Archive for May, 2008

Distribution of fitness effects of mutations?

By Razib Khan | May 31, 2008 2:47 pm

Haven’t had a time to check this paper out, but looks real interesting, Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome:

Although mutations are known to cause varying degrees of harmful effects, it is difficult to quantify the distribution that best describes the variation of fitness effects of these mutations. Here we present a new method for inferring this distribution and inferring population history using Single Nucleotide Polymorphism (SNP) data from human populations. Using 47,576 SNPs discovered in 11,404 genes from sequencing 35 individuals (20 European Americans and 15 African Americans), we find evidence of an ancient population expansion in the sample with African ancestry and a relatively recent bottleneck in the sample with European ancestry. In both populations, the patterns of variation are consistent with a leptokurtic distribution of selection coefficients (e.g., gamma or log-normal) peaked near neutrality. Specifically, we predict 27-29% of amino acid changing (nonsynonymous) mutations are neutral or nearly neutral, 30-42% are moderately deleterious, and nearly all the remainder are highly deleterious or lethal. Furthermore, we infer that 10-20% of amino acid differences between humans and chimpanzees were fixed by positive selection, with the remainder of differences being neutral or nearly neutral.

Leptokurtosis describes a more acute peak around the mean.



By Razib Khan | May 30, 2008 12:37 pm

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First Greenlanders left no descendents?

By Razib Khan | May 29, 2008 8:41 pm

Here’s another example of how genetic methods can shed light on archaeological questions, Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland:

The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World’s northern extremes. However, their origin and genetic relationship to later cultures is unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human, using 3400- to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This suggests that the earliest migrants into the New World’s northern extremes derived from populations in the Bering Sea area, and were neither directly related to Native Americans nor the later Neo-Eskimos that replaced them.

New Scientist has a popular press profile of the research & findings. Remember last year when it was confirmed that Polynesians had to have been visiting the coast of South America because of the phylogeny of chicken DNA extracted from subfossils? Though there have always been hints, I think this suggests greater complexities to our picture of the pre-Columbian world. Do note that this is one mitochondrial DNA lineage. It shows lack of perfect continuity, but does not entail total replacement….
Update: “Polynesian” chickens might not be in the bag yet. See comment.


Measuring the age of white supremacy

By Razib Khan | May 29, 2008 3:13 pm

vickers.jpgI’m getting into an exchange with Luis below about the rise of European domination. Unfortunately with historical questions I can’t “prove” my case as in mathematics, nor can I cite an empirical result that is extremely generalizable as in much of the natural sciences. I’m trying to describe a distribution of facts over time and space, and I can’t really make my own position clear without plugging into Luis’ mind all my priors (the inverse might apply from Luis’ perspective). That takes time and is basically impossible in blog-format, though I’ve had better success I think in face-to-face conversation because the per unit density of data which can be transmitted quickly. So, two quick points.

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Short Guide to the Human Genome

By Razib Khan | May 29, 2008 8:43 am

shortguidehumangenome.jpgJust got a copy of Short Guide to the Human Genome, put out by Cold Spring Harbor Laboratory. It’s a fun little review; appropriate for browsing during your “in-between” time. As the title emphasizes this guide is characterized by extreme brevity, under 200 pages. Nevertheless it attempts a survey of the major results which have come to light over the past decade in human genomics. This isn’t really a primer, it assumes you know what UTR stands for and why spliceosomes are important. In other words, return on investment is probably only there if you are reasonably familiar with the basics of molecular genetic terminology so that you don’t always have to keep running for references. The guide is divided into broad thematic sections, for example, “RNA” or “comparative genomics.” Within these chapters are compact sections with headings in the form of aquestion. After some short introductory exposition (usually a sentence or two), you are presented with a table or chart which summarizes the main finding, followed by further clarifying exposition. Methods and data sources are always appended, and quite frequently you’ll also find a citation to papers which cover the topic being addressed. The author notes that this book was written as an extended response to the most common questions asked about the human genome, so don’t be surprised if you stumble upon something you might have wondered about but never followed up.


Postgrad education vs. Biblical literalism, nonlinear?

By Razib Khan | May 28, 2008 10:11 pm

BibLitPG.jpgA good critique of my posts which explored the correlates of Biblical literacy. It isn’t surprising that some transformations make the relationship clearer….


The Post-American World by Fareed Zakaria

By Razib Khan | May 28, 2008 8:31 am

postamericanworld.jpgFive years ago Fareed Zakaria, Newsweek‘s International Edition editor, splashed onto the public intellectual scene with The Future of Freedom: Illiberal Democracy at Home and Abroad. It’s somewhat heterodox, at least for the mainstream, observation that liberal democracy is more than simple majoritarianism, earned him some notoriety. Enough so that he could receive a fawning profile in New York Magazine. But while five years ago Fareed promoted some rather academically well known but transgressive ideas about the necessity for institutional, economic and cultural supports for a flourishing democratic polity, in The Post-American World he plays the role of the golden-tongued expositor of conventional wisdom. The basic thesis of the The Post-American World is that as the 21st century proceeds the United States will have to resituate itself in a multi-player world where it is the most powerful actor, instead of being the only agent on stage. China & India rise, globalization brings wealth, terrorism is a manageable, and no longer being #1 in every metric does not imply decline. The big picture is dime-a-dozen, but Fareed’s fleshing out of the argument is littered with facts which shed light on subtle points in regards to the precise dynamics across which the arc of history will be played out.

