Wednesday, December 30, 2009

The engineer terrorist   posted by Razib @ 12/30/2009 10:25:00 AM

Slate reviews the scholarly literature. Explaining the mechanics of the over-representation of engineers at the higher echelons of transnational terrorism is a guessing game, but the empirical reality seems relatively robust. Though I suspect that sociological and economic factors are necessary (see the linked paper in the article), I think the ultimate precondition has to be the psychology and training of engineers, who are geared toward analysis of a problem and devising a solution. The most ingenious/ridiculous models of Young Earth Creationism seem to spring from the minds of fundamentalist engineers, who must resolve their Biblical literalist premises with the world as it is. One can foresee how the same sort of mentality would be much more explosive in the Islamic world, where the fundamentalist premises lead to a set of inferences (e.g., Islam's manifest superiority over the West) which seems at variance with the state of the world. The engineer resolves this contradction by devising "solutions."


Tuesday, December 29, 2009

Why do we delay gratification even when there is no downside?   posted by agnostic @ 12/29/2009 09:10:00 PM

Earlier this year, John Tierney reviewed several studies on how delaying gratification makes us feel better in the short term by preventing guilt but makes us feel more miserable in the long term by causing regret over missed opportunities. I added my two cents here, just to note that this sounds like part of the Greg Clark story about recent genetic change in the commercial races that adapted them to the emerging mercantile societies they found themselves in. What I had in mind was the delaying of vice -- investing a dollar today rather than splurging, moderating the amount of drink or sweets you enjoy, and so on.

But now Tierney has another review of related studies which show that we delay gratification even for what should be guilt-free pleasures like redeeming a gift card, using frequent flier miles, and visiting the landmarks in your local area. And don't we all have enjoyable books and DVDs we've been putting off? After indulging in these cases, there is no potential bankruptcy, no hangover, and no tooth decay -- so why do we indiscriminately lump them in with genuine vices and put off indulging in them? Obviously this tendency too is a feature of agrarian or industrial groups -- hunter-gatherers would never leave gift cards lying around in their drawers.

It must be because of how recent the change toward delaying gratification has been. Given enough time, we might evolve a specialized module for delaying gratification in vices and another module for doing so in guilt-free pleasures, which would be better than where we are now. But when our genetic response to a change is abrupt, typically we have broad-brush solutions that take care of the intended target but also leave plenty of collateral damage. Over time our solutions get smarter, but it takes awhile. Just look at how crude the responses to malaria are.

We see this domain-general taste for (or aversion of) risk in other areas. People who lead more risky lifestyles buy much less insurance than people who lead cautious lifestyles. Those who ride motorcycles without helmets would be richer and more likely to pass on their genes if they bought a lot of insurance, while those who play it safe would be richer by not buying all that superfluous insurance. Instead, daredevils are daredevils all the way -- including a contempt for insurance.

This casts doubt on how easy it is to change our behavior so that we no longer postpone our indulgence in guilt-free pleasures. Because we have a domain-general delay of gratification, it will still just feel wrong. You can also argue the logic of buying lots of insurance to the motorcyclist who rides without a helmet, but that won't change his mind because his tastes for risk is across-the-board.

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One year after the financial collapse, Gotham in a downward spiral   posted by Razib @ 12/29/2009 12:59:00 AM

Actually, not really. New York on Track for Fewest Homicides on Record. I assume that those who project long term fiscal problems due to a contraction in the financial sector in New York City are probably correct (assuming that the financial sector actually doesn't expand back to its pre-2009 size). But the assumption that the economic fallout would lead to 1970s levels of anomie doesn't seem to be panning out. As I indicated earlier I found suggestions of such a reversion plausible at the time because I had a rather economistic mental model of the "root causes" of crime. But that seems less plausible when you look over the arc of the past century. Another model of course is that in fact it was financial sector workers who were driving much of the crime directly by subsidizing illicit activity through their enormous incomes generated by the efficiencies of capital allocation which they drove (I'm not being serious here).


Sunday, December 27, 2009

New comment format   posted by Razib @ 12/27/2009 03:34:00 PM

A lot of people (including paying readers! kidding!) are complaining about the new commenting format. I'll be euphemistic and observe that it's suboptimal. But I don't have time to work on tweaking and beautifying it now, so please be patient. Over time it'll move up the stack of my priorities, and hopefully your awesome contributions to the discussion will be facilitated by a more elegant and user-friendly commenting interface by the end of January.

Additionally, I am thinking that posting "admin" messages in this space is also suboptimal. It uses space which should be allocated to real posts about science and such. If you're in the minority of readers who actually cares enough about your blog-reading experience to gripe in the comments, I invite you to subscribe to/follow my twitter feed, I'm gonna put "admin" related stuff there from now on. You can also send messages via twitter. Email is fine as always, but if you're someone who I don't recognize, there's a non-trivial chance that you'll stay at the bottom of the task stack and I'll never get back to you. I have my twitter feed on my Google homepage, so I am more likely to see random direct messages (as I noted earlier, I get a non-trivial number of messages from PR people, so it isn't unlikely that I'm forgetting emails in the "none of the above" folder).


Mutation and selection in stickleback evolution   posted by p-ter @ 12/27/2009 08:46:00 AM

Understanding the precise molecular mechanisms underlying changes in animal morphology is a tricky problem--usually two species which have diverged morphologically (say, mice and humans) are now so unrelated as to make genetic study exceedingly difficult, if not impossible. For years, a group led by David Kingsley has been addressing this problem in a cleverly-chosen model--three-spined sticklebacks. Importantly for the question of morphological evolution, freshwater populations of this fish have lost many of the spines and pelvic girdle carried by the saltwater populations (there are a number of hypotheses, probably not all mutually exclusive, for why this has been under selection).

In a new paper, this group demonstrates the precise genetic alteration underlying this change in a number of freshwater populations. Perhaps surprisingly, it appears to be due to the recurrent deletion (in different freshwater populations) of an enhancer of an important developmental gene. Strikingly, creating a transgenic freshwater fish with a copy of this enhancer (which normally is missing) leads to freshwater fish with a pelvis like the saltwater fish.

In fact, this enchancer seem to fall in a "fragile" (read: repeat-laden) region of the genome, which presumably increases the rate of deletion at this site. If one imagines there are a number of genetic paths to get to the reduced pelvis size favored in freshwater environments, the probability of each path depends on the mutation rate of each genetic change. In this case, many (though not all) freshwater populations have independently taken the same path, likely due to the increased mutation rate at this fragile site.


Citation: Chan et al. (2009) Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer. Science. Published Online December 10, 2009 [DOI: 10.1126/science.1182213]


Thursday, December 24, 2009

Merry Xmas   posted by Razib @ 12/24/2009 02:20:00 PM

& a happy New Year.

Wednesday, December 23, 2009

The old old time religion   posted by Razib @ 12/23/2009 10:55:00 PM

Ross Douthat, Into The Mystic:
But as the Pew chart suggests, there is one sense in which religion was less influential in mid-century American life than it is today, and that's the realm of personal mystical experience. Slightly more people went to church in 1962, but many fewer people went out looking for their own private encounters with the numinous. This isn’t a surprising correlation, since the traditional Christian churches tended to either discourage mystical freelancing or (in the case of Catholicism) encourage it only within the framework of monastic discipline. The churches constrained and channeled Americans' religious impulses; their declining influence let a hundred mystic flowers bloom. Christianity became less culturally powerful, but religion itself - whether you were a tongues-speaking Pentecostal, a Gaia-communing pantheist, or some combination thereof - became much more freewheeling and intense.

Whether atheists, agnostics, and secular-minded Americans should prefer this dispensation depends on which raises their hackles more: Having laws and moral norms that are heavily influenced by Christianity, or having a culture that's heavily influenced by mysticism and supernaturalism. If you favor legal abortion, no-fault divorce, and easy access to pornography, today's America is a more pleasant place to live than the America of mid-century. (Especially if, like some atheists, you find pantheism to be the most congenial form of theism.) But if you don't like having your seatmate on an airplane ask if you've been born again...if you don't like being harangued at cocktail parties about the Mayan apocalypse or the healing power of crystals...if you don't like seeing the shelves at your local bookstores filled up by authors who claim to have conversed with the Almighty...well, then you might legitimately feel nostalgia for an earlier, less mystical America.

I recently recorded a diavlog with Nicholas Wade on The Faith Instinct. In that book Nicholas outlines the change in religion from its "primitive" state to what we would term "higher religion." Higher religion is built on the foundations of primitive religion, as institutional religion becomes less powerful in the lives people in the Western world people seem to be reverting back to their cognitive "default" settings. More often when you strip away adherence to theology you do not get atheism, you get animism.

Is this good for the small set of atheists and asupernaturalists? On an interpersonal level it might add a bit more confusion to one's life, as you never know which direction someone trying to sell you on supernaturalism is going to come from. But on a societal level it probably reduces the ability of religious elites to manipulate sects as cohesive functional units toward their ends.


The diversity of the east   posted by Razib @ 12/23/2009 09:33:00 PM

Just a weird random thought. In the early 20th century the Ainu of Japan were considered by many physical anthropologists a branch of the white race. This fit in nicely with the historical fantasy of the period which often featured "Lost Races," with a lost white race the best of all. By contrast, the Negrito and Melanesian populations were considered outliers of the black race. Though the idea of Ainu as white seems to have diminished, in part because those sorts of ideas aren't too popular today, and partly because hardly any Ainu remain who do not have substantial ancestry from the Japanese. On the other hand, there remain pan-Africanists and black nationalists who talk about the unity of black peoples, from India to Melanesia. To the left is a photo where I've placed an Ainu man from the 19th century next to contemporary Andaman Islanders. I think you could understand why physical anthropologists of the period classified populations as they did based on appearance.

