Saturday, March 31, 2007

Spencer Wells interview   posted by p-ter @ 3/31/2007 04:28:00 PM

PLoS Genetics has published an interview with Spencer Wells of the Genographic project. A very good read.

Friday, March 30, 2007

Skin color & sexual dimorphism?   posted by Razib @ 3/30/2007 10:24:00 AM

Some new data to throw into the argument about the origin of light skin (it seems that dark skin obviously arose when we lost our fur, seeing as functional constraint is strong in dark-skinned populations and unexposed skin in our nearest primate relatives is pink). From Dienekes:
Women have lighter skin than men do across a wide range of populations, even on the unexposed skin of the upper inner arm, possibly because of sexual selection by men for lighter-skinned women. If this hypothesis is true, human skin color should become more sexually dimorphic with increasing distance from the equator, since sexual selection for lighter skin in women would be less constrained by natural selection for darker skin in both sexes. Yet when Madrigal and Kelly (2006) analyzed skin reflectance data from 53 different samples, they found that the most dimorphic human populations were actually those of medium skin color at medium latitudes.

Dienekes presents some values, and suggests that "In these data points it looks to me that Iranians and Kurds have the highest sexual dimorphism." I don't know what to make of that. Recall that sexual dimorphism often arises rather slowly as a genetically coded trait because obviously if you select for one sex at one end of the population range (sexual selection usually operates via male reproductive skew in most populations), their opposite sex offspring should also skew in that direction. A more complex genetic architecture which takes into account modifier genes on sex chromosomes (which will differ across sexes), or modulation via expression of sex hormones (which are dependent upon loci on those sex chromosomes ultimately, like SRY), seems necessary. Also, I was skimming through Nina Jablonski's Skin:A Natural History and on page 89 she states: " consistent observation is that women have lighter skin color than men. This is true for all indigenous peoples, even for those who are very dark-skinned, among whom such differences are not readily visible...." Jablonski's own hypothesis is presented in her paper The Evolution of Human Skin Color:
...the lighter skin pigmentation of females is needed to permit relatively greater UV light penetration of the integument for previtamin D3 synthesis. The extra calcium needs of females during pregnancy and lactation are met by increasing plasma concentrations of 1.25-dihydroxyvitamin D, which in turn enhances calcium absorption in the intestine....

Pregancy and lactation are critical periods which determine fitness. By focusing on this Jablonski gets a pretty good yield in terms of differential fecundity. She does not dismiss the importance of sexual selection as a secondary or subsequent factor in generating or heightening dimorphism. For the general interpopulation variation in skin color Jablonski focuses upon the balance between the need to prevent the breakdown of folate (due to UV) and produce enough vitamin D (also due to UV). She points to the Inuit as exceptions that prove the rule, insofar as their dark-skin is comprehensible because their diet is rich in vitamin D.

From the genomic perspective we know that the architecture varies by location for similar phenotypic outcomes in regards to skin color. Even if the locus where a derived allele emerges is the same across two populations to generate the same phenotype (or contribute to the overall effect), that allele is often different, suggesting an independent mutational event. I would not be surprised if varied selective forces end up shaping human skin color variation. Though the correlation between UV and skin color is pretty clear, that may simply be the first principle component, with other factors rounding out the variation....

Update: Just an additional thought: a lot of the genomic data suggests recent selective sweeps on some of the genes for light skin (e.g., a variation of MC1R in China, the SLC45A2 derived allele in Europe, etc.). I think this is a big weakness in the model proposed by Jablonski, after all, it isn't like humans just showed up in northern Eurasia within the last 10,000 years. So what gives? I suspect that the lack of variety in the diets of agricultural peoples is an important factor. In other words, the more varied diet of hunter-gatherers (or late Ice Age big game hunters) didn't necessitate skin lightening to increase Vitamin D synthesis. Or, there are other selective pressures which we don't know about.

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Thursday, March 29, 2007

The seeds of fundamentalism?   posted by Razib @ 3/29/2007 04:32:00 PM

In the discussion thread for the Ayaan Hirsi Ali post there was some mooting of the nature of Islamic fundamentalism. I think this story is illustrative of the issues at work that might surprise:
...Khan told him he first became attracted to radical Islam because the tradition he grew up with was forcing him into an arranged marriage. The radical Imams were offering him a way out.

"A lot of guys I know, actually, have become radicalized, or initially took the first steps towards learning more about Islam and their way of life as a result of them being tried to being forced to marry someone they don't want to marry," Butt tells Simon.

Of course "traditional" South Asian youth don't object to arranged marriages, it is those who are inculcated with "Western" values who tend to find them abhorrent in conception. The fact is that the folkways that immigrants from Third World countries bring with them aren't really appropriate for their new cultures, and so their children have to find their own way (I know whereof I speak!). Fundamentalist Islam rooted in the Salafist movement is a safety valve for many of these first generation immigrants because it is a modern creation. I don't want to get into the details of the origins of the Salafi movement, but the reality is that some of its early thinkers were actually quite liberal. The manner it which it mutated makes that seem a bizarre possibility, but it is as it is. My own personal experience is that my more "fundamentalist" relatives are amongst the most open to rejection cultural tradition, so long as that rejection can be grounded in Islamic principles. The malleability of such principles are, I believe, the root of the mutagenic nature of an ideology which presents itself as timeless, and yet is very much a sign of the times. Most immigrant youth do not have the orientation to become atheists whose individualistic self-absorption transcend deep group ties. That's why the emergence of more "liberal" Islams is essential. Some of that process is going on now as Muslims rework the meaning of their religion in a Western cultural context. But part of the dynamic also has to be from without, just as Western culture forced Jews to accommodate outside of the ghetto, and America denied the Roman Catholic Church any status but that of just another denomination amongst many, so we must get our heads out of the multicultural sand and delegitimatize the sense of entitlement that many "community leaders" of a reactionary bent have in the Muslim community (this is more true for our friends across the pond).


But don't they all look alike?   posted by Razib @ 3/29/2007 03:13:00 PM

A face you can trust?:
The Intopii computer firm of Helsinki, Finland, announced in February that it has installed software to help voters find candidates who look like them. Intopii is basing this idea on studies that suggest Finnish voters tend to select candidates who most resemble themselves....


Culture vs. genes   posted by Razib @ 3/29/2007 03:03:00 PM

From page 56 of Ancient Greece:
...Sometimes the colonists [that is, Greek founders of colonial settlements outside of Greece] enjoyed a friendly welcome from the local inhabitants where they settled; sometimes they had to fight to win land for their new community. Since colonizing expeditions were apparently usually all male, wives from the colonists had to be found among the locals, either through peaceful negotiation for violent kidnappings.

This is the second time I've seen a reference to the non-Greek women who were present at the founding of Greek colonial cities (from Naples to Syracuse in the West to Byzantium in the East). Pretty soon I'll have to dig into the scholarly literature. My interest is stimulated by the fact that I don't know of any aspects of these Greek colonies which were culturally non-Greek (though "in the know" can enlighten me!). That is, it seems that the fathers determined the culture of their children. Of course, later colonial males would have arrived, diluting the impact of the initial hybrid generations, but it seems quantitatively this would pale in comparison to the demographic expansion that the founders would have engaged in. Makes me wonder about the Rape of the Sabine Women. Another factor is of course our perception of the ancient world comes through texts filtered through the preconceptions of the authors, a lot of variation "on the ground" is being elided as common motifs are highlighted.


Lab courses & MRI & Neutral Theory   posted by Razib @ 3/29/2007 10:06:00 AM

RPM has a long post about the importance of lab courses (in response to a philosopher with some background in physics who suggests doing away with undergraduate lab courses) and Aziz points out that the father of magnetic resonance imaging has died.

Update: From the author of the original post (in the comments):
Actually, I don't advocate doing away with undergraduate labs. Undergraduate labs, done well, can be valuable and are essential in training undergraduate majors in the sciences. What I argue is that the attitude prevailing at many institutions that every or most theory classes needs a corresponding lab keeps science departments from being able to teach classes that would be of great value to students, especially non-majors.

Update II: Also, I'd be remiss in not pointing to RPM's excellent intro post to Neutral Theory (check out the graphs!).


INFIDEL, by Ayaan Hirsi Ali   posted by Diana @ 3/29/2007 07:53:00 AM

Note from Razib: This discussion thread will be heavily moderated. If you're not going to be interesting, be banal and polite. Otherwise, be interesting. My point in Islam threads isn't to sit there listening to self-important prigs repeat the same talking points I've heard since 9/11. Been there, done that (myself). Let's add some value.
End Note

Reviewers of Hirsi Ali's autobiography, Infidel, should be required to put relevant cards on the table. Accordingly, here are mine: I am a reluctant atheist, which I mean that I wish I could believe in some comforting suprapersonal code, but I don't (and I have a particular contempt for the latterday "god of the gaps"); that said, I am nervous about and wary of Islam finding a beachhead in the West, even as I reject anguished warnings of the immanence of Eurabia and creeping dhimmitude.

Also, I had no particular interest in reading Hirsi Ali's book. (Parenthetically, I knew of her long before the Theo Van Gogh murder, and it occurred to me when I first heard of her and apprehended her striking physical presence, that she would eventually end up in the United States. I did not, of course, foresee the terrible events that precipitated her move, but I suspected that Holland was simply too small a country to contain her.) I have so far been unimpressed by the intellectual calibre of other Muslim critics. They have zero credibility in the Muslim world and their criticisms of Islam may be valid but the only noteworthy thing about them is that they are undergoing enlightenment two centuries after it became unremarkable in the West. I sympathize, but for my crowd, the thrill is gone.

What sparked my interest in reading Hirsi Ali's was a fierce irritation at the constant references to religion in American public life since 9/11. This was bad enough when the hectoring came from the right, but now it's coming from the left. I could and did ignore the Baptist who said that god doesn't hear the prayers of a Jew, because he's a hick that no one in the cultural elite, among whom I live and work, takes seriously. I don't pray and I don't care. I scorned the leftists who brandished this nobody in my face as an example of the horrors of American anti-Semitism, when it was nothing of the sort.

Now these same people go on Air America to tell the world that Jesus was a leftist (no links, but I heard it) and they supply ludicrous, a-historical examples to prove their non-existent case. This "who can be more sanctimonious" religious competition is driving me crazy, but it has had the salutary effect of clarifying my attitudes. So I paid renewed attention to this literal firebrand. I wanted to see if I could learn anything from her book than the fact that another smart girl grew up and left god-as-daddy with her dolls.

I did. Ayaan Hirsi Ali, I am pleased to report, is a much more interesting, deep (and flawed, like all heroic figures) person than any collection of newspaper reports can convey. Those looking for a simple "I hate Islam" manifesto will be disappointed by Infidel. The book -- which should more properly be called "Apostate"-- is a calm, lucid, balanced account of a nightmarish upbringing. She wasn't really raised, as Westerners understand it, she just grew taller while being dragged around to various third world hellholes (Saudi Arabia, Ethiopia, and then Nairobi), due to her father's clan-based opposition to Somali dictator Siad Barre. Hirsi Ali's mother, grandmother, older brother and younger sister existed on charity doled out by her father's clan members. Hirsi Ali watched her once-vibrant and enterprising mother become distorted with bitterness, subjecting Hirsi Ali's to routine beatings, while turning her outwardly docile middle child into the family drudge.

It is revealing that Ayaan Hirsi Ali divides her autobiography into two parts, entitled "My Childhood," and "My Freedom." The animating force of her life is to tell the world that Islam is essentially infantilizing. The first half of the book, which encompasses the first 22 years of her life, is riveting reading. She describes the ideal of Somali womanwood: to be baarri, whose closest approximation in English would be virtue: "If you are a Somali woman you must learn to tell yourself that God is just and all-knowing and will reward you in the Hereafter." Hirsi Ali explains: "If her husband is cruel, if he rapes her and then taunts her about it, if he decides to take another wife, or beats her, she lowers her gaze and hides her tears. And she works, faultlessly."

Have you ever wondered about the bewildering complexity of Somalia's clan structure? This is the book for you. Somali life, as she describes it, consists of complete, utter, subservience to family and clan, yet it is pervaded by suspicion and violence. When she is a little girl, her one-year older brother pushes her into a shit-filled latrine. And whose fault is it? Ayaan's, because she failed to be suspicious. It's a world where feelings are considered weakness, and pride is everything.

No review can do justice to how crowded with incident and packed with colorful, fantastic characters the first half of the book is. She is moved from Saudi Arabia to Ethiopia to a series of dwellings in Nairobi. She and her younger sister are gentially mutilated by their nomad-born grandmother. She learns Arabic, Amharic, English and Swahili. She becomes infatuated with Islamic fundamentalism but describes the process as so natural we never question its inevitability. A crazed Quran teacher shoves her head against a wall and fractures her skull; the hospital costs are covered by (what else?) the clan. Other wandering preachers of Islam drift in and out of the exile Somali community. She elopes with a gorgeous cousin strictly for the sex; they ditch each other quickly and figure out a way to "unmarry" each other. (Hint: the clan works out the details.) She rescues family members streaming out of Mogadishu by bribing Kenyan border police. This is all portrayed expertly, with deft omissions (to keep the story in control; whole books could be written about the era of African history she witnessed), swift pacing, and tight narrative.

The amount of human suffering that Hirsi Ali witnesses in Africa is sometimes overwhelming, and one wonders whether the second part of the book doesn't show evidence of some post-traumatic stress disorder. As Ian Buruma points out, her account of Dutch life is a bit too pat, too admiring. But should we not empathize with Hirsi Ali? after living the life she has, and witnessing what she has, Holland is a paradise. But, as she herself points out, it's a hard-won paradise, created by centuries of conflict between Catholic and Protestant, reclaimed from the sea. Her Dutch experience sounds reported and not fully lived, as her life in Africa was. (Perhaps this is true of the difference between life in Africa and life in Europe and has nothing to do with Hirsi Ali's specific experience -- I report, you decide.)

In Holland, Hirsi Ali committed two signal mistakes. The first was that she fabricated the reasons for claiming asylum in Holland. The fabrications were minor and were common knowledge, but her status could and should have been legally regularized before she stood for Parliament. More seriously, Hirsi Ali's collaboration with Theo Van Gogh on Submission occurred after she was elected to Parliament. Van Gogh's November 2004 murder was not her fault, but Hirsi Ali was a public servant at the time, and would have done her cause of protecting Muslim women greater service by focusing on the passage of laws to protect them, than by auditioning to be the Karen Finlay/Andres Serrano of Holland. These judgement mistakes made her vulnerable to a Swift Boat slandering on a Dutch television show from which her reputation suffered. Family members denied that Hirsi Ali was forced into an arranged marriage and was not genitally mutilated. These slanders continue to be retailed in the Muslim blogosphere and are thoroughly and convincingly refuted in the book. No one who reads the description of her mutilation can doubt that she experienced this horrific abuse; her detailing of the arranged marriage is as watertight as the grass jugs her grandmother used to weave by hand.

Hirsi Ali isn't the first prophet to experience dishonor in her country. What she can do to modernize and moderate Islam is doubtful, as she is now by public profession no more a part of the Ummah. She's our girl now and part of our furious debate about how to get along with Islam. The same neoconservatives whose chief guru cynically valued religion as social control for dummies have insincerely gushed over her book not because she has embraced enlightenment, but because she has rejected Islam.

Hirsi Ali thinks the West is falling apart. I disagree: we've never had it so good, and it's getting better all the time. She thinks that Muslims will destroy the West with higher birthrates: I doubt this. Pim Fortuyn favored a Cold War with Islam. I don't think that's necessary.

However, Fortuyn also said, "I don't want to fight for the rights of women and homosexuals again," and that, I think, is the heart of the issue, although I wouldn't put it that way. Here's how I would put it: "the law of the land is the law." Those of you who wish to keep your youth Muslim and live in the West must figure out a way to reconcile Islam with the dominant culture. If you can't, expect more Hirsi Alis. In fact, expect more Hirsi Alis even if you do -- it's the price of the ticket. The stupid among your children will be seduced by bling; the brilliant, by science.

And, unlike the chicken littles of the Right blogosphere, I think that is exactly what we are saying, if rather mumblingly, hesitantly and stammeringly. Sometimes, it's not way you say, it's what you do. That Puerto Rican girl on the subway isn't exchanging her t-shirt that says, "I must, I must, I must improve my bust," for a burqa. Our industrialists and molecular biologists and physicists aren't going to stop thinking and innovating and creating. They are an army much more powerful than the Quran, yes. We will insist, acidly, on our freedoms, on our laws, on our science, and our crummy t-shirts. If the Muslims in our midst can't handle it, that's their problem. The fact that Hirsi Ali needs bodyguards is disgusting and unacceptable but it is evidence of Islam's fragility, not our weakness.

Finally, we will protect the apostates from Islam who come to our free societies for refuge. If Hirsi Ali has helped us to focus our minds on that task, she deserves our gratitude.

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Darwin's Origin: the Variorum Edition   posted by DavidB @ 3/29/2007 07:27:00 AM

In 1959, 100 years after the publication of the first edition of Darwin's The Origin of Species, the University of Pennsylvania Press published a 'Variorum Text', edited by Morse Peckham, containing all the variants in the six editions published during Darwin's lifetime. Anyone who reads historical studies of Darwin's work will have seen references to the Variorum edition, but the book itself has been out of print and virtually unobtainable for many years. I have occasionally seen it in bookdealers' lists at a price of hundreds of pounds or dollars, but even my enthusiasm for Darwin doesn't run quite that far.

It is therefore a pleasure to report that it has recently been republished in paperback:

Charles Darwin: The Origin of Species: A Variorum Text, edited by Morse Peckham, University of Pennsylvania Press, Philadelphia, 816 pages.

The price is about $30 in the US or £20 in the UK.

