Razib Khan One-stop-shopping for all of my content

September 30, 2010

Friday Fluff – October 1st, 2010

Filed under: Blog,Friday Fluff — Razib Khan @ 11:03 pm

FF3

1. First, a post from the past: Levels of selection & the full Price Equation

2. Weird search query of the week: “politcal correct cultures in science-fiction.” I direct you to Ursula K. Le Guin.

3. Comment of the week, in response to Mormons are average:

I am a Mormon convert with 11 children (11 is allot, even for a Mormon family). I joined the church at age 24 and am now 60. I have about 2 years of college (no degree) and have a good job at Hewlett Packard that I grew into.

It is expected that my kids will all have college degree’s (and so far, the adults all do). Among the younger generation in the Mormon culture it is normal to obtain at least a Bachelors degree. A person (especially a male) who does not go to college is not normal in the Mormon culture. It shows a lack of initiative and the more desirable, faithful Mormon girls may not consider this person as a desirable mate. The same is true for boys who do not go on missions. It shows a lack of initiative and faithfulness. In a Mormon lifestyle of high achievement and active church and community service, women do not want to be married to a sluggard for the rest of their lives.

Mormon youth grow up in an environment where most would not even consider skipping college.

4) 15% of you think that the sex bias of the blog’s readership is a problem, 75% do not, 10% don’t care.

Poll question….

5) And finally, your weekly fluff fix:

honkingsouth

Daily Data Dump – Thursday

Filed under: Blog,Daily Data Dump — Razib Khan @ 10:21 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.”


Bronze Age Mediterraneans may have visited Stonehenge. “The new evidence shows that ‘the Boy with the Amber necklace’ spent his childhood in a warm climate typical of Iberia or the Mediterranean. Such warm oxygen values are theoretically possible in the British Isles but are only found on the extreme west coast of South West England, western Ireland and the Outer Hebrides. These areas can be excluded as likely childhood origins of his on the basis of the strontium isotope composition of his teeth” Migrations in the days of yore….

The Uncanny Accuracy of Polling Averages*, Part I: Why You Can’t Trust Your Gut. The Cowles Commission found that stock market newsletters weren’t effective in increasing returns to subscribers. But they also concluded that the “demand” was too strong for them ever to not be a part of the investment scene. The same with verbal punditry which doesn’t take model-based quantitative form. Of course the proof is in the pudding, macroeconomic models haven’t done better than simple heuristics in predicting economic performance, but the economy is a more complex system than an election.

The Judgment of the Future. Remember that history is not always Whiggish. Secular intellectuals in the 19th and early 20th centuries of a progressive bent, such as Jack London and H. G. Wells, were amongst the most enthusiastic promoters of a systematic and more efficacious race-based Social Darwinism. Even though conservatives, whether they be Christians in the West or Confucians in the East, were racialist in any modern sense, they were much more moderate than the more ’scientific’ progressives in their attitudes toward the ‘lower races,’ and definitely closer to contemporary ‘right thinking’ norms than the secular futurists of 1900.

Mormons are average

Filed under: data,Data Analysis,Latter Day Saints,Mormons,Religion — Razib Khan @ 10:07 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:

mormoncuny

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:

mormed

OK, now let’s look at income:
incmorm

As you can see Mormons rank below Mainline Protestants, and well below Jews. A notable trend though is that Mormons seem to have lower variance than the national sample. There are fewer Mormons at the extremes.

Finally, here’s how Mormons stack up on IQ using a NLSY sample:

IQbyreligion

These data data seem to imply that Mormons are average white folk. So why the perception that they’re more educated? Part of it probably has to do with the reality that the “floor” of Mormon achievement is above the national norm. Fewer high school dropouts, fewer poor people. But I think another issue is what I’ll call “The Mitt Romney Effect.” Romney is conventional Mormon genealogically. His roots are in the Mountain West. But he was raised in Michigan, and spent much of his adult life in Massachusetts. I suspect with Mormons there is a much milder version of what has gone on with the Indian American community: strong selection biasing on migrants toward achievers. This gives Americans a skewed view of what Indians are like. While half of Indian Americans have graduate degrees, 1/3 of Indians are illiterate! How’s that for a difference? Similarly,bi-coastal Americans don’t meet many Mormons, and the ones they do are more likely to be achievers, not those of more downscale or modest means who never left St. George, Utah.

The Bushmen are not primitive! (not necessarily)

Filed under: Biology,Cladistics,Evolution,Systematics — Razib Khan @ 1:38 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.


abofig1Here’s a figure from Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry. This tree has a smaller number of populations, but the broad geographical relationships are the same. West Eurasians are one cluster, while East Eurasians, Native Americans and Oceanians are their own super-cluster which divides further. Among the Africans you see that the Bushmen and the Mbuti again exhibit more distance from the other groups. But the biggest difference is that the tree is unrooted, so you don’t immediately orient yourself from outgroup to ingroup in a serial manner.

Now let’s look at a headline inspired by one of the papers: African San people – the world’s most ancient race. Going by the figures which paper do you think it was? It was the first paper of course. There’s a huge problem when these phylogenetic trees are generated that human outgroups, or basal clades, are defined as ‘ancient,’ the ‘oldest,’ or the most ‘antique.’ This is just confusing. Not only that, as a person deeply committed to the dignity of the indigenous peoples I am offended! I generally get irritated or blow a gasket when people make that confusion in the comments, because I think it leads to lazy inferences. One of my main quibbles with The Faith Instinct is that Nicholas Wade used the Bushmen as proxies for ur-humans to reconstruct prehistoric religious practice, implicitly relying on the fact that they’re the basal lineage in most genetic studies as if they’re a fossil which we can use to paint the past.

phytreeIn any case, I was going to recommend to readers that they just refer to ‘basal clades.’ Well, I’m not a taxonomist obviously so I decided to look in the literature, and I found this paper, Which side of the tree is more basal? The tree they use to illustrate the lack of utility of terms like ‘basal clade’ is to the left. Let me quote them:

Both branches originating from a node (i.e. the two sister groups) are of equal age and have undergone equivalent evolutionary change. Whether a group has branched off early (basal) or later in the phylogeny contains no information about this particular group, but information about both this group and its sister group, because both branched off at the same time. By notation we tend to portray one branch (the species/taxa-poor one) as being on the left, and the other (species/taxa-rich) as right – but this infers nothing about their evolutionary development, only about their taxon richness (speciation less extinction) at a given geological period (mostly the present), or, even worse, about the taxon sampling pattern in the particular study. Different taxon sampling leads to different interpretation about ‘the most basal clade’….

Considering clades or taxa as ‘basal’ is not only sloppy wording, but shows misunderstanding of the tree and may have severe semantic and argumentative implications. Declaring one sister group to be basal gives the other sister group a higher or at least a different value (‘the basal clade’ vs. ‘the derived clade(s)’). If the Polyneoptera is the most basal clade of the Neoptera, then the rest of the Neoptera (the Eumetabola) is given a higher value (as the ‘main’ body of the group). Admittedly, it contains more species, but this is not a quality necessarily granting it higher value…..

If the phylogenetic tree in Fig. 1 is correct, Polyneoptera and Eumetabola are sister groups. There is no necessity to term either as ‘basal’. Even if one wants to avoid the little-used name Eumetabola, it is easy to describe the Polyneoptera as the sister group of the remaining Neoptera. Argumentation with sister-group relationships is easy and shows relationships much more clearly than declaring one sister group to be basal. The ‘basal position’ within an ingroup always means ‘sister to the remaining taxa’, so say so!

The argument here is obviously embedded in the milieu of systematics and their particular concerns. But their objection to the term ‘basal clade’ is actually pretty much my main qualm which using terms like ‘ancient.’ I don’t think using ’sister to the remaining taxa’ is going to be informative to most people, so at this point I don’t know what I’ll use for short hand. Outgroup seems viable.

I don’t really think about systematics in a deep philosophical sense. But the problem of terminology here, and the evolutionary implications therein, have brought home to me utility of a precise and accurate systematic framework in biology.

* The term “San” is like the term “Lapp” or “Welsh,” what others call them, so I’ll use Bushmen.

September 29, 2010

A world almost built

Filed under: science fiction,Space — Razib Khan @ 3:35 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.

Daily Data Dump – Wednesday

Filed under: Blog,Daily Data Dump — Razib Khan @ 1:04 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.”


Bangladesh, ‘Basket Case’ No More. The headline is hyperbolic. But this is key: “As a percentage of gross domestic product, Islamabad spends more on its soldiers than on its school teachers; Dhaka does the opposite. In foreign policy, Pakistan seeks to subdue Afghanistan and wrest control of Indian Kashmir. Bangladesh, especially under the current dispensation, prefers cooperation to confrontation with its neighbors.” By any measure Bangladesh is one of the poorest and most corrupt nations in the world. Because of widespread malnutrition and low literacy it has major human capital deficits. But, it has managed to avoid excessive wasteful military adventures (though the military is still too big and serves the same role as a cushy bureaucratic job; I know, I have relatives who are officers in the Bangladesh army).