But with all the more recent genetic studies it seems pretty clear that the Ainu and the Andaman Islanders are part of a broader swath of "easterners" who swept out of Africa (in fact, there are Y chromosomal haplogroups which the Ainu share with Andaman Islanders). Older classical markers suggested that the Ainu were an East Asian people, and the uniparental markers suggest the same thing (I don't see any more recent SNP array studies which look at the Ainu). As for the Andaman Islanders, it seems very likely that they're simply an island population of the ancient "eastern" substrate of South Asia, which has been admixed on the mainland with a "western" quasi-European element, which in many regions and castes is now dominant. The Ainu and the Andaman Islanders are probably just the remains of the physical diversity which was once much more common in eastern Eurasia than it is today. That diversity may have gone by the wayside because of the expansion of the Han and the Austronesians, but it may serve as a hint that there may be only a few basic human racial morphs which reoccur, whether by chance or adaptation.

Addendum: The non-Bantu populations of southern Africa look East Asian. Also, since the Reich et al. paper on Indian genetics came out I've been reading up, and now I can see how the Andaman Islanders do kind of "look Indian." More specifically, there are some subtle facial features which South Asians have which must have come down from people distantly related to the Andaman Islanders. Look at the individual on the left in the photo above.


Transhuman Goodness   posted by Razib @ 12/23/2009 08:56:00 PM

Most of the readers of this weblog probably have as much use for the Singularity as John Derbyshire, but for those of you who dig Overcoming Bias and Less Wrong, you might check out Transhuman Goodness. The author, Roko Mijic, is so normal he could almost pass as a civilian!

Why are Mormons the American success story?   posted by Razib @ 12/23/2009 03:53:00 PM

I was skimming through a book on Scandinavian migration to Utah the other day, these Scandinavians being converts to Mormonism. The author noted that while most Scandinavian Americans settled in areas where farming was relatively easy, these converts went to Utah, which is a less than optimal territory when it comes to per unit productivity. Fair enough. But it got me thinking about why Mormons are so successful: perhaps it's just a function of migration. There were lots of American sects which arose during the early 19th century. The Disciples of Christ and the Seventh Day Adventists derive from the same period of religious ferment during the Second Great Awakening. But the Mormons have been the most successful. Why?

Perhaps it was the Mormon theology, the awesomeness of Joseph Smith. Or perhaps Mormons really are the One True Faith and god is on their side. But then I remembered that the original Mormons were New Englanders, and that most of New England's population in 1800 derived from the period between 1630-1640. The 20-30,000 who left England to establish a Puritan utopia in the New World. In the colonial period, and up to the Civil War, New Englanders were the most fertile group of Americans. Those Puritans who emigrated to New England in the 17th century, and remained (many went back to England during the period of Cromwell), have been extremely successful genetically in relation to their relatives in the home country. The reason is the simple Malthusian nature of biological increase; America had more room for growth (though England's population did grow very fast in the two centuries after the Puritans left, it did not match America).

The Utah Mormons are not the only descendants of Joseph Smith's religious idea. The Community of Christ, once the Reorganized Church of Latter Day Saints, and long under the stewardship of the Smith family, remained in the Midwest while Brigham Young led the migration west. Today the Community of Christ is in many ways a small mainline Protestant denomination, having lost or never developing the uniqueness of the Utah Mormons in terms of their theology. Numerically and socially it is relatively marginal, to the point where many Americans would be surprised as its existence (splinter Mormon sects which practice polygamy get a lot more press for obvious reasons).

The Community of Christ might illustrate the dynamic of attraction and absorption which occurs to splinter sects within a mature society. Over time minorities standardize their norms with that of the majority as they become respectable. This means they lose their distinctive cohesion. By contrast, the Utah Mormons were a people apart for several generations because of the nature of geographical distance in the 19th and early 20th centuries. Only with the rise of modern communication have they been assimilating, deemphasizing (at least in public) some of the more exotic aspects of their theology which might shock mainstream Christians. But because of the long incubation period in Utah the Church of Latter Day Saints remains fundamentally separate from what most Christians refer to as the "Great Tradition" of orthodox Christianity. By analogy to biology what occurred was an instance of allopatric religious speciation. In this model the great success of Mormons rests on their human geography during their formative period.

Some world historians point out that it has been nearly 1,500 since the last great distinctive world religion arose which challenged the status quo. Sikhism and Mormonism are instances of religious speciation, but they are small potatoes compared to Islam. Additionally, both of these traditions have shown some evidence of drifting back into their parent tradition (though Sikhs resist this, Hindus often claim Sikhs as simply a Hindu sect, while some Mormons have been slowly emphasizing their shared commonalities with other Christians). Perhaps modern communication technology and mobility will prevent future religious fissions on planet Earth? Perhaps subsequent to Islam the technological and communication gaps which new religions utilized to overturn older orders simply closed? In fact, if you read the travels of Ibn Battuta you might conclude that Islam itself served as a critical catalyst in closing up all the remaining gaps and discontinuities across the Old World oikoumene!


Selection & African Americans   posted by Razib @ 12/23/2009 02:12:00 PM

I already posted on the new paper on African American Genetics. I noticed that Frank Sweet says:
It is interesting that the 18 percent mean of Euro DNA markers in A-As has been holding steady for about 8 years now, having replaced the prior estimate of 25 percent.

Where did the prior estimate come from? I recall seeing it as well too. Were the older markers biased towards ones which might have been shaped by recent selection? The new paper doesn't have anything definitive in regards to this (they they mention the variance in African vs. European across different regions of the genome), though certainly some genes which affect malaria seem to have been shifted away from what you'd expect.


NPR has a science blog   posted by Razib @ 12/23/2009 01:25:00 PM

Cosmos and Culture.

Tuesday, December 22, 2009

Reminder on comments, enter a handle   posted by Razib @ 12/22/2009 11:13:00 PM

Please remember to enter a name when you put in a comment. Can be fake and such. Just something distinctive. I'm deleting comments from "Guests."

Canada & North American theocracy   posted by Razib @ 12/22/2009 12:45:00 AM

In the comments Europeans often point out that nations we Americans consider very secular, such as the United Kingdom and the Netherlands, actually provide state subsidy to religious schools. Part of the issue here is that Americans have a caricature of Europeans in mind, just as Europeans often have a caricature of Americans. Though in terms of their personal beliefs most Europeans are more secular than most Americans, that does not mean that we Americans can infer from that particularities of how Europeans organize their relationship between church & state. When the American republic was founded a proactive effort was made to separate the national government from any particular church or religion (a precedent which was eventually followed by the states in the early 19th century). At that time even nations with a reputation for religious tolerance, such as the Netherlands, arguably treated their minorities as what we would recognize today as "dhimmis" (see Divided by Faith: Religious Conflict and the Practice of Toleration in Early Modern Europe).

And yet despite the lack of national promotion of one particular sect America remains an exceptionally religious nation, at least by belief. Most European societies took different tracks (I think one major confusion by Americans is the idea that there is one European outlook on particular questions). Which brings me to a weird historical oddity I recently stumbled upon: Newfoundland had a purely sectarian public school system until 1997. You can read about it here. This system seems to be what the Catholic Church would have preferred in the 19th century for the United States, as the public school system was strongly tinged with Protestant presuppositions (e.g., reading Protestant Bibles). In the United States the Church lost. In Newfoundland it looks like they obtained a satisfactory compromise.

(the title is a joke, Canadians supposedly have a sense of humor)

Addendum: Before a Canadian points this out, yes, I'm aware that some provinces still allow for tax-support of sectarian schools.


Monday, December 21, 2009

Brain size & microcephaly genes   posted by Razib @ 12/21/2009 10:22:00 PM

Microcephaly Genes Associated With Human Brain Size:
Highly significant associations were found between cortical surface area and polymorphisms in possible regulatory regions near the gene CDK5RAP2. This gene codes for a protein involved in cell-cycle regulation in neuronal progenitor cells -- cells that migrate to the cerebral cortex during the second trimester of gestation and eventually become fully functioning neurons. The cerebral cortex is the outer layer of the brain, often referred to as "gray matter." The most highly developed part of the human brain, the cerebral cortex is responsible for higher cognitive functions, such as thinking, perceiving, producing and understanding language, some of which is considered uniquely human.

Similar but less significant findings were made for polymorphisms in two other microcephaly genes, known as MCPH1 and ASPM. All findings were exclusive to either males or females but the functional significance of this sex-segregated effect is unclear.

"One particularly interesting feature of this new discovery is that the strongest links with cortical area were found in regulatory regions, rather than coding regions of the genes," said Andreassen. "One upshot of this may be that in order to further understand the molecular and evolutionary processes that have determined human brain size, we need to focus on regulatory processes rather than further functional characterization of the proteins of these genes. This has huge implications for future research on the link between genetics and brain morphology."

Wouldn't be the first time that genes which have a connection to pathologies turn out to be useful in illuminating normal human variation. It'll be on the site of PNAS someday.