I can recommend the book to anyone who wants to make a serious study of the Origin. Let me be clear: it is not a suitable edition for anyone who just wants a reading copy. For this purpose, the text of the first or the sixth editions, both of which are easily available, would be more convenient. The layout of Peckham's Variorum edition is unusual. Each sentence of the first edition text is printed in full, followed by any amendments or additions in each of editions 2 - 6 in turn. Often this means that a whole page or more is devoted to one sentence of the original text. This makes it difficult (though not impossible) to follow a continuous text of any of the editions. I have seen the Variorum edition criticised for this reason, but this is missing the point. As Peckham himself says in his Introduction (page 27) 'this arrangement makes the text difficult to read, but I cannot imagine anyone reading such an edition in order to obtain a general knowledge of the book'. Its purpose is to enable historians and others interested in the development of Darwin's thought, and his reactions to criticisms and new evidence, to trace how this was shown in his revisions of the Origin. For this purpose it seems to me well-designed, and I don't know of any substitute for it. It is true that all six editions of the Origin are now available online from the Darwin Online Project, but even if you can find some way of getting all six texts on screen at the same time, it would be extremely laborious to compare them. One of the most striking lessons of the Variorum text is to show just how much revising Darwin did. As Peckham points out, around three quarters of all the sentences in the first edition were amended, often several times, and as a result of numerous additions the sixth edition is nearly a third as long again as the first.

And yet the substance of Darwin's views is remarkably little changed. The common view that he watered down his emphasis on natural selection in favour of 'Lamarckism' does not stand up to examination: changes in this direction are few, and do not greatly affect the balance of the book.

So congratulations to the publishers for making this available again.

Wednesday, March 28, 2007

The genetics of population differentiation   posted by p-ter @ 3/28/2007 07:41:00 PM

PLoS One has a new article on detecting recent natural selection in the human genome. As opposed to previous studies mentioned on this site [1][2], this study looks for fixed differences between populations, rather than those on their way to fixation. This is a potentially very important set of differences between populations, and one that is as of yet unexplored.

My inital reaction to this study was lukewarm, but their approach isn't biased in any way, rather it's just not particularly rigorous-- the statistic they use is based on blocks of homozygosity, an approach which is strongly influenced by demographics. They note themsevles that, among the candidates for being under selection, "a relatively large proportion...are false positives". This makes it particularly difficult to judge any single gene as being under selection from this dataset. However, some of the genes they report as being under selection are worth mentioning.

First, when comparing African and European-origin samples (the data used are from the HapMap), they find a number of pigementation related genes, as well as genes involved in skeletal development. These genes could be involved in the notable phenotypic differences between Western European and Nigerian populations. Some gene involved in fertility also show up, as do immune-reponse related genes. But as mentioned before, it's tough to make any strong statements with an approach like this.

How would I attack this problem? The limited amount of data, along with some amount of prior information, cries out for a Bayesian approach. Plus, the fact that the chimpanzee genome is also available could be used to one's advantage. This paper is a decent first strike at the problem of identifying important population-specific adaptations, but expect much more rigour in the future...

UPDATE: I've started a discussion on this paper on the PLoS One website (see the first link in the post). Feel free to join in.


The round-eyed Buddha   posted by Razib @ 3/28/2007 05:14:00 PM

Over at my other blog I've posted several times about Buddhism. The main reason was to clarify a boundary condition when it came to the discussion of the evolution and psychology of religion. When addressing the intersection of these two disciplines and their relevance to modeling religious phenomena it was important to emphasize the relative lack of importance of written texts and elite formulations upon the modal mental representation amongst the believers. In large part this is because many Westerners who are by temperament anti-religious, and in their personal ontology scientific materialists, will tend to excuse Buddhism from the general critique which they apply to other faiths. When discussing religion as a natural phenomenon, that is with an analytic gaze, one must approach it from some remove, and the view that many secularists have of Buddhism as being the "atheistic religion" tends to result in less skepticism then would otherwise be the case. That being said, I am not as ignorant of the elite traditions of Buddhism, and the view from the "commanding" heights, as some SB readers assumed. Additionally, I do not believe that elites or their formulations are irrelevant. Rather, their importance must be modulated and held in perspective, people may kill each other over the fact that they are Shia or Sunni, and tens of millions may be expended to "convert" a people from the profession of belief in one god to another, but all the while the conflicts may not be based on any substantive psychological distinction. In any case, with that in mind I picked up All is Change: The Two-Thousand-Year Journey of Buddhism to the West, a history of the interplay of Buddhist ideas and Western intellectual history.

The author, Lawrence Sutin, is a secular Jew who is clearly a religious seeker and sympathetic with a broadly ecumenical world view (he states as much in the forward). It shows in the text, as he is very conversant in the details of the contemporary American Buddhist "scene," and sympathetic toward the community while being objective enough to shed light upon shortcomings (e.g., ethical lapses amongst the leadership). But his treatment of the first thousand years is a bit sketchier, Sutin is obviously relying on only partially digested secondary sources. For example, at one point he states that Buddhism was introduced into Japan in the 4th century, and later on he says it arrived in the 5th century. Actually, it was the 6th century. In covering the last flowering of Buddhism in the Indian subcontinent centered around pre-Islamic Bengal he states that the Buddhist Pala kings were conquered by Muslim warlords from central Asia, but in fact the Palas fell to the Hindu Sena dynasty (who are often considered anti-Buddhist), who were then defeated by Turkic invaders. These are minor historical errors in the broad sweep of the story, but it does suggest that the author has a relatively vague sense of early Asian Buddhism. On the other hand, as you shift the time scale closer to the present, and address the various flirtations with Buddhism by modern European intellectuals starting with the Sinophilia of late 17th century, the author becomes far more confident and detailed in his description and analysis. Fundamentally, Sutin's narrative is one which focuses on the transformation of Buddhism into a modern Western religion through several centuries of interaction, spanning the Age of Exploration down to the post-colonial period. As such, it will be of special interest to Western converts to Buddhism and those who are "fellow travelers" in regards to Buddhist beliefs.

Nevertheless, despite its contemporary skew All is Change is still illuminating as a guide to the literature of Eurasia's cultural development after the rise of the "world" religions. Though not an expert himself, Suttin does a good job of offering bite-sized summaries of the current state of scholarship in regards to questions about the possible influence of Buddhism upon Christianity, and Christianity upon Buddhism. The reality seems to be that the exact answer to most of these questions are not extractable from the morass of human history, the possibility remains that features of Buddhism such as monasticism might have played a role in serving as an indirect template for early Christianity. Or, inversely, that Nestorian Christianity, or religions influenced by this eastern variant of Christianity such as Manichaeanism, may have played a role in the genesis of Pure Land Buddhism, whose evangelical flavor and theistic bent have long been observed by Westerners as at least superficially analogous to religions with which they are more familiar with. But from the perspective of cultural science it is also critical to entertain the possibility that many aspect of transcultural religions which exhibit similarities may also be naturally evoked properties of the human mind's interaction with its environmental substratum. For example, the idea in parts of the early Christian Church that the soul may enter into a process of transmigration need not necessarily imply an influence of Indian religious thought (with Buddhism as the vector). Reincarnation seems a common religious idea which can be found in a variety of pre-Christian religious traditions in Europe (e.g., the Celtic world). This does not mean that an influence from Buddhism was not possible, it simply suggests that a hard reliance on diffusionism of universally recurrent motifs should be treated with caution. In contrast to the typical muddle the tale of Barlaam and Josaphat is clearly a garbled retelling of the life of the Buddha, which can be attested by the 8th century in Christian Georgia. In terms of specific & precise "small ideas" it seems that diffusionism is far easier to appeal to, unless one believes in a sort of Jungian meta-consciousness. I think Sutin's narrative converges upon the most plausible explanation for cross-cultural influences and similarities, between the 6th century BCE and 6th century CE Eurasia was slowly shifting from "civilization" being defined as islands in a sea of tribal barbarism toward a robust network of cultures and meta-civilizations with multiple foci of creativity (e.g., even though the Western Roman Empire fell, the Byzantines during the 6th century fundamentally maintained continuity with late antiquity and kept the fire of Roman Christian civilization alive). Within this common pool of networked cultures idea could move relatively fast if they were selected, e.g., bureaucratic states arose all across Eurasia within a few centuries. But, one might also offer that bureaucratic states might simply be a 'natural' form which large political agglomerations focused upon urban areas must take as a necessity for their perpetuation.

With the rise of Islam the Buddhist and Christian worlds were separated and interacted only via the new mediator civilization. Sutin's story is therefore relatively brisk until one reaches the 16th century, when European colonialism began to make inroads into societies where Buddhism was the dominant religion. The early interactions also show the importance of semantics and form to elites. In Japan the Jesuits dressed like Buddhist monks because Buddhism had a relatively high status there in the eyes of the ruling caste. In China the Jesuits switched to aping Confucian officials in their style of dress and avoided associations with Buddhist monks because they were considered to be rabble. Additionally, across the chasm of centuries and languages problems arose because the Christians had to make sure that their religion was not viewed as just another sect of Buddhism. Catholics initially adopted some of the terminology of Pure Land Buddhism only to abandon this because of the ensuing confusion. Latin religious phrases which had no intelligible Chinese resonance were necessary lest the similarity of terminologies (e.g., for "God") result in the lack of distinction between the faiths.

This brings me to reiterate the point that modal religiosity on the ground was often little different between the various world religions. One reason that semantics was crucial was that conventional beliefs of the culturally naive could easily confuse devotions to bodhisattvas with that of the Christian religion. Such confusions were not unknown going in the other direction, along the coast of western India the Portuguese spared some Hindu statuary which depicted the three faces of the godhead precisely because they assumed that it must be their familiar Trinity. Histories of the Chinese Jews consistently reiterates that the native elite had difficulties distinguishing this religion from Islam, and to some extent Christians also were easily confused with the other monotheistic religions. Perhaps because of these confusions the early missionaries, such as Francis Xavier, focused on bringing lettered elites to Christianity first. In late Ming China a small core group of intellectuals along with members of the court had sympathy with Catholic Christianity, while in Japan the conversion of the populace in Kyushu was primarily a top-down affair through the conversion of daimyos. The choice to "start at the top" during the early centuries caused problems due to the connection between Christianity and a particular political faction. The fall of their patrons was one reason that Catholicism went into decline in China (with the rise of the vigorous Manchus and their suspicion of the Jesuit's foreign connections and the rejection of the ancestor cult by the Catholic Church) and was exterminated in Japan (where the ruling shoguns looked with suspicion at Christians who seemed to be allying with Iberian powers). It is important to remember that for several centuries the Jesuits were the face of Christianity for many East Asians. I think this prefigures in some ways the introduction of Buddhism to the West.

Jumping to the 19th century Sutin's story really starts kicking into high gear. This is when Arthur Schopenhauer makes a strong case for Buddhism as a religion superior to Christianity, which is fundamentally non-theistic. Like many intellectuals of the time Schopenhauer contended that many core features of Christianity were derivable from Buddhism, and the racial conceptions of the time played into his model, as he conceived of the Buddhist element as what made Christianity distinct from Semitic Judaism. Since Schopenhauer thought of of Buddhism as an "Aryan" religion he believed in the future northern Europeans would naturally defect from the "Mediterranean" derived Christianity to the new religion, which was non-theistic to boot. Other intellectuals had differing opinions, racialist thinker Arthur Gobineau believed Buddhism was rooted in an anti-Aryan cultural rebellion in the Indian subcontinent, so he did not believe that the religion was fundamentally a sound basis for European spirituality. From a few intellectuals the Buddhist ideas spread by the end of the 19th century to have cultural influence via the rise of spiritualism and neo-Eastern religions, centered around the Theosophical Society. Though many of the new religious adepts claimed tutelage under Eastern mentors, in general the primary mode of transmission seems to be textual. Transcendentalism in New England was less shaped by real Brahmins from India than the readings of Hindu scriptures enabled by Orientalist translators. On occasion a Western enthusiast would also produce a translation of a Buddhist text. Obviously Buddhism was not a mass religion being spread through a "Great Awakening" (as men like Schopenhauer might have dreamed), but an elite sect which combined elements of esoterica and rationalism. Schopenhauer's contention that Buddhism was non-theistic was and remains a common viewpoint among Westerners, who dismiss forms which seem operationally theistic (Pure Land) as debased or culturally muddied (e.g., "that's not real Buddhism").

But the influence of Buddhism upon a small core of Western intellectuals was not without consequences for lands traditionally Buddhist. Men like Anagarika Dharmapala, born David Hewavitarne to a Christian Sinhalese family, were strongly influenced by individuals from the Theosophical society to fight back against the inroads of Christianity in Sri Lanka. Though a resistance movement to Christian missionaries was already emerging, the impact of Westerners was clearly non-trivial in the emergence of what has sometimes been termed a "Protestant Buddhism." The term is meant to be ironic, but I think it reflects the crystallization of an elite Buddhism which could communicate effectively and intelligibly with Westerners, Christian and non-Christian. Though elite Buddhism has always had a transparent and fundamental non-theistic side, Buddhism does exhibit some axiomatic logic, many of the 19th century intellectuals in the West reinterpreted Buddhism through a definite Enlightenment lens. This sensibility has also spread to many elite Asians, many of whom already saw Buddhism as a meditative avocation as opposed to a mass religion. Just as Native Americans sincerely embrace a self-perception of being "close to Nature" after several centuries of European depiction as Noble Savages, so educated Asian Buddhists can see in their religion's ambiguities and complexities vis-a-vis the uncompromising simple message of the Abrahamic faiths as a testament to its sophistication. Dharmapala was also a man of his time insofar as he fused Buddhism with Sinhalese racial identity (mimicking Western racialists who would declare that Europe was the faith, and that the faith was Europe), formulating the precursor to the compound identity espoused by many Sinhalese nationalists today.

In many ways it seems to me that Christianity and Buddhism are inverted in their sociological role in the Pacific Rim and the West. I have spoken to many Taiwanese converts to Christianity who speak of how it is a more rational religion than "superstitious" Buddhism. And yet one can find the exact same sentiments from Westerners who accept Buddhism after leaving a Christian background. In South Korea Christians tend to be more well educated than Buddhists, while in the United States the reverse is true. In Japan Christianity and its ideas are culturally prominent in relation to its numbers, and one may say the same about Buddhism in much of the West. This illustrates I think a parallel process to modal religiosity, and that is the systematic rational religiosity of segments of the elite. If by chance Buddhism had lodged itself in the lower classes of the West its modal nature in the West would be, I suspect, far different. Similarly, in Taiwan Christianity is a middle class religion, while in parts of North India is fundamentally a lower class religion. These social realities may strongly shape belief and practice.

The history of the Buddhist Churches of America is shows the nature of the cleavages in Western Buddhism. This ethnic Japanese offshoot of Pure Land Buddhism has been present on American soil for a century, but it remains by and large stuck in its ghetto, and has had very little impact upon the convert community. In contrast, Zen has been far more influential, and I think that that is due to Zen's more individualistic and less devotional orientation. Western "seekers" aren't looking for another "Church," they are looking for the Way. Similarly, Sokka Gakkai devotional form of Buddhism is known to have a far larger proportion of blacks and Latinos than is common amongst converts. I believe this is a function of the fact that Sokka Gakkai resembles religion as these communities experience and understand them to a far greater extent than mainstream American Buddhism, which has been shaped by an elite white sensibility.

In regards to the elite sensibility, I think it is important to observe, as Sutin does, that a disproportionate number of Buddhists in the United States are of Jewish ancestry. Sutin states that about 1/3 of American Buddhist leaders are Jewish ethnically, and offers that some have estimated that 3/4 of the whites who reside in Dharamsala are Jewish. Sutin offers that the attraction of Buddhism is of a spirituality that speaks to Jews who can not find what they are looking for in their natal religion, but do not wish to turn to "rival" religions like Christianity. Sutin is under the impression that Jews did not convert to Christianity in great numbers in the past, or today. This is false. The American Jewish Identity Survey shows that a large minority of Jews are Christian, and the historical record is clear that converts formed a large minority of "Jews" in many nations of the West in the past few centuries. But, surveys of Jewish identity do show that Christian Jews, for lack of a better word, tend to be much closer in socioeconomic profile to the Christian population than Jews. I would argue that Jews attracted to "New Religions" or neo-Eastern faiths are of a different orientation than those who would be attracted to conservative Christianity. In The Future of Religion the authors show that Jews are very over represented in "New Religion Movements" (e.g., Hare Krishna), as the educated as a whole are. This doesn't surprise insofar as small exotic sects often have an appeal to avant garde elites. Some have made the case that Hellenistic Jews were the core of the early Christian community, viewing this faith as a way to assimilate into Roman society without turning their back on their Jewishness, so I think we are seeing the same process again in a different guise.

Finally, the entrance of an enormous immigrant Buddhist community in the last generation is changing things. Theravada traditions arrived from southeast Asia with the waves of Cambodian refugees, as did Mahayana movements with the Vietnamese. A new pulse of Chinese immigrants in the last generation also has resulted in a boom for Buddhism in that community (which, like the Japanese, had been nominally Christianized after the Oriental Exclusion Act). These factions haven't interfaced much with the large convert community, the small Japanese Buddhist Church, or the devotional movements. Religion is a hard thing to define, and it means many things to many people. The difficult part is to keep all the various elements in mind and assign them their appropriate quantitative weights in making our model of the world, and making each weight appropriate to the context. This means an exploration of psychology, evolution, sociology and history, in the general and specific cases.

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Will an infection become an epidemic? A simple model   posted by p-ter @ 3/28/2007 03:17:00 PM

One subject I've developed a mild interest in is the modeling of epidemics. So in that vein, here is a post (the first of a possible series, if I feel really inspired) on mathematical epidemiology:

Let's start with a simple discrete-time model for the evolution of an infection: imagine an infinite population of people, of which one has become infected with a disease. This one person will infect each of the other susceptible members of the population with some probability p. In the next time unit, the infected individual will recover and become immune to further infection (i.e. he either has developed resistance to the disease or is dead). Each of the newly infected individuals then independently can infect each of the remaining susceptible individuals with probability p once more (so note that the probability of being infected is p if there is one infected individual in the population, 2p if there are two, 3p if there are three, etc), and so on and so forth. The basic model is shown in the figure-- asusceptible individual (S) can be infected, becoming an infected individual (I). Infected individuals then always recover and are removed from the population (R).

One of the first (and most mathematically tractable) questions to ask of this model is: will an infection become an epidemic?

