Archive for January, 2009

Gene Genie #42

By Razib Khan | January 20, 2009 1:07 am

@ Genetic Future.


Deadweight bankers

By Razib Khan | January 19, 2009 2:52 pm

The End of Banking as We Know It:

The bright side is that all those displaced financial services professionals can now set their sights on doing something, well, truly useful.
Still, this adjustment will be painful for all those who have to carve out new careers, as well as for New York and other places these companies call home.
Finally, what will a humbled financial services industry mean for consumers? Higher borrowing costs, Mr. Miller said.
“The leverage that these companies were using allowed them to lower their rates,” he said. “Rates have to go higher for the banks to operate in a safe and sound manner and make money.”
Credit is also likely to remain tight, in Mr. Miller’s opinion. A result is that consumer spending won’t recover to bubble levels.

The bloated banking sector did have a use: propping up conspicuous consumption in a culture where for a small moment everyone fancied themselves a potential real estate millionaire in the making. It seems the current opinion is that all those extra iBankers were like all the extra bureaucrats at any large corporation; no value added except for their own bottom line. To be fair, I think this argument could be made about most scientists and science. But there is a structural difference between science & finance. Just because 99.99% of scientific possibilities are false leads, it doesn’t mean that it is then acceptable that 99.99% of financial decisions are also missteps. In finance the remaining 0.01% of decisions won’t result in something like electricity or the railroad.


Ivory & teak, how related are South Asians & Europeans?

By Razib Khan | January 19, 2009 9:40 am

The post yesterday about the deletion which results in heart disease later in life had some interesting ancestry related material. This makes sense, the genetic maps which I post on now and then ultimately have a medical rationale behind them; eliminate population structure so that you don’t have spurious correlations confusing you when you try and get a fix on the genetic underpinnings of a disease. By example, consider a study with cases & controls, and individuals with the trait or disease have five times the likelihood of carrying a particular allele at a particular gene. But you look more closely, and you see that if you control for race this doesn’t hold, in fact you are just picking up the fact that one population has a greater propensity for the trait or disease as well as the reality that populations differ in allele frequencies on many genes. The old chestnut about correlation not equaling causation applies here. But, causation can ascertained using correlation as a precondition. Eliminating cryptic population substructure with ancestrally informative markers (AIMs) is the way you would do this, so that there’s nothing in the genetic background confounding the associations you pick up.
In any case, the supplementary material has some graphs that I thought would be of interest.

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Where is MYBPC3 deletion found?

By Razib Khan | January 19, 2009 2:03 am

In some of the popular press pieces on the genetic variant which is implicated in heart disease among South Asians there are references to the fact that only 1% of the world’s population carries it. Actually, that’s obscuring an important piece of information: that 1% is almost exclusively South Asian, so that the 1% is simply 5% X 20% (20% being the proportion of the world’s population that is South Asian). I’ve placed the table from the supplementary data which shows the populations in the HGDP data set which do, and don’t, have the deletion on MYBPC3.

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Gene causes heart disease in South Asians

By Razib Khan | January 18, 2009 9:01 pm

gandhi.jpgA common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia:

Heart failure is a leading cause of mortality in South Asians. However, its genetic etiology remains largely unknown1. Cardiomyopathies due to sarcomeric mutations are a major monogenic cause for heart failure…Here, we describe a deletion of 25 bp in the gene encoding cardiac myosin binding protein C (MYBPC3) that is associated with heritable cardiomyopathies and an increased risk of heart failure in Indian populations (initial study OR = 5.3…replication study OR = 8.59…combined OR = 6.99….and that disrupts cardiomyocyte structure in vitro. Its prevalence was found to be high (4%) in populations of Indian subcontinental ancestry. The finding of a common risk factor implicated in South Asian subjects with cardiomyopathy will help in identifying and counseling individuals predisposed to cardiac diseases in this region.