Crime way down. Who exactly knows stuff?   posted by Razib @ 12/21/2009 03:19:00 PM

Despite recession, crime keeps falling:
In times of recession, property crimes, in particular, are expected to rise.

They haven't.

Overall, property crimes fell by 6.1 percent, and violent crimes by 4.4 percent, according to the six-month data collected by the FBI. Crime rates haven't been this low since the 1960's, and are nowhere near the peak reached in the early 1990's.

Who expected crime to increase? Did you? I did. But I didn't know anything about crime statistics over time so I was working off naive intuition. Did social scientists expect this? I recall a lot of worry in the media about a year ago that the crime drop which started in the 1990s would be reversed, and I shared the worry. Here's Matt Yglesias worrying last January:
I think this is worth worrying about. One thing we know about crime is that when wages and employment levels for low-skill workers are high, crime goes down. Another is that mass incarceration works - increase the number of beds in prison and the number of sentence-years handed out and the crime rate drops. But the first of these is the reverse of what happens in a recession, and the second we've already pushed well past the limit of cost-effectiveness (see here) and it's inconceivable to me that you could actually push this far enough to compensate for the declining economy in the context of declining state budgets.

It's easy to find national uniform crime reports data back to 1960, and unemployment rates. Quick correlations between 1960-2008 are:

Violent Crime Aggregated 0.37
Murder 0.52
Rape 0.37
Robbery 0.53
Assault 0.24

Property Crime Aggregated 0.53

One seems to see a modest expectation for a rise in crime then over this time period. But poking around the ICPSR I came across Eric Monkkonen's data sets on homicide in New York City going back to the 19th century. Below are homicides per capita by year between 1900 and 2000. The second chart is log-transformed.

It seems that there's another "Depression Paradox" here. The economic distress of the Great Depression seems to have been associated with less crime, while the economic exuberance of the 1920s led to more crime. So if I constrained the time series from 1920-1940 the correlations might be quite different.

All things equal the recent past is a better guide to the near future than the less recent past. But it's important to remember that history does sometimes work in cycles, and the deeper past can occasionally give us insights which the recent past can not. One could construct a tentative model whereby basal crime rates reflect cultural norms, and once norms and crime hit a particular "equilibrium" it may take a bit of a "shock" for it to shift out of the stable state.

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Sunday, December 20, 2009

Coincidence or adaptation?   posted by Razib @ 12/20/2009 01:48:00 AM

Different Evolutionary Histories of the Coagulation Factor VII Gene in Human Populations?:
Immoderate blood clotting constitutes a risk factor for cardiovascular disease in modern industrialised societies, but is believed to have conferred a survival advantage, i.e. faster recovery from bleeding, on our ancestors. Here, we investigate the evolutionary history of the Coagulation Factor VII gene (F7) by analysing five cardiovascular-risk-associated mutations from the F7 promoter and nine neutral polymorphisms (six SNPs and three microsatellites) from the flanking region in 16 populations from the broader Mediterranean region, South Saharan Africa and Bolivia (687 individuals in total). Population differentiation and selection tests were performed and linkage disequilibrium patterns were investigated. In all samples, no linkage disequilibrium between adjacent F7 promoter mutations −402 and −401 was observed. No selection signals were detected in any of the samples from the broader Mediterranean region and South Saharan Africa, while some of the data suggested a potential signal of positive selection for the F7 promoter in the Native American samples from Bolivia. In conclusion, our data suggest, although do not prove, different evolutionary histories in the F7 promoter region between Mediterraneans and Amerindians.

The primary aim of this research seems to have been to figure out if the variance in a medical trait (prevalence in cardiovascular disease) could be traced to variance in this coagulation factor gene. Doesn't seem like that panned out. But their "Native American" sample happened to consist of Bolivian highlanders, Quechua and Aymara speakers. There are long haplotypes amongst these populations for the variant which seems result in increased risk for cardiovascular disease. I don't know much about physiology, but I immediately wondered if modulating traits which effect hematological system might have nasty side-effects. The populations of the Andes of course have developed some genetic tricks to optimize their functioning at high altitudes, bt tricks often have trade-offs. Of course this doesn't necessarily mean it's selection which drove up the frequency of the variant in question. Native populations of the New World seem to have gone through a population bottleneck, which can generate some of the same patterns. But there are enough non-highland groups whereby one could check to see if they have the high risk variant and a long haplotype as well.

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Friday, December 18, 2009

Cultures of constraint; Islam, India and Marxism   posted by Razib @ 12/18/2009 10:11:00 PM

Pew has a new report, Global Restrictions on Religion (HT JohnPI). It illustrates rather clearly some general trends which I've been mulling over for several years looking at cross-cultural data. Here's a 2-dimensional chart which plots the 50 most populous nations in their data set along an axis of governmental vs. social restrictions on religion.


There are the set of countries which have been shaped by Marxism in the recent past, or still are officially Marxist, which have strong legal sanctions against organized religion. China, Eritrea and Uzbekistan fall into this camp. But look at Russia. Perhaps Russian intolerance is a function of its Eastern Orthodoxy, but it seems plausible that Communist era elites have simply continued the tendency to control "subversive" religious groups that they had honed during the Soviet period (most Western nations were very restrictive of minority religions when the Russian Revolution occurred, but during the Soviet period many evolved toward a more tolerant state).

Then there are the Muslim countries. While China has official atheism, religious groups can flourish (at least within the natural bounds of the religiosity of the Chinese people, which seems to be set rather low) so long as they keep a low profile and don't get on the wrong side of the state. But in many Muslim countries hostility toward non-mainstream religious movements runs very deep. I don't need to elaborate on this, Muslims are the modern apotheosis of the Abrahamists of old, atheists toward other gods and promoters of their own (listening to the radio recently I noticed how talk show hosts given Muslims a pass when they get all effusive about how incredible their religion is. If a white Christian did this it would seem gauche). This probably explains on some level the extreme outrage in Muslim majority countries when Muslim expression in the non-Muslim majority countries is restrained. This response is totally not dampened by the strong tendency for Muslims to severely constrain the rights of non-Muslims when they themselves are in the majority. The Single Truth needs no apology, and why would one want to be fair and balanced between Truth and delusion? (I think back here to debates between pagans and Christians in Late Antiquity, as the latter brushed aside the pleas from the former for tolerance of belief and practice by arguing in effect that freedom of religion would only give succor to delusion and was therefore ultimately an obscenity. This stance remained dominant in the West down to the Enlightenment)

Finally, there's India. By India, I don't mean the nation of India. I mean the civilization, which includes Bangladesh, Nepal, Sri Lanka and yes, Pakistan. Poking through survey data it seems that Hindus are quite religious, like Muslims, but they are far less atheistic, as one would expect. The philosophical aspects of Hinduism which tend toward universalism and cultural parallelism seem to percolate down rather far (though the survey data I see probably excludes the illiterate masses). On the other hand, like Muslims Hindus seem to have really strong attitudes when it comes to religious defection or switching. India has laws discouraging or banning conversion which might be appropriate in the Muslim or (post-)Marxist world. When looking at survey data on South Asians from India in the UK or USA it is interesting to me that though the Hindus are only moderately religious in their self-conception, very few avow that they have "No Religion." This is in strong contrast with East Asia, and among East Asian immigrants, who routinely assert that they have no religious affiliation. While Indian Hindus by and large have no need to convert the world in totality to their religion, as Muslims and Marxists must in regards to their faiths, they are strong believers in the necessity of some religious identity. Additionally, they have an attachment to the idea that people should not defect or switch between identities, lest inter-communal harmony be disrupted.

In the report they express some surprise that Africa is relatively tolerant. I am not. From what I have read religious conversion and switching is very common in Africa, from Protestantism to Catholicism to Islam and back. Even heads of state have switched religions without extreme controversy. Perhaps this has something to do with the sheer fragmentation and diversity of most African nations, which are cleaved along many dimensions besides religion. Additionally, the roots of any given organized religion are generally rather shallow in most of these nations. So unlike Indian civilization switching religion doesn't carry a lot of historical baggage. The best analogy to Africa seems like the United States, which also have a huge diversity of religious sects, and where switching is generally not particularly surprising or controversial. Individual preference is balanced with communal identification.

Finally, I want to note the distinction between some European nations which are secular (France) and East Asian ones (Korea, Japan). Without the totalist influence of Marxism East Asian nations tend to take a relatively muted stance toward religion. Just as Sri Lankan Buddhists show that the identitarian reflex of Indians is not a function of Hinduism, Taiwan, Singapore and Hong Kong all illustrate that without official Marxism there is relatively robust tolerance of religious sectarianism. The power of one organized religion in East Asia was always much less than it was in Europe. Talking to many Europeans who are secular, though they themselves are not believers, they often find "non-traditional" religions rather weird. There is clearly a particular favoritism toward the traditional religion of a society, and a suspicion of new religions. This in some ways resembles the Indian attitude, except it is much more stripped of any supernatural content in terms of belief.

Here are two maps which illustrate the axes above:



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Avatar   posted by Razib @ 12/18/2009 11:12:00 AM

Open thread for reader reactions. Don't plan on watching it in the near future myself, but curious....

Wikipedia Article on Group Differences in IQ   posted by dkane @ 12/18/2009 10:28:00 AM

As penance for my sins, I have been involved in a lengthy mediation process at Wikipedia concerning the Race and Intelligence article. Check the links and the history for examples of how the (controversial) sausages are made.

