Thursday, May 31, 2007

Watson genome sequenced   posted by Razib @ 5/31/2007 08:03:00 PM

Genome of DNA Discoverer Is Deciphered.

Related: In defense of the celebrity genome.


Are conservatives not crazy?   posted by Razib @ 5/31/2007 12:33:00 AM

Chris of Mixing Memory has a post up titled Are Conservatives Less Creative?. I joked with him that basically creativity is strongly coupled with being mentally on edge, after all, who would really follow their muse on the high risk stakes of a creative career which will likely be characterized by penury? But in any case, check it out. I've seen other stuff which show small correlations like this, but, as I mentioned to him what really matters are the tails. Sure, a statistically significant greater number of Leftish folk might cough up the cash for the rec center finger-painting class, but the more important possibility is that the threshold above which one sees artistic virtuosity might be overwhelmingly dominated by those of Left sensibility. This matters of course over the course of history as art is an essential propagandistic tool. Similarly, the recurrent finding that amongst the high IQ those more verbally adept tend to be on the Left and those with stronger mathematical aptitudes tend to be on the Right is also significant in terms of modeling the trajectory of societal evolution and dynamics.


Wednesday, May 30, 2007

Sam Brownback & evolution   posted by Razib @ 5/30/2007 11:30:00 PM

Sam Brownback offers a cryptic op-ed in regards to his attitude toward evolution (he, one of the three Republican candidates for president who raised their hand when Chris Matthews asked if any of them do not believe in the theory of evolution). As they say, read the whole thing, Brownback is definitely a politician. He seems to have believed that Chris Matthews asked if any of the candidates rejected scientific materialism. Nary a word about common descent in the op-ed, the typical genuflections toward microevolution, and a peculiar objection to both "determinism" and "chance."


Introducing the book   posted by Razib @ 5/30/2007 02:46:00 PM

Read top subtitles....


Glia are just support cells   posted by amnestic @ 5/30/2007 02:44:00 PM

People who study glia are getting all excited about the 'tripartite synapse' where astrocytes that wrap around the synaptic cleft play an active role in controlling neurotransmission. Well TAKE THAT glia researchers!

Selective Stimulation of Astrocyte Calcium In Situ Does Not Affect Neuronal Excitatory Synaptic Activity

Todd A. Fiacco, Cendra Agulhon, Sarah R. Taves, Jeremy Petravicz, Kristen B. Casper, Xinzhong Dong, Ju Chen and Ken D. McCarthy


Astrocytes are considered the third component of the synapse, responding to neurotransmitter release from synaptic terminals and releasing gliotransmitters—including glutamate—in a Ca2+-dependent manner to affect neuronal synaptic activity. Many studies reporting astrocyte-driven neuronal activity have evoked astrocyte Ca2+ increases by application of endogenous ligands that directly activate neuronal receptors, making astrocyte contribution to neuronal effect(s) difficult to determine. We have made transgenic mice that express a Gq-coupled receptor only in astrocytes to evoke astrocyte Ca2+ increases using an agonist that does not bind endogenous receptors in brain. By recording from CA1 pyramidal cells in acute hippocampal slices from these mice, we demonstrate that widespread Ca2+ elevations in 80%–90% of stratum radiatum astrocytes do not increase neuronal Ca2+, produce neuronal slow inward currents, or affect excitatory synaptic activity. Our findings call into question the developing consensus that Ca2+-dependent glutamate release by astrocytes directly affects neuronal synaptic activity in situ.

I kid. I'm sure glia are more than support cells. They really are more active and reactive than people had given them credit for. Perhaps if they don't directly affect fast neurotransmission they could modulate glutamate driven synaptic plasticity.

Lenin vs. God   posted by Razib @ 5/30/2007 10:08:00 AM

Michael Shermer's Skeptic Society has an interesting article up based on And God Created Lenin: Marxism vs Religion In Russia, 1917-1929, which chronicles the futile attempt by the Communists to exterminate religion. One must make a distinction here between religion and a specific religious system and organization.

In The Rise of Western Christendom by Peter Brown I was struck by two simultaneous processes as the Roman Empire withdrew from portions of Germany and Britain and the barbarians rushed in. First, there is the archaeological record of the persistence of folk Christianity for centuries (e.g., amongst the presumably post-Roman peasant subjects of the Avars, or the British remnant under pagan Anglo-Saxon rule). But second, there is the almost invariable creeping advance of doctrinal deviation and religious syncretism once the institutional "police" disappear from the scene. This was in clear evidence in portions of Germany which came under Carlognian direct rule after a long period of Merovingian neglect. St. Boniface records nominally Christian priests regularly taking part in pagan cults and garbling the most basic professions of their faith. A more recent example are the Kakure Kirishitan, Japanese "Hidden Christians" who reemerged after the opening of their nation to the West during the 19th century. In the early 17th century hundreds of thousands of Japanese on Kyushu were at least nominal Roman Catholic Christians (Nagasaki was a Catholic city). The victorious Tokugawa Shogunate persecuted and suppressed Catholicism because of its perception as a "foreign" religion and made every Japanese family register with a Buddhist temple. Though the vast majority of Christians seem to have left the religion (many of these were only notional in any case), a small minority kept their religious identity as Catholics under a mask of crypto-Buddhism. Over the centuries they absorbed outward Buddhist motifs and passed on their Christianity orally. By recontact many of these "Christians" needed to be reoriented toward orthodoxy, so deviated had their religion become from its original character without institutional support. Note that though the surface layer of ritual and belief became distorted rather quickly, the basal psychological attachments with the ancestral faith along with the religious impulse still drove these believers forward to put their lives at risk (one can see this clearly among "Hidden Jews" as well).

Earlier, I have pointed to the fact that Russia seems to have gone through religious "awakening" in the last 15 years. This, despite 70 years of state supported atheism. Boris Yeltsin and Vladimir Putin were both baptized into the Orthodox Church & professed believers, a signal as to the direction of the wind. But, I will not reject the assertion that many of these "conversions" are superficial. A few years back I read a piece which pointed out that a disproportionate number of devout Christians during the Soviet period were of Jewish ethnic origin, a group already under suspicion during the later phases of the Communist state which looked toward Russian Orthodoxy as a source of solace. With the reconversion of much of the non-Jewish Russian elite after the fall of Communism many of these Jewish Christians were shocked to observe that those who had once persecuted them on account of their religious convictions were now attempting to marginalize them within the Russian Orthodox Church itself, presumably driven by anti-Semitic convictions. In Evolution for Everyone David S. Wilson holds out the hope that a non-theistic "religion" may serve some of the same group cohesive functional roles (the "horizontal" aspect) without any nod to a supernatural element (the "vertical" dimension). To some extent I think the reassertion of religious identification in places like Russia and Serbia fits this mold in that many people who affiliate with the Orthodox religion are likely only minimally interested in, or believers in, the supernatural. Slobodan Milosevic never disavowed his atheism, but during the late 1980s he built up his power within what was then Yugoslavia by aligning himself with the Eastern Orthodox religion, even attending ceremonies presided over by clerics. Of course, what one generation might do out of expedience another might accept with sincerity. The conversion of the pagan aristocracy of Rome to Christianity in the early 5th century was a forgone conclusion, their own religious traditions to which they had stubbornly clung to in the face of a century of Christian Roman Emperors was simply no longer a viable option in a polity which now proscribed their rituals and persecuted their beliefs. But by the 6th century no doubt the descendants of once proudly pagan families were now sincere and devout Christians (as attested by their patronage of the Church).

The point here is that religious systems and beliefs are embedded within functionally relevant institutional structures. Even if the former are altered or eliminated, the latter are often needful. Observe the cults of personality, mass rallies and cultivation of youth within the Party structure within Communist states which ostensibly have banished religious feeling. Similarly, even with the collapse of the latter as scaffolding the basal religious impulse will seek outlet in the psychology of a great many human beings. The synergy of both have often been powerful and historically significant forces, as attested by the relationship between Christianity and the rise of monarchy in northern Europe or the spread of Islam during the 7th century.


Steven Pinker's new book   posted by Razib @ 5/30/2007 01:56:00 AM

Just noticed that Amazon is taking pre-orders for The Stuff of Thought: Language as a Window into Human Nature, Steve Pinker's latest. His website states that Pinker will start his book tour on the publication date listed on Amazon, a little over 3 months from now, so that seems sufficient confirmation. Here is Steven Pinker on The Stuff of Thought from his 10 Questions last year:
(10) Most GNXP readers probably know you for The Blank Slate and your work as a public intellectual. However, your next book (entitled The Stuff of Thought) returns to the themes of language and cognitive science. Now, as you may or may not know, GNXP readers are interested in genetics and evolution; politics, religion, and world affairs; and the past, present, and future of the human species. What can you tell us about your upcoming book that might whet the appetites of GNXP readers?

The subtitle of the book is "Language as a Window Into Human Nature," and The Stuff of Thought deals with many aspects of human cognitive and social evolution--how a mind that evolved to think about rocks and plants and enemies can invent physics and math and democracy; why people impose taboos on topics like sex and excretion and the divine; why they threaten and bribe and seduce in such byzantine ways. I also discuss many real-world applications of semantics--words that have impeached one president and that many feel should impeach another; language that continues to embroil the Middle East; whether Democrats can win back the White House by winning the metaphor wars; whether language traps us in a self-referential circle (as the postmodernists believe) or offers us contact with truth and reality.


Tuesday, May 29, 2007

ASPM & Microcephalin & tonal languages?   posted by Razib @ 5/29/2007 01:08:00 PM

Note: The authors have a website which summarizes their research (via Language Log).

Speaking in tones? Blame it on your genes:

People who carry particular variants of two genes involved in brain development tend to speak nontonal languages such as English, while those with a different genetic profile are more likely to speak tonal languages such as Chinese.

In tonal languages, which are most common in South East Asia and sub-Saharan Africa, subtle differences in pitch can change the meaning of vowels, consonants and syllables. Nontonal languages, which prevail in Europe, the Middle East and North Africa, use pitch only as a way of conveying emphasis or emotion.
He cautioned, however, that the research had so far found only an association that appears to be more than chance, and that more work was needed to confirm a causal effect.

I first started hearing stuff this sort of research (i.e., the correlations between particular alleles and language forms) in 2006, so I'm not too surprised. We'll see how this pans out, look for it in PNAS.

But, which alleles on which genes? From Scientific American:
The new research, published this week in Proceedings of the National Academy of Sciences USA ties this difference to two genes, ASPM and Microcephalin. The exact functions of both genes are still open to debate, but they are known to affect brain size during embryonic development. "They presumably have something to do with brain structure, because there are deleterious mutations of the genes that lead to microcephaly" (a condition in which a person's brain is much smaller than the average size for his or her age), says senior study author, Robert Ladd, a professor of linguistics at the University of Edinburgh in Scotland.
Ladd and Dediu compared 24 linguistic features-such as subject-verb word order, passive tense, and rounded vowels-with 981 versions of the two genes found in the 49 populations studied. Most of the language contrasts could be explained by geographic or historical differences. But tone seemed to be inextricably tied to the variations of ASPM and Microcephalin observed by the authors. The mutations were absent in populations that speak tonal languages, but abundant in nontonal speakers.

First, note that the authors here imply that derived (more recent) forms of the genes in question under strong selection are connected to the spread of non-tonal languages around 6,000 years ago. There's a lot of question begging here, are tonal languages ancestral? Is this association causal? But look, there's one thing that jumps out at me from a cursory examination of the various times suggested here: it sees possible that the rise to prominence of non-tonal languages (assuming their derived character) dovetails with the posited expansions of Indo-European and Afro-Asiatic languages around the core of the World-Island (Eurasia + Africa).

Here is the wiki info on the geography of tonality:
In Europe, only Norwegian, Swedish, Scottish Gaelic, the Limburgish language (according to some a dialect of Dutch), Lithuanian, Serbian, Croatian, and some dialects of Slovenian possess tonality, and only Lithuanian regularly marks it in text other than in dictionaries. The tones of Lithuanian are believed to be especially authentic, as they agree for the most part with the tones of Vedic Sanskrit, its ancient cousin. Another Indo-European tonal language, spoken in the Indian subcontinent, is Punjabi.

Most languages of sub-Saharan Africa (notably excepting Swahili in the East, and Wolof and Fulani in the West) are tonal. Hausa is tonal, although it is a distant relative of the Semitic languages, which are not.

There are numerous tonal languages in East Asia, including all the Chinese "dialects", Thai, Vietnamese and Burmese (but not Mongolian, Cambodian, Malay, standard Japanese or standard Korean). In Tibet, which is riven by harsh geography, the Central and Eastern dialects of Tibetan (including that of the capital Lhasa), are tonal, while the dialects of the West are not. Much speculation has been generated over the reasons for this partial tonogenesis.

Some of the native languages of North and South America possess tonality, especially the Na-Dene languages of Alaska and the American Southwest (including Navajo), and the Oto-Manguean languages of Mexico. Among the Mayan languages, which are mostly atonal, Yucatec, with the largest number of speakers, has developed tones.

Finally, from the authors' website:
The next step is to do experiments in which we look for evidence of the nature of the predisposition or bias. The work of Patrick Wong and his colleagues provides one possible lead here: they have shown that some monolingual adults find it much harder than others to learn an artificial language vocabulary that makes use of tone or pitch distinctions, and that the differences between these groups show up in subtle differences of brain structure as well. If we could show that these differences also reflect differences in genetic make-up, it would go some way to showing that the correlation we have found is based on a real causal link.

Related: This is Bruce Lahn's brain on ASPM and MCPH1. ASPM, Microcephalin, and intelligence. Developmental cell biology of ASPM. Brain size & genes.


Monday, May 28, 2007

Facilitating selection   posted by agnostic @ 5/28/2007 01:12:00 PM

Recently Razib walked readers through a scenario where a population passing through a bottleneck would, by sampling error, experience a change in allele frequencies and thereby convert some of the variance due to dominance into additive genetic variance -- the kind that matters most for a population to respond to selection. If we recall the Breeder's Equation -- R = S*h^2 -- the increase in the population mean for a trait (R) equals the mean of the sub-population selected for breeding (S), multiplied by a fraction between 0 and 1 that shows how fully the potential for change is exploited by selective breeding (h^2). This fraction is called the heritability and equals the fraction of the entire phenotypic variance that is accounted for by just additive genetic effects. Clearly, this fraction increases as additive variance increases.

To review a key difference between additive vs multiplicative scenarios, the components in an additive case don't interact, or the context in which they appear doesn't matter. Since such effects are blind to all other contingencies, they matter most in trying to breed a trait in a desired direction. Non-additive effects throw sand in the gears: for instance, if the alleles within a particular locus interact, we have dominance. The other type is due to epistasis, or the interactive effects between loci. Since these effects blunt the power of directional selection, we ask what if we could magically convert the retarding type into the promoting type? Razib's post linked above has already showed how, in detail, this could happen when a bottleneck converts dominance variance into additive variance. Now, to see how a bottleneck could convert epistatic variance into additive variance, consider the following table*:

---- AA -- Aa -- aa
BB.. 8....... 6...... 4
Bb.. 2....... 4...... 4
bb.. 1........ 1..... 3

Let's call the locus with the A and a alleles locus 1, and that with the B and b alleles locus 2. We'll say the entries correspond to a phenotype that depends on the genotypes at both loci, and that fitness is positively correlated with this phenotype. Consider locus 1: the A allele is associated with greater fitness if you look just at the first row, where it interacts with just the BB genotype. In fact, A's effect is perfectly additive: each copy of A adds 2 units to the baseline, and the heterozygote's value is the average of those of each homozygote. If the b allele were lost somehow, then the only possible genotype at locus 2 would be BB (only the top row would show up), and the greater fitness of A combined with its non-trivial heritability (i.e., greater additive variance) would then drive A to fixation. The trouble is that when A teams up with the Bb and bb genotypes, its effect is non-additive and it's associated with lower fitness. We therefore have epistatic variance in this trait: the fitness of the alleles at locus 1 depend on the larger genetic context in which they appear.

For readers not used to this jargon, consider a real-world case of the market success of musical styles. Let's say that locus 1 represents the musical styles, such that AA is a pure classical, Aa is classical-jazz fusion, while aa is pure jazz. Now, locus 2 represents the critics, such that BB prefers classical and increasingly winces as he hears more jazz intrude into a style; Bb prefers music that has even a hint of jazz; while bb is a jazz purist. Here, the success of a particular style depends on who's judging it, and since the judges have dissimilar opinions, a diversity in musical styles will be maintained.

But suppose that, due to the whims of fashion in criticism, the pool of critics was suddenly depleted of those who valued jazz at all, leaving only the classically minded critics (BB). Then we would quickly see jazz musicians removed from the concert halls and record stores, replaced by pure classical musicians. This loss of diversity in the pool of critics wouldn't have to result from caprice -- maybe somebody important in the world of criticism fired all of the critics even somewhat sympathetic to jazz.

To bring this back to genetics, the loss of the b allele at locus 2 could result from a population bottleneck, which increases sampling error, or it could result for more selective forces. We already see that b is associated with lower fitness (values descend as you move down any of the three columns), so it could also be lost due to selection against it. In the past 10,000 years, it has been possible for a few people to affect large numbers of others -- maybe a satrap decides that he doesn't like people with blue eyes and tries to kill them off. Or perhaps an imperial ruler or ruling elite make good on a promise to execute anyone who steals. By purging a locus or loci of their diversity in any of these ways, any other loci that had been interacting with the suddenly homogenous loci are now more free to undergo directional selection. Crucially for humans, the new socio-cultural and institutional structures that came into being only after agriculture probably rubbed out some diversity at loci that were only of marginal importance in a hunter-gatherer society, but whose diversity could not be tolerated in an agricultural one. This applies equally to loci affecting traits above the neck as well as below.

* Shamelessly using the same numbers as Table 2.3 on p.21 of Mazer & Damuth (2001). Evolutionary significance of variation, in Fox, Roff, & Fairbairn (eds.). Evolutionary ecology: Concepts and case studies. New York: OUP.

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Yu Hong, round-eyed in China   posted by Razib @ 5/28/2007 12:38:00 PM

Kambiz @ has an excellent review of the case of the Chinese warlord with "European" ancestry.


Building a Better Mouse   posted by Fly @ 5/28/2007 11:04:00 AM

'Smart' mice teach scientists about learning process, brain disorders

Mice genetically engineered to lack a single enzyme in their brains are more adept at learning than their normal cousins, and are quicker to figure out that their environment has changed, a team led by researchers at UT Southwestern Medical Center has found.
The group is also beginning a search for drugs that might create the same effects without genetic manipulation and monitoring the animals' health and behavior over time.
The key in this study was being able to "knock out" the gene for Cdk5 only in the brain, and only when the mice were adults. This technique, only recently developed and called conditional knockout, allows much more sophisticated experiments than traditional knockout, which entirely eliminates the gene.
Normally, Cdk5 works with another enzyme to break up a molecule called NR2B, which is found in nerve-cell membranes and stimulates the cell to fire when a nerve cell signaling molecule, or neurotransmitter, binds to it. NR2B previously has been implicated in the early stages of learning.

The new research showed that when Cdk5 is removed from the brain, the levels of NR2B significantly increase, and the mice are primed to learn, Dr. Bibb said.

Evolved biological systems aren't optimal...just good enough. Knowing how the system works should lead to interventions that improve function. In the coming decades there should be nutritional, drug, training, genetic, and cybernetic enhancement of brain function.


Sunday, May 27, 2007

Everything and nothing   posted by amnestic @ 5/27/2007 10:47:00 AM

Redefinition / turnin' your play into a tragedy / exhibit level degree on the mic / passionately - Kweli

Nature has an Insight section up ostensibly about epigenetics starting with an article by Adrian Bird suggesting a re-definition. It's free. I think the term is useful to the extent that you can predict something about a phenomenon or mechanism by knowing that it is 'epigenetic'. Bird's suggestion is to make the term less useful and more inclusive. The last section is labeled 'Refining a definition' when in fact he is doing just the opposite:
...there might be a place for a view of epigenetics that keeps the sense of the prevailing usages but avoids the constraints imposed by stringently requiring heritability. The following could be a unifying definition of epigenetic events: the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states. This definition is inclusive of chromosomal marks, because transient modifications associated with both DNA repair or cell-cycle phases and stable changes maintained across multiple cell generations qualify.

