Archive for September, 2010

Daily Data Dump – Thursday

By Razib Khan | September 30, 2010 11:21 am

Should you go to an Ivy League School? “Clearly, going to a top-ranked school seems to deliver far higher earnings at age 28 than poorer ranked schools. In fact, the relationship is highly non-linear. Contrary to what you may have heard (“All top-ranked schools are the same”); it in fact looks like the difference between top-ranked Harvard and 9th ranked Dartmouth is on the order of ~$4,000 a year (perhaps $100,000-$200,000 over the course of a lifetime?).”

The Other Social Network. Speaking of non-linearities: “And of course there’s the H-Factor. “I think the name had a lot to do with it,” says Ting. “When we go to a school and say this site is from Columbia, it doesn’t carry the same marketing punch as, This is from Harvard.”

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Mormons are average

By Razib Khan | September 30, 2010 11:07 am

Clark of Mormon Metaphysics says below:

My impression is that atheists, Mormons and Jews did best simply because all three groups tend to be well educated. (Someone mentioned stats adjusted for education but I couldn’t see where that was noted although maybe I just missed the obvious)

This is not an unfounded assertion, as it is “common knowledge” in the Zeitgeist that Mormons are high achievers. Ergo, posts such as The Latter Day Ruling Class. There’s one problem here: it’s not really true in a full-throated sense. The sample size for Mormons in the GSS is very small, so that’s not what we need to look at. First, American Religious Identification Survey 2008:


As you can see Mormons have about the average proportion of college graduates for an American ethno-religious group. We can drill-down further with the Religious Landscape Survey. First, comparisons of various religious groups by educational attainment class as proportions:

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CATEGORIZED UNDER: Data Analysis, Religion

The Bushmen are not primitive! (not necessarily)

By Razib Khan | September 30, 2010 2:38 am

324_1035_F1To the left is a figure from the 2009 paper The Genetic Structure and History of Africans and African Americans. This paper happens to have excellent coverage of African populations, and the figure is a phylogenetic tree generated from distances between those populations, as well as some non-African ones. I’ve labelled the broad clusters. The Bushmen* branch off first, along with the Pygmies. The other clade represents all other humans, African and non-African. Following the non-Bushmen/Pygmy clade down its branching pattern all non-Africans eventually go their own way, and differentiate into their various groups. South Asians form a clade with Europeans and Middle Easterners. East Asians, Native Americans, and more broadly Oceanians, form their own clade. Outside of Africa you basically have a west vs. east & further east division.

These trees are essential in helping us visualize genetic relationships. Tables of pairwise distances are simply not as informative as representations of the data for the human mind. More colloquially, they blow. Trees and two-dimensional plots are much better representations of the data which we can digest in a more gestalt fashion. We see, therefore we know. Ah, but even the innocent tree can lead a mind astray. Or at least this particular tree. So let’s try something different.

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A world almost built

By Razib Khan | September 29, 2010 4:35 pm

By now you’ve probably seen headlines such as A Habitable Exoplanet — for Real This Time. Phil Plait has a more sober assessment. Still, he concludes:

But perhaps the most interesting and exciting aspect of all this is what it implies. The Milky Way galaxy is composed of about 200 billion stars, and is 100,000 light years across. The fact that we found a planet that is even anything like the Earth at all orbiting another star only 20 light years away makes me extremely optimistic that earthlike planets are everywhere in our galaxy. 20 light years is practically in our lap compared to the vast size of our galaxy, so statistically speaking, it seems very likely it’s not unique. I don’t want to extrapolate from a data set of two (us and them), but if this is typical, there could be millions of such planets in the galaxy. Millions.

So we don’t know if this planet is all that much like Earth — the surface gravity may be quite high if it’s dense and small, for example, or it may not have any air, or it may have a thick atmosphere like Venus — but what it’s telling us is that smaller, lower mass planets at the right distance from their star for liquid water are almost certainly common in the galaxy.