To answer this question, let's think of the first stages of the infection of the population as a Galton-Watson process (see this wikipedia link if you're wondering what role Francis Galton played in outlining this process). That is, each infected individual infects a random number of susceptible individuals in the next time point according to some probability distribution (called the "offspring distribution") X. If the probability of infecting each individual person is sufficiently low, we can say this distribution is Poisson(lambda).

The quantity of interest, then, is the probability that this Galton-Watson process goes extinct; that is, that there exists a time point in which zero people are infected. Let's call this probability E. At a given point in time, if there is one infected individual, the probablity of excinction is E. If there are two infected individuals, the probability of extinction is E^2. Three infected individuals: E^3. And so on. Given that we start with one infected individual, we can than write:

E = P(X=0) + P(X=1)E + P(X=2)E^2 + P(X=3)E^3 + P(X=4)E^4 ...

Mathematically oriented readers will notice that the right-hand side of this equation is the probability generating function of the offspring distribution, evaluated at E. Indeed, the extinction probability of a Galton-Watson process is the minumum solution to the equation E = A(E) [1].

For our Poisson distribution, this has simple consequences: if the mean of the offspring distribution is less than 1, the infection will not become an epidemic (the only solution to the equation is E = 1). If the mean of the distribution is greater than or equal to one, there is some probability that the Galton-Watson process will never die (in a real population, of course, the epidemic will eventually run out of gas, but we're not interested in those dynamics here). This may seem rather intuitive (if on average, each infected individual infected less than one individual, the infection will die out quickly), but the mathematical formalism allows one to construct more complex models. Plus, reducing lambda (the mean of the Poission distribution), of course, is then the goal of nearly all anti-epidemic precautions-- quarantines, hand-washing, etc.; all can be though of as practical ways to reduce a mathematical parameter.

[1] The probability generation function A(z) of a distribution X is the sum over all possible values of X of P(X=x)z^x.


Short memories   posted by Razib @ 3/28/2007 11:45:00 AM

Several people have pointed me to the articles which quote a nationalist Japanese minister as stating, to the effect, that Arabs won't trust blonde & blue-eyed Westerners, but have no historical aversion to East Asians. I found this kind of funny because of course the Sack of Baghdad was at the hands of the Mongols. Though the current post-colonial vogue is to attribute Arab failures to European exploitation, many scholars have long made the argument that the Mongol invasions dealt the Arabs a blow from which they never recovered (the Turks were ascendant from then on).1 It highlights the importance of history as propaganda and ideology to consider that the Crusades were relatively minor affairs compared to the later invasion of the Mongols, and yet the former loom far larger in the contemporary Arab mind.

1 - The Arab world had been in decline already during this period with the rise of Turkic warlords, but the Mongols snuffed out a late renaissance of the Caliphate in Baghdad.


The Unchurched   posted by Razib @ 3/28/2007 02:12:00 AM

Unchurched Population Nears 100 Million in the U.S.:
A new survey released by The Barna Group, which has been tracking America's religious behavior and beliefs since 1984, reveals that one out of every three adults (33%) is classified as unchurched - meaning they have not attended a religious service of any type during the past six months....

Some population segments are notorious church avoiders. For instance, 47% of political liberals are unchurched, more than twice the percentage found among political conservatives (19%). African Americans were less likely to be unchurched (25%) than were whites (32%) or Hispanics (34%). Asians, however, doubled the national average: 63% were unchurched....

There has been some talk about the boom in Asian American evangelical Christianity, but it is important to keep in mind that the rate of growth is in part a function of the fact that the "untapped" market is still rather large. Of course, The American Religious Identification Survey found:
...between 1990-2001 the proportion of the newly enlarged Asian American population who are Christian has fallen from 63% to 43%, while those professing Asian religions (Buddhism, Hinduism, Islam, etc) has risen from 15% to 28%.

Many of the non-Christian religions don't have as strong a congregational tradition as Christianity. But, the finding that Asian Americans are more secular than other ethnicities is a pretty robust and consistent finding.


Why we're not all hot?   posted by Razib @ 3/28/2007 12:35:00 AM

Why some people are more attractive than others:
Professor Petrie theorised that since genetic mutations can occur anywhere in the genome, some will affect the 'DNA repair kit' possessed by all cells. As a result, some individuals have less efficient repair kits, resulting in greater variation in their DNA as damage does unrepaired.

Although unrepaired DNA is generally harmful - causing tissue to degenerate or develop cancers - it is useful in some parts of the genome, such as those parts resposible for disease defence where variation can help in the resistance to disease. It has long been known that greater variation of DNA in the disease defending regions makes it more likely that an individual can resist attacks by bacteria and viruses.

Using a computer model to map the spread of genes in a population, Professor Petrie demonstrated that the tendency towards reduction in genetic diversity caused by sexual selection is outweighed by the maintenance in greater genetic diversity generated by mutations affecting DNA repair.

I haven't read the paper...and the press release sounds kind of garbled. I guess the results here are suggesting that polymorphism at the disease resistence loci (e.g., MHC) is so important that DNA repair mechanisms can't get too good. A byproduct of this is variance in the mutational load across the population. I suppose this sort of answer to "why we're not all hot" is like the answer to why we're not all parthenogenetic.


Tuesday, March 27, 2007

A visual approach to statistics   posted by agnostic @ 3/27/2007 06:44:00 PM

I was recently recommended an excellent book with the irresistibly seductive title The Geometry of Multivariate Statistics, which offers more visually oriented people a crisp way of thinking about statistics that still captures what the algebraic formulas say. To be sure, the author is aware that diagrams, pictures, and so on are employed anytime someone draws a histogram, but he seeks to ground the gamut of the most important ideas in statistics -- variance, correlation, regression, and so on -- in a geometric view, focusing mostly on vectors and trigonometry.

I have found this 160-page book to be quite helpful in fully wrapping my brain around the core ideas of statistics*, although it is best used in conjunction with a standard textbook containing the algebraic and computational sides of things. It would also help to read it after or concurrent with a first course in linear algebra: while there is no use of eigenvalues / eigenvectors or matrix algebra, you should be familiar with the basic idea of what vectors and vector spaces are (though some complain that many students memorize the matrix algorithms without "getting" the more basic ideas). The book does provide an overview of these fundamentals, but it is more of a reminder.

Both to share this exciting new way of looking at statistics, as well as to help me get a solid lock on the perspective, I thought I'd give a little taste of what the book has to offer. Unfortunately, I'll be using fake data since I don't have enough time to collect my own or search for that of others, but the goal here is more didactic than empirical. Caveat: anyone who's already read the book or studied statistics in this way will be pretty bored by this post.


The basic idea is that, unlike when we graph scatter-plots, which plot (in variable-space) how various subjects scored on different variables -- say, height and weight -- we're going to plot the variables themselves in "subject-space," to see directly how the variables relate to one another (since usually we don't care about the subjects themselves except as a way to figure out the relationships between the variables). For instance, let's say we tested two subjects on their height and weight, such that the height in inches and weight in pounds (respectively) for subjects A, B, and C were (69, 135), (72, 150), and (79, 200). In a scatter-plot, we'd have 2 axes (height and weight) and 3 data-points corresponding to the 3 subjects.

Standing this view on its head, let's instead create a 3-D graph with one axis for each of the 3 subjects, and just 2 data-points (one for height, one for weight). The height data-point would "score" 69 on the A-axis, 72 on the B-axis, and 79 on the C-axis. The weight data-point would "score" 135, 150, and 200 on these axes, respectively. So then, our new data-points (69, 72, 79) and (135, 150, 200) are just vectors whose components are the heights and weights of all the subjects. Instead of trying to infer the properties of and relationships between the height and weight variables from a scatter-plot, we can see them more directly by examining the magnitude of the vectors and the angle between them.

Notice that if we center each variable by subtracting the mean from each component, the new vector's components are deviations from the mean. Consider two such centered vectors x and y. If we take the dot product of x with itself, we get the sum of the squares of each component. And since the components are deviations from the mean, x dot x is equal to the variance; square-rooting this gives us the standard deviation. Now, recall the following dot product formula for the angle between x and y:

cos(x, y) = (x dot y) / (|x| times |y|)

Since any vector is collinear with itself, the angle between "them" is 0, making the cosine 1. If both vectors on the right-hand side of the equation are the same, then x dot x must equal |x| times |x| or |x|^2 to make the ratio equal 1. Because in our case x dot x equals the variance of the variable it represents, then the variance also equals the square of the length or magnitude of the vector. Thus, the length itself equals the square-root of the variance, or standard-deviation. That's a pretty neat way to see how spread out the values of a variable are: just look at how long the vector representing it is.

As for their correlation, refer to MathWorld's entry on the correlation coefficient, specifically line 22 (the notation for sum of squares, SS, is defined in the first 9 lines). Square-root both sides to get r by itself. Since we've centered our variables, we could re-write the formula as:

r = (x dot y) / (|x| times |y|)

Of course, that's equal to the cosine of the angle between x and y, so taking the inverse-cosine of the ratio on the right-hand side gives us the correlation coefficient. Thus, the larger the cosine -- and so, the smaller the angle -- the larger the correlation. That makes it an easy task to see the correlation: draw the vectors from the same point and look at the angle formed between them.

An example

So, let's take a look at how this might play out in the real world. Suppose we test 50 people on two distinct IQ tests and create a scatter-plot of an individual's score on Test 1 and Test 2. It might look something like this (again, this is fake data for illustration):

Let's just focus on two aspects of the data, the correlation between scores and the variance in scores for each test. Clearly, there is a high correlation between scores, as we'd expect if IQ tests measure pretty much the same underlying construct (general intelligence). As a correlation always lies in [-1, 1], eyeballing the correlation from a scatter-plot forces you to judge angles that range from 0 to 45 degrees in magnitude. When we redraw the two variables as vectors, however, the angle between them (which again indicates the correlation) can range from 0 to 90 degrees in magnitude, which places less stringent demands on our visual acuity to get the gist of the picture. Judge for yourself (this shows the centered variables, but the correlation between them and their variances are unaffected by translating the mean to 0):

Even as a more visually oriented person, I find the small angle between the vectors (~6.9 degrees) easier to grok than the discrepancy of the trend-line's slope from +/- 1. Turning now to the variance in scores, it's not so clear from the scatter-plot which test has greater variance -- to my eye, it looks wider than taller, suggesting Test 1 has greater variance, but this is wrong. In fact, the standard deviations for Test 1 and 2 are 14.6 and 18.3, respectively. I suspect my misjudging the spread of the two variables on the scatter-plot is due to a bias of the human visual system that finds horizontal lines longer than vertical lines of equal length, but who knows? Returning to the vector picture above, it is immediately clear that the Test 2 vector is longer than that of Test 1, indicating greater variability. Since Test 2's SD is 18.3 / 14.6 = 1.25 times larger than that of Test 1, the corresponding vector is 1.25 times longer. Admittedly, if the variables were close to uncorrelated -- and so, if the vectors were nearly orthogonal -- the task of judging their respective lengths would be a bit more difficult than when they're more closely related, but most of the interesting results that people have to share are when there is at least a weak or modest correlation between variables.

So that's it, really -- not a difficult viewpoint to understand, but I find it much more illuminating than a raw algebraic derivation of formulas. Remember that this way of thinking is no less formal or rigorous, but just taps into a different modality of thinking, which some find more natural. There is a lot more in the book (regression, ANOVA, and more), so I hope this brief post has piqued your curiosity enough to at least browse through it in your library. It's not very long either, so why not add it to your list of must-reads?

*I started studying stats way back in high school when I took AP Statistics, so I'm no stranger to the subject. Still, the (to me) novel appeal to geometric reasoning makes a lot of it pretty intuitive now. One of the reviews at the Amazon entry claims that a lot of early work in statistics was guided by geometry, which, not being a statistician, I was unaware of -- though given that the inveterate geometer R.A. Fisher pioneered a lot of modern statistics, it's not surprising to hear.

Addendum: By request, here are pictures that show the difference between plotting subjects as points in variable-space (a familiar scatter-plot) and plotting the variables as vectors in subject-space. Subject 1 scores 1 on Variable A and 3 on Variable B, so his data-point is (1, 3), and likewise for the other two Subjects.

To plot the Variables themselves, we gather their values across all three Subjects -- so Variable A "scores" 1 on Subject 1 (since that is S1's value on A), 2 on Subject 2, and 4 on Subject 3; likewise for Variable B.

The idea is to draw a vector a from the origin to (1, 2, 4) and b to (3, 6, 7). I omitted these lines since it would clutter the picture, but you can see that they point in pretty similar directions, which here means that they're highly correlated. In fact, the cosine between them is 0.968 -- their correlation.

If you measured the same 2 Variables but included data from 100 Subjects, it's obviously impractical to try to draw a 100-dimensional coordinate grid just to plot the two vectors representing the variables. But since you can draw the length of a vector according to its SD, and draw an angle between them to indicate their correlation, you don't really need 100 dimensions to see how the Variables relate. The simpler 3-D picture above is to illustrate the rationale: represent a Variable as a vector whose components are the scores on that Variable across all the Subjects tested.

Monday, March 26, 2007

Swappable DNA Module in Bacteria Gives Light Harnessing Ability   posted by Fly @ 3/26/2007 12:17:00 PM

Engineering Bacteria to Harvest Light
Some bacteria, such as cyanobacteria, use photosynthesis to make sugars, just as plants do. But others have a newly discovered ability to harvest light through a different mechanism: using light-activated proteins known as proteorhodopsins, which are similar to proteins found in our retinas. When the protein is bound to a light-sensitive molecule called retinal and hit with light, it pumps positively charged protons across the cell membrane. That creates an electrical gradient that acts as a source of energy, much like the voltage, or electromotive force, supplied by batteries.

First discovered in marine organisms in 2000, scientists recently found that the genes for the proteorhodopsin system - essentially a genetic module that includes the genes that code for both the protein and the enzymes required to produce retinal - are frequently swapped among different microorganisms in the ocean.
Intrigued by the prospect that a single piece of DNA is really all an organism needs to harvest energy from light, the researchers inserted it into E. coli. They found that the microorganisms synthesized all the necessary components and assembled them in the cell membrane, using the system to generate energy.
The findings have implications for both marine ecology and for synthetic biology, an emerging field that aims to design and build new life forms that can perform useful functions. Giant genomic studies of the ocean have found that the rhodopsin system is surprisingly widespread. The fact that a single gene transfer can result in an entirely new functionality helps explain how this genetic module traveled so widely. In fact for microbes, this kind of module swapping may be the rule rather than the exception.


Population substructure in Europe - Northwest to Southeast cline?   posted by Razib @ 3/26/2007 04:52:00 AM

The American Journal of Human Genetics has an article up examining population substructure within Europe (or, more precisely, the varation of genes), Measuring European Population Stratification with Microarray Genotype Data. From the discussion:
PC1 [the largest principle component of variance] largely separates northern from southeastern individuals...and is consistent with the clines observed in classic gene-frequency...Y-chromosome...mtDNA...and whole-genome...studies of European diversity. PC2 [the second largest principle component of variance] reflects mainly east-west geographic separation and, particularly, identifies the two Iberian populations (Spanish and Basques) in our analysis as distinct...Furthermore, PC3 and PC4 emphasize the separation of the Basques and Finns, respectively, from other Europeans...The Basques are known to have unusual allele frequencies for several marker systems...and speak a unique non-Indo-European language. In line with their non–Indo-European Uralic language and previous study of their Y-chromosomesthe Finns show evidence of an increased affinity to the Central Asian populations when placed in an intercontinental context...STRUCTURE analysis of the European populations is highly consistent with PCoA; for example, when the number of populations (K) is 3, the major divisions correspond to the northern, southeastern, and Iberian populations...In cases of higher K values, first the Finns (K = 4) and then the Basques (K = 5) emerge as distinctive....

The southeast-north cline that they speak of is straight out of L.L.Cavalli-Sforza's History and Geography of Human Genes. Cavalli-Sforza argued in that book that this reflected the "demic diffusion" of agriculture and was a residue from a genetic wave of advance generated by population expansion initiated in the region of the Levant-Anatolia. By its nature a wave of advance is exhibits a weaker genetic signal in relation to the source because of dilution via intermarriage, so it is no surprise that the British, for example, are predominantly descended from the Paleolithic hunter-gatherers of northern Europe. The detection of east-west gradients, as well as the diversity of the Iberian sample, also points to the demographic expansions out of the Ice Age refugia when the glaciers retreated and northern Europe was repopulated. Note that the sample sizes for some of the local populations were very small. From the paper, "western Irish (n = 6), eastern English (n = 8), French (n = 1), German (n = 8), Valencian Spanish (n = 20), Basque Spanish (n = 8), Italian (n = 9), Polish (n = 8), Greek (n = 8), Finnish (n = 7), Armenian (n = 8), and Ashkenazi Jewish (n = 5)...." I've placed the most informative figure below the fold as a high res image.

Related: Jaakkeli says....


Sunday, March 25, 2007

Nature Reviews Epigenetics Focus   posted by amnestic @ 3/25/2007 09:51:00 PM

I'm working on a follow-up to my knee-jerk negative reaction to Miller and Sweatt last week. Surveying the field, I found that Nature Reviews Genetics just dropped an issue focusing in epigenetics with a complementary website.

At least a couple of the reviews spotlight our recently acquired ability to assay DNA methylation states on a genome-wide scale. I'm reading the Jirtle and Skinner piece now. Go check it out and report back.


White and Nerdy   posted by Darth Quixote @ 3/25/2007 11:28:00 AM

On Reading Wright   posted by DavidB @ 3/25/2007 08:49:00 AM

Last year I discussed the views of R. A. Fisher on population size, and said I would later cover Sewall Wright's views on the subject. It has taken me a while to come back to this, as I soon realised that my knowledge of Wright was too superficial for the task. On reading more of Wright's work, I think there are also several other issues worth exploring.

I aim to write notes on the following subjects:

1. The measurement of kinship.

2. Inbreeding and the decline of genetic variance.

3. Population size and migration.

4. The adaptive landscape.

5. The shifting balance theory of evolution.

It will take me some time to actually write these notes, but as a starter here are a few comments on the range of Wright's work and its influence...

Wright's Works

Where possible I will quote from the collection Sewall Wright: Selected Papers on Evolution, edited by William B. Provine, U. Chicago Press, 1986 (SPE). Provine's biography of Wright: Sewall Wright and Evolutionary Biology, 1986, (SWEB) is also useful.