He wants to allow transience and yet use epigenetics to explain stable phenomena:
A growing idea is that functional states of neurons, which can be stable for many years, involve epigenetic phenomena, but these states will not be transmitted to daughter cells because almost all neurons never divide.
Without such epigenetic mechanisms, hard-won changes in genetic programming could be dissipated and lost;
With this refinement, epigenetics is everything and nothing. The only thing you can infer about an epigenetic event is that it doesn't change the DNA sequence. Bird wants to claim that a unifying trait is that epigenetics is 'responsive' rather than 'proactive'. I don't understand. If you're going to introduce new terms, why not choose to bring into to broader use the distinction between meiotically and mitotically heritable or force people to be specific about which chromatin modification they are referring to instead of saying 'epigenetic modifications'? Responsive and proactive are more loosely defined concepts destined to muddy waters and lead away from insight.


Saturday, May 26, 2007

Cognitive biases and science - II   posted by Razib @ 5/26/2007 03:04:00 PM

The Science article, Childhood Origins of Adult Resistance to Science, has now been re-packaged for Edge. I have read Paul Bloom's work before so none of this is surprising, though I would offer that he has the cognitive psychologist's bias, so to speak, of not addressing the impact of the variation of human intelligence on the ability of people to comprehend scientific concepts. Even if you can't reproduce all the findings of a given science, high IQ people often have a large database of facts they can cross-reference, a toolkit of rough & ready heuristics and raw analytic power through which concepts can be filtered. The less intelligent often can't make recourse to these cognitive faculties, so the power of authorities looms large and there must be an extra sensitive focus on their credibility. Interestingly, I've found that google actually makes stupid people even more efficiently stupid, they simply proceed to use the search engine to collect an enormous assemblage of moronic sources to reinforce their beliefs. Of course, there's the reality that smart people are often quite stupid outside of their knowledge domain, though eminence within their own field often results in self-deception as to the source of their beliefs outside of their area of expertise (i.e., they attribute their positions to reasoned analysis when in many cases they are simply expressing the beliefs of their social set).


Friday, May 25, 2007

Why the gods will not die   posted by Razib @ 5/25/2007 04:35:00 PM

Over at my other weblog I have a long response to the Edge piece which argues for the power of the Secularization Hypothesis, roughly, that with modernity there comes a falling away from supernaturalism. In short, the authors dig into some data, but like those who make arguments about the inevitable conquest of secularity by religion, their narrative is characterized by selection bias. That is, where the data is powerfully in favor of their argument they draw upon surveys, where it is not powerful or argues against their case they just quote impressions about how non-religious people really are, and sometimes they just pull data out of context (e.g., focus here on South Korea). In any case, I'm just here to remind people of a little history: atheism and theism have basically always been around. The finally victory of either will likely not be won in the human future, as retreat seems to herald future advances. The relative power of atheism or theism varies over time and space, but neither morph ever seems to fix. The sample space of data is so large that like a high school essay it isn't that hard assemble a list of data which support your thesis. It is natural then that the various camps will have their court propagandists outlining their case. But this just really masks the true variation and diversity on this character and its multi-dimensional nature.


Round-eyed Chinese, part n   posted by Razib @ 5/25/2007 11:21:00 AM

European Man Found in Ancient Chinese Tomb, Study Reveals. This is a follow up on an earlier story, worth reading for a lot of quotes. One might ask why the Chinese look so "Chinese" with this ancient evidence of gene flow. Well, non-trivial gene-flow is not the same as a non-trivial flow of peoples. The low level introgression of selectively favored alleles via isolated matings may be genetically significant, but leave little overall signatures on the genome (ergo, ancestry and other characters keep on a truckin' as before). I recall once reading an ethnography of the Hui people, roughly, Chinese speaking Muslims, where local villagers presented an old man with a large nose, a full beard and round eyes and declared that "this is a true Hui man!" Even though generations of intermarriage has resulted in the bleeding into the Chinese Muslim population (presumably founded by Central Asians who settled during the Yuan dynasty of the 13th and 14th century) of the general cultural and genetic character of the surrounding Han population (and likely some flow in the other direction too) these people still remember what they once supposedly looked like.


Thursday, May 24, 2007

In defense of the celebrity genome   posted by p-ter @ 5/24/2007 05:46:00 PM

According to a news article in Nature (subscriber only), some scientists are "alarmed" that a number of high-profile scientists and public figures are going to be the first people to have their genomes sequenced (the published public sequence is a mish-mash of a number of people, and the now-public Celera sequence, though largely Craig Venter, was also from more than one person).

For those unaware of this, 454 Life Sciences is currently in the process of sequencing James Watson's genome, Craig Venter claims to have an analysis of his finished sequence in review at PLoS Biology, and the X Prize in Genomics will be given to the first person to efficiently sequence a number of genomes, including those of "celebrities such as television journalist Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul Allen and former junk-bond trader Michael Milken".

Some quotes from those who don't like this:
"This is almost like recreational genomics, or the molecular equivalent of a whole-body scan, for those who have boundless curiosity and cash," says Kathy Hudson, director of Johns Hopkins University's Genetics and Public Policy Centre in Washington DC. "It will be sort of a sad statement if that's what we end up getting out of the Human Genome Project."


"If all the sequences obtained over the next year or two are done on scientists with strong financial positions, that will send a message quite contrary to what the genome project aimed to achieve," says Francis Collins, head of the US National Human Genome Research Institute (NHGRI) in Bethesda, Maryland.


"I'd hate the availability of single-genome sequencing to be based purely on money and fame," says Michael Ashburner, a geneticist at the University of Cambridge, UK. "Just doing famous or very rich people is bloody tacky, actually."
I'll grant that celebrating sequencing the genomes of a bunch of celebrities is pretty tacky. Fair enough. But these critcs are entirely missing the point.

1. I haven't thought to hard about this, but can anyone think of a major technology that was not first used by the rich? Cars, comupters, the internet, air travel, any major medical technology-- all of these things were first available to those with the money to buy them. After the frontier has been broken and the technology proven, it will be improved, made more cost effective, and eventually be available to the more general public. In the article, a comparison is made between sequencing your genome and getting a private space flight, with the implication that both are ridiculous luxuries for the rich. The explcit goal of the X Prize for space flight, of course, is "to make space travel safe, affordable and accessible to everyone through the creation of a personal spaceflight industry." The same principle is at work here.

2. Many people are wary of genetic technologies and what they bring. There are issues with privacy, with "genetic discrimination", with what to do if you know you could pass on a genetic disease, etc. These are not issues to be taken lightly, but the critics above seem to think that the first people to have their genomes sequenced should be the people that have no idea what genetics is. According to the article, one institutional review board required that any person having their genome sequenced in a given study had to have at least a masters degree in genetics. That's not a bad idea, because in the end, the best way to show you think that something is safe and effective is to do it to yourself first. If the first people having their genomes sequenced were individuals with no knowledge of genetics, there is no doubt the scientific community would be accused of taking advantage of ignorance get people to participate, of using less-educated people as guinea pigs, of scientific irresponsibility, and worse. Damned if you do, damned if you don't...

N.B. if anyone wants to sequence my genome (one hell of a genome, if I do say so myself), please be in touch.


Tuesday, May 22, 2007

Who's the daddy? Evolution says both!   posted by Razib @ 5/22/2007 11:04:00 PM

Who's Your Daddy? Paternity Battle Between Brothers (who are identical twins). Pretty bizarre story.


Adaptive radiation in biology and academia: Why math matters   posted by agnostic @ 5/22/2007 10:42:00 AM

The idea that a species will undergo diversifying selection as it begins to colonize an environment made up of many niches never seen before -- adaptive radiation -- is pretty intuitive. It's obvious enough qualitatively that you'd figure it out on your own if thinking about biology were your day job: the forms of life around us seem so different mostly because they are adapted to different habitats. That idea should probably scale down to sub-populations of a single species. What biologists get paid to do is flesh out the finer-grained quantitative details of how that happens, how much diversity will be maintained by what conditions, and so on. We talk a lot here about recent human evolution (that is, after the invention of agriculture), and so it's worth knowing some of the key points that emerge from quantitative studies of adaptive radiation.

Toward that end, here is a free journal article from PNAS by Gavrilets & Vose which has pointers to the lit and is brief / very readable (although if you want, you can skip their "model" and "methods" sections and focus on "results and interpretations" and "discussion"). Since it's pretty short, I'll let readers peruse it themselves rather than report its contents, but one thing's worth noting: speciation in their model occurred in huge initial bursts. This is yet more evidence that it's foolish to argue that natural selection "hasn't had enough time" to differentiate human populations within 10,000 years, since adaptation doesn't creep steadily. See also the review and simulation articles by H.A. Orr to this effect. Clearly, to the extent that we've moved from one form of society to another more quickly over this time period, these bursts are probably occurring more frequently than in pre-agricultural times. If anything, the only thing that there "hasn't been enough time for" is the settling down of the adaptive process toward a steady state.

Now, the non-math-phobes will have noticed a few phrases lifted from math lingo in the previous paragraph -- the rate of change is increasing (acceleration), are we in a steady vs transient state, etc. But how many here -- not least of which is me -- would know what to do with the jargon of knots, braids, links, or anything else from the field of topology? The only incorporation of these kinds of ideas that I've seen is the chapter on evolutionary graph theory in Martin Nowak's Evolutionary Dynamics. Maybe there are similar articles or book chapters out there, but the point is that there is a mostly unsettled niche begging to be exploited by biologists whose math toolkit contains more than "engineering math" (i.e., non-expert levels of calculus & differential equations, linear algebra, and statistics & probability).

That's no slight to knowing this much math -- but since these tools have been applied for so many decades, it makes it harder to create something original using them. If you were the first to learn, say, knot theory and apply it to biology, you'd blaze a new trail. Even if you personally didn't perform optimally in this area, your intellectual descendants would become increasingly adapted to it and really exploit it (you'd still get credit as the progenitor). Hell, you wouldn't even need to invent new math -- you could absorb what's already understood in math, and maybe roughly how it's used in applications (which would probably be in physics). All you'd have to do is use a bit of analogical reasoning to figure out what pattern in biology it looks like -- or perhaps predict a biological phenomenon that's currently not known, and investigate that.

Edison didn't give much of a role to inspiration, but we could go farther and say that sometimes inspiration is 99% canny opportunism: taking already invented tools to excavate a virgin mine in your own neck of the woods. Most "big ideas" in evolutionary biology are like this: the diffusion equation to model the spread of alleles through a population, game theory to study altruism, extreme value theory to deal with a mutation more beneficial than all extant alleles, and so on. I'm just harping on topology because of a neat little pop-math book I just read called Knots (review by Derbyshire; review by knot theorist). You'd better start settling now, since the corresponding niche in physics appears very crowded, and many of them must feel pressure to migrate to biology where they'd find it much easier to make a name for themselves.

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Copy number variation & autoimmune diseases   posted by Razib @ 5/22/2007 10:06:00 AM

FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. The "Brief Communication" in Nature is open access. Here's a popular press summation.

Related: The HapMap and copy number variation. Potentially massive human genetic variation detected.


Monday, May 21, 2007

Cognitive biases and science   posted by p-ter @ 5/21/2007 09:52:00 AM

It may be obvious that people tend to trust their intuition over data, but some counterintuitive facts or forces are questioned (i.e. evolution), while other are not (i.e. electricity, the non-flatness of the earth). This review (entitled Childhood Origins of Adult Resistance to Science-- I can't tell if the title is deliberately clever or entirely serious) takes a look at why, concluding (perhaps unsurprisingly) that resistance to scientific information is exacerbated in societies "where nonscientific ideologies have the advantages of being both grounded in common sense and transmitted by trustworthy sources." I tried to pick out some select quotes, but instead I'm just putting the whole thing below the fold. It's a fascinating article, and very well-written:
Scientists, educators, and policy-makers have long been concerned about American adults' resistance to certain scientific ideas (1). In a 2005 Pew Trust poll, 42% of respondents said that they believed that humans and other animals have existed in their present form since the beginning of time, a view that denies the very existence of evolution (2). Even among the minority who claim to accept natural selection, most misunderstand it, seeing evolution as a mysterious process causing animals to have offspring that are better adapted to their environments (3). This is not the only domain where people reject science: Many believe in the efficacy of unproven medical interventions; the mystical nature of out-of-body experiences; the existence of supernatural entities such as ghosts and fairies; and the legitimacy of astrology, ESP, and divination (4). This resistance to science has important social implications, because a scientifically ignorant public is unprepared to evaluate policies about global warming, vaccination, genetically modified organisms, stem cell research, and cloning (1).

Here we review evidence from developmental psychology suggesting that some resistance to scientific ideas is a human universal. This resistance stems from two general facts about children, one having to do with what they know and the other having to do with how they learn.

The main source of resistance concerns what children know before their exposure to science. Recent psychological research makes it clear that babies are not "blank slates"; even 1-year-olds possess a rich understanding of both the physical world (a "naïve physics") and the social world (a "naïve psychology") (5). Babies know that objects are solid, persist over time (even when out of sight), fall to the ground if unsupported, and do not move unless acted upon (6). They also understand that people move autonomously in response to social and physical events, act and react in accord with their goals, and respond with appropriate emotions to different situations (5, 7, 8).

These intuitions give children a head start when it comes to understanding and learning about objects and people. However, they also sometimes clash with scientific discoveries about the nature of the world, making certain scientific facts difficult to learn. The problem with teaching science to children is thus "not what the student lacks, but what the student has, namely alternative conceptual frameworks for understanding the phenomena covered by the theories we are trying to teach" (9).

Children's belief that unsupported objects fall downward, for instance, makes it difficult for them to see the world as a sphere—if it were a sphere, the people and things on the other side should fall off. It is not until about 8 or 9 years of age that children demonstrate a coherent understanding of a spherical Earth (10), and younger children often distort the scientific understanding in systematic ways. Some deny that people can live all over Earth's surface (10), and when asked to draw Earth (11) or model it with clay (12), some children depict it as a sphere with a flattened top or as a hollow sphere that people live inside.

In some cases, there is such resistance to science education that it never entirely sticks, and foundational biases persist into adulthood. One study tested college undergraduates' intuitions about basic physical motions, such as the path that a ball will take when released from a curved tube (13). Many of the undergraduates retained a common-sense Aristotelian theory of object motion; they predicted that the ball would continue to move in a curved motion, choosing B over A in Fig. 1. An interesting addendum is that although education does not shake this bias, real-world experience can suffice. In another study, undergraduates were asked about the path that water would take out of a curved hose. This corresponded to an event that the participants had seen, and few believed that the water would take a curved path (14).

The examples so far concern people's common-sense understanding of the physical world, but their intuitive psychology also contributes to their resistance to science. One important bias is that children naturally see the world in terms of design and purpose. For instance, 4-year-olds insist that everything has a purpose, including lions ("to go in the zoo") and clouds ("for raining"), a propensity called "promiscuous teleology" (15). Additionally, when asked about the origin of animals and people, children spontaneously tend to provide and prefer creationist explanations (16). Just as children's intuitions about the physical world make it difficult for them to accept that Earth is a sphere, their psychological intuitions about agency and design make it difficult for them to accept the processes of evolution.

Another consequence of people's common-sense psychology is dualism, the belief that the mind is fundamentally different from the brain (5). This belief comes naturally to children. Preschool children will claim that the brain is responsible for some aspects of mental life, typically those involving deliberative mental work, such as solving math problems. But preschoolers will also claim that the brain is not involved in a host of other activities, such as pretending to be a kangaroo, loving one's brother, or brushing one's teeth (5, 17). Similarly, when told about a brain transplant from a boy to a pig, they believed that you would get a very smart pig, but one with pig beliefs and pig desires (18). For young children, then, much of mental life is not linked to the brain.

The strong intuitive pull of dualism makes it difficult for people to accept what Francis Crick called "the astonishing hypothesis" (19): Dualism is mistaken—mental life emerges from physical processes. People resist the astonishing hypothesis in ways that can have considerable social implications. For one thing, debates about the moral status of embryos, fetuses, stem cells, and nonhuman animals are sometimes framed in terms of whether or not these entities possess immaterial souls (20, 21). What's more, certain proposals about the role of evidence from functional magnetic resonance imaging in criminal trials assume a strong form of dualism (22). It has been argued, for instance, that if one could show that a person's brain is involved in an act, then the person himself or herself is not responsible, an excuse dubbed "my brain made me do it" (23). These assumptions about moral status and personal responsibility reflect a profound resistance to findings from psychology and neuroscience.

The main reason why people resist certain scientific findings, then, is that many of these findings are unnatural and unintuitive. But this does not explain cultural differences in resistance to science. There are substantial differences, for example, in how quickly children from different countries come to learn that Earth is a sphere (10). There is also variation across countries in the extent of adult resistance to science, including the finding that Americans are more resistant to evolutionary theory than are citizens of most other countries (24).

Part of the explanation for such cultural differences lies in how children and adults process different types of information. Some culture-specific information is not associated with any particular source; it is "common knowledge." As such, learning of this type of information generally bypasses critical analysis. A prototypical example is that of word meanings. Everyone uses the word "dog" to refer to dogs, so children easily learn that this is what they are called (25). Other examples include belief in germs and electricity. Their existence is generally assumed in day-to-day conversation and is not marked as uncertain; nobody says that they "believe in electricity." Hence, even children and adults with little scientific background believe that these invisible entities really exist (26).

Other information, however, is explicitly asserted, not tacitly assumed. Such asserted information is associated with certain sources. A child might note that science teachers make surprising claims about the origin of human beings, for instance, whereas their parents do not. Furthermore, the tentative status of this information is sometimes explicitly marked; people will assert that they "believe in evolution."

When faced with this kind of asserted information, one can occasionally evaluate its truth directly. But in some domains, including much of science, direct evaluation is difficult or impossible. Few of us are qualified to assess claims about the merits of string theory, the role of mercury in the etiology of autism, or the existence of repressed memories. So rather than evaluating the asserted claim itself, we instead evaluate the claim's source. If the source is deemed trustworthy, people will believe the claim, often without really understanding it. Consider, for example, that many Americans who claim to believe in natural selection are unable to accurately describe how natural selection works (3). This suggests that their belief is not necessarily rooted in an appreciation of the evidence and arguments. Rather, this scientifically credulous subpopulation accepts this information because they trust the people who say it is true.

Science is not special here; the same process of deference holds for certain religious, moral, and political beliefs as well. In an illustrative recent study, participants were asked their opinion about a social welfare policy that was described as being endorsed by either Democrats or Republicans. Although the participants sincerely believed that their responses were based on the objective merits of the policy, the major determinant of what they thought of the policy was, in fact, whether or not their favored political party was said to endorse it (27). Additionally, many of the specific moral intuitions held by members of a society appear to be the consequence, not of personal moral contemplation, but of deference to the views of the community (28).

Adults thus rely on the trustworthiness of the source when deciding which asserted claims to believe. Do children do the same? Recent studies suggest that they do; children, like adults, have at least some capacity to assess the trustworthiness of their information sources. Four- and five-year-olds, for instance, know that adults know things that other children do not (like the meaning of the word "hypochondriac") (29), and when given conflicting information from a child and from an adult, they prefer to learn from the adult (30). They know that adults have different areas of expertise: Doctors know how to fix broken arms, and mechanics know how to fix flat tires (31, 32). They prefer to learn from a knowledgeable speaker than from an ignorant one (29, 33), and they prefer a confident source to a tentative one (34). Finally, when 5-year-olds hear about a competition whose outcome was unclear, they are more likely to believe a person who claimed that he had lost the race (a statement that goes against his self-interest) than a person who claimed that he had won the race (a statement that goes with his self-interest). In a limited sense, then, they are capable of cynicism (35).