Another School Says Christine O’Donnell Did Not Attend. Resume padding is as American as apple pie…but this is a problem for Christine because it feeds into the narrative that she’s a dull ditz. OK, depending on your perspective, perhaps not really a problem….

Some ADMIXTURE estimates in Eurasia. Dienekes is doing some interesting things with the ADMIXTURE program.

Every variant with an author!

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.


fig1bIn this study they pooled together several studies into a meta-analysis. One thing not mentioned in the abstract: they checked their GWAS SNPs against a family based study. This was important because in the latter population stratification isn’t an issue. Family members naturally overlap a great deal in their genetic background. Also, if I read it correctly they’re focusing on populations of European origin, so this might not capture larger effect alleles which impact between population variance in height but don’t vary within a given population (note that if you explored pigmentation genetics just through Europeans you would miss the most important variable on the world wide scale, SLC24A5, because it’s fixed in Europeans). In any case, as you can see what they did was extrapolate out the number of loci which their methods could capture to explain variation with the predictor being the sample size. At 500,000 individuals they’re at ~700 loci, and around 20% of the heritable variation. My initial thought is that I’m not seeing diminishing returns here, but since I haven’t read the supplements I’ll let that pass since I don’t know the guts of this anyhow. They do assert that they are likely underestimating the power of these methods because there may be be smaller effect common variants which can top off the fraction.

But even they admit that they can go only so far. Here are some sections from the conclusion that lays it out pretty clearly:

By increasing our sample size to more than 100,000 individuals, we identified common variants that account for approximately 10% of phenotypic variation. Although larger than predicted by some models26, this figure suggests that GWA studies, as currently implemented, will not explain most of the estimated 80% contribution of genetic factors to variation in height. This conclusion supports the idea that biological insights, rather than predictive power, will be the main outcome of this initial wave of GWA studies, and that new approaches, which could include sequencing studies or GWA studies targeting variants of lower frequency, will be needed to account for more of the ‘missing’ heritability. Our finding that many loci exhibit allelic heterogeneity suggests that many as yet unidentified causal variants, including common variants, will map to the loci already identified in GWA studies, and that the fraction of causal loci that have been identified could be substantially greater than the fraction of causal variants that have been identified.

In our study, many associated variants are tightly correlated with common nsSNPs, which would not be expected if these associated common variants were proxies for collections of rare causal variants, as has been proposed27. Although a substantial contribution to heritability by less common and/or quite rare variants may be more plausible, our data are not inconsistent with the recent suggestion28 that many common variants of very small effect mostly explain the regulation of height.

In summary, our findings indicate that additional approaches, including those aimed at less common variants, will likely be needed to dissect more completely the genetic component of complex human traits. Our results also strongly demonstrate that GWA studies can identify many loci that together implicate biologically relevant pathways and mechanisms. We envisage that thorough exploration of the genes at associated loci through additional genetic, functional and computational studies will lead to novel insights into human height and other polygenic traits and diseases.

The second to last paragraph takes a shot at David Goldstein’s idea of synthetic associations.

We’re still where we were a a few years back though, old fashioned Galtonian quantitative genetics, a branch of statistics, is the best bet to predict the heights of your offspring. As with intelligence, “height genes”, are not improvements upon common sense. But if you’re going into the 10-20% range of variation explained it’s certainly not trivial, and the biological details are going to be of interest.

September 28, 2010

Religious illiteracy is the norm

Filed under: Culture,data,Religion — Razib Khan @ 11:01 pm

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.


If you are part of a minority group you’ll often get into discussions about religion. Since I “look” Hindu/Muslim and am pretty frank about my atheism I’ve gotten into discussions more frequently than most (perhaps the weirdest experience was a conversation with an evangelical acquaintance in high school who was ready to argue with me about how demonic Hinduism was; as I wasn’t Hindu, and I didn’t know much about Hinduism, it was somewhat disappointing for my acquaintance). By chance when I was 18 I was at an InterVarsity Christian Fellowship event (I was young and wasn’t told about the nature of the “party”) and the pastor started talking about how “we all believe in Christ.” At that point I raised my hand and explained that 1) I didn’t believe in Christ, and, 2) I didn’t believe in God. Didn’t want to implicitly mislead. After a bit of awkwardness the fun went on.

Obviously over the years I’ve read up a fair amount on religion. You’d probably be aware of that if you read the blog. One of the weirder outcomes of my religious literacy is that it occasionally happens that people will simply refuse to believe I’m an atheist. I had a friend in college who was an evangelical and half-joked that I had to be some sort of crypto-Christian, and I’d eventually “come out” and accept in my heart what I obviously already knew with my head. In the end I wasn’t a fool. In a less amusing case I had a Jewish individual accuse me of being a crypto-Muslim intent on undermining the state of Israel, as I just knew too much about Judaism for there to be any other possibility.

You too can take Pew’s religious knowledge quiz. 15 questions which take only a few minutes. Since readers of this weblog are among the minority of humans which fall into the class intelligent I suspect you’ll beat the average American at this game (I scored a 15 out of 15).

To gain pallor is easier than losing it

journal.pbio.0000027.g002

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:


skinvarianceWhat you’re seeing here are patterns of relationships by population when it comes to the select subset of genes which we know are implicated in between population variation in pigmentation. The peoples of Melanesia are arguably the darkest skinned peoples outside of Africa (and perhaps India), and interestingly they are closer to Africans than any other non-African population. But in total genome content they’re more distant from Africans than other non-African populations, excluding the peoples of the New World.

This disjunction between phylogenetic relationships when looking at broad swaths of the genome, as opposed to constraining the analysis to the half a dozen or so genes which specifically encode between population differences on a specific trait, is indicative of selection. In this case, probably functional constraint on the genetic architecture. From the reading I’ve done on skin pigmentation genetics there is an ancestral “consensus sequence” on these genes which result in dark complexions. In contrast, as has been extensively documented over the last few years there are different ways to be light skinned. In fact, the Neandertals which have been sequenced at those loci of interest also turn out to have a different genetic variant than modern humans.

How to explain this? I think here we can go back to our first course in genetics in undergrad: it is easier to lose function than gain function. The best current estimate is that on the order of one million years ago our species lost its fur, and developed dark skin. And it doesn’t look like we’ve reinvented the wheel since that time. All of the peoples termed “black” across the world, from India, to Australasia, to Africa, are dark because of that ancestral genetic innovation. In contrast, deleterious mutations which “break” the function of the genes which gave some of us an ebony complexion occur relatively frequently, and seem to have resulted in lighter skinned groups in more northerly climes. It turns out that some of the pigmentation genes which are implicated in between population variance in complexion were actually originally discovered because of their role in albinism.

So how does this relate to the New World? I think the difficulty in gaining function once it has been lost explains why the people of Peru or the Amazon are not as dark skinned as those of Africa, Melanesia, or South Asia. They haven’t had enough time to regain function which they lost as H. sapiens traversed northern Eurasia. So there you have it. A nice little illustration of how the genetics taught to 18 year olds can be leveraged by the insights of modern genomics and biological anthropology! In the end, nature is one.

Image Credit: Dennis O’Neil

Daily Data Dump – Tuesday

Filed under: Blog,Daily Data Dump — Razib Khan @ 9:52 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.


Why Charity Ratings Don’t Work (as of now). People want an easy number, but summary metrics can’t replace really legwork. Though perhaps Holden & company can help us develop our own personal heuristics.

Tragedy at the Virginia Quarterly Review. This is of a piece with Emily Bazelon’s previous reporting on bullying, but check this out: “It had a staff of six, including Genoways and Morrissey, and a circulation of less than 5,000.” This weblog gets 2,000-3,000 visitors on a given day. Much more if you evaluate over the month as some people only drop in once or twice a week or every other day. Of course there’s a lot of editing and such which goes into those high quality small circulation periodicals, so apples to oranges, but still….

How California Became America’s Greece. The climate’s the same. I wonder….