The odds ratio is showing a large effect for this deletion; the likelihood of heart related problems if you carry the deletion are very high. On the order of 90% of older individuals who carry it have heart problems. On the other hand, only around 5% of the heart disease among South Asians is due to this locus of large effect. Why is this genetic variant so common? The authors suggests that since it has an effect only later in life, beyond reproductive age, selection has not been able to purge the allele. On the other hand, a 5% frequency is rather high, perhaps it is just a neutral variant which become common due to some population bottleneck in South Asia within the last 30,000 years. Or, perhaps antagonstic pleiotropy, by which I mean benefits early in life (which would increase reproductive fitness greatly) outweighing the relatively limited fitness effects later on in life (older individuals can increase the fitness of their offspring through investment in resources, but this is less important or likely than direct increase in fitness during peak reproductive years). In some ways this deletion in MYBPC3 is the South Asian cystic fibrosis, at least in terms of frequency. But CF hits people early on it life and so its evolutionary impact is much stronger. Here’s a figure which shows the effect in those with the allele:

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Korean genetic relationships

By Razib Khan | January 17, 2009 12:11 am

There’s a new paper, The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers:

Methodology and Results
We analyzed mitochondrial DNA…sequence variation in the hypervariable segments I and II…and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations…In addition, published mtDNA haplogroup data…mtDNA HVS-I sequences…Y chromosome haplogroup data…and Y chromosome STR da…were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations.
The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.

Last month I posted on the genetic map of East Asia. That paper surveyed hundreds of thousands of variant loci in the autosomal genome, and mapped the variation in the populations on a 2-dimensional chart. Like the genetic maps of Europe there wasn’t too much of a surprise. So what value-add is there in this sort of study which examines uniparental lineages, that is, genes inherited only through the maternal (mtDNA) and paternal (Y) lineages? Here’s the table to look at:

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Judeo-Zensufi-Hindianity, yes indeed

By Razib Khan | January 16, 2009 8:47 pm

I have a big round up of various responses to my posts on Judeo-Christianity at Secular Right. Ross Douthat responds:

Indeed, the only real problem with the term for his purposes may be that it isn’t intellectually lazy enough – that it doesn’t create an umbrella big enough for liberal-Protestantized Muslims and Hindus and Buddhists to huddle under as well. And reading his post again, maybe that’s what he’s getting at: That we need Christians and Jews to “retain their distinctiveness in at least a notional sense,” as he puts it, in order to make other faiths feel comfortable joining the liberal tent – rather than remaining outside out of fear that they’ll be swallowed in a Judeo-Christian sea. But ultimately, he does want religious distinctions to be swallowed in a Judeo-Christian (or liberal Protestant) sea: He wants us to emphasize the distinctions between Christians and Jews in the short run, because that’s the only way to de-emphasize the distinctions between Muslims and Christians or Jews and Hindus over the long run. No to Judeo-Christianity, in other words, but yes, eventually, to Judeo-Zensufi-Hindianity.

I think Ross hit the nail on the head. Unlike some New Atheists I don’t see supernatural belief declining toward triviality, therefore, I want it to be “manageable.” Additionally, unlike someone like Sam Harris I don’t view religious moderates as milquetoast gateway drugs to “authentic” fundamentalist religion. Some atheists are prone to accepting the position that fundamentalists are the most honest religionists, that they take the beliefs of their faith seriously and consistently. For various reasons I do not believe this (though I once did when I was younger). Fundamentalist and non-fundamentalist religion may both be grounded in supernatural claims, but the former is dangerous to a pluralistic society, so I naturally favor the latter. I have no theoretical problems with exclusive religious claims, and take no offense if someone believes that I am going to hell, but the social consequences of several fundamentalisms coexisting within one society is not one of amity in the long term. So yes, I want to diminish the differences to the point where there is an operational syncretism, and affiliation to specific religious traditions is one of personal preference or family tradition. I think we’re going in that direction already. The vacuous assertion common in the mainstream that one is “spiritual” and not “religious” is another sign….


