Archive for May, 2009

Fisher's Wave of Advance & Hybrid Zones

By Razib Khan | May 24, 2009 3:04 pm

Waves of stationary shape:

Over at Scienceblogs, people are talking about waves. Of course, everyone thinks that waves are in the domain of physics, and people always forget about one of my favorite subjects: waves of advance. Way back in the day, RA Fisher wondered what might happen if genes had to spread not just locally but across space, and he published his findings in a landmark article called The Wave of Advance of Advantageous Genes. This paper was not just important for its contributions to population genetics, but because of fundamental contributions to applied mathematics. As far as I can tell, Fisher and the great mathematician Kolmogorov published similar findings on this same subject in the same year. To that end, these kinds of waves of advance are often referred to as “Fisherian” waves.
What was Fisher’s model, what did he find, and how has it been extended?

CATEGORIZED UNDER: Genetics

Optimism across the world

By Razib Khan | May 24, 2009 2:51 pm

090524122539-large.jpgPeople By Nature Are Universally Optimistic, Study Shows:

Data from the Gallup World Poll drove the findings, with adults in more than 140 countries providing a representative sample of 95 percent of the world’s population. The sample included more than 150,000 adults.
Eighty-nine percent of individuals worldwide expect the next five years to be as good or better than their current life, and 95 percent of individuals expected their life in five years to be as good or better than their life was five years ago.

At the country level, optimism is highest in Ireland, Brazil, Denmark, and New Zealand and lowest in Zimbabwe, Egypt, Haiti and Bulgaria. The United States ranks number 10 on the list of optimistic countries.
Demographic factors (age and household income) appear to have only modest effects on individual levels of optimism.

I suspect that a sunny outlook isn’t just relevant in a cross-country sense. Without optimism where would all the entrepreneurs be? Would anyone start a new restaurant? Optimism helps people think they’ll beat the odds in a risky proposition. Though there’s some interpersonal variation in risk aversion, I suspect that there isn’t enough to explain the types of people who repeatedly enter into very low probability of success, though high reward, activities. And these very activities are often the motors behind economic growth through positive externalities.

CATEGORIZED UNDER: Culture

Patty Barreiro & Edmund Andrews & their finances

By Razib Khan | May 23, 2009 5:08 am

Megan McArdle posts Edmund Andrews’ response to her revelation of his wife’s bankruptcies. Megan concludes:

On a very broad note, I don’t see this as a story about the goodness or badness of Andrews or Barreiro–and I’ve been dismayed by some of the nastiness about her in comments here and elsewhere. Rather, I think this matters because the story Andrews told was basically about the subprime crisis, and the book casts him as a sort of everyman, lured in by cheap credit and a likeable scoundrel of a mortgage broker. That may be what happened to many, or most people in the mortgage crisis–but the back to back bankruptcies strongly suggest that this is not what happened to Andrews. That said, I think the story told with the bankruptcies included would still be a story well worth telling.

As Megan notes, even if Patty’s bankruptcies weren’t relevant, he should have brought them up to show they weren’t relevant.

CATEGORIZED UNDER: Culture

Katz

By Razib Khan | May 22, 2009 9:37 am

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CATEGORIZED UNDER: Blog, Culture

Obesity inversely correlated with European ancestry among African Americans

By Razib Khan | May 22, 2009 8:23 am

It is well known that different ethnic groups vary when it comes to diseases such as Type II Diabetes. Or, more specifically they vary in terms of risk, all things equal (if you use an online Type II Diabetes calculator you’ll see immediately as they sometimes have a parameter for ethnicity). American blacks for example are heavier than American whites. This seems to be true even when you control for socioeconomic status (though as Oprah once said, “You don’t need to do a ‘study’ to figure that out”). There has been research on genetic loci correlating to obesity in European populations before, but there is now a new one which looks at African Americans, and tries to ascertain whether some of the loci might be unique to them because of their racial ancestry.
Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X:

Obesity is about 1.5-fold more prevalent in African Americans than European Americans. To determine whether genetic background may contribute to this observed disparity, we scanned the genomes of African Americans, searching for genomic regions where obese individuals have a difference from the average proportion of African ancestry. By examining genetic data from more than 15,000 African Americans, we show that the proportion of European ancestry is inversely correlated with BMI. In obese individuals, we detect two loci with increased African ancestry on chromosome X (Xq13.1 and Xq25) and one locus with increased European ancestry on chromosome 5 (5q13.3). The 5q13.3 and Xq25 regions both contain genes that are known to be involved in appetite regulation. Our results suggest that genetic factors may contribute to the difference in obesity prevalence between African Americans and European Americans. Further studies of the regions may identify the causative variants affecting susceptibility to obesity.