Obnoxious speech and trusting the Other

Filed under: Culture,Data Analysis,GSS,Religion,Tolerance,WVS — Razib Khan @ 9:09 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:


Demographic Ban preaching by Anti-American Muslim in community
Male 51
Female 65
Northeast 57
Midwest 56
South 63
West 56
White 56
Black 70
Hispanic 74
Protestant 62
Catholic 65
Jewish 68
No religion 42
No High School Diploma 82
High School 62
Junior College 57
Bachelor 45
Graduate 30
Dumb (Wordsum 0-4) 75
Average (Wordsum 5-8) 61
Smart (Wordsum 8-10) 34
Atheist and agnostic 30
Know god exists 68
Bible Word of God 76
Bible Inspired Word 55
Bible Book of Fables 38
Liberal 45
Moderate 62
Conservative 61
Democrat 56
Independent 66
Republican 59

Can I get some hallelujahs for the Bill of Rights and elites who will defend them? If you’re curious why “moderates” and “Independents” are as intolerant, or more so, than conservatives and Republicans, I think it’s because they’re generally stupid, and stupid people in particular are suspicious of deviations in speech and thought. Ideologues tend to be brighter. There is more than a dimes worth of difference.

Now that we’ve established that Americans are probably hypocrites, I recall that The Future of Religion reported that excepting Seventh Day Adventists the more fundamentalist a person was the more likely they were to support banning missionaries from non-Christian religions in the USA. In other words, preaching for me but not for thee. How does trust of other religious correlate with religiosity? Let’s look at it internationally. The WVS has a question about how important religion is in your life, very important, rather important, not very important, and not at all important. I constructed an index of religiosity by recoding these responses into numbers and multiplying by weights. So, 50%*3 + 25%*2 + 10%*1 + 15%* 0 = 2.1. 3 would be 100% who say that religion is very important, 0 would 100% not important at all. There is also a question about trusting people of “another religion.” The answers were trust completely, trust a little, not trust very much, and not trust at all. I constructed an index of trust of other religions in the same manner. On the X axis I placed religiosity, and on the Y axis trust of other religions. Here’s the scatterplot with r-squared:

rel1

There’s really no relation here. Only 10% of Y can be explained by variation in X. But, rescaling a bit we can generate quadrants of values. I now label the nations as well:

reltrust2

As you can see Muslim nations can be trusting or not trusting of other religions. One of the main issues with international perceptions of Islam is that we take Middle Eastern Islam as the normative Islam, and Middle Eastern Muslims tend to be among the most religiously intolerant people in the world, along with Chinese, and well as assorted group from the Orthodox Christian world. In contrast, as you can see with Mali and Burkina Faso, African Muslims are more tolerant of pluralism. As I have noted before, Senegal is more than 90% Muslim, but the “father of the nation” was a Roman Catholic. In contrast, Boutros (the equivalent of Peter) Boutros-Ghali’s political career always had an implicit glass-ceiling because he was a Coptic Christian, even though Christians are about the same percentage of the population in Egypt. Now, if Egyptian religious liberals would have the same heft and authority when they said “but in Senegal Muslims do….” or “in Indonesia they practice Islam….” as when Pakistani or Indonesian religious conservatives did when they stated “in Arabia….”, we’d be in a better place. But as it is, I do think it is a little misleading to state that “only 20% of the world’s Muslims are Arab.” That 20% “counts” more than the 30% which is South Asian.

Here’s the raw data….



Trust of other religions
Country Trust completely Trust a little Not trust very much Not trust at all Weighted index
Sweden 16.40% 72.40% 8.70% 2.60% 2.03
New Zealand 23.60% 59.90% 10.80% 5.70% 2.01
France 29.00% 48.70% 14.70% 7.60% 1.99
Norway 14.70% 64.80% 16.40% 4.00% 1.90
Great Britain 11.50% 69.40% 13.60% 5.50% 1.87
Mali 23.60% 44.50% 25.20% 6.70% 1.85
Finland 12.20% 64.60% 19.00% 4.20% 1.85
United States 6.10% 73.40% 16.00% 4.50% 1.81
Canada 5.10% 74.70% 14.90% 5.20% 1.80
Australia 6.00% 67.00% 22.20% 4.70% 1.74
Switzerland 5.30% 65.60% 24.60% 4.60% 1.72
Andorra 3.20% 72.80% 15.40% 8.60% 1.71
South Africa 14.80% 48.60% 27.90% 8.70% 1.70
Rwanda 5.30% 61.90% 27.40% 5.40% 1.67
Argentina 11.80% 51.00% 25.40% 11.80% 1.63
Trinidad 6.40% 56.90% 26.80% 9.90% 1.60
Burkina Faso 13.50% 41.90% 30.20% 14.40% 1.55
Uruguay 12.70% 44.60% 24.30% 18.40% 1.52
Ghana 12.20% 40.60% 32.00% 15.20% 1.50
Taiwan 1.80% 44.90% 46.50% 6.80% 1.42
Serbia 4.30% 42.20% 43.30% 10.10% 1.41
Poland 1.70% 47.60% 39.90% 10.90% 1.40
Brazil 5.70% 44.60% 33.60% 16.10% 1.40
Netherlands 2.70% 43.00% 44.20% 10.10% 1.38
Spain 7.50% 39.70% 35.20% 17.60% 1.37
India 12.60% 32.70% 32.80% 22.00% 1.36
Ethiopia 12.00% 27.70% 44.50% 15.90% 1.36
South Korea 3.90% 37.80% 48.10% 10.20% 1.35
Bulgaria 4.50% 40.30% 41.30% 14.00% 1.35
Indonesia 1.60% 38.30% 50.80% 9.20% 1.32
Georgia 3.00% 36.10% 49.60% 11.20% 1.31
Germany 1.50% 41.30% 42.70% 14.50% 1.30
Ukraine 5.70% 33.10% 43.50% 17.70% 1.27
Zambia 8.70% 30.80% 38.30% 22.20% 1.26
Italy 0.70% 40.40% 43.00% 16.00% 1.26
Malaysia 2.20% 33.30% 50.20% 14.20% 1.23
Chile 4.10% 32.90% 43.30% 19.70% 1.21
Egypt 3.50% 35.70% 38.70% 22.10% 1.21
Thailand 5.00% 23.70% 53.40% 17.90% 1.16
Russia 2.30% 33.90% 40.40% 23.40% 1.15
Vietnam 1.00% 26.90% 58.20% 13.90% 1.15
Slovenia 4.60% 23.60% 49.90% 21.90% 1.11
Romania 2.40% 28.20% 46.00% 23.50% 1.10
Jordan 4.90% 27.40% 35.40% 32.30% 1.05
Mexico 4.50% 27.80% 32.50% 35.30% 1.02
Turkey 2.40% 26.00% 42.00% 29.60% 1.01
Cyprus 1.90% 25.80% 42.90% 29.40% 1.00
Moldova 1.20% 25.00% 44.10% 29.60% 0.98
Morocco 1.20% 21.30% 45.00% 32.40% 0.91
Peru 2.30% 23.20% 35.60% 38.90% 0.89
China 1.90% 15.60% 51.90% 30.60% 0.89

Importance of religion in life

Very important Rather important Not very important Not important at all Weighted index
Egypt 95.40% 4.20% 0.20% 0.20% 2.95
Jordan 94.50% 5.20% 0.20% 0.20% 2.94
Indonesia 94.70% 4.10% 0.90% 0.30% 2.93
Morocco 90.60% 7.90% 1.30% 0.30% 2.89
Mali 90.20% 8.60% 0.90% 0.30% 2.89
Ghana 90.40% 7.50% 1.70% 0.40% 2.88
Burkina Faso 84.30% 12.20% 2.70% 0.70% 2.80
Georgia 80.20% 17.00% 1.90% 0.90% 2.77
Malaysia 80.50% 15.50% 3.30% 0.70% 2.76
Ethiopia 81.00% 13.20% 3.80% 2.00% 2.73
Zambia 77.50% 16.70% 4.60% 1.20% 2.71
Trinidad 76.80% 13.00% 7.90% 2.30% 2.64
Turkey 74.70% 16.60% 6.20% 2.50% 2.64
South Africa 70.30% 20.20% 6.50% 3.00% 2.58
Thailand 56.30% 37.90% 5.40% 0.40% 2.50
Romania 58.00% 32.50% 7.20% 2.40% 2.46
Mexico 59.00% 26.10% 11.50% 3.40% 2.41
Brazil 50.60% 40.40% 6.20% 2.70% 2.39
Rwanda 38.90% 56.90% 4.10% 0.10% 2.35
Poland 47.80% 39.00% 10.40% 2.80% 2.32
Cyprus 54.10% 27.20% 12.10% 6.60% 2.29
India 51.40% 29.30% 13.90% 5.50% 2.27
Peru 49.60% 26.70% 18.90% 4.80% 2.21
United States 47.40% 24.20% 19.70% 8.70% 2.10
Chile 39.90% 33.50% 18.40% 8.20% 2.05
Italy 34.40% 41.70% 17.00% 6.80% 2.04
Moldova 31.80% 41.20% 20.40% 6.60% 1.98
Argentina 33.40% 32.00% 24.00% 10.60% 1.88
Serbia 25.70% 40.90% 26.80% 6.60% 1.86
Canada 32.00% 27.10% 25.30% 15.60% 1.76
Ukraine 18.30% 38.80% 27.70% 15.20% 1.60
Bulgaria 18.90% 31.90% 32.20% 17.00% 1.53
Taiwan 12.40% 39.30% 35.80% 12.50% 1.52
South Korea 21.20% 25.80% 34.50% 18.60% 1.50
Finland 17.60% 27.50% 40.60% 14.30% 1.48
Russia 13.70% 35.10% 32.50% 18.70% 1.44
Uruguay 22.80% 23.20% 27.80% 26.20% 1.43
Switzerland 17.20% 28.30% 31.70% 22.80% 1.40
Great Britain 21.00% 19.70% 33.90% 25.40% 1.36
Slovenia 15.30% 27.60% 31.00% 26.10% 1.32
Australia 19.50% 19.70% 31.40% 29.30% 1.29
France 13.00% 27.90% 30.70% 28.40% 1.26
Spain 14.90% 24.20% 31.10% 29.80% 1.24
Vietnam 7.20% 25.60% 47.60% 19.60% 1.20
New Zealand 17.30% 18.50% 30.70% 33.60% 1.20
Norway 10.50% 22.20% 41.30% 26.00% 1.17
Sweden 9.30% 20.10% 40.90% 29.80% 1.09
Germany 11.20% 22.70% 29.00% 37.00% 1.08
Netherlands 12.50% 19.00% 28.40% 40.20% 1.04
Andorra 8.00% 21.20% 31.30% 39.50% 0.98
China 6.70% 15.20% 31.00% 47.10% 0.82