I assume this means we can play around with the Drake equation? In any case, I am now reminded of Poul Anderson’s essay “The creation of imaginary worlds: the world builder’s handbook and pocket companion.” You can read most of the essay online at Google Books. Or, find it in Writing Science Fiction & Fantasy. For us “squishy science” lovers the biochemist Hal Clament has an essay which follow’s Anderson’s which outlines how to create imaginary life.

CATEGORIZED UNDER: Science Fiction, Space

Daily Data Dump – Wednesday

By Razib Khan | September 29, 2010 2:04 pm

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation. Edmund Yong has already written this paper up. Sheril Kirshenbaum offers up her thoughts, stimulated by personal communication with the first author.

Inferring the Dynamics of Diversification: A Coalescent Approach. The title is more forbidding than the topic: “Applying our approach to a diverse set of empirical phylogenies, we demonstrate that speciation rates have decayed over time, suggesting ecological constraints to diversification. Nonetheless, we find that diversity is still expanding at present, suggesting either that these ecological constraints do not impose an upper limit to diversity or that this upper limit has not yet been reached.”

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Every variant with an author!

By Razib Khan | September 29, 2010 1:36 pm

I recall projections in the early 2000s that 25% of the American population would be employed as systems administrators circa 2020 if rates of employment growth at that time were extrapolated. Obviously the projections weren’t taken too seriously, and the pieces were generally making fun of the idea that IT would reduce labor inputs and increase productivity. I thought back to those earlier articles when I saw a new letter in Nature in my RSS feed this morning, Hundreds of variants clustered in genomic loci and biological pathways affect human height:

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits1, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait2, 3. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

The supplements run to nearly 100 pages, and the author list is enormous. But at least the supplements are free to all, so you should check them out. There are a few sections of the paper proper that are worth passing on though if you can’t get beyond the paywall.

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Religious illiteracy is the norm

By Razib Khan | September 29, 2010 12:01 am

By now you probably know that:

Atheists and agnostics, Jews and Mormons are among the highest-scoring groups on a new survey of religious knowledge, outperforming evangelical Protestants, mainline Protestants and Catholics on questions about the core teachings, history and leading figures of major world religions.

On average, Americans correctly answer 16 of the 32 religious knowledge questions on the survey by the Pew Research Center’s Forum on Religion & Public Life. Atheists and agnostics average 20.9 correct answers. Jews and Mormons do about as well, averaging 20.5 and 20.3 correct answers, respectively. Protestants as a whole average 16 correct answers; Catholics as a whole, 14.7. Atheists and agnostics, Jews and Mormons perform better than other groups on the survey even after controlling for differing levels of education.

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CATEGORIZED UNDER: Culture, Religion
MORE ABOUT: Data, Religion

To gain pallor is easier than losing it

By Razib Khan | September 28, 2010 5:21 pm


John Hawks illustrates what can be gained at the intersection of old data and analysis and new knowledge, Quote: Boyd on New World pigmentation clines:

I’m using some statistics out of William Boyd’s 1956 printing of Genetics and the Races of Man[1]. It gives a good accounting of blood group data known more than fifty years ago, which I’m using to illustrate my intro lectures. Meanwhile, there are some interesting passages, from the standpoint of today’s knowledge of the human genome and its variation.

On skin pigmentation – this is the earliest statement I’ve run across of the argument that the New World pigmentation cline is shallower than the Old World cline because of the relative recency of occupation….

Looking at what was said about pigmentation generations ago is of interest because it’s a trait which in many ways we have pegged. See Molecular genetics of human pigmentation diversity. Why humans vary in pigmentation in a deep ultimate sense is still an issue of some contention, but how they do so, and when the differences came about, are questions which are now modestly well understood. We know most of the genetic variants which produce between population variation. We also know that East and West Eurasians seem to have been subject to independent depigmentation events. We also know that some of the depigmentation was relatively recent, probably after the Last Glacial Maximum, and possibly as late as the advent of agriculture.

