deal with an sympathetic audience and seem to demand a level of sycophancy so there's a lot of garbage to wade through.

Rather, I'll leave the thread open to ID believing GNXP readers to flesh out their axioms. Specifically, I want some insight to why Behe is totally unconvinced by all the rebuttals which have been offered in the 15 years since he came on the scene.

(Obviously this is not an invitation to religious argument or preaching)

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Obese regions do vote for McCain, but McCain voters may not be especially obese   posted by Razib @ 10/20/2009 09:09:00 PM

A friend pointed me to this article in Slate which noted:
This size bias may ultimately play out along party lines. The last presidential election revealed a startling overlap between statewide obesity figures and support for the GOP. Despite losing in a landslide, John McCain carried all nine of the fattest states in the union and 16 of the top 20. (Obama prevailed in 17 of the 20 thinnest states, including New Jersey.) In the race for governor of a very blue state, Christie's girth marks him as an outsider-a member of the chunky-monkey Fox News demographic, the kind of guy who rides around in an SUV and eats Double Down sandwiches. If Christie stands in for America's boorish consumer culture, then Corzine-slender, bearded, and bespectacled-represents the cosmopolitan elite.

The issue though is that black Americans are more obese, and extremely black states exhibit a lot of racial polarization whereby McCain actually those states. My friend wondered if I could look on a more granular level. If I could find obesity data on all the counties in the nation, that would be easy, but I didn't find that. But, I did find obesity data for race, so the proportion of each state which are classified as obese who are non-Hispanic white, as well as exit polls of the white vote for McCain. The scatterplot below shows the outcome.

What about individual level data? In 2004 there was a variable which was interviewer perception of weight. Here's what the GSS says:

The 95% confidence intervals are their, including the N's. Not much difference. Perhaps the sample size is too small to tell, or perhaps how interviewers perceived people differed from region to region. I limited the sample to Non-Hispanic whites. Here's the variables:

Row: INTRWGHT(r:1 "Below Average"; 2 "Average"; 3-4 "Above Average")
Col: partyid(r:0-2 "Democrat";3 "Independent"; 4-6 "Republican") polviews(r:1-3 "Liberal";4 "Moderate" ;5-7 "Conservative")

Oh, and about fat people voting for fat candidates. I think the issue is that many fat people imagine that one day they won't be fat, so it's hard to create an identity around something you want to escape, and think you can, with enough hard work, or a miracle drug, or gastric bypass.

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Did you pass a paper to me last december?   posted by Razib @ 10/20/2009 06:49:00 PM

There are lots of weird search queries which come into this weblog. Or any website, period. But this month 3 times someone arrived via this query: "last december i passed a paper along to razib."

1) If you're the person who arrived in this way, could you tell me what's up? Was I supposed to blog on something? Did I not give you credit? I'm genuinely perplexed.

2) Especially over the past year the number of publicists contacting bloggers has increased. A lot. So my regular correspondence is getting drowned out, and I'm probably not as good about responding to people, crediting them appropriately, etc. (though often readers of this weblog know what I'd be interested in, and I get nearly simultaneous emails from several different people, so crediting is an issue). Some of these publicists are rather chatty and send emails which look to be personally targeted. Just so you know.

Note: People might be curious, but two of the top 10 searches relating to me coming into this weblog over the past 3 years (how long I've had Google Analytics installed) involve Matt Yglesias and Cosma Shalizi :-)


Language(s), then and now   posted by Razib @ 10/20/2009 02:31:00 PM

One of the trends which L. L. Cavalli-Sforza pointed to years ago is that linguistic and genetic cladograms exhibit a great deal of similarity. More recently geneticists such as Marcus Feldman have suggested that the reason behind this is that people tend to marry those who they can communicate with. Once the genetic data becomes more granular in Europe it will be interesting to see if this works on the national level. Though it is true that languages such as French or German are relatively new standards within the boundaries of their nation state, it is also true that people from village to village were intelligible with each other, until presumably they hit upon a major linguistic boundary such as between Romance and Germanic languages (though presumably here bilingualism would have been common).

But one of the problems which crops up now and then trying to think of the past, especially with all the new results coming out of historical genetics, is that we project the linguistic homogeneity of the present back. For example, in ancient Mesopotamia there were two languages which are linguistic isolates to the best of our knowledge, Sumerian and Elamite. If we didn't have extant written records, or, more accurately if writing hadn't arrived in Mesopotamia so early, we'd have no idea that there were non-Semitic languages in that region today. Not only that, but the ancient records from that period in Mesopotamia hint at other language groups which were not literate and so left no record. In the Roman Empire the vast majority of our extant records are in Greek and Latin. We know the existence of other languages, such as Celtic dialects, Punic, and such, but there are also indications of the flourishing of local lingua franca such as "Iberian" in southern Spain which have left only a marginal literary impact. The emergence of large polities led to linguistic homogenization; I have read that the dominance of Quechua, the language of the Incas of Cuzco and its environs, actually dates to the Spanish colonial period. In the chaos after the fall of the Inca Empire the language of the Incas gave the local peoples are a sort of solidity.

I'm thinking about this because I am corresponding with some people about the David Reich paper on Indian genetics, and people are asking questions such as "did the ancestral South Indians speak Dravidian languages?" I doubt it, but I also doubt that the language families of ancient India were as cleanly sorted out as they are today. Even the languages of the Andaman Islanders may not be one family! Over the past 10,000 years, and especially the last 2,000 years, much of the World Island has seen cultural positive feedback loops which have resulted in linguistic homogeneity. The rise of nation-states, literate elites, class stratification, etc., are I think part of the whole package which has given rise to this dynamic. Some of these are general phenomenon which presumably apply to H. sapiens 30,000 years ago, but I suspect the powerful magnitude is a new feature.


Monday, October 19, 2009

Humans still evolving, etc.   posted by Razib @ 10/19/2009 04:26:00 PM

Are Humans Still Evolving? Absolutely, Says A New Analysis Of A Long-term Survey Of Human Health:
"There is this idea that because medicine has been so good at reducing mortality rates, that means that natural selection is no longer operating in humans," said Stephen Stearns of Yale University. A recent analysis by Stearns and colleagues turns this idea on its head....

Taking advantage of data collected as part of a 60-year study of more than 2000 North American women in the Framingham Heart Study, the researchers analyzed a handful of traits important to human health. By measuring the effects of these traits on the number of children the women had over their lifetime, the researchers were able to estimate the strength of selection and make short-term predictions about how each trait might evolve in the future. After adjusting for factors such as education and smoking, their models predict that the descendents of these women will be slightly shorter and heavier, will have lower blood pressure and cholesterol, will have their first child at a younger age, and will reach menopause later in life.

