Gene Expression

To crush your enemies, and steal their cattle for your sons!

Mon, 02 Nov 2009 10:49:44 -0500

As I gave a nod to statistical tricks and subtle shell games very recently, the material I review subsequently should be viewed with skepticism and caution. A few days ago I also pointed to a paper which describes and models intergenerational transfers of wealth across various societies. In other words, what parents transmit to children. From the perspective of someone who reads this blog, obviously parents transmit genes to their offspring.

To the left is an old scatterplot from Francis Galton which shows the dependence of the height of children upon the average height of parents. Obviously you have to take into account sex, but if you use standard deviation units and control for gender it works fine. There is a close relationship here between the axes, though it is not perfect. In modern developed societies the heritability of height is ~0.8-0.9. That means that 80-90% of the variance of the trait within the population can be explained by the variance in genes within the population. On an individual level this would result a relatively good correspondence between parental and offspring heights. In terms of the scatterplot, as heritability approaches 1, the slope converges upon 1. As heritability approaches 0, the slope approaches zero. This makes graphical sense, insofar as slope of 0 indicates no ability to predict the value of Y (children) from X. It's just random noise.

Of course there is the problem of confounds in these sorts of studies. One has to control for environmental effects, interactions and correlations. The paper that I would like to put a spotlight on in fact focuses on these issues, and not so much on genetics, except in passing. But the general formalisms resemble those of quantitative genetics, and the issue under examination is heritability of wealth, and therefore the variance in well-being across generations which persists.

To the paper, Intergenerational Wealth Transmission and the Dynamics of Inequality in Small-Scale Societies:

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William Gunn is looking for another job

Mon, 02 Nov 2009 00:52:19 -0500

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

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Against multiculturalism (multireligionism)

Sun, 01 Nov 2009 03:12:18 -0500

I rarely post much political commentary here, because it would add little value as I have nothing distinctive to say in that domain. At Secular Right I am wont to do data analysis because I think data is something that needs to be injected into political discussions and commentary. But in any case, today I put up an essay, Religious diversity & its discontents. In it I make clear my distaste for multiculturalism, so if you are a reader who would find such opinions to your distaste, I invite you not to click! My own opinion is that multiculturalism as it is presented is not a noble lie, but a silly one.

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Andrew Gelman's "Applied Statistics"

Sat, 31 Oct 2009 20:01:47 -0500

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

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Mosque offended by alcohol & roast pig...in New York City

Sat, 31 Oct 2009 17:58:04 -0500

Spotted Piglet Hiccups: Boozy Breslin Clashes With Mosque:

The much-hyped, soon-to-open Breslin restaurant, situated in the 12-story Ace Hotel on Broadway and 29th, is giving members of the Masjid Ar-Rahman mosque across the street some agita. "Five times a day, there's a hundred cabs on the street--the good news is you can always get a cab," co-owner Ken Friedman told the Transom the other evening. He said some mosque visitors "object to seeing people drink alcohol."

After the recent FergusStock, a festival during which famed British chef Fergus Henderson cooked whole pigs for a rapt crowd of New York chefs and foodies, Mr. Friedman said the mosque's leaders called a meeting with the hotel. "They said, 'Can you move the bar?'" he said. "And I laughed. And the guy said, 'Oh, you think that's funny?' And I said, 'Yeah, that is funny, that is really funny, because we're not going to move the bar just because you discovered we're serving booze.' Can you name one restaurant in New York that doesn't serve booze?"

Mr. Friedman and his partner, Spotted Pig chef April Bloomfield, did agree to nix plans for a dive bar in a townhouse next door, but as for the restaurant, "I said, 'This is the United States of America and we'll do whatever the fuck we want.'" He said the mosque had suggested it couldn't control the behavior of "a few bad eggs"; i.e., "we could get a brick through our window." Mr. Friedman said he made the police aware of this threat.

If you move to a country that is 98% "kuffar" STFU is all I have to say. As Muslims like to remind us there are 1.5 billion of them, but despite being adherents of the One True Religion countries dominated by Muslims tend to kind of suck-ass. Therefore, they queue up to immigrate to countries where the majority is non-Muslim. But they expect to carry on as usual, as evident by some Muslim cab drivers refusing to pick up those who've had alcohol, or people with seeing eye dogs (because Muslims consider dogs unclean, though this is true of Hindus too last I checked).