These developmental data suggest that resistance to science will arise in children when scientific claims clash with early emerging, intuitive expectations. This resistance will persist through adulthood if the scientific claims are contested within a society, and it will be especially strong if there is a nonscientific alternative that is rooted in common sense and championed by people who are thought of as reliable and trustworthy. This is the current situation in the United States, with regard to the central tenets of neuroscience and evolutionary biology. These concepts clash with intuitive beliefs about the immaterial nature of the soul and the purposeful design of humans and other animals, and (in the United States) these beliefs are particularly likely to be endorsed and transmitted by trusted religious and political authorities (24). Hence, these fields are among the domains where Americans' resistance to science is the strongest.

References and Notes

* 1. H. Nowotny, Science 308, 1117 (2005).[Abstract/Free Full Text]
* 2. "Teaching of Creationism is Endorsed in New Survey" New York Times, 31 August 2005, p. A9.
* 3. A. Shtulman, Cognit. Psychol. 52, 170 (2006). [CrossRef] [ISI] [Medline]
* 4. M. Shermer, Why People Believe Weird Things: Pseudoscience, Superstition, and Other Confusions of Our Time (Owl Books, New York, 2002).
* 5. P. Bloom, Descartes' Baby (Basic Books, New York, 2004).
* 6. E. Spelke, Cognition 50, 431 (1994). [CrossRef] [ISI] [Medline]
* 7. G. Gergely, Z. Nadasdy, G. Csibra, S. Biro, Cognition 56, 165 (1995). [CrossRef] [ISI] [Medline]
* 8. V. Kuhlmeier, K. Wynn, P. Bloom, Psychol. Sci. 14, 402 (2003). [CrossRef] [ISI] [Medline]
* 9. S. Carey, J. Appl. Dev. Psychol. 21, 13 (2000). [CrossRef] [ISI]
* 10. M. Siegal, G. Butterworth, P. A. Newcombe, Dev. Sci. 7, 308 (2004). [CrossRef] [ISI] [Medline]
* 11. S. Vosniadou, W. F. Brewer, Cognit. Psychol. 24, 535 (1992). [CrossRef] [ISI]
* 12. S. Vosniadou, in Mapping the Mind, L. Hirschfeld, S. Gelman, Eds. (Cambridge Univ. Press, New York, 2003), pp. 412–430.
* 13. M. McCloskey, A. Caramazza, B. Green, Science 210, 1139 (1980).[Abstract/Free Full Text]
* 14. M. K. Kaiser, J. Jonides, J. Alexander, Mem. Cogn. 14, 308 (1986). [ISI] [Medline]
* 15. D. Kelemen, Cognition 70, 241 (1999). [CrossRef] [ISI] [Medline]
* 16. M. Evans, Cognit. Psychol. 42, 217 (2001). [CrossRef] [ISI] [Medline]
* 17. A. S. Lillard, Child Dev. 67, 1717 (1996). [CrossRef] [ISI] [Medline]
* 18. C. N. Johnson, Child Dev. 61, 962 (1990). [CrossRef] [ISI] [Medline]
* 19. F. Crick, The Astonishing Hypothesis (Simon & Schuster, New York, 1995).
* 20. This belief in souls also holds for some expert ethicists. For instance, in their 2003 report Being Human: Readings from the President's Council on Bioethics, the President's Council described people as follows: "We have both corporeal and noncorporeal aspects. We are embodied spirits and inspirited bodies (or, if you will, embodied minds and minded bodies)" (21).
* 21. The President's Council on Bioethics, Being Human: Readings from the President's Council on Bioethics (The President's Council on Bioethics, Washington, DC, 2003).
* 22. J. D. Greene, J. D. Cohen, Philos. Trans. R. Soc. London Ser. B 359, 1775 (2004). [CrossRef] [ISI] [Medline]
* 23. M. Gazzaniga, The Ethical Brain (Dana, Chicago, 2005).
* 24. J. D. Miller, E. C. Scott, S. Okamoto, Science 313, 765 (2006).[Abstract/Free Full Text]
* 25. P. Bloom, How Children Learn the Meanings of Words (MIT Press, Cambridge, MA, 2000).
* 26. P. L. Harris, E. S. Pasquini, S. Duke, J. J. Asscher, F. Pons, Dev. Sci. 9, 76 (2006). [CrossRef] [ISI] [Medline]
* 27. G. L. Cohen, J. Pers. Soc. Psychol. 85, 808 (2003). [CrossRef] [ISI] [Medline]
* 28. J. Haidt, Psychol. Rev. 108, 814 (2001). [CrossRef] [ISI] [Medline]
* 29. M. Taylor, B. S. Cartwright, T. Bowden, Child Dev. 62, 1334 (1991). [CrossRef] [ISI] [Medline]
* 30. V. K. Jaswal, L. A. Neely, Psychol. Sci. 17, 757 (2006). [CrossRef] [ISI] [Medline]
* 31. D. J. Lutz, F. C. Keil, Child Dev. 73, 1073 (2002). [CrossRef] [ISI] [Medline]
* 32. J. H. Danovitch, F. C. Keil, Child Dev. 75, 918 (2004). [CrossRef] [ISI] [Medline]
* 33. M. A. Koenig, F. Clement, P. L. Harris, Psychol. Sci. 15, 694 (2004). [CrossRef] [ISI] [Medline]
* 34. M. A. Sabbagh, D. A. Baldwin, Child Dev. 72, 1054 (2001). [CrossRef] [ISI] [Medline]
* 35. C. M. Mills, F. C. Keil, Psychol. Sci. 16, 385 (2005). [CrossRef] [ISI] [Medline]
* 36. We thank P. Harris and F. Keil for helpful comments on an earlier version of this manuscript. Neither author received any funding for the preparation of this article.


Sunday, May 20, 2007

Who are the descendants of Genghis Khan?   posted by Razib @ 5/20/2007 09:51:00 PM

Via Dienekes this paper about the distribution of the Genghiside patrilineage amongst Eurasian peoples:
...The highest frequency of haplotypes from the cluster of the Genghis Khan's descendants was found in Mongols (34.8%). In Russia, this cluster was found in Altaian Kazakhs (8.3%), Altaians (3.4%), Buryats (2.3%), Tyvans (1.9%), and Kalmyks (1.7%).

It is no surprise that the Mongols have a high frequency of the Genghiside lineage. But, it is interesting that the Kalmyks have the lowest frequency, they are the western (European) branch of the Oirat Mongolian tribes. During the rise of Genghis Khan the Oirats of western Mongolia were forest dwellers at the margins of the grand historical forces which reshaped the heart of Eurasia. Centuries later they rose to the fore to become the most ferocious power of Inner Asia, triggering mass migrations of other nomadic peoples before them, reminiscent of the folk wanderings caused by the depredations of the Huns. The Mongolian peoples to their east, the Khalkha Mongols, allied with the Manchus to eventually defeat the Oirats. The Khalkha elite rejected domination by the Oirat in part because they were not of Genghiside descent. The high frequency of Genghiside lineages amongst non-Mongolian peoples, for example, the Altaian Kazakhs, attests to the cultural power that descent from Genghis Khan had as a way of accruing status and asserting the right to rule amongst the various Turkic Islamic peoples of Inner Asia. It is of course via the Turks, and particularly the Moghuls, that Khan became a common titular surname amongst the Muslims of South Asia. This is an illustration of how exceptional and rare phylogenetic events can sweep across populations and confound previously clear relationships. Two thousand years ago the proto-Oirat and proto-Khalkha male lineages would have been obviously closely related in comparison to Turkic outgroups. But less than one thousand years one subgroup of the proto-Khalkha lineage expanded across the semi-civilized region of Innner Asia, which naturally excluded the forests of the Oirats. Now on top of the short range genealogical networks facilitated by deme-to-deme mate exchange there is a larger system which corresponds to a social force that emerged at a precise historical point.


Synaptic Census   posted by amnestic @ 5/20/2007 01:28:00 PM

Morgan Sheng and Casper Hoogenraad just published a through review of recent attempts to understand the synapse at a quantitative level using mass spectrometry and electron microscopy. The focus is on the receiving end of synaptic transmission (the post-synapse). There is a highly organized, disc-shaped protein architecture just inside the post-synaptic side of a synapse called the Post-Synaptic Density. This is where neurotransmitter receptors are anchored in the membrane along with various scaffolding and signaling molecules. We learn things such as the average size of the PSD (300-400 nanometers wide and 40 nanometers thick), the average number of AMPA receptors ~15. The number of molecules per average synapse, maybe up to 1000, seems almost manageable, as though we could perhaps one day do computations and make predictions. There are two major caveats associated with the type of studies reviewed though: 1) They rely on averages rather than quantitative studies of individual synapses. As Sheng and Hoogenraad point out, there are probably synapses with 30 AMPARs and 0 AMPARs, and this is very important for function. 2) The studies freeze the synapse in time and provide no indication of the dynamic nature of synaptic molecular architecture. Hence this electron microscope-generated post-synaptic mountain range should probably look more like molten lava:

Recent advances in imaging technologies and molecular genetics in vivo have allowed studies such as the one discussed here. The amount of diffusion and protein turnover makes one despair of ever getting a handle on post-synaptic architecture. This is captured in a rather apt analogy at the end of the review:
"Even as we struggle to reach a stoichiometric and geometric description of the PSD and its constituent proteins, it is clear that we are chasing a moving target that changes rapidly and substantially in response to neural activity and developmental experience (akin to taking a census of a fluid society)."

To fully appreciate the analogy one would have to ask how much use a census is for a society. We know how much good it did David. I think one of the major uses of the census is to identify global trends across decades. Here the metaphor fails a bit because we have to destroy the synapse to identify its molecular constituents, but it does point toward a useful experimental design. The census of synaptic components must be taken over time to observe the evolution of synapses in response to stimuli or development. Some developmental data exists, but I would very much like to see a fine scale time course of PSD content following LTP induction. Easy for me to say; if it were really easy it would've been done already.

Saturday, May 19, 2007

Confucianism & China   posted by Razib @ 5/19/2007 12:49:00 PM

The Economist has an article up about the revival of Confucianism in China. There has been a lot of talk about Christianity & Christianesque cults in China over the past 15 years (see Jesus in Beijing). It seems plausible that ~5% of the citizens of the People's Republic of China are now Christian or Christianesque, and this number is likely to go somewhat higher. But, it is important to remember that the number of Christians in Taiwan has long been stabilized at 5%, and in the 5-10% range in Hong Kong, both jurisdictions where Christianity was somewhat favored by the powers that be for decades. Meanwhile, South Korean Christianity seems to have plateaued at about 25% of the population after decades of rapid growth. The point is that one would probably bet against China becoming a Christian nation anytime soon, and without that Christianity being able to assume center stage as a unifying ideology seems unlikely.1

So Confucianism is an interesting alternative. Below I talked about the fact that even in a post-Christian continent the basic raw material of Christian belief is still abundant amongst the population which remains as a reservoir of older practices and outlooks. Is the same true of China? Though State Confucianism fell in the first decades of the 20th century as the organizing principle of the Chinese polity, the the idea of Confucianism as central to the Han Chinese identity did not really suffer major body blows until the Communist take over of the mid-20th century. While most Europeans remember a time when Christianity was ascendant as the central motivating belief structure of their culture, and some European nations still have Christianity embedded in their organizing political documents, the same is not true of Confucianism. Rather, Confucian ideas floated outside of the power structure and passed from generation to generation informally. Outside of China (e.g., Taiwan) Confucianism did not go through the gauntlet of the Cultural Revolution, so even if there was not within China some memory of this ideology it could conceivably be re-planted from without.

But what exactly is "Confucianism"? The "original" Confucianism, as elaborated by Confucius himself and preserved in The Analects, was basically an elaboration of the ideals of Zhou Dynasty China. Its core, family values and traditionalism, are not particular controversial. Later on thinkers such as Mencius and Xun Zi added layers of philosophy on top of the original system, and the rise of Buddhism, and the counter reaction religious Daoism, gave birth to synthetic ideas of Neo-Confucianism, exposited effectively by intellectuals such as Zhu Xi. Some have also asserted that State Confucianism, as promulgated first by the Han Dynasty, had more in common substantively with Legalism (though Legalism was strongly influenced by one of the three fathers of Confucianism, Xun Xi), the bete noire of early Confucianism, with only stylistic flourishes being carried over from the original ideas of Confucius. Whatever the exact truth is, I think the critical overall point is that it is less important what Confucianism is, then that it served as a common anchor for the Chinese bureaucratic elite. Until recently the common anchor for the modern Chinese mandarinate were the texts of Marx & Engels, the policies of Lenin and later the thoughts of Mao (the Little Red Book was actually modeled on the Christian pocket pamphlets ubiquitous in the China of Mao's youth). For obvious reasons that is now less appealing, and attempting to reconstruct them to be congenial to nationalist capitalism is a difficult project. Confucianism is also in some ways an odd fit, especially with its historical contempt for the merchant classes and non-primary producers in general, but at least most Chinese can accede to the fundamental value of Confucian ideas and perhaps make them relevant to the modern age.2 Just as the Constitution of the United States serves as a unifying document for the American nation, so a reconstructed Confucianism might serve as the hub around which the various spokes of Han Chinese culture revolve.

1 - I use the word "Christianesque" because many of the new Christian inspired "cults" are really pretty strange, and mix a lot of folk beliefs within Christian orthodoxy. Since so much of the growth is outside conventional channels and uncoordinated from above it tends to span a lot of "idea space."

2 - One could observe that the synthesis of Christianity and capitalism which is the norm in much of modern Western culture is also rather unexpected.


Latency in Haloscan   posted by Razib @ 5/19/2007 09:53:00 AM

Just an FYI, Haloscan seems to be forcing a delay between posting a comment into their database and displaying it on the message board. Please wait a few minutes before posting again! Your comment might show up.


Friday, May 18, 2007

God's Contintent, Christianity, Islam and Europe's Religious Crisis   posted by Razib @ 5/18/2007 08:33:00 PM

Philip Jenkins' God's Continent: Christianity, Islam and Europe's Religious Crisis is a very good book. In fact, I recommend anyone interested in Islam & Europe to buy it and read it! It is dense on data and citation, and the narrative benefits from the author's multi-faceted understanding of the history and development of religions and religious institutions. While Jenkins' previous two books, The Next Christendom & The New Faces of Christianity, painted a vibrant & fresh portrait of Christianity across the world, from Africa to Latin America and Asia, God's Continent is geographically more narrow-focused, though thematically broader. Unlike many academics Jenkins has the ability to be sympathetic toward his subjects without seeming patronizing or turning into an advocate (though on occasion he does verge upon the latter). Importantly, as an Episcopalian he does not necessarily view all religions as fundamentally outmoded and primitive, allowing contempt to cloud the narrative. Though his sympathies and potential biases are pretty obvious, the data are so abundant that it takes little effort to arrive at conclusions at variance with the author's.

Despite the occasional lapses from objectivity, God's Continent is not a work of rhetoric steeped in anecdote and reliant upon shared norms to render it credible scholarship, its empirical bent is central, the narrative is an extended argument awash in data. The Next Christendom was a tightly presented brief that the future of the Christian religion lay the Third World, specifically, in Latin America, Africa and Asia. In it Jenkins' made the case that the Secularization Hypothesis is false, that it applies primarily to Europe, and that the United States is not an exceptional nation in its religiosity, rather, it is reflective of the worldwide vitality of organized religion. In large measure The Next Christendom and The New Faces of Christianity were aimed at a secular and progressive Western audience out of touch with the realities of religious expression, but whose own lives might soon be impacted by the changes being wrought by demography. After all, it is entirely plausible that within the next generation the Pope is more likely to be an African prince of the Church than a conservative German theologian. This is a very different book with a different audience. Though Jenkins does spend a fair amount of time engaging secular liberals and their confusions regarding the nature of the religion of the masses of "Europeans," his most biting rebuttals seem to be aimed at American conservatives who glory in visions of Eurabia. There are numerous quotations of Front Page Magazine, Mark Steyn and Claire Berlinski, mostly to emphasize the exaggerations and substantive weakness of the claims. God's Continent relays clearly the message that the reports of Christendom's demise are greatly exaggerated. I won't repeat the general arguments made by the likes of Steyn and Berlinski, rather, the first half of Jenkins' book does the leg work by simply collecting data and doing elementary school level math. Here are, for example, the number of just evangelical Christians vs. Muslims in Europe, inclusive of the Russian Federation:
Some Religious Minorities in Europe (includes Russia)

Evangelicals, Charismatics and Pentecostals 8%4.6%8.2%9.8%

The author's point in offering these data is that no one speaks of the evangelical "bounce back" in Europe, even though it is a reality, and numerically more significant than the Muslim presence. Jenkins does suggest that there are those on the Left who are wedded to the Secularization Hypothesis, and continue to view religion as the opium of the masses which is naturally going to fade away. And so they dismiss, ignore, or minimize, the vitality of Christian religious movements within the continent. But it seems his greater irritation is toward American conservatives, who prematurely mourn a religious civilization as if it is dead and buried for the sake of politics and propaganda.

Jenkins offers several reasons why commentators have a tendency to view Europe as "Allah's Continent" even though only a small proportion of the residents of Europe are Muslim. First, scholars tend to count one as "Muslim" on the slightest pretext, because Islamic identity is viewed as a catchall. In contrast, Christian affiliation is associated more closely with a pro-active identification. This results in the exaggeration of the number of religious Muslims and an underestimate of Europeans with sentiment or sympathy toward Christianity. In other words, while secular individuals from a Muslim background can be assumed to have some relationship with the Islamic cultural complex, the same certainly applies to secular individuals from a Christian background! Jenkins himself regularly repeats the claim that "8-10% of French are Muslims or of Muslim origin." The latter is key, it is well known that French "Muslims" are nearly as secular in their habits as French "Catholics," and a recent survey found that 4% of respondents identified as Muslim. This implies that a non-trivial number (assuming that around 1 out of 10 French citizens is of ethnic identity which is conventionally Muslim) of French Muslims have even disavowed a nominal association with the religion, which is parallel with a concurrent decline of Catholic identification in the mainstream French population since the 1960s. Second, there is the regional concentration of Muslims. Rotterdam is half Muslim (in a nation that is 4% Muslim). Greater London is 10% Muslim (in a nation that is 2.5% Muslim). Paris is surrounding by suburbs dominated by ethnic North Africans. There are other dense "pockets" of Muslims throughout Europe, from the industrial heartland of Germany to Malmo to Copenhagen. Muslims are highly concentrated in particular locales, and this ties in to the third issue, and that is that the European elites also concentrate in the same urban conurbations where Muslims are preponderant. Brussels, the capital of the EU, is 20% Muslim! I am always surprised when I read papers in England complaining that a television show with one non-white character out of 10 does not "reflect Britain." But a quick survey of the UK Census shows that this is in fact a proportional representation of Britain (in fact, more than a proportional representation). Nevertheless, it is not a representation of London, and that I believe is the critical variable, because the chattering class naturally conflates its own circumstance with that of the nation. Fourth, Muslims are a problem. Issues of class and race are confounded with the role of religion, but Islam qua Islam and its relation to the West are obviously of some importance in the world at this point. Even if only half of South Asians in Britain are Muslim, they are the half which grips the attention of the media and the public because their impact is not banal or workaday. Discussions about "Asians" and their problems in Britain elide the reality that the "Asians" are invariably the Muslims. Fifth, there is politics at work. Parties on the Far Right in the late 20th century emerged in large part because of the Muslim problem, so it is in their interest to heighten its threat. Elites on the Left co-opt Muslims as tools in their own conflicts and culture wars with the Right, high and low. If Muslims serve as the new revolutionary class then it is in the Left's interest to promote them and encourage the perception of the power of this constituency, as well as to facilitate its mobilization under the leadership of individuals with whom other segments of society can negotiate. In the United States there is the peculiar synergy of jingoism and anti-Europeanism that is the hallmark of much of the New Right combined with the neoconservative perception that anti-Semitism is locally on the rise across Europe and that Islam and Islamism are both regional and worldwide problems which the continent is not addressing.