Since large numbers of humans forgo reproduction in an evolutionary sense they might as well have died (excluding some inclusive fitness effects). If reproductive variance and heritable variation in traits correlated with that variance continues then naturally selection will be an operative phenomenon.

The paper is coming out in PNAS, so no guarantee when it'll be online, Byars, S., D. Ewbank, et al. Natural selection in a contemporary human population. Proceedings of the National Academy of Sciences, 106(42) DOI: 10.1073_pnas.0906199106.

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At the intersection of evolution & intelligence   posted by Razib @ 10/19/2009 09:29:00 AM

If you're at ASHG, a session you might want to attend, Scale Effects and Recent Brain Evolution: Theory and Preliminary Evidence. Here's the abstract:
What forces have driven human evolution since the grand human diaspora? In this paper, I argue that the scale effects so central to endogenous growth theory in the field of economics (e.g., Kremer's widely-cited "Population Growth and Technological Change: 1,000,000 B.C. to 1990," Quarterly Journal of Economics, 1993) have been important drivers of human brain development since the diaspora. Scale effects have made prominent appearances in recent explanations of continent-level outcomes. For instance, in Kremer’s model, big continents create larger, denser, faster-growing populations. In Diamond’s Guns, Germs, and Steel model, wide continents raise the chance that an innovation will arise at a given latitude, an innovation which can then disperse across that latitude, enriching those who live on wider continents. In both models, the Malthusian nature of pre-Industrial Revolution existence imposes strong conditions on the general equilibrium outcome. My model takes those channels as given, and works out the theoretical implications for the divergent evolution of human brains on these continents. Brains are biologically costly, so evolution will only select for larger brains if there is a substantial payoff. And since larger brains tend to have higher levels of intelligence [corr(Brain Size, IQ)= 0.4 in recent in brain-scan studies], larger brains tend to have more processing and memory power. Under certain parameter values, Kremer’s and Diamond’s models both imply that the payoff to a big brain—a brain that can better adopt someone else’s ideas—will be higher on wider, larger continents. Thus, we would expect human populations living on larger, wider continents to develop larger, more powerful brains. I model this relationship formally. This result should only hold on average: intra-group diversity is central to evolutionary theory, and massive intra-group diversity is an important fact of quantitative human genetics. The main purpose of the paper is to set forth the model, but I include some tests of its implications. I discuss whether, as the model predicts, human brain size and average IQ correlate positively with continent size and continent width. Indeed, evidence generally supports this hypothesis. Further empirical testing of the model’s predictions will occur as future researchers employ genetic diversity databases. I plan to present the results in a manner intelligible to non-economists.

Here's the info:

Session Title: Evolutionary and Population Genetics Session

Session Location: Exhibit Hall II, Convention Center Session Time: Wed 9:30AM-3:30PM

Program Number: 643/W Poster Board Number:301 Presentation Time: Wed, Oct 21, 2009, 1:00PM-2:00PM

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Sunday, October 18, 2009

What Darwin Said: Part 6 - Gradualism (B)   posted by DavidB @ 10/18/2009 04:40:00 AM

This is the sixth in a series of posts about Charles Darwin's view of evolution. Previous posts were:

1: The Pattern of Evolution.
2: Mechanisms of Evolution.
3: Heredity.
4: Speciation.
5. Gradualism (A) , which dealt with Darwin's views on gradualism in the rate of evolutionary change.

The present part deals with another aspect of gradualism: the size of the variations adopted by natural selection. A gradualist in this respect maintains that successful variations (mutations, in modern terminology) are always or usually relatively small in effect.

[Added on 20 October: there is an article on Panda evolution (discussed below) here.]


Unless otherwise stated, all page references are to Charles Darwin: The Origin of Species: a Variorum Text, edited by Morse Peckham, 1959, reprinted 2006.

To denote small variations, Darwin usually refers to 'individual differences', which he describes as 'many slight differences which may be called individual differences, such as are known frequently to appear in the offspring of the same parents, or which may be presumed to have thus arisen, from being frequently observed in the individuals of the same species inhabiting the same confined locality' [122]. 'Individual differences' are therefore envisaged by Darwin as being both small and relatively common.

To denote larger or rarer variations, Darwin uses several terms, with some differences of meaning. Occasionally he refers to 'single variations', meaning those occurring only in rare and isolated individuals. Single variations may be either 'slight or strongly-marked' [178]. He also sometimes refers to 'sports', a traditional term used to describe unexpected new characters such as buds different from the rest of a plant [81]. Another term is 'monstrosity': 'some considerable deviation of structure in some part, either injurious to or not useful to the species, and not generally propagated' [120].

But Darwin most often uses the phrase 'great and sudden', 'great and abrupt', or related terms, to describe variations larger than individual differences [264, 267, 345, 362, , 713, 735, 751] : 'As natural selection acts solely by accumulating light, successive, favourable variations, it can produce no great or sudden modification; it can act only by very short and slow steps' [735; the word 'very' is omitted in the 5th and 6th editions].

The adequacy of individual differences

Darwin believed that in general individual differences were sufficient for the observed pattern of evolution: 'A large amount of inheritable and diversified variability is favourable [to natural selection], but mere individual differences probably suffice' [192].

Some authors have interpreted Darwin's concept of individual differences as covering only continuous variations (quantitative traits, in the modern jargon). I find no strong evidence to support this interpretation. Darwin himself does not use the terms continuous and discontinuous. In the first edition of the Origin he does twice refer to 'insensibly' small gradations [321, 714], and on one occasion to 'infinitesimally small' inherited modifications [185], expressions which might be taken to imply strict continuity. But the words 'insensibly' and 'infinitesimally' were removed in later editions. Darwin moreover says that 'Every one who believes in slow and gradual evolution, will of course admit that specific changes may have been as abrupt and as great as any single variation which we meet with under nature, or even under domestication' [263]. He also says that 'the general pattern of an organ might become so much obscured as to be finally lost, by the atrophy and ultimately by the complete abortion of certain parts, by the soldering together of other parts, and by the doubling or multiplication of others, - variations which we know to be within the limits of possibility' [679]. It is a general rule that when the same body part is repeated many times in the same individual, like the vertebrae of snakes, the number is variable [297]. These statements clearly imply that 'meristic' (numerical) changes can occur in evolution.