The short goodbye

By Razib Khan | January 16, 2009 3:47 pm

Farewell to evolgen. I guess the Facebook account must occupy all his time….


Humans have adapted on genome-wide level?

By Razib Khan | January 16, 2009 2:50 pm

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans. Here’s the author summary:

There is much reported evidence for positive selection at specific loci in the human genome. Additional papers based on comparisons between the genomes of humans and chimpanzees have also suggested that adaptive evolution may be quite common. At the same time, it has been surprisingly hard to find unambiguous evidence that either positive or negative (background) selection is affecting genome-wide patterns of variation at neutral sites. Here, we evaluate the prevalence of positive or background selection by using two genome-wide datasets of human polymorphism. We document that levels of neutral polymorphism are substantially lower in the regions of (i) higher density of genes and/or regulatory regions, (ii) higher protein or regulatory divergence, and (iii) lower recombination. These patterns are robust to a number of possible confounding factors and suggest that effects of selection at linked sites cannot be ignored in the study of the human genome.

Here’s the critical bit from the discussion:

Because recurrent adaptive substitutions leave local (on the order of 0.1 s/ρ) and transient (on the order of Ne generations) dips in neutral polymorphism, persistent adaptation should lead to lower levels of neutral polymorphism in regions of lower recombination and regions where selective sweeps are more frequent and/or stronger on average. Here we have confirmed these predictions by showing that levels of SNP density are lower in the regions of lower recombination and in the regions of higher functional density and functional divergence.

Areas subject to selection, positive or negative, naturally have lower neutral variation because selection “cleans” them either, through through purifying selection (as deleterious mutants are purged from regions of the genome with important functional significance) or due to the homogenizing effect around the locus in the population of a selective sweep. In the later case one haplotype, which can be a particular sequence of alleles derived from one individual which has come under selection, increases in frequency during the selective process. After selection has ceased due to the fixation of a haplotype, recombination and mutation begins to breakdown down the uniformity around area of homogeneity. The extent of the resultant new variation is obviously proportional to time of sweep, as well as recombination, mutation rate, etc.
The authors have some good quotes in ScienceDaily:

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Genetic variation in space & time – Iceland

By Razib Khan | January 16, 2009 12:55 am

A neat new paper on Icelandic genetics, then and now, Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool:

A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.

This shouldn’t be that surprising. Iceland is an island, and an island with little immigration after its first few centuries. This genetic isolation allows for the building up of differences because there is no gene flow evening out the differences in random variation which is generated by drift. This is why Iceland and Sardinia often show up as outliers on principle component maps which illustrate genetic variation between different groups.

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Pigments: zebrafish and humans

By Razib Khan | January 14, 2009 8:50 pm

About 3 years ago a paper was published on pigmentation which heralded the breaking of the dam when it comes to skin color genetics, SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. The zebrafish, a model organism familiar to evo-devoists the world over, played an important role in the paper. The new issue of Zebrafish is totally devoted to pigmentation. The press release was kind of weird, Zebrafish Journal Publishes Skin Pigmentation Studies That Shed Light on the Evolution of Race:

“With the election of the first African-American president of the United States, our society has taken a landmark step towards deracializing human conduct,” says Stephen C. Ekker, PhD, Rochester, MN, Editor-in-Chief of Zebrafish. “As scientists, we contribute to this work by sharing genetic insights to demystify skin color and race.”

OK…. In any case, there are two papers (both OA) that readers might find interesting. Skin Color in Fish and Humans: Impacts on Science and Society:

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In defense of Judeo-Christianity

By Razib Khan | January 14, 2009 8:18 pm

Ross Douthat (also, James Poulos) makes an intelligent, well-informed defense of the term using the general framework that I began with (as opposed to some people who simply insist on digressing immediately to forward their own position). There are also intelligent comments below. Instead of responding in a point-by-point fashion to Ross’s rejoinder in this post, I’ll just elaborate in the comments here and below. Rather, I want to tack to a different issue. My main concern as an atheist who lives in a progressively more religiously pluralist society characterized by liberal democratic values is to turn all religions into operational variants of mainline Protestantism. Implicit in this is that the extinction of organized religion will not occur in the near future, so in a pragmatic sense religion has to be take as one of the parameters which define our society.