As a result of this process, there is a new article entitled Between-Group Differences in IQ. As you can see, the article is a mess right now. But it could be great! Are there any GNXP readers willing to help out? Editing Wikipedia is the sort of experiences that you ought to try at least once. Main short term goal is to add the material from Rushton, J. P., & Jensen, A. R. (2005). Thirty years of research on race differences in cognitive ability. Psychology, Public Policy, and Law, 11, 235-294 (pdf). Any help much appreciated.

Thursday, December 17, 2009

The new comments   posted by Razib @ 12/17/2009 10:57:00 PM

Make up a name if you want to comment. I'm not going to let any "Guest" comments through from now on, since they seem to mess up the recent comments, and it makes it hard to know who is who.

Social science data sets   posted by Razib @ 12/17/2009 02:11:00 AM

At the Inter-University Consortium for Political & Social Research. Registration is free.


Wednesday, December 16, 2009

Shellfish & the human bottleneck   posted by Razib @ 12/16/2009 06:02:00 PM

How shellfish saved the human race:
Turns out, somewhere between 130,000 to 190,000 years ago, the human species was reduced to less than 1000 breeding individuals--just a few thousand people in total. Ancient, naturally driven climate change pushed our species to the brink, said Curtis Marean, Ph.D., a professor with the Institute of Human Origins and the School of Human Evolution and Social Change at Arizona State University.

What saved us? According to Marean, the answer may be "shellfish".

"They're a great source of protein," he said. "And shellfish are immune to colder ocean temperatures. In fact, when the water gets colder, those populations go up."

Marean used climate models to pinpoint locations in Africa where human hunter-gatherers could have hunkered down during a long glacial period that dried out the continent and expanded deserts. Of the four-to-six possible locations, he focused in on an area along the coast of South Africa.

This is probably wrong. Though one of the many ideas about this period in human history have to be right. And there's always the tricky problem of falsification and testing alternative hypotheses when it comes to models of human evolution. From what I know humans are a relatively homogeneous species which underwent some sort of demographic expansion within the last 100,000 years. The tacit assumption seems to be that the proto-modern African lineage nearly went extinct, and then bounced back, possibly due to an exogenous shock. My own question: why couldn't it just be that a few bands simply exterminated or marginalized all the other African lineages? This is an assumption by many about modern humans as they expanded into Eurasia, more or less, so why not in Africa? Humans can certainly reproduce up to the Malthusian limit. In 1800 1.2 million humans were resident in New England, the vast majority of whom were descended from the 20,000-30,000 who arrived in the 1630s. And remember that the reproductive population is going to be a fraction of the census size.

I could speculate on what gave a small subset of African humans an advantage, but I'll leave that to the comments.


Settlers, Slaves & Immigrants   posted by Razib @ 12/16/2009 02:09:00 AM

A few weeks ago I referenced Campbell Gibson's paper, The Contribution of Immigration to the Growth and Ethnic Diversity of the American Population, which estimated that ~1990 50% of the population of the United States could be attributed to those enumerated in the Census of 1790. In other words, the first generation of white settlers who were citizens of an independent republic, and the free and enslaved blacks. More specifically, 61.4% 69.2% were British & Irish (mostly English), 11.6% of continental origin (2/3 German) and 19.3% were black. In Gibson's analysis he does take into account mixing. He notes that the probability of a given "Old Stock" American having only American ancestors ~1800 is very low (the inverse situation, where a "white ethnic" has only immigrant grandparents or great-grandparents, is less unlikely simply because potential set is smaller, 4 or 8, as opposed to 64 or 128), so he takes admixture into account. From a genetic perspective though one can see how important being somewhere first can be. Below I've reproduced two tables from Gibson's paper. The second table shows the dilution over time of the founding population. It is interesting that though we are a "nation of immigrants", in actually actuality only during the Reagan administration was the demographic preponderance of the descendants of enslaved Africans and white settlers of a domain of the British monarch surpassed by that of immigrants seeking opportunity in an American republic.


Tuesday, December 15, 2009

What Heritability is Not   posted by ben g @ 12/15/2009 09:11:00 AM

Because so many people abuse or misunderstand the concept of heritability, I decided that it would be nice to have a list of what heritability is not in one place. If you have questions or if there is a misconception about heritability you'd like me to address here, feel free to comment. This post will serve as an updated reference.
  • Heritability is not an indicator of malleability. Entirely genetic disorders such as phenylketonuria can be cured through the proper diet.
  • Heritability is not a measure of straightforward genetic effects. For example, genes that affect physical appearance have an effect on personality development.
  • Heritability is not independent of the population. It may differ from one group of individuals to the next, because groups differ environmentally and genetically.
  • Heritability is not independent of age. The effects of genes or environments may grow in potency through development.
  • Heritability is not an indicator of the causes of group differences. A trait can be highly heritable, as in the crop field metaphor, and group differences may still be due to environment. This applies also in the real world situation for humans, where the environmental differences between groups are not as systematic.
  • Heritability is not necessarily homogeneous within a population. A heritability of 50% may be hiding the heritabilities of 40% and 60% in subgroups.
  • Heritability is not a measure of intergenerational transmission. A trait may be highly heritable but not pass on from one generation to the next. This is because the relevant genes and environments may differ from one generation to the next.
  • Heritability is not a statistic for individuals. If you are using your knowledge of heritability to understand a single individual you are a biographer, not a scientist.
So, some of you may be wondering, why is heritability a useful statistic? That's easy to answer: it's a measure of how much phenotypic variation in a given population at a given time is due to genetic variation in that population. Measuring heritability allows us to say that, for adults in the modern world, variation on IQ and personality measures is primarily due to genetic variation. That's a pretty remarkable, and important finding if you ask me.


Monday, December 14, 2009

Who argues the most from authority?   posted by agnostic @ 12/14/2009 01:00:00 PM

Google results for +"nobel laureate" +X, where X is one of the following:

Chemistry: 317,000
Physics: 415,000
Medicine: 467,000
Economics: 484,000

Of course, there are more winners to refer to in Physics than in Economics, so we should control for that. Dividing the number of Google results by the number of winners gives these per capita rates:

Chemistry: 2032
Physics: 2231
Medicine: 2395
Economics: 7446

If the intellectual merit of a body of ideas is not so well established, you're more likely to deflect attention by reassuring everyone that, hey, it can't be that crazy -- after all, the guy is a Nobel laureate. Perhaps that's why physics ranks above chemistry here, what with string theory etc. taking it further into speculation compared to more grounded chemistry.

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Comments   posted by Razib @ 12/14/2009 11:22:00 AM

Haloscan is forcing an upgrade something called Echo. I am not inclined to switch comment systems since this has worked since 2004. So commenting may not work for a bit. But blogging will be light from me for a bit anyway.

Update: The new comment system is working, after a fashion. But I can't install it fully because if I do it will interrupt their migration of Haloscan era comments into the new system, so I will leave it be until they give me the go ahead via email. Despite the fact that the comments box states "0" comments, that is not necessarily so. The new comment system is rather flexible, and I've turned on the feature which allows for trusted commenters to go through the mod queue. That means that after an X number of comments over an Y period of time of approved comments you're listed as trusted. This will probably be good since the active comment community here is relatively small. I'll start doing other things when I think it won't break everything.

P.S. There's a 5,000 character limit on comments. If you regularly go over this, you need a blog.


Thursday, December 10, 2009

Carbs & ancestry   posted by Razib @ 12/10/2009 11:43:00 PM

Stable Patterns of Gene Expression Regulating Carbohydrate Metabolism Determined by Geographic Ancestry:
Methodology/Principal Findings
Using a combination of genetic/genomic and bioinformatics approaches, we identified a large number of genes that were both differentially expressed between American subjects self-identified to be of either African or European ancestry and that also contained single nucleotide polymorphisms that distinguish distantly related ancestral populations. Several of these genes control the metabolism of simple carbohydrates and are direct targets for the SREBP1, a metabolic transcription factor also differentially expressed between our study populations.

These data support the concept of stable patterns of gene transcription unique to a geographic ancestral lineage. Differences in expression of several carbohydrate metabolism genes suggest both genetic and transcriptional mechanisms contribute to these patterns and may play a role in exacerbating the disproportionate levels of obesity, diabetes, and cardiovascular disease observed in Americans with African ancestry.

Figure 2 had me thinking of Me, Myself & Irene.

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Wednesday, December 09, 2009

Monkeys & language   posted by Razib @ 12/09/2009 05:44:00 PM

The paper is out, Campbell's monkeys concatenate vocalizations into context-specific call sequences. Nicholas Wade and Ed Yong review the evidence. One of the issues is that chimps don't seem to have syntax, so how can a monkey? But since domesticated dogs have better human-comprehensible theory of mind than chimps I don't think genetic distance or general intelligence should weight that highly.


More Jewish Genetics   posted by Razib @ 12/09/2009 02:22:00 PM

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. I posted on it at ScienceBlogs. Nothing too new.


The Mating Mouth   posted by Razib @ 12/09/2009 02:12:00 AM

Gingival Transcriptome Patterns During Induction and Resolution of Experimental Gingivitis in Humans:
A relatively small subset (11.9%) of the immune response genes analyzed by array was transiently activated in response to biofilm overgrowth, suggesting a degree of specificity in the transcriptome-expression response. The fact that this same subset demonstrates a reversal in expression patterns during clinical resolution implicates these genes as being critical for maintaining tissue homeostasis at the biofilm–gingival interface. In addition to the immune response pathway as the dominant response theme, new candidate genes and pathways were identified as being selectively modulated in experimental gingivitis, including neural processes, epithelial defenses, angiogenesis, and wound healing.