No great and sudden changes

Darwin makes several statements against the likelihood of 'great and sudden' changes. Perhaps the strongest is that: 'If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down' [344] This still leaves open the possibility of 'great and sudden changes' which do not produce a new complex organ, but some other change such as a large increase in size. Darwin was sceptical about the likelihood of any great and sudden changes. Many of his comments on the subject was added in the 3rd or later editions of the Origin, for example: 'It may perhaps be doubted whether monstrosities, or such sudden and great deviations of structure as we occasionally see in our domestic productions, more especially in plants, are ever permanently propagated in a state of nature' [121, 3rd edn. onwards]. Darwin's position is not that such changes are impossible, but that he sees little evidence for them, and several arguments against them. His reasoning is considered further below.

Darwin does make a partial exception for two kinds of sudden change. One is where a plant has flowers, etc, of two different kinds. If for some reason the plant ceased to produce one of these, there would be a sudden change, though the different types might originally have been produced gradually. [121] Darwin also acknowledged the case, raised by E. D. Cope, of what is now called heterochrony, where different stages of the life cycle of an organism are speeded up or slowed down. In such circumstances some parts of the life cycle may eventually be omitted entirely, and this could be a relatively sudden change, but 'Whether species have often or ever been modified by this comparatively sudden mode of transition, I can form no opinion; but if this has occurred, it is probable that the differences between the young and mature, and between the mature and the old, were primordially acquired by graduated steps' [349]

Darwin's reasons for gradualism

Curiously, in the first edition of the Origin Darwin gives little argument against 'great and sudden changes'. This was not because he had not thought about the matter. In the draft 'big species book' which he was working on before receiving the celebrated letter from Wallace, he included the following passage:

I cannot believe that in a state of nature new species arise from changes in structure in old species so great & sudden as to deserve to be called monstrosities. Had this been so, we should have had monstrosities closely resembling other species of the same genus or family; as it is comparisons are instituted with distant members of the same great order or even class, appearing as if picked out almost by chance. Nor can I believe that structures could arise from any sudden & great change of structure (excepting possibly in the rarest instances) so beautifully adapted as we know them to be, to the extraordinarily complex conditions of existence against which every species has to struggle. Every part of the machinery seems to have been slowly & cautiously modelled to guard against the innumerable contingencies to which it has to be exposed [p. 319, Charles Darwin's Natural Selection, ed. R. C. Stauffer, 1975]

In abridging his draft for the Origin, Darwin omitted this passage, apparently because he did not expect his position to be controversial. In the event, several commentators, including T H Huxley, thought he had been unwise to rule out great and sudden changes or 'saltations'. Darwin's correspondence shows that he was surprised at this objection, and in subsequent editions of the Origin he gave fuller reasons for his position. These may be broken down into the following main points:

1. It is improbable that large and sudden changes would produce the refinement of adaptation we observe in nature: 'almost every part of every organic being, at least with animals, is so beautifully related to its complex conditions of life that it seems as improbable that any part should have been suddenly produced perfect, as that a complex machine should have been invented by man in a perfect state' [121]

2. It is very rare for wholly new organs to appear 'as if created for some special purpose...nature is prodigal in variety, but niggard in innovation' [361] In his chapters on 'Difficulties of theory' and 'Miscellaneous objections' (in the 6th edition) Darwin discusses at length the evidence for transitional stages in the evolution of organs.

3. Closely related species usually differ only slightly, by a number of small differences, and cannot be sharply distinguished from sub-specific varieties, which in turn are merely well-marked individual differences. There is a continuity of variation which suggests that the differences between species are the accumulated effects of individual differences [135, 265]

4. 'Monsters' are usually sterile [121]

5. Embryology shows gradual rather than sudden transitions [267]

6. Great and sudden changes occur only rarely and in isolated individuals. Even if they have some selective advantage, such changes are likely to be eliminated by chance extinction, or diluted by interbreeding with other individuals, before they can establish themselves. [178]. Darwin based this argument on an anonymous article in the North British review (in fact by Fleeming Jenkin). Jenkin intended it as an argument against natural selection in general, but Darwin welcomed it as supporting his position against the importance of 'single variations'.

7. As in his pre-Origin draft, Darwin pointed out that if evolution often occurred through large and sudden changes in a single trait or organ, we ought to be able to find many cases of closely related species, resembling each other in most respects, but differing sharply in some particular way resembling a monstrosity. Darwin claimed that he had diligently searched for such cases but not found any [121]

Was Darwin right?

Mainstream neo-Darwinian evolutionists generally follow Darwin in minimising the role of 'great and sudden' variations. Gradualism usually goes together with a belief in the importance of adaptation and natural selection. In contrast, critics of natural selection, from Darwin's lifetime onwards, have often favoured some kind of saltationism: Mivart, Bateson, Goldschmidt, and Schindewolf being notable examples. More recently, punctuationists such as Stephen Jay Gould and Stephen Stanley have combined acceptance of macromutations with a lukewarm attitude towards natural selection. On the other hand, there is no logical incompatibility between macromutation and natural selection, if large mutations are favoured by selection. A minority of evolutionists, including Francis Galton, De Vries and J. B. S. Haldane, have combined selectionism with acceptance of macromutation as a possibility.

It is sometimes supposed that R. A. Fisher proved the impossibility of large mutations being selected. I am not sure that Fisher himself made such a bold claim. What he did prove, given a few reasonable assumptions, was that:

a. a small mutation is more likely to be beneficial than a large one

b. the probability that a mutation will be beneficial declines as the number of different traits affected by the mutation increases.

These points fall short of the strong claim that macromutations can never be beneficial. Confusion on this point has perhaps arisen from Fisher's informal 'microscope' analogy. If a microscope is already fairly well focused (corresponding to an organism which is fairly well adapted, as it must be to survive at all), a small adjustment of the focus has a 50:50 chance of making an improvement, whereas a large adjustment is bound to make things worse. But the latter conclusion depends on the tacit assumption that there is only a single optimum focus. In the case of a microscope we know that this is true, but if instead of a microscope we have some instrument with more than one locally optimal setting, such as an FM radio receiver with many stations, then a large adjustment has a non-zero probability of improving on the current position. Whether the probability is significant will depend on the number and spacing of local optima within the range of possible adjustment. Turning to the biological case, we can make use of the phenotypic version of the 'adaptive landscape' concept. Assuming that an organism is close to a peak in the landscape, a mutation will take its offspring to some other point of the landscape. Whether this is higher or lower in fitness than the parent will depend on the structure of the landscape. If peaks of fitness are few and far between, relative to the range of possible mutational effects, then the probability of a large mutation being beneficial will be very small. If on the other hand there are many peaks within the range of feasible mutations, then a large mutation may well be advantageous. I do not know of any rigorous argument against this scenario.

