Archive for June, 2008

Synteny – who is right?

By Razib Khan | June 30, 2008 11:09 pm

PZ Myers outlines synteny. RPM says he’s kind of wrong. Check out the definition in Wikipedia. Since RPM came down on me for confusion on this term I knew he would bring this up. I don’t really care much about which definition is “correct,” but I thought I’d point interested readers to the debate…..


George Lakoff's The Political Mind

By Razib Khan | June 30, 2008 3:50 pm

Chris of Mixing Memory is doing us the service of a chapter by chapter review of George Lakoff’s The Political Mind. This should be fun! I told Chris that reading Lakoff talking about the minds of conservatives is kind of like me opining with supreme confidence as to the deep motivations behind why so many homosexual men prefer being “bottoms.” The is fact that I’m not a homosexual male myself, nor have I read a great deal of literature on the topic, or even communicated with homosexual males about the issue and their motivations behind their preferences, is besides the point. Now only if there was a large audience of heterosexuals who knew no gay people interested in buying books about the topic!


The paucity of libertarianism

By Razib Khan | June 30, 2008 3:42 am

A few weeks ago I read Brink Lindsey’s The Age of Abundance: How Prosperity Transformed America’s Politics and Culture. One strange thing is that because I’ve watched Brink on BloggingHeads.TV on occasion could hear the prose with his particular cadence and delivery. Really weird. In any case, The Age of Abundance is a social history of the 20th century which makes the case that despite the persistence of a partisan divide our culture has operationally congealed around a rough libertarian consensus. In short, a free market of money and lifestyle choices. I think there is a strong argument that can be made for this, as evidenced by Matt Yglesias’ qualified admission as to the rapprochement between the Left and the market, or the phenomenon of South Park Conservatism.

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We have to the technology; we can rebuild the race!

By Razib Khan | June 29, 2008 7:50 pm

Baby to be born free of breast cancer after embryo screening:

The couple produced 11 embryos, of which five were found to be free from the gene. Two of these were implanted in the woman’s womb and she is now 14 weeks pregnant.
By screening out embryos carrying the gene, called BRCA-1, the couple, from London, will eliminate the hereditary disease from their lineage.

Obviously the headline is hyperbolic in this specific case. Changing probabilities is not necessarily a guarantee. But I think the bigger picture here warrants serious notice. Armand Leroi has outlined the major issues, so I won’t review them again….



By Razib Khan | June 28, 2008 6:58 pm

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Heritability of voting

By Razib Khan | June 27, 2008 4:39 pm

I just read an interesting new paper, Genetic Variation in Political Participation:

The decision to vote has puzzled scholars for decades…The results show that a significant proportion of the variation in voting turnout can be accounted for by genes. We also replicate these results with data from the National Longitudinal Study of Adolescent Health and show that they extend to a broad class of acts of political participation. These are the first findings to suggest that humans exhibit genetic variation in their tendency to participate in political activities.

Here’s a figure which really cuts to the chase:

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Bird phylogeny

By Razib Khan | June 27, 2008 6:10 am

The best summary so far here of the bird phylogeny paper. Also, Greg Laden. Most definitely I was surprised and interested to learn that falcons are not closely related to eagles & hawks.


Pigmentation loci, TPCN2 and ASIP

By Razib Khan | June 26, 2008 2:48 pm

Sandy pointed me to letter to Nature by a group which has done some earlier pigmentation work, Two newly identified genetic determinants of pigmentation in Europeans:

We present results from a genome-wide association study for variants associated with human pigmentation characteristics among 5,130 Icelanders, with follow-up analyses in 2,116 Icelanders and 1,214 Dutch individuals. Two coding variants in TPCN2 are associated with hair color, and a variant at the ASIP locus shows strong association with skin sensitivity to sun, freckling and red hair, phenotypic characteristics similar to those affected by well-known mutations in MC1R.

All well and good, but do note that in the fine print that it is the odds ratio for OCA2 really jumps out at you.
Related: SLC24A5, SLC45A2, TYRP1, OCA2 and KITLG.