Against the salience of the Islamic presence on the European continent Jenkins makes a powerful case that Christianity is still a vital, if not preeminent, force on the cultural landscape. He rebuts the common assertion that Europeans are atheistic & materialistic in the majority with a simple appeal to the same survey which I have pointed to. Europeans have become sharply detached from organized Christianity, but majorities still retain sympathy with supernaturalism broadly construed, and large minorities (in some nations the majority, e.g., Greece, Spain, Poland and Ireland) of religious believers remain with a strong Christian identity. And then there is the gray land of Europeans who are weakly connected to Christian orthodoxy, but have powerful cultural affinities with their traditional denominational backgrounds (Edward Said, an atheist from an Anglican religious background, often said that Islam was his civilization. Similarly, it seems plausible to say that many atheists in the West are of the Christian civilization, whether they like to admit it or not). The large numbers of Europeans who make recourse to rituals such as baptism & confirmation attest to this sentimental attachment. Additionally, there are some metrics on which Europeans might be said to exhibit greater religiosity than Americans. For example, the enormous numbers of Catholics who make pilgrimages to holy sites throughout the continent dwarfs any cognate in North America, no doubt in part because of the relative dearth of "sacred spaces" in the United States in comparison to Europe, but also perhaps because that is part of European religious practice which has no equivalent in the United States. Though it seems fair to say that the average European is less religious than the average American, it is also important to remember that many European cultures are not characterized by the wall of church-state separation which Americans take for granted, and religious assumptions may "guide" the society in a manner surprising to some. For example, on the issue of abortion Europeans have had a range of responses, with some states as liberal in their laws as the United States (generally in Scandinavia and Britain), but most more conservative (Germany), and some rather restrictive (Portugal). This diversity is a function of the fact that religious forces, especially the Catholic Church, are political actors who serve to act as breaks upon "progressive" social tendencies. While in the United States such as activism might be seen as improper, or evidence of the power of the Religious Right, in nations where the church is given a nod in the Constitution (though not necessarily established) and explicitly religious parties have long existed such objections are not feasible.

Jenkins also bridges some of the ideas in his previous books by pointing out that a substantial proportion of the immigrants to Europe are Christian. These communities serve as vital hubs of religious evangelism and Christian belief. To some extent one might wonder what Third World Christianity has to do with European Christianity, but of course many religious denominations are international. Just as there is a global Islam, the revivalism of which has world-wide ramifications, so the beliefs of Christians outside of Europe impacts those within Europe. The Anglican Communion is now demographically a predominantly African Christian community. Similarly, Roman Catholicism is a religion with a representation on every continent, and its primary regions of growth lay in Africa and to a lesser extent Asia. For Roman Catholicism this is critical because the sharp decline in the number of seminarians across Europe, excepting Poland, has resulted in the common presence of non-white priests and monastics. In parts of France immigrants and transplants from Francophone West Africa have been critical in filling the breach left by the lack of replenishment of clerical ranks from the native populace. In other situations we have peoples who are reaching & pushing back to the "mother church." African Lutherans are uncompromising in their criticism of the Lutheran hierarchy of northern Europe, who they accuse of being decadent and ineffectual. The Mizo peoples of northeast India were originally converted to Christianity by Welsh Protestant nonconformists, but with the decline of fidelity to organized Christianity in Britain they have now sent missionaries back to Wales (in some ways one might contend this is an expanded recapitulation of the evangelization of Anglo-Saxon Britain from Ireland during the late 6th and early 7th century, as the Irish themselves were converted to Christianity by the Romano-British). The zeal of Korean missionaries is also well known, and their recent problems in the Middle East show just how seriously they take the "Great Commission" (I do find it rather peculiar when 3/4 of their fellow Koreans remain non-Christian that they venture off to foreign lands like the Irish who ventured into the pagan lands of barbarian Europe). The point here is not that the Scotch will be converted back toward "orthodox" Presbyterianism by the Koreans, it is that the same international religious tendrils which have wafted the embers of Islam across the Mediterranean also have resulted in an indwelling of Christians from across to the world to the continent which has been the faith's traditional home. Even if native Europeans were totally lacking in any religious vision or sentiment, Islam is certainly not the only alternative on the scene, for immigrants from other Christian hands have replanted a very vital strand of contemporary Christianity, heavily influenced by the Pentecostal movement, upon European soil.

Emphasizing the native European attachment to Christianity (revival movements, staunchly Christian nations like Poland), as well as immigrant Christianity communities, allows Jenkins to make his case that Islam does not look across a godless continent filled with nihilists, unchallenged and unassailable. When intellectuals, American and European, speak of the death of Christianity and the post-Christian landscape, they are highlighting two distinct dynamics. First, the European elite is in many ways post-Christian. Tony Blair, though an Anglican of some religious convictions, is diffident and tentative in expressing his Christian faith in public. European statesmen such as Francois Mitterrand have been openly irreligious, while even in Catholic Poland until recently the head of state was personally an unbeliever. Though American elites are often accused of being "out of touch," Jenkins argues that European elites exhibit a far greater distance from their "hinterlands" in terms of outlook and world-view (he suggests that the small size and low number of cultural capitals results in a far greater centralization in terms of elite socialization). Dutch elites in the immigrant filled cities no doubt find it easy to forget that their nation is host to a "Bible Belt" of Calvinist believers. Nations as disparate as Norway, France and Scotland have regions of elevated Christianity commitment. But these concentrations of organized Christianity highlight the second trend: the reemergence of the ancient classical pattern where Christianity is simply a major cult within a religiously diverse landscape. The analogy is not totally apt insofar as unlike late antiquity Christians and Christianity still command the heights of the culture, and are a far greater proportion of the population identify as Christians. Additionally, while late antique Europeans lived in a landscape where pagan religious assumptions were normative and served as the cultural backdrop, today's post-Christians live in the shadows of their Christian cultural past. Nevertheless, Europeans have ushered in an age where a wide range of beliefs are acceptable and in currency, just as it was so in late antiquity. This is a time when the Prince of Wales admits that he would prefer to be a defender of the faiths, not a faith. European is post-Christian insofar as Christian assumptions are not unchallenged and always at the center of the cultural discourse because the culture is by definition and necessity explicitly Christian. In decades past the Roman Catholic Church in Italy would not have to reiterate its central role in Italian life, because that would be a given. But today the presence of a Muslim minority, as well as the rise of secularity, means that Italian Catholicism must pro-actively make the case for its relevance and centrality.

And it is this counter-reaction which Jenkins argues is nearly inevitable. He offers a historical perspective, in 1798 the Pope was held captive as anti-Christian revolution swept Europe. Many savants of the age predicted the death of Christianity and the ancien regime. Despite the restoration after the fall of Napoleon, the ancien regime did fall and transform into the modern era of nation-states, but Christianity did not die. It is also important to remember the power of anti-clericalism throughout much of the 19th and early 20th century, and the allure and appeal of radical politics for the European working classes. In 1881 Italian nationalists attempted to seize the body of Pius IX and throw it into the Tiber river. In France the Catholicism and laicism have been at tension for two centuries. If Europeans tire of the ennui of secular materialism and consumer decadence it seems far more plausible that indigenous religious traditions, prominently local Christianities, will serve the role as the vehicle for a revived organized supernaturalism as opposed to Islam. There are already signs that in parts of northern Europe where Islam is prominent that locals are exploring their relationship with Christianity anew. In Scandinavia the Lutheran churches were (or are) arms of the state. In Denmark they term it the Distant Church, and these churches exhibit all the sclerotic tendencies of government bureaucracies. But just as Pietism arose in response to the cooling of Reformation embers, so a second look at religious traditions visited only in passing, at confirmation and marriage, may be induced by the alternative example of Islamic religious communities which are defined by their relationship to their god. The pessimism in regards to European Christianity seems to resemble the nostalgia that some intellectuals felt toward classical paganism, which encapsulated a native spirituality more congenial with nationalist sentiment. European neo-Paganism is in fact a reconstructed tradition which serves as a religious focus for a wholesale re-identification with a national past, mythic or not. But in the generality it failed as a mass movement, and the reason is simple: paganism died in Europe as an organized and explicit movement, its influence was felt within the cultural substratum in custom and tradition, and re-scaffolding these folkways in a systematic manner into a new religious movement proved impossible because the chain of connection across the generations had been broken. The same is not true of Christianity, hundreds of millions of Europeans remain Christian believers, the chain of belief has not been broken! Christianity is not a memory, but a living tradition in some recess, but that recess has been a draw down from a high point after the revivals of the 19th century in the face of 18th century rationalism.

God's Continent spends a great deal of time on the role and nature of Islam in Europe. Jenkins offers many ideas and posits future trends which might surprise some. I won't cover these in detail in this post, but rather will follow up later, as I want to keep the focus on Christianity. But I have to ask, why the relative ignorance of much of the data that Jenkins presents in his book? Part of it is surely human psychology. Readers of this weblog are intelligent, but they can get carried away as much as anyone. A regular reader of this weblog (going on 5 years) conflated the fact that the majority of elementary age children in Rotterdam were Muslim (the city is, as I said, half Muslim) with the possibility that the majority of Dutch children were Muslim! Another reader in a chat was worried about the numbers of Muslims in France, and when I asked him numbers he assumed they were in the 20-30% range. I respectively offered that the concern is laudable, but one should take 5 seconds and go to Google to look at the range of data (15% is probably the high bound). Another reader responded that in France the problem was that one can't speak out against immigrants and Islam. I was busy so I didn't respond that the National Front has been a powerful anti-immigrant force (though ineffectual) for a generation now, winning 10-20% of the national vote, so such a contention seems highly misleading. Th reader was likely not stupid, but they were simply blurting out impressionistic thoughts and telegraphing sentiments common in the right-wing press (i.e., the inevitable "Death of Europe," its weakness in the face of Islam and jihadism, etc.). I have been guilty of this myself. A few years ago I asked on an e-list I was a member of "what northern European nation will become Muslim first?" By "first" I meant in this generation, within 10-20 yeas. I was stupid and lazy, and basically engaging in intellectual masturbation instead of courting the data.

I regret the time wasted on this, though it was enjoyable at the time. In some ways it was a byproduct of the web-masturbatory tendencies of the whole "warblogger" period, where people who knew nothing felt free to say anything about everything. I wasn't a total retard, but my working hypothesis was that a "tipping point" might be reached where Europeans start to convert to Islam. Now, if I was an absolute ignoramus this sort of model might be plausible, but, I did know some history. I'd read a fair amount of Roman, Byzantine and Islamic history, and I had a sense of how "religious change" occurs. I also knew that the idea that Christianity wasn't a lower class religion, that in fact it was a cult of the urban "middle class," and that it spread to the society at large via elite patronage after the conversion of Constantine and the suppression of pagan cults during the reign of Theodosius. Finally, I'd also read a fair amount of sociology of religion and knew of the importance of social networks in the spread of new religions, and the utility bundles which they needed to bring to be successful. In expressing views which seem laughably simplistic in hindsight I was catering to my masturbatory tendencies and my detestation of Islam, using worst case scenarios to stoke my own sense of Schadenfreude, that the Europeans were getting what was coming to those pussies. My own animus toward the central tendency of the Muslim religion remains, but I have come to grips to the likelihood that to grapple with reality one must model it properly. So small details matter, for example, 1/3 of the Muslims within Europe (excluding Russia) aren't immigrants or their children. Rather, they're part of the old communities of the Balkans. This is relevant to projecting the impact that non-white immigrants have upon European Islam, and making an identity between racial minorities and Islam. The cultural influence of Islam and is relationship with race and class are important, plausible high bound estimates of the number of Muslims (e.g., assuming no defection and a broad definition of "Muslim") allow us to arrive at a ~20% figure for what proportion of the residents of European are of that faith in 2050. The Republic of Macedonia is about 33% Muslim. These are members of the Albanian ethnic minority, a long established community in the Balkans. Though today a co-dominion between the Christian Slavs and Muslim Albanians has been achieved, it is only after a civil war in which the Albanians reacted to what they perceived to be overbearing domination and prejudice. An analogy between Macedonia in the 1990s and Europe in 2050 is not totally apt, insofar as Muslims in Macedonia are established as one ethnic community speaking a common language, sharing a common history, and also deriving some support from neighboring Albania. But, this might be a situation which allows us to get a sense of the outer boundary of the problems which Islam might cause, in regards to serving as a focus for rebellion of a minority community which demands concessions from the majority. Nevertheless, it is a far cry from the imposition of Sharia across Europe and domination by mullahs and clerics.

My own concern with this issue as an American has to do with my interest in Europe, the font of Western civilization, and the source of modernity as we understand it. To Americans "Europe" can mean many things. To some liberals it is a socialist utopia of secularism. To many conservatives it is a decadent civilization which we must look to as a warning, a caution about what America might become if it turns its back on its own peculiar cultural traditions. I think that we Americans have to get over some of these issues, and take and accept Europe on its own terms. It is a great civilization, of which we Americans are a branch. It lives to validate its own purpose, and not serve as a prop for our own political quarrels forward our own national interest. Of course, I believe that acknowledging this reality does serve American national interests, but that is a separate issue altogether. Do most liberals know that German abortion laws are stricter than those of the United States? What about the prevalence of right-wing parties which promote a racialist ideology? Do conservatives know that the greatest number of Christians still reside on the European continent? If they are Catholic do they give thought to what their pessimism implies for the Bishop of Rome and the great religious centers and sites of their faith? Presumably conservatives glory in the canon of Western civilization, but will they sit still in the face of the transformation of the lands from which that canon emerged? There is one particular issue which I think puts into stark relief the wrongheaded attitude that Americans have toward Europe: Turkey. Some conservatives seem to want Turkish admission to the E.U. solely for its proximate impact, as it might please our military ally and somehow aid in the "War on Terror." Many liberals see it as part of the multicultural project, a testament to the inclusiveness of modern civilization. But what about the Europeans? After all, they're the ones who have to live out this experiment! The European elite is conflicted, and the populace seems dead set against it. I won't elucidate the reasons why Turkish admission is not a "good idea," but the promotion of this position on the shallow grounds which I have seen on both the American Right and Left highlights the fact that in some ways my nation's elites look to Europe as if it was just another part of the great world "Out There," just as blacks and other minorities are charming and "diverse" people in the far off lands away from the Upper East Side or the other redoubts of the American oligarchy. In the interests of short term tactical position within their own social systems, their own set of hierarchies, they are willing to sell down the river the civilization with which we most definitely have a "special relationship."

The birth, death, and evolution of cultures are complex topics. Like a ball of yarn it is almost impossible with untangle all the strands to get a clear picture of the underlying structure. That being said, the largest threads can be extricated and they serve as a infrastructure which scaffolds the overall structure. Religion is one of the those "infrastructures" within "culture" in its broadest sense. Religion is either the justification or the cause of social change, of public debate, the trigger for cataclysmic wars and the mediator of the most banal of social exchanges. I have written copiously about the different things that religion can mean, that it can be. Like the felicitous alignment of molecules within ore to generate a magnetic field, organized religion can be a powerful cultural force to channel social impulses in concurrent directions. But the basic raw material of magnetism is always there within a molecule, even if they are not aligned together within the ore. We can not project demographics with a linear model which assumes that fertility rates will stay constant, nor can we assume that the increased "secularism" in the West which began during the 1960s will continue without end. We can also evaluate hypotheses about mass conversions of Europeans to Islam by using models and analogies to other situations and scenarios where such things did occur. Masses of Africans converted to Islam and Christianity within this century, while Papuans accept the "white man's religion" so as to imbibe some of his magical technology. European warlords took upon the mantle of Christianity to validate their monarchies within the commonwealth of post-Roman states, one God and one King. And with them came peoples, willingly or not. It does not take a deep understanding or knowledge of history to dismiss the probability that Europeans will look to the ghettos and housing projects for their spiritual renewal, even assuming that they are the soulless golems which some of their critics accuse them of. Rather than focusing on the Europeans it is more important to look to European Islam, because it seems highly like that though it will be a junior partner in the dance with post-Christendom, it will definitely have something to say and help shape the course of events.

Note: I'm going to delete any comments that I perceive do not add value. If you reply to a non-valued comment I'll just delete your whole comment too, so just be warned. This post is partly for Google, and partly to encourage people to read this book and draw their own conclusions. More data is welcome! Your uninformed opinion, not so much.


Culture and wave of advance   posted by Razib @ 5/18/2007 03:46:00 PM

Cultural hitchhiking on the wave of advance of beneficial technologies:
...Decoupling of the advantageous trait from other "hitchhiking" traits depends on its adoption by the preexisting population. Here, we adopt a similar wave-of-advance model based on food production on a heterogeneous landscape with multiple populations. Two key results arise from geographic inhomogeneity: the "subsistence boundary," land so poor that the wave of advance is halted, and the temporary "diffusion boundary" where the wave cannot move into poorer areas until its gradient becomes sufficiently large. At diffusion boundaries, farming technology may pass to indigenous people already in those poorer lands, allowing their population to grow and resist encroachment by farmers. Ultimately, this adoption of technology leads to the halt in spread of the hitchhiking trait and establishment of a permanent "cultural boundary" between distinct cultures with equivalent technology.

Application? Trace the spread of agriculture in Europe and haplogroup J2, and map it onto "diffusion boundaries."


What -ogamy are we?   posted by Razib @ 5/18/2007 01:51:00 PM

Martin mulls over the question, Are Humans Polygamous? There is lots of interesting discussion, with a FinnXPer & reindeer lover in the fray. I think part of the confusion here is simply semantical. Cultural anthropologists often tend to define an -ogamy based on the preferred ideal within a society. So you have circumstances where the social ideal is polygyny, but for various reasons most males (and even females) aren't in polygynous relationships. In contrast, behavioral ecologists tend to look at it a different way, the extent of polygyny can be thought of as the ratio of the reproductive skew of males to females. In other words, if males exhibit high skew (so that only a few males reproduce in a generation) and females exhibit low skew (so that most females reproduce) then you have a species which is highly polygynous. Traditionally one would have to use the tricks of the ecologist's trade and make observations and count broods/offspring from pairings to do this, but with modern genomics this is less critical. You can test for paternity directly within the context of a group of individuals being studied, or, you can examine population level genomic trends. For example, this paper, Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea, allows us to infer a long history of polygyny within a given society. Males have a few ancestral lineages while females have many more across a given time period because so many more females reproduce per generation. Also, in many organisms the "ideal" is not necessarily the reality. "Monogamous" birds for example were found to be not so monogamous when genetic tests were performed to ascertain paternity.

In regards to our own species there are two primary issues which I think need to highlighted. First, it isn't a distribution along a simple polygyny-monogamy axis. If you use primate analogs this would be the gorilla-gibbon range. Male gorillas have harems when they are at their reproductive peak. In contrast, gibbons enter into male-female pair bonds. The size differential between males & females of the species correspond to what you would expect, since gorillas engage in a great deal of male-male competition, males are far larger than females. In contrast, gibbons are more balanced in size because there isn't a large differential between sexes in competition (females always have to "represent"). Additionally, in both species individuals seem to "cheat," so the breeding systems are ideals which are not always fully realized (both sexes are "jealous" and try to guard territory among gibbons). But there is another group of great apes which we have to look at, the chimpanzees. They don't fit the gorilla-gibbon range because females in both chimp species exhibit levels of polyandry, that is, they mate with more than one male over a short period of time . This explains the relatively large ball sacks of males chimps as well as their gooey sperm. If gorillas are at one end of this dimension and chimps at the other (gorilla females have been observed to attempt to cheat, but they don't seem to succeed much), humans seem to be in the middle (check the reliability of paternity confidence across cultures here). I think the question would be better framed as one of polygyny vs. polyandry vs. monogamy, as opposed to a one dimensional spectrum it is a multi-dimensional behavior space. Second, generalizing about the whole of humanity might not really be informative. Variation in behavior and phenotype is not an uncommon phenomenon. Humans may be characterized by alternative behavioral morphs which are extant at different proportions within various populations contingent upon the environment and society. Orangutans are a clearer case of this, there seems to be a "small male" type which females reject when offered the opportunity to male with "large males." But, the small male may remain within the population because its mobility and speed allows it to pursue a raping "strategy." That is, while large males need to be attractive to females because of their lack of agility, the smaller males can simply catch and inseminate the females. One can imagine various higher organisms being characterized by a flux of strategies within the population with might be evolutionarily stable, especially those subject to negative frequency dependence. For example, imagine that among orangs the small males are at a low frequency within the population. In this scenario it seems plausible that most females would be caught unawares because they would only rarely deal with the "threat" of approaching small males. Once the frequency of this morph rises to an appreciable level then socially (or genetically) conditioned defensive responses might arise which prevent it from increasing in frequency. In the case of gorillas, gibbons or elephant seals the modal (most common) strategy is almost exclusively practiced. But in species like orangs, gorillas or even chimpanzees, where more variation over time and tribe is the norm one must keep in mind both the central tendency (the mean) as well as the variance, and, possible multi-modalities (which would map onto the common morphs).

