Archive for April, 2009

Vitamin D & asthma

By Razib Khan | April 27, 2009 10:28 am

Serum Vitamin D Levels and Markers of Severity of Childhood Asthma in Costa Rica. See ScienceDaily. Anecdote: my own asthma has gotten much better since I started Vitamin D supplementation. Not only have I had many fewer bouts of bronchitis the past few years, but my basal respiratory functioning is much improved.

CATEGORIZED UNDER: Biology

Folate & fertility & skin color

By Razib Khan | April 27, 2009 9:18 am

On the order of ~1 million years ago humans seem to have evolved dark skin. While light skin evolved several times, it looks like dark skin exhibits an “consensus sequence,” so that all dark skinned peoples seem to have the same genetic architecture.
skincolormelan.pngThis chart (from Signatures of Positive Selection in Genes Associated with Human Skin Pigmentation as Revealed from Analyses of Single Nucleotide Polymorphisms) shows that when it comes to skin color related genes the populations of Bougainville Island (off the eastern coast of Papua New Guinea) and Sub-Saharan Africa are far closer than you would expect based on total genome content alone. Bougainville Islanders are simply a branch of non-Africans, so they should cluster with other such populations. In contrast you can see that the lighter skinned populations exhibit a lot more variance. Plainly there are many more ways to tear down than built up when it comes to this trait. To develop lighter skin you can simply build up loss of function mutations across the genes which result in dark skin in H. sapiens sapiens. But that still begs the question, why did humans develop the consensus sequence which results in dark skin in the first place?

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CATEGORIZED UNDER: Evolution, Genetics

People should stick with "their own kind"

By Razib Khan | April 26, 2009 6:37 pm

Since the post on anti-miscegenation laws got a lot of attention, I was curious about analogs in the World Values Survey. There are two such questions of interest:
Important for succesful marriage: Same ethnic background(D042)
and
Important for succesful marriage: Religious beliefs(D031)
These data are skewed toward European nations. Below the fold are data are % who assert that same ethnic background is NOT very important, or that same religious beliefs are NOT very important. I will admit that the international pattern is surprising to me.

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CATEGORIZED UNDER: Culture

Katz return

By Razib Khan | April 26, 2009 3:56 pm

The sabbatical is over. Normal hours are Fridays….

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CATEGORIZED UNDER: Culture

Jake Young & myself on bloggingheads.tv

By Razib Khan | April 26, 2009 3:52 pm

The episode is titled “your brains & your genes.” There’s more emphasis on economics than you think.

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CATEGORIZED UNDER: Culture, Psychology

Abortion vs. homosexuality – trends since the 1970s

By Razib Khan | April 26, 2009 12:47 pm

One of the arguments of some younger social conservatives (e.g., Ross Douthat) is that while the abortion wars are in stasis, the Right is losing ground when it comes to opposition to gay marriage. Is this true? Below are charts from the GSS with each column representing a year, from the mid-1970s to the 2000s (not necessarily every year, but every few years).

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CATEGORIZED UNDER: Blog, Culture

Culture doesn't cause borderline personality disorder

By Razib Khan | April 26, 2009 10:24 am

Thankfully. Familial Resemblance of Borderline Personality Disorder Features: Genetic or Cultural Transmission?:

Borderline personality disorder is a severe personality disorder for which genetic research has been limited to family studies and classical twin studies. These studies indicate that genetic effects explain 35 to 45% of the variance in borderline personality disorder and borderline personality features. However, effects of non-additive (dominance) genetic factors, non-random mating and cultural transmission have generally not been explored. In the present study an extended twin-family design was applied to self-report data of twins (N = 5,017) and their siblings (N = 1,266), parents (N = 3,064) and spouses (N = 939) from 4,015 families, to estimate the effects of additive and non-additive genetic and environmental factors, cultural transmission and non-random mating on individual differences in borderline personality features. Results showed that resemblance among biological relatives could completely be attributed to genetic effects. Variation in borderline personality features was explained by additive genetic (21%; 95% CI 17-26%) and dominant genetic (24%; 95% CI 17-31%) factors. Environmental influences (55%; 95% CI 51-60%) explained the remaining variance. Significant resemblance between spouses was observed, which was best explained by phenotypic assortative mating, but it had only a small effect on the genetic variance (1% of the total variance). There was no effect of cultural transmission from parents to offspring.

The book Evil Genes focused to a large extent on BPD. Here are some correlations across relatives for this trait:

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CATEGORIZED UNDER: Genetics

Bernie, the man & the madness

By Razib Khan | April 26, 2009 6:19 am

Fortune has a massive profile of Bernie Madoff’s life, career and scam. Some new material too.