Darwin himself [121, 267] objects to the sheer improbability that a single, sudden transformation would produce an organism perfectly adapted to its environment. But the macromutationist does not need to claim this much: he need only claim that the organism would on balance be fitter than its predecessors. The adaptation might then be refined by smaller changes.

Turning to Darwin's other points, the argument from embryology is a weak one. It assumes that the evolutionary sequence of mature organisms is closely followed in the embryonic development of an individual, so that there can be no sudden transitions in the former without sudden transitions in the latter. This requires a strong 'recapitulation' theory of embryology, which would not now be accepted.

Fleeming Jenkin's arguments against the selection of 'single variations' depend on the assumption of 'blending inheritance', according to which an offspring is always intermediate between its offspring. But for single gene mutations, which would include many mutations of large effect, the 'blending' assumption fails.

The argument that 'monsters' are usually sterile carries some weight. Large mutations are sometimes due to chromosomal abnormalities, which reduce fertility, while even in the case of single gene mutations the resulting 'monster' may have difficulty finding a mate.

Darwin's remaining arguments are empirical. He claims that it is rare to find an organ in one species which cannot be traced through transitional forms in other species. New organs or body parts are evolved from old ones: for example the wings of birds and bats are evolved from the standard tetrapod forelimb, and not wholly new parts. Related species differ by a number of small differences, not by single radical mutation of the kind known to occur in 'monstrosities'.

It would be difficult to evaluate these claims without a wide-ranging survey of the animal and plant kingdoms. It seems to be true that closely related species often differ by numerous small changes. Cases like the 'geminate species' on the opposite sides of the Panama Isthmus, where several million years of separate evolution have produced slightly differing pairs of species, support this position. There is however evidence that single mutations of striking phenotypic effect have had a larger role in evolution than Darwin supposed. The classic cases of melanism and mimicry in insects seem to be of this kind: a melanic or mimic form first appears by a relatively large mutation, which is then refined by smaller changes. It is also claimed (by Vorontsov) that the hairlessness of the naked mole rat and of the bat species Cheiromeles is due to a single mutation. Whether we call these 'macromutations' is a matter of taste, but they go beyond what Darwin described as 'individual differences'.

There are some cases where the nature of the variation itself seems to require a sudden change. For example, some snail shells coil in the opposite direction to the standard one, and a single-step reversal of chirality (of a kind known to occur by rare mutations) is more credible than a transition through an uncoiled stage. In starfish, most species have five rays, which is evidently the 'primitive' condition, but some species have more than five. A transition through forms with 'five-and-a-bit' rays seems highly improbable, so there was presumably a sudden increase in some lineages. When significant sudden changes do occur, they may conceivably mark the origin of a new higher taxon, such as a family or order. Macromutationists have often argued for this. However, most such claims are vague and poorly supported. For example, Stephen Jay Gould endorsed the view of Dwight Davis that the distinctive features of the Panda (Ailuropoda) may have resulted from a few large mutations (with some subsequent 'polishing'), but there seems to be no direct genetic or fossil evidence for this. On perusing Davis's original 1964 monograph, he really had no reason for his view other than a gut feeling that the changes, such as the enlargement of the radial sesamoid bone, could not have been gradual. It has also been claimed (e.g. by Oliver Rieppel) that Chelonia (tortoises and turtles) must have evolved their armoured shell by large mutational steps. There were until recently no intermediate stages in the fossil record, but some transitional forms have now been discovered, which casts doubt on the macromutationist argument.

Overall, Darwin's gradualism probably went too far. There is no reason (Fisher notwithstanding) to be opposed in principle to macromutational changes, and there is evidence that they have sometimes occurred (perhaps more often in plants than animals). On the other hand, enthusiasm for 'saltationism' has often been linked with hostility towards natural selection, and a subjective inability to see how such-and-such a change can have been gradually selected. 150 years after the Origin, evolutionists should arguably be more open-minded than Darwin to the role of large mutations in evolution, but still cautious in claiming that any given change 'must' have been sudden.

Saturday, October 17, 2009

John Hawks &   posted by Razib @ 10/17/2009 01:31:00 PM

Another episode with me interviewing John Hawks on Mostly we're talking about about Ardipithecus. The last 1/3 is about Indian genetics. We recorded on Thursday, but since then I've changed my mind on some issues and now disagree with some of what I said. I will likely post on my revisions soon, though have a rather low degree of certitude as to the accuracy of what I suspect, so I am poking through the literature to see if I can become more confident, or just falsify (if you missed my last discussion with John from two weeks ago, it's here).


Thursday, October 15, 2009

UNICEF, boo!   posted by Razib @ 10/15/2009 11:02:00 PM

What's different about Kiva:
Contrast Kiva with, for example, UNICEF. Kiva makes it possible to trace the path of your donation, to the extent that such tracing is realistic (and it largely turns out to be more along the lines of "you funded a certain MFI" rather than "you funded a certain person"). UNICEF doesn't even seem to have a breakdown of how much money is going to each continent. We definitely can't find information on questions like (a) What specific projects are you funding? (b) What is your role in each? (c) What new projects are planned, and where? (d) How is each project going, whom is it affecting, and how?

There are no strange patterns in UNICEF's numbers because there are no numbers. There are no contradictions because there is no concrete information. And the intent here isn’t to single out UNICEF - it's merely one of the vast majority of international aid organizations about which we know essentially nothing.

If you're not an Objectivist, you might consider adding The GiveWell Blog to your RSS.


Wednesday, October 14, 2009

Version 2.0 of Montana & Gretzky   posted by Razib @ 10/14/2009 05:09:00 PM

Since we're talking about athletics & heritability, California School Has a Montana and a Gretzky at Quarterback. Unfortunately regression toward the mean implies you'd have to bet against the sons of some of the greatest players in professional sports having anything close to the same impact. On the other hand, having a professional athlete parent is going to increase your odds of being a successful athlete in the pros by orders of magnitude I suspect. The expectation is that children of professional athletes, who are many standard deviations above the norm, will regress back toward the mean as a function of heritability. But the expectation of their athleticism is going to be far higher than the norm, and because there is going be variance around that expectation it also increases the probability that those children will match their parent, or even outperform them. The Manning brothers and Barry Bonds are cases where the offspring are more exceptional than their parent.