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Godless elites?

By Razib Khan | May 28, 2008 3:33 am

My two posts on religion & IQ/education are getting a lot of attention. I didn’t spend more than 30 minutes on both entries combined, so the attention to unit time invested ratio is rather out of wack. Doing some digging it’s funny how interested people are in this topic, while at the same time being totally disinclined to do their own leg work. Multiple message boards have also pointed to another similar survey which shows the relationship between religiosity and IQs in international comparisons. You might be amused to find out that I wrote that up in 30 minutes 5 years ago as a joke! All the data is real, I didn’t make it up, but in all honesty I connect these particular dots to see peoples’ prejudices slam up against their anti-prejudices. Most atheists are Good Enlightened people who are often skeptical of IQ tests because Good Enlightened people know that standardized tests are false (except of course in the cases where they make sure everyone knows their really high standardized test score while at the same time admitting that it “doesn’t mean anything….”). But atheists also generally believe that religious people, especially fundamentalists, are stupid and lacking in reasoning capabilities. So how about pointing out that religious fundamentalists don’t do as well on tests which supposedly measure reasoning ability? If you track some of the reaction on the message boards you see repeated instances of excitement and glee before someone pipes up to remind the assembled godless that “IQ isn’t a valid measure of intelligence.” Gosh darnit!
For the record, I believe IQ and standardized tests in general have predictive power. I also don’t believe in God.
In any case, a few people have questioned the relationship between education & Biblical literalism. I’ve pointed out that that’s a pretty robust trend over many decades, but I’ll offer some quick “proof.” Then I’ll repost some data I found in regards to elites and their religious affiliations and views which might interest.

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New recommended levels of Vitamin D?

By Razib Khan | May 27, 2008 10:19 am

Current Vitamin D Recommendations Fraction Of Safe, Perhaps Essential Levels For Children:

The current recommended daily allowance (RDA) of vitamin D for children is 200 International Units (IUs), but new research reveals that children may need and can safely take ten-times that amount. According to new research this order-of-magnitude increase could improve the bone health of children worldwide and may have other long-term health benefits.

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By Razib Khan | May 26, 2008 10:31 pm

Via Reihan, Instapaper. Need to not get behind on my Tech Crunch feed….


Pizzly shot

By Razib Khan | May 26, 2008 5:10 pm

A few weeks ago I mentioned that there is some debate as to the taxonomy of the Polar Bear; specifically, as to whether it was simply a clade of the Brown Bear species. Interesting, I note that today a Polar Bear-Grizzly hybrid was shot in Canada:

There have long been stories of oddly coloured bears living in regions where the two territories overlap.
But until now, grizzly-polar hybrids, dubbed “grolar bears” or “pizzlies”, have been found only in zoos.
The hybrid bear was shot last month by an American big game hunter on Banks Island, Northwest Territories, Canada.
His guide, Roger Kuptana, noticed the creature had the long claws and slightly humped back of a grizzly bear and thought it might be a hybrid.
The body was seized by officials, who sent a DNA sample for tests which confirmed its unusual origins.

If this is not a “one-off” or sterile hybrid that leaves the opening for gene flow between these populations.


Educational levels & denomination

By Razib Khan | May 26, 2008 3:01 pm

The post below where I show that belief in the literal truth of the Biblical tends to correlate well with IQ scores from the General Social Survey on a denominational scale is getting a lot of response; enough of it is of low quality that I’ll close the comment thread soon enough. As I observed the “truth” which I had extracted out of the data is rather banal; I doubt it surprised anyone that a “fundamentalist” attitude toward religious scripture tends to be associated with low cognitive ability. The correlation here is probably not one of simple causality in either direction. It seems the most plausible model is one which notes that various denominations tend to have particular socioeconomic profiles which shape a general cultural outlook. In the American South this was made most explicit, with a rank order of status from Episcopalians, to Presbyterians, to Methodists, to Baptists, and finally on down to marginal sectarians. These denominations tend to run in families, but, one may change denomination with relative ease in the United States in comparison to other nations. According to The American Religious Identification Survey reports that 16% of the adult population changes their affiliation during their lifetime. This level of churn is also probably not random; those who change their socioeconomic status may “trade up” or “trade down” in their church so as to feel more comfortable among their peers. I like to point out that the presidential candidate and wealthy lawyer John Edwards was raised a Baptist, but switched to Methodism as an adult. This is probably partially a reflection of his class status shift as well as his social liberalism. In contrast, though George W. Bush was raised an Episcopalian, he now worships in a Methodist church. This is a pretty good illustration of Bush’s reinvention of himself as Middle American despite his patrician New England origins.

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Biblical literalism or low IQ: which came first?