ScienceDaily has a more awesome title, Nearly One Third of Human Genome Is Involved in Gingivitis, Study Shows:
Research conducted jointly by the University of North Carolina at Chapel Hill and Procter & Gamble (P&G) Oral Care has found that more than 9,000 genes -- nearly 30 percent of the genes found in the human body -- are expressed differently during the onset and healing process associated with gingivitis. Biological pathways associated with activation of the immune system were found to be the major pathways being activated and critical to controlling the body's reaction to plaque build-up on the teeth. Additionally, other gene expression pathways activated during plaque overgrowth include those involved in wound healing, neural processes and skin turnover.

Perhaps then bad breath and poor oral hygiene are simply a fitness indicator, and kissing evolved as a method for humans to evaluate each other's health as an "honest" signal?


Tuesday, December 08, 2009

Food stamps & unemployment go together (duh)   posted by Razib @ 12/08/2009 02:41:00 PM

Derek Thompson at The Atlantic has a post Are America's Fattest States Also the Most Jobless?. The county-level data on unemployment only goes back to 2008 (at least that I can find online). But I do have data on obesity at the county-level too. What's the correlation? 0.32. Pretty modest. If I correlate for white obesity it goes down a little, 0.23 (though remember that I estimated white obesity, so be cautious about this). Since I also have food stamp utilization data I looked at that. Correlation is 0.56. If you think of this as r-squared, how much of variance of Y can be explained by X by squaring the correlation, it's a much stronger association. I constructed a quick regression where % unemployed on the county-level was the dependent variable, and % black, obese, median household income and % on food stamps were the independents. Except for food stamps none of these variables generated statistically significant beta coefficients. In other words, regional level differences in unemployment in 2008 which tracked obesity are probably best explained as emerging out of a general poverty factor (though do note that median household income itself isn't very predictive once % on food stamps gets put into the equation).

I don't doubt that all things equal the obese would be fired first. That being said, all things are often not equal.

Update: I realized I left something out. Looking at the correlation college degree holding on the county-level and unemployment in 2008, I found it to be -0.43. So I popped that into the regression, and here are the coefficients with standard errors (all statistically significant):

Black 1.20987610 (0.33416977)
College Degree -7.64273043 (0.62394667)
Percent on Food Stamps 0.14095962 (0.00946762)
Median Household Income 0.00002967 (0.00000523)
Obesity -0.06840311 (0.01494881)

I'll let readers wonder what's going on here, though I assume it has something to do with the changes in the education premium and such with globalization.

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Does the family matter for adult IQ?   posted by ben g @ 12/08/2009 05:57:00 AM

A frequent claim in the IQ debates is that which family you are raised in has no lasting impact on your IQ. Jensen argues in The g Factor that the only causes of IQ similarities between adult identical twins are genetic. Many researchers go so far as to argue that by 12 years of age, the shared environment has no impact.

Based on my limited knowledge of the behavior genetic research, I used to hold this position as well. But thanks to some recent in depth reading, I have come to the conclusion that which family you are raised in matters significantly for your IQ as an adult, especially so for people of lower socioeconomic status. I'll detail the behavior genetic evidence here, and argue that it points to significant shared environmental influences on adult IQ scores.

Twin Studies

The most recent and comprehensive survey of twin studies on IQ comes from Haworth et al (2009). Using pooled twin data from around the world, they modeled genetic and environmental influences as a function of age. Here is what they found regarding the effects of the shared environment:
[S]hared environment shows a decrease from childhood (33%) to adolescence (18%) but remained at that modest level in young adulthood (16%).
In an email exchange with Dr. McGue (one of the co-authors of the paper) he told me that while the latest data may not fit with earlier estimates, it's actually more reliable due to the unprecedented sample size (11,000 pairs of twins).

One failing of this study, though, is that it doesn't go far enough into adulthood. The young adult group ranges from 14 to 34 years of age, with an average age of 17. In contrast, McGue (1993) looked seperately at data on adults over 20 years of age. He found that the shared environment diminished to zero impact at that point. Here's his chart:
Looking at that chart, you might quickly conclude that shared environmental influence evaporates by age 20. However, this conclusion is premature. Twin studies make a great number of assumptions, some of which increase and others of which decrease estimates of the shared environment. A straightforward way of bypassing these assumptions is to compare monozygotic twins reared apart (MZAs) to monozygotic twins reared together (MZTs). The following data comes from a comparison of MZTs and MZAs, of average age 41, in Bouchard (1990):

MeasureMZA correlationMZT correlation
WAIS IQ-Full Scale0.690.88
WAIS IQ-Verbal0.640.88
WAIS IQ-Performance0.710.79

Differences between MZA's and MZT's on Raven's Progressive Matrices follow the same pattern but are even more extreme. Bouchard (1981) reported a median correlation of only 0.58 for adult MZA's on the Raven's. Curiously, though, MZA's are equally if not more correlated than MZT's on the Mill-Hill vocabulary test. Apparently, the pattern is that more g-loaded tests tend to show stronger evidence of lasting shared environmental impact.

It's worth noting that MZT vs. MZA comparisons are actually biased towards an underestimation of shared environmental impact. Bouchard's study of twins reared apart found an environmental correlation of .22 for MZAs on various environmental measures, with some having a small but significant correlation with IQ scores. Also MZA's share the womb. To summarize: when the assumptions of the twin method are effectively controlled for, lasting shared environmental impacts are revealed.

Adoption Studies

To date, most adoption studies of IQ have concluded that being adopted by a new and typically well-off family has no effect on adult IQ scores. Here is a chart of adoption studies from Bouchard (2009):As you can see by clicking it, the IQ correlation between unrelated individuals in the same family decreases (on average) from .26 in childhood to .04 in adulthood (which begins at age 17 for the purposes of this graph).

However, as with the previous chart, the quick conclusion that shared environmental influences don't matter in adulthood shouldn't be so quickly accepted. To begin with, we can see that the adoption data underestimates the shared environment relative to the twin literature. This most likely occurs because of the assumptions that go into adoption studies.

Stoolmiller (1999), for example, highlighted the issue of range restriction-- the idea that the limited range of adoptee and adoptive family environments will lower estimates of the shared environment. This idea is supported by studies which make the extra effort to include individuals of lower SES. The French adoption studies that made such an effort buck the trendline seen above, in finding that nurture matters almost as much as nature for the IQ of 14 year olds. Scarr (1993) is the outlier in the adoption graph above, finding a .19 correlation between unrelated adolescent siblings. Perhaps her results differed from others because her sample was multi-racial and therefore less range restricted. Lastly, there are other lines of evidence supporting the idea of range restriction, such as Turkheimer's work on SES and cognitive ability.

It's worth noting, however, that McGue (2007) looked for evidence of range restriction effects within the "broad middle class" and did not find any. He used statistical methods that are over my head to estimate the effects of range restriction based on a range restricted sample and state census data. Unfortunately there are no studies which have critiqued his as of yet. Any commenters who are familiar with the statistics involved are invited to comment. Even if McGue is right about restriction of range, my point stands that assumptions inherent in the adoption studies deflate c^2 estimates.

Future Directions

Future work will help sort out the still unanswered question of shared environmental influences on adult IQ scores. There are large longitudinal adoption studies currently under way, and I believe that Haworth's twin study will be followed-up on and include data on older twins. There are also interesting (albeit less methodologically agreed upon) studies coming out like this one, which find significant shared effects on IQ in adulthood.

My reading of the available evidence is that there is a significant shared environmental input to adult IQ, and that it is associated with socioeconomic status. To what extent it's the neighborhood or the parents themselves that matters is unclear. Just as the most g-loaded tests show the most shared environmental effects in the MZA-MZT comparison, so too does the Flynn effect occur on the most g-loaded tests, suggesting that whatever is loading onto the "shared environment" within generations is also responsible for differences between them.

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Monday, December 07, 2009

Roman Britain to Anglo-Saxon Britain   posted by Razib @ 12/07/2009 02:11:00 PM

Peter Frost on Roman Britain:
Historians often assume that the Romans changed Britain politically but not demographically. The indigenous elites adopted Roman culture while the mass of the population remained Celtic. When the Anglo-Saxons arrived in the fifth century, much of this population fled to Wales and Cornwall, where they would retain their language and traditions. Meanwhile, those who remained behind were obliterated through a process of ethnic cleansing and coerced assimilation.

This historical account may be false....


Once Rome had pulled its troops out of Britain in the early 5th century, there was no longer an inflow of people to offset the demographic deficit. The local population fell into decline, and the decline accelerated in the 6th century when plagues killed three out of every ten people. The Romano-British needed no help from the Anglo-Saxons to die out. They did it largely on their own.

Peter's summation of the historical consensus is correct. This view is exposited in Norman Davies' The Isles. The historians have had a bias for several generations of assuming that population movements have been marginal in shaping cultural change. In some cases this is correct; I've looked and it is very difficult to detect a discontinuity among the Hungarians in relation to their neighbors despite this nation's putative origins among an Inner Asian group (and later settlement of Turks who fled the Mongols within the Magyar kingdom). The emergence of Hungarian is therefore most plausibly modeled as a process of elite emulation, where Romance, German and Slavic speaking peasants adopted the speech and identity of their Magyar overlords. The Hungarian case is easy to test because the geographical distance of the Magyar homeland in the Volga-Ural region is great enough that they would have been a genetically distinct population who would introduce alleles which couldn't be explained except as exogenous inputs (the Hazara are a case of this).