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Genes vs. environment, athletics   posted by Razib @ 10/14/2009 04:26:00 PM

The GSS variable GENENVO4:
Character, personality, and many types of behavior are influenced both by the genes people inherit from their parents and by what they learn and experience as they grow up. For each of the following descriptions, we would like you to indicate what percent of the person's behavior you believe is influenced by the genes they inherit, and what percent is influenced by their learning and experience and other aspects of their environment. The boxes on handcard D1 are arranged so that the first box on the LEFT (which is numbered 1) represents 100% genetic influence (and 0% environment). The next box (numbered 2) represents 95% genes (and 5% environment), and so on. The RIGHTMOST box (numbered 21) represents 100% environmental influence (and no genetic influence). After each description, please type the number of the box that comes closest to your answer. Please use the numbered scale on handcard D1 to indicate, FOR EACH OF THE BEHAVIORS DESCRIBED, what percent of the person's behavior you think is influenced by the genes they inherit, and what percent is influenced by their learning and experience. After each question, type the number of the box that comes closest to your answer. Remember, the higher the number, the more you think the behavior is influenced by learning and experience; the lower the number, the more you think it is influenced by genes 981. George is a Black man who's a good all-around athlete. He was on the high school varsity swim team and still works out five times a week. (Please type in a number from 1 to 21):

In other words, if someone gives the response 1, they think that George's athleticism is 100% a function of genes. 21, 100% a function of environment. The N for this variable is in excess of 2,000, and the question was asked in 2004. I decided to recode a bit so that responses were aggregated across 25% intervals like so: GENENVO4(r:1-6 "75% or more";7-11 "50% or more"; 12-16 "25% or more"; 17-21 "less than 25%"). If you want to poke around the GSS you can just cut & paste that into the "ROW" box. I was surprised at some of the results, first, the lack of difference across ages, as well as the similarity between liberals and conservatives. On the other hand, the dumb and uneducated were more likely to put an emphasis on genes, which went along with my expectations. The data are below in table form, and as well as a line graph (just to show you visually which ones deviate from the others).

% Genetic All Whites Black Male Liberal Conserv No College Degree College Degree Dumb Average Smart
75-100 21.1 19.3 29.6 21 21.7 19.6 24.2 13.8 28.2 23 15.1
50-75 27.8 28.7 28 26.4 29.4 24.6 26.5 31.1 31.9 26.8 27.6
25-50 22.4 23.4 16.2 23.1 24.8 24.5 20.5 27.1 11.2 22.4 25.6
0-25 28.6 28.6 26.2 29.4 24.1 31.3 28.9 28 28.7 27.8 31.7

At first when I saw little difference between liberals & conservatives and across age groups I wondered if it was coded wrong. But the outcomes for intelligence & education seem to fit. Perhaps it has something to do with George being a black athlete, so the intelligent and educated know what they should say about this sort of question?

Note: Dumb = WORDSUM 0-4, average WORDSUM 5-7 and smart WORDSUM 8-10.


Less than nations   posted by Razib @ 10/14/2009 02:59:00 PM

Since Afghanistan is in the news a lot, I keep hearing about it. I decided to double check some numbers, and here's some weird stuff:

Afghanistan, 11 million Pashtuns, Pakistan, 27 million Pashtuns
Azerbaijan, 8.1 million Azeris, Iran, 17.75 million Azeris
Mongolia, 2.3 million Mongols, China, 5 million Mongols


Chronic fatigue & infection   posted by Razib @ 10/14/2009 01:18:00 PM

The New York Times has a long article on the implications of the new paper in Science, Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome. Here are the numbers: "Studying peripheral blood mononuclear cells (PBMCs) from CFS patients, we identified DNA from a human gammaretrovirus, xenotropic murine leukemia virus-related virus (XMRV), in 68 of 101 patients (67%) compared to 8 of 218 (3.7%) healthy controls."


Biological Egalitarianism   posted by dkane @ 10/14/2009 11:36:00 AM

Bruce Lahn and Lanny Ebenstein write (pdf) in Nature: "Let's celebrate human genetic diversity." (Hat tip: Steve Sailer.)

The current moral position is a sort of 'biological egalitarianism'. This dominant position emerged in recent decades largely to correct grave historical injustices, including genocide, that were committed with the support of pseudo scientific understandings of group diversity. The racial-hygiene theory promoted by German geneticists Fritz Lenz, Imbler Fischer and others during the Nazi era is one notorious example of such pseudoscience. Biological egalitarianism is the view that no or almost no meaningful genetically based biological differences exist among human groups, with the exception of a few superficial traits such as skin colour. Proponents of this view seem to hope that, by promoting biological sameness, discrimination against groups or individuals will become groundless.

We believe that this position, although well intentioned, is illogical and even dangerous, as it implies that if significant group diversity were established, discrimination might thereby be justified. We reject this position.

Agreed. I have made this same argument with regard to debates over higher education, although I prefer the terminology "genetic egalitarianism" since it better captures the fundamental assumption that genetics don't matter.

Tuesday, October 13, 2009

There are no NFL genes (?)   posted by Razib @ 10/13/2009 01:34:00 PM

23andMe performs genome-wide association study on NFL players, fails to find athlete genes:
It's unsurprising that the results of this study are negative (more on this below), but the conclusions they draw from this are fallacious. In fact we know from twin and family studies that many (but not all) traits related to athletic performance are highly heritable; researchers just haven't been able to track down the vast majority of the genetic variants responsible yet, and this study is no exception.

What 23andMe have actually shown here is that the limited subset of genetic variation captured by their genotyping chip (which almost exclusively targets genetic variants with a frequency of greater than 5%) doesn't include any variants with an extremely strong association with NFL prowess.

That shouldn't come as a surprise to anyone who's been following advances in human genetics for the last few years; a genome-wide association study on a highly complex trait with a sample size of 100 has, historically speaking, a vanishingly small chance of yielding any positive results at all. (Yes, there are exceptions, but I don't think a sensible prior expectation would be that athletic performance has a similar genetic architecture to macular degeneration.)

NFL players are taller and heavier than average, in addition to being able to run the 40 in 4.5 seconds. Seems like a lot of these are quantitative traits.