The hobbits were cretins. Perhaps. Or perhaps not

Filed under: Anthroplogy,H. floresiensis,Hobbits,Human Evolution,paleontology — Razib Khan @ 12:53 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.

On the varieties of Roma

Filed under: Genetics,Genomics,Gypsies,Historical Population Genetics,Roma — Razib Khan @ 12:05 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:

romaY

Remember that that’s just the Y chromosomes, the male lineages. There are some broad affinities, but note how scattered the Gypsy groups are. I assume that’s an artifact of large shifts in Y lineage frequencies because of genetic drift through bottlenecks. Additionally, the Vojvodina Roma group which was surveyed specifically in this study is a definite outlier (VOJ). As I stated above they typed three Roma groups from Serbia. They were resident in Kosovo, Belgrade and Vojvodina (which is north of Belgrade, near Hungary). They calculated admixture estimates for the three groups based on their Y haplogroup proportions, and found that ~100% of the male line ancestry of the Kosovo Roma was South Asian, ~75% of the Belgrade Roma was South Asian, but ~0% of the Vojvodina Roma sample had South Asian male ancestry. For what it’s worth, they estimate that the balance of the Belgrade Roma ancestry was Slavic European (based on the frequency of the given haplogroups in regions and ethno-linguistic groups of Europe), while the Vovjodina Roma had all non-Slavic ancestry. The Vovjodina Roma men overwhelmingly carry a variant of haplogroup E1b1b1a2. Here’s the frequency map from Wikipedia:

800px-HgE1b1b1a2

Since they’re Kosovo Roma, and they seem to be a subclade of a lineage at high frequency among Albanians, it stands to reason that at some point in history a group of Albanian men, or a Albanian man, was culturally assimilated into a Roma identity. From the earlier charts I posted using variation on autosomal loci, instead of just a uniparental lineage, that shouldn’t be too surprising. The interesting point, as Dienekes noted, is that despite the genetic variation the Roma are surprisingly similar culturally across Europe. In particular it is striking that they tend to continue speaking an Indo-Aryan language. It’s not like this is unprecedented though. Some commenters have already observed striking analogies between Gypsies and Jews genetically and culturally, or at least in terms of the ethnogenesis of both groups as genetic and cultural compounds on the European scene. The analogy is tight enough that you have papers such as Multiple Origins of Ashkenazi Levites: Y Chromosome Evidence for Both Near Eastern and European Ancestries, which I believe will be recapitulated for the Gypsies broadly, and even the particular subset who are termed Roma.

Image Credit: Wikimedia Commons

September 27, 2010

American family values: where even the dull can dream!

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.


Minnesota is to some extent the Scandinavia of America, so the cross-cultural difference is particularly notable. You wouldn’t be surprised for example by big differences between Mississippi and Sweden. But looking at a comparison between the Upper Midwest and Scandinavia is closer to seeing the impact of national culture and policy differences on populations which were originally very similar.

Their methodology was simple, though as with much of this sort of behavior genetic work the statistical analysis can be somewhat labored. In both Sweden and Minnesota you had samples of dizygotic and monozygotic twins which give you a way to compare the effect of genes on variation in life outcomes. Sweden has large data sets from male conscription for behavior genetics analysis. They compared this with the Minnesota Twin Family Study data set.

Since the topline results are pretty straightforward, I thought I’d give you some statistics. Table 1 has raw correlations. Note that they converted educational attainment into a seven-point scale, less than 9 years of education to completion of doctoral studies.

swed1

You see the expected drop off in correlation between identical and fraternal twins. Identical twins share more genetic identity than fraternal twins, so they’re going to be more identical on a host of metrics aside from appearance. Those are just raw correlation values of traits though across categories of twins. The core intent of the paper was to explore the relationship between genes, family environment, and other environmental factors, and educational attainment. To do this they constructed a model. Below you see estimates of the variance in the trait explained by variance in genes, shared environment (family), non-shared environment (basically “noise” or error, or it could be something like peer group), from Sweden to Minnesota, and, at three intelligence levels. Two standard deviations below the norm is borderline retarded, ~2.5% of the population or so, and two standard deviations above the norm is at Mensa level.

swed2

It’s interesting that as you move up the IQ scale the genetic variation explains more and more of variance the educational attainment. Someone with an IQ of 130 is likely to be university educated. But there are many who are not. Why? The way I interpret these results is that if you are that intelligent and do not manage to complete university you may have heritable dispositions of personality which result in you not completing university. If, for example, you come from a family which is very intelligent, but is low on conscientiousness, then there may be a high likelihood that you just won’t complete university because you can’t be bothered to focus. Or, you may have personality characteristics so that you don’t want to complete university. A second major finding here is that Sweden and the USA go in totally different directions when it comes to the sub-average and dull in prediction of years of education. Why? The explanation in the paper seems plausible: Sweden strongly constrains higher education supply, but makes it available to those with proven academic attainments at a nominal price. Family encouragement and connections don’t matter as much, if you can’t pass the university entrance examination you can’t pass it. In contrast in the USA if you’re dull, but come from a more educated or wealthier family, you can find some university or institution of higher education which you can matriculate in. Supply is more flexible to meet the demand. I actually know of a woman who is strongly suspected to be retarded by her friends. I have been told she actually tested in the retarded range in elementary school but was taken out of that  track because her family demanded it (she’s the product of a later conception, and her family made their money in real estate, not through professional advancement). Over the years she has enrolled in various community colleges, but never to my knowledge has she completed a degree. If she had not had family connections there is a high probability she wouldn’t have completed high school. As it is, she can check off “some college” on demographic surveys despite likely be functionally retarded.

The next table is a bit more confusing. It shows you the correlations between the effects of the variable on education and intelligence. In other words, does a change in X have the same directional effect on Y and Z, and what is the extent of the correspondence between the effect on Y and Z.

swed3

Shared environment had almost the same effect on intelligence and education, while genetics had a more modest simultaneous effect. Not too surprising that non-shared environment didn’t have a strong correlation in effect across the traits, the authors note that much of this is going to noise in the model, and so not systematically biased in any direction. Though the confidence intervals here are a little strange. I’m not going to get into the details of the model, because frankly I’m not going to replicate the analysis with their data myself. That’s why I wanted to present raw correlations first. That’s pretty straightforward. Estimates of variances out of models with a set of parameters is less so. Here’s an interesting point from the correlations in the last table:

The patterns of genetic correlations in the two samples differed. In Sweden, genetic correlation was steadily in excess of .50 across the range of intelligence, indicating a genetically influenced direct effect of intelligence on educational attainment that was weaker than the shared environmental effect on educational attainment. In the MTFS [Minnesota] population, however, genetic correlation was in excess of .50 when level of intelligence was low, but was halved at higher levels of intelligence. This indicated that genetic influences on intelligence tended to limit educational attainment when the level of intelligence was low, but not when the level of intelligence was average or high.