CATEGORIZED UNDER: Culture, History

Revenge of the roader: Chinese atheists are reactionary

By Razib Khan | April 25, 2009 10:22 am

One of the major problems in most societies, subject to “great sorts” of various kinds, is the fact that people observe correlations of attitudes & beliefs, and infer from those necessary relations. For example, if one of the first things that someone finds out about me is that I am an atheist, there is a general presupposition that I am a Left-Liberal. It is true that there is a robust relationship between atheism and liberalism in the United States, the problem I have, as an admittedly illiberal atheist, are those who believe that atheism entails liberalism. In a specific instance I have encountered secular proponents of abortion rights and gay marriage who simply find it hard to conceive that someone would have reasoned objections to these policy positions which were not fundamentally rooted in religion. A cursory examination of the treatment of homosexuals in Cuban or the old East Germany would show religion is not necessary for intolerance of homosexual behavior.
But instead of focusing on such details of history, I think it is important to note there are societies which are both far more secular than the United States, and more socially conservative: those of East Asia. Instead of asserting this, let’s look at the World Values Survey. I use both the WVS 2005-2008 & Four-wave Aggregate of the Values Studies, explaining the duplicates for nations in the tables below. Additionally, I would caution some care in overemphasizing any specific row because of some small sample sizes, in particular the number of convinced American atheists in the Four-wave Aggregate of the Values Studies (n = 17).
Below are attitudes to a host of social and political issues in several East Asian countries and the United States. I also later broke these out by religious criteria.

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CATEGORIZED UNDER: Culture

Swine flu…2009 as annus horribilis?

By Razib Khan | April 24, 2009 10:26 pm

See FuturePundit & Effect Measure. Also see H5N1. CDC recommends (especially for residents of California & Texas):

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CATEGORIZED UNDER: Biology

Vitamin D & autism?

By Razib Khan | April 24, 2009 3:56 pm

What If Vitamin D Deficiency Is a Cause of Autism?:

As evidence of widespread vitamin D deficiency grows, some scientists are wondering whether the sunshine vitamin–once only considered important in bone health–may actually play a role in one of neurology’s most vexing conditions: autism.
The idea, although not yet tested or widely held, comes out of preliminary studies in Sweden and Minnesota. Last summer, Swedish researchers published a study in Developmental Medicine and Child Neurology that found the prevalence of autism and related disorders was three to four times higher among Somali immigrants than non-Somalis in Stockholm. The study reviewed the records of 2,437 children, born between 1988 and 1998 in Stockholm, in response to parents and teachers who had raised concerns about whether children with a Somali background were overrepresented in the total group of children with autism.
In Sweden, the 15,000-strong Somali community calls autism “the Swedish disease,” says Elisabeth Fernell, a researcher at the Karolinska Institute in Stockholm and a co-author of the study.
In Minnesota, where there are an estimated 60,000 Somali immigrants, the situation was quite similar: There, health officials noted reports of autism among Somali refugees, who began arriving in 1993, comparable to those found in Sweden….

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CATEGORIZED UNDER: Genetics

Don't hit the white ones!

By Razib Khan | April 24, 2009 9:38 am

Funny clip from the “Fatbeard” episode of South Park. Interesting how Cartman turned into a White Rajah with ease.

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CATEGORIZED UNDER: Blog

Media meltdown hits science journalism

By Razib Khan | April 24, 2009 4:49 am

Bora points to this report about mega shakeups at Scientific American. The editor for nearly a generation, John Rennie, is out. Nature Publishing Group is now calling the shots. In non-science news Ezra Klein, king of all journolism, is moving to The Washington Post. We live in the age of creative destruction when it comes to media. I’m a dabbler in in writing about science, but as the years go by it seems that the media itself is converging upon my own bloggish means of production. I know that Ross Douthat is going to produce print-worthy column prose for The New York Times, but I have to think there’ll be a qualitative stylistic difference from the days of William Safire influenced by Douthat’s “New Media” exposure.
Speaking of converged New Media, there should be a bloggingheads.tv episode up Sunday or Monday which features myself & Jake Young.

CATEGORIZED UNDER: Blog, Culture

Cattle genetic variation & evolution

By Razib Khan | April 23, 2009 7:15 pm

There are some papers out on the genome of the domestic cow out right now. ScienceNews has an overview:

Two competing research teams have cataloged the “essence of bovinity” found in the DNA of cattle, but not without disagreement on some essential points.
Reporting online April 23 in Science and April 24 in Genome Biology, the two groups compiled drafts of the bovine genome, identifying genes important for fighting disease, digesting food and producing milk.