This dovetails with the issues I pointed to in "On Offense". Muslims, and for that matter Mormons, many Hindus, etc., would naturally find inebriation with alcohol offensive and disrespectful, especially around a religious center. If a Mongolian beef establishment opened up across from a Hindu temple I think one might wonder as to the sensitivity of this sort of behavior as well. But how many sets of norms can we accommodate before we go get bogged down in norm tracking? In much of India Hindus and Muslims avoid consumption of pork and beef as a form of reciprocal sensitivity* (though I think this is easy in part because so many Hindu elites are vegetarian, period). I understand where food taboos come from, it is taboo to eat dolphin or dog in the United States. But any given society needs to have some semblance of restraint and common norms on boundaries, or we'll become like those Hasidic Jewish sects where people are vegetarian because they don't trust anyone to be properly kosher. A whole society of Hasidic Jews is not viable.

Note: Some Europeans find Muslim animal sacrifice and male circumcision offensive. Of course Muslim react naturally with their catchall accusation of Islamophobia, and haven't had to modify their own practices yet.

* One thing I never understood about this is why Muslims would care that non-Muslims ate pork. Unlike Hindus Muslims don't venerate the pig.

H/T Anna

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Bernie Madoff only squandered $21 billion

Sat, 31 Oct 2009 16:24:20 -0500

In a piece that outlines SEC follies:

In fact, Mr. Madoff said in the jailhouse interview that, on two occasions, he was certain it was only a matter of days or even hours before he would be caught. The first time, in 2004, he assumed the investigators would check his clearinghouse account. He said he was "astonished" that they did not, and theorized that they might have decided against doing so because of his stature in the industry.

"I'm very proud of the role I played in the industry," he said. "Of course I destroyed that now."

In Mr. Madoff's second close call in 2006, investigators actually asked for his clearinghouse account number on a Friday afternoon, but then never followed up. He said he firmly expected the following Monday would bring the curtain down on his crime. Again, nothing happened. He recalled thinking at the time: "After all this, I got away lucky."

His investors did not. According to estimates by a court-appointed trustee who is liquidating his estate, Mr. Madoff's crime cost thousands of victims at least $21 billion in cash losses, part of the $64.8 billion in paper wealth that vanished when his scheme collapsed.

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Materialism leads to inequality

Sat, 31 Oct 2009 15:13:24 -0500

Intergenerational Wealth Transmission and the Dynamics of Inequality in Small-Scale Societies:

Small-scale human societies range from foraging bands with a strong egalitarian ethos to more economically stratified agrarian and pastoral societies. We explain this variation in inequality using a dynamic model in which a population's long-run steady-state level of inequality depends on the extent to which its most important forms of wealth are transmitted within families across generations. We estimate the degree of intergenerational transmission of three different types of wealth (material, embodied, and relational), as well as the extent of wealth inequality in 21 historical and contemporary populations. We show that intergenerational transmission of wealth and wealth inequality are substantial among pastoral and small-scale agricultural societies (on a par with or even exceeding the most unequal modern industrial economies) but are limited among horticultural and foraging peoples (equivalent to the most egalitarian of modern industrial populations). Differences in the technology by which a people derive their livelihood and in the institutions and norms making up the economic system jointly contribute to this pattern.

See ScienceDaily for a summary. Two immediate thoughts come to mind:

1) Many people have long suggested in many ways "advanced" industrial nations are shifting back toward the values which are more common among hunter-gatherers. "Traditional" values the norm among pre-modern agriculturists may be a peculiar interlude, when native human intuitions and the range of personal choice were constrained by powerful lineages which monopolized wealth.

2) I wonder if the differences in wealth & inequality track reproductive variance. Specifically, if the range of relative fitness is higher in societies with more inequality. This could have an evolutionary impact, one can posit that more variance in fitness means more rapid change in phenotypic values. Genghis Khan wouldn't have been possible among hunter-gatherers.

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Katz

Fri, 30 Oct 2009 18:32:46 -0500

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On offense

Fri, 30 Oct 2009 06:51:41 -0500

Ruchira Paul has a post up, "Religious, superstitious, nonsense" and other harsh words. The point at issue is the fact that a teacher who expressed anti-Creationist views in harsh tones was sued. Ruchira asks somewhat rhetorically as to the sort of things parochial schools say about other religions and atheists. The bigger issue is one of public decorum, and decorum is very contextual. When my 7th grade teacher had us read Medea she explained a bit about the context of Greek society, including the nature of their religion. She spoke of "their gods" and "our God." Her reference to "our God" was absolutely ecumenical, and in the most general of tones, while her reference to "their gods" was clinical and disrespectful. Disrespectful because she perceived Greek paganism to be superstitious, if interesting, nonsense, and said so (I agreed with her, but my own sentiments were a bit more catholic). Ludicrous on the face of it was her stance, which she made plain. There were no Greek pagans to protest.