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Menopause with a purpose   posted by Razib @ 10/13/2009 01:14:00 AM

Virpi Lummaa is at it again, Fitness benefits of prolonged post-reproductive lifespan in women:
Using complete multi-generational demographic records, we show that women with a prolonged post-reproductive lifespan have more grandchildren, and hence greater fitness, in pre-modern populations of both Finns and Canadians. This fitness benefit arises because post-reproductive mothers enhance the lifetime reproductive success of their offspring by allowing them to breed earlier, more frequently and more successfully. Finally, the fitness benefits of prolonged lifespan diminish as the reproductive output of offspring declines. This suggests that in female humans, selection for deferred ageing should wane when one's own offspring become post-reproductive and, correspondingly, we show that rates of female mortality accelerate as their offspring terminate reproduction.

The effect of a grandmother being around seems to be ~10% increase in the survival likelihood of grandchildren. Not trivial.

Update: Yep, it's an old paper. If you haven't read it, still work checking out Lummaa's work.


Monday, October 12, 2009

Answering ancient history questions with an equation   posted by Razib @ 10/12/2009 04:03:00 PM

Peter Turchin is at it again, Coin hoards speak of population declines in Ancient Rome (ungated version):
In times of violence, people tend to hide their valuables, which are later recovered unless the owners had been killed or driven away. Thus, the temporal distribution of unrecovered coin hoards is an excellent proxy for the intensity of internal warfare. We use this relationship to resolve a long-standing controversy in Roman history. Depending on who was counted in the early Imperial censuses (adult males or the entire citizenry including women and minors), the Roman citizen population of Italy either declined, or more than doubled, during the first century BCE. This period was characterized by a series of civil wars, and historical evidence indicates that high levels of sociopolitical instability are associated with demographic contractions. We fitted a simple model quantifying the effect of instability (proxied by hoard frequency) on population dynamics to the data before 100 BCE. The model predicts declining population after 100 BCE. This suggests that the vigorous growth scenario is highly implausible.

The figure to the left shows the reasoning. A simple model which related population size (dependent) to coin hordes (independent) was fitted before 100 BCE. The correlation between coin hordes to population size and political stability are well attested for many polities. In any case, using the model and projecting outward with the coin hordes known for the early imperial period a theory which suggests that multiplicative increases in census size during the Julio-Claudian age were a function of a shift in the accounting method (instead of simply males, including the whole household) was supported. The high count was already implausible on other grounds (e.g., if true, that means that Italy never attained the early Roman imperial population size until the mid-19th century), but that the model fits so well with the lower projections previously offered by other scholars is very suggestive. Contra extreme subjectivists some models of the past are probably right, and some are probably wrong.

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Maybe it was agriculture   posted by Razib @ 10/12/2009 12:46:00 AM

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium:
The number and volume of cells in the blood affect a wide range of disorders including cancer and cardiovascular, metabolic, infectious and immune conditions. We consider here the genetic variation in eight clinically relevant hematological parameters, including hemoglobin levels, red and white blood cell counts and platelet counts and volume. We describe common variants within 22 genetic loci reproducibly associated with these hematological parameters in 13,943 samples from six European population-based studies, including 6 associated with red blood cell parameters, 15 associated with platelet parameters and 1 associated with total white blood cell count. We further identified a long-range haplotype at 12q24 associated with coronary artery disease and myocardial infarction in 9,479 cases and 10,527 controls. We show that this haplotype demonstrates extensive disease pleiotropy, as it contains known risk loci for type 1 diabetes, hypertension and celiac disease and has been spread by a selective sweep specific to European and geographically nearby populations.

In ScienceDaily:
By comparing human data with genetic data from chimpanzees, the team were able to conclude that the genetic variant was the result of a selection event favouring variants that increase the risk of heart disease, coeliac disease and type 1 diabetes in European populations 3,400 years ago. The authors suggest that the risk factors were positively selected for because they gave carriers an increased protection against infection.

"The study of blood traits is challenging because of the difficulty of teasing apart biological processes underlying the origin of blood cells," explains Dr Christian Gieger, Head of the Genetic Epidemiology research unit at the Helmholtz Zentrum and co-lead of the HaemGen consortium. "Until now, few genome-wide association studies have looked beyond single traits. But, through a systematic analysis of correlated traits we can begin to discover such shared genetic variants, forming the basis for understanding how these processes interact to influence health and disease.

This sort of disease-based pleiotropy is of course interesting because disease really bites. On the other hand, I think other many interesting phenotypes are out there which probably emerged due to pleiotropy. East Asian hair and European eye color are two guesses. Looking for these clusters of traits associated with one genotype might be a nice way to crank-down the probability of an adaptive-story.


Sunday, October 11, 2009

Effects of Toxoplasma gondii   posted by Razib @ 10/11/2009 11:40:00 PM

An older article on the effects of Toxoplasma gondii in Schizophrenia Bulletin:
Consistent and significant differences in Cattell's personality factors were found between Toxoplasma-infected and -uninfected subjects in 9 of 11 studies, and these differences were not the same for men and women. After using the Bonferroni correction for multiple tests, the personality of infected men showed lower superego strength (rule consciousness) and higher vigilance (factors G and L on Cattell's 16PF). Thus, the men were more likely to disregard rules and were more expedient, suspicious, jealous, and dogmatic. The personality of infected women, by contrast, showed higher warmth and higher superego strength (factors A and G on Cattell's 16PF), suggesting that they were more warm hearted, outgoing, conscientious, persistent, and moralistic. Both men and women had significantly higher apprehension (factor O) compared with the uninfected controls.

I was thinking about this because I was trying to convince a friend who hadn't had cats that he should really think about getting some. It reminded me a bit of the old Garfield episode, "King Cat," where the Egyptians worshiped and pampered their cats. The feline dominated society was overthrown thanks to the influence of dogs upon human beings. There has been plenty of stuff on the differences of Toxoplasma gondii between nations, but I wonder about the effect over time. I haven't been able to find the data, but I recall that widespread pet ownership was a practice which emerged with the rise of the middle class.

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Friday, October 09, 2009

The uninsured, by county, by voting   posted by Razib @ 10/09/2009 07:43:00 PM

The New York Times has a piece, The Divided States of Health Care:
Those who lack health insurance now are far more likely to live in states that usually vote Republican — the states whose senators and representatives are least likely to support a law to extend coverage.

That would seem to indicate that Republican constituents are the ones who would most benefit from passage of universal health insurance coverage. But an analysis of Congressional districts within those states indicates that those without health insurance are much more likely to live in strongly Democratic Congressional districts. Many of those contain large minority populations with relatively low incomes.