Finally, there is the issue of culture, the environmental and non-genetic aspect of behavioral causality. Obviously a trait must be expressed within a particular environment, and the expression of a genetic "switch" must then be properly contextualized. Consider the relationship between MAOA and abuse. The correlation between one allele and abuse on the population level needs to be understood in the context of early childhood environment at the level of the individual. The "abuse" morph will not express without particular environmental inputs. One can characterize this as a norm of reaction, or simply treat the environment as another component of the variance. The point is that a genetic component toward a behavioral bias does not imply that social & environmental forces can not play critical roles in how the phenomenon is realized (or not!). An emphasis on alternative morphs and behavioral strategies, and facultative responses, also implies that a range of behaviors might be realized dependent on the range of environments which a population is subject to over time. Ultimately I think a focus on instrumental attitude toward explanations are essential in the case of our own species because the biosocial toolkit is so multifaceted and flexible. Models need to be "thick" and microscale, nested within a set of contingent facts and amenable toward accommodating the reality of variation, heritable and non-heritable. No need for determinism, genetic or cultural, here.


Dumb things guys do to impress girls   posted by agnostic @ 5/18/2007 01:19:00 PM

Retrospectacle gives the low-down on the Schmidt Sting Pain Index, which measures the pain of insect stings. The winner is the Bullet Ant that plays a central role in boy-to-man initiation rites of the Satere-Mawe tribe in Amazonia, as seen in this video. Returning to my post on daredevils, one episode of Jackass spin-off Wildboyz features Steve-O and Chris Pontius undergoing the ritual. See this video (some censored non-nudity). Their hysterics are somewhat affected, but no doubt it takes a bad MF to undergo this ritual multiple times for 10 minutes each time.

Why would a sane person do this? Easy: study the facial expressions of the local women after Steve-O and Chris undergo the ritual (about 2:15 in the video). Since facial expressions are pretty universal, we Westerners can recognize them as "my romantic curiosity has been piqued." And the girls are pretty, too -- now we understand why guys do stupid stuff like this. Not surprisingly, the creators of the two sting scales (Schmidt and Starr), are both male. I'm sure other obscure pain scales were developed by males as well, even if they're uncredited -- fraternity initiations must involve calculations of pain from similar sources. Scoville was male, but he measured spiciness according to what a panel of tasters thought.

This is yet another example of how culture could influence evolution: a ritual like the ant-gloves unmasks the ability to "take it like a man." Since the signal of manliness is amplified by extraordinary circumstances like these, the females now don't have such a hard time teasing it out from the noise of quotidian goings-on and can thus make better decisions about who to mate with. Branding and tattoo-ing likely serve similar functions, aside from whatever other roles they may play.

On a personal note, I'm not a paragon of machismo, but I figured out early on that I have a very high tolerance for needle pain. At 22 I decided to have my forearms tattooed (tastefully), and I'm surprised by how intrigued girls have been by them. They often fondle your arms as they inspect them -- not the worst thing in the world. A co-blogger has also noted that girls dig non-tasters, i.e. someone who can eat fire without flinching (though in his case the attention is unwanted, as he has a girlfriend). Males have duller palates (see here too), making non-tasting a more masculine trait. That could be why men with overly refined palates are perceived as effeminate. In any case, here too culture could unmask who is manly vs wimpy.

True, not all cultural / technological advances will allow previously unnoticed males to become manly men -- World of Warcraft addicts will always be dateless -- but that still allows for adaptive radiation into many other "now open for business" niches. There is also the not mutually exclusive possibility that selection is acting on other, correlated traits (e.g., for certain personality types).

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Thursday, May 17, 2007

Arrays on the way out?   posted by p-ter @ 5/17/2007 09:57:00 PM

A few months ago, I wondered out loud if next-generation sequencing techniques would render microarrays obsolete. There's no need to estimate abundances of any nucleic acid by hybridization if you can just count up frequences of mRNAs or DNA or whatever directly via sequencing. I must have heard that idea somewhere, because this week's Cell has an example of just that principle.

The assay in question here is chromatin immunoprecipitation (ChIP), a classic technique for testing whether your protein of interest is bound to a DNA sequence of interest. In the assay, you crosslink proteins to the DNA, then use an antibody to your favorite protein to isolate the DNA it's bound to. In the old days (or now, if you have a specific hypothesis to test), you would then do PCR on said DNA to test for the presence of a sequence of interest. With arrays, you could blindly hybridize the DNA to the array, generating a map of where your protein bound in the genome (in this case, the assay is cutely called ChIP-chip). But this is subject to all the problems of arrays-- isolating the signal from the noise, possible low resolution, a need to amplify the DNA, etc. One way around this is to simply sequence the DNA-- binding sites can then be directly imputed from the sequence data (the quality of which will depend on the efficiency of the IP). This is exactly what the authors do, and it seems to work.

Moral of the story: technology moves fast.


Wednesday, May 16, 2007

Origins of disease...   posted by Razib @ 5/16/2007 05:44:00 PM

Origins of major human infectious diseases:
Many of the major human infectious diseases, including some now confined to humans and absent from animals, are 'new' ones that arose only after the origins of agriculture. Where did they come from? Why are they overwhelmingly of Old World origins? Here we show that answers to these questions are different for tropical and temperate diseases; for instance, in the relative importance of domestic animals and wild primates as sources. We identify five intermediate stages through which a pathogen exclusively infecting animals may become transformed into a pathogen exclusively infecting humans. We propose an initiative to resolve disputed origins of major diseases, and a global early warning system to monitor pathogens infecting individuals exposed to wild animals.


Strength in numbers   posted by Razib @ 5/16/2007 03:22:00 PM

The Benefits of Bee-ing Social:
By measuring how much of each solution it took to stop the staph's growth, the researchers determined the strength of each kind of bee's body coating. All the coatings killed bacteria, but the social bees' antimicrobials proved much more powerful than expected, says Stow. Antimicrobial armor from the most social bees was 314 times stronger than that from the most solitary bees, the team reports online this week in Biology Letters, and even the most mildly social bees were 10 times more protected than their solitary counterparts.

The general inference about the impact of the rise of dense human settlements 10,000 should be pretty obvious.


Genetics of obesity   posted by p-ter @ 5/16/2007 02:45:00 PM

I realize I'm sort of beating a dead horse by reporting every single high-profile genome-wide association scan (for example), but it's worth pointing out their successes, as there was serious opposition to the HapMap project that laid the groundwork for these studies. So in that spirit, I'll point out this paper, which identifies a common variant in the FTO gene as being associated with obesity:
An additive association of the variant with BMI was replicated in 13 cohorts with 38,759 participants. The 16% of adults who are homozygous for the risk allele weighed about 3 kilograms more and had 1.67-fold increased odds of obesity when compared with those not inheriting a risk allele. This association was observed from age 7 years upward and reflects a specific increase in fat mass.
One of the most important points about genome-wide association studies is that they're (more or less) unbiased-- that is, you don't have to think about which genes could be involved in the phenotype before studying it. Some people consider this a liability, some a blessing. I'm in the latter group, as a strong signal in a genome-wide association can in some cases lead to new candidate genes, new hypotheses and expose interesting biology. This is precisely one of those cases. Here's what's known about the gene identified in this study:
FTO is a gene of unknown function in an unknown pathway that was originally cloned as a result of the identification of a fused-toe (Ft) mutant mouse that results from a 1.6-Mb deletion of mouse chromosome 8. Three genes of unknown function (Fts, Ftm and Fto), along with three members of the Iroquois gene family (Irx3, Irx5, and Irx6 from the IrxB gene cluster), are deleted in Ft mice. The homozygous Ft mouse is embryonically lethal and shows abnormal development, including left/right asymmetry. Heterozygous animals survive and are characterized by fused toes on the forelimbs and thymic hyperplasia but have not been reported to have altered body weight or adiposity. The fused-toe mutant is a poor model for studying the role of altered Fto activity, because multiple genes are deleted. Neither isolated inactivation nor overexpression of Fto has been described.
So essentially, nothing is known about this gene. Thanks to this study, this is unlikely to be the case for long.

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Herpes, it does a body good   posted by p-ter @ 5/16/2007 02:25:00 PM

Check this paper, which shows a latent herpesvirus infection confers resistance to bacterial infections in a mouse model:
All humans become infected with multiple herpesviruses during childhood. After clearance of acute infection, herpesviruses enter a dormant state known as latency. Latency persists for the life of the host and is presumed to be parasitic, as it leaves the individual at risk for subsequent viral reactivation and disease1. Here we show that herpesvirus latency also confers a surprising benefit to the host. Mice latently infected with either murine gammaherpesvirus 68 or murine cytomegalovirus, which are genetically highly similar to the human pathogens Epstein–Barr virus and human cytomegalovirus2, respectively, are resistant to infection with the bacterial pathogens Listeria monocytogenes and Yersinia pestis [the plague]. Latency-induced protection is not antigen specific but involves prolonged production of the antiviral cytokine interferon-gamma and systemic activation of macrophages. Latency thereby upregulates the basal activation state of innate immunity against subsequent infections. We speculate that herpesvirus latency may also sculpt the immune response to self and environmental antigens through establishment of a polarized cytokine environment. Thus, whereas the immune evasion capabilities and lifelong persistence of herpesviruses are commonly viewed as solely pathogenic, our data suggest that latency is a symbiotic relationship with immune benefits for the host.


Tuesday, May 15, 2007

Count down to triple digits!   posted by Razib @ 5/15/2007 02:49:00 PM

Remember back in the late 90s when there were all those "countdown to legality" websites? Well, take note, Jacques Barzun, author of From Dawn to Decadence: 500 Years of Western Cultural Life 1500 to the Present, will be turning 100 on November 30th of this year! In homage to Barzun's centenary you will note to the right a ticker which will countdown until his 100th.

Oh my god!!!   posted by Razib @ 5/15/2007 02:39:00 PM

Monday, May 14, 2007

Heights of comedians: Average Joes   posted by agnostic @ 5/14/2007 07:54:00 AM

Continuing the series on the maintenance of variation in human height, let's have a look at how comedians measure up. (See the previous entry in the series here, which has links to the other entries.) I could see their heights go either way: maybe they're shorter than average, and their comedy routine is their way of getting attention -- or maybe they're taller than average, since you might need a more commanding height to put hecklers in their place.

As explained in the previous entry on daredevils, females in general prefer a male who is taller than average. For a man who's average or below-average in height, then, he had better have something to make up for his unremarkable stature. Since a sense of humor is typically listed near the top of women's preferences (search this page for "humor"), perhaps perfecting comic skills could save a shorty from romantic oblivion. In a recent advice column for short guys, we read:

Bill, a 35-year-old publishing executive from Rochester, NY, who's 5'6", says he's had a good response online from women of all heights. "I have taller girls emailing me a lot, even though I don't meet the height they say they're looking for," he says, "They all tell me my profile made them laugh. I think the key is having something to capture their attention other than height. Humor's the best."

To investigate this possibility, I took a list of the Top 100 comedians as ranked by Comedy Central in 2004 [1], and looked up their heights at the CelebHeights website, for which I found 42 data-points. I then looked up the remaining individuals on Imdb, which gave me new total of 61 heights. But to correct for ubiquitous lying in self-reported height, I subtracted 1 inch from the heights listed at Imdb (a generous assumption). The means and SDs were not different for the group of 42 culled only from CelebHeights vs. the pooled group of CelebHeights plus Imdb data, so I used the larger sample to increase N.

I ignored the 8 or so females who made the ranking, and I left out individuals who were born before 1935, in order to make sure their height wouldn't have been affected by growing up during the Great Depression or anything like that [2]. See here (PDF) for data on a representative sample of male American height.

Below is a frequency distribution of heights in this sample of comedians:

The points show what percent of the group lies strictly above the next-lowest height and up to & including the height where the point is (e.g., 26% were above 68 inches and at most 70 inches). It's an almost normal distribution, and its skewness of 0.29 means that it's more or less symmetrical. Comedians here have a mean height of 69.5 inches (median = 69 inches), with one SD = 3.0 inches. If that sounds like a perfectly representative sample of the general population, that's because it is: a two-tailed t-test to test the difference from the population mean of 69.6 inches gives t = -0.26, which is nowhere near significant (p = 0.8). Out of curiosity, I checked whether height and rank in the Top 100 list were correlated -- they were not: Spearman's rank correlation = -0.06, but p = 0.64.

It's pretty clear that variation in height will not be eroded by female preferences for tall males, provided the average and short males have some way to compensate. Upon realizing that they are not cut out for most sports, hand-to-hand combat, executive positions, and so on, they carve out a niche where this flaw of theirs is unimportant. They still manage to do all right for themselves, and enjoy the side-effect that they are probably much better flirts than their competition. While not knowing much about the history of comedians, I still doubt that a person was able to earn a living as a comic until very recently, so I don't claim that the benefit of comic skills was in attaining high financial status and attracting a bevy of groupies like some modern comedians do.

At the same time, most comedians -- until they are very rich and famous -- typically hold down a day job and perform before an audience during their leisure time. So being a comedian would not have meant that you couldn't have earned a living some other way. And even if there weren't large audiences to tell jokes to, a first-rate comic would surely have acquired a reputation for his skills and would have impressed enough women -- either via reputation or by face-to-face flirtation -- that he would've earned distinction as a local star. After that, mating opportunities would have ensued.

So, there are at least four ways for men to compensate for unimpressive stature: as rockstars (and perhaps as musicians broadly), daredevils, and comedians. All involve cultivating a talent which one can display in front of an audience and which is difficult to copy (as anyone who's tried to make up their own jokes has quickly figured out). This increases their social status. The other way we've seen is to simply be a pretty boy -- no talent there, really, but it's conceivable that women would be attracted to pretty boys due to "good genes" selection. I don't think this necessarily says that short guys will tend to gravitate toward performance-based niches -- it's just that the CelebHeights website only keeps data on celebrities. It would require funding that I don't currently have in order to investigate what other pursuits are shorty-friendly.

Again, let this serve as "news you can use" for sub-tall men currently in the dating arena, or men who plan to have sub-tall sons but still wish for them to do well with girls.

[1] You can bicker about who should be where, but it's a representative sample of famous comedians.

[2] Actually, Jackie Mason's data-point (65 inches) made it into the first round of data collection, and I forgot to throw it out when I calculated the statistics, made the graphs, made these into images, and so on. Rather than waste another 30 minutes to correct all of these just to weed out this one point, I'll keep it in, since its exclusion wouldn't affect any of the results.

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Sunday, May 13, 2007

Behavioral Economics and IQ   posted by Herrick @ 5/13/2007 06:13:00 PM

We all know that homo economicus fails as a complete description of human behavior, as the new field of behavioral economics makes abundantly clear. So while the homo economicus model does a good job explaining things like the interaction of supply and demand, the random walk nature of stock prices, and photo #16, it misses quite a lot of important facts about human behavior. By now, there's a rich literature on this, and any book you can find on the subject by Bowles, Camerer, or Thaler would give a good overview.

But of course, both h. economicus and h. behavioralis are ideal types--and so the question arises: Are some people more behavioral than others? Are some people more economistic that others? And is there any simple way to predict who will fit into which part of the spectrum?

Economists have started working on this question over the last few years, and right now I'll just stick to one small issue: Patience. The behavioralists have done a good job proving that people are generally much less patient than economic models predict. And recent work seems to show that smarter people are quite a bit more patient, a fact that may have important social implications.

In a recent study, Benjamin and Shapiro found that among Harvard undergrads, "A one-standard-deviation increase in mathematical performance raises the propensity to be patient by 18 percentage points, relative to a base of 28%." So if math scores rise by two standard deviations, patience more than doubles. Their summary:

In two laboratory studies [with Harvard students and Chilean high school students], we show directly that cognitive ability is associated with more standard time and risk preferences.

And what does "standard" mean to Benjamin and Shapiro? More like h. economicus.

Shane Fredrick of MIT showed much the same in this quite readable paper. He has a nice review of the earlier literature and in his own experiments found that "[t]hose who scored higher on the [cognitive reflection test] were generally more 'patient.'"

Both of those papers involve experiments with students playing for small sums of cash. This paper, published in what is arguably the top journal in economics, showed that when people were making decisions involving thousands of dollars, people with higher AFQT scores were much more patient.

The military drawdown program of the early 1990s provides an opportunity to obtain estimates of personal discount rates based on large numbers of people making real choices involving large sums. The program offered over 65,000 separatees the choice between an annuity and a lump-sum payment. Despite break-even discount rates exceeding 17 percent, most of the separatees selected the lump sum--saving taxpayers $1.7 billion in separation costs. Estimates of discount rates range from 0 to over 30 percent and vary with education, age, race, sex, number of dependents, ability test score, and the size of payment.

And when officers were broken down by careers, who were the most patient?


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Coevolution of Male and Female Genital Morphology in Waterfowl   posted by Darth Quixote @ 5/13/2007 01:25:00 PM

Here is something that caught my eye over at PLoS ONE:
Most birds have simple genitalia; males lack external genitalia and females have simple vaginas. However, male waterfowl have a phallus whose length (1.5-40 cm) and morphological elaborations vary among species and are positively correlated with the frequency of forced extra-pair copulations among waterfowl species. Here we report morphological complexity in female genital morphology in waterfowl and describe variation vaginal morphology that is unprecedented in birds. This variation comprises two anatomical novelties: (i) dead end sacs, and (ii) clockwise coils. These vaginal structures appear to function to exclude the intromission of the counter-clockwise spiralling male phallus without female cooperation. A phylogenetically controlled comparative analysis of 16 waterfowl species shows that the degree of vaginal elaboration is positively correlated with phallus length, demonstrating that female morphological complexity has co-evolved with male phallus length. Intersexual selection is most likely responsible for the observed coevolution, although identifying the specific mechanism is difficult. Our results suggest that females have evolved a cryptic anatomical mechanism of choice in response to forced extra-pair copulations.

This paper has some interesting figures.


Saturday, May 12, 2007

Pro forma hand wringing?   posted by Razib @ 5/12/2007 08:09:00 PM

The New York Times has a piece which goes over the issue of genetic testing and abortion. Most of the coverage is given over to people who support abortion rights but are not particularly happy about the consequences of the rhetoric of "choice." I'm not old enough to remember, but does this airing of "concerns" remind anyone of some of the sounds made when "test tube" babies were a big social issue? I suspect that most "progressives" given space in this article would concede the importance of points the disability rights activist person makes. That being said, I also suspect that they won't do anything about the inevitable shift toward consumer genetics and the selective abortions of fetuses with disabilities.


A simpler Middle East   posted by Razib @ 5/12/2007 06:39:00 PM

Just stumbled onto this article about the exodus of Mandaean community from Iraq, to Sweden. We know that the Christians of Iraq are leaving in droves, but, it is not always appreciated that this is the second great emigration of Iraqi Christians. Early last century the more numerous members of the Church of the East, which was the dominant Christian confession in Mesopotamia since the time of the Sassanid Empire, left their homeland after cooperating with the British and experiencing persecution. The Christian remnant in Iraq was represented by the Chaldean Church (Tariq Aziz is a member), and these are the refugees of today. Of course, the even more antique community of Iraqi Jews were also expelled during the 20th century. In Syria and Lebanon the proportion of Christians has decreased in part because of massive emigration to the West. The ancient Palestinian Christian community is vanishing to triviality.