Now let me jump to conclusion:

This finding indicates that genetic influences common to intelligence and educational attainment may have been more effective in limiting educational attainment in individuals with low levels of intelligence than in encouraging educational attainment in those with high levels of intelligence. As in Sweden, shared environmental influences on intelligence and educational attainment were completely linked, indicating a direct contribution from shared environmental influences on intelligence to educational attainment. The decrease in shared environmental variance with higher intelligence, however, indicated that shared environmental influences were more effective in encouraging educational attainment in higher-intelligence individuals than in limiting educational attainment in lower-intelligence individuals. In other words, in populations in which shared environmental influences such as family history and values encouraged high levels of educational attainment, individuals were able to surmount limitations in intelligence.

Our analysis does not permit the conclusion that these differences in educational systems cause the differences in environmental and genetic influences on educational attainment observed in this study, but it is reasonable to hypothesize that this is likely. In particular, the greater expense of higher education and greater subjectivity of admission standards in the United States compared with Sweden may partially explain the very different patterns of shared environmental influences in the two population samples. Regardless of the causes underlying the differences we observed, the results of our study make clear that the degrees of environmental and genetic influences can vary substantially between groups with different circumstances, and even within such groups. Our results also suggest that the ways in which social systems are organized may have implications for how and to what extent environmental and genetic influences on behavior will be expressed.

This discussion about the role of environment, genes, and culture, on various outcomes should not hinge on one paper. But, these sorts of results are often not widely disseminated among the intellectual classes. One aspect of the American educational system in contrast to some other nations is that not-too-brights have university degrees. Education has long been a project for social engineering in the USA, going back to Horace Mann. Legacies, underrepresented minorities, the poor, those with particular talents, etc., are all part of the decentralized system of university admissions in the United States. In contrast, in nations such as Sweden or Japan there is a more centralized and universal set of criteria. This results is more perfect sorting by the metrics of interest without considerations of social engineering. I know that Sweden has traditionally had a small aristocratic class, while the Japanese aristocracy were basically abolished after World War II. Additionally, both are relatively homogeneous societies so considerations of racial representativeness are not operative. Or weren’t until recently in the case of Sweden. But consider one reality: if such a system is perfectly meritocratic over time if the traits being evaluated are heritable then you will have genetic stratification and reduction of social mobility assuming assortative mating at university.

Currently there is some handwringing by the elites about the fact that so few poor kids get admitted to Ivy League universities. I think there’s a simple way to change this: get rid of the implicit Asian quotas. After all, there was a lot of socioeconomic diversity after the Ivy League universities got rid of their Jewish quotas, but the children of the Jews who didn’t have to go to CUNY and went to Harvard are well off themselves. But more socioeconomic mobility through removing the implicit Asian quota would cause other difficulties, as elite private universities need their slots for both legacies as well as underrepresented minorities for purposes of social engineering/fostering diversity/encouraging donations. Additionally, just as with the Jews the welter of mobility in one generation of the children of Asian immigrants would settle into quiescence in the next if the traits which enable university admission are genetically or culturally heritable.

Citation: Johnson W, Deary IJ, Silventoinen K, Tynelius P, & Rasmussen F (2010). Family background buys an education in Minnesota but not in Sweden. Psychological science : a journal of the American Psychological Society / APS, 21 (9), 1266-73 PMID: 20679521

Daily Data Dump – Monday

Filed under: Blog,Daily Data Dump — Razib Khan @ 11:42 am

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.


Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model Traits. ” We also show that the accuracy of predicting genetic values is higher for traits with a proportion of large effects (proportion black and fat percentage) than for a trait with no loci of large effect (overall type), provided the method of analysis takes advantage of the distribution of loci effects.”

The World Is Fat. Wow, Mexico finally got fatter than the USA! Lay off those beans & rice!

September 26, 2010

Story of X

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.


But biology is obviously more than just armchair analysis. Though there were always quantitative thinkers such as  R. A. Fisher who made great contributions to the field, naturalists and anatomists such as Charles Darwin and Thomas Huxley were the predecessors of the vast majority of working biologists today. Even molecular biologists arguably descend from the laboratories of the physiological geneticists of the early 20th century. With a more robust understanding of the biophysical embeddedness of genetic inheritance in genomic structures a new dimension has been added to analysis from first principles. The fact that genetics is mediated through chromosomes matters.

One obvious aspect in mammals is that males are the heterogametic sex. All males have one X chromosome, while all females have two. This means that an X chromosomal lineage will “spend” 2/3 of its “time” in females, all things equal. This physical reality has been spun out to fascinating effect by evolutionary biologists, outlined in Matt Ridley’s The Red Queen: Sex and the Evolution of Human Nature. In this way the concrete nature of genetics has yielded another axiom to insert into the analytic engine of evolutionary biology.

Of late one finding that has been emerging out of the area of human evolutionary genomics is that the X chromosome may experience selective dynamics differently than the autosome. This possibility turns out to be critical in explaining some strange results reviewed in the communication. The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes:

The ratio of X-linked to autosomal diversity was estimated from an analysis of six human genome sequences and found to deviate from the expected value of 0.75. However, the direction of this deviation depends on whether a particular sequence is close to or far from the nearest gene. This pattern may be explained by stronger locally acting selection on X-linked genes compared with autosomal genes, combined with larger effective population sizes for females than for males.

At issue are some statistics presented in two papers, Accelerated genetic drift on chromosome X during the human dispersal out of Africa and Sex-biased evolutionary forces shape genomic patterns of human diversity. The first group found much less nucelotide diversity, π, on the X chromosome than the second group. From π and D, the divergence between humans and a primate outgroup, they could ascertain a rough proxy of effective population size. The smaller the effective population, the less nucleotide diversity as drift will tend to expunge variation out of the genome. The ratio of effective population size inferred from the X and the autosomes was given by NeX/NeA. The value was on the interval 0.65-0.75 for the first group (depending on the human samples used), and 0.75-1.08 for the second group.

From this the first group concluded that female effective population sizes were smaller for our species. Recall that the X spends more time in females. Naturally from their results the second group concluded that there were more breeding females. In science it is not optimal when two groups come into conflict when looking ostensibly at the same question using similar methods. But, their were subtle differences in their methods which may have biased the results. The first group looked at large regions of the genome, while the second group focused on intergenic regions with recombination. In the second case the aim was to look for patterns of variation away from genes which might have been targets of natural selection (recombination would break apart associations). The logic of the first group was presumably that increasing the proportion of the genome surveyed would mitigate the distorting affect of a few genes which had been subject to natural selection. To check for this they examined the statistics when constraining the data set to regions far away from genes. This did not change their finding.

s1But the second group, which submitted this communication to Nature Genetics, observes that it is not physical distance which is the appropriate variable, but genetic distance. To explore this question they looked at the dependence of π upon genetic distance from genes, and it is clear that the difference in π between the X and the autosome decreases as a function of genetic distance. Obviously the X chromosome has sharply reduced genetic variation near the genes. Why?

The general answer is that the X chromosome experiences selective pressures differently from the autosome. That is a function of the cytogenetics of mammals. Unlike the autosomes a substantial minority of X chromosomes are exposed to the full force of natural selection in the haploid state. To make this concrete males have only one copy of the X, so positive or negative fitness implications would have a much stronger immediate impact. The negative aspect is famous from “sex-linked diseases,” where sons inherit defective genetic variants from their mothers, who are carriers. Since the mothers have two X chromosomes they do not manifest illness. But the positive impact is that if there is a favored allele, and it only expresses recessively, then natural selection is going to be much more efficacious on the X chromosome because a substantial minority of allelic variants will express even at low frequencies. The problem with recessive traits being the primary target of positive selection is that at low frequency the traits almost never express. If, on the other hand, the frequency of the allele rose because of its exposure in males, then that would have a positive feedback loop effect as more and more females would also express the trait in the homozygous state.

In sum the authors conclude that different regions of the X chromosome are telling us different stories. Genic regions are witness to the powerful impact of natural selection upon the genome. In contrast, neutral sites are representative of the demographic history of the species, and in particular its females. I’ll let them finish:

If this hypothesis is correct, multiple evolutionary processes may confound inferences based on wholesale comparisons of full genome sequence data. If we wish to disentangle the history of selection, recombination and demography, a targeted set of carefully chosen regions at sufficient genetic distances from functional elements is needed. Intriguingly, at least for the human X chromosome, the signature left solely by demographic history may be hidden in the small fraction of selectively neutral polymorphisms that reside far from genes.

Citation: Hammer MF, Woerner AE, Mendez FL, Watkins JC, Cox MP, & Wall JD (2010). The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nature genetics PMID: 20802480

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

Filed under: Christine O'Donnell,creationism,Data Analysis,Evolution,GSS,Poll — Razib Khan @ 11:01 am

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?

