Gene Expression

Applied Statistics over at ScienceBlogs

2009-11-07T19:19:00.001-08:00

Just a reminder, Andrew Gelman is now blogging at ScienceBlogs under "Applied Statistics".

Coffee or not

2009-11-02T10:56:00.000-08:00

Real vs Placebo Coffee. There's a real effect. Though interestingly those who secretly were given decaf didn't notice it in their self-reports.

Inequality & wealth

2009-11-02T10:27:00.001-08:00

A review over at ScienceBlogs of a new paper, Intergenerational Wealth Transmission and the Dynamics of Inequality in Small-Scale Societies. I'm going to comment more in the near future, as I think this an give us insight into historical dynamics. An interesting find is that pastoralists and settled agriculturalists exhibit the same levels of heritability of material wealth (as well as the same values on material wealth). Hunter-gatherers and slash & burn agriculturalists seem to be at the other end of the spectrum.

Sunshine and SEC Football

2009-11-02T07:35:00.000-08:00

The cover story for Sports Illustrated two weeks ago described the dominance of the South Eastern Conference (SEC) in US college football.

"More players are invited to the NFL combine each year from the SEC than from any other conference," Ole Miss's [Head Coach] Nutt says when asked about the quality of the athletes who compete in the league. "The most players drafted just about every year going back 10 years come from the SEC." Indeed, dating to the 2000 NFL draft, the conference has had 400 players selected; the next-best league is the ACC, with 364.

It's no mystery to Nutt why an SEC team has won the BCS national championship each of the last three years (Florida in 2006 and 2008, LSU in 2007) and is favored to produce the champ again this season. "I watch [teams in] other conferences all the time and I think, Boy, I'd like to play them," Nutt says.

But, for GNXP readers, this is the most fun comment.

It all starts with recruiting. Nutt says that players from the South, particularly those who reside in Florida, become better college players than kids from other parts of the country, though he can't explain why. "Maybe it's the sunshine," he says. "In any given year an average of 335 young men [from Florida] sign with Division I schools. When I was coaching at Murray State [in Kentucky], I remember going to Florida and seeing, maybe, coaches from Wake Forest down there. But now? You've got Wisconsin, Minnesota, Purdue, Virginia, Virginia Tech. You've got schools from North Carolina. They're all down there, and they're coming for the speed. We signed nine from Florida this year. Nine!"

Yeah! It's the "sunshine" that causes the "quality of the athletes" in the SEC. Caste Football calculates that the percentage of white starters at SEC teams is 25%, lower than any other major conference.

Of course, from a GNXP point of view, sunshine may be actually have played a role, but not in the way that Nutt implies . . .

William Gunn is looking for another job

2009-11-01T21:49:00.000-08:00

Early (2002) reader of this weblog, William Gunn, is leaving a biotech company in San Diego and is looking for another job. Here's his Linkedin.

How European is New England...not as much as I thought

2009-11-01T13:53:00.000-08:00

One hypothesis I have held is that there is a cultural gap in the United States whereby the West Coast and the Northeast are more "European" than the rest of the nation. So you have ideas crop up like Jesusland. I decided to see if I could compare European nations and American subregions using the WVS, Eurobarometer and GSS. I looked at two issues:

1) Belief in God
2) Nationalism

These two had equivalent questions in the 2000s for the WVS & GSS. I created an index of religiosity whereby:

Atheists & agnostic = 0
Higher Power = 1
Theist = 2

And:
Very Proud of Country = 3
Somewhat Proud of Country = 2
Not Very Proud = 1
Not Proud at All = 0

On these two traits I don't see much of a Blue America + Europe clade....

Note: Limited GSS results to the 2000s.

Andrew Gelman's "Applied Statistics"

2009-10-31T17:01:00.000-07:00

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

2009-10-31T15:11:00.000-07:00

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.

Names frequency changes not always stochastic

2009-10-30T11:15:00.001-07:00

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

2009-10-30T00:15:00.000-07:00

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.

Center-Right world?

2009-10-29T15:49:00.000-07:00

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.

Germs, collectivism and serotonin

2009-10-28T13:38:00.000-07:00

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

2009-10-28T00:13:00.000-07:00

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):

religwave2.xls

religwave4.xls

religwave5.xls

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!

What Darwin Said: Part 7 - Levels of Selection

2009-10-27T05:43:00.000-07:00

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.

References:
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.

The slob factor

2009-10-26T23:01:00.000-07:00

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

2009-10-26T22:29:00.000-07:00

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

2009-10-26T16:25:00.000-07:00

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."

Svante Paabo believes modern humans & Neandertals interbred

2009-10-26T14:20:00.000-07:00

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.

H/T: Anthropology.net

When you can meet online, will colloquia disappear?

2009-10-24T19:08:00.000-07:00

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.

EDAR & lubrication

2009-10-23T23:18:00.000-07:00

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?

2009-10-23T22:11:00.000-07:00

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.

Inferring demographic history

2009-10-23T12:52:00.000-07:00

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.

Welcoming Nicolae Carpathia

2009-10-22T20:00:00.000-07:00

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

2009-10-22T19:00:00.000-07:00

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).

People can't judge their own political ideology

2009-10-21T19:17:00.000-07:00

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 identication in predicting both presidential and congressional voting. In fact, conventional denitions of ideology, predicated on self-reporting, show themselves to be completely inadequate.

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