Friday, May 11, 2007

Tasmanian Aboriginal DNA not extracted...   posted by Razib @ 5/11/2007 05:28:00 PM

Here is a story about a museum which returned Tasmanian Aboriginal remains to a community group without doing DNA analysis, because they argued that this sort of compromise would preserve them for future analysis. This is a tricky area. I'm obviously generally disinclined to sympathize with "communities" who claim bones because the individuals making the decisions are simply individuals, and often individuals playing politics. That being said, the history of the Tasmanian Aboriginals was characterized by proactive bestial treatment on the part of Europeans, and the relationship of the native peoples of Australasia and "civilization" has been highly "problematic." I think that from a cost vs. benefit standpoint targeting descendants of Aboriginal groups is perhaps a better bet, community groups can't make a strong argument that they have a right to decide whether someone gives genetic material or not. I'd honestly be curious to hear what John Hawks thinks, seeing as he's an anthropologist and so has presumably thought this issue through to some extent.


Romney on evolution   posted by Razib @ 5/11/2007 09:49:00 AM

Mitt Romney elaborates his position on evolution. Here's the thing: some are wondering if this will hurt Romney with evangelicals. But imagine the opposite, what if he pandered to Creationism? Well, perhaps someone would have asked how he could believe in the evolution of humans into gods while rejecting evolution as a general process! I know, low blow, but an elite scorned might go there. After all, Jacob Weisberg has elucidated one strain of elite thinking which declares honestly that believing in stuff made up thousands of years ago is less egregious than believing in stuff made up hundreds of years ago.

P.S. you can watch all four hours of PBS' The Mormons online.


Terror from the skies....   posted by Razib @ 5/11/2007 09:21:00 AM

When I saw this picture taken from the California fires I couldn't but help thinking about Mt. Vesuvius.


Thursday, May 10, 2007

Neutral origins of complexity?   posted by p-ter @ 5/10/2007 06:31:00 PM

Reading an agressively-stated scientific opinion is an acquired taste-- in published work, academics prefer to subtly hint that their colleague is ass, rather than just saying it directly like we do here on the internets. But when one is used to the dry writing of the scientific research articles, those subtle (or sometimes not so subtle) digs come to be rather enjoyable.

Which is why I enjoyed this piece by Michael Lynch [pdf], just published in PNAS. Dr. Lynch has long been an advocate for taking population genetics forces into account when studying genome evolution and innovation, and here he makes his case:
Although the basic theoretical foundation for understanding the mechanisms of evolution, the field of population genetics, has long been in place, the central significance of this framework is still occasionally questioned, as exemplified in this quote from Carroll (4), "Since the Modern Synthesis, most expositions of the evolutionary process have focused on microevolutionary mechanisms. Millions of biology students have been taught the view (from population genetics) that 'evolution is change in gene frequencies.' Isn't that an inspiring theme? This view forces the explanation toward mathematics and abstract descriptions of genes, and away from butterflies and zebras. . . The evolution of form is the main drama of life's story, both as found in the fossil record and in the diversity of living species. So, let's teach that story. Instead of 'change in gene frequencies,' let's try 'evolution of form is change in development'." Even ignoring the fact that most species are unicellular and differentiated mainly by metabolic features, this statement illustrates two fundamental misunderstandings. Evolutionary biology is not a story-telling exercise, and the goal of population genetics is not to be inspiring, but to be explanatory.
His argument is that many of the features of the eukaryotic cell, often assumed to be products of adaptations, may be largely the result of deleterious fixations due to a much smaller eukaryotic effective population size. It remains unclear how these features-- introns, large genomes, some aspects of gene regulation-- came to arise given their apparent costs. According to Lynch, population genetics provides a simple framework for testing neutral versus adaptive hypothesis on this subject (he favors neutral explanations). This has been largely ignored due to, well, the fact that math is hard:
The field of population genetics is technically demanding, and it is well known that most biologists abhor all things mathematical. However, the details do matter in the field of evolutionary biology.
Overall, he presents a sort of neutral theory of genome evolution, or at least the beginnings of one. And I must admit I'm intrigued by this possibility that "a long-term synergism may exist between nonadaptive evolution at the DNA level and adaptive evolution on the phenotypic level".

Some possibile examples of this: one of the current roles of the nuclear membrane is to segregate the actions of transcription from those of translation so that introns can be spliced out before a protein is made. It's an interesting hypothesis, then, that the nuclear membrane itself (one of the defining hallmarks of a eukaryotic cell) evolved in response to the existence of introns. Lynch cites another paper arguing that the nonsense-mediated decay pathway could also have evolved to prevent the translation of transcripts resulting from splicing errors. Finally, I've also heard much speculation that many of the regulatory mechanisms we take for granted-- methylation, histone modifications, etc.-- could have evolved to silence selfish DNA elements before taking on the broader roles they play today.

Sewall Wright put much emphasis on the role of genetic drift in allowing the evolutionary process to cross regions of low fitess to find other adaptive peaks. Maybe early population geneticists really did discover everything worth knowing about evolution.

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Long distance migration....   posted by Razib @ 5/10/2007 05:33:00 PM

I've been having a correspondence with a reader about phylogeographic issues, and one thing that I told him was that I think he underestimates the possibility of long distance travel for steppe peoples. It may be correct that in pre-modern times that "most people did not move more than 10 miles from where they were born." I also believe that it is likely correct that the size of "barbarian hordes" was relatively small in proportion to the local peasant population which they ruled after the fall of Rome. But, none of this negates the possibility that in particular circumstances long distance travel and migration did occur. Obviously living a world where European descended peoples dominate North American, Australasia and are non-trivial presences in South America, we are aware that such migrations do occur. But even 4,000 years ago, a man born in what is today Switzerland found himself buried at Stonehenge! Though the expectation of travel was low in pre-modern times, there was a variance. I think one illustration of this can be the Alan peoples. Today the remnants of this Iranian speaking ethnic group reside in the North Caucasus region as the Ossetes. 2,000 years ago their precursors as the Alans were part of the Sarmatian hordes which battled the Roman Empire. In the 4th century some were driven forward from the plains of Pannonia (Hungary) and they eventually settled parts of France as Roman federates. Others became the dominant power in early 5th century Spain, but after their defeat at the hands of Roman armies they were absorbed by the Vandal monarchy. When the Vandals set up their kingdom based out of Carthage in modern Tunisia the Alans were still a distinctive part of their nation. The rulers of North Africa were the "kings of the Vandals and Alans" up until their conquest in the early 6th century. Another portion of the Alan peoples roamed the West Eurasian steppes (between the Carpathian mountains and the Volga). These eventually gave rise to the Ossetes. But, interestingly, I read once that there were Christian priests in the Mongol capital in the 13th century because there were Alans who served the Khan. So here you have an ethnic group whose members have spanned the World Island, from Tunisia to China.

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Wednesday, May 09, 2007

Infidelity around the world....   posted by Razib @ 5/09/2007 09:42:00 PM

Update: I forgot a major note, the data below refers to extramarital relationships within the past year. Specifically, a sexual partner not your spouse.

I got Lust in Translation: The Rules of Infidelity from Tokyo to Tennessee, a few weeks ago. It's a pretty fluffy book that really doesn't have much meat. But, there was a nice collation of world wide data (that is available) on infidelity. I've reproduced it below the fold. Note: if you are going to comment, please don't analyze one particular data point, the regional trends are what you need to look at. This data is merged from a host of different surveys and obviously isn't entirely representative nationally.

Togo (1998)37.00.5
Cameroon (2004)36.54.4
Ivory Coast (1998)36.11.9
Mozambique (2003)28.93.1
Tanzania (2005)27.62.6
Niger (1998)27.20.1
Haiti (2000)25.40.8
Benin (2001)23.40.6
Zambia (2002)22.61.5
Mali (2001)22.40.7
Uganda (2001)22.31.2
Burkina Faso (2003)20.10.5
Chad (2004)19.90.7
China urban (2000)18.33.2
Dominican Republican (2002)18.00.8
Malawi (2000)16.30.5
Nigeria (2003)15.20.6
Mexico City (2001)15.0n/a
Zimbabwe (1999)13.80.7
Peru (1996)13.50.1
Ghana (2003)13.00.4
Namibia (2000)13.01.2
Brazil (1996)12.00.8
Kenya (2003)11.51.6
Norway (1997)10.86.6
China ( 2000)10.5n/a
Great Britain****9.35.1
Bolivia (2003)8.60.4
Ethiopia (2000)6.91
Armenia (2000)4.70.1
Philippines (2003)4.50
U.S.A. (2004)*3.93.1
France (2004)**3.82
Italy (1998)3.50.9
Rwanda (2000)3.20.1
Nepal (2001)3.00
Switzerland (1997)3.01.1
Australia (2002)2.51.8
Bangladesh (2004)1.6n/a
Kazakhstan (1999)1.60.9

* married only; ages 18 or older
** married only, ages 18.54
*** married and cohabitating, ages 16-44

Caveats? Well, obviously the differential between males & females needs to be explained. Some of it is a real outcome of the structure of societies. That is, males will marry later, and young women will enter into affairs with older men. In societies like Russia and parts of Africa there is a large imbalance in the sex ratio as one goes north of 30, so males indulge in operational polygyny. Obviously this probably isn't the whole story, there are cultural expectations, and it seems likely that women will under-report infidelities more than males (in some cultures the author implies that males may actually exaggerate how unfaithful they are to prove their virility). Not only will women consciously lie, it seems possible that women will engage in more self-deception (because of cultural expectations). I had a female friend who didn't count a one night stand as infidelity because "it wasn't a relationship." In contrast, male acquaintances that engage in this sort of behavior not only count, but revel, in their additions to their head count.

Now, as for the rough geographic differences, what's going on here? Some of this again might be due to variations in the perception of the questions being asked and the survey methodology, but looking across nations some trends emerge. African countries seem to exhibit a lot more infidelity than, for example, Nepal or Bangladesh. Being who I am I know a bit about the culture of Bangladesh, and I will offer that Bangladeshi males are not faithful because of their moral fiber, rather, they have no opportunity. When transfered to a context where infidelity is a possibility, "nature takes its course." In Bangladesh the reality is that young women who enter into sexual relationships with older males outside of the bounds of marriage are simply not "respectable" (and very rare). Women are closely watched by their male kinfolk, it is a patrilineal and patrifocal society, and despite Islam, predominantly exogamous (i.e., wives are "strangers" in the houses of their husbands, surrounded by his relatives). Female honor is essential in a society where property is passed down through the male lineage. Additionally, males are the primary economic producers, being in evidence in the fields, while women are more likely to be found working within the home or in the matrix of the village of her husband (remember, women tend to move to the household of their husbands, and so that means that they are surrounded by her husband's relatives). In Africa the situation is different, garden based agriculture means women are much more independent economic players, and matrilineal inheritance means that paternity certainty is not so inextricably tied to transfers of wealth across the generations. If most of your wealth is coming from your mother and her family, your father's line is less relevant.

There is also another issue in Africa which I think needs be brought up: Christianity. I've just finished reading some material on the period in Europe between 500 and 1000, and one point to note is that it was rather difficult for Christian clergy of a Greco-Roman orientation to stamp out polygyny amongst elite males in "barbarian" societies. That is, the nobility of Ireland and Francia were commonly polygynous, even on high up to the Merovingian dynasty. Sometimes this tension between Christian priests and the rulers upon whose patronage they depended played out centuries after the introduction of Christianity. In Africa Christianity is generally less than a century old, with much of the conversion occurring within the last two generations. While the churches preach monogamy, in keeping with Christian models ultimately derived from the Greco-Roman precedent, elite males still tend to enter into operationally polygynous relationships. Because these males are often Christian (Christianity often correlates with high socioeconomic status, and so ability to support extra wives and mistresses) they do not solemnize their relationships with their "secondary" wives. So by definition, if not operation, these are extramarital relationships.


Notes on eugenics   posted by p-ter @ 5/09/2007 10:37:00 AM

PZ Myers is against forcibly sterilizing low-IQ people (or sending them into space). This is a brave, progressive position, and I applaud him for standing up to those who would have the underclass living off nothing but moon dust. However, his righteous argument makes an absolute butchery of much of population/quantitative genetics. Let's take two examples:

1. One issue at hand here is whether, should low-IQ people reproduce at a rate higher than high-IQ people, lower IQ could then evolve in humans. This should be self-evident, but perhaps must be spelled out more clearly.

What is necessary for a phenotype to evolve by natrual selection? Richard Lewontin, in 1970, set out the three requirements (I limit myself to considering the evolution of phenotypes; Lewontin considers the evolution of any "unit"). They are:

1. There must be phenotypic variability in the population.

2. The phenotypic variation must have fitness consequences.

3. The phenotype (and thus fitness) must be heritable.

IQ is obviously variable, there is an inverse relationship between IQ and fertility (for example), and heritability estimates for g are in the range of 60%. Thus, intelligence satisfies all the requirements for phenotypic evolution. Note that there is no claim made about the precise molecular machinery or genes underlying intelligence; this knowledge is irrelevant to the arguement-- as long as there is variability, heritability and selection, the breeder's equation will do the rest.

2. Another issue here is whether there are populations with different distributions of genetic variants underlying intelligence. Dr. Myers writes, "You'd be hard-pressed to argue that the diverse groups marked by ethnic and class distinctions in the U.S. even count as distinct populations in any biological sense. There are social barriers to breeding, but they are sufficiently porous that over the course of time needed to set up genetic differences that matter, they're negligible." This is absurd. Ethnic groups can be distringished based on genetic data alone (at least in the US, where this has been explicitly tested, and see also my longer post on the topic of race). And unless he doesn't consider things like hair color and skin color to be genetic, some genetic differences, at least, should be readily visible.

Different population groups have different distributions of intelligence, and different distributions of genetic variation genome-wide. True, the explicit connection between the two has not yet been made, but the study of human genetic variation is in its infancy. The genetic change underlying much of the variation in skin color between European and African populations, for example, was discovered less than two years ago. There is much to be learned, and not all of it will be palatable.

Unless one believes that biologically identity is required for political equality, this should not have any major political consequences. But knowledge of the genetics underlying "desirable" traits does raise the spectre of eugenics. Is this necessarily a bad thing?

As Razib has pointed out before the "new eugenics" will not take the heavy-handed route of forced sterilization or government coersion; it will likely be an entirely individually-pushed enterprise-- many parents would choose to give their children a boost of a couple IQ points if doing so were simple and painless. Dr. Myers seems to be a fan of Richard Dawkins, so I'll quote a couple paragraphs from him:
IN THE 1920s and 1930s, scientists from both the political left and right would not have found the idea of designer babies particularly dangerous - though of course they would not have used that phrase. Today, I suspect that the idea is too dangerous for comfortable discussion, and my conjecture is that Adolf Hitler is responsible for the change.

Nobody wants to be caught agreeing with that monster, even in a single particular. The spectre of Hitler has led some scientists to stray from "ought" to "is" and deny that breeding for human qualities is even possible. But if you can breed cattle for milk yield, horses for running speed, and dogs for herding skill, why on Earth should it be impossible to breed humans for mathematical, musical or athletic ability? Objections such as "these are not one-dimensional abilities" apply equally to cows, horses and dogs and never stopped anybody in practice.

I wonder whether, some 60 years after Hitler's death, we might at least venture to ask what the moral difference is between breeding for musical ability and forcing a child to take music lessons. Or why it is acceptable to train fast runners and high jumpers but not to breed them. I can think of some answers, and they are good ones, which would probably end up persuading me. But hasn't the time come when we should stop being frightened even to put the question?


Performance-enhancing alleles   posted by p-ter @ 5/09/2007 08:46:00 AM

Yann points to an article on a mutation in dogs that leads to increased muscle mass and speed:
Here we describe a new mutation in MSTN found in the whippet dog breed that results in a double-muscled phenotype known as the "bully" whippet. Individuals with this phenotype carry two copies of a two-base-pair deletion in the third exon of MSTN leading to a premature stop codon at amino acid 313. Individuals carrying only one copy of the mutation are, on average, more muscular than wild-type individuals (p = 7.43 × 10-6; Kruskal-Wallis Test) and are significantly faster than individuals carrying the wild-type genotype in competitive racing events (Kendall's nonparametric measure, τ = 0.3619; p ≈ 0.00028). These results highlight the utility of performance-enhancing polymorphisms, marking the first time a mutation in MSTN has been quantitatively linked to increased athletic performance.
The myostatin gene in humans plays a similar role in muscle growth-- a deletion in the gene leads to extreme muscularity, as evidenced by the "Baby Superman". The gene has also been shown to be under recent selection in humans--variants presumed to lead to more muscularity are far more common in Sub-Saharan Africa. This paper in dogs shows that increased muscularity also leads to better performance in competititve racing events; it's not such a strech to believe the same could be true in humans as well.

Tuesday, May 08, 2007

Really ancient morphs?   posted by Razib @ 5/08/2007 11:59:00 PM

A few years ago Henry Harpending & Greg Cochran published In our genes in PNAS. They focused on the D4 dopamine receptor (DRD4) locus as "a model system for understanding the relationship between genetic variation and human cultural diversity." Check this out, Drd4 gene polymorphisms are associated with personality variation in a passerine bird:
Polymorphisms in several neurotransmitter-associated genes have been associated with variation in human personality traits. Among the more promising of such associations is that between the human dopamine receptor D4 gene (Drd4) variants and novelty-seeking behaviour....Frequencies of the three Drd4 SNP830 genotypes, but not the ID15 genotypes, differed significantly between two P. major lines selected over four generations for divergent levels of 'early exploratory behaviour' (EEB). Strong corroborating evidence for the significance of this finding comes from the analysis of free-living, unselected birds where we found a significant association between SNP830 genotypes and differing mean EEB levels. These findings suggest that an association between Drd4 gene polymorphisms and animal personality variation predates the divergence of the avian and mammalian lineages. Furthermore, this work heralds the possibility of following microevolutionary changes in frequencies of behaviourally relevant Drd4 polymorphisms within populations where natural selection acts differentially on different personality types.


Nice 'N Slow: how to make more GCN4   posted by amnestic @ 5/08/2007 08:58:00 PM

Let me take you to a place nice and quiet. There ain't no one there to interrupt. Ain't gotta rush. I just wanna take it nice and slow. - US-HER RA-YM-OND

I just summarized in a previous post how eIF2alpha kinases can reduce the amount of a crucial resource needed for initiation of protein synthesis, namely eIF2-GTP. There are four well-characterized eIF2alpha kinases: PKR, PERK, GCN2 and HRI. I was previously a little vague in my characterization of the inducing conditions for this pathway. The four kinases are activated by double-stranded RNA (representing viral infection), ER stress (i.e. protein misfolding), amino acid starvation, and low heme (iron scarcity), respectively. Regardless of the specific cause, the general effect is to suppress protein synthesis cell-wide while the cell deals with some perturbation. Still, for the cell to go about the business of handling its biz, it has to make a few key proteins. Indeed, it might even want to make more of these proteins than it was making before.

By far, the most heavily studied of these pathways is the GCN2 response to amino acid starvation. Recall that proteins are a string of amino acids. The secret decoder ring to translate the language of nucleotides into that of amino acids is the transfer RNA (tRNA). Transfer RNAs usually have a triplet of nucleotides at one end and an amino acid at the other, like an adapter. If a cell is low on amino acids, tRNAs might get made with on amino acid on the other end. if GCN2 finds out this type of tomfoolery has been going on it brings the hammer down and phosphorylates eIF2alpha, putting a large restraint on protein synthesis. That's all well and good; it's like putting your state under martial law for a minute during a crisis. It's not enough though because if the authoritarian GCN2 regime just repressed every attempt to get a message out, the cell would lose its vitality. Instead, the global repression of protein synthesis has an immediate positive effect: GCN4 synthesis increases. GCN4 is a transcription factor and can thus affect exactly which types of programs the cell is putting its resources toward. GCN4 is a practical transcription factor. Given the situation of amino acid shortages, and it drives the cell to produce more genes in the amino acid biosynthesis pathway.