First, to gauge a sense of Delaware’s religious culture I looked at the Religious Landscape Survey. Because of the small sample size the margin of errors were large, but going through the data I think it is safe to say that Delaware is near the “middle of the road” in reference to the national sample, perhaps just a bit on the more secular and/or religiously liberal end of the spectrum. In the South it seems that Delaware would be very religiously liberal, while in the Northeast it is probably a touch on the more conservative side.

Next, I used the GSS data set. There are four variables which address evolution:

CREATION:

1. God created man pretty much in his present form at one time within the last 10,000 years

2. Man has developed over millions of years from less advanced forms of life. God had no part in this process.

3. Man has developed over millions of years from less advanced forms of life, but God guided this process, including man’s creation

EVOLVED: Human beings, as we know them today, developed from earlier species of animals. Is that true or false?

SCITESTY and SCITEST4: Both also ask if human beings developed from earlier species of animals. Answers though are definitely true, probably true, probably not true, and definitely not true.

I looked to see who voted in the year 2000, variable VOTE00. Note that the questions were asked between 2000-2008, so the “Not Eligible” category simply points to the individuals in the samples in the mid-to-late 2000s who were not yet 18 and could not vote in the 2000 election.


Voted in 2000 Election Did not vote in the 2000 Not eligible to vote 2000
God Created Man 43 44 32
Man Has Evolved, But God Guided 41 42 45
Man Has Evolved 13 10 16
Human Beings Developed From Animals (EVOLVED)
True 50 46 59
False 50 54 41
Human Beings Developed From Animals (SCITESTY)
Definitely True 16 12 21
Probably True 28 31 38
Probably Not True 15 15 15
Definitely Not True 41 41 27

It does not seem to me that the electorate is much less Creationist than the non-voters. The bias toward evolution in the not eligible to vote category is because these are younger age cohorts, who are more secular and less Creationist.

censdivNext I wanted to do some regional analysis of attitudes toward evolution. The GSS has a variable REGION which is broken down into nine categories. The map to the left shows the divisions, as they’re from the Census definitions. 1 = New England, 2 = Mid-Atlantic, 3 = Great Lakes, 4 = Upper Midwest and Plains, 5 = Atlantic South, 6 = Central South, 7 = South Southwest, 8 = Mountain West, and finally, 9 = Pacific West. To increase sample sizes I aggregated some of these together, so 1 + 2 = Northeast, 3 + 4 = Midwest, 5 + 6 + 7 = South, and 8 + 9 = West. Unfortunately the divisions don’t always quite map onto real social and geographical divisions. Missouri is in the same class as North Dakota. The Mid-Atlantic border states of Maryland and Delaware are thrown together into the same category as Florida. In contrast, the Mountain, Great Lakes, New England and Pacific regions are coherent. New York, Pennsylvania and New Jersey do form a tight unit in the Mid-Atlantic (though I think today Maryland and Delaware should be included in the same class).

In any case, I took REGION and recombined it like so: REGION(r:1-2 “Northeast”;3-4 “Midwest”;5-7 “South”;8-9 “West”). Delaware might be in the South in this system, but the Northeast is probably more representative of its values and attitudes. All of the results are for the year 2000 and later.


Northeast Midwest South West
God Created Man 31 41 54 34
Man Has Evolved, But God Guided 50 46 33 45
Man Has Evolved 15 11 9 16
Human Beings Developed From Animals (EVOLVED)
True 64 52 40 57
False 37 48 60 43
Human Beings Developed From Animals (SCITESTY)
Definitely True 22 13 11 21
Probably True 40 34 23 30
Probably Not True 11 13 15 20
Definitely Not True 27 40 51 30
Human Beings Developed From Animals (SCITEST4)
Definitely True 22 9 12 21
Probably True 39 34 26 30
Probably Not True 16 20 19 15
Definitely Not True 23 38 43 34

Let’s limit the sample to non-Hispanic whites:


Non-Hispanic Whites Only
Northeast Midwest South West
God Created Man 29 40 53 35
Man Has Evolved, But God Guided 42 46 34 40
Man Has Evolved 15 12 10 19
Human Beings Developed From Animals (EVOLVED)
True 70 54 41 55
False 30 46 59 45
Human Beings Developed From Animals (SCITESTY)
Definitely True 24 13 12 24
Probably True 42 35 23 25
Probably Not True 11 14 16 20
Definitely Not True 24 39 49 32
Human Beings Developed From Animals (SCITEST4)
Definitely True 22 10 13 25
Probably True 46 32 25 32
Probably Not True 16 22 20 12
Definitely Not True 16 37 43 32

Observations? First, both the Northeast and West tend to be much more accepting of evolution than other regions of the nation. But the West is more polarized, with a larger Creationist minority. This makes sense, as the American West tends to be more secular than the Northeast, but the religious institutions which do exist are generally more fundamentalist in orientation. In the Northeast Roman Catholicism and mainline Protestantism are much more influential than evangelical Protestantism. In the West the situation is more balanced between Catholics and evangelicals, and includes Mormons who tend to have skeptical attitudes toward evolution. The South is more Creationist than the Midwest, though the Midwest tends toward more fundamentalism in belief than the Northeast and West. This I think aligns with our intuitions, the Midwest tends to be the “swing-vote” in culture and politics, though part of this is because there are more “Southern” regions of the Midwest. The “Butternut” areas of Illinois, Indiana and Ohio were settled from the South, while Missouri is also split between Southern and Midwest leaning areas. In contrast, northern Ohio and Illinois, Michigan, and the Upper Midwest states were part of “Greater New England,” and later settled by Scandinavians and Germans who were not congenial toward American Protestant fundamentalism (with the exception of Missouri Synod Lutherans).

As for as Christine O’Donnell and her Creationism, I think she would have benefited from running in Alabama or Mississippi. In some ways the coastal elites are out of touch with how common and pervasive Creationism is, but though Delaware may not quite be part of BosNyWash megalopolis, it’s on the margin of its sphere of influence.

The view from somewhere smart

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:

“Much to my surprise, the Islamic scriptures in the Quran were actually far less bloody and less violent than those in the Bible,” Jenkins says.

Jenkins is a professor at Penn State University and author of two books dealing with the issue: the recently published Jesus Wars, and Dark Passages , which has not been published but is already drawing controversy.

Violence in the Quran, he and others say, is largely a defense against attack.

“By the standards of the time, which is the 7th century A.D., the laws of war that are laid down by the Quran are actually reasonably humane,” he says. “Then we turn to the Bible, and we actually find something that is for many people a real surprise. There is a specific kind of warfare laid down in the Bible which we can only call genocide.”

It is called herem, and it means total annihilation. Consider the Book of 1 Samuel, when God instructs King Saul to attack the Amalekites: “And utterly destroy all that they have, and do not spare them,” God says through the prophet Samuel. “But kill both man and woman, infant and nursing child, ox and sheep, camel and donkey.”

“By the standards of the time” is critical. Much of the genocidal coloring of the Bible comes from the passages in the Hebrew Bible, a product of the late Bronze Age. In contrast the Koran is a product of a world where “higher religions” with formally developed ethical theories were waxing. The rhetoric of genocide as grand strategy was replaced with the implementation of genocide as a tactic of necessity. Similarly, the Book of Mormon reflects an understanding of archaeology totally in keeping with early 19th century America.

Despite the fact that Philip Jenkins is a believing Christian who presumably accepts that the Christian religion is the true religion in some deep sense he does not tend to whitewash the history of Christianity or deny the virtues of other religions. This sort of epoché, stepping away from one’s own normative preferences to assess the world as it is and was, is admirable and all too rare. It is alas especially rare in scholarship which is aimed toward the public. This does not mean that everything Philip Jenkins asserts in his books should be taken as Truth, but, it does tell you that he is making a sincere attempt at getting at the heart of what was and is, not what he would prefer it to have been or be.

Jenkins’ most recent book, The Lost History of Christianity: The Thousand-Year Golden Age of the Church in the Middle East, Africa, and Asia–and How It Died, is a perfect exemplar of his strengths. It has a definite perspective, Jenkins does not hide his plain admiration for the lost Christian civilizations of the Middle East, but his partisanship does not compromise his integrity as a scholar. I believe that Philip Jenkins’ identity as a Christian in the Anglican tradition may explain some of his sympathy toward the world of Middle Eastern Christendom. The ancient Christian traditions of the Middle East emphasize liturgy and continuity with the past, just as the Roman Catholic Church does, but traditionally rejected the supremacy of the Pope* (and before that the Emperor). Similarly, there is a strand in the Anglican Church which is also rooted in the historic traditions of the Christian religion going back to antiquity, and yet they too reject the claims of the Bishop of Rome to primacy. This is not purely a detached work of scholarship for Philip Jenkins, the narrative is delivered in a manner which makes clear his regret and sadness at the passing of the great Christian tradition of the East into marginality, and then oblivion.