On the New World cline, which is clearly shallower than that of the Old World. The chart below from Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms is useful:

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Daily Data Dump – Tuesday

By Razib Khan | September 28, 2010 10:52 am

Just a minor note: if you want an admin update on this weblog, go to my twitter account. You don’t need to subscribe, as you might not be interested in all my random interactions with other bloggers. But if I don’t post for a few days, please don’t email me or post a comment in the thread wondering if I’m well, just check the twitter account. Easier that way not to clutter up the content on this website. You can always find the link to twitter right under my head shot on the sidebar. You can’t miss it.

Getting even with the odds ratio. To some extent it’s “common sense,” context matters. But nice to be reminded. Especially when in some cases context doesn’t matter.

Complexity Not So Costly After All: Moderately Complex Plants and Animals Can Be Better Equipped to Adapt. “By incorporating a more realistic representation of pleiotropy, Zhang’s analysis found the reverse of Orr’s arguments to be true. Although Fisher’s observation still holds, reversing Orr’s assertions minimizes its impact, thus reducing the cost of complexity.” I plan on blogging this, so I won’t say more.

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Obnoxious speech and trusting the Other

By Razib Khan | September 28, 2010 10:09 am

Update: After watching the videos of what went down at the cultural festival I seem to have unwittingly slandered the Act 17 missionaries. They behaved well and were obviously unjustly arrested. Their YouTube site is testimony to the reality though that they’re pretty shallow and obnoxious in some contexts, but that’s frankly not atypical for this sort of evangelical Christian from where I stand. I apologize for engaging in stereotyping in this case, because my expectations were out of line with what I saw on the tapes (though their attempt at apologia is stereotypically laughable, and the goonish response of some of the Muslim youth to Act 17′s antics unfortunately predictable).

Ed Brayton points to a resolution of a case of aggressive and seemingly obnoxious Christian missionaries being arrested for “public disturbance”. Ed observes:

Those four Christian missionaries I wrote about who were arrested for disorderly conduct and breach of the peace while preaching at the Dearborn International Arab Festival in June were acquitted by a jury on Friday. That’s the right result, but frankly the charges should have been dismissed by the judge in the first place.

Nabeel Qureshi of Virginia, Negeen Mayel of California and Paul Rezkalla and David Wood, both of New York, were acquitted of breach of peace, 19th District Court officials in Dearborn said after the verdict. Mayel was found guilty of failure to obey a police officer’s order.

[my emphasis - R]

That last result is still a bit disturbing because the order she was given was an unlawful one. The officer had no legitimate reason to give her the order to stop videotaping what was going on and therefore she should not be held liable for violating that order.

Unfortunately, the mayor of the town continues to be confused about the legal realities….

I’ve only followed the case casually. From what I can gather it seems that these preachers were sort you find around college campuses, or sometimes in downtown areas of big cities. Going by stereotypes of how objectionable Middle Eastern Muslims tend to find proselytization by Christians in their own countries I assume that this sort of behavior would result in a public disturbance, because this sort of preaching tends to be “in your face” and confrontational. The politician is behaving in the craven manner politicians are wont to behave. That’s why we have the Bill of Rights. And I say we in particular to the readers of this weblog, we tend to be irreligious and unloved by the public. If for example I simply stood on a street corner in some small American towns and kept shouting “there is no God” in a monotone voice I suspect I’d attract attention, hostility, and perhaps threaten public disturbance. But all I’d be doing was stating my simple belief.

In any case, enough commentary. How about if the shoe was on the other foot? In the last iteration of the GSS, in 2008, they had a question: SPKMSLM: Now consider a Muslim clergyman who preaches hatred of the United States. If such a person wanted to make a speech in your community preaching hatred of the United States, should he be allowed to speak, or not? Here are the results by demographic:

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CATEGORIZED UNDER: Culture, Data Analysis
MORE ABOUT: GSS, Religion, Tolerance, WVS