The question of Britain is a bit more confused. Historians rely on textual evidence which points to Anglo-Saxon rule of Celtic-speaking populations in their kingdoms in the 7th and 8th century, in particular stipulations of different wergild ('blood money') for Saxons, noble and commoner, and Celts, noble and commoner. The existence of an elite Celtic speaking class suggests that Gildas' allusions to genocide were exaggerations. Over the past 10 years a lot of exploration of the genetic variation within Britain has simply muddied the picture. Though some early Y chromosomal studies suggested sharp breaks between Wales and England, autosomal data don't seem to show this. Rather, a reasonable model is that the Anglo-Saxons contributed a significant, but minority, element to England's contribution. Their genetic impact drops as a decaying function of the distance from East Anglia, which was the heart of the "Saxon Shore," but their cultural influence was not diluted along the wave of advance. This highlights the stark difference between genetic and cultural inheritance, the former is constrained in the nature of transmission in a way the latter is not. In fact, during the high tide of the Viking era in Britain's history, the Saxon redoubt was Wessex, which genetic data show seem to has been minimally affected by German settlement. Rather, Wessex was likely conquered by the Saxonized.

Finally, what happened to multicultural Britain? The genetic data show a small effect, a random African lineage here and there which can not be explained by recent genealogy. An orders of magnitude less important than the Saxon migration. I think the reason is the simple that that urban areas were population sinks, and unless immigrants "went native" they disappeared into the genetic black hole. A reasonable historical analogy may be Lithuania. After the official union of the political structures of Lithuania and Poland in the 16th century the Lithuanian nobility was Polonized. The emergence of modern Lithuanian identity was to a great extent an elevation of Lithuanian peasant culture, which was left unaffected by Polonization. If extant literary or high cultural artifacts are used to reconstruct Lithuania's history one might posit that Lithuanian's disappeared in the early modern era, only to reemerge in the 19 century due to the ideology of nationalism.

There has long been a supposition that Latinization in Britain was relatively restricted and superficial compared to Gaul, where Celtic speech seems to have disappeared in the 5th century. This may be a inference made plausible by hindsight, because Britain was one region (the Balkans the other) where the ornaments of Roman high culture was totally extinguished in the face of barbarian invasions. By contrast, Gaul, Iberia and Italy all produced culturally hybrid elites who were Romanized. But from what I know the archaeological evidence does suggest a shift even among Romano-British warlords from a Roman to a British style in their material possessions over the 5th and 6th centuries (additionally, Roman commanders and legions stationed in Britain had a tendency to relocate to the continent in part because that was where the "action" was in terms of advancement and glory, so there may have been a sorting process whereby the most Romanized elites emigrated, while those who were willing to become barbarized, whether by going back to their Celtic roots, or becoming Saxonized, remained).

Here's some gene related charts to support what I'm saying above about the muddle. On first inspection a Netherlandish affinity to many Briton's is obvious (also, you can see it in Structure). Uniparental markers show the clines I'm alluding to above though, so where these samples come from within Britain matters a great deal at the scale we're talking about. But the main problem is that some might argue that there have long been interactions between the low countries and southeast England because of their proximity, and not one particular Anglo-Saxon migration. Perhaps at some point it will be feasible to analyze the decay linkage disequilibrium (or see if there's linkage disequilibrium) in southeast England to date the time of a putative admixture event. But of course the peoples of the North European Plain and those of England are relatively close genetically, so I'm not going to hold my breath. Ancient DNA will probably yield more sooner.


Technical difficulties   posted by Razib @ 12/07/2009 10:40:00 AM

There were some difficulties with the site overnight. Probably best place to check for updates is my twitter feed, 99% of the stuff there are just re-posts of my blog content. If you don't have my email address, you can also contact me Additionally, I set up an aggregator weblog a few weeks ago, which is basically all the stuff from GNXP.COM, ScienceBlogs GNXP and my posts from Secular Right (just a feed of the "David Hume" author archives). Mostly useful for its RSS feed, since the links all point back to the individual blogs and comments are off.


Sunday, December 06, 2009

Finding the missing heritability   posted by ml @ 12/06/2009 09:31:00 PM

In a recent special issue of The Economist magazine, evolutionary psychologist Geoffrey Miller of the University of New Mexico writes that there is a "looming crisis in human genetics". Setting aside a number of mistakes Miller makes, a core truth he reports is that to date most genetic variants that have been associated with complex diseases such as diabetes and complex phenotypes such as height can account for only a small percentage of the estimated genetic contribution to population variation in these traits (~5% in total for the cases of type-2 diabetes and height). This residual unexplained variability has been dubbed the "missing heritability".

The missing heritability is an open and fascinating research question, not a crisis, although it has become fashionable to characterize it as such. First, it's important to realize that a primary goal of genetic studies of human disease is to identify the biological underpinnings of these diseases and thus advance work toward improved diagnoses, cures, and mechanisms of prevention. Important work has already been done towards these ends with many new and unexpected biological pathways now associated with diseases thanks to the recent successes of genome-wide association studies (GWAS). Thus, it may not be necessary to explain all of the missing heritability in order to make great strides towards these goals.

Second, the first generation of GWAS were not realistically expected to find loci of large effect as they focused on common variant; although the potential benefits of first-generation GWAS may have been oversold by some. Nonetheless, first-generation GWAS have explained a substantial fraction of the heritability of some traits, such as age-related macular degeneration.

Third, where should we look for the missing heritability? A recent review in Nature offers some suggestions:
Many explanations for this missing heritability have been suggested, including much larger numbers of variants of smaller effect yet to be found; rarer variants (possibly with larger effects) that are poorly detected by available genotyping arrays that focus on variants present in 5% or more of the population; structural variants poorly captured by existing arrays; low power to detect gene–gene interactions; and inadequate accounting for shared environment among relatives. Consensus is lacking, however, on approaches and priorities for research to examine what has been termed 'dark matter' of genome-wide association—dark matter in the sense that one is sure it exists, can detect its influence, but simply cannot 'see' it (yet). Here we examine potential sources of missing heritability and propose research strategies to illuminate the genetics of complex diseases.

A key consideration is the genetic architecture of each trait--the number, type, effect size and frequency of variants affecting a trait. Because the genetic architecture of a complex trait cannot be known a priori (although theory can suggest which architectures are more probable) it is an open question as to which approach to finding the missing heritability will yield the most success. Until more approaches are attempted, it is premature to predict a crisis. This does not mean, however, that success is guaranteed. It is possible that the genetic architecture of some complex traits is too complex to dissect practically with current methods. Rather than a crisis, we might instead expect more slow but steady progress in upcoming years. Some traits will be more amenable to new methods (as age-related macular degeneration was to fist-generation GWAS). Other traits will likely remain largely intractable.


Religious identity vs. religious activity (and God is not back!)   posted by Razib @ 12/06/2009 01:47:00 PM

One of the more irritating things which seems to crop up in popularizations of international trends is the idea that religion is reviving all over the world. It is probably not as plainly false as the idea in common currency from the Enlightenment down to the 20th century that religion will disappear in the generation to come, but it sure sells a lot of books. God Is Back is one of the more mindless and superficial books in this line of thought which has come out recently, but re-reading some of Samuel Huntington's books in the last few months it is clear that the idea there is a world wide religious revival did seep into the background assumptions of academics around the turn of the century as well. In fact, in Who Are We? Huntington operated under the assumption, and related data, that there was a mass religious revival occurring in the United States at the time that there was actually a second mass wave of secularization occurring since the 1960s (the reality was already evident from the data, but Huntington's theoretical filter or expectation led him to simply selection bias the data appropriately to fit his narrative).