The Lost History of Christianity is a peculiar book insofar as it has two halves, and one of those halves is not that lost at all. The “lost” component is the history of what we term today Oriental Orthodoxy and the Church of the East, known in the West as the Monophysite and Nestorian traditions. More concretely these were the churches with rejected the theological tutelage of the Byzantine Empire, and so are not part of the Western Christian tradition even broadly understood. The Monophysite faction was dominant in the non-Greek portions of the Byzantine Empire before the rise of Islam, and today is represented by Christian minorities in Syria and Egypt, as well as the Armenian and Ethiopian churches. The Nestorian faction was for all practical purposes the Christian church as it emerged and evolved within the lands of the Sassanian dynasty of Persia, the Persian church (even if the majority of adherents were not ethnic Persians, but Syriac speakers who were resident in Mesopotamia). The first half of The Lost History of Christianity is a panoramic survey of these Eastern Christianities in the period between their separation from Byzantine Christian Orthodoxy and their final marginalization after the conquest of the Middle East by the Mongols.

After the survey of the history of Christianities lost Jenkins jumps centuries into the future, and chronicles the unexpected death of the churches of the East. These are the years not so lost. The centuries between Mongols and the late Ottoman period are passed over, in large part because these were generations when the eastern sects kept a low profile and focused on survival. And survive they did, as Jenkins observes the reality that there were large and vibrant Christian communities from Egypt to Iraq in 1900, before the unforeseen catastrophes of the 20th century rendered many of them irrelevant or moribund.

800px-Abbasids850Anyone who reads historical monographs would be well aware of the vital role that the Eastern traditions played in the spiritual life of the early Byzantine and Islamic polities. But as a rule this is not highlighted, or well understood, in histories written from a Western perspective. One aspect of The House of Wisdom: How the Arabs Transformed Western Civilization which I did not emphasize in my review is that the author seems to have a very weak grasp on the specific nature of religious pluralism in the early centuries of Islam. Part of the reason was that his real focus was on the late High Medieval and early early Renaissance era, but part of it was either ignorance or lack of interest in Eastern Christianity. This was evident to me in the fact that he repeatedly confused Monophysites for Nestorians, and didn’t seem to have a good grasp of the dynamics of the various players in the religious “great game” of that era. There is a natural reason for this: Eastern Christianity was a cultural dead-end. Jenkins notes correctly that as Eastern Christianity shifted from being majority to minority status in the lands of Islam it went from being intellectually productive to totally moribund in the domain of the mind. In the early years of Western Christianity around 700 there were a series of Syrian popes. When Western Christians began to penetrate the Ottoman heartland in the 19th century they found that the Syriac clerisy was often illiterate and had become hereditary (going from uncle to nephew, as the elite clergy were still often expected to celibate). They had become historical footnotes.

So why should we care? First, because the Eastern Christian tradition, and its rise and fall, give us a window into the waxing and waning of cultures and civilizations. Even granting the classical Islamic narrative whereby the religion exploded out of Arabia fully formed in the early to mid 7th century, Eastern Christians did not view the new dispensation as one which would in the end marginalize them. After all, they had experienced centuries of domination by an Imperial Roman (Byzantine) Christian Church which viewed them as heretics, but had persisted and flourished (perhaps only in Palestine was the Byzantine Orthodox Church the numerically preponderant in the non-Greek lands of the East). More recently in the decades before Islam much of the traditionally  Byzantine Near East had been under Persian rule.

Christianity remained the dominant religion of most of the lands under Muslim rule for at least two centuries after the Arab conquests at a minimum. The Patriarch of the Church of the East between 780 and 823, Timothy, presided over a Christian international network which stretched from the Euphrates to China! Timothy’s missionaries were active in Central Asia, China, Tibet, and India. Mesopotamia was the heartland of his church, but most of the former Persian lands hard large Nestorian minorities, who remained in place while the Zoroastrians slowly disappeared. Jenkins makes the case that Timothy’s Church of the East was the largest of his day, superior in numbers to the Western Church headed by the Bishop of Rome. Remember than in 800 much of Germany was only marginally Christianized, while Scandinavia and almost all of Eastern Europe remained fully pagan. In the days of Charlemagne the Western Christian Church had barely expanded beyond the former Roman Empire, having added Ireland and the regions of Germany closer to the old imperial limes (Charlemagne famously forcibly converted the continental Saxons to Christianity, at least nominally). In contrast the Church of the East had connections and tendrils far outside of the boundaries of the Abbasid Caliphate in which the Timothy was a major political player.

Moving forward centuries the Mongols who conquered the Middle East in the 13th century had some Nestorian connections, due to the successful conversion of several tribes beyond the lands of Islam. The leader of the Mongol horde which sacked Baghdad, Hulagu, had a mother of the Nestorian faith. After centuries of decline since their preeminence in the early Abbasid period the Church of the East took heart in the rise of the Mongols, and the collapse of Islamic hegemony. The Christian connections, and even Christian affiliation, of the Mongol ruling elite opened up a possibility that after over five hundred years of Isle famic domination Christianity would come back to the fore as a religion of rulers in the former Persian lands. This was not to be, after a few decades of flirtation with Christianity and Buddhism, the Mongols of Mesopotamia and Iran opted for Islam. The window of tolerance was over, and the newly empowered Muslims put Christians back into the subordinate place that they’d had before the fall of the Abbasids. In fact they ground them down further in retribution for the perceived and real assistance that they’d provided the Mongols during their years when there had been a possibility for a new religious order. A simple lesson here is that pride cometh before the fall. In the first few Islamic centuries the center of the Christian world was arguably in the lands of Islam. These Christians had extended their reach beyond the domains of their Muslim overlords through a vigorous and conscious campaign of proselytization. For centuries their numerical heft within the Arab polity meant that the Muslim Caliphs would have to treat their religious officials with respect and due deference.

Plato-raphaelThis world of Christianities in 800 was no more in 1800. By then the faith was Europe, and Europe was the faith. Most of the Christianities had been lost, leaving Europe standing nearly alone, the Western Church sundered between the Catholics and Protestants, and the Eastern Roman Church having given rise to the Orthodox Christian churches of Eastern Europe. But it is here that Philip Jenkins brings us back to The Next Christendom: today Europe is no longer the faith, and the faith is no longer Europe. Western Christians are wont to assert that their religion is a compound, a Hebrew heart (revelation), Greek mind (theology), and Roman body (the institution of the Church). But Jenkins observes in The Lost History of Christianity that for much of the history of the religion the traditions of Oriental Orthodoxy and the Church of the East were more parsimonious in their application of Greek philosophical style and substance**, while Oriental Orthodoxy emerged in large part as an institutional counterpoint to the Roman state religion, and the Church of the East grew organically from the seedbed of the Persian Empire. The history of Eastern Christianity before its decline may offer us a window into the possibilities of the Christianity dominated by non-Europeans, at least numerically. As a non-Christian I do not take a deep interest in such topics, but I do know that Asian and African Christians in particular bring a new perspective as to the understanding of the necessary cultural preconditions of their religion.  The Latin Church Father Tertullian once quipped, “What has Athens to do with Jerusalem?”  This may become more relevant in the near future, as non-European Christians challenge the cultural assumptions of a religion which has for 1,000 years been dominated by Europeans and people of European descent.

418px-Kim_Kardashian_6The second half of in The Lost History of Christianity deals with the death of the the Eastern churches in the last century. This is as Jenkins admits something of an exaggeration. Nearly 1 out of 10 Egyptians remains a Copt, an adherent of Egypt’s Monophysite Christian tradition. The Ethiopian and Armenian Orthodox churches retain their central roles in the national identity of these peoples. Lebanon still has a robust Christian population, albeit one which is almost certainly a minority today. The true story of the death of Christianity in the East is in the former Persian lands, Iraq and Iran. In the early 20th century the Iraqi government engaged in a genocide to purge the nation of its Assyrian minority, those Christians who adhered to the tradition of the Church of the East of Timothy. Operationally they succeeded, as the Assyrian community is now almost wholly a Diaspora. This left the Chaldean Catholic Church, of which Tariq Aziz is a member, as the dominant Christian presence in Iraq. This Christian community comes out of the Church of the East, but aligned itself with the Roman Catholic Church during the Ottoman period. This seems a tendency within Eastern Christianity in its terminal phases: a susceptibility to being absorbed into the more robust Western Church. In any case, the American occupation of Iraq and the emergence of a democratic popular regime resulted in the decimation of the Chaldean Catholic community. Most now live in the West, Syria, or Jordan, fleeing Iraq because of their untenable position as a marginal player caught in the cross-fires of sectarian conflict.