SPE is a large collection, including Wright's classic 1931 paper on 'Evolution in Mendelian Populations', his 1943 paper on 'Isolation by Distance', and most of his other general writings on evolution prior to his 4-volume book on Evolution and the Genetics of Populations (EGP), published from 1968-78. EGP itself is a strange work, which despite its length deals with some important issues far too briefly, while others are pursued in excruciating detail.

There are two important omissions from the collection SPE. For reasons of length it does not contain Wright's 5-part 1921 paper on 'Systems of Mating', which is the foundation of all his later writings. Fortunately, all 5 parts of the paper are available free online: search Google Scholar for 'Sewall Wright', and 'Systems of mating'. Part 1, which contains most of the essential points, is here.

The other major omission from SPE is that there is no substantial piece on Wright's technique of path analysis. This is Wright's major contribution to statistical theory, and he constantly makes use of the technique. Fortunately, many of his papers on path analysis are also available online, and links are provided here. The most useful paper is the 1921 paper on 'Correlation and Causation', but I noticed that a page (p.561) is missing from the pdf file. As the missing page contains Wright's definition of a path coefficient, this is a serious loss. I have therefore consulted the original print version and transcribed the missing part of the definition at Note 1 below.

Wright's influence

As for Wright's influence, he is routinely cited (along with R. A. Fisher and J. B. S. Haldane, in various permutations) as one of the three founding fathers of population genetics. Unlike Fisher and Haldane, Wright's work was largely confined to genetics, with the important exception of path analysis. Within genetics, Wright was probably the most systematic of the three founding fathers, and his active career in the subject was longer. Wright remained active into the 1980s, whereas Fisher and Haldane both died in the early 1960s. On the other hand, Wright's influence may have been limited by the fact that he wrote no book on the subject (or on evolutionary theory more widely) until EGP, the first volume of which appeared in 1968. EGP itself is highly technical and very heavy going. Meanwhile, Haldane's book The Causes of Evolution (1932) was accessible both literally and metaphorically, and Fisher's Genetical Theory of Natural Selection (1930), despite its difficult mathematics, has a great deal of stimulating verbal discussion.

Fisher has a notorious reputation for obscurity, but Wright is hardly any easier to read. The difficulty lies partly in the mathematics and partly in the verbal explanations. Unlike Fisher, Wright seldom uses very advanced mathematics, but his algebra is still difficult to follow. Characteristically, he will set out a few definitions, and then say something like 'it follows that', followed by a complicated formula bearing no obvious relation to what precedes it. Sometimes a few substitutions and rearrangements will produce the desired result, but often (in my experience) repeated attempts leave the mystery unsolved. As an example, consider the equation r = (etc) on p.117 of 'Systems of mating Part 1'. This does not bear any close resemblance to the standard formula for the correlation coefficient, except for being a fraction with a square root in the denominator. By some laborious algebra I have verified that it can be derived from the standard formula, together with Wright's stated assumptions about the value of the quantities to be correlated, but I still have no clue as to how Wright himself obtained his equation. I have also checked by numerical trials that the formula in the next paragraph is correct for the case of Hardy-Weinberg equilibrium, but I have not been able to derive the formula itself algebraically [note 2]. Of course, this may be because I am not a very good mathematician (which is true) but I doubt that most biologists were any better until comparatively recently. Wright's closest colloborator, Theodosius Dobzhansky, once said:

He has a lot of extremely abstruse, in fact almost esoteric, mathematics. Mathematics, incidentally, of a kind which I certainly do not claim to understand. I am not a mathematician at all. My way of reading Sewall Wright's papers, which I still think is perfectly defensible, is to examine the biological assumptions the man is making, and to read the conclusions he arrives at, and hope to goodness that what comes in between is correct. "Papa knows best" is a reasonable assumption, because if the mathematics were incorrect, some mathematician would have found it out' (quoted in SWEB, p.346).

Dobzhansky was far from unique. Among other examples, the geneticist Harrison Hunt complained in a letter to Wright:

I have one very serious criticism, however, to offer to all these papers. I have expended, yes wasted, an enormous amount of time upon them because as a rule too few key equations are given in the mathematical analysis. You have a marked tendency to state your assumptions very briefly and then give the end results of the mathematical analysis without giving a sufficient number of the intermediate steps to make it easy for a non-mathematical person to follow your reasoning. Upon enquiry I have found other geneticists have the same difficulties that I do. (for more examples and Wright's defence see SWEB pp.400-02).

Wright's verbal explanations also present some difficulties. The problem is not with any obscurity of the language itself (unlike Fisher's often convoluted sentences, Wright's are usually short and simple) but in the excessively concise treatment of difficult subjects. Key concepts like those of path coefficient, correlation between gametes, adaptive landscape, and fitness function are introduced in just a few words, and important assumptions are either not stated at all or stated so inconspicuously that they are easily overlooked. This is not just my impression: even W. G. Hill, an admirer of Wright, and an expert geneticist, comments that Wright's methods 'were not then and are still not easy to understand... partly because critical points were dealt with very tersely'.

The difficulty of Wright's work has probably limited its direct influence on biologists. Here it is necessary to distinguish between specialists in population geneticists and other biologists. Wright is the population geneticist's population geneticist. In Crow and Kimura's textbook, for example, Wright gets more references than any other author. Many of Wright's concepts and methods, such as his kinship coefficients, the FST statistic, the effective size of a population, the treatment of migration between subdivided populations, and the proof that genetic diversity declines by approximately 1/2n per generation (where n is the effective size of the population) are part of the indispensable basis of population genetics, perhaps more so than any specific contribution of Fisher or Haldane.

Among general evolutionary biologists, on the other hand, Wright's influence in the last 40 years or so seems to have been limited. This is partly because the general trend in evolutionary biology, at least since George C. Williams's 1966 book Adaptation and Natural Selection, has been strongly adaptationist, whereas Wright has been seen as ambivalent, if not actively hostile, towards the effectiveness of natural selection. (As Provine pointed out in his biography (SWEB pp.289-91), Wright later tended to re-write history, playing down the extent to which his early writings were non-adaptationist.) Differences between Britain and the United States have also affected Wright's influence. In Britain most biologists learned their genetics directly or indirectly either from Fisher (notably E. B. Ford and the school of 'ecological genetics' at Oxford) or from Haldane (John Maynard Smith and his numerous students). W. D. Hamilton, the most influential of all recent theorists, was largely self-taught in genetics, but took Fisher's Genetical Theory of Natural Selection as his main inspiration. In much British writing on evolution Wright is therefore either ignored or presented only as the advocate of 'genetic drift', which seriously distorts his actual position. (An important exception is the strong school of agricultural genetics at Edinburgh, including Hill, Robertson, Falconer and others, where Wright was a visiting professor around 1950. Another partial exception is Julian Huxley, whose influential book Evolution: the Modern Synthesis summarised Wright's theories respectfully and at reasonable length.)

It might be expected that Wright would be a more powerful influence in the United States. His work is doubtless more widely read there than in Britain. But his influence on evolutionary biologists, as distinct from population geneticists, may have been weaker than expected. Major evolutionary theorists like G. G. Simpson, Ernst Mayr, and George C. Williams referred to Wright with respect, but were not enthusiasts for his shifting balance theory. Dobzhansky, Wright's closest collaborator, expounded Wright's theories very fully in his books on evolution, but his empirical studies tended to undermine some of Wright's key ideas. Wright has perhaps been most influential on those theorists, such as Gould, Lewontin, and D. S. Wilson, who may be considered heretics or rebels against the prevailing trend of Fisherian adaptationism.

As for my own assessment, for what little it is worth, in reading Wright I have realised that his achievement was truly massive. At the same time, I find it difficult to work up any great enthusiasm for his writings. This is partly due to the obscurities I have already mentioned, but also to a certain dryness and narrowness of scope. Whereas one can still read Fisher and Haldane and hope to find new insights and speculations, there is relatively little in Wright that cannot be found in more digestible form in a good textbook. Perhaps this is what every scientist should aspire to: to be absorbed into textbook nirvana.

Note 1.
Extract from p.561
"Where there is a network of causes and effects, the interrelations could be grasped best if a coefficient could be assigned to each path in the diagram designed to measure the direct influence along it. The following is an attempt to provide such a coefficient, which may be called a path coefficient.

We will start with the assumption that the direct influence along a given path can be measured by the standard deviation remaining in the effect after all other possible paths of influence are eliminated, while variation of the causes back of the given path is kept as great as ever, regardless of their relations to the other variables which have been made constant. Let X be the dependent variable or effect and A the independent variable or cause. The expression sX.A [where s stands for small sigma, and X and A are printed as subscripts] will be used for the standard deviation of X, which is found under the foregoing conditions, and may be read as the standard deviation of X due to A. In a system in which variation of X is completely determined by A, B, and C we have s.X.A = sACsX [where s stands for small sigma, and all letters except the first and third sigmas and the second X are printed as subscripts] representing the constant factors, B and C, and also the variation of A itself (sA) by subscripts to the left. The path" [/p.562]

Note 2: In the same paragraph the equation p = root,uv is a misprint or slip of some kind, as it should clearly be p = 2.root.uv. (I have checked that the error is in the original printed text, and not just a glitch in the pdf.) Whatever its origin, the error does not appear to affect the remainder of the paper, which uses the correct value.

Saturday, March 24, 2007

Noruz & Iran   posted by Razib @ 3/24/2007 12:06:00 PM

A few weeks ago we discussed the extent of non-Islamic cultural practices in Iran, in particular, Noruz, the Zoroastrian New Year. In an article about the Kurds and Noruz here is a tidbit of interest:
The holiday is a much bigger deal next door in Iran - ancient Persia is the birthplace of the Zoroastrian religion, and the government practically shuts down for weeks. The Kurds are given fewer days off and hold fewer rituals, but Noruz remains an important holiday, in part because it is used to commemorate one of the founding myths of Kurdish identity.

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Friday, March 23, 2007

The poll, reviews   posted by Razib @ 3/23/2007 11:35:00 PM

Well, the poll has been running for a week. Nothing changes around these parts. 85-90% of regular readers are male. A plural majority identify as "libertarians," though there is a rough political balance along the normal Left-Right range with a slight Center-Right skew. One thing that I will comment on though is the fact that though we have many readers who have been around various periods of time, there is a definite dearth of those who say they've been reading for less than 6 months vs. 1 week. Only at 1-2 years do we surpass those who say they've been reading for less than a week. Do we have an influx of new blood? I doubt it. Rather, the half life of a GNXP reader is likely pretty low. The majority of those of you who count yourselves as "regular" readers, but have only sampled a few weeks worth of posts, will find us too boring, too offensive or too obnoxious, and take yourselves off to other parts. This is normal. It seems plausible many "short termers" stumbled upon this blog via a link from another blog when we talked about something you were interested it...but it turns out that's not the real focus of the blog. It happens. I read Stephen Bainbridge because he was a conservative who was against Intelligent Design. But, it turns out that most of the time I'm not really that into what Bainbridge is talking about, I just checked out his blog because one day he was talking about what I was interested in. Such is life.


The well educated reader   posted by Razib @ 3/23/2007 11:21:00 PM

On the chat over the past few weeks I've been recommending that people just read the first half of The Genetical Theory of Natural Selection to get the most out of GNXP. I say this because I know time is finite, and it isn't like most people have time to read The G Factor, Hartl & Clark or Falconer. Though there is a lot that is wrong with The Genetical Theory of Natural Selection (e.g., a whole chapter on R.A. Fisher's theory about the evolution of dominance?), it still seems a succinct introduction to thinking about evolution as more than an open-ended description about the natural world (in contrast, Sewall Wright or W.D. Hamilton were both more expansive in their prose, whiel J.B.S. Haldane seems to be a bit scattershot and without the thematic coherency that one would prefer). Do readers have other suggestions? The amount of marginal time individuals have varies, so restricting to one book isn't really necessary, though for those in careers which require 60-70 hours (in which case, why the hell are you reading a weblog???) only one book is likely practicle.

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Blogging Heads, is it worth it?   posted by Razib @ 3/23/2007 11:00:00 PM

Virginia Postrel was asking whether Blogginheads.TV was worth it. Most of your probably know that I'm a regular watcher. Some of you might wonder, "Why???" The reason is simple, I don't own a TV, nor do I read many political blogs or newspaper articles, so it is a cheap way for me to stay hook in to the Zeitgeist of what people who think politics matters think matters right now. Normally I listen to the "debate" in one tab while I'm browsing or doing work. Also, it gives me an opportunity to make fun of the way people look, and mock M. Yglesias, which I enjoy for purely childish reasons. But back to the main issue, is the format worth it? Postrel mentions technical issues, and it seems every other episode has problems with unrecorded diavlogs and what not. Well, check this out:

Jesus. I know ALEXA sucks, but not by an order of magnitude. Blogginheads.TV doesn't really beat, let alone someone like M. Yglesias. I am pretty shocked to be honest, but I guess only hardcore nerds are really interested in what other nerds have to say.

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Blowhard on 300   posted by Razib @ 3/23/2007 03:39:00 PM

Via Steve, Michael Blowhard's magisterial review of 300.


Thursday, March 22, 2007

Genetic Engineering Color Vision in Mice   posted by Fly @ 3/22/2007 06:20:00 PM

Genetic studies endow mice with new color vision

Although mice, like most mammals, typically view the world with a limited color palette - similar to what some people with red-green color blindness see - scientists have now transformed their vision by introducing a single human gene into a mouse chromosome. The human gene codes for a light sensor that mice do not normally possess, and its insertion allowed the mice to distinguish colors as never before.

In a study published in the March 23, 2007, issue of the journal Science, Howard Hughes Medical Institute researchers at Johns Hopkins, together with researchers at the University of California at Santa Barbara, demonstrated in a series of cleverly designed color vision tests that the genetic modification allows mice to see and distinguish among a broader spectrum of light waves. The experiments were designed to determine whether the brains of the genetically altered mice could efficiently process sensory information from the new photoreceptors in their eyes. Among mammals, this more complex type of color vision has only been observed in primates, and therefore the brains of mice did not need to evolve to make these discriminations.

The new abilities of the genetically engineered mice indicate that the mammalian brain possesses a flexibility that permits a nearly instantaneous upgrade in the complexity of color vision, say the study's senior authors, Gerald Jacobs and Jeremy Nathans.
"Our observation that the mouse brain can use this information to make spectral discriminations implies that alterations in receptor genes might be of immediate selective value not only because they expand the range or types of stimuli that can be detected but also because they permit a plastic nervous system to discriminate between new and existing stimuli," the authors wrote in the Science paper. "Additional genetic changes that refine the downstream neural circuitry to more efficiently extract sensory information could then follow over many generations."

I'm surprised that the mouse brain visual system is sufficiently plastic that the altered mice gained significant color differentiation ability.

Update: Carl Zimmer on Mouse Color Vision

Poll time!   posted by Razib @ 3/22/2007 12:21:00 AM

Every now and then I take polls of GNXP readers. Been a while, so here I go.... (please check it out only if you are a regular reader, etc.)

How long have you been reading GNXP regularly?
less than 1 week
less than 1 month
less than 6 months
less than 1 year
less than 2 years
less than 3 years
less than 4 years
less than 5 years (i.e., since the blog began)
Free polls from

Are you a male or female?
Trans (please answer seriously)
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What are your politics? (please normalize to American standard if possible!)
Far Left
Far Right
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What are your religious beliefs (or lack of)
I believe in God
I suspect there is a God
I am not really sure
I doubt there is a God
I don't believe in God
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What is your racial identity?
East Asian
South Asian
Middle Eastern
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What is your class? (if you are a student, your parents' class)
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Middle class
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How did you find out about GNXP?
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Free polls from


Wednesday, March 21, 2007

Chat update   posted by Razib @ 3/21/2007 04:18:00 AM

I know many of you are probably sick of chat updates, but please note.

1) The way the app works right now it autologs you on. But,

2) I've set up a filter so that your randomly assigned nickname ("zanon123...") won't show up. You can talk, but you aren't seen. If you want to be seen on the nick list, just change your nickname with the gray button where your "zanon" handle is, or, type "/nick theNameyouWant" in the command box (IRC-like). If you want to lurk, then keep it "zanon."

3) Also, your connection won't show. I'll figure out a way to fix the problem with the disconnects which show (but shouldn't).


Blue-eyed babies & the evolution of light skin   posted by Razib @ 3/21/2007 12:35:00 AM

Over at her website Judith Rich Harris has posted her article, Parental Selection: A Third Selection Process in the Evolution of Human Hairlessness and Skin Color. When I asked Judy 10 questions I expressed some skepticism about this theory:
4) In your 2005 response to the Edge Question, "What Do You Believe Is True Even Though You Cannot Prove It?," you alluded to two things, 1) selection for light skin 2) hairlessness by parents in infants. When you pointed to these facts, did you do so in light of recent genetic work which suggests that dark skin might have evolved in humans as a response to loss of body hair? In other words, one trait would never been selected for if not for the other.

No, I hadn't heard of that work. But it doesn't matter. All humans have more or less hairless bodies, so I assume that the characteristic of hairlessness is at least as old as our species - at least 100,000 to 200,000 years old. Racial differences in skin color, on the other hand, are no more than 50,000 years old. If humans turned dark-skinned as a response to hairlessness (a theory I find dubious), then an explanation is still needed for why their skin turned white again so quickly when they inhabited Northern Europe, thousands of years later. My response to the 2005 Edge question offered a possible explanation.

By the way, I've expanded that essay into an article for a journal called Medical Hypotheses. It will be published in a few weeks.

Here is the abstract from the artice:
It is proposed that human hairlessness, and the pale skin seen in modern Europeans and Asians, are not the results of Darwinian selection; these attributes provide no survival benefits. They are instead the results of sexual selection combined with a third, previously unrecognized, process: parental selection. The use of infanticide as a method of birth control in premodern societies gave parents - in particular, mothers - the power to exert an influence on the course of human evolution by deciding whether to keep or abandon a newborn infant. If such a decision was made before the infant was born, it could be overturned in the positive direction if the infant was particularly beautiful - that is, if the infant conformed to the standards of beauty prescribed by the mother's culture. It could be overturned in the negative direction if the infant failed to meet those standards. Thus, human hairlessness and pale skin could have resulted in part from cultural preferences expressed as decisions made by women immediately after childbirth.