The sample here is ~20% European in ancestry, in line with a large body of research on African Americans. Additionally, there is variance in the black community in terms of how much European ancestry an individual has (e.g., a rule of thumb is that around 10% of black Americans are actually 50% or less African in ancestry). This study find a weak but statistically significant negative correlation between European ancestry and Body Mass Index (BMI), ρ = −0.042 & P = 1.6×10−7. Here’s the figure (modified to fit on the screen) which illustrates it:

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CATEGORIZED UNDER: Genetics

Patty Barreiro's personal credit history?

By Razib Khan | May 21, 2009 2:52 pm

Most people have probably read Edmund Andrews’ piece in The New York Times, My Personal Credit Crisis (expanded into the book Busted: Life Inside the Great Mortgage Meltdown). Many raised eyebrows when reading this:

We had very different ideas about money. Patty spent little on herself, but she refused to scrimp on top-quality produce, Starbucks coffee, bottled juices, fresh cheeses and clothing for the children and for me. She regularly bought me new shirts and ties to replace the frayed and drab ones in my closet. She thought it wasn’t worth agonizing over nickels and dimes. I was almost exactly the opposite. My answer to any money squeeze was to stop spending. I would skip lunch at work to save $7. If I arrived at the Metro just before the end of rush hour, I would wait for five minutes to save 50 cents on the fare.

Fresh juices? I like Odwalla but I usuall think the better of it. In any case Megan McArdle has found that there’s a lot more in this direction:

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CATEGORIZED UNDER: Culture

Superfreaks about the face

By Razib Khan | May 21, 2009 9:29 am

A few years ago I commented a fair amount on the topic of prosopagnosia, face blindness. Turns out that ~2% of the population can’t really recognize faces, and this is a cryptic trait as many of these individuals have developed compensatory tendencies so that people don’t know. Not only that, but there seems to be a strong genetic component so that it runs in families. At the time I was fascinated by this because it made me wonder at how much more “cryptic” variation there could be in the human population. It seems that face recognition is such a basic and universal “competency” that it is hard to fathom that 1 out of 50 humans would lack the capability.
Now the same team has come out with new research reporting that there are individuals at the other end, those who are extremely good at recognizing and remembering faces. Super-recognizers: People with extraordinary face recognition ability:

We tested 4 people who claimed to have significantly better than ordinary face recognition ability. Exceptional ability was confirmed in each case. On two very different tests of face recognition, all 4 experimental subjects performed beyond the range of control subject performance. They also scored significantly better than average on a perceptual discrimination test with faces. This effect was larger with upright than with inverted faces, and the 4 subjects showed a larger “inversion effect” than did control subjects, who in turn showed a larger inversion effect than did developmental prosopagnosics. This result indicates an association between face recognition ability and the magnitude of the inversion effect. Overall, these “super-recognizers” are about as good at face recognition and perception as developmental prosopagnosics are bad. Our findings demonstrate the existence of people with exceptionally good face recognition ability and show that the range of face recognition and face perception ability is wider than has been previously acknowledged.

Here’s a figure showing how the three categories relate to each other:

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CATEGORIZED UNDER: Evolution, Genetics

The myth of the rational electorate

By Razib Khan | May 21, 2009 8:31 am

California, a Broke State, Reels as Voters Rebuff Leaders:

Direct democracy has once again upended California — enough so that the state may finally consider another way by overhauling its Constitution for the first time in 130 years.