The hobbits were cretins. Perhaps. Or perhaps not

By Razib Khan | September 28, 2010 1:53 am

I was thinking a bit about H. floresiensis today. Probably my thoughts were triggered by John Hawks’ post on the propensity for paleontologists to be “splitters,” naming new finds as species when they’re not. The issue with H. floresiensis is a little more cut & dried: if they weren’t a separate species they were obviously pathological. The original paper on the Flores hobbits came out in 2004. Is it too much to ask for a little clarity here six years on? Carl Zimmer has covered this story in depth before, so perhaps he’ll have some insights or inside sources who can shed some light at some point in the near future. John Hawks was sure that the specimens were pathological in the early days, but he hasn’t said much for a bit now. And from what I hear there are new controversies about “Ardi”. I was at a talk years ago where Tim White played up the importance of fossils as the final word, as opposed to the more indirect inferential methods of statistical genetics, but this is getting ridiculous. After the Neandertal admixture paper and the Denisova hominin, genomic inferences are looking pretty good. I assume there’s more coming in the near future (though Svante Pääbo may have kidnapped family members of people working in his lab to gain leverage, so word probably won’t start leaking until a few weeks before the paper breaks). Ötzi the Iceman is going to have his genome published next year.

With all that as preamble, here’s a new paper, Post-Cranial Skeletons of Hypothyroid Cretins Show a Similar Anatomical Mosaic as Homo floresiensis. It’s in PLoS ONE, so read it yourself. Does anyone care? I don’t know enough about about anatomy and osteology to make well-informed judgments about these sorts of things, so to the experts I absolutely defer. But frankly some of the experts strike me jokers. Here’s the problem: I don’t know who the jokers are!

I just went back and reread some of the press when the hobbit finds were revealed. New member of the human family tree! Evolution rewritten! And so forth. If H. floresiensis turns out to be pathological, I don’t know what to think about paleontology. More honestly, I might start slotting the discipline in with social psychology or macroeconomic modeling.

CATEGORIZED UNDER: Anthroplogy, Human Evolution

On the varieties of Roma

By Razib Khan | September 28, 2010 1:05 am

Dienekes has a pointer to a new paper on Gypsy genetics which surveys Y lineage variation among three Roma groups from Serbia in the context of Europe-wide Gypsy genetic variance, as well as their potential host (European) and source (Indian) populations. Since I recently posted on the topic, and Dienekes didn’t post some of the figures, I thought I’d do so. In particular here’s the MDS of the Gypsy groups in the international context:


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CATEGORIZED UNDER: Genetics, Genomics

American family values: where even the dull can dream!

By Razib Khan | September 27, 2010 5:03 pm

ResearchBlogging.orgOne of the issues when talking about the effect of environment and genes on behavioral and social outcomes is that the entanglements are so complicated. People of various political and ideological commitments tend to see the complications as problems for the other side, and yet are often supremely confident of the likely efficacy of their predictions based on models which they shouldn’t even been too sure of. That is why cross-cultural studies are essential. Just as psychology has overly relied on the WEIRD nature of data sets, so it is that those interested in social science need to see if their models are robust across cultures (I’m looking at you economists!).

That is why this ScienceDaily headline, Family, Culture Affect Whether Intelligence Leads to Education, grabbed my attention. The original paper is Family Background Buys an Education in Minnesota but Not in Sweden:

Educational attainment, the highest degree or level of schooling obtained, is associated with important life outcomes, at both the individual level and the group level. Because of this, and because education is expensive, the allocation of education across society is an important social issue. A dynamic quantitative environmental-genetic model can help document the effects of social allocation patterns. We used this model to compare the moderating effect of general intelligence on the environmental and genetic factors that influence educational attainment in Sweden and the U.S. state of Minnesota. Patterns of genetic influence on educational outcomes were similar in these two regions, but patterns of shared environmental influence differed markedly. In Sweden, shared environmental influence on educational attainment was particularly important for people of high intelligence, whereas in Minnesota, shared environmental influences on educational attainment were particularly important for people of low intelligence. This difference may be the result of differing access to education: state-supported access (on the basis of ability) to a uniform higher-education system in Sweden versus family-supported access to a more diverse higher-education system in the United States.