First, on a pedantic note, let me lodge my general protest in regards to the assumed decomposition of natural, sexual, and, Judy's putative third factor, parental selection. I'm reading some cognitive psychological work now about categorization and one thing that struck me as very apt in regards to how humans conceptualize the world is that we're always trying to break nature apart its joints, so to speak. Most regular readers know I'm a fan of consilience, and so I must reiterate and be a nag about the fact that many dynamic selective processes may bound in nature, but fundamentally they're all of a piece. As J.B.S. Haldane said: fitness is a bugger, naming selection is easy, characterizing it both accurately and precisely can often be very hard. The gene is the unit of selection, the various levels and dimension are all equal under God's eye.

In any case, to the thrust of the hypothesis. First, in the past few years a lot of work has been done on skin color. Last year I observed that Armand Leroi's afterward to Mutants where he notes that we don't understand skin color will need a coda in future editions. Here's what we know, so far....

1) In the 1960s human geneticists using classical pedigree analysis determined that 4-5 loci, genes, explained most of the intergroup variation between blacks and whites in regards to skin color.

2) In the past few years genomics has generally confirmed this view, there are a few loci of large effect (e.g., SLC24A5 in Europeans vs. non-Europeans) which explain intergroup differences in complexion.

3) But, equivalent phenotypic values can be attained via alternative genetic architectures, and this seems to have happened. In other words, light-skinned northeast Asians are not necessarily light for the same reason that Europeans are. Even if the change occurs upon the same locus, the allele or haplotype may be different.

4) Different evolutionary dynamics might affect the various loci. For example, in Europeans MC1R is highly polymorphic, suggesting either diversifying selection (e.g., frequency dependence) or a deep coalescence time (perhaps MC1R built up a great deal of variation during the residence of hominid lineages in Europe and modern humans simply assimilated the local depigmentation alleles?).

5) Also, some of these loci under selection seem to be relatively recent (e.g., perhaps within the last 10,000 years). Like LCT (lactase persistence) they leave a powerful imprint on the genome via a selective sweep.

How does this square with the hypothesis presented above? First, some prelims. Selection of all sorts can be hard to get a grip on. After all, we bandy about selection coefficients, s, in a vacuum, when they vary within their environmental contexts. Environment in this case can mean the natural world, the social world and other genetic parameters (via genetic interactions). Negative frequency dependence also throws a monkey wrench into these processes by making the selection coefficient a function of the frequency of the traits. But we need to start from simple models and build up in complexity.

The example of the !Kung woman who did not want to kill her light-skinned daughter is illustrative of Judy's hypothesis, but, it is simply a starting point. Nevertheless, I think it highlights a weakness: the genomic data is shedding light on the possibility that selection for loci which cause light skin (or, more properly explain a proportion of the intergroup variance) occurred long after the first humans settled the temperate zone. If the parental preference for light skin (which derives from the deep seated sensory bias which is also the root of sexual selection) existed prior to the arrival in the northern latitudes why is it that Eurasian populations seem to exhibit pulses of selection relatively late in history? One could make the argument, assuming that parental and sexual selection were paramount, that child and mate choice were simply not operative prior to this time period. Sexual selection works ideally through polygynous mating systems where there is a great deal of reproductive skew. Peter Frost has argued that blondeness in European females emerged through a form of sexual selection where males selected from a finite sample space of females because of the nature of the low latitude tundra, but the operative principle is the same, selection upon heritable variation. Perhaps within the last 10,000 years large boom and bust cycles in populations through the World Island has resulted in truncation selection events which reshaped the genomes (and generated high selection coefficients who show up in the long haplotypes)? I really don't know, but, I think one must say that it is more complex and contingent than a simple relaxation of functional constraint and the operation of innate preferences.

Additionally, I don't see much exposition of the details of sexual selection theory in Judy's article. For example, runaway sexual selection occurs very fast, and is often quickly checked by functional constraints. I believe that her hypothesis about light skinned preference being very deep implies some sort of sensory bias.

The intersexual difference in coloration is obviously real. There are biological reasons for this (hormone levels), but the cultural amplifiers of this tendency are rather universal. On this point the hypothesis is on strong ground, civilizations throughout the world seem to value female (relative) paleness. But, I think this point still goes back to my previous issue in regards to time scale: is this a phenomenon of the mass societies?

In any case, I'll leave it at that. There's a lot to chew on here. My main point of contention with this hypothesis is that I think the time depth is off. The most current results out of genomics suggest repeated and independent evolutionary sweeps in northern Eurasia at various times generating the phenotype of light skin. If the preference for light skin is deep within our natures, even predating bipedalism, it seems that it should have manifested immediately with the move of H. sapiens sapiens to the northern latitudes 30,000 years ago.

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Nominations for creepiest hair-band song   posted by Razib @ 3/21/2007 12:02:00 AM

OK, something for the elderings amongst us: nominations for the creepiest hair-band song. Post the link in the comments for YouTube. Mine is below....


Tuesday, March 20, 2007

A Turkish analogy for Indo-Europeans?   posted by Razib @ 3/20/2007 03:01:00 PM

After reading J.P. Mallory's In search of the Indo-Europeans I am much more convinced of a possible analogy with the expansion of th Turkic peoples for the rise of the Indo-Europeans. Roughly, in 400 Turks would have been confined to the area around where presently the borders of Russia, China, Mongolia and Kazakhstan converge. 1,200 years later Turks ruled vast swaths of middle-west Eurasia. Both India and Iran were ruled by Turk dynasties. The Ottomans were self-consciously of Turkish origin. Much of central Asia was going through turnover from being predominantly Iranian speaking to Turkish speaking. In Sons of the Conquerors journalist Hugh Pope traveled around the Turkish world, and one thing he offers (which I had understood before) is that the many Turkic "languages" are very close, and pretty much intelligible. So linguistically Turks are very close, but what about genetically? Not so much. I won't review the studies here, you can google them, but, if you've met a Turk from central Asia and another from Anatolia, it is pretty obvious that the former is way too hairy to be a true blue "Mongoloid" (Borat = Turk from Turkey, not Kazakhstan). The studies I've seen suggest anywhere from 5% to 25% admixture between local Anatolian substrate and immigrant central Asian Turks over the last thousand years (they seem to converge around 15%). This means that some Anatolian Turks do look Asian, because the alleles that code for Asianness are going to be distributed unequally throughout the population, but, most look pretty much like what you would expect being situated between Iran, Greece and the Arab Middle East.1

Of course, Turk cultural domination did not entail wholesale Turkicization. Though modern Iran is about 1/3 Turk (Azeris plus other odd groups), Indo-Iranian elements still dominate. Similarly, Turk rule in India didn't leave a strong cultural imprint (aside from names and adherence to the Hanafi school amongst Muslims). Interestingly, one could argue that in India Turk rule served as a vector for Persian cultural ascendancy, as Farsi was the court language of the Mughals. Similarly, Farsi was also in high esteem at the court of the Ottomans. So the rise of Turk rule also resulted in the spread of Persian cultural forms, and in places like India the Turkic military elite recruited heavily from Persia to fill their civilian bureaucracies.

So what does this have to do with Indo-Europeans? Well, I speak two Indo-European languages. English and Bengali. I am familiar with a third (I took several years of French). Even as a child I was struck by the similarities between Bengali and English, though not knowing of the Indo-European language family I had a difficult time understanding why the cognates would exist. A new position in Indo-European studies is that this language group spread from Anatolia with the Neolithic revolution, beginning 8 to 9 thousand years ago. This would place the diversification of Indo-European very far back in time, and historical linguists have a serious problem with this: Indo-European languages are just too similar. There are many variants of the Out-of-Anatolia theory, but they all suffer from this conflict with historical linguists. Some of the wrinkles include adding secondary homelands, epicycles if you will. In the case of Indo-Iranians their precursor culture, the Andronovo, is known. Believe it or not, a disproportionate number of borrowings of Indo-European words into Finno-Ugric are clearly Indo-Iranian forms! (take that you uncreative Finns!) This dovetails well with the Andronovo as the predecessors of the Indo-Iranian groups, as this culture was extant to the south and east of the Finno-Ugric "homeland" (or, roughly the central tendency of these languages). Explaining these findings is a difficult project for the Out-of-Anatolia hypothesis, and at some point the complexity begins to resemble apologia in my opinion.2

In any case, it seems to me that the odds on favorite is still the Pontic-Steppe hypothesis. And this is where I think the Turk analogy is so obvious: Indo-Europeans could have expanded rather quickly as mobile war bands. In some places, like Syria (the Mitanni) the dynamic was similar to India or Iran for the Turks, the local substrate absorbed the Indo-Europeans (who in Syria were Indo-Aryans). On other regions, such as Europe and India, the dynamic was more like Anatolia, though some genetic signatures can be discerned (perhaps M17/R1a?), the local population was large enough that the demographic impact was not substantial, but, the cultural impact was enormous (i.e., the language you speak is a big deal, even though I think a good argument can be made that pre-Indo-European forms still predominate in the civilizations of Greece or India, for example, or that the non-Indo-European Etruscan input into Latin culture was a fundamental distinctive characteristic).

Addendum: On the map, Turks were dominant through most of the area shaded by 1200. Anatolia was already dominated by Turkic tribes, most of the Middle East was controlled by various Turkic military elites, Turks were soon to be dominant in the make up of the Mongol Golden Horde, and India was being invaded and conquered by Turkic warlords. 1600 was simply the apogee before the long decline.

1 - Many Balkan Turks were resettled after the great exchange with Greece in the early 20th century, so modern Turkish citizens might be somewhat less Asian then they would be otherwise.

2 - Renfrew's model was on the heels of Cavalli-Sforza's demic diffusion wave of advance regarding the spread of agriculture in Europe.

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Group selection, the parameters   posted by Razib @ 3/20/2007 10:10:00 AM

I wanted to a wait a bit before I posted this, but the essential part of Elisabeth Lloyd's essay Units and Levels of Selection is this:
It is widely held, for instance, that the conditions under which group selection can effect evolutionary change are quite stringent and rare. Typically, group selection is seen to require small group size, low migration rate, and extinction of entire demes.[3] Some modelers, however, disagree that these stringent conditions are necessary. Matesi and Jayakar, for example, show that in the evolution of altruism by group selection, very small groups may not be necessary (1976, p. 384; contra Maynard Smith 1964). Wade and McCauley also argue that small effective deme size is not a necessary prerequisite to the operation of group selection (1980, p. 811). Similarly, Boorman shows that strong extinction pressure on demes is not necessary (1978, p. 1909). And finally, Uyenoyama develops a group selection model that violates all three of the "necessary" condition usually cited (1979).

In short, if there is too much migration between demes (breeding groups) then selection upon group heritable traits can not occur. Between group variance is diminished too quickly. The emphasis on the extinction of demes is due to the fact that that this makes the selective punch strong (i.e., the selection coefficient upon the group level trait). As for group size, David S. Wilson often uses an "organismic" analogy. Increased size means increased complexity, so a model which already suffers from a lack of parsimony benefits from simplicity. A large group is presumably less cohesive, and at a certain point it is pointless to speak of a "group" in any real sense (e.g., the "deme" of North Americans?). The main issue I have with group selection is that between group movement seems to be a major parameter in human societies, "exterminating" another group often involves killing them men and taking their women. In a marginal society this may not be viable as "big men" might not be able to support extra wifes, but with societies with some stratification and excess surplus, this is the norm (more realistically, surplus allocated in an equal fashion). In the comments below Jason points to this paper:
My empirical estimates show that genetic differences between early human groups are likely to have been great enough so that lethal intergroup competition could account for the evolution of altruism. Crucial to this process were distinctive human practices such as sharing food beyond the immediate family, monogamy, and other forms of reproductive leveling.

Monogamy generally implies some sort of resource constraint. Though I think that pre-Neolithic group selection is more plausible than post-Neolithic group selection (see the parameters above!), the work looks at modern hunter-gatherers as his models. A primary objection to this back extrapolation is that modern groups, like the Bushmen, have been marginalized and driven to the least desirable locales by agricultural groups. They might not be good representatives of pre-modern hunter-gatherer groups, some of whom might have been rather complex. I will agree though that the non-group selective explanations for "food sharing" have struck me as unsatisfactory (e.g., enhancement of reputation).

Anyway, here is a verbal description how a group selective mechanism could. Let's assume a trivial amount of migration/mutation, so demes have a mix of strategies in various proportions. Take two demes, Mostly Cooperator (MC) and Mostly Defector (MD). Cooperators are selfness, and so they increase their group fitness. Defectors don't increase group fitness. In the MC average fitness is higher than in the MD group because the former has more group contributors. On the other hand, within MC and MD the defectors are both fitter than the cooperators, they're free riders. Over time, MC would marginalize MD, but, MC itself would be effected by a turn over from cooperation to defection since the latter strategy is fitter within group. How can cooperation persist? A solution would be for the initial MD to go extinction, and MC to them redistribution itself into smaller groups. At this point, these smaller groups would exhibit imbalances in the number of cooperators, and so the process would recapitulate itself.

Addendum: From this explanation, and an internalization of the parameters above, I think you can intuite while cultural group selection is more plausible than biological group selection to most workers.

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Monday, March 19, 2007

An Indo-Europeanist on Etruscans   posted by Razib @ 3/19/2007 11:50:00 PM

I'm rereading In Search of the Indo-Europeans by J.P. Mallory. Here is Mallory (1989) on the Etruscans:

...This raises the entire problem of Etruscan origins which has filled volumes...and is as heatedly debated as the problems concerning Indo-European origins. There is no easy solution, since the evidence is extremely self-contradictory. Nevertheless, the present tendency in Etruscan research is to adopt the most economical hypothesis: the Etruscans were a non-Indo-European people native to Italy who adopted many items and styles of east Mediterranean provenience by way of trade....

Mallory is an outsider to Etruscan studies, but I think it goes to show that the dominant view was the 'economical' one. I don't see any problem with this, the fact is that researchers did have confusing, contradictory and fragmentary pieces of evidence to go on. The idea of a mass folk migration from western Anatolia by a mysterious people to the northwest coast of Italy does seem far fetched. But, I think the the character of the mtDNA phylogeny strongly suggests just such a movement. This is a case where reading passages like this can be very illuminating, because the scholars did have many somewhat instructive variables which just didn't "gel" together in an authoritative manner. In many ways the tentative consensus was the inverse of the reality, it was the Etruscans who adopted the customs and ways of the local indigenous substrate, not the locals adopting Etruscan culture from the eastern Mediterranean. With the powerful genetic evidence the priors are reshaped, and what were once variables of uncertain veracity can now be sifted appropriately, and the contradictions melt away. Interestingly, Mallory notes that many of the theories about the origins of the Indo-European peoples of Anatolia are dependent on Herodotus.

Related: Etruscans - the consensus?

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Levels of selection (group selection)   posted by Razib @ 3/19/2007 08:44:00 PM

The topic of "group selection" emerges many times on this blog. My own issue with this debate is that semantics are often rather tortured...and people have to be on the same page for any intellectual utility to be derived. With that in mind, I would like everyone who wishes to discuss groups selection to read Elisabeth's Lloyd's entry in the Stanford Encyclopedia of Philosophy, Units and Levels of Selection. It's long, but pretty definitive as far as surveys go. I think it will suffice as a semantic recalibrator. Also, David S. Wilson, the main promoter of higher level selection, has a new paper out, Human groups as adaptive units. If the topic interests you, I suggest you check it out. I've only skimmed the paper, but I'll give it a closer look soon....

Update: I read Wilson's paper...and it really doesn't push the ball beyound what you'd find in Unto Others. I am reminded of an anecdote that Martin Gardner related about Rodulf Carnap and the animosity that Karl Popper held toward him, "...the distance between him and Popper was not symmetrical. From Carnap to Popper it was small, but the other way around it appeared huge...." It seems Wilson wants it both ways, on the one hand, the mainstream is already where he is, they simply don't recognize it, on the other hand there is going to be a seismic Kuhnian paradigm shift in the near future. I will excise a portion of Wilson's paper which I think illustrates the problem with his sort of theorizing:
As an example, consider a single group consisting of two types of individual, A and B. Type A individuals behave in a way that increases the fitness of everyone in their group (including themselves) at no cost to themselves. The idea of providing a public good at no private cost might seem unrealistic but is useful for illustrative purposes. Type B individuals are free-riders that enjoy the benefits provided by A-types without providing any benefits of their own. By increasing the fitness of everyone, the frequency of A-types does not change within the group (except by drfit)....

Continuing this example, suppose that there are many groups, not just one, that vary in their frequency of A and B types. Even though the frequency of A does not change within any group (except by drift), groups with a higher frequency of A will contribute more to the total gene pool than groups with a lower frequency of A. In effect, we have added a process of natural selection at the group level: a population of groups, that vary in their genetic composition, with corresponding variation in their contribution to the gene pool (fitness). Group selection provides the fitness differences that were lacking within groups. In the case of a no-cost public good, any variation among groups is sufficient for the A-type to evolve to fixation in the total population, because positive among-group selection is unopposed by within-group

Yes, and money grows on trees! Group selection will not be validated by a priori analysis, it needs to be supported by empirical examination. A few examples already exist, and more will no doubt emerge, but evolution is a science of variation. The issue is not whether something occurs, but its importance in the order of things. As Wilson states in his paper, everyone agrees in principle that group selection can occur, so why the need for a toy model to illustrate that it can occur in the best of all worlds? I guess I feel that I want my 20 minutes back.

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Galor and Moav: Property rights as an evolutionary force   posted by Herrick @ 3/19/2007 12:32:00 AM

Recently, I've posted on economists' attempts to use genetics to explain long-term economic growth. So far, I've talked mostly about data. Today, theory gets its due.

Oded Galor (Brown) and Omer Moav (Hebrew U and Royal Holloway) have a simple story: The agricultural revolution set off a process of rapid human evolution that itself created the industrial revolution.