The problem is simple. Voters approve services through ballot measures, and reject taxes which might result in revenues to pay for those services, through simple majorities. Fair enough. But the legislature needs a 2/3 vote for tax & budget related actions. So the problem here is that the stupid electorate is complemented by a paralyzed legislature.
In the age of Animal Spirits, Predictably Irrational and How We Decide it seems ridiculous to continue to bow before the dogma that the American voter is smart. They’re not. If they can’t be trusted to make rational decisions in their personal financial decisions, how do you expect they would make rational decisions in regards to public finance?

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CATEGORIZED UNDER: Culture, Politics

ScienceBlogs Brazil, in English

By Razib Khan | May 20, 2009 9:41 pm

Turns out there is a new weblog which showcases some Brazilian ScienceBlogs posts, translated into English.

CATEGORIZED UNDER: Blog, Culture

On Financial Foolishness

By Razib Khan | May 20, 2009 3:52 pm

Check out this Felix Salmon’s interview (video) with Gillian Tett, author of Fool’s Gold: How the Bold Dream of a Small Tribe at J.P. Morgan Was Corrupted by Wall Street Greed and Unleashed a Catastrophe (the reference to “Tribe” is a wink to Tett’s background as an anthropologist). Also, she was recently on NPR.

CATEGORIZED UNDER: Culture

Around ScienceBlogs

By Razib Khan | May 20, 2009 9:52 am

Poor, poor Ida, Or: “Overselling an Adapid”
Physics in Star Trek
Online social networking isn’t for everyone
Decoding the brain’s response to vocal emotions
Philosophy and evolution

CATEGORIZED UNDER: Blog

Habitable planets & Alpha Centauri

By Razib Khan | May 20, 2009 4:38 am

ffddpm.jpgSeed‘s Mr. Space Lee Billings has an interesting piece, The Long Shot:

“If planets are found around Alpha Centauri, it’s very clear to me what will happen,” Marcy said. “NASA will immediately convene a committee of its most thoughtful space propulsion experts, and they’ll attempt to ascertain whether they can get a probe there, something scarcely more than a digital camera, at let’s say a tenth the speed of light. They’ll plan the first-ever mission to the stars.”

The premise seems to verge on science fiction. But then much of science could be fiction if it weren’t fact. In any case, some perspective:
Alpha Centauri is 136,379 times as far from Earth as Mars is currently.
Mars is 793 times as far from Earth as the Moon is currently.
If New York to Chicago = from Earth to Alpha Centauri, then Earth to the Moon is equivalent to 0.3 millimeters.
Discovering the habitable planets would be the easy part. Waiting for WolframAlpha to become sentient so it could make the trip is the hard part.

CATEGORIZED UNDER: Science, Space

"Missing link," hype & science

By Razib Khan | May 19, 2009 4:03 pm

You’ll be seeing a lot of media hype about a new paper, Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. Here’s some perspective, A Discovery That Will Change Everything (!!!) … Or Not and There is no missing link. Bora has just about every commentary on this paper in his link list….

CATEGORIZED UNDER: Evolution

Why the indigenous still dominate the Andean region

By Razib Khan | May 19, 2009 8:24 am

400-500 years ago in the midst of the Great Dying somewhere the indigenous inhabitants of the New World suffered mortality rates on the order of 90-95%. This was almost certainly due to the facts of evolutionary history; the indigenous peoples had little defense against Eurasian pathogens. A result has been the reality that most of the New World is inhabited by European, African or mixed populations. But there are exceptions. In Mesoamerica there is still an indigenous dominated region from southern Mexico into the highlands of Guatemala. More substantially the highlands of the Andes, and therefore Peru and Bolivia, remain strongholds of indigenous groups.
Why? We know that prior to the arrival of the Spaniards the Inca Empire was being hit by plagues, no doubt of Eurasian provenance. So there was almost certainly demographic contraction. But there are also records which suggest that Spanish women had a difficult time with carrying children to term in the highlands, so whatever population crash there was, unlike other regions of the New World world Europeans and part-Europeans did not expand into the demographic vacuum. The fact that the indigenous peoples of the Andes have adaptations to highland living is not news. But there is a new paper which reviews data which suggest that Andean women give birth to healthier infants at high altitudes, Augmented uterine artery blood flow and oxygen delivery protect Andeans from altitude-associated reductions in fetal growth:

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CATEGORIZED UNDER: Anthroplogy, Culture, Genetics

The Onion on data overload

By Razib Khan | May 19, 2009 4:56 am

Amusing web view parodying the data-bleed overload of today’s youth, from 5-minute-twitter-updates to a sea of cellphone pictures at parties of people posing like tools. Perhaps a transparent society is a society of trivialities?