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CATEGORIZED UNDER: Cognitive Science, Culture, Psychology

Daily Data Dump – Monday

By Razib Khan | September 27, 2010 12:42 pm

Wow, it sure feels like summer!

No one cares about your blog (part 2). “The thing is – it’s just writing, isn’t it? Talking extensively about science blogging is like having intense discourses about what you can do with pen and paper. “Should we staple all our pieces of paper together, or only the ones on which we wrote about our work?…” This is a generalized issue. Talking about blogging is a major topic on blogs, and is bound to get discussion going. On the other hand, when I post data or reviews of paper there’s less engagement of the subject, though there are a fair number of tweets.

Dinesh D’Souza’s poison. Heather Mac Donald rips into Dinesh D’Souza. Many on the Right don’t pay much attention to D’Souza because of his penchant for provocation and sloppiness. I take Heather’s main point to be that operationally Barack Hussein Obama is a standard issue liberal Democratic politician. Quantum mechanics is’t necessary when Newtonian mechanics will do.

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Story of X

By Razib Khan | September 27, 2010 12:35 am

A month ago I pointed to a short communication in Nature Genetics which highlighted differences in the patterns of variation between the X chromosome and the autosome. I thought it would be of interest to revisit this, because it’s a relatively short piece with precise and crisp results which we can ruminate upon.

ResearchBlogging.orgSometimes there is a disjunction between how evolutionary biologists and molecular biologists use terms like “gene.” The issue is explored in depth in Andrew Brown’s The Darwin Wars. Brown observes that one of the problems with Richard Dawkins’ style of exposition is that it did not translate well to the American context. He spoke of genes as units of analysis, from which logical inferences could be made. This was the classical Oxford style of evolutionary biology which Ernst Mayr objected to. In contrast American biologists were used to thinking of genes in more concrete biophysical terms, and tended to miss the theoretical context which Dawkins was alluding to in his arguments. In Dawkins’ defense, it must be remembered that the gene does have its origins as an abstract entity whose biophysical substrate, DNA, was not known for decades. In my post Simple rules for inclusive fitness I outlined a paper which is very much in keeping with the analytic tradition. Start with an abstract model and allow the chain of inferences to be made, and see where it takes you.

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CATEGORIZED UNDER: Biology, Genetics, Genomics

Is Christine O'Donnell a kook because she's a Creationist?

By Razib Khan | September 26, 2010 12:01 pm

Christine O’Donnell has said a lot of kooky things. Right now people are focusing on her Creationism. Though I’m obviously not a Creationist I think mocking someone for this belief in a political context is somewhat strange: the survey literature is pretty robust that Americans are split down the middle on opinions about evolution. More specifically most of the polling shows that around ~50% of Americans tend to reject the validity of evolutionary theory when asked. This is what I like to call a broad but shallow belief; for the vast majority of Americans attitudes about evolution are really just cultural markers, not stances of deep feeling or impact. One point of evidence for this conjecture is that polling on evolution is easy to massage through framing. Another is that Republican candidates for the presidency do not invariably hew to a Creationist line despite the likelihood that the majority of primary voters are Creationist. Politicians react to incentives, and my own hunch is that there isn’t a strong push from the Christian Right on evolution as there is on abortion or gay marriage.

I’ve posted plenty on how Creationists are more female, less intelligent, more conservative, more likely to be ethnic minorities, less educated, etc. Here I want to put the spotlight parameters which might shed some light on the O’Donnell race. Is her kooky opinion on evolution a particular liability in Mid-Atlantic Delaware? Are Creationists less likely to vote? And what are the regional breakdowns which might explain the bi-coastal shock and amusement at O’Donnell’s opinions?

