If BusinessWeek is doing it, why aren't you?

Check it, got this note from Adam Bly of Seed:

So I’m flipping through the new issue of BusinessWeek (April 3, 2006; Cover: The
Top Performers) and on page 14 in the BLOGSPOTTING section, I happen upon this article:

BLOGSPOTTING
LIFE, THE UNIVERSE, AND ALL THAT
http://scienceblogs.com

WHY READ IT A sister project of Seed magazine, this blog bills itself as the Web’s largest conversation about science. Its members include physicists, surgeons, and historians.

NOTABLE POST “…If life doesn’t exist on Enceladus [one of Saturn’s moons]…I suggest seeding the moon with Terran organisms that might be able to survive and flourish. In a few decades genetic engineering might also progress to a point where exotic…metabolisms could be synthesized with the physiology of more complex aquatic organisms.” [that’s me, that’s me, that’s me! -Razib]

If BusinessWeek is reading my other blog, shouldn’t you be? 🙂

Genes don’t “make” you be a certain way….

Apropos of my earlier post relating to heritability…this is the sort of confusing gibberish that ends up making it into the press, Professor researches genetics of gambling. He tries to clear up problems of communication:

This quote has been misconstrued. In the logical development of any investigation of the genetics of a disorder, once something is shown to run in families and appears to have some heritable component, molecular genetic approaches follow. Studies can be done with small numbers of DNA samples, as I propose doing, but definitive studies require thousands of DNA samples. I doubt such an ambitious undertaking will take place for many years.

Good luck on getting nuance across to the press. All the while, genetic association studies will continue.

Distribution of a religious meme

This whole conversion story in Afghanistan has been in the news recently. The Christian Science Monitor attempts to put the issue of conversion from Islam to another religion in an international perspective. Most readers of this weblog know that I am cautious about making large generalizations without qualifications, but I will offer that as a civilization, “Dar-al-Islam,” has particular issues with conversion when set against “Hindu” or “Christian” civilization. Though the difference is quantitative, not qualitative, some facts are so naked that caveats can not truly cover up the shame.

There are “Muslim” nations where conversion to other religions is socially acceptable. Albania and Indonesia are two such cases. In Albania the dereligionization of Communist period has been followed by a feeding frenzy of religious activity as Muslim and Christian groups have entered the country and turned it into a rational choice competitive marketplace of memes. I am to understand the current issue of First Things has an article by Stephen Schwartz where he notes that Muslim clerics in Albania do not begrudge conversions to Christianity (specifically, Roman Catholicism, another one of Albania’s traditional religions, as evidenced by Mother Theresa). In Indonesia after the 1960s there were widespread conversions to Hinduism by Communism sympathetic nominal Muslims (whole villages sometimes converted due to animus against orthodox santri Muslim landlords and their right-wing thugs), and to this day there tends to be acceptable religious flux in this nation as Christians, Hindus and Muslims make conversions from each other’s camp. In Africa there are also many conversions from Islam to Christianity, I recall Pat Robertson bragging that thousands of members of a tribe that was traditionally Muslim was converted to Christianity in Burkina Faso thanks to the activities of missionaries.

Nevertheless in wide swaths of the Muslim world standard sharia injunctions against conversion away from Islam are normative. For example, in Pakistan and Bangladesh Christian missionaries have targeted the Hindu minorities because the Muslim majority will not tolerate evangelization. The same pattern can be found in Malaysia, where Christians proslyetize amongst Buddhists, Chinese folk religionists and Hindus, but avoid the Muslims for fear of political retribution. I also recall that back in the 1990s Go Chok Tong warned Christian fundamentalists about upsetting the religious balance of the city-state in part because of anger from the Muslim Malay minority.

How to interpret this? First, one must note that horror at conversion to another religion has never been limited to Islam, one only need to look at the Hebrew Bible, or injunctions against Jews owning Christian slaves and statues against Judaizing to know that other branches of the Abrahamic family tree have been ill at ease with individual defections of creed. The long history of interaction between pagan and Christian in Europe between the 4th and 12th centuries was one of transition from the former to the latter, in large part because reversion from the latter to the former was rarely accepted. Within bounds Christians still are not especially comfortable with conversion away from their own flock, the “anti-cult” movements on the fundamentalist fringe of American Christianity are often focused on critiquing New Religious Movements which are perceived as a missionary threat bent on “stealing” their youth (in the course of being instruments of Satan of course). In The Future of Religion Rodney Stark and William Bainbridge report data which shows that Americans who are most supportive of the Great Commission are also the least favorable toward allowing non-Christian missionaries to freely operate within the United States (Seventh Day Adventists were an exception). I also recall years back when John Paul II proudly told Indians that the Catholic Church would not turn aside from its missionary program in South Asia, this, at the same time the Church was vociferously objected to the intrusion of evangelical Protestants into Latin America (Roman Catholics might fairly contend that the analogy does not work because the latter case was “sheep stealing,” but of course my understanding is that Catholicism has always been a missionary religion in Protestant lands where such activity is feasible).