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CATEGORIZED UNDER: Blog

Killing you with poison, not sepsis

By Razib Khan | May 18, 2009 10:12 pm

Ed Yong has an excellent review of new research which casts substantial doubt on the trivia chestnut that Komodo dragons kill their prey with their extremely pathogen rich saliva. The more prosaic answer seems to be that they utilize poison, not particularly surprising or trivia worthy for a reptile. But the truth is not always sexy.

CATEGORIZED UNDER: Ecology, Evolution

Genes which affect female development

By Razib Khan | May 18, 2009 8:41 am

There are several papers and letters in Nature Genetics on the relationship between menarche, menopause, etc. and genetics.
Meta-analysis of genome-wide association data identifies two loci influencing age at menarche:

We conducted a meta-analysis of genome-wide association data to detect genes influencing age at menarche in 17,510 women. The strongest signal was at 9q31.2 (P = 1.7 10-9), where the nearest genes include TMEM38B, FKTN, FSD1L, TAL2 and ZNF462. The next best signal was near the LIN28B gene (rs7759938; P = 7.0 10-9), which also influences adult height. We provide the first evidence for common genetic variants influencing female sexual maturation.

Loci at chromosomes 13, 19 and 20 influence age at natural menopause:

We conducted a genome-wide association study for age at natural menopause in 2,979 European women and identified six SNPs in three loci associated with age at natural menopause: chromosome 19q13.4 (rs1172822; -0.4 year per T allele (39%); P = 6.3 10-11), chromosome 20p12.3 (rs236114; +0.5 year per A allele (21%); P = 9.7 10-11) and chromosome 13q34 (rs7333181; +0.5 year per A allele (12%); P = 2.5 10-8). These common genetic variants regulate timing of ovarian aging, an important risk factor for breast cancer, osteoporosis and cardiovascular disease.

Genome-wide association studies identify loci associated with age at menarche and age at natural menopause:

Age at menarche and age at natural menopause are associated with causes of substantial morbidity and mortality such as breast cancer and cardiovascular disease. We conducted a joint analysis of two genome-wide association studies of these two traits in a total of 17,438 women from the Nurses’ Health Study (NHS, N = 2,287) and the Women’s Genome Health Study (WGHS, N = 15,151). For age at menarche, we identified ten associated SNPs (P = 1 10-7-3 10-13) clustered at 6q21 (in or near the gene LIN28B) and 9q31.2 (in an intergenic region). For age at natural menopause, we identified 13 associated SNPs (P = 1 10-7-1 10-21) clustered at 20p12.3 (in the gene MCM8), 19q13.42 (in or near the gene BRSK1), 5q35.2 (in or near genes UIMC1 and HK3) and 6p24.2 (in the gene SYCP2L). These newly identified loci might expand understanding of the biological pathways regulating these two traits.

Genetic variation in LIN28B is associated with the timing of puberty:

The timing of puberty is highly variable1. We carried out a genome-wide association study for age at menarche in 4,714 women and report an association in LIN28B on chromosome 6 (rs314276, minor allele frequency (MAF) = 0.33, P = 1.5 10-8). In independent replication studies in 16,373 women, each major allele was associated with 0.12 years earlier menarche (95% CI = 0.08-0.16; P = 2.8 10-10; combined P = 3.6 10-16). This allele was also associated with earlier breast development in girls (P = 0.001; N = 4,271); earlier voice breaking (P = 0.006, N = 1,026) and more advanced pubic hair development in boys (P = 0.01; N = 4,588); a faster tempo of height growth in girls (P = 0.00008; N = 4,271) and boys (P = 0.03; N = 4,588); and shorter adult height in women (P = 3.6 10-7; N = 17,274) and men (P = 0.006; N = 9,840) in keeping with earlier growth cessation. These studies identify variation in LIN28B, a potent and specific regulator of microRNA processing2, as the first genetic determinant regulating the timing of human pubertal growth and development.

Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche:

Earlier menarche correlates with shorter adult height1 and higher childhood body fat2. We conducted a genome-wide association study of age at menarche (AAM) on 15,297 Icelandic women. Combined analysis with replication sets from Iceland, Denmark and the Netherlands (N = 10,040) yielded a significant association between rs314280[T] on 6q21, near the LIN28B gene, and AAM (effect = 1.2 months later per allele; P = 1.8 10-14). A second SNP within the same linkage disequilibrium (LD) block, rs314277, splits rs314280[T] into two haplotypes with different effects (0.9 months and 1.9 months per allele). These variants have been associated with greater adult height3, 4. The association with adult height did not account for the association with AAM or vice versa. Other variants, previously associated with height…did not associate significantly with AAM. Given the link between body fat and AAM, we also assessed 11 variants recently associated with higher body mass index (BMI)…and 5 of those associated with earlier AAM.

These work are interesting because if the genetic mechanisms by which menopause occurs are elucidated, perhaps the question of whether it is an adaptation, or not, will be resolved (or greater clarity attained). Below are some figures on the global distribution of some of the larger effect SNPs identified from the HGDP browser.

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CATEGORIZED UNDER: Genetics

Are Gulf Arabs fat?

By Razib Khan | May 17, 2009 5:11 am

I was looking up some data on obesity rates, mostly for American states, and I stumbled onto the maps below on obesity rates by nation for males & females (in that order):

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CATEGORIZED UNDER: Culture

Social capital ∝ to religion? (or not?)

By Razib Khan | May 16, 2009 9:00 pm

Does secularization of the USA spell social meltdown?:

That’s certainly what two European sociologists, Loek Halman and Thorleif Pettersson, have concluded. Using data from the European Values Survey, they found that there was no relationship between how religious a country was (on average) and a rich it was in social capital.
For example, the Czech Republic and Slovakia have similar levels of social capital, although Slovakia is far more religious than the Czech Republic. Some of the countries with the most social capital, Sweden and Denmark, were also the least religious.
In fact, in Western Europe, the trend is the reverse of what you might expect – the least religious nations have the most social capital!
Now, the important fact to bear in mind is that, in Europe as in the USA, more religious people are more civically engaged. It’s just that, at the aggregate level, other factors are overwhelmingly more important.
For example, social trust, a key generator of social capital, is driven at a cross-national level by the same factors that build a strong democracy – such as open institutions and free speech. Although religious are generally perceived to be more trustworthy on an individual level, that really has no bearing at a national level.
In other words, this is another example where extrapolating from the individual effects of religion to the social effects just does not work.

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CATEGORIZED UNDER: Culture

Opposition to gay marriage; region & race

By Razib Khan | May 16, 2009 10:39 am

There was a somewhat funny, if stupid, comment below in regards to minority opposition to gay marriage:

This has to be one of most ignorant and race obsessed articles I have ever read. Since you are so blinded by race you decided to leave out the most determinative factors in ones opinion concerning sexuality. The fact of the matter is black people are products of being enslaved and socialized in the bible belt. Black people are actually more tolerant of homosexuality then there white counterparts from the same cultural/geographic areas. Compare black opinions on homosexuality to Scotts-Irish in Georgia, South Carolina, and Texas then we can have a conversation.

As I have pointed out before most of the black American opposition to gay is probably due to their propensity toward Christian fundamentalism, which is the most well developed of any American racial group (Asian Americans are the most secular).* In any case, is it true that blacks are actually more supportive than whites when you control for region? Let’s look.
Again, the GSS variable MARHOMO measures opposition or support for gay marriage. I limit to the years 2006 and 2008 (there was very little change in the sample in terms of opinion). Additionally I select only whites and blacks, and break it down by Census Region. Finally I discarded all regions where the number of blacks surveyed was < 50. I added together those who "disagree" and "strongly disagree" with gay marriage into one category, and plot them on a graph where the X axis are the regions where the sample sizes for blacks are relatively large.

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CATEGORIZED UNDER: Culture
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