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CATEGORIZED UNDER: Creationism, Data Analysis, GSS

The view from somewhere smart

By Razib Khan | September 26, 2010 4:15 am

9780061472817When it comes to scholarly explorations of religion and history it is very difficult to find works which I can recommend to casually interested friends. On the one hand you have very narrow monographs on a specific topic, for example the possible connection between Monothelitism and Maronite Christianity. Set next to these you have broadly written and engaging works of semi-scholarship with very strong viewpoints which operationally reinforce the preconceptions or biases of the audience. Karen Armstrong’s body of work is an exemplar of this. Much of it is filled with fascinating detail, but she invariably shades the framing of the past so as to make it congenial to her religiously liberal Western audience. Armstrong’s opposite in viewpoint would be Rodney Stark. A sociologist by training Starks’ early work on religion always came with a large dollop of opinion, but it was sound in terms of scholarship. But of late he’s moved in a far more polemical direction, exemplified by books such as God’s Battalians: The Case for the Crusades. Starks’ recent work can be compared to the more crass Afrocentric projects, they’re long drawn out arguments which show that the greatest of human achievements necessarily come from the tradition which conservative Western Christians are singular modern representatives of (not just Western, Stark attempts to dismiss the intellectual achievements of Classical Greeks in The Victory of Reason; rather atrociously in my opinion).

A strong viewpoint is not always a problem. The ideal of objectivity is often an illusion, and only produces a muddle. But in the case of both Stark and Armstrong’s work if you are moderately familiar with their area of focus you can pick out many errors of omission and interpretation. Naturally these flaws in their reading of the literature are always in the direction of their conclusion of preference. If you have a thick network of background facts and frames into which you can inject data and analysis, bias need not be a problem. I am an atheist but I have no issue reading the New Testament for its historical and literary value, despite the fact that it has a clear viewpoint. But that viewpoint is very transparent and obvious to someone who does not share it. Much of popular historical writing has the problem that the audience is not aware of the bias and selectivity of the authors as they frame their arguments. Rodney Stark and Karen Armstrong have a much more fluent grasp of medieval history than the vast majority of their readers, so their obfuscations and distortions, conscious or not, will not be transparent to the audience. It is with all this said that I wholeheartedly recommend Philip Jenkins oeuvre to anyone who will listen. Jenkins’ own perspective colors his scholarship, but he is frank and honest with the reader as to his sympathies, while at the same time correcting the enthusiasms of his “own side.” This is far preferable to the illusion of the “view of from nowhere.” Because his cards are on the table the lay audience can weight his assertions appropriately.

Jenkins is an Episcopalian who has an affinity for the more traditionalist streams of Christian faith and practice coming out of what is now termed the “Global South.” He is probably most well known for his lengthy exposition on this topic in his book The Next Christendom: The Coming of Global Christianity, though I personally find that his book on Europe, God’s Continent: Christianity, Islam, and Europe’s Religious Crisis, more original. In his popular works Philip Jenkins writes in a manner which makes it clear that he is broadly in agreement with the claims of the Christian religion. There is no doubt in that. But he is also a man who can say something like this:

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Open Thread, September 25th, 2010

By Razib Khan | September 25, 2010 12:11 am

Being Wrong: Adventures in the Margin of Error is in my “stack,” though I don’t know when I’ll get to it. A few things I’ve been wrong about in the last 10 years:

- I was more optimistic about reproducible I.Q. QTLs in 2000 than I should have been. Here’s a 1998 article on Robert Plomin’s “discovery” of an I.Q. gene, and now his recent finds.

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Friday Fluff – September 24th, 2010

By Razib Khan | September 24, 2010 1:41 pm


1. First, a post from the past: Historical Dynamics and contingent conditions of religion

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By Razib Khan | September 24, 2010 2:02 am

I didn’t realize that Elmo is almost 40 years old. Not only that, apparently some “Sesame Street Traditionalists” refer to him as the “Little Red Menace”. Since I haven’t watched the show regularly since the 1980s I don’t have a strong opinion about his influence, malevolent or not, but generally I’m pro-Elmo. He’s not quite in the class of Mickey, but he’s definitely got a spot in the history books at this point. Here’s Elmo in the now nixed Katy Perry video:

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MORE ABOUT: elmo, katy perry

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