401px-Shakira_Rio_02Philip Jenkins contends that in 1900 Christians formed at a minimum 10% of the population of the Fertile Crescent, while in much of eastern Anatolia Armenian Christians were a prominent presence. In 2000 the Armenians no longer were a presence in eastern Anatolia. Christians were ~5% of Jordan’s population (30% in 1950), and are nearly gone from Iraq and Palestine. They are now a minority in Lebanon, whereas they had once been a solid majority. Some of this can be attributed to differential birthrates, as Christians tend to be more educated and Westernized, and so have smaller families. But the preponderance of the proportionate decline is probably due to emigration. There may be as many 10 million people of Arab descent in Brazil, almost all of Syrian and Lebanese Christian origin. There are substantial populations of Christian Arab provenance across Latin America, in France, and the United States. A quick back-of-the-envelope indicates to me that more Christian Arabs live in the New World than in the Middle East by at least a factor of two, and probably more (there are some ambiguities with identifying Arabs in the New World in part because many of them, such as Salma Hayek and Shakira, are of only part-Arab descent). With 10% of the population remaining Christian, Syria is probably the exception which proves a rule: the rise of populist nationalism in the Arab world has not been good for the region’s ancient Christian communities. Syria is dominated by a family of Alawite origin. Jenkins introduces the possibility that the Alawites may be derived from the Gnostic Christian tradition, but all that really needs to be stated is that Alawite heterodoxy is such that the regime can not afford to tolerate exclusive Islamic chauvinism from its Sunni majority. In Dining with al-Qaeda the author observes that it is not uncommon in Syria that Christians have authority over Muslims in the bureaucracy, something which he asserts would be totally unheard of elsewhere in the Arab world excepting Lebanon, where they form a much larger and more powerful segment of the populace than in Syria. It is to Syria that Iraqi Christians tend to flee, and a large fraction of the world’s Chaldean Catholics now calls Damascus home.

The Lost History of Christianity shows that when history, power, and presence, are lost, one becomes invisible to the world. Though Western Christians were shocked and appalled at pogroms directed against their religious brethren in the Ottoman Empire in the 19th century, their interventions went only so far. The Ottomans did manage to extirpate the Armenian community from their lands. The Iraqi government did expel the Assyrians. More recently the Christians of Palestine and Israel have been caught between Jews and Muslims. Ironically Jenkins observes that Christian Palestinian radicals who were of Leftist orientation were seen as enemies by the West during the Cold War, a time when the United States in particular viewed an assertion of Islamic identity in Muslim lands as a bulwark against secular socialism. More recently the American hegemony over Iraq has witnessed the de facto ethnic cleansing of a Christian community whose roots date back to 1st century. It is a commonly told story that at some point in their life a Christian Arab in Jerusalem will encounter an evangelical Protestant from the Southern United States who is not well versed in the region’s history, and finding out that they are a Christian, will inquire of the Arab when they converted to Christianity. Europe is still the faith, and the faith is still Europe. At least for some.

Saint_Elijah's_Monastery_1The story which Philip Jenkins tells is negative, positive, or neutral, depending on perspective. A Christian may see the decline into dhimmitude of the people who were once the root of the faith. A Muslim may see the spread among people who adhered to an imperfectly preserved revelation of true religion the genuine true religion. A Japanese Buddhist may view the change in religious culture as simply a sectarian and political matter in the history of an alien people. It is a tale of memories lost, and consigned to the dustbin of history. The great traditions of Eastern Christianity are dying, the liturgies, processions, and the public buildings. In northern Iraq the cistern of an ancient Christian monastery was being used as a latrine by the Republican Guard before the arrival of American troops. The Iraqis were literally shitting on their own past, as they were almost certainly mostly descendants of Syriac Christians. But that past was one that was lost to them, no longer claimed by them. And so it was that in ages past the ancestors of the Muslims who had been Christians had torn down or neglected the idols of Marduk for the Christ. Such is the way of the world, civilizations and cultures rise and fall, a fact reiterated repeatedly in The Lost History of Christianity.

We live today on the cusp between ages, a time of demographic, cultural, and technological tumult. People are recreating their own past, reshaping their own present, and concocting fantastic futures. Philip Jenkins reminds us that cultural memory can be ephemeral, that even a thousand years may fade into imperceptibility. The values which we hold right, true, and proper, may simply be the fashion of the age. Our ideas may not echo down the generations, but hurtle toward oblivion. I do not know Philip Jenkins’ personal beliefs in the details despite his professed adherence to Anglican Christianity, but his work is a sobering reminder to Christians who believe that the day is coming when all will bend the knee to their Lord that that day will not arrive at their pleasure. Their Lord works in mysterious ways, He giveth and He taketh.

* Over the past few centuries many of the churches have come into the Roman Catholic fold, though retaining their ancient liturgies.

** One has to be be careful not to overdo this, and I would assert that Jenkins does do so in this section. Many Syrian Monophysites in particular were Greek speakers.

Image Credits: Andres Arranz, Doug, Luke Ford, Wikimedia Commons

September 24, 2010

Open Thread, September 25th, 2010

Filed under: Blog,Open Thread — Razib Khan @ 11:11 pm

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.


- I was too credulous about lots of things before the Iraq War. This was egregious, but unfortunately the moronic company here are legion. Here’s Joshua Micah Marshall in June of 2002: “In other words, to give the go-ahead to war with Iraq, you’d have to decide that the experienced hands are all wrong, and throw in your lot with a bunch of hot-headed ideologues. Oh, and one other thing: The last few times, the ideologues have turned out to be right.”

- I thought minarchist libertarianism was a viable model of governance. I do not believe this to be so now, in large part because of my current understanding of how the modal mind works.

- I accepted the inevitability of secularization cross-culturally. I think the story is more complex now, for coarse sociological and historical reasons, as well as fine-grained psychological ones. I think atheism is definitely a minority disposition rooted in peculiarities of neurology.

- I thought Muslims behaved in a crazy manner because they accepted the validity of a crazy book (Koran) and traditions (Hadith). I think the reality is much more complex now.

- I totally accepted G. C. Williams line on the overwhelming dominance of individual level selection. I am more of an agnostic now, though I still believe individual level selection is the best null.

- I accepted the historical consensus that in recent times change in culture occurred overwhelmingly through the flow of memes, not genes, excluding obvious exceptional cases such as the New World. I think the reality is more complex now.

- I used to think that the Right was more intellectually vibrant than the Left. I now am generally skeptical that intellectual life within ideological movements can ever be “vibrant.”

- I thought George W. Bush would pursue a “humble” foreign policy, and feared Al Gore’s association with the “hawkish” wing of the Democratic party. Wrong-headed.

- I accepted the argument of economists about the Great Moderation. I think they were wrong, and I was wrong to accept their authority.

- I thought open source relational databases would cannibalize Oracle’s core product lines. I was wrong, Oracle swallowed the open source flavors whole and their firm is still robust.

- I thought Facebook would peak in 2008. I was wrong.

- I thought twitter would be a fad which came and went. Wrong. I’m on twitter, and see its utility.

- I thought I’d be fatter in 2010 than I was in 2000. I was wrong.

- I thought talk therapy was ridiculous and that prescription antidepressants were far superior in efficacy. I believe I was wrong.

- I thought the Netherlands or Sweden would become Muslim names in the near future. I was wrong. More precisely, I had a lot of dumb ideas in my head and combined them in a dumber fashion.

- I thought Thomas Malthus was a fool. I think I was wrong. He was wrong, but he was a sophisticated thinker.

- I thought we broke out of the Malthusian trap because of innovation. Wrong, only half of the puzzle. The demographic transition occurred, and productivity gains were not swallowed up by population increase.

Were you wrong within the last 10 years? About what?

Friday Fluff – September 24th, 2010

Filed under: Blog,Friday Fluff — Razib Khan @ 12:41 pm

FF3

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

2. Weird search query of the week: “porn makes you straight.”

3. Comment of the week, in response to Swedes are not sexist or nativist:

I’ve been living in Sweden for somewhat more than a year now. I previously lived in Canada, the USA, and Germany. From those countries, the Swedes are at least in my impression the most backward thinking nation I’ve encountered. Nowhere else have I heard so often the replies “Because we’ve always done it like that.” or “That’s just how we do it in Sweden,” when I inquired about the reason for a particularly dumb procedure or policy. (An example: You won’t get a contract for a phone unless you’ve paid taxes for at least 7 months. WTF, I wonder, is that business of the phone company? And let me not get started about the rental situation in that country, but hey, they’ve always done it like that.) I always want to tell them, if we’d all be thinking that way, we’d still live in the stone age. But then, the Swedes are way too polite to tolerate my bickering.

4) Poll question….

(last week’s results were 30% accept peak oil, 40% reject it, and 30% don’t know)

5) And finally, your weekly fluff fix:

topspeed

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