So how can GCN4 escape the crackdown and curry the favor of the ribosomes? The answer lies in the first ~600 nucleotides of the mRNA coding for GCN4. The sequences in this area, called the 5' untranslated region, allow GCN4 to play it kind of coy with the ribosome. If the ribosome gets things started with GCN4 mRNA, it might get to keep going for a little bit, but it eventually hits roadblocks. The only way for a ribosome to get to the main task of really translating GCN4 is to take it nice and slow and sometimes skip opportunities to make a move. You may not know about the primary structure of mRNAs though, so let's take a brief look.

The main thing to note is that I am an artistic genius. After that, you can note that the whole RNA doesn't code for protein. There are big chunks that hang off the 5' and 3' ends of the protein-coding region (AKA the open reading frame). 5' and 3' refer to specific features of nucleic acid structures, but all you need to know is that ribosomes read from 5' to 3', and since we speak American around here, we will put the 5' end on the left. To initiate translation the ribosome assembles with several other factors including eIF2-GTP at the very 5' end of the mRNA. There is a structure here called the 5' cap that is recognized by the initiation complex. The assembled ribosome et alia start scanning the mRNA from 5' to 3'. As it moves from left to right it will first encounter the 5' untranslated region (UTR). The 5'UTR is made up of nucleotides, but the ribosome does not translate them into amino acids yet. The signal for a ribosome to start translating the genetic code and creating a new protein is a Start Codon. Start codons have the sequence AUG. The scanning ribosome carries a tRNA with it (called the initiator tRNA) that can base-pair with AUG and which carries the amino acid, methionine, on the other end. I don't want to get involved with the mechanism for adding amino acids onto the chain. Suffice it to say that the once the ribosome "opens" a "reading frame" it reads the nucleotide code triplet by triplet and builds a protein. The final feature of the open reading frame is the Stop Codon. There are three nucleotide triplets that do not code for any amino acid. When the ribosome reaches these, it usually pauses for a while and then stops making proteins. I would've said that it falls off, but I am about to describe a process that depends on it continuing along in the 3' direction. The last two features of your average mRNA are not of great importance to the current discussion. They are the 3' UTR (more nucleotides not coding for proteins) and the polyA tail. The polyA tail promotes translation and RNA stability.

So to be very clear: an Open Reading Frame (ORF) is the part of the RNA that a ribosome actually reads between the Start and Stop codons. The role of eIF2-GTP is to bring the initiator tRNA to the ribosome, so that it can be used as soon as the ribosome finds a Start Codon. When the peptide is started, the eIF2-GTP is used up, and if that ribosome wants to start any other peptides, it has to have a new eIF2-GTP.

Now imagine that I lied to you about 5' UTRs. You don't have to imagine very hard. There are quite a few 5' UTRs that contain open reading frames. They just aren't the main course as it were. They are called upstream open reading frames (uORFs). A ribosome can start at the cap, read an uORF and synthesize a short protein, and then scan further down the mRNA to the real ORF. GCN4 mRNA, for instance, has four uORFs before the ORF that codes for the GCN4 protein. If you artificially construct a GCN4 mRNA that lacks these uORFs, you get a lot more GCN4 protein. The uORFs thus have the effect of inhibiting translation of the downstream ORF under normal conditions. Many of the experiments detailing the 5' UTR pretty much ignore the middle uORFs and focus on uORF1 and uORF4 because these seem to be enough to get eIF2 kinase dependent expression.

The ribosome always reads uORF1 first because that's what it encounters first during scanning. Under normal conditions, it is reloaded with eIF2-GTP and an initiator tRNA relatively rapidly and it can read ORF4. ORF 4 is a hangup. It causes the ribosome to tarry right at the end. This is partially because its last amino acid is proline, which is relatively rare and difficult to find, so the ribosome is losing momentum by the time it reaches the end of ORF4. As it tries to scan even further down to the GCN4 ORF, it encounters a little more opposition, throws up its hands, and dissociates from the mRNA. As a result, we get no GCN4. The magic of eIF2 kinases is that they reduce the availability of eIF2-GTP and thus delay re-initiation after translation of uORF1. If the ribosome takes just a little bit longer to be ready again, it an skip ORF4. See? Isn't that cool? If it only reads ORF1 and takes its sweet time getting ready it can get all the way to the GCN4 start codon. In this way, GCN4 protein is increased while translation of the majority of other mRNAs is inhibited.

The protein of interest in Costa-Mattioli et al is not GCN4, but it has a similar mechanism. Next I hope to describe some of the experiments one has to do to discover that an mRNA is controlled in this manner. I will focus on the articles that showed that the production of ATF4 protein is regulated by eIF2 kinases in mammalian cells.

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Egg protection   posted by Razib @ 5/08/2007 03:19:00 PM

Evidence of Amino Acid Diversity - Enhancing Selection within Humans and among Primates at the Candidate Sperm-Receptor Gene PKDREJ:
Sperm-egg interaction is a crucial step in fertilization, yet the identity of most interacting sperm-egg proteins that mediate this process remains elusive. Rapid evolution of some fertilization proteins has been observed in a number of species, including evidence of positive selection in the evolution of components of the mammalian egg coat. The rapid evolution of the egg-coat proteins could strongly select for changes on the sperm receptor, to maintain the interaction. Here, we present evidence that positive selection has driven the evolution of PKDREJ, a candidate sperm receptor of mammalian egg-coat proteins. We sequenced PKDREJ from a panel of 14 primates, including humans, and conducted a comparative maximum-likelihood analysis of nucleotide changes and found evidence of positive selection. An additional panel of 48 humans was surveyed for nucleotide polymorphisms at the PKDREJ locus. The regions predicted to have been subject to adaptive evolution among primates show several amino acid polymorphisms within humans. The distribution of polymorphisms suggests that balancing selection may maintain diverse PKDREJ alleles in some populations. It remains unknown whether there are functional differences associated with these diverse alleles, but their existence could have consequences for human fertility.

To my understanding this sort of barrier between sperm & egg is a variant of prezygotic isolation, a gene flow barrier which crystallizes speciation. If I read their last sentence correctly it seems that the researchers are implying that polymorphism in regards to this character might be a source of reduced fertility between some individuals because of the gametic incompatibilities.

Note: Sperm related genes are always a good target of adaptive evolution because of their proximal relationship to fitness. For example, Pervasive adaptive evolution in primate seminal proteins.

Related: Sperm competition.


Mendel's Garden #14   posted by Razib @ 5/08/2007 10:07:00 AM

Is at Epigenetics News.


Monday, May 07, 2007

Humans rule! Chimps do not?   posted by Razib @ 5/07/2007 11:18:00 PM

So, I found this this strange press release in my RSS feed. Here's the important bit:
Gene sequencing revealed a mutation specific to humans that triggers a change in the splicing pattern of the neuropsin gene, creating a new splicing site and a longer protein. Introducing this mutation into chimpanzee DNA resulted in the creation of type II neuropsin. "Hence, the human-specific mutation is not only necessary but also sufficient in creating the novel splice form," the authors state.

The full article is titled Human-Specific Mutation Leads to the Origin of a Novel Splice Form of Neuropsin (KLK8), a Gene Involved in Learning and Memory, and it is in a journal called Human Mutation. There seems something really stilted in the English in the press release, and the claims feel way too grandiose, but I figure if there is a 1% chance this is accurate I'll throw up a post. Those of you with neuro chops will probably sniff out the crap earlier then I....


Female physical variation   posted by Razib @ 5/07/2007 07:15:00 PM

Most of the delegates for Miss Universe 2007 now have their profiles up. I don't have time right now to engage in any phenotypic analysis, but comments are welcome.


Human v. chimp: the evolutionary showdown   posted by p-ter @ 5/07/2007 06:04:00 PM

A recent paper on the relative number of genes that have undergone positive selection in chimps and humans recieved quite a bit of press (see Razib's comments here, here, and here). The title is quite provocative ("More genes underwent positive selection in chimpanzee evolution than in human evolution"), so I finally gave it a read. Frankly, if you haven't read it already, don't waste your time.

Let's grant the authors their starting position-- that there is a "common belief" that more genes have undergone positive selection in the human lineage than in the chimpanzee lineage (I would argue that this belief isn't all that widespead, though ultimately the reasons for the intiation of the study are irrelevant). In theory, addressing the veracity of this claim is easy-- make a list of the genes that have undergone positive selection along the human lineage, make a list of the genes that have undergone positive selection along the chimp lineage, and start counting. The devil, of course, is in the details.

Due to the fact that not every selected gene will leave a detectable signature, the major assumption of the authors' analysis, then, is that the fraction of detected selected genes along the human lineage is the same as the fraction of detected selected genes along the chimp lineage. That is, if the number of genes that have undergone positive selection in both lineages is the same, but 75% are detected in chimps and only 50% are detected in humans, one might erroneously conclude that more genes have undergone selection in chimps than in humans, while in truth the number of selected genes is the same. This, I will argue, is precisely the mistake made in this paper.

Let's take a look at how the authors identified genes that have undergone positive selection. The basis of the test is essentially the ratio of non-synonymous to synonymous changes in a given gene along a given lineage (non-synonymous changes alter the amino acid sequence of a protein and are presumed to be functional, while synonymous changes do not changes the sequence of a protein and provide a sort of background substitution rate). So if there is an excess of non-synonymous changes (a ratio > 1), one might conclude that the gene has been subject to positive selection. The power of this test to dectect selection is contingent on finding an excess of amino acid-changing substitutions in a lineage.

So what could alter said power? First, it's clear that a single selected site will alter the ratio only slightly, two selected sites will alter it a little more, three even more, etc. So the more selective fixations that occur in a gene, the more power the test will have to conclude for selection. On the other hand, take the number of synonymous substitutions-- if there are more of these, the levels of "noise" are elevated relative the levels of "signal", and there is lower power to conclude for selection.

There is a major difference between historical human and chimpanzee populations that alters the power of the test in the two lineages; indeed, the authors mention this difference without really grasping why it discounts their conclusions. That difference is population size. Humans have historically had a smaller effective population size than chimpanzees and, as the authors note, natural selection is more efficient in a larger population. Thus, advantageous alleles can be pushed to fixation with greater probability, while neutral or deleterious alleles are fixed at a lower rate. So smaller populations should have overall higher levels of substitution (assuming positively selected changes are a minority of all fixations). This is exactly what is seen in the data-- humans have 30,083 synonymous fixations and 19,000 non-synonymous fixations, while the numbers for chimp are 29,644 and 17,701, respectively.

These changes in the rates of allele fixations should lead to a weaker signal of selection in humans, and thus less power to detect it. It's no surprise, then, that the authors find less selected genes in humans than in chimps. Even if the number of selected genes were exactly the same, the relatively stronger signal of selection in chimps should produce exactly the same result. Perhaps the authors want to argue that fewer amino acid changes have been fixed by positive selection in humans than in chimps; this is what population genetics theory predicts, and may be true. However, to extrapolate from a number of amino acid changes to a number of genes is problematic; a single adaptive change in a gene could have major phenotypic consequences without being detected with the sorts of tests employed in this study.

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Australian Aborignals, a people that dwelt alone?   posted by Razib @ 5/07/2007 02:40:00 PM

Ancient Australians Were a People Apart. Money shot:
A team headed by Georgi Hudjashov of Tartu University in Estonia analyzed variation in the Y chromosome and mitochondrial DNA (mtDNA, which is inherited only from women) in several hundred people from Australia and New Guinea. By knowing the mutation rate of mtDNA and comparing Australian samples with those from Asian populations, the team ascertained that the Australian and New Guinean populations branched off from a parent population 50,000 years ago, and that no significant additions to the aboriginal Australian gene pool had been made until modern times. "Australia was colonized, then nobody else came," says co-author Peter Underhill of Stanford University in Palo Alto, California.

The study will be published in PNAS this week. The article notes that there seems to have been morphological evolution in Australia over the past 50,000 years (e.g., from gracile to robust). Some have adduced from this that waves of migration of disparate peoples. But, remember, phylogeny does not necessarily track morphology over evolutionary time scales. In Dragon Bone Hill two paleoanthropologists make the argument that the robust physique of Australian Aboriginals was a response to selective pressures derived from intercommunal melees (!?!?! You read that right!). Whatever the truth, I don't doubt that 50,000 years is long enough a time period that in situ selection upon extant genetic variation could reshape the modal morphology of populations. Additionally, we know that Australia was an not island ark totally separate from the rest of humanity, dingos were introduced within the last 10,000 years. It seems almost certain that the northern coast of Australia was occasionally visited by sailors from the Indonesian archipelago (for supplies such as water). Let's take at face value the results derived from these two neutral lineages and assume it is an accurate representation of total genome content in regards to ancestry. Explicitly, the vast majority of lines of ancestry of Australian Aboriginals today coalesce back to a founding population which reached the continent's shores 50,000 years ago. That does not negate the possibility that alleles may have crossed from the Eurasian mainland and so driven adaptive evolution amongst Australian populations. Just as they picked up the dingo from traditions of canine domestication originating in Eurasia, so Aboriginals may exhibit a non-ancestral genetic signature on many loci which are phenotypically salient.


Sunday, May 06, 2007

Ancient technology   posted by Razib @ 5/06/2007 11:04:00 PM

The New Yorker has an article on the Antikythera Mechanism.


Intro to stress-induced translation regulation   posted by amnestic @ 5/06/2007 01:57:00 PM

"Ya stressed out. Depressed out ya brain." - Baatin

I've been meaning to write about the Costa-Mattioli et al paper in the early April issue of Cell. It's got some very cool findings, but there is a lot of background to get on board. So maybe we can take a running start by covering some of their references and some basic biology. The basic idea is that some proteins are counterintuitively upregulated while the protein synthesis machinery is globally inhibited. The mechanism is pretty clever and it may be used in a relatively large number of eukaryotic mRNAs.

First off, just a little bit about the mechanism of translation. Of course you know the central dogma of genetics. DNA --transcription-> mRNA --translation-> protein. The mRNA is supposed to act an intermediary between the nucleus and the cytoplasm so the two worlds can communicate. An mRNA contains a nucleotide 'recipe' that is decoded by translation machines called ribosomes and a special type of RNAs called transfer RNAs (tRNAs). Numerous cofactors help the process of translation along at its various stages: initiation, elongation, termination, and release/recycling. In eukaryotes, these factors are named in a semi-organized system indicating which stage they have been implicated in. For instance, initiation factors are named eIFsomething for eukaryotic Initiation Factor X. You can't always trust nomenclature systems based on function though, because new knowledge renders the naming system inaccurate. For instance, new studies indicate a role for eEF1a in initiation of translation. I apologize for all the nomenclature, but the names are the names and we all have to live with it.

So I want to talk about a particular initiation factor, eIF2. There are three eIf2 subunits: alpha, beta, and gamma. We are going to pretend gamma doesn't exist. Alpha is crucial to the assembly of ribosomes on an mRNA. In its GTP-bound form, it is responsible for bringing the first amino acid for any given protein (which is always methionine) to the ribosome. As initiation actually occurs, the Guanidine TRI - phosphate is converted to Guanidine DI - phosphate (GDP) releasing energy and allowing the machine to change shapes in the necessary ways to start scootching down the mRNA reading codons. You have to have eIF2alpha-GTP to start synthesizing a new protein, and it is a resource that must be replenished with every round of translation initiation. The job of exchanging the GDP falls to eIF2beta.

All of that is the normal process carried out by cells day-to-day. Under a range of circumstances, cells will want to regulate the amount of new proteins being synthesized on a more-or-less global level. For instance, during viral infection it may be to the cell's advantage to reduce synthesis of new proteins and go into a more protective, stressed-out state. Also, if something in the protein folding process starts going haywire, the cell may want to slow down on creating new proteins until they can get the post-translational processing sorted out. These cellular stress states are communicated to the translation machinery by way of a group of enzymes called eIF2alpha kinases. They are capable of phosphorylating eIF2alpha. I'm not sure how many times I've explained what phosphorylation is, but you can think of it in basic terms as adding a reactive group to a protein to change its shape and electronegative characteristics. It is a very common way of 'throwing a switch' to activate or deactivate a given protein. A kinase, by definition, is an enzyme that phosphorylates other proteins.

EIF2alpha that has been phosphorylated becomes a qualitatively different protein. Rather than promoting translation initiation, it now acts as an inhibitor. It is still bound by eIF2beta, but eIF2beta can no longer load it up with a new GTP. Instead alpha sticks in its craw and ruins it even for other unphosphorylated alphas. The net effect is to reduce the amount of eIF2-GTP and thus the amount of ready-to-roll translation machines. The pathway to remember here is this:
Cellular Stressor -> Cellular Stress Response -> eIF2alpha Kinases -> eIF2alpha phosphorylation > eIF2beta inhibition -> reduced eIF2alpha-GTP -> globally reduced translation initiation.

This is a lot of names and a lot of pathways to get up on. In coming posts I hope to build on this knowledge to examine a specific type of mRNA that can circumvent this global translation reduction. In fact, certain mRNAs gain an advantage during cellular stress states. Generally these mRNAs code for proteins that are important for dealing with the stressor. Once we have the mechanism on board we will be at the very starting point for understanding the Costa-Mattioli paper I mentioned at the beginning. By the way, for our Spanish speaking audience, I think I found an interview with Costa-Mattioli en espanol. Three classes later I still don't know any spanish science terminology, so if anyone listens to it and I am entirely mistaken about the content, lemme know.

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Saturday, May 05, 2007

Nussbaum on brownland   posted by amnestic @ 5/05/2007 06:01:00 PM

I just listened to Martha Nussbaum's discussion of her new book, The Clash Within: Democracy, Religious Violence, and India's Future, on the Carnegie Council Podcast. Given that I know essentially nothing about India's history or politics I would be interested if any of the more informed cats around could critique or corroborate her assessment of the events surrounding the Gujarati riots of 2002. She uses these riots as a counter-example to the 'clash of civilizations' framework for understanding Islam. As Nussbaum paints it, in the riots, far right Hindu folks informed by a British ideal of masculinity killed and did all sorts of other horrible things to Muslims who were otherwise living peacefully side-by-side with other cultures. I'm currently suspicious of attempts to paint Muslims as oppressed (even though this goes against my guilty liberal inclinations) because I read this article in Commentary about how Muslim's in Europe don't really have it so bad off.

Oh, and I also thought it was interesting how she characterized Nehru's disdain for religion as problematic because he (and his party) lost the ability to use deep cultural symbols to connect with the public at large. In the context of the new Atheism and Hitch's new book, this example illustrates an unforeseen danger of strident atheism. If you're not willing to fill that void in your community's life, someone else with more pernicious aims might be willing to do so. Like Mr. Raymond says, "After tonight, don't leave your girl alone with me, true playa for real."


Conservatives & Darwin   posted by Razib @ 5/05/2007 09:45:00 AM

The New York Times has an article up about the recent AEI event (which you can watch online), Darwinism and Conservatism: Friends or Foes?. Let me reiterate what I've stated before, if you do a head count, "against Darwin or not?," the 1/3 of Americans who would self-label as "conservative" would mostly be against (see the opinions of white Evangelicals here). That being said, there does exist a "split" among elite conservatives. Humans have multiple affiliations and affinities, and Jonah Goldberg's embarrassment is comprehensible via his identity as a member of the East Coast Pundit Class. If you weight sentiment about Creationism, assign it a positive or negative value, and sum across all self-identified conservatives, I suspect the value would be much closer to 0 then you would have expected because of the shallowness of negative sentiment and the intensity of feeling from the elites.*

Related: TNR surveys conservative movers and shakers.

* And of course, no on really knows much about the process of evolution. It's more a cultural marker.


Friday, May 04, 2007

A different kind of SNP   posted by Razib @ 5/04/2007 05:08:00 PM

Apropos of David's post from earlier this week, Labor bites it! Sunday will likely be Sarko's....