I don’t see the Genome Biology paper on the site yet, but there are two in Science. First, The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution:

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

This paper focuses on the big picture taxonomic context of bovines within the bigger family tree of mammals, and how their genome is similar and/or different. Orthologs are just genes in different species which had a common ancestor before speciation, and often retain similar functions (though not always). They look at which genes have reorganized or seem to have been subject to selection in cattle, and not unsurprisingly note:

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CATEGORIZED UNDER: Genetics

Sharia friendly prostitution

By Razib Khan | April 23, 2009 3:37 pm

Misyar: Prostitution By Another Name:

Over the past year many Muslim converts have had the “opportunity” to discover something called a “misyar marriage”, or Sunni version of temporary sexual relationship sanctioned by shariah law. From where I stand as a convert, the entire affair appears to be nothing more than prostitution by another name. I just find it interesting how in the over twenty five books on Islamic marriage that I read in English, not once was this little business about temporary marriage mentioned. The fact is that it was hidden from western students and converts to Islam because we would recognize it for what it is and be repulsed. This practice breeds fraud and duplicity in both men and women. For example…

As I told a Muslim friend who pointed this piece to me, humans will do as they wish. Religion is man made, and so at the service of man. In this case, literally. Here’s the original article that the blog post is based on….

CATEGORIZED UNDER: Anthroplogy

Which nationalities are trusting

By Razib Khan | April 23, 2009 8:35 am

Reading Dan Ariely’s Predictably Irrational I was struck and concerned by his data which suggested that once social norms of reciprocity break down it is difficult to regenerate them. In other words, social capital can be thought of as a limited nonrenewable resource, at least proximately. On the macroscale Peter Turchin offers up a historical theory where social capital translated into group cohesion serves as the motor behind the rise & fall of states. And over 10 years ago Francis Fukuyama wrote Trust: The Social Virtues and The Creation of Prosperity, which surveyed differences across nations in terms of how economic and social variation hinged on the trust, or lack of, across non-kin within a culture.
As it happens, both data sets in the World Values Survey has a binary question on trust:

Generally speaking, would you say that most people can be trusted or that you need to be very careful in dealing with people?
1 – Most people can be trusted
2 – Can´t be too careful

Below I report the % who answered #1 for all the nations in the two data sets. Some nations are therefore duplicated.

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CATEGORIZED UNDER: Uncategorized

Is wife beating acceptable in Slovenia?

By Razib Khan | April 22, 2009 9:20 pm

See the data that The Audacious Epigone reports. Hope other bloggers will start using the World Values Survey!

CATEGORIZED UNDER: Culture

Confucius against Peter Singer?

By Razib Khan | April 22, 2009 6:37 pm

I have another piece in The Guardian, A Confucian calculation.

CATEGORIZED UNDER: Blog

Beyond the sequence

By Razib Khan | April 22, 2009 12:32 pm

Dan MacArthur’s post, Can’t find your disease gene? Just sequence them all…, is worth a read. He concludes:

But sequencing won’t be enough: we need much better methods for sifting out the truly function-altering genetic variants from the biological noise. This is already difficult enough for protein-coding regions (as this study demonstrates); we currently have virtually no way of picking out disease-causing variants in the remaining 98% of the genome. There’s a clear need for developing highly accurate and comprehensive maps of the functional importance of each and every base in the human genome, using all of the tools at our disposal – something that will keep us geneticists busy long after we’ve run out of genomes to sequence.

CATEGORIZED UNDER: Genetics

Cryptic variation & melanoma risk

By Razib Khan | April 22, 2009 8:18 am

One of the funnier aspects of the discovery of genes correlated with physical traits is that finding the genetic variant which explains 75% of the variation in blue eyes is interesting, but it isn’t as if you now have a better way to find blue eyed people (though it is important for forensic work). But now there is apparently working on looking at pigmentation genes and how they effect melanoma risk in a manner which isn’t visible to the eye: Dark Hair? Don’t Burn? Your Genes May Still Put You At Risk For Melanoma:

Overall, the presence of certain MC1R variants was associated with a more than two-fold risk of melanoma, but this risk was largely confined to those patients who would not usually be considered to be at elevated risk.
Although those with dark hair are not thought to be at increased risk for melanoma, if they had dark hair and also inherited certain MC1R genetic variants, their risk for melanoma increased 2.4-fold. However, no elevated risk was associated with these same MC1R variants in those with blond or red hair.
MC1R was also associated with increased risk among those with dark eye color (3.2-fold increase), who did not freckle (8-fold increase), who tanned after repeated sun exposure (2.4 fold increase) or who tanned immediately without burning (9.5-fold increase). People with these characteristics are usually thought to be at reduced risk for melanoma.

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CATEGORIZED UNDER: Genetics
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