This is not a surprising finding. Some of the most Democratic districts due to variables of race & income are in "Red States." The text alludes to more granular analysis, but it doesn't show up in the graphics, which is focused on the state level. But the county level data is freely available from the Census. To the left is a map of uninsured (those 18-64) by county. It does seem to me that state regulations or policies have some influence, look at the Pennsylvania-Ohio border with Kentucky and West Virginia, and Pennsylvania's border with New York. Culturally the Appalachian areas of Pennsylvania are extensions of West Virginia. Or look at the Missouri-Iowa border. But we can do more than just look at maps. Let's compare the county-by-county variation against other metrics. For example, how about voting for this year's Nobel Peace Prize recipient in the fall of 2008. What's the correlation?

I was a little surprised when I got a correlation of -0.33. That is, a negative correlation for voting for Barack Obama and proportion of uninsured on the county level. This assumes a level of linearity which really isn't there when you look more closely. You can see in the scatterplots at the bottom of this post, but let's just go with the linear for the moment so I can stick to correlations; you can correct by looking at the loess curves later on. Here are some other correlations with the proportion uninsured in each county (most of the dta are from the American Community Survey 2005-2007 of the Census, the "Foreign Born Males" data are for males over the age of 18):

-.36 - White (not Latino)
0.07 - Black (not Latino)
0.48 - Latino
0.43 - Foreign Born Males
-.29 - Age
-.24 - Median Household Income (2006)
-.15 - Median Home Value (2006)

I was a little curious about the lack of correlation with health insurance for blacks, but this from the Census clears it up:
At 89.4 percent, non-Hispanic Whites were more likely to have health insurance coverage than any other racial group. Those reporting 'some other race' were the least likely to have coverage, 66.0 percent [most of 'some other race' are probably Latino -Razib]. The health insurance coverage rates for the remaining single-race groups fell in that range - 85.5 percent for Asians, 83.8 percent for Native Hawaiians and Other Pacific Islanders, 82.0 for Blacks, and 68.4 percent for American Indians and Alaska Natives. The health insurance coverage rate for Hispanics was 68.5 percent.

This includes both private health insurance and public health insurance (Medicaid) for those under 65. Look at the map for those at or below 200% of the poverty rate. It looks like Medicaid is covering many people in the Black Belt, while regions in Appalachia which aren't quite as destitute in northern Alabama and Mississippi are relatively underinsured. The Census also reports that those ages 18-24, and 25-34, have coverage rates of 71.4 and 73.3 respectively, before jumping up to nearly 81% in the 35-44 range. For non-citizens the rate is around 50%.

How about limiting the data set to those counties where 90% of the population is white, not hispanic. That leaves 1477 counties in the data set.

-.48 - Obama
-.30 - Income
-.12 - Home Value

As you can see, in very white counties the inverse relationship between proportion uninsured and proportion voting for Barack Obama holds. I played around with limiting geographically. In New England and Tennessee there's no correlation between voting for Obama and insurance rates. But New England had really uniform voting. Tennessee might be a special case where lower insurance coverage rates among blacks are at play. In California and Texas the lack of insurance among Latinos positive correlations between voting for Obama and underinsurance, but only on the order of ~0.10.

I'm a little confused by these results. You can get the original data as a csv and see if I switched the sign or did something wrong. I wouldn't be surprised. My general model though is that this is a case of:

1) The Dems tending to get high and low socioeconomic status groups (not necessarily the super-rich, but the middle and upper-middle class college-educated).

2) The poor get insurance through Medicaid. And public sector workers and small business people of approximately same incomes are likely to differ in their insurance rates (public sector workers are overwhelmingly insured from what I know).

3) Democratic leaning states have more robust insurance systems for the poor. Take a close look at some of the inter-state differences on the borders; rather stark. In a lot of data county level variation doesn't give you a sense of state borders, especially those dictated by latitude or longitude. Not so here.

Here are the some plots.

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Migration & evolution   posted by Razib @ 10/09/2009 12:11:00 PM

Evolution with Stochastic Fitness and Stochastic Migration:
As has previously been shown with selection, the role of migration in evolution is determined by the entire distributions of immigration and emigration rates, not just by the mean values. The interactions of stochastic migration with stochastic selection produce evolutionary processes that are invisible to deterministic evolutionary theory.

I haven't read the paper yet, but on my "To-Read" list....


Get credit   posted by Razib @ 10/09/2009 10:31:00 AM

I don't usually post this sort of stuff, but I suspect that this might be of interest to readers of this weblog, What Happens When You Need a Loan but You Don't Have Any Credit?:
I don't own a credit card. Never needed one. By the time I was old enough to carry plastic, the convenience of the card had been cleaved from the possible dangers of credit. The debit/ATM card allowed me to buy goods without holding cash, and did it without exposing me, particularly as a teenager, to the temptations of credit. As I got older, I had the money to live within my means, and so I did so. I figured this meant I had a good credit score. It wasn't until a few years ago, when I tried to open a Banana Republic credit card to get a few bucks off some fall purchases, that I realized it meant I had no credit score. Not a bad credit score. No credit score.

Then I tried to buy a house.

Without a credit score, Fannie Mae and Freddie Mac wouldn't hold my loan. That meant most big banks wouldn't loan to me at particularly favorable terms, as they'd have to carry the loan themselves. My other option was going through the Federal Housing Administration, which meant that the banks would require that I pay extra for private mortgage insurance.

I talked to another GNXPer recently who didn't have a credit card. Until last year I didn't have one either. My theory was that I lived within my means, have few expenses, was healthy, etc. etc. I know plenty of people like me, young, intelligent and not too interested in signalling with positional goods and such, who didn't get caught up in the real estate craze, and so made a calculation that there was no need for credit (at least for the time being).

And then you run into issues like above. At some point you may need credit, and you're a "credit ghost." I actually wasn't a credit ghost because I had had credit cards in college (when my cash flow was a little more unpredictable, if you get my drift), and for some reason two of the accounts remained open (though with no activity in nearly 10 years). I found this out after checking my credit score after hearing about this problem in early 2008.

There are many ways your credit score is calculated. Here are three variables:

1) the amount of credit you have access to matters (i.e., add up your credit lines)
2) the amount of utilization of that credit matters (i.e., how much of your lines are you drawing on)
3) the length of time you've had an account matters

So one easy way for people who don't live beyond their means to increase their credit score is apply for a card every 6 months and barely use them (but enough so that they won't close the account for lack of use). A problem with compulsive spenders is that if they have more cards, they spend more. But for people who shy away from credit this isn't an issue (presumably), so this is an easy way to increase your credit score. The reason to apply every 6 months is that if you apply for too much credit at the same time you get a bunch of "inquiries" and that drops your score, and you might simply get rejected because it seems like you're hard up for money and so a bad risk.