Why "Asian" mice have straight hair

By Razib Khan | June 25, 2008 1:17 am

Humans, being who we are, are really interested in how our external phenotype is shaped. Since the year 2000 many of the genetic underpinnings of the gross physical features which we use to categorize people, the sort of thing that might show up in a people description, have been elucidated. We know, for example, the genes which control variation in skin color to a first approximation at this point. It also seems that we’ve zeroed in on the primary gene responsible for eye color variation. Additionally, recently there’s been the discovery of the gene which seems to control East Asian hair form, EDAR. At my other weblog p-ter posts on a new paper, Enhanced ectodysplasin-A receptor (EDAR) signaling alters multiple fiber characteristics to produce the East Asian hair form. Go there for the summary and awesome picture of the “Asian” mice.


Selection, drift, disease and complexity, all rolled into one….

By Razib Khan | June 24, 2008 2:59 pm

One of the great things about evolutionary genetics is that it is such a diverse field in terms of the cognitive toolkit which one must access as a matter of course. Since R. A. Fisher’s The Genetical Theory of Natural Selection (along with the contemporaneous work of Sewall Wright and J. B. S. Haldane) we’ve been habituated toward thinking of evolutionary processes on an abstract level which might allow us to make general deductive inferences from first principles. Genetic drift, selection, migration, etc., are parameters which are used to construct models that allow us to generate predictions and obtain deeper insight. The discovery of DNA and the elucidation of the biophysical substrate which constrains the modes of inheritance in a concrete manner opened up the startling vistas of molecular evolutionary genetics. This discipline has allowed an inspection of how the predictions of evolutionary theory are born out on a more fine grained level. And today the genomics revolution is ramping up the data sets as computational power enables more powerful extraction of the patterns and dynamics which emerge out of these discrete streams of information.
But this is all rather philosophical and abstract. Yesterday I posted on a paper which showed how selection and drift might have operated upon the frequency of an allele which has a disease implication, and so has a pragmatic impact on quality of life. Today I’d like to bring your attention to another paper which synthesizes the big picture ideas which might entail consequences in terms of the utilitarian details of daily life, Natural Selection on Genes that Underlie Human Disease Susceptibility:

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Postgrad education vs. literalism: update

By Razib Khan | June 23, 2008 6:35 pm

Last month my posts Biblical literalism or low IQ: which came first? and Educational levels & denomination got a lot of play around the blogosphere. I used the US Religious Landscape Survey to get demographic data for denominations, but I had to cobble together numbers on Biblical literalism, etc. But with a further release of data I can now flesh out almost all the denominations plotting postgrad education % vs. belief that the Bible is the literal word of god.
Clarification: Y axis = % with postgrad education. X axis = % who believe the Bible is the literal word of god.
As you can see, the trend still holds with more denominations. I decided to do this since people were curious about denomination X, and I didn’t have that included. Click the image or here for a larger version so you can see the labels. And here is a chart with all religious affiliations included (e.g., includes non-orthodox Christians such as Mormons as well as non-Christians). Below the fold I’ve put the raw data I used, but if you want to snatch it for yourself, here it is as a CSV file (if you do some statistical analysis of the data post a link in the comments and I’ll link next week).

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Evolutionary genetics in Iceland; it's about the parameters

By Razib Khan | June 23, 2008 4:18 pm

Another story about recent human evolution, this time, really recent. The paper in PLOS is A Drastic Reduction in the Life Span of Cystatin C L68Q Carriers Due to Life-Style Changes during the Last Two Centuries. A mouthful, but the authors are really good at explaining what they’re finding and why it’s important:

….The detrimental phenotypic impact of the L68Q mutation appears to have emerged in reaction to common life-style changes almost three centuries after the mutation occurred. We believe that this is the first report of phenotypic flexibility of a monogenic disease in reaction to life-style changes that fall within the normal range of behavior of a single population in the space of a few generations. Our results underline how single gene disorders with simple Mendelian inheritance can be affected by environmental factors, resulting in changed disease status.

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Perfidious Neandertals

By Razib Khan | June 23, 2008 3:35 pm

Britain’s Last Neanderthals Were More Sophisticated Than We Thought. I don’t need to comment/summarize because already has….


Buddhists do believe in god

By Razib Khan | June 23, 2008 1:46 pm

One of the points that I run into all the time is that Buddhism is a religion without god, that is it is an atheistic religion. I admit this assertion as an ideal or elite belief, but contend that the vast majority of the world’s Buddhists are theists, so one can’t simply present Buddhism as an atheistic religion when most Buddhists are not atheists. I do tend to agree that Western converts to Buddhism are often atheists, and that’s one reason Westerners view it as atheistic religion since the Buddhists they are most likely to know are not ethnically Asian ones. The US Religious Landscape Survey actually has some questions which assess the beliefs of American Buddhists.