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Rot at the top, rot at the bottom

By Razib Khan | January 14, 2009 2:02 pm

Arnold Kling put up a chart which shows how the Masters of the Universe were empty suits. He says:

The pattern is big egos, big money, and big power offering big promises, getting big media play, and making big mistakes (Spitzer’s mistakes were relatively small, to be honest). To me, the fiscal stimulus represents yet another redistribution of power away from ordinary people and toward the elite, when already the imbalance is too high. I am more worried about rot at the top of society than at the bottom.

Kling notes that there is also rot at the bottom; the speculative credit binge mentality trickled down, you know what I’m talking about. American consumer spending has been based on foreign credit for years now. But we don’t have sober elites, rather, it’s public choice theory gone wild in application. Power corrupts. What to do? I’m an atheist, but I’m incline to say pray and hope for a miracle.
My main consolation is that just as humans are prone to irrational exuberance, we can get into dark funks insulated from the shades of gray. Hopefully my pessimism can be abolished by the reality that despite the evil of individuals, our institutional frameworks are fundamentally robust and so will eventually channel the animal passions appropriately.


Vitamin D & diabetes?

By Razib Khan | January 14, 2009 3:17 am

Vitamin D and Diabetes:

Diabetes is a leading cause of cardiovascular disease. Persons with diabetes are at greater risk for early cardiac mortality, and for repeat events if they survive their first cardiac event. Recently, low serum concentrations of vitamin D have been associated with increased risk for cardiac events. Evidence indicates that persons with diabetes have lower serum concentrations of vitamin D. In addition, persons at risk for diabetes or metabolic syndrome have inadequate serum concentrations of vitamin D. This review will assess the evidence relative to the impact of vitamin D in the development of diabetes, metabolic syndrome, and diabetes complications. Studies that address vitamin D and its impact on metabolic outcomes as well as possible mechanisms of action are provided. Finally, the assessment and suggested treatment for vitamin D deficiency is addressed. Effective detection and treatment of inadequate vitamin D concentrations in persons with diabetes or those at risk for diabetes may be an easy and cost-effective therapy which could improve their long-term health outcomes as well as their quality of life.

I got to this article via this ScienceDaily piece, Vitamin D Is The ‘It’ Nutrient Of The Moment. I’ve wondered about this before, my RSS is pretty much peppered constantly by Vitamin D related literature right now. I got into this because of its possible role in the evolution of human skin color, but I’m not surprised about the diabetes connection. South Asians have really high rates of diabetes, so I’ve read a fair amount on how to prevent diabetes, and Vitamin D supplementation is in there. As it happens, South Asians at high latitudes might suffer chronic Vitamin D deficiencies due to lower radiation levels…though honestly it looks like many South Asians are fat,* so I think that’s probably a bigger population level factor right now.
* There are interpopulational differences in obesity in the United States. Some of it breaks down by race; black people are fatter than white people. Some of it by region; Southerners are fatter than Coloradans. Some by socioeconomics; poor people are fatter than rich people. As far as “Asian Americans” goes, I’m willing to bet that the majority of obese Asian Americans in the United States are South Asian. I’m not sure if we’re fatter on average than whites (I wouldn’t be surprised if we are, especially if you control for SES), but we sure are fatter than East Asians.


Dispatches from bizarro world!