The longer version: In a hunter-gatherer society, everything's a team effort. Each day's successes and failures are shared with a fairly large clan. That provides insurance, which is quite valuable. However, since there's no "I" in team, that means that in a hunter-gatherer world, evolution can only work at the group selection level. And as Razib has noted, group selection is simply a weaker force than family-level selection.

Then comes the agricultural revolution. Such a world, they say, led to the rise of the nuclear family as the unit of production, as the unit of wealth transmission, and hence, as the unit of evolutionary selection. More productive nuclear families, working on their own plots of land, were wealthier and hence healthier and hence passed on more of their genes into future generations. The end of insurance meant the end of group selection.

In the main body of their paper, Galor and Moav emphasize the "quality v. quantity" choice as the key evolutionary choice: Parents who chose to have lots of kids would pass on fewer genes, while parents who chose to invest more in the education/nutrition of a smaller number of kids passed on more of their genes. So the "choosing child quality" allele become the favored allele. However, they explicitly note that they could have just as easily written the model as one where more intelligent offspring were more productive.

My subject line is disingenuous: Galor and Moav nowhere claim that property rights were an evolutionary force. However, they do need some mechanism in their model to move them from the group-sharing of the hunter-gatherers to the family-sharing of the agriculturalists. "Property rights," whether tacit or explicit, seem to do that just fine. What's mine is (sorta) mine, even if the king takes half and I share some with my neighbor. Still a far cry from the hunter-gatherer world.

It's easy to see how this theoretical model can fit into a Diamond-style Guns, Germs, and Steel model: Regions of the world that have more easy-to-domesticate plants and animals ex ante (e.g., Eurasia) have a more thorough agricultural revolution, which leads to more rapid spread of the human-capital-promoting alleles throughout the population ex post. Rice begat 'rithmetic.

Galor and Moav's paper, "Natural Selection and the Origin of Economic Growth," was published in the Quarterly Journal of Economics (a top-5 econ journal) in 2004. A working paper version is here. A less-technical review of the new field that Galor and his coauthors created, known as "Unified Growth Theory," is here. Section 5.2 of the latter paper gives a quick overview of their theory. The closing paragraph of the review is worth citing:

The most promising and challenging future research in the field of economic
growth....would be the exploration of the interaction between human evolution
and the process of economic development.

Sunday, March 18, 2007

The Greeks   posted by Razib @ 3/18/2007 09:04:00 PM

Here's a question: what "invention" of the Greeks was the most significant? This is a subjective question as I'm not going to specify criteria to constrain you, I'd like get some nominations is all. And I'll offer mine: the mathematical proof. I think one can make a case that the Greeks basically invented formal systematic thinking.*

* I stipulate both formal & systematic because it seems that ad hoc formalisms (e.g., Babylonian mathematics) existed prior to the Classical Greeks, and certainly philosophical systems emerged in other civilizations (e.g., Indian philosophy). But, it seems that the prior formalisms weren't philosophical (i.e., their ends were often engineering or astrological), nor was the philosophy truly formal (i.e., their ends were often religious or ethical and framed in culturally conditioned verbal narratives).


De facto universal DNA database   posted by the @ 3/18/2007 01:04:00 PM

I've previously argued for the expansion of DNA databases to universal coverage. The reasoning being in part that all-or-nothing coverage is in many ways preferable to the patch-work system now in place. I'm not alone in making this argument, and I find it comforting that most authors commenting on this subject agree that some kind of changes are needed. The consensus of most commentary is that greater legislative regulation and oversight is needed regardless of what direction we take.

Making action on this issue more urgent, several developments have occurred which bring us to a situation where de facto universal coverage seems likely to occur merely as an extension of current policy (without further legislative action). The first development is the finding that the STR profiles currently used in law-enforcement DNA databases are good enough to allow identification first-degree (and even second-degree) relatives in a substantial percentage of cases. While there are technical limitations to this approach, this development has the net effect of significantly expanding the number of individuals who are identifiable. The second development is one of law-enforcement technique -- the surreptitious collection of discarded DNA from targeted individuals. Regardless of the legality of individual methods used, it seems inevitable that certain forms of surreptitious collection will be legally permissible. This has the net effect of making any targeted individual's DNA open to law enforcement without a court order. Lastly, the pace of development of genotyping technologies is quickly bringing us to a point of virtually-limitless genotyping capacity. The possibilities of surreptitious DNA collection that this will open up are limited only by imagination (and the cost of human labor).

All of these developments point towards a situation where a de facto universal DNA database (or a functional near-equivalent) will develop even in the absence of any changes in legislation. This appears to be a largely-unexamined issue, but it seems to call for debate and legislative action.


Emma Darwin, novelist (again)   posted by DavidB @ 3/18/2007 05:54:00 AM

I mentioned last year that a highly-praised new novelist, Emma Darwin, was yet another descendant of you-know-who.

I will therefore provide a link to this interview with her in today's (UK) Sunday Telegraph. I see that her novel is now available in paperback, and nominated for a prize.

American readers may be puzzled by the reference to Annie's Box, by Randal Keynes. This was given a different title for its US publication. I can't imagine why.

What kind of genomics is this?   posted by Razib @ 3/18/2007 12:01:00 AM

OK, just checking out books on Amazon (I usually check reviews before looking for the books elsewhere), and I found this: A Discourse with Our Genes: The Psychosocial and Cultural Genomics of Therapeutic Hypnosis and Psychotherapy. Also, check out The Psychobiology of Gene Expression. No. I'm not making this up. Click the links. I dare you.


Saturday, March 17, 2007

Climate change & size   posted by Razib @ 3/17/2007 10:55:00 PM

Climate change said to affect evolution:
Researchers found that while more of the largest sheep survived in the harshest winters, smaller sheep also survived mild winters, bringing down the average size and reducing natural selection among the sheep, the Times reported.

This seems to be confirmation of Bergmann's Rule:
In zoology, Bergmann's Rule is a principle that correlates environmental temperature with body mass in warm-blooded animals. It asserts that within a species, the body mass increases with latitude and colder climate.

As size increases, the ratio between surface area and mass decreases, resulting is less loss of heat through radiation. This is obviously convenient if you are a warm-blooded mammal trying to maximize metabolic efficiency in a low temperature clime. Since it is a "Rule," it isn't always operative. But, for example, humans became smaller after the Ice Age. The only issue I would quibble in regards to the press release is the idea that natural selection was "reduced." It seems to assume that there is a set species size which the population regresess to naturally, when in reality large size likely comes with some cost which might exceed the reduced payoff in regards to metabolic efficiency at higher temperatures (or, smaller individuals might develop and reproduce faster).

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Numbers, numbers   posted by Razib @ 3/17/2007 11:20:00 AM

The survey about medical doctors & evolution from a few years back has been nicely reformatted. Interestingly, adding the % of Hindu docs and assuming that 1/3 of the Muslims are South Asians gives the regularly quoted figure that "5% of American doctors are Indian American" some backing. I was surprised that males were such a large % of docs, but I suppose that there are a lot of older practitioners in the field from before the time that med school graduation rates were around 50/50 gender wise. Also, recently The New York Times repeated the standard "estimated six million Muslims who live in the United States" figure. The number comes from Muslim groups, so some skepticism is warranted because most religious groups try and inflate their numbers (more estimates) when possible (and Muslims in particular have been aiming to find figures which would show that they are nearly as numerous as Jews). The American Religious Identification Survey found only 1.1 million Muslims. But, I realized there is another way to check which numbers might be correct: these quotes also imply that 1/3 of American Muslims are South Asian. That sounds about right, either South Asians or blacks are the most numerous group of Muslims. Unlike religious data, the Census does collect ethnic data. Checking the most recent Census data it seems likely that the total number of South Asian Americans (Indian + Pakistani + Bangladeshi + Sri Lankan + Nepali) is somewhere between 2.5 and 3 million (here are the numbers for Asian Indian in 2005, you can also find Pakistani American by selecting "population group" to the left, though Bangladeshis and other groups will take some googling or trolling the Census site). Let's take 3 million to err on the side of a high number, and use 6 million for Muslims since it is nice & round. If 1/3 of American Muslims are South Asian, that means 2/3 of American South Asians are Muslim! This is not true. Around 85-90% of American South Asians are from India. Let's be generous (to Muslims) and assume that all 15% of the non-Indians are Muslim (obviously most Sinhalese are not, and a disproportionate number of Bangladeshis in the USA are likely Hindu and Pakistanis likely Christian). Let's also assume that 15% of Indians are Muslim, since that's about their proportion in the Indian population (this is probably an overestimate as American South Asians are biased toward particular regions and ethnic-caste groups, and none of these are Muslim). You get a total of 825,000 Muslim South Asians. Assuming that 1/3 of Muslims are South Asian, you get 2,475,000 American Muslims. Assuming 1/5 of Muslims are South Asian, you get 4,125,000 Muslims. To reach 6 million fewer than 15% of American Muslims must be South Asian. 1) This is not plausible, all the proportions are between 1/4 and 1/3. Though aggregate numbers are not something you can guess by visual inspection, proportions are. People couldn't pretend that half of American Muslims were Albanian, for example, because the number of brown, white, black and Asian Muslims is pretty obvious in a mixed gathering (yes, I know there are ethnic mosques, but you can count those up separately). Note that I'm also being a bit generous with the number of South Asians (it is likely closer to 2.8 million than 3), and the % who are are Muslim (likely less than 10% of Asian Indians are Muslim, groups like Gujarati Hindus, Punjabi Sikhs and Malayalee Christians are highly overrepresented among American Asian Indians). Anyway, checking the numbers took me all of 15 minutes (I'm including writing up this post, double checking it for errors). I know people are on a deadline, but seriously, "the paper of record"?

Update: Here is how not to comment on a post which took me 15 minutes of simple multiplication and division. Please, do read what I write before offering an opinion!

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Friday, March 16, 2007

Chat   posted by Razib @ 3/16/2007 05:55:00 PM

As some of you have noticed I've added the chat feature to the right sidebar. If you click the pop up you'll get a bigger screen. I'll be making more changes soon. I decided to put it on site so people could see what was going on...the down side is that the app auto logs in everyone who visits the front of the site (I'm not outputting the chat window on individual entries and archives for those of you reading via RSS), though I gave them nicks of the form "zanon" so they'd be at the bottom of the list. I'll be tweaking/fixing as we go along time & inclination permitting.

P.S. My philosophy is to test on Firefox and fix on everything else, so warned....


The March of Civilizations   posted by Razib @ 3/16/2007 02:20:00 PM

Over at Aziz's blog there has been some discussion about ideas like "the West." On a level of serious intellectual discussion this is a complicated and expansive topic. On the level of unintellectual cheerleading it is all rather simpler. To some extent this is apropos as we've been discussing 300 a lot recently, and it relates to my earlier post on Al-Andalus in regards to how people view, and use, history. Defining a "civilization" is difficult, basically you're trying to describe a cluster of characters in which span many dimensions. It is the same problem which crops up when we talk about "race," essentialism becomes the straw man which everyone likes to knock-down. This was in fact one of the main ways that people attacked Huntington's "Clash of Civilizations" thesis, it was a coarse enough model that you didn't need to know much to poke holes in the categorizations.

Aziz said over at his blog:
As far as whose civilization precedes whose, I just don't see any meaningful lines to be drawn between Persia, Greece, etc. Obviously they were distinct but they also were built on the same shared foundation of previous civilizations. It's like genetics - mixtures and sharing of ideas/genes freely flowing. Rewind the the tape far enough and everything that looks distinct today just melds into the amorphous mass.

Yes, and no. Obviously like genetic evolution, cultural evolution is marked by mixing & matching various elements together in combinations, and an inevitable spread of selected traits (e.g., iron usage, rice farming, etc.). But, there is a marked difference in the nature of variation between genes and cultures: two adjacent populations are far more likely to exhibit more between group variation culturally than genetically. An obvious example would be the peoples of Bengal. The eastern 2/3 of the historic Bengal now form the nation of Bangladesh. The western 1/3 is now the province of West Bengal in India. Going back to the blood group studies of the early 20th century little distinction could be made between these two regions, one where Muslims predominated and the other where Hindus did. But, there is obviously a strong cultural difference, that of religion. And that religious difference bleeds into various areas of life, in regards to speech, dress, food and manners. Cultural evolution can occur very fast, in my own family a great-grandfather of mine converted from Hinduism to Islam, and therefore there is a sharp discontinuity in cultural traditions, at least outwardly, across the generations. Of course, Hindus and Muslims in Bengal are not cultural aliens, they share a culture, broadly speaking. But, their between group difference is far greater than what one would predict based on genetics. The moral here is that cultures can have relatively sharp boundaries which emerge very fast because of the nature of the human capacity to absorb new ideas, and, the high fidelity that some of these traits exhibit when spread within a group. Language is a perfect example, within a tribe there is no dialect difference because everyone has approximately the same accent. What does this have to do with civilization? Differences do exist, and they manifest in a relatively sharp fashion in comparison to genetics. This is starkest when it comes to language and religion. Consider the border between Turkey and Greece in in the southeast Balkans, linguistically and religiously the difference across a few tens of miles can be enormous (in part because of ethnic cleansing in the early 20th century on both sides of the border), but genetically the difference will be far smaller. Though Greeks and Turks do not intermarry much because of the religious and linguistic differences, the Turkish cultural complex spread through the substratum of Anatolia and left only a minor genetic impact. Many of the ancestors of modern day Turks would likely be Greek speakers, and their non-Greek antecedents likely lived in Anatolia long before the arrival of nomads from Central Asia in the 11th century.

But though there can be sharp differences in civilizations over short periods of time (e.g., the conversion from a Greek dominant culture in central Anatolia in the 10th century to a Turkish one in the 12th) and space (the convergence of Turkic, Greek and Slavic cultural complexes in Thrace in the Balkans), there is also a great deal of cultural exchange, and a particular ethnic group or tribe is not always easily boxed into one civilizational category. For example, though the Javanese are overwhelmingly Muslim, they retain their Indian derived script, and aspects of custom and tradition from their Hindu-Buddhist past. In fact, the pre-modern state which the Indonesian government uses as justification for its dominion over the far flung archipelago, the Majapahit Empire, was based on Indian (Hindu) cultural foundations. So what civilization do the Javanese belong too? The Indian one, or the Islamic? Clearly they are a synthesis of various cultural elements from both major civilizations, which serve as an overlay upon their own indigenous cultural traditions. Similarly, the Thai nation emerged from the milieu of southern China, and their co-ethnics, the Dai, are still a national minority in the People's Republic. But once in southeast Asia they took the Khmer Empire as their exemplar and adopted more "Indian," as opposed to Chinese, cultural forms. For example, Theravada Buddhism and court Brahmins. Though the Thai king was often a vassal of the Emperor of China (and the Thai ruling dynasty has Chinese ancestry!), the royal system was based more on Indian precepts than Chinese ones. Further east the Vietnamese also emigrated south from what is now southern China, but whereas the Thai adopted an Indian cultural model, the Vietnamese were much more directly influenced by Chinese culture, the dominant form of Buddhism being Mahayana, and an emulation of Confucian models occurred here just as they did in Korea, and to a some extent, Japan. On the other hand, the Vietnamese state absorbed the Saivite Hindu Malay speaking Champa Empire. So today there still remain an ethnic minority of Chams in the Vietnamese highlands of the central coast who remain Hindus. The point is that though the disparate nations of southeast Asia were different influenced by other civilizations, we can estimate very approximately the weights, without denying that the influences were not singular or uniform.

Now, with the technicalities addressed, let me address another point Aziz made in his post:
I look at history and I see two civilizations - that of the Islamic-Christian arc, and the East (China). I also see a vast struggle between barbarians and nations.

Aziz has stated this before, but, I would offer that there is a third civilization: that of South Asia. Though on the "rank order" of influence I would place the West first, and China second, I do believe Indian civilization deserves to be counted as a major one simply because it is the only one besides the West which has produced world religions (and, it did it first, and there is evidence that later Abrahamic forms of organization, such as monasticism, had original Indian models mediated through Persia and Rome). Among higher religions there are two broad streams: the Abrahamic, and the Dharmic. Indian influence was predominantly through religion, though they also participated non-trivially in the cultural lines of communication which stretched from the Atlantic to Persia (e.g., the Indian numeric system). From an Abrahamic perspective (Aziz is a Muslim) it stands to reason that one would divide the world into Heathen and non-Heathen, and in modern America there has been an attempt to generate a pan-Asian identity which includes Indians by appealing to the cultural glue of Buddhist civilization (but this seems a stretch). But these three civilizational streams are but principle components which sketch out particularly powerful cultural pulses across time and space. Back-projecting "Indian" or "Western" identity 2,000, or 3,000, years ago is clearly problematic. When Westerners say "our forebears the Greeks" there are issues with such an assertion.

A major factor is that most people are not interested in history aside from the bricks and mortar it can provide for our ideology, our patriotism, our sense of identity and place in history. The past consists of symbols, and for most humans the reality of its existence and the manner in which it played out is irrelevant. In From Plato to NATO classicist David Gress outlines what he perceives to be the attempt by some intellectuals (preeminently Will Durant) to draw a connection between the modern West, and especially the United States, and democratic Athens of the 5th century. In the process Gress argues that these intellectuals dismissed and marginalized the impact of the Roman Empire, the Christian religion, the post-Roman Germanic feudal states. Concisely put, Gress argues that the creation of the West, what was once termed Christendom, was a organic process, while historians such as Will Durant wished to retell the story so that Athens was rediscovered in the 18th century, and subsequently served as the model for the liberal democratic present we now live in. But the reality is that even in the United States our classically educated founding fathers looked less to Athens than Rome, for we are first and foremost a republic, and the system of checks and balances reflects more properly the mixed government and indirect representation of the Roman Republic than the more uniform participatory polity which Athens was.

The emergence and crystallization of civilizations and cultures and the self-identity of a people is subject to many contingencies. But, as I note above, this can occur relatively fast and with sharpness when set against biological evolution. The French Revolution imposed a national self awareness upon what had been a more amorphous entity, a French nation of villages, with local dialects and languages, under the personal rule of a king. As a child of the late 20th century the myth of Athens was taught to me with clarity and finality, and yet this was a creation of the mid-20th century. But what is the past but a strange and forgotten land? As I noted earlier this week, at the same time that the Muslim government of Iran burnishes its religious credentials, it can take offense at the insult direct at its pagan past, which it might otherwise wish to deemphasize. Pakistani Muslims can cheer and identify with the depredations of Turkic warlords upon the Hindus of the Punjab and Sindh, even though those Hindus were their own ancestors!