Here's some data from the Pew Global Project. I've ordered by the biggest % drops between the young and middle aged cohorts:

Religion “Very Important” by age

18-39 40-59 60+
Spain 9 21 30
South Korea 11 20 *
Argentina 27 43 57
Poland 20 29 49
Russia 13 17 27
Japan 7 9 22
Mexico 52 61 77
US 48 55 64
France 8 9 15
Egypt 69 76 *
India 70 77 75
Jordan 77 84 *
Lebanon 46 50 *
Britain 15 16 23
Australia 18 19 29
Brazil 72 75 84
South Africa 80 83 82
Turkey 83 84 88
Pakistan 95 96 *
German 21 21 25
Indonesia 95 95 *
Nigeria 94 94 *
Tanzania 94 92 *

Currently the data on cross-generational differences in religiosity resemble those of sex-differences in religiosity: either no difference, or one category (men or the young) is invariably less religious than the other. But here's another result which I haven't harped on quite as much:

Attitudes toward Christians

Unfavorable Favorable Ratio
US 3 87 29
Tanzania 6 92 15.33
Russia 7 88 12.57
Britain 7 83 11.86
Poland 8 88 11
Australia 8 84 10.5
South Africa 10 83 8.3
Germany 12 83 6.92
Lebanon 14 85 6.07
France 17 82 4.82
Argentina 14 66 4.71
Nigeria 17 78 4.59
Brazil 21 79 3.76
Jordan 25 73 2.92
Spain 24 67 2.79
Mexico 28 47 1.68
S. Korea 36 53 1.47
India 37 49 1.32
Japan 38 48 1.26
Indonesia 41 51 1.24
Egypt 46 52 1.13
Pakistan 60 24 0.4
China 55 22 0.4
Turkey 74 10 0.14

This is the ratio of fav. to unfav. in relation to Christianity. It is no surprise that the United States is at the top. But look at how low China is on the list. Christians aren't special here, the Chinese tend to be unfavorable toward Jews and Muslims too. I think this is to some extent a measure of nationalism. But I also think it sheds light on the thesis of a book from a few years ago, Jesus in Beijing: How Christianity is Transforming China and Changing the Global Balance of Power. Evangelical Christians often claim that over 100 million Chinese are already Christian. The Chinese state gives numbers closer to 20 million. Independent estimates are somewhere in the middle. But the general thesis is China will follow in the wake of South Korea, and become a partly Christianized society. Though Christians remain a minority in South Korean society they are very influential, and the current President has been accused of bias in favor of Protestants. In terms of geopolitics the assumption is that an Evangelically-tinged China will lean toward a pro-Israel position against the Islamic world. I have argued before that this is all premature, and Christianity's success in South Korea is somewhat dependent on particular cultural and historical streams which may not be repeated in China. These data show that the Chinese population are still unfamiliar with Christianity, and do not view it positively, leaning against the likelihood of mass conversion in the near future (in South Korea Christianity was associated with the anti-colonial movement, and the colonial power, Japan, was non-Christian).

The connection between nationalism and religion explains I think what's going on with Turkey being at the bottom of the list. In the rest of the survey Turkey does show itself to be on the moderate/liberal end as far as Muslim nations go (only a minority of Turks have a positive view of Saudi Arabia, whereas most Muslims in the other nations surveyed had a positive view). But historically the identity of Turks has been connected to their role as ghazis, warriors for the faith, who are on the front line pushing into Christian Europe. Turkey's rivalry with Greece has clear civilizational aspects. Though Turks are by and large religious Muslims, and their attitudes toward Christianity and Islam are suffused with their perceptions of what it means to be a Turk, and their national identity. This makes sense when you see the numbers for Russia and the secular nations of Western Europe; despite the fact that Western European nations are now dominated by populations which dissent from the core propositions of the Christian faith their populations are still strongly connected emotionally to Christianity. The Christian religion is the religion that they are not.

I suspect all of this seems curious as unintelligible from the American perspective. Many authors who write about religion and its 21st century revival assume an American model, where religion is a matter of individual choice and personal fulfillment. In other words, religion can be treated as a consumer good of a sort, with more transcendent valence perhaps, but still a matter of individual volition in theory if not practice. This is less intelligible in other nations. Even atheist Americans can take these stances as a given. Consider the reaction to a book written about secularity in Denmark, to which the Danes reacted with irritation, as they perceived the American author as incorrectly assuming that the Danes were secular because they lacked strong religious beliefs!

Of course I do think religion can come back. This charts show how:


Friday, December 04, 2009

David Sloan Wilson & Razib Khan (me) on BHTV   posted by Razib @ 12/04/2009 11:37:00 PM

Here. All I have to say is that 60 minutes really isn't that much time.

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Thursday, December 03, 2009

Vox Dei   posted by Razib @ 12/03/2009 10:53:00 PM

David Killoren points me to this Ed Yong post, Creating God in one's own image. It is based on the paper Believers' estimates of God's beliefs are more egocentric than estimates of other people's beliefs:
People often reason egocentrically about others' beliefs, using their own beliefs as an inductive guide. Correlational, experimental, and neuroimaging evidence suggests that people may be even more egocentric when reasoning about a religious agent's beliefs (e.g., God). In both nationally representative and more local samples, people's own beliefs on important social and ethical issues were consistently correlated more strongly with estimates of God's beliefs than with estimates of other people's beliefs (Studies 1–4). Manipulating people's beliefs similarly influenced estimates of God's beliefs but did not as consistently influence estimates of other people's beliefs (Studies 5 and 6). A final neuroimaging study demonstrated a clear convergence in neural activity when reasoning about one's own beliefs and God's beliefs, but clear divergences when reasoning about another person's beliefs (Study 7). In particular, reasoning about God's beliefs activated areas associated with self-referential thinking more so than did reasoning about another person's beliefs. Believers commonly use inferences about God's beliefs as a moral compass, but that compass appears especially dependent on one's own existing beliefs.

Ed hits the main points well as usual, so let me jump to the discussion:
these data provide insight into the sources of people's own religious beliefs. Although people obviously acquire religious beliefs from a variety of external sources, from parents to broader cultural influences, these data suggest that the self may serve as an important source of religious beliefs as well. Not only are believers likely to acquire the beliefs and theology of others around them, but may also seek out believers and theologies that share their own personal beliefs. If people seek out religious communities that match their own personal views on major social, moral, or political issues, then the information coming from religious sources is likely to further validate and strengthen their own personal convictions and values. Religious belief has generally been treated as a process of socialization whereby people's personal beliefs about God come to reflect what they learn from those around them, but these data suggest that the inverse causal process may be important as well: people's personal beliefs may guide their own religious beliefs and the religious communities they seek to be part of.

Finally, these data have interesting implications for the impact of religious thought on judgment and decision-making. People may use religious agents as a moral compass, forming impressions and making decisions based on what they presume God as the ultimate moral authority would believe or want. The central feature of a compass, however, is that it points north no matter what direction a person is facing. This research suggests that, unlike an actual compass, inferences about God's beliefs may instead point people further in whatever direction they are already facing.

There is always debate about how religion affects cognition and culture, and how cognition and culture affects religion. I suspect that in religious environments the default stance is that religion affects cognition and culture. Religion is after all assumed to be true, a reflection of some transcendent reality. It stands to reason that its impact upon humans would be significant if you believe that it is an expression of the ultimate reality (if you are a person to whom "ultimate reality" means something, you know what I mean, though I don't really myself). But many atheists hold to the same view. The New Atheists often put at religion's feet all the evil done in its name (though generally minimizing power of religion as a force for altruistic action or social cohesion). This view seems to hold that religion is something clear and distinct. More generally in civilized societies religion is a matter of rational and systematic reflection, detailed practice, and mindful contemplation.

On the other hand, there are those who emphasize how religion reflects social and cognitive presuppositions. For example, most American Christians would assert that their religion naturally leans toward an anti-racist perspective. This would not be something recognizable to R. L. Dabney. Consider the arguments of Susan Wise Bauer, a Reformed Christian historian, on the stance of many Christian Southerners to slavery. But in other writings she cites Dabney, who is still apparently influential among conservative Presbyterians (some have even attempted to defend slavery because it is Biblical, but to my knowledge very few conservative Christians will follow along here, instead relying in interpretations such as Bauer's). Even "conservative" and "orthodox" and "traditional" Christians seem quite clearly influenced by the distribution of norms around them. Similarly, I recall several years ago finding rather interesting the arguments of Indian Christians on why arranged marriage is Biblically preferred to love matches, with citations of specific instances in the Bible (consider the marriage of Isaac and Rebecca). Over the last few decades cognitive anthropologists who study religion have described models and reported results which show how religious phenomena, the bundle of traits which we bracket into religion, emerge from normal human psychological and social dynamics. Some scholars have even shown that the mental model of gods across cultures is actually invariant, though the verbal descriptions are very distinct. If you consider the power of culture to change religion, the shift from pacifist to non-pacifist stance among early Christians, or pro-racist to anti-racist stance among 20th century Christians, becomes more intelligible.

I tend toward the second model in terms of its utility in what can be gleaned about human social processes. If, for example, I read the Hebrew Bible and the New Testament would I be able to predict which group was the more pacific, American Jews or white Evangelicals? I don't think so. Scott Atran reported in In Gods We Trust that religious believers showed little correlation above expectation in the inferences they made about correct behavior in specific situations in relation to their avowed religious beliefs. In other words, when people couldn't talk to each other and reach a religiously correct consensus, they simply gave a random range of answers. Both the Chinese Muslims and "Hidden Christians" of Japan moved in strange directions in relation to their co-religionists due to isolation. It seems plausible that to a great extent Emile Durkheim was right, religion is a reflection of society. But, it is also strongly constrained by human cognitive biases.

The connection between some of these ideas and what Ed Yong asserts is obvious:
Epley's results are sure to spark controversy, but their most important lesson is that relying on a deity to guide one's decisions and judgments is little more than spiritual sockpuppetry.

David Killoren has an alternative model:
I can think of at least one other plausible interpretation of this study.

If you believe in God, you probably think God is morally omniscient. That is: you believe that, if any given action X is wrong, then God knows that X is wrong - and conversely, if God believes that any given action X is wrong, then X really is wrong. (You might think God is morally omniscient because you are a theological voluntarist. But even if you deny voluntarism, as many believers do, you probably still think God is morally omniscient, if you believe in God.)

But if you think God is morally omniscient, then you would be irrational if you believe that, say, abortion is wrong (or permissible, or whatever) without thinking that God shares your belief. Given God's omniscience, a given judgment is correct if and only if God agrees with it. So your endorsement of any given judgment has the immediate implication that God shares your view.