The issue and dynamic are general. In the ancient world the Jews and Christians were considered atheistic because they denied the existence of all gods but their own.This was an offense to the pagan majority, who did not exhibit reciprocal disbelief. I have talked to Hindus who are hurt by the exclusive and atheistic stance by the Abrahamic religions about other gods (from the perspective of a non-Abrahamist much of the scriptures of those religions and the writings of their most respected divines are hate screeds). In any case, with the rise of Christianity to be called heathen or pagan was an offense, and the old gods became blasphemous demons (and naturally fundamentalist Christians are wont to identify Hindu deities such as Shiva with demonic figures in the Book of Revelation). When the Chinese encountered Christianity (again) in the 16th and 17th centuries, in particular its Catholic forms, the exact same accusations of cannibalism which were common in the ancient world reemerged. Outside of the proper cultural context, a plain explanation of transubstantiation seems more offensive than sacred.

One can expand the point outside of religion. In much of pre-modern Europe a bare breast was reputedly less sexually charged than exposed shoulders or legs. Sexuality is not totally culture variant, even societies where nudity is common have norms (e.g., notice that Amazonian women in the older National Geographic specials never squat). But there's enough variation that software differs from society to society. The human mind operates on autopilot much of the time, and internalizes particular cues and contexts, and fires programs which come preloaded. When put into an exotic circumstance it takes some time to adjust, and when two individuals come together when there are cultural differences confusion can often ensue (immigrants may often never become totally acculturated).

Back to religion. In the World Values Survey there's a question about how much you "Trust People Of Other Religions." There are 4 responses, trust complete, trust a little, not trust very much, and not trust at all. I created an index of trust, whereby the above response were coded as 0, 1, 2 and 3. So if 100% in a country did not trust at all, the value would be 3. Below are the responses for nations in WVS wave 5. I've ordered them. You might be surprised.

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The grandmothers effect, paternal or maternal matters (?)

Fri, 30 Oct 2009 06:02:08 -0500

I've discussed menopause as an adaptation and the grandmother effect before. I was also pleased to see the responses of Larry Moran's readers when he presented his standard anti-adaptationist line of argument. I don't want to retread familiar ground here, I'm not sure if menopause is an adaptation, but let's assume so for the purposes of reviewing a new paper which has come out and offers a slight but fascinating twist on the grandmother hypothesis. Grandma plays favourites: X-chromosome relatedness and sex-specific childhood mortality:

Biologists use genetic relatedness between family members to explain the evolution of many behavioural and developmental traits in humans, including altruism, kin investment and longevity. Women's post-menopausal longevity in particular is linked to genetic relatedness between family members. According to the 'grandmother hypothesis', post-menopausal women can increase their genetic contribution to future generations by increasing the survivorship of their grandchildren. While some demographic studies have found evidence for this, others have found little support for it. Here, we re-model the predictions of the grandmother hypothesis by examining the genetic relatedness between grandmothers and grandchildren. We use this new model to re-evaluate the grandmother effect in seven previously studied human populations. Boys and girls differ in the per cent of genes they share with maternal versus paternal grandmothers because of differences in X-chromosome inheritance. Here, we demonstrate a relationship between X-chromosome inheritance and grandchild mortality in the presence of a grandmother. With this sex-specific and X-chromosome approach to interpreting mortality rates, we provide a new perspective on the prevailing theory for the evolution of human female longevity. This approach yields more consistent support for the grandmother hypothesis, and has implications for the study of human evolution.

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Power ballads

Fri, 30 Oct 2009 04:57:50 -0500

In the wikipedia entry for "ballad" there's the image with caption to the left. Am I weird for finding that just really, really, funny? I start having these weird flashbacks to lots of pink hair,screaming weirdos, and Every Rose Has Its Thorn. Am I the only one who feels that the fashions and styles of the 70s and 80s were just way stranger than those of the 50s and 60s? Or is it just that the 50s and 60s are so far back that we've forgotten their own variant of Cherry Pie?

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Remember the lizard men

Thu, 29 Oct 2009 17:22:35 -0500

Carl Zimmer points me an article about a former anthropologist who has some weird ideas about the origin of man:

Since his resignation from the university in 1990, however, Horn has changed his tune. Once a staunch Darwinist and tenured CSU anthropology professor, Horn has devoted the last 19 years of his life to the study of alternative theories of human origin.

After receiving a doctorate in anthropology from Yale University and while teaching at CSU, Horn focused his energies on the study of the evolution of non-human primates, his wife Lynette Horn said.