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Engaging theism & engaging Creationism

By Razib Khan | June 22, 2008 2:59 pm

I happen to personally accept both of these assertions:
1) A scientific world-view entails atheism
2) A scientific world-view contradictions Creationism
That being said, as matters of debate & discussion I think the former is an open question, while the latter is not an open question. When it comes to Creationism from where I stand there’s nothing to talk about; the facts of the universe manifestly falsify Creationism. Creationism is a rather clear & distinct idea. I know what I’m rejecting, and I know what the Creationists believe. Aside from the Amish and a few other groups the vast majority of Creationists are embedded in a world whose technological apparatus is contingent upon a network of facts which taken together naturally lead to the inference that Creationism is false. When I was younger I did expend marginal time trying to explain to my Creationist friends why their model of the world is problematic, but at this point I have zero interest in personally investing marginal time in this task. The persistence of Creationism in the United States, and to a lesser extent other regions of the developed world, is a functional of historical and sociological processes. For a variety of reasons a subculture has emerged in the United States which rejects the authority of the scientific elite. Authority is very important, because most people who “believe” in evolution doesn’t understand it with any plausible detail, rather, they accept that scientists in general tend to know what they’re talking about, and they also are signaling their status as a modern educated individual who identifies with the establishment.

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Black, but how black?

By Razib Khan | June 22, 2008 2:29 am

Comparing Genetic Ancestry and Self-Described Race in African Americans Born in the United States and in Africa (H/T Yann):

Genetic association studies can be used to identify factors that may contribute to disparities in disease evident across different racial and ethnic populations. However, such studies may not account for potential confounding if study populations are genetically heterogeneous. Racial and ethnic classifications have been used as proxies for genetic relatedness. We investigated genetic admixture and developed a questionnaire to explore variables used in constructing racial identity in two cohorts: 50 African Americans and 40 Nigerians. Genetic ancestry was determined by genotyping 107 ancestry informative markers. Ancestry estimates calculated with maximum likelihood estimation were compared with population stratification detected with principal components analysis. Ancestry was approximately 95% west African, 4% European, and 1% Native American in the Nigerian cohort and 83% west African, 15% European, and 2% Native American in the African American cohort. Therefore, self-identification as African American agreed well with inferred west African ancestry. However, the cohorts differed significantly in mean percentage west African and European ancestries…and in the variance for individual ancestry…Among African Americans, no set of questionnaire items effectively estimated degree of west African ancestry, and self-report of a high degree of African ancestry in a three-generation family tree did not accurately predict degree of African ancestry. Our findings suggest that self-reported race and ancestry can predict ancestral clusters but do not reveal the extent of admixture. Genetic classifications of ancestry may provide a more objective and accurate method of defining homogenous populations for the investigation of specific population-disease associations

So how does this jive with Genetic Structure, Self-Identified Race/Ethnicity, and Confounding in Case-Control Association Studies:

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The American professoriate: godless liberals?

By Razib Khan | June 21, 2008 2:36 am

In short, liberal, yes, but godless, far less so. Religious Beliefs and Behavior of College Faculty:

Faculty are, however, not monolithic. There are divisions among faculty ranks. Science and math faculty are the least religious in belief and behavior. Business faculty are the most conservative and most religious. Humanities faculty, though the most politically liberal, are not less religious than other faculty and on some measures are more religious. Faculty, while less religious than the general population, are complex in their religiosity.

Am I the only one who has had the experience of a non-science background friend who is surprised that I’m not terrified by the idea of fish genes being spliced into tomatoes? In other words, yes, a modern liberal arts education might make one more skeptical of conventional “mainstream” world-views, but that skepticism is often not complemented much with a commitment toward rational & empirical analysis of the issues at hand. So naturally intuitive morality with roots in our cognitive hardware kick in.
Most interesting figures below the fold….

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Steven Pinker interview

By Razib Khan | June 20, 2008 6:45 pm

Steven Pinker: The evolutionary man. Also check out the GNXP interview with Pinker from 2 years ago.

CATEGORIZED UNDER: Cognitive Science


By Razib Khan | June 20, 2008 4:54 am

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Time preference as a parameter in life history

By Razib Khan | June 20, 2008 3:54 am

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