Aziz's post began as a reaction to a comment thread over at Dean Esmay's group blog. The gist is that some individual was making caricaturish assertions about the West vs. the East, and others pointed out that a) the classical Greeks might only tenuously be connected to the West now, and b) Persia was the font of a great deal of culture. Additionally, there came the conventional argument about the contributions of Islam to the development of the Western intellectual tradition. My own opinion is this:

a) The Greeks were special, especially in regards to intellectual and political life. But much of what they wrought did not "take" as Roman autocracy resembled "oriental" despotism far more than the vibrant political life that was Athens. Greece serves as an important retrospective model, but we should be cautious in drawing a straight line between 5th century Greece and the modern West.

b) The Persia of Xerxes was not quite yet Zoroastrian, but it was the seedbed from which that religion arose. Zoroastrianism has been highly important in the history of the world via its influence on Exilic Judaism (ergo, Christianity and Islam). One can model Christianity as a combination of Hebrew religious ideas synthesized with Persian ones, and then flavored with a strong Geek philosophical spice.

c) In regards to the influence of Islam on the West (e.g., Aristotle):

1) My most current reading implies that intellectual development preceded the importance of "the Commentator" in the 13th century ("the Commentator" was Ibn-Rushd). The Islamic influence amplified and enriched the Western intellectual milieu in the 13th century, and was an important ingredient in the "Aristotelian Renaissance," but a major reason that it is emphasized is ideological.

2) I say the last because the emigration of Greeks from Byzantium during the same centuries to Italy was also extremely important, and unlike the Andalusian impact it was via classical authors in the original Greek (as opposed to translations into Latin from Arabic which were translated from the original Greek or Aramaic translations themselves). This is not to dismiss the Andalusian contribution, but, it is to suggest that the outsize importance that it is given is perhaps a reflection on the intellectual and cultural currents of the 19th and 20th centuries above and beyond what occurred in the 13th century (part of it is perhaps that Anglo-Saxon scholars are probably biased toward the influence that Ibn-Rushd it had on the relatively nearby University of Paris as opposed to the intellectual ferment that occurred in Italy because of the Greek learning imparted by the Byzantines).

Of course, no offense, but I don't have any hope that the "rabble" that Aziz alludes to will be influenced by this post at all. I say this, and state this, in the interests of capturing the world as it is, and as it was, to the best of my current knowledge and analytic capacity. And in hopes that others will also be willing to muddle along with me....

Further Reading:
From Plato to NATO
Aristotle's Children
The Closing of the Western Mind
Medieval Foundations of the Western Intellectual
The Classical World
Sailing from Byzantium
Not by Genes Alone
Indonesia: Peoples and Histories

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Epigenetics in memory   posted by amnestic @ 3/16/2007 08:13:00 AM

There's a new article by Miller and Sweatt in Neuron claiming that DNA methylation is a step in memory formation. They show methylation and demethylation of particular genes (reelin and PP1) following fear conditioning, and they show that inhibition of DNA methyl transferases (the name says it all) during the memory consolidation can disrupt memory. I hope now that they've started naming genes at which the methylation matters they'll study something more specific. The idea of inhibiting all DNA methylation in a cell for any length of time seems too blunt an instrument. The cells responsible for that memory could've just keeled over or radicaly changed because some cell cycle regulator got turned up too high for instance. They do show that animals can form a new, strong memory a couple days after administration of the drug, but in some cases, animals with a hippocampal lesion can perform these tasks. The nervous system can achieve learning (especially learning as important as conditioned fear) through many means, so seemingly normal behavior after an insult isn't that strong a control.

The scope of the processes disrupted by a DNMT inhibitor is indicated by this sentence from Miller and Sweatt:
Many developmentally important processes utilize this "prima donna" of epigenetics (Scarano et al., 2005 and Santos et al., 2005), including gene imprinting, cell differentiation, X chromosome inactivation, and long-term transcriptional regulation (Bestor et al., 1988 and Okano et al., 1998).

Sorry to be such a naysayer. It is an interesting hypothesis. It is likely the case that DNA methylation is regulated during memory formation. If we just think that memory will require transcriptional regulation then probably some DNA modifications will have to be done and undone. Cis-regulatory sequences that control a gene's level of activation can act through recruitment of histone acetyl transferases and other chromatin modifiers, so a precedent exists. But I don't think there is any special connection between epigenetics and memory. Memory requires cells to be cells and work properly, so it will require transcriptional regulation and DNA/chromatin modification. For any further connection, I think we have to start naming names.

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The Faiths of the Founding Fathers   posted by Razib @ 3/16/2007 12:07:00 AM

Just read The Faiths of the Founding Fathers. Summary:

George Washington - Deistic Episcopalian, rejected orthodox beliefs & sacramental practices

John Adams - Unitarian Christian or Deist, a anti-Trinitarian, but a strong believer in the supernatural

Thomas Jefferson - Deistic Episcopalian, leaned toward a more materialist Deism, firmly anti-Orthodox

James Madison - Deistic Episcopalian, leaned toward a more impersonal Deism, firmly anti-Orthodox

James Monroe - Deistic Episcopalian, extremely silent in regards to religion publicly or privately (though averse to evangelicalism)

These are the first five presidents of the United States, John Quincy Adams, the sixth, was the son of John Adams, and like him a Unitarian of Christian inclination. Though the modern Unitarian-Universalist Association has a non-Christian majority, and a large non-theist "Humanist" minority, in the late 18th and early 19th century Unitarianism was a form of Christianity which rejected the Athanasian Creed in regards to the Trinity. It emerged out of the "Left-wing" of the Congregationalist Church in New England. Some of them were explicit in claiming to be latter day Arians, a heretical sect which was popular in the 4th century, and persisted amongst Germanic peoples into the 6th century (the Lombards of Italy were Arians as late as the 7th century). Though there is firm evidence for Thomas Jefferson's rejection of orthodox Christianity in his private letters, he, like the other presidents besides Adams, were often affiliated with Episcopal churches. The behavior of Washington and Monroe though did not indicate a deep faith in the cardinal points of this church, while Madison was clearly more Unitarian in the beliefs he held then conventionally Protestant. Nevertheless all of these men would have counted themselves as Christians, while a large majority of contemporary Americans might reject that label for them. Over the past generation most American presidents (Carter, Reagan, Clinton and Bush II) have expressed an evangelical faith, and yet the first five presidents were very different, and highly anti-mystical Christians who abhorred "enthusiasm."

What happened? Though there is evidence that John Quincy Adams was more conventionally Christian than his father (that is, his Unitarianism was less thorough or deep), the first Christian in a sense that many Americans would find intelligible would be Andrew Jackson. Jackson was a conventionally orthodox Presbyterian, if not necessarily fundamentalist (there is private correspondence where praises all Christian religions, and includes Catholicism). After this period to our knowledge most of the presidents did not approach the heterodoxy of someone like Thomas Jefferson, though as late as the first decade of the 20th century William Howard Taft was a confirmed Unitarian who rejected the divinity of Jesus Christ. And yet today we have a scenario where Mitt Romney's peculiar religion makes nomination as candidate for president more difficult than it would otherwise be. What's going on here? Are Americans fundamentally more religious and orthodox?

I doubt it. I believe what is happening is that the broad populism of American politics has percolated upward the necessary values which a tribune of the people must possess to represent that people. During the first half of the 19th century most states abolished their property qualifications, and so the pool of voters became far broader than that which would elected a George Washington or Thomas Jefferson. These voters would come from a lower social station, and perhaps be less open to a Deism whose roots lay in the Freemason clubs and university campuses of the early nation. But universal white male sufferage was not the end of the story, as I note above religious orthodoxy was not a necessary prerequisite into the 20th century. The rise of mass culture and communication, the invasiveness of modern media into the lives of public figures, all these have likely pushed politicans to flatten the distinctions which might separate them from their constituents. Some have characterized the United Statse as a country where the elite are as secular as Swedens and masses as religious as Indians, but the reality is that at the founding the political elite was far more out of step with popular religious opinion, and what we are seeing now is more of a convergence.

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Thursday, March 15, 2007

Speciation in the temperate zone?   posted by Razib @ 3/15/2007 10:29:00 PM

There's a new paper in Science which posits that speciation might be more common in the temperate zone than in the tropics. From a summary:
...For nearly a century, researchers have assumed that new species are constantly popping up here, while speciation is far more stagnant at Earth's relatively deserted poles. But a new study claims the opposite: Species evolve much more readily at higher latitudes. It's just that the new arrivals die off so fast that most of them never get counted.
The pair studied 309 pairs of bird and mammal sister species (the most closely related pair from a common ancestor) living from the tropics to the poles. DNA analysis revealed that, on average, birds and mammals near the equator diverged from a common ancestor 3.4 million years ago; in contrast, those near the poles diverged less than 1 million years ago....

One of the researchers, Dolph Schluter, has done work on sympatric speciation of 3-spined sticklebacks. It stands to reason that he would be interested in angles besides conventional allopatric speciation. The fact that temperate lineages have relatively shallow coalescence times due to extinction rates also suggests to me that their long term effective population will be smaller. For humans this is likely true, e.g., the withdrawal of Europeans into Ice Age "refugia" during the Last Glacial Maximum, while tropical populations would be less perturbed by the climatic change. The neurobiologist William Calvin had speculated in the 1980s about the role that the oscillating Ice Ages might have had in reshaping our hominid lineage, though the Out of Africa Hypotheses have shunted that idea aside.

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Wednesday, March 14, 2007

DNA ancestry testing-- a uniter, not a divider?   posted by p-ter @ 3/14/2007 11:48:00 AM

From today's NY Times: "At a Harlem Reunion, a Rancher From Missouri Meets His 'DNA Cousins'".
[I]n walked the new cousin: a Missouri cattle rancher named Marion West, 76. It was Mr. West's first visit to New York City, and he stood out partly because of his rancher outfit: black cowboy hat, shiny boots, string tie and a jacket advertising a feed company. But he also stood out because he was a white man greeted by a roomful of black New Yorkers embracing him as a long-lost member of their family.
"If it's my story, it's many people's story too," Ms. Higginsen said. "It's the real story of America. People are finally asking: 'Whose blood is running through our veins? Who are we? Who of us is black, and who's white?' They're realizing there are no thoroughbreds among us, and nobody's 100 percent anything in this country."

As a stickler, I have to note that being 100% black or white is a pretty meaningless number to non-geneticists (in terms of posterior probability of belonging to a certain group, there are definitely people that are close to 100% something, but that doesn't mean all those people are genetically the same, as I imagine John Q. Public would interpret it), but whatever. So a white dude in Missouri shares a Y chromosome haplotype with a black family in Harlem. This is not surprising (African-Americans are an admixed population, after all), but I suppose this is a serious advance in the understanding of genetics for your average man on the street. As genetics gets involved more in our day to day lives, it's likely that your average person's intuitive sense for what genetic information "means" will improve. This can only be a good thing. I mean, hell, these people are laughing at jokes about heterosis!
He brought laughter to the room when he spoke of cattle breeding.

"I've been breeding cattle all my life, and I'll tell you, cross-breeding is better," he said. "You mate the black angus with the other breeds, and you have better, healthier offspring."
If things continue at this rate, who knows? Maybe agnostic will get his own talk show.


The games people play   posted by Razib @ 3/14/2007 12:45:00 AM

I purchased The Origin and Evolution of Cultures and Foundations of Human Sociality as a 1-2 theory + data survey of culture. Two things that have jumped out at me immediately:

1) In Foundations of Human Sociality the authors show that the variance in 'rational' behavior by universities students world wide (Western and non-Western) is very small. In contrast, in the 15 world wide cultures they surveyed there is an enormous variance in the modal outcomes. If man had a paleolithic mind, then it is very diverse indeed. The differences don't seem to track phylogeny well at all (that is, genetically close groups can behave very differently, and similarly to distant groups). Part of the answer seems to be that analogical reasoning plays a big role in how these peoples respond to these "games." Remember the whole schtick about how human universals are what matter, and they're hard-wired by the Stone Age EEA? That is a lot easier to assert when your study subjects are undergraduate college students apparently. On the other hand those barely out of the Stone Age seem to exhibit more behavorial plasticity.

2) In one paper there was a peculiar finding re: the Ultimatum Game, defined by wiki as:
...two parties interact anonymously and only once, so reciprocation is not an issue. The first player proposes how to divide a sum of money with the second party. If the second player rejects this division, neither gets anything. If the second accepts, the first gets her demand and the second gets the rest.

This experiment wasn't that anonymous. The researchers found that when tracking gender, women in mixed players pools tended to accept far lower offers from men than women. Men did not accept low offers from either gender. But, it turns out that on average women in mixed player experiments (that is, repeated plays with different individuals) had the highest overall take. Why? Because half the players were men and they tended to have a higher offer acceptance rate in those cases. The men tended to reject many offers when they felt they were too low no matter the context, though they did net the bigger offer when the giver gambled on their stubborn pride. I don't know what that says for human sociality, but one thing I have mooted on this blog is that males are high risk players, and women keep it safe. The Trivers-Willard Hypothesis is an extension of this insight when considering the nature of reproductive skew: female offspring are a sure bet, but male offspring are a bigger bet.

...more later.

Related: The games genes play.

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Tuesday, March 13, 2007

St. Paul vs. the Pharisee on 300   posted by Razib @ 3/13/2007 10:50:00 PM

Dienekes loved 300, while an academic specializing in Hellenistic history did not. I did know about the hoplites from Thespiae (700 of them)...that bothered me, but can you imagine how confusing it would have been to refer to "Thespians" throughout the film?


Sleep Affects IQ   posted by Fly @ 3/13/2007 12:13:00 PM

Sleep Disorders Can Impair Children's IQs As Much As Lead Exposure

UVa researchers have been studying sleep disturbances in children with enlarged tonsils and adenoids for the past seven years. In a recent study, they discovered that youngsters who snore nightly scored significantly lower on vocabulary tests than those who snore less often.
According to Dr. Suratt, the vocabulary differences associated with nightly snoring are equivalent to the IQ dissimilarities attributed to lead exposure. "Studies show that, even at nontoxic levels, lead exposure can reduce a child's IQ by more than seven points," he notes.
In a series of studies involving six to twelve-year-olds, researchers have been piecing together a list of risk indicators. So far, snoring frequency combined with sleep lab results have proven to be the most reliable predictors of intellectual impairment and behavioral problems. Sleep duration and race appear to be important risk factors, too.

This study only shows correlation but when combined with research showing the importance of sleep for consolidating memories the story becomes interesting. Perhaps treatments that improve sleep quality will increase IQ?

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Imprinted gene undergoing accelerated evolution in humans?   posted by Razib @ 3/13/2007 10:38:00 AM

From PLOS Genetics Identification of the Imprinted KLF14 Transcription Factor Undergoing Human-Specific Accelerated Evolution:
Imprinted genes are expressed in a parent-of-origin manner and are located in clusters throughout the genome...By sequence analysis of numerous species, we place the timing of this event after the divergence of Marsupialia, yet prior to the divergence of the Xenarthra superclade. We identify a large number of sequence variants in KLF14 and, using several measures of diversity, we determine that there is greater variability in the human-lineage with a significantly increased number of non-synonymous changes, suggesting human-specific accelerated evolution. Thus, KLF14 may be the first example of an imprinted transcript undergoing accelerated evolution in the human lineage.

Genomic imprinting has evolutionary implications, and could suggest a recent change in hominid mating systems.

Update: I was in a hurry when I posetd so I didn't clarify some issues. First:
Under this hypothesis, the maternally expressed KLF14 is predicted to suppress embryonic growth. This, together with its predicted function as a transcriptional repressor, suggests that the protein may suppress the expression of genes which enhance fetal or placental development.

Why would a female want to restrain the resource consumption of the fetus? Because it reduces her own fitness, and therefore the chance of her reproducing in the future. In a polygynous species where the male will likely not inseminate the same female twice this is acceptable for the "paternal" allele, as future paternal alleles will be unrelated. In contrast, the "maternal" allele is going to be related to the future offspring (coefficient 0.5, since females contribute one of two alleles). So you haev intralocus conflict. The confusing sexual dynamics are alluded too in the earlier link.

Also, this from the discussion might interest some:
Due to KLF14's increased expression in neuronal cells, as well as the accelerated evolution observed in the human lineage, this gene may have played a role in the acquisition of human-specific traits. Such a function would agree with our hypothesis postulated above, describing the role of imprinting in the variability of the gene. Despite being imprinted in ancestral mammals, we observe that the evolutionary aspects of KLF14 are unique to the human lineage. This observation could be due to selective pressures unique to this species, and possibly unique to demographic populations within the human population, which have accelerated the evolution of the gene. Consequently, the variations seen in KLF14 may be beneficial to humans or subpopulations of the human species, particularly the variations that are fixed or are going towards fixation. However, further studies are required to determine the gene's function in the brain, particularly in neurons, in order to assess its contribution to human speciation and its putative role in cognitive disease.

Finally, please be cautious, as much of the paper is littered with "not statistically significant" as they are looking for signs of positive selection, not rejecting neutral evolution and suggesting a possible role for relaxation of purifying selection. Kind of messy, but they looks like they might have been the first to snatch at some new fruit....

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The attack against Persian civilization?   posted by Razib @ 3/13/2007 01:26:00 AM

Not unpredictably some Iranian officials see 300 as a cultural attack. I find this interesting because the Iranian government itself has been attacking and reviling the pre-Islamic past since the revolution. From what I have read most of the tourists at Persepolis, the seat of the Achaemenid Empire, are Parsees. That is, Zoroastrians from India, not native Iranians, whose Muslim government does not smile upon reverence for the glories that came before Allah. The government has also apparently attempted to dampen the celebration of Noruz, a pre-Islamic holiday. Of course Iranian identity is a synthesis of many elements, and it seems likely that a counter-reaction to excessive Islamicization of the national identity at the expense of the cultural richness attested in Ferdowsi's work is now afoot at the grassroots. Nevertheless, my point is that situation and context matters. As a matter of historical reality it seems likely that Zoroastrianism during the reigns of the early Achaemenid was thin on the ground, and that conventional Aryan polytheism (the worship of the daeva) was the predominant dispensation. The depiction of Xerxes as a lush character indulging in pagan hedonistic pleasures in 300 was likely not that far off from reality, it was good to be King of Kings. The Islamic government should be glad that film depicts the pagan excess of ancient Persia, which did not know the light of the true religion. Without God one has nothing, including victory on the plains of battle.