There are several issues here. First, intolerance and disgruntlement at defection from group identity is normal. The recent flair ups against Christian missionaries in India and the occassional “Satanism” hysteria in the United States show that it lurks under the surface in cultures where conversion is accepted and protected. I think it is to some extent an emergent property of human “groupishness,” of “doing what your neighbor does.” In some societies, like the United States conversion from various religions to others is common enough that the social stress is limited to an interpersonal level, community censure is simply too weak to be powerful. There are exceptions, for example I have heard of Mormons who leave the religion not being able to live a normal life in parts of southeastern Idaho because day-to-day interaction is not possible due to ostracism. But in most of the United States the intersection between religious pluralism and social mobility results in a cocktail where “church shopping” is common.

Other nations are not like this. And to some extent the United States is an aberration, the only real analogy being countries like Albania where traditional religious institutions have been totally demolished and have not had the time to recover and monopolize the social space they once held. Most nations with long histories do have “established” churches, whether via custom or law. Russia has the Orthodox Church. Sweden has the Lutheran Church. Malays are Muslim. Spaniards are Roman Catholic. Jews are, well, Jews. These are what I term “cartel cultures” where higher order religious goods & services are monopolized by one particular umbrella institution. Some of these cultures have sizable secular minorities who no longer participate in the transactions mediated by the monopoly (communal prayer, mass, etc.), but there is little competition from other umbrella institutions. In cultures like Russia the monopoly religious institution is not just a religious institution, it is an organic and necessary part of the communal culture. This inseparability means that defection from the Russian Orthodox Church toward a Protestant Christianity is far more threatening than simply lapsing in practice. This might explain the phenomenon of Jews and Muslims in Christian cultures expressing more hostility toward converts to Christianity from their own ranks as opposed to the non-religious who reject the creedal points but do not replace them with an alternative set of beliefs. Unbelief does not necessarily imply rejection of the community, but alternative beliefs do.

The cartel system has been the modus vivendi for many cultures over the past few thousand years. The millet system under the Ottomans was one of the more explici
t manifestations of this, each religious leader was responsible for his own community. Elsewhere, rabbis in much of Eastern Europe became princes of their people, and where Roman Catholics were a minority they organized their own counter-cultural institutions against the Protestant majority. In The Netherlands the “pillar” system reflected the self-organization of Catholics, Protestants and the unaffiliated. Of course this system isn’t etched into our cultural DNA. Small-scale peoples do not construct doctrines and institutional churches which promote and execute creeds and practices. Nevertheless, the basic tools were already in place, ostracism and other social pressures already had developed to an advanced stage to enforce group conformity and coherence. They were simple scaled up, with an extra layer of rationalistic sophistication (theology, doctrine, etc.) wielded by a specialist class (clerisy) sitting atop the system.

Where does this leave us? In regards to Islam as it is practiced and enforced in much of the Middle East and South Asia it seems that the cultural form is simply a refined expression of a common stable state. Familial, clan and ethnic honor are intertwined with religious profession in a set of interlocking contingent norms and practices with serve as cultural boundaries. In some parts of the Muslim world, in the Balkans, Africa and parts of Southeast Asia the magnitude is attenuated and there is more give and take with other cultural communities. Similarly, in India and and in much of Europe conversion from one religion to another is legal, but subject to social costs and strain. In the United States and South Korea and in parts of Africa conversion is so common, and switching so ubiquitous, and the pace of economic and social development so rapid, that the normal modus vivendi has been overturned and religion has become, to some extent, McChurch. It has been torn away from custom and tradition and stability of generations, and into more ad hoc fluid organizations which serve individualized needs and preferences.

This is important because to some extent in international contexts there seems to be tendency to frame the debate as if the religiously fluid situation in the United States is the norm throughout the world, or that it should be. George W. Bush is a Methodist, his father is an Episcopalian, while his brother converted to Roman Catholicism. Karl Rove is not religious. Marvin Olasky, the father of “compassionate conservatism,” is a convert to evangelical Christianity from Judaism. The point is that George W. Bush’s experience has primed to see conversion as only a personal choice, when in most of the world it is a profoundly transgressive act that is a rebuke to kith and kin. The recent problems caused by South Korean Christian missionaries in Iraq also point to the same mentality, taking for granted religious conversion as a normal part of life when it isn’t. Some of the Christian Churches of the Middle East have a nearly 2,000 year old history, so they are particularly affronted when evangelicals from the United States attempt to “convert” their youth.

Myself, I think the instability of the new world is a byproduct of radical individualism. I like this, I enjoy the choice that volition it introduces into the self-creation of individuals. But, I do not think that its future ascendence is going to be without bumps and rocky patches. And, I don’t think it is “normal” in any straightforward sense of the word, humans are a social animal, and the customs and traditions of almost all traditions rebels against the radical choice which enslaves the culture to the whim of the individual.

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How much is coding?