Thursday, October 08, 2009

The urban vs. rural baby gap   posted by Razib @ 10/08/2009 06:54:00 PM

A comment on the post below made me wonder about fertility differences between urban and rural areas of the United States today. I used the GSS variables "childs" and "srcbelt" (the latter recoded a bit), and limited to whites age 40 and over between 1996-2006. Chart of distributions & means below

Mean # of children
City 1.99 12 Largest cities 1.79
Suburb 2.16 Other cities 2.09
Town 2.41 12 Largest suburbs 2.18
Rural & farm 2.5 Other suburbs 2.14
Towns 2.41

Rural & farm 2.5

Seems like cultural clustering. I disaggregated in the means to show how the super-cities are somewhat different; New York is a different beast from Minneapolis I assume when it comes to cost of living. One thing to note of course is that many people who are suburbanites at 45 are likely urbanites at 25 and suburbanites at 15, and so forth. It it interesting that suburbanites and urbanites converge at around 4 children, while those in rural and small town locales have a higher frequency of very large families. This is probably reflecting that "2 child norm" is stronger in urban and suburban areas where college degree holders predominate.


Semitocracy   posted by Razib @ 10/08/2009 02:15:00 PM

Reading Sumer & the Sumerians to see if there are any new facts known about these people and period since I was a kid. Unfortunately, as noted in the preface, after 1991 and until the mid-2000s (when the book was published) archaeology in Iraq wasn't feasible. So not so much. But, the author does note and reiterate an old dynamic: the slow but persistent decline in the proportion of those for whom Sumerian is a native language in the cities of Mesopotamia. Semitic speakers (e.g., Akkadians) were a presence in the earliest extant cuneiform tablets ~3000, and were likely dominant in the north of Mesopotamia. Earlier and more speculative works in fact have suggested that the Sumerians, whose language seems an isolate (unrelated to any other in the world), were outsiders who arrived from the south. So the Semitic speaking peoples may in fact have been indigenes who were temporarily dispossessed.

In any case, the text makes it clear that it seems two types of rural nomads moved into the cities of Sumer. Very wealthy individuals who experienced diminishing marginal returns as their herds expanded in size, and who found in cities more opportunities for efficient allocation of their capital. And secondly, very poor nomads who simply no longer had herds which were numerous enough for them to subsist. For the whole period of Sumerian cultural ascendancy, from 3000 to 2000 BCE, one presumes that the nomadic population reserves were stocked then with the "middle class" which hovered around the margins of subsistence. From what can be gathered by the textual evidence the nomads were invariably populations which were Semitic. The Sumerians were city-dwellers, though no doubt they also formed the peasantry around the canals and irrigation works during much of this period. Somehow we know that gradually between 3000 and 2000 the Sumerians went from being the majority in the cities of Sumer, to being a likely minority (though still culturally and to some extent politically dominant). By 1800 BCE it is likely that Sumerian was a dead language (one can't dismiss the possibility of Sumerian speaking communities here and there, but they're gone from the written record).

So what happened? The gradualism is of particular interest to me, and the likely concentration of Sumerians in the cities. It seems plausible that because the Sumerians were the first to settle in the cities, and concentrate disproportionately within them, natural increase would have been reduced for them relative to less urban populations. The slow replacement by Semitic speakers may have been due to the fact that Semitic speakers had a demographic reservoir which the Sumerians did not. There is of course a way to balance this out, and that is cultural assimilation. It seems likely that this did occur, but for some reason this was not a powerful enough effect so as to prevent the Semitic takeover. Or was it? 1,000 years is a long time. For all we know the Sumerians may have arrived as a small minority form the outside, and their lasting 1,000 years, as well as leaving a cultural impact which redounded down the generations, was a rather good show. That being said, I do wonder if the edifice of cultural complexes were more primitive during the time of Sumer than they became later, as the long road of cultural evolution of written & institutional civilization was only beginning.


Friday, October 02, 2009

Religion & teen birthrate, a real relationship   posted by Razib @ 10/02/2009 01:25:00 AM

A few weeks ago I pointed to a paper which suggested a state-level relationship between teen births and religiosity. I did the calculation, and added in race as a control, as well as breaking out birthrate of the 15-17 age bracket. My results differ a little because 1) I didn't impute states like Rhode Island, 2) I think I used 2000 Census household income numbers, not later American Community Survey numbers (my bad).

Teen Birth Rate

15-17 Birth Rate

r r (control Black) r (control Household Income) r r (control Black) r (control Household Income)
Black 0.41
0.41 0.39
Median Household Income -0.59 -0.59
-0.49 -0.49
Religiosity Index 0.72 0.64 0.55 0.65 0.56 0.49

Race didn't make that big of a difference. Here's a map with the states:

Click it for the big version. But Utah is an outlier now because its 15-17 teen birthrate is way lower than when you include 18-19. The social reason for this is obvious; young marriage among Mormon women.

I'm skeptical of the conclusions or at least the explanatory framework in the model in the paper. I will do an analysis of Hispanics, as there's something there. The states well above the trendline have large Hispanic populations, and Hispanics aren't that much more religious than whites (so they would push a state in the vertical direction, but not to the right). But I think if I can get county level data I might see some interesting correlation with Scotch-Irish ancestry. Some of the states with high teen birthrates, like Oklahoma, have a higher proportion of Non-Hispanic whites than nationally, so there's some other story to be told here.

Addendum: I suspect that a lot of the time when it come to religion and social data the causality is inverted. Both the anti and pro-religious tend to take the efficacy of religion for granted (though their value judgments would be inverted). But in many cases it may be that particular religious "styles" (e.g., low church vs. high church) reflect the state of a given society. There is a body of social science data which shows the strong relationship between socioeconomic status and particular Protestant denominations, and the strongly biased "switching" of those who move up or down the socioeconomic ladder in their lifetimes. A similar effect might be at work on the aggregate social level.


Thursday, October 01, 2009

Science to publish Ardipithecus ramidus paper   posted by Razib @ 10/01/2009 09:58:00 AM

That's what Kambiz Kamrani is saying. Significance:
Owen Lovejoy is one of the authors of the paper, and he says that the fossil changes the notion that humans and chimps, our closest genetic cousins, both trace their lineage to a creature that was more like today's chimp and we'll have to be rewriting our text books soon. This is big folks. What this means is that our common ancestor was a bipedal forest forager and that chimps were an evolutionary offshoot.

Update: John Hawks & Carl Zimmer.

Update II: Science's Ardipithecus page is up. You can get the papers free with registration.