The result is that, if you believe God is morally omniscient, then your moral beliefs also serve as conjectures about God's attitudes. Thus, in order to explain Epley's results, we don't need Yong's "Sockpuppet Hypothesis," as I'll call it. Epley's results are precisely what we should expect if religious believers consider God to be morally omniscient, regardless of whether religious believers treat God like a ventriloquist treats a dummy.

Killoren has an analogy clarifying what he's trying to get at:
An analogy can help here. Suppose I think that Dr. Smith, a famous scientist, knows everything there is to know about biology. Then, if I believe that platypuses are not mammals, I should believe that Dr. Smith believes that platypuses are not mammals. (After all, if I believed that Dr. Smith considers platypuses to be mammals, and believed that Dr. Smith knows everything about biology, then I would be crazy to think platypuses are not mammals.) But this doesn't mean Dr. Smith is my sockpuppet. If Dr. Smith were to tell me that platypuses are mammals, I’d believe him, even if I previously thought otherwise.

I can see where Killoren is coming from. When I was more deeply interested in philosophy of religion, and to a great extent thought religion was mostly about belief systems, I would probably be willing to go along with it. But at this point I think Ed Yong's thesis is more plausible because it is simple and dumb, and most people are simple and dumb. If you need to use an analogy that suggests that some cognitive cycles are being eaten up here, and I believe most moral cognition which has a religious tinge is actually "hard and fast" and more reflexive than this. Of course, in Tim Harford's The Logic of Life he shows that in the aggregate human behavior can quite often operate in a logical fashion as if it is undergirded by a chain of clean propositions derived from axioms. But I wasn't quite convinced by Harford's apologia; I'm still with Dan Ariely.

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On insults and religion   posted by Razib @ 12/03/2009 09:59:00 AM

When I was a younger man I recall watching a documentary on missionaries in Mississippi. They were Southern Baptists who were on a mission to "save" everyone (this included Roman Catholics and Protestants who had not had a "Born Again" experience). At one point the missionaries encountered a man from Pakistan, who was a Muslim. They confronted him aggressively as to whether he worshiped "idols." From what I saw their tactics seemed more a way to allow these individuals to act out and be obnoxious than convert people (social science research shows that conversions usually happen through networks of friends, not from encountering the random missionary). Later that year a friend of my younger brother, who was Baptist, saw my dad praying. He asked me whether we worshiped idols. He even slipped a little doll in front of my dad's prayer rug, an act which my brother found really offensive. At the time I wondered if conservative Baptist churches around the country were sharing literature and tactics which verged in this obnoxious direction (I also had another friend inquire if I was Hindu after there was a sermon on Hinduism. I told him I was not, at which point he still regaled me with the gist of how horrible demonic Hinduism was).

This sort of behavior is very boorish. On the other hand, it brought home to me the importance of intersubjectivity. As an atheist to me all religion was human-created, so the behavior of my Baptist friends and acquaintances when it came to other religions was boorish, but not offensive. But religion is important for most humans. Religions, and societies more generally, tend to share explicit and implicit norms and values. They allow individuals to differentiate between the acceptable and unacceptable. In a society where there is pluralism this is a more difficult task.

The importance of intersubjectivity is why I roll my eyes when Egypts grand mufti talks about an "insult to Islam". It is important to remember that Islam by its very nature is an insult to many religions. That is, the core beliefs of Islam are an offense. There is a lot of exegesis on exactly what Islam says about the People of the Book, but there is little doubt about what it says about "idolatry." For example, Hindus who revere idols and consider themselves polytheists are insulted by Islam constantly.* The holiest books of Islam are basically hate-texts against polytheists and those who revere idolts. Among South Asian Muslims the "idolatrous" practices of Hindus are fodder for much humor in social situations.** Even the command to convert the world is offensive to many.

At one point I was a regular participant on the comment boards of Talk Islam and Sepia Mutiny. It was interesting to contrast the two, for though Sepia Mutiny is not explicitly a religious weblog, most participants are from Hindu or Sikh religious traditions (Dharmic). On Talk Islam I repeatedly explained, and made the argument, that one could be sincerely religious, and, accept a common underlying and equivalent truth of all religions. Aziz found this an implausible or false assertion, as for him the nature of religion is such that you adhere to a faith you believe the closest to the truth, and you wish others would also adhere to the nearest approximation of the ultimate truth. By contrast, on the Sepia Mutiny it was clear that many simply could not comprehend why Christians and Muslims had to proselytize by the nature of their faith. For them, it was a given that all religions express aspects of the ultimate truth, and attempts to convert individuals to another tradition is simply cultural aggression which sows discord and is an implicit affront. From long discussions it was clear that the two groups had a very primitive or non-existent understanding of the perspective of the other. Some of the concerns of adherents of Indian religions also emerge among Jews. They perceive Christian attempts to convert them as a form of cultural genocide, but that is because their presuppositions about religion are fundamentally different from those of Evangelical Christians. Jews also have issues with Christians who "compliment" their tradition by asserting that their own religion is simply a "completion" of Judaism. Muslims often prove their pluralist bona fides by observing that they respect all prophets who have come before, and view the People of the Book of having received a true message from God. Of course, these traditions are less than flattered, because most Muslims also believe that their traditions are distortions and degenerations from Islam (Muslims view their faith as the "primal religion." This view is shared by many conservative Christians as well), ergo, the necessity of Muhammad as the seal of prophets.

As an atheist with no strong emotional connection to any religion I view this with some curiosity and intellectual interest. But, I also think that it brings up a pragmatic issue: genuine religious pluralism has to lead toward religious segregation. The Ottoman millet model, which also existed in Europe in the relationship of Jews to the polity, is in some ways the "natural" state of religious pluralism. But what about the United States? I think we have turned Catholics and Jews into operational Protestants. To assimilate then Muslims have to cede ground on the importance of orthopraxy and Hindus have to accept the ubiquity of religious defection. In Muslim countries Christians no longer act out on the injunction in the New Testament to preach their faith, because they've been turned into People of the Book, who exist as religious fossils. The Parsi attitude toward conversions is probably shaped in part by their inculcation of Hindu attitudes. And so forth.***

Addendum: For many religious people I've found that the very avowal of atheism is somewhat offensive to them. At least judging by their negative and uncomfortable body language. A few times people have even asked if atheism is too strong of a world, and perhaps I'm just "not religious" or "secular."

* Many Hindus reject idol reverence and consider themselves monotheists. Perhaps most in the West. But many Hindus will assert that they are polytheists, and accept the importance of the representation of gods in worship.

** When I was a child some old guy at a party where everyone was a South Asian Muslim started talking about how Hindus consumed cow feces. I really hated this stuff, since this was invariably before we ate, but people always thought this was really funny. But at this party there was a younger man who was offended by this. He asserted that in fair play Muslims should not mock other religions, even in private. I recall everyone was shocked and dumbfounded. It was clear they'd never even run into this sort of argument, and the conversation moved to other topics. I have been told by Hindus that the inverse mockery also occurs. No surprise.

*** There was always an implicit ethnic Persian aspect of Zoroastrianism. But the historical record attests to Zoroastrians among many non-ethnic Persians, from Armenians to Turks, to converts from Christianity.

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Wednesday, December 02, 2009

A shifting mode   posted by Razib @ 12/02/2009 11:02:00 PM

picture-31-(1)Here's the source. The fact that there's been so much change since 1990 is what is striking to me.


The Deadweight Loss of Gift Giving   posted by Razib @ 12/02/2009 04:57:00 PM

Q&A: Scroogenomics Author on the Holidays' 'Orgy of Wealth Destruction'.


Being a Popperian about charities   posted by Razib @ 12/02/2009 12:02:00 PM

Reading The GiveWell Blog is interesting, as it allows one to exclude charities because they do all the leg-work. For example, a few days ago they put up a analysis of Smile Train's usage of funds (or lack of transparency). Prompting an evasive response from Smile Train.

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Tuesday, December 01, 2009

There is no society, just homicidal individuals   posted by Razib @ 12/01/2009 10:48:00 AM

There's a new book out, American Homicide, which has some interesting arguments:
He concluded that people's views about the legitimacy of government and how much they identify with their fellow citizens play a major role in how often they kill each other -- much more so than the usual theories revolving around guns, poverty, drugs, race, or a permissive justice system.

"The predisposition to murder is rooted in feelings and beliefs people have toward government and their fellow citizens," said Randolph Roth, author of the book and professor of history at Ohio State.


That includes theories held dear by both conservatives and liberals. If you look at the evidence over time, poverty and unemployment don't lead to higher murder rates, as many liberals argue, he said. But locking up criminals, using the death penalty, and adding more police don't hold the murder rate down either, as conservatives claim.


In his analysis, Roth found four factors that relate to the homicide rate in parts of the United States and western Europe throughout the past four centuries: the belief that one's government is stable and its justice and legal systems are unbiased and effective; a feeling of trust in government officials and a belief in their legitimacy; a sense of patriotism and solidarity with fellow citizens; and a belief that one's position is society is satisfactory and that one can command respect without resorting to violence.

When those feelings and beliefs are strong, homicide rates are generally low, regardless of the time or place, Roth said. But when people are unsure about their government leaders, don't feel connected to the rest of society, and feel they don't have opportunity to command respect in the community, homicide rates go up.

The main issue I have with the explanations for crime variance out there is that the 1960s spike and the 1990s abatement were synchronous internationally. So I'm skeptical of policy changes being the ultimate cause of these cycles.