By Razib Khan | May 26, 2008 3:29 am

Update II: Many links into this entry are labeling this a “study.” It wasn’t a study, I literally took 10 minutes before I went to sleep to collect the data and produce the chart. The data on literal interpretation of the Bible is from a book which you can read via Google. The IQ scores are from the General Social Survey as reported by The Inductivist. I already knew that this sort of correlation existed, it’s pretty unsurprising as I noted. The same pattern shows up if you use post-graduate eduation as the dependent variable. And I spot checked SAT scores by denomination, and again the association shows up. All that being said, the title was obviously tongue-in-cheek.
Update: Follow up post….
A few months ago I posted data which showed, unsurprisingly, that Unitarian-Universalists tend to have high IQs and Pentecostals not so much. What about something like Biblical literalism and IQ? Well, I plotted the IQ values from the General Social Survey for selected denominations and plotted them against the proportion which believed in a literal interpretation of the Bible. Prepare to be greeted by a very banal reality below the fold….

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The Phoenix has landed

By Razib Khan | May 26, 2008 12:22 am

As you probably know, the Phoenix has landed on Mars. No problems so far. I assume the best place to track the data as it comes back is the NASA mission page for Phoenix. Here are the mission goals:

–Determine whether Life ever arose on Mars
–Characterize the Climate of Mars
–Characterize the Geology of Mars
–Prepare for Human Exploration


Bloggingheads ScienceBlogs edition

By Razib Khan | May 24, 2008 6:55 pm

PZ Myers & John Wilkins for this week’s Science Saturday


Gender gap in politics

By Razib Khan | May 23, 2008 8:37 am

One of the truisms of American politics for the past generation has been the “gender gap” whereby women tend to lean toward the Democrats and men toward the Republicans. This gap has become part of the background assumptions of American political commentary to the point that right-wing polemicist Ann Coulter has proposed restricting the vote to men. Though Coulter’s proposal is obviously ludicrous, there isn’t that much objection to the assumption she makes that women support the Left party and men the Right. That’s been empirically a valid judgment in the United States for the past generation. The problem is when pundits begin to create grand theories about how the Democrats and their liberal program are naturally the “Mommy Party” and the Republicans and their conservative plank the “Daddy Party.” I generally don’t buy it, because I read, and so when I was a teenager I read a paper which showed that if suffrage had been limited to men in the United Kingdom then almost every Conservative victory in the 20th century would have been overturned. A similar tendency also holds for Australia. This is not to suggest that men are naturally liberal, or women naturally conservative. Rather, it is to suggest that locally contingent conditions are important, and generalizing from one case might lead one astray. Since we Americans don’t know much about other nations we need to fall into this trap quite a bit.
Nevertheless, there are some interesting cross-cultural dynamics within the past generation worth noting. The Developmental Theory of the Gender Gap: Women and Men’s Voting Behavior in Global Perspective:

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By Razib Khan | May 23, 2008 1:22 am

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Religion & public attitudes: Europe vs. USA

By Razib Khan | May 22, 2008 7:45 am

A few years ago a poll came out, Religious Views and Beliefs Vary Greatly by Country, According to the Latest Financial Times/Harris Poll. My title is a bit misleading insofar as the survey compared several European countries as well as the United States. Below the fold I’ve placed a few of the tables which I think might surprise, or not, depending on where you stand. One thing I will observe is that despite the substantive differences which lay at the heart of the rivalry between France and the United States, there are also similarities between these two “universal nations” that lead to some of the enmity since they both perceive each other to be brands competing in the same market.

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Fear of a white planet

By Razib Khan | May 21, 2008 7:08 am

barackraila.jpgOne of the main facts about American life is hypodescent, “the practice of determining the lineage of a child of mixed-race ancestry by assigning the child the race of his or her more socially subordinate parent.” Barack Obama & the Kenyan politician Raila Odinga (who, probably falsely, claims to be Obama’s first cousin) are both “black,” despite the fact that when compared to each other Obama’s substantial European ancestry is rather clear. I recall years ago watching the Oprah Winfrey television show where they were discussing the issue of self-hatred with a young black woman who was attempting to become impregnated by a white man (any white man) so that her children would “look white” and be beautiful. An adoption counselor rose up and told this young woman that her agency had many biracial children who they were attempting to place, and “none of them look white, they all look black.” The clear and present background axiom here is that the power of black phenotype ensured the futility of this young woman’s “quest.”

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Notes on Sewall Wright: Wright's F-statistics

By Razib Khan | May 20, 2008 4:08 pm

Notes on Sewall Wright: Wright’s F-statistics:

A preliminary question is one of terminology. What, if anything, does the letter ‘F’ stand for? One plausible answer is that it stands for ‘fixation’, since among other things the F-statistics can be used to measure the rate at which alleles tend to be ‘fixed’. Wright himself in his later writings sometimes refers to F as an ‘index of fixation’.

Believe it or not, Fst is one of thos population genetic concepts you’ve almost certainly encountered no matter your background.
Related: On Reading Wright, Notes on Sewall Wright: Path Analysis and Notes on Sewall Wright: the Measurement of Kinship.


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