Treatments for some Mendelian diseases in the works?   posted by p-ter @ 5/04/2007 09:58:00 AM

One of the most consistent complaints about medical genetics research is that it's great at finding the gene/genes underlying a disease, but finding the gene/genes doesn't necessarily lead to any sort of treatment. The genes for cystic fibrosis and Duchenne muscular dystrophy, for example, were both identified in the late '80s. Both remain uncured. In fact, the genes underlying a large number of so-called "Mendelian" diseases (named because they are essentually due to defects in a single gene, unlike "complex" or "multifactorial" diseases) were identified in a mad rush after the realization in 1980 that disease genes could be found without knowing anything a priori about a disease or its genetics. As far as I know, no treatments have come out of these studies.

But as they say, Rome was not built in a day. If the precise genetic defect underlying a disease can be indentified, someone will find a way to fix it, though it may take many years, new technologies, and a lot of luck. So it's heartening to see a report in this week's Nature on the identification of a compound that may one day be a treatment for disorders caused by nonsense mutations (mutations that cause a truncated protein). From the abstract:
Nonsense mutations promote premature translational termination and cause anywhere from 5-70% of the individual cases of most inherited diseases. Studies on nonsense-mediated cystic fibrosis have indicated that boosting specific protein synthesis from <1% to as little as 5% of normal levels may greatly reduce the severity or eliminate the principal manifestations of disease. To address the need for a drug capable of suppressing premature termination, we identified PTC124-a new chemical entity that selectively induces ribosomal readthrough of premature but not normal termination codons.
The selectivity of PTC124 for premature termination codons, its well characterized activity profile, oral bioavailability and pharmacological properties indicate that this drug may have broad clinical potential for the treatment of a large group of genetic disorders with limited or no therapeutic options.
Clinical trials have apparently been initiated; this is a story to watch.

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Thursday, May 03, 2007

Ideofact is back   posted by Razib @ 5/03/2007 09:47:00 PM

Every few months I check in on blogs which were around and active when GC & I first started back in 2002. Most of them remain inactive, but I just noticed that Bill Allison is back at Ideofact. If you didn't check him out the first time, swing by.


GOP candidates & evolution   posted by Razib @ 5/03/2007 08:54:00 PM

I don't follow politics, but I see via CNN that only 3 out of the 10 current GOP candidates reject evolution, Mike Huckabee, who is aiming for the social conservative vote, Tom Tancredo, a convert from Roman Catholicism to evangelical Christianity, and Sam Brownback, a convert from mainline Christianity to evangelical Christianity to Roman Catholicism who still attends Protestant services with his wife. So 7 out of 10 candidates for president from the party of choice of American theocrats accept evolution! What's going on here? I suspect this is reflecting SES & and the shallow roots of anti-evolutionary sentiment. In other words, I do believe that those who oppose evolutionary theory are sincere, but their attitude is simply a subsidiary of a host of positions which serve as notional markers for social conservatives. When push comes to shove cultural elites on the Right have generally balked at embracing Creationism, and this has been tolerated by the grassroots because it is a marginal issue. In contrast, 9 out of 10 candidates would not defend Roe vs. Wade, which suggests that opposition to abortion rights is a far deeper sentiment which elicits a stronger emotional valence.

Update: Jason Rosenhouse has a roundup of links. Jonah Goldberg says:
I know there are Intelligent Design fans among our readers, but I found the string of hands going up from candidates last night admitting they didn't believe in evolution to be more than a little dismaying. I'm sure they had very intelligent, nuanced, explanations. But that doesn't help that much as far as I'm concerned.

Clearly an out of touch Metrocon! Where's the love for democracy!

Meanwhile, Mike Huckabee clarifies. Pretty tepid a supporter of Creationism, he. Just goes to show a) the power of elites b) the lack of importance this issue for the grassroots, since he is focused on being the genuine conservative candidate.


Wednesday, May 02, 2007

Is fertility heritable?   posted by Razib @ 5/02/2007 06:24:00 PM

Correlation of Intergenerational Family Sizes Suggests a Genetic Component of Reproductive Fitness:
Reproductive fitness is a complex phenotype that is a direct measure of Darwinian selection. Estimation of the genetic contribution to this phenotype in human populations is confounded by within-family correlations of sociocultural, economic, and other nongenetic factors that influence family sizes. Here, we report an intergenerational correlation in reproductive success in the Hutterites, a human population that is relatively homogeneous with respect to sociocultural factors that influence fertility...We interpret these results as indicating a significant genetic component to reproductive fitness in the Hutterites.

The Hutterites are notoriously fecund, I wouldn't be surprised if recent, recent, human evolution is at work here....


Tuesday, May 01, 2007

Toxoplasma gondii's South American origins and its influence on culture   posted by agnostic @ 5/01/2007 11:03:00 PM

Would there have been a Goya without the Columbian Exchange?

It would require many volumes to catalogue the ways in which human gene flow from Iberia and Africa into South and Central America has affected the history of the New World, while at first blush the matter of human gene flow from the Americas into Iberia and Africa might merit little more than a book or two. However, humans are not the only living things whose genes might flow in one direction or another. A simple example is corn, which when introduced into Spain became a popular staple among peasants -- so much so that many were plagued by an epidemic of pellagra for relying solely on corn, which lacks niacin. But is it possible that gene flow of another sort might have affected European high culture? After all, when we think of the culture of Spain, we typically think of The Golden Age writers, Goya, Gaudi, Segovia -- not outbreaks of pellagra.

A short and freely available article
from last year in PNAS argues pretty persuasively that the pathogen Toxoplasma gondii, which has already been shown to affect human personality and culture, originated in pre-Columbian South America. The reasoning is simple: it is much more polymorphic at neutral sites within South America, and shows a striking lack of diversity elsewhere. The less diverse forms elsewhere likely reflect smaller founder populations that were carried away on European ships. (The same reasoning suggests that Africa is the ancestral homeland of human beings.) As the Europeans returned from their initial voyages to South America, they probably brought back with them infected cats and rats, as well as soil contaminated by cat feces. Because Iberia was an agricultural society with greater population density than pre-Columbian South America, T. gondii likely found much more ideal conditions for increasing its virulence, not to mention that European populations were innocent of its existence and so likely had no defenses. The authors argue that, from there, maritime travel spread the pathogen to the rest of the world.

As Razib mentioned in his review of the study that showed T. gondii's effect on human personality, the germ has somewhat different effects on men vs women. Since we're considering high culture, we need only concern ourselves with its effect on males. The short and skinny is that it raises levels of novelty-seeking and Neuroticism, a trait that measures how easy it is for a person to become emotionally worked up. One study by Cattell found that eminent researchers he interviewed tended to be more emotionally stable. For artists, though, you don't really need me to tell you that they tend to be emotionally excitable. Novelty-seeking is obviously important for both domains.

To return to the theme of genius germs, artists show a stronger bias toward being born during the Winter and Spring than scientists, which is consistent with the hypothesis that an early infection (more likely during the "flu season") starts the individual's personality off on a more Neurotic groove. So perhaps the flourishing of T. gondii among a virgin European population contributed to the explosion of artistic creativity that we see starting about the 17th Century. Greg Clark's new book, A Farewell to Alms, argues that the Industrial Revolution could not have happened far earlier than it did, in part because the English were simply not genetically prepared for it -- they were predisposed to abandon rather than conscientiousness. Maybe the same is true for artistic revolutions -- a population may have to wait for an outbreak of nuttiness in order to produce a Beethoven or a Goya. As the population adapts defenses against pathogens that affect personality, and as sanitary conditions improve, the frequency of bona fide weirdos diminishes, and what remains are faux iconoclasts like we see in Modern Art. Andy Warhol is a good example: his eccentricity was probably little more than an affectation.

The case of Western Classical music is particularly instructive, and anyone's theory of what produces artistic genius has to contend with this medium and time-frame. Unlike all other art forms, there is almost nothing of impressive value from "Ancient music" or even most Medieval music. There is a hint of sophisticated music during the Renaissance, and then suddenly there is an explosion during the Baroque, Classical, and Romantic eras -- after which there is a figure here or there who you might compare to a "mediocre" Baroque composer, but none you would comfortably rank alongside Bach. The early great works of the Baroque begin about the 1720s, and by the mid-1800s most of the rest of the Greats were dead; Wagner died toward the end of the 19th C., and most of the leading candidates for "Great 20th Century compositions" debuted before 1920. How can the near entirety of an artistic domain have been created within scarcely 200 years, burning out as abruptly as it caught fire?

I initially thought an epidemic of some infectious disease was likely, since there were plenty of outbreaks of cholera, typhoid, and others back then. Syphillis, maybe? That seems plausible at first, but that disease really does appear to make you quite nuts. If it were something less severe, but that still affected the brain and personality, it could have been the newly introduced T. gondii germ, which would have taken some time to reach Germany and France. England actually has quite low levels, despite Britons' reputation as cat-lovers, and they have never produced a composer on the level of any Continental -- and not because there was no demand for or encouragement of such music. When Haydn arrived in London, he was overwhelmed by how greatly he and other Continental composers were worshipped in England. The only composer of high eminence who can claim to be an Englishman was in fact a German import: Handel. The Scandinavian countries likewise were not principal actors during the great period of classical music; the population there is more spread out, and the climate is much colder, so T. gondii might have had a harder time causing epidemics there (current levels are also very low there). Iberia and Italy would have been struck early since they have more hospitable climates and have many ports that would have welcomed ships returning from the New World.

Surely there are many necessary conditions for artistic genius to flourish, and to reiterate the point of another post on extreme deviations, if one component is lacking, the entire edifice collapses. Before and after the great period of Western music, all of the other components may well have been in place, waiting for an outbreak of oddballness. These days, no one would allow a purposeful epidemic in the hopes that it might produce one Beethoven among the millions of other lives it would ruin, so we may have to just wait for something similar to happen naturally and hope that some good comes of it. Until then, if my conjecture is on the right track, those who treasure Western high culture may owe a debt of gratitude to an obscure South American parasite that we contract via infected cat shit.

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Untied Kingdom?   posted by DavidB @ 5/01/2007 05:06:00 AM

Today is the 300th anniversary of the Act of Union between England and Scotland. But many commentators doubt whether the Union will last another decade. I discuss some of the issues this raises below the fold.

First, will it happen? The immediate reason for expecting the breakup of the Union is that the Scottish National Party is likely to win the forthcoming elections to the devolved Scottish Parliament. The SNP will then have a mandate for a referendum on independence. The result of such a referendum is not a foregone conclusion. Much of the current support for the SNP is a protest vote against the ruling Labour Party, at both Edinburgh and Westminster. In opinion polls the majority of Scots do not want full independence. Before any referendum takes place, Tony Blair (a crypto-Scot) will be replaced as Prime Minister by Gordon Brown ( a Scot). But there is also likely to be a general election to the UK Parliament before any Scottish referendum. If the Conservatives under David Cameron (an Anglo-Scot) win the UK election, the secession of Scotland is almost inevitable. [Added on 2 May: This is probably an overstatement. Let's just say that a Conservative victory would greatly increase the pressure for independence. ] On the other hand, if Labour is re-elected, the Scots may be satisfied with something short of full independence. But this raises another intriguing possibility. If Labour wins the UK election, but only by virtue of a majority in Scotland and Wales, or with the support of the Liberal Democrats (led by Menzies Campbell, a Scot), there may be agitation for leaving the Union by England. [Added 2 May: This is also an overstatement. There would be agitation for more equitable treatment, rather than breaking up the Union.] Of course, there is nothing intrinsically wrong with the balance in a United Kingdom Parliament being tipped by Scottish or Welsh votes. It has happened several times in the past. But that was before devolution. The creation of the Scottish Parliament and the Welsh Assembly has given the Scots and Welsh a degree of self-government which is denied to the English. If the English find themselves governed by Scots and Welsh, whom they subsidise, but over whom they do not have reciprocal power, the sleeping dog of English nationalism may finally wake up. The West Lothian Question would be raised with a vengeance. But the outcome would probably not be independence but just some arrangement within the UK Parliament for purely English matters to be reserved for English MPs to decide.

Second, what about Wales and Northern Ireland? At present the Welsh seem much less enthusiastic for independence than the Scots. Support for Plaid Cymru is weak outside the Welsh-speaking areas. So I would bet against Welsh secession from the Union in the foreseeable future. Northern Ireland is a very different matter. I suspect that there will be some form of united Ireland within the next 15 years, regardless of what happens in Scotland. The flourishing economy in the Republic is one factor, but recent political realignments are equally important. The most startling political sight of the last year was that of the Reverend Ian Paisley laughing and joking with the Taoiseach in Dublin. The reality is that the progressive elements in Irish society and politics detest Sinn Fein almost as much as the Unionists do. So I would expect to see some kind of revised Irish Constitution - secularised and with safeguards for the North - that the majority of the Northern Irish can sign up to. And if both Scotland and Northern Ireland have left the United Kingdom, the remainder will surely need a new name. I suggest 'Kingdom of England and Wales', which abbreviates nicely to KEW.

Finally, is all this desirable? Viewing it from an English perspective, I don't care strongly either way (though I would care rather more in the event of the 'West Lothian' nightmare scenario). In politics, as in other matters, 'if it aint' broke, don't fix it'. I cannot see anything so badly wrong with the present system that a breakup of the Union is necessary as a remedy. Breakup would also involve a host of complications over international obligations, the EU, finance, the monarchy, and the armed forces. But I assume that these could be resolved without insuperable difficulties. In particular, I assume that Scotland, a united Ireland, and KEW (or whatever) would be members of the EU, so that free movement of goods, labour, and capital would continue. The loss of revenues from North Sea oil (asuming that these go mainly to Scotland) would be roughly balanced by the end of tax subsidies from England to Scotland. The economic effects of a breakup would therefore be modest.

Subject to these complications being dealt with, I think there would be considerable potential advantages for England. The centre of political gravity would shift towards the free-enterprise right, and both Labour and Conservatives would respond by reshaping their policies. But the greatest advantage might be psychological. With the end of the United Kingdom, we could draw a line under the errors of the post-war years, with their delusion of continuing great power status. We could stop pretending to be a world policeman, and reshape the armed forces for the purpose of national defence and internal security. The UK's nuclear weapons could be decommissioned or converted to a small, flexible, genuinely independent 'force de frappe' (i.e., not under de facto American control, like the present Trident system). [Added: The Bliar government characteristically refuses to give a straight answer to questions about whether Trident could be used without American agreement, from which I take it that the answer is 'No'.] We could stop apologising for the British Empire, which was as much Scottish and Irish as English anyway. We could pursue foreign, internal security, and immigration policies based on national self-interest. But I stress that these are only potential advantages, and they would depend on finding English politicians with balls, which have been in short supply in recent years.

Do girly names obstruct scientific progress?   posted by agnostic @ 5/01/2007 01:05:00 AM

Update: In the comments, Arosko has collected data contradicting the study's claims.

Via Omni-Brain, a press release is circulating wildly about a new study by David Figlio (an economist), which suggests that girls with more feminine-sounding names are less likely to pursue math and the sciences compared to girls with less feminine names.* First, let me admit that out of laziness I didn't read the press release in full and conjectured at Omni-Brain's blog that it might be an effect of genes (i.e., masculine parents giving their daughters masculine names plus masculine genes), but it's a twin study. Whenever I hear an argument of the form, "group X does / doesn't tend to do well in activity Y because of social expectations," my toes curl.**

There are several puzzling, unanswered questions, such as how exactly is the femininity of a girl's name measured? In languages with grammatical gender, there are regularities that allow you to predict better than chance if a word is masculine or feminine, but English doesn't have that. Then again, some sound sequences might be more frequent in male than female names, or something like that. But is there independent evidence that this something that ordinary people are sensitive to, enough to behave differently toward Abigail than Isabella? I don't think these are that hard to answer, and the metric may be perfectly sound.

The problem I want to focus on is more dull but potentially more damning: it may be that the "result" is not due to anything other than sampling error. The reason is that non-feminine names are not that popular, and therefore the variance in outcomes will be greater among Abigails than Elizabeths, due only to the much smaller sample size of the former. Below the fold is a graph showing the relationship between femininity of a name and its popularity.

The 15 names and their femininity scores are as reported at the end of the press release linked to at the beginning. To judge popularity, I entered the names into the HowManyOfMe search engine and rounded the figure to the nearest thousand. I couldn't search by sex, so for "Alex," this returned male as well as female names. Note that "Alex" is the full name, not the nickname, since "Elizabeth" is not reported as "Liz," for example. I went with the figure for "Alexandra" (that of "Alexis" was about the same), which is probably an upper-bound, again since it's unlikely to give a girl the full name Alex. As the graph shows, feminity is moderately correlated with its popularity, with r = +0.39 (r^2 = 0.15). That's not surprising if there really is something to the idea that some names are more feminine than others, and if parents in general don't want to give their daughters manly names.

Thus, the statements about girls with less-feminine names must be based on very small sample sizes, which we know would increase the variance in their outcomes. The same is true for the one outlier at the very-feminine end -- "Isabella" is the most feminine but least frequent, so pronouncements about Isabellas are premature. To be concrete, Figlio's study used 1000 twin pairs, or 2000 girls total. Based on the figures reported at HowManyOfMe, together with that site's estimate of the US population as 301,734,581 (the female half of which is ~150,867,000), I multiplied the population frequency of each name times the sample size of 2000 to see how many individuals of each name we might expect to see. True, there are probably age effects for frequency of names, but this at least gives a rough idea. We would expect to see 18.7 Elizabeths, 9.8 Jessicas, and 8.8 Annas (more feminine), but only 0.8 Alexs, 0.5 Abigails, and 3.8 Graces (less feminine). For the outlier of Isabella (more feminine), we'd expect 0.2.

Even if we partitioned the names into equivalence classes of femininity, it's still clear that the least-feminine group is going to be small, while the most-feminine group will be pretty big. Concretely, dividing the number of girls with a given name by the total number of girls with any name that was covered in the sample (rather than out of all girls), and multiplying this relative frequency by 2000 still gives us just 35 Alexs and Abigails combined, and 4 Isabellas, compared to 774 Elizabeths and Jessicas combined. Maybe girls with names as non-feminine as Abigail are more likely to pursue math because, just by chance, the handful of girls with such names in the sample happened to prefer science. The name Isabella is getting a lot of attention (it gets 4 mentions in the brief press release, apart from its entry in the list of names and their scores), but these conclusions must be based on 1 or 2 individuals at most. For what it's worth, in my 26 years, I've met one Isabella (and I lived in Barcelona for a year, where I should've met many more!), and she was struggling in and hated math. Why my anecdote isn't being given a megaphone, I don't know.

So, there are three take-home messages here. First, smaller sample sizes produce greater variance, which despite being taught in any statistics class is still not widely appreciated, as Howard Wainer illustrates in his essay "The Most Dangerous Equation". Second, since journalists in search of a juicy scoop and academics in search of recognition make a perfect pair to collude against public understanding, don't believe any popular press release about an unpublished study; delay judgment until the study becomes publicly available and you can inspect it yourself. And third, extra caution is probably wise when the academic is an economist writing about anything other than economics -- this isn't a credentialist turf-war, but just an observation that economics must be a hard way to earn fame, since economists are increasingly trying to invade other fields. That may or may not work out fine: physicists who invade typically do better than you'd expect for career-changers, but the track record for economists who invade is less impressive.

* This is another one of those studies that gets a lot of PR but hasn't yet been published (though it is at least in press at Journal of Human Resources). These episodes drive me nuts because while everyone is busy gossiping about them, we have to take the PR department's word for it that the interpretation is sound, but once the data are finally made public, everyone has stopped caring. This makes an easily broadcastable critique impossible. Obviously my critique is subject to this as well: maybe my complaints will prove baseless -- but I want to know. It's almost as obnoxious as the increasing trend toward publishing the data in online supplements, which often tell a more watered-down story than the headline and "Discussion" section of the article, but where most lay readers aren't going to bother to look. So, we'll have to really see what's up once the study comes out.

** Consider a trivial example: very physically attractive girls project femininity at least as much as do girls with very feminine names. And at least to judge anecdotally, they tend to go into more feminine careers like PR, advertising, and so on, rather than mathematics, sports, etc. Is this because they have succumbed to social expectations about what feminine women ought to do? Or did they just figure out that some niches are more tailored to feminine women than others, and rationally decided to play their strong suit?