I need an estimate of the fraction of selected variants that involve an amino acid change, as opposed to noncoding changes in promoters and enhancers and such. Something for mammals would do. Can anyone find one?

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Come the reductionist revolution….

There is an important paper out on calculating heritability (JAVA applet). Heritability is an important and misunderstood concept. Some people have argued that heritability is fallacious reification, a biostatistical construct which has no real relevance (or reality) outside of its utility in quantitative genetic models. But its entwinement with various concepts within evolution and genetics means it can’t be ignored, love it or hate it.1 Heritability is the proportion of phenotypic variation within a population that is attributable to genotypic variation.

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No cheat left behind

Seems like a Jersey principal was instructed to cheat on state tests.

Principal Joseph Carruth was riding down the slow, paneled elevator at Camden’s district office, ready to cave in to pressure from a superior who he says had just given him a tutorial on how to cheat on state tests.

“My head is spinning,” Carruth recounted to The Inquirer of his feelings that day in January 2005. “I can’t believe it.”

Still green on the job at Camden’s Dr. Charles E. Brimm Medical Arts High, Carruth needed medical benefits for his ill daughter. He did not have tenure. He was tempted to take whatever steps necessary to keep his job.

“I was thinking, ‘How can I do it?’ ” Carruth said about that day. “And then it’s, like, ‘What are you doing? You can’t do this.’ “

Good thing the cheater was caught, so that this thing won’t ever happen again.

ADDENDUM: From the Wikipedia article on Camden:

The racial makeup of the city was 16.84% White, 53.35% Black or African American, 0.54% Native American, 2.45% Asian, 0.07% Pacific Islander, 22.83% from other races, and 3.92% from two or more races. 38.82% of the population were Hispanic or Latino of any race. 8.9% are foreign-born.

La Griffe has a nifty solution all ready to go for just this kind of situation.

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Amusing stuff

Nothing big enough for its own post, just a bunch of things that caught my attention:

PLoS Genetics: AVPR1a and SLC6A4 Gene Polymorphisms Are Associated with Creative Dance Performance

We therefore hypothesize that the association between AVPR1a and SLC6A4 reflects the social communication, courtship, and spiritual facets of the dancing phenotype rather than other aspects of this complex phenotype, such as sensorimotor integration.

PLoS Medicine: Are Racial and Ethnic Minorities Less Willing to Participate in Health Research? Nope.

TSC: The Stone Age Trinity wherein a libertarian realizes that humans have an egalitarian instincts which will get in the way of a libertarian society.

TNR: Blue State Blues — Criticizing “red state snobbery”, Jonathan Chait writes “I wonder if Wolfe and his fellow travelers realize how much their mau-mauing of blue staters is, well, Maoist.” — Ironic new meaning of “Red state”.

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Calculating heritabilty using only full siblngs by genotyping

A paper in PLoS Genetics, Assumption-Free Estimation of Heritability from Genome-Wide Identity-by-Descent Sharing between Full Siblings, describes a way to determine heritability using actual genotypes in leiu of estimated kinship coefficients.

From the synopsis:

Quantitative geneticists attempt to understand variation between individuals within a population for traits such as height in humans and the number of bristles in fruit flies. This has been traditionally done by partitioning the variation in underlying sources due to genetic and environmental factors, using the observed amount of variation between and within families. A problem with this approach is that one can never be sure that the estimates are correct, because nature and nurture can be confounded without one knowing it. The authors got around this problem by comparing the similarity between relatives as a function of the exact proportion of genes that they have in common, looking only within families.

While children inherit more or less exactly half of their genomes from each parent (and thus — usually — have a coefficient of kinship of 1/2) due to the mechanism of two hapolid genomes combining at feritilization, for full siblings the actual coefficient is merely distributed around a mean of about 1/2. Due to chance segregation, some siblings have an actual relatedness which is greater than 1/2 and others less than 1/2. Here’s the actual distribution of relatedness that they measure:

The rest of the synopsis:

Using this approach, the authors estimated the amount of total variation for height in humans that is due to genetic factors from 3,375 sibling pairs. For each pair, the authors estimated the proportion of genes that they share from DNA markers. It was found that about 80% of the total variation can be explained by genetic factors, close to results that are obtained from classical studies. This study provides the first validation of an estimate of genetic variation by using a source of information that is free from nature–nurture assumptions.

They get a h^2 of 0.8. My reading of there paper is that this may be an underestimate:

We have ignored the contribution of the sex chromosomes to genome-wide IBD. In humans, the X chromosome accounts for 4% of genes and 5% of physical length [29]. If all chromosomes account for genetic variation in proportion to the number of genes or physical length, then our estimate of heritability will be biased downwards by about 4% to 5%.

This is a very important paper for several reasons. First, it should permit the verification of heritability coefficients for phenotypes like IQ where there has been some dispute. Second, it will permit the estimation of heritability in tandem with mapping projects that have sibs. I imagine there are already suitable datasets out there waiting to be mined.

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