He now advocates the theory that modern man is not the result of a natural process of evolution, but that evolution was artificially aided by reptilian extraterrestrials. The reptilians bred mankind as servants and continue to rule the planet today, Horn said.

Reptilians have manipulated perceptions of world history and hold power over humankind through their influence over an elite and powerful group of humans, known as the Illuminati, Arthur said. Throughout human history, the reptilian beings have been recorded as dragons or gods.

Thought it was a joke, but it looks real.

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Hutterites are like Icelanders

Thu, 29 Oct 2009 05:15:07 -0500

The Spittoon points to a new paper, Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes, which I've been meaning to look at more closely. Unlike some attempts to use genetics to illuminate questions about the human past here the historical record is rather complete. The 16th century was the high tide and maximal efflorescence of German Protestantism. Not only were vast swaths of what we think of as redoubts of German Catholicism in the Austrian lands brought into the Protestant fold, but the diversity was also at a peak, as the religious status quo was in flux and indeterminate. In the 17th century the Hapsburg Emperors won back the Austrian lands for the Roman Catholic Church,* while Lutherans and Calvinists began turning on the smaller radical sects, generally Anabaptists, in their midst.

Groups like the Amish and the Hutterites are echoes of that time, taking root and flourishing in the United States because of its laissez-faire attitude toward religious belief and practice. The Hutterites are also of note because for a long time they were reputedly the highest fertility population in the world. That explains why their numbers have increased by a factor of 30 in the past 150 years, and also points to why they're of genetic interest. Like many sects Hutterites don't accept many converts, so their growth is due to their own fertility. Additionally, the history of the Hutterites in Europe seems to be one of bottlenecks due to persecutions. It's a nice way to see if what one assumes would happen with fluctuating populations did happen when it comes to the genomes of populations.

As expected the Hutterites are of Central European origin. In any admixture model where the two parent populations were Central and Eastern European, the Hutterites are 80% Central European. But, their mtDNA and Y chromosomal lineages are a restricted subset of the parental populations, and they exhibit a great deal of genetic novelty.

I think this is visually obvious when you look at the Y & mtDNA phylogenies of Hutterites within the context of Central & Eastern European populations. Note how concentrated the Hutterites are in particular branches; they're subsets, but only a slice.

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Alberta has no rats!

Thu, 29 Oct 2009 02:11:59 -0500

There's something cool about Canada, I just found out that Alberta is the only large region of permanently inhabited human territory which lacks brown rats. One thing you have to remember is that the brown rat only began spreading within the last 1,000 years (in the process displacing the black rat), and it seems to have arrived in the British Isles only within the last two to three centuries. North America did not have the rat until Europeans arrived, and it didn't show up in Alberta until 1950. At that point the government attempted an eradication program. Apparently this can work because there aren't ecologically congenial corridors for the rats to constantly reappear through migration.

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Old tricks never die

Wed, 28 Oct 2009 05:35:18 -0500

This critique by Ted Goertzl, Myths of Murder and Multiple Regression, is making the rounds. It made me think of this old apocryphal story:

There is a famous anecdote inspired by Euler's arguments with secular philosophers over religion, which is set during Euler's second stint at the St. Petersburg academy. The French philosopher Denis Diderot was visiting Russia on Catherine the Great's invitation. However, the Empress was alarmed that the philosopher's arguments for atheism were influencing members of her court, and so Euler was asked to confront the Frenchman. Diderot was later informed that a learned mathematician had produced a proof of the existence of God: he agreed to view the proof as it was presented in court. Euler appeared, advanced toward Diderot, and in a tone of perfect conviction announced, "Sir, (a + bⁿ)/z = x, hence God exists--reply!". Diderot, to whom (says the story) all mathematics was gibberish, stood dumbstruck as peals of laughter erupted from the court. Embarrassed, he asked to leave Russia, a request that was graciously granted by the Empress.

The second law of thermodynamics talking point is an unsophisticated descendant of Euler's gambit, while William Dembski's whole career is a homage to the trick. In regards to the shenanigans that Goertzl refers to, you can go to UC Berkeley's GSS interface, and after reading the documents, "massage" the outcomes yourself. I do think that econometric methods are still useful tools, their frequent misuse shouldn't lead us down the path to epistemological nihilism. Many use the law to further their own selfish ends and pervert its intent, but that doesn't mean that the general idea of an objective legal framework has to be discarded. Specifically, I think the Cowles Foundation has done some worthwhile work (e.g., showing that stock newsletters add no value).

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