By Razib Khan | January 14, 2009 1:51 am

Bizarro.jpgAfghan Schoolgirls Under Attack:

One morning two months ago, Shamsia Husseini and her sister were walking through the muddy streets to the local girls school when a man pulled alongside them on a motorcycle and posed what seemed like an ordinary question.
“Are you going to school?”
Then the man pulled Shamsia’s burqa from her head and sprayed her face with burning acid. Scars, jagged and discolored, now spread across Shamsia’s eyelids and most of her left cheek. These days, her vision goes blurry, making it hard for her to read.


Carnival of Liberals

By Razib Khan | January 14, 2009 1:16 am

Ruchira Paul is hosting the Carnival of Liberals. Check it out!


Justify Judeo-Christianity!

By Razib Khan | January 13, 2009 9:22 pm

One of my more quixotic quests has been to dispute the use of the term “Judeo-Christian” in normal conversation. Many people who use the term do so without much forethought, it’s just one of the definitions you use to point to the bracketing of the two traditional religions of Western civilization. In our modern context where there are great tensions between the world of Islam and the West it also alludes to a cleavage between the Abrahamic faiths where Islam is painted as the outgroup.
My own contention is that the term misleads, and emerged out of an attempt to acknowledge the rise of religious pluralism in what used to be called “Christendom,” that pluralism being tested on the margins by the predominant non-Christian tradition of the West, that of the Jews. As a matter of fact for most of the past 2,000 years, or more precisely the period between the Christianization of the Roman Empire (circa 300-500) and the Jewish Enlightenment (circa 1800), Jews were not part of Western civilization.* Rather, Jews were in the West, and in the Islamic World, but they were generally not of them, with the exception perhaps of Al-Andalus.

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Is this profiting on stupidity bad?

By Razib Khan | January 13, 2009 3:09 pm

The Man Who Made Too Much:

Hedge fund manager John Paulson has profited more than anyone else from the financial crisis. His $3.7 billion payday in 2007 broke every record, and he made it all by betting against homeowners, shareholders, and the rest of us. Now he’s paying the price.

There’s a lot of talk about how this is equivalent to currency speculation, but is it? I mean morally.


Less sleep = more illness?

By Razib Khan | January 13, 2009 1:05 pm

Sleep Habits and Susceptibility to the Common Cold:

There was a graded association with average sleep duration: participants with less than 7 hours of sleep were 2.94 times…more likely to develop a cold than those with 8 hours or more of sleep. The association with sleep efficiency was also graded: participants with less than 92% efficiency were 5.50 times …more likely to develop a cold than those with 98% or more efficiency. These relationships could not be explained by differences in prechallenge virus-specific antibody titers, demographics, season of the year, body mass, socioeconomic status, psychological variables, or health practices. The percentage of days feeling rested was not associated with colds.

Even if there’s a big confound that they haven’t accounted for, this is a large effect. It also goes along with our intuitions and common sense. There are plenty other correlations between less sleep and illness out there, but respiratory illness is a great proximate dampener on productivity for many of us. Also, ScienceDaily.


Topology to teleos?

By Razib Khan | January 13, 2009 3:27 am

Over at Culture11, Will Wilson (a mathematics student at Yale) has an interesting article up, Screaming Shapes & Seven-Dimensional Donuts:

It is clear that reductionist and demiurgic approaches to science have stood unchallenged on the intellectual landscape for too long, and their profound philosophical and cultural implications left to unfold freely. Many will complain that explanation and understanding — which shift the purpose of inquiry away from mere accuracy and toward knowledge of propriety — is not the role of science. This may be true in the aftermath of the divorce of science from philosophy won by the positivists, but perhaps it is time that this split be healed in a way that allows us to gain in both humility and wholeness. Thom’s theory alone may be unsatisfactory, but it points the way towards what is needed: a rigorous unification of prediction and explanation that is aware of its political and cultural implications; a postmodern natural philosophy for the masses.

That’s the conclusion. You have to read the whole thing to understand what Will is getting at. I am myself a “Three cheers for reductionism!” fellow, but I’m curious if any mathematicians might weigh in (I’m not familiar with René Thom’s work, which is the launching point for Wilson’s essay).


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