Update: Kambiz has the expat view. Salman argues against the expats in the comments. To my knowledge questions like "how anti-pre-Islamic is the Iranian government?" have not been subject to quantitative analysis, so a lot of this is going to be impressionistic. One issue I would have with Kambiz's post, I read A Persian Strongholad of Zoroastrianism in college, and persecution of Zoroastrians in that nation pre-dates the Islamic Revolution. There is a reason that Zoroastrians were to be found in the most remote and isolated regions of pre-modern Iran (or that more Zoroastrians live(d) in India than Iran). And of course, the Towers of Silence were shut down by the Shah's regime in the 1970s, not the the Islamic government.


The "God Gap"   posted by Razib @ 3/13/2007 01:09:00 AM

Christian pollster George Barna has a new report out which addresses the religious differences between Republicans and Democrats. Money shot:
A new survey from The Barna Group explores the so-called "God gap" between Republicans and Democrats, examining 32 measures of religious commitment, belief and activity. The study shows that while Republicans continue to hold advantage in attracting born again Christian voters, Democrats are not as far behind on measures of Christian commitment as might be assumed.
The eight most significant differences were almost exclusively in the domain of beliefs and commitment, rather than the arena of behavior.

Update: Inductivist has the goods. Not surprisingly, the God Gap does exist for whites, and more so for Latinos. But not for blacks.


Overseas books   posted by Razib @ 3/13/2007 12:11:00 AM

I like to buy technical books, and generally I use, and cross-reference with Amazon, Froogle and MySimon. One thing I've noticed (especially Abebooks and Froogle) is that some overseas sellers are dirt cheap. But, being overseas I'm generally reluctant to purchase because I wonder about the hassles if something gets messed up in the chain of delivery. When I mean "overseas," I'm talking India or Argentina, not Britain (where the books aren't than much cheaper, if at all, especially taking into account shipping). Any experiences to relate?


Monday, March 12, 2007

Phylogenetics of the yeti   posted by p-ter @ 3/12/2007 09:41:00 PM

Cosma Shalizi points to a study on the phylogenetics of the yeti [pdf], based on a sequence of mitochondrial DNA from a hair sample. The results are striking:


DNA databases and DNA profiling   posted by the @ 3/12/2007 07:25:00 PM

Everything I've read about DNA profiling and DNA databases suggests the following:
  1. A universal national DNA database should be constructed
  2. DNA profiling for this database should switch to SNP genotyping
DNA database - The U.S. national and state governments operate a number of DNA databases. Most law enforcement databases are integrated under the FBI's CODIS system, which now contains several million DNA profiles in its "offender" index. Privacy advocates raise a number of concerns about these databases, but most political action concerns the criteria for getting profiles into and out of these databases. As far as I can tell, all of the concerns about inclusion/exclusion criteria would be circumvented by the existence of a universal database. For example, issues of contention include:
  • What crimes warrant the collection of DNA?
  • Should DNA be automatically collected at arrest or not until conviction?
  • If DNA is collected at arrest, should DNA profiles be expunged if no conviction is made?
  • Does the mass collection of DNA raise the risk of false positives and subsequent false convictions? [Note, ostensibly it does - especially when imperfect forensic profiles are used to search for a match.]
The retention of DNA samples is a second concern for privacy advocates. This is a real issue which should be addressed by maximizing protections of stored samples or by choosing to discard samples. Other concerns are aimed at the application of DNA databases in criminal prosecution. These criticisms exist regardless of the databases' size/scope, but there is reason to believe that the increased attention to the caveats of DNA evidence that a universal database provides would improve these conditions. Along those lines, there are a number of benefits which come from universal coverage:
  • Universal coverage is perhaps the best way to ensure proper privacy protection and oversight of the database.
  • False positives would be more easily detected and corrected.
  • The advantages to law enforcement would be obvious.
  • Paternity would be known for all children.
  • It would have beneficial uses for identification outside of law-enforcement.
DNA profiling - The most common form of DNA profiling used for DNA databases (and other DNA-identification applications) is STR genotyping. Even with the best foreseeable technological advancements, STR genotyping has many disadvantages to SNP genotyping. If we were to implement a universal DNA database, it would be prudent to make the switch to SNP genotyping.
  • While STR genotyping is currently performed on ~13-16 highly polymorphic loci, it would be technically trivial to genotype hundreds (or thousands or more!) of biallelic SNPs.
  • High-throughput SNP genotyping platforms are advanced, and the pace of development (i.e. reduction in costs) is enormous.
  • SNP genotyping is technically simpler than STR genotyping, and it would be easier to miniaturize.
  • Huge databases of SNPs are already known, making it possible to select a panel of SNPs to meet almost any reasonable requirements. For example, SNPs could be chosen to minimize the chance that they are actually markers for socially-important phenotypic differences between individuals or groups.
  • Multiple correlated SNPs can be chosen for redundancy against genotyping error.
  • Poor quality forensic samples can be more accurately assigned to database profiles when there are hundreds (or thousands) or points of comparison, in contrast to the 13 STRs used in CODIS.
  • You can imagine the on-demand genotyping of a select subset of SNPs as an identity-verification scheme.
Previous posts: [1],[2],[3]

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An operational definition of the neutral theory?   posted by p-ter @ 3/12/2007 06:12:00 PM

I've often had the impression that debates about the neutral theory of molecular evolution are made confusing by people not defining their terms. Qualitative statements like "drift is more important than selection" tend to get tossed around. So this is from a recent paper:
This theory [the neutral theory] posits that the overall pattern of DNA evolution can be accounted for by mutation, genetic drift, and negative selection. It does not deny the operation of positive selection on some loci but only asserts that the overall pattern of genomic evolution can be explained without invoking adaptive evolution. Presumably, adaptive changes at any given time involve too small a fraction of the genome to be a statistically significant factor, despite their overwhelming biological significance.
I wonder if this is a generally accepted definition. If so, can the neutral theory officially be declared dead (at least for the protein-coding regions of the genome in Drosophila and human)?

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Sunday, March 11, 2007

What's in a brain?   posted by amnestic @ 3/11/2007 11:28:00 PM

One sweet day I shall provide more original neuroscience content. In the meantime, enjoy the neuroanatomy refresher below the fold via Toothpaste For Dinner.

Bawdy genetics joke   posted by agnostic @ 3/11/2007 09:52:00 PM

I'm sure someone out there's come up with a similar joke, but here goes.

A woman married to a geneticist decides to file for divorce, although when pressed by her friend, she refuses to say exactly why. She claims it is because she has absorbed too much of her husband's technical jargon, which has impaired her ability to converse with ordinary people.

However, her friend remains incredulous and inquires further: "I'm afraid I don't understand -- is he not a tenured and respected researcher who brings home a handsome salary? Does he not send you unexpected love letters penned in dulcet tone?"

"Yes, he does all of those things," she says. "...But let's just say I'd rather be with someone with whom penetrance were not so stochastic."


The unbelieving conservatives   posted by Razib @ 3/11/2007 08:49:00 PM

Daniel Larison points me to this piece in The New English review which discusses intersection of unbelief and conservatism, sparked in part by Heather Mac Donald's "coming out" last year. The article references my 10 questions with Heather. Over at Real Clear Politics there is a response to the piece in TNE. Finally, Larison offers his critique.

(you can view the technorati responses to the interview here)

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PLoS One genetics and genomics   posted by the @ 3/11/2007 12:01:00 AM

PLoS One has been out for a couple months now. They currently list 70 papers in the category of genetics and genomics. They rely in part of community feedback for peer review, so give feedback where you have comments.


Saturday, March 10, 2007

GOOD JOBS FOR AVERAGE AMERICANS   posted by Diana @ 3/10/2007 02:49:00 PM

What career path would you advise a younger person to take? This entry at Vdare got me to wondering. [Note: I had genuine reservations about linking to Vdare, which I read about once per fiscal quarter, but facts are facts. It should be accepted among adults that you can read incendiary things without necessarily agreeing with them.]

I realize that the vast majority of GNXP readers' kids and the kids of their friends are all winners in the brains sweepstakes. Extreme intelligence makes its own rules. But the rest of us must follow immutable laws of the economic universe and have to be beady-eyed about how our talents and capacities dovetail with demand. We've got to be brutally realistic.

For those in your acquaintance who are only somewhere above average, what secure career choices would you suggest?

My own would be to advise a young man to go into some kind of building contracting, and allied trades (such as carpentry, landscaping, glaziers, bricklayers, etc.). Contractors are making out like bandits in any locale where development is going on, and that's in lots of places. I had a conversation with a building contractor in Warwick, New York, in 2004, and he told me that he had to turn down work. Warwick used to be a dreary pit; due to its proximity to New York combined with a picturesque setting, it is now chi-chified and booming. The contractor grew up there when it was poor; he is now turning down business from the people who have moved there. He drove a Ford pickup and was probably a high school graduate. There must be thousands of such counties in these great United States.

Too many middle-class parents look down on trades such as these -- what are they thinking? Isn't it better to be a self-sufficient carpenter than a nervous middle manager who is scared that his job is going to be exported? There will always be a market for superior craftsmanship.

For women those kinds of jobs would be either not attractive or too physically demanding. I suggest cosmetology. Don't laugh; you can charge a lot for one hair-coloring. Fine motor coordination might make women better at jewelry-making. Another career path would be dressmaking. Back in the day, a good seamstress was able to make a dress without patterns. They fit, they draped and they were beautiful. There are very few custom dressmakers left in New York; people tell me that they are all in Jackson Heights, where the Indian immigrants have moved.

I realize that these jobs can be physically taxing can't have everything.

Suggestions welcomed! (But please, keep it proper.) The idea is to suggest professions that do not require freakish ability. Just a job that an average but dedicated and persevering yeoman can accomplish.

The comments have proved an interesting exercise. What happens with fruitful comment lines is that certain principles manifest. In this case, the main principle that jumps out at me is that you may not need to be brilliant to be a successful small businessman, but you do need above-average drive and organizational ability. Even a micro-mini-Martha Stewart (who started as a local caterer, another career choice) needs to be very dedicated. A lot of folks simply aren't. They want to collect a paycheck and let The Man take care of everything.

While I sympathize with this mentality, I can't agree with it. The Man has taken care of things so well that entire sectors of our economy have been exported. Average America has to start mistrusting The Man, and that's what I tried to point out with this post. Henry Ford is seriously dead.

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300   posted by Razib @ 3/10/2007 10:12:00 AM

I went an saw 300 yesterday. The historical inaccuracies were legion of course. That being said I went into it expecting a film adaptation of a comic book (they call them "graphic novels"?). I'm not a fan of comics, so I didn't read Frank Miller's work, nor do I bring a comic sensibility. Daniel Larison has a really good post up on this film which made many of the points I would have made, and without seeing the film! (he read the original work though) You can extract out of this film whatever you want really if you focus on the lull between the battle scenes. A war between the white male West and the multiracial imperium of Asia is pretty straightforward interpretation. Or, one between rational secularity and faith based mysticism is also there. Finally, there is the angle of a progressive and liberal view of history (a "New Age") vs. a static and traditionalist once. As you can tell, for a film which lacks much subtly the broad brush strokes sweep in all directions. Ultimately, 300 was more a lushly realized video game than a live action movie, so the somewhat attenuated plot and character elements loom larger due to their scarcity on the ground, and I think this explains the over-reading by some. For example, the Ru Paulish elements of Xerxes are notable precisely because this character exhibits some depth and personality, repulsive though it is. The user rating over at Yahoo Movies is an A-, with 4,600 votes in so far. At IMDB it is getting 8.4 out of 10 with over 8,000 votes. The core audience is liking it. If you're not a straight male between the ages of 18-35, there is a strong chance you "just won't get it."

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Friday, March 09, 2007

Drugs Policy Report   posted by DavidB @ 3/09/2007 05:48:00 AM

As I have previously posted on the subject of drugs policy, I was interested to see a new report in the UK from a Commission appointed by the Royal Society of Arts (RSA). This is not to be confused with the better known Royal Society of London for the Improving of Natural Knowledge, usually known simply as the Royal Society. Nevertheless, the RSA is a respected independent body promoting discussion of public policy issues. In this case it had appointed a Commission chaired by a professor of politics and including experts on various aspects of drugs policy, not least a senior officer at Scotland Yard.

The full report is available here as a 2Mb pdf file. While I haven't read the full 330-page report line-by-line, it certainly contains a lot of useful information and will contribute to rational debate.

Thursday, March 08, 2007

Etruscans - the consensus?   posted by Razib @ 3/08/2007 06:13:00 PM

As some of you know I've lately posted on the genetic evidence which implies a non-trivial Near Eastern, in particular Anatolian, element in the Etruscan population of the ancient world. This is of interest because there has been controversy from the time of Herodotus about the origin of this enigmatic people (who influenced Rome). Roughly, there was a camp which held that the Etruscans were a settler population, perhaps from Lydia, while another group held that they were indigenous. The genetic data seems strongly to suggest that there was a non-trivial exogenous input, exactly from the region of the world where ancient oral history suggests they emigrated. In response to my spate of posts one individual left an irate and angry comment, suggesting that for several decades everyone has known that the Etruscans were from Anatolia, and sarcastically offered that the only issue is that one must have the approval of a "real science" like genetics. I deleted the comment due to its rude and insulting tone. But, I'm not a specialist in Etruscan studies, so I didn't totally dismiss it. I have read a bit about Rome though, and the consensus seemed to be that the Etruscans were indigenous. Today I was at the library and checked out The Etruscans (1998) by Graeme Barker and Tom Rasmussen. Here is what I found.

Page 44:

Virtually all archaeologists now agree that the evidence is overwhelmingly in favour of the 'indigenous' theory of Etruscan origins....

Page 83:

...The overwhelming evidence of the archaeological record is that the origins of Etruscan society lie fundamentally in the later prehistoric communities of Etruria....

One book is not definitive, but, it is in keeping with the general bias of late 20th century archaeologist, and, what I have read in the historical literature. Myself, I assumed that the indigenous theory was of a higher likelihood until the recent data, and certainly the Etruscans were a hybrid peoples, genetically and culturally, even assuming an exogenous element (though the exogenous female lineages imply a folk wandering of some scale). But in any case, I do have to wonder about the abusive commenter. Either they were stupid, of they were lying. Or, Barker and Rasmussen don't report the consensus accurately. I'll probably look at a few other books just to make sure, but I can't communicate how enraged I get at righteous commenters that either lie or don't know they're talking about. It wastes everyone's time.

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The Lamp Post Rule   posted by Matt McIntosh @ 3/08/2007 10:46:00 AM

There's a problematic tendency, particularly prevalent when dealing with emotionally-charged subjects, for people with little or no understanding of a complex subject to handle numbers that come out of that subject in much the same way that Moses handled the Ten Commandments: They are handed down from higher intellectual powers, whose ways are mysterious to us but whose authority is without question. They are the outputs of a black box whose inner workings are completely opaque, but which is quite useful to those looking for a blunt object with which to bash their opponents over the head.

Examples are not hard to find: Creationists making reference to Haldane's limit, global warming deniers talking about arctic ice cores, price control fetishists banging on about Card & Krueger, race-skeptics quoting Lewontin's infamous 85/15 figure, etc etc etc. We've all seen it, many of us have probably even done it at some point, and it's a stupid human trick that's centuries old.

Good old Arty Schopenhauer knew what this one was about:

This is chiefly practicable in a dispute between scholars in the presence of the unlearned. If you have no argument ad rem, and none either ad hominem, you can make one ad auditores; that is to say, you can start some invalid objection, which, however, only an expert sees to be invalid. Now your opponent is an expert, but those who form your audience are not, and accordingly in their eyes he is defeated; particularly if the objection which you make places him in any ridiculous light. People are ready to laugh, and you have the laughers on your side. To show that your objection is an idle one, would require a long explanation on the part of your opponent, and a reference to the principles of the branch of knowledge in question, or to the elements of the matter which you are discussing; and people are not disposed to listen to it. For example, your opponent states that in the original formation of a mountain-range the granite and other elements in its composition were, by reason of their high temperature, in a fluid or molten state; that the temperature must have amounted to some 480 degrees Fahrenheit; and that when the mass took shape it was covered by the sea. You reply, by an argument ad auditores, that at that temperature - nay, indeed, long before it had been reached, namely, at 212 degrees Fahrenheit - the sea would have been boiled away, and spread through the air in the form of steam. At this the audience laughs. To refute the objection, your opponent would have to show that the boiling-point depends not only on the degree of warmth, but also on the atmospheric pressure; and that as soon as about half the sea-water had gone off in the shape of steam, this pressure would be so greatly increased that the rest of it would fail to boil even at a temperature of 480 degrees. He is debarred from giving this explanation, as it would require a treatise to demonstrate the matter to those who had no acquaintance with physics.

There's always going to be a lot of assumptions underlying any specific truth-claim pertaining to a complex subject. Altering one or more of these assumptions will have an impact on the plausibility of the specific claim in question, and often it takes a trained eye to see what assumptions are being made, which are likely to be sound and which are highly questionable. But the unfortunately large intersection between the set of subjects people have strong feelings about and the set of subjects that take a non-trivial amount of education to adequately comprehend ensures that people are always going to end up arguing beyond their range of competence. So how do we deal with this combination of ignorance and importance?

I propose an informal rule for any sort of argument where the participants involved are not competent to evaluate specific truth-claims: All arguments conducted in a state of relative ignorance must be algebraic. I don't mean speaking in math -- I mean that such arguments should focus on the relations between variables rather than on what specific values to assign them. And if someone does plug specific values into the argument, they have to either A) be unobjectionable, i.e. everyone in the argument can agree that the values are reasonable, or B) be supported with at least a cursory explanation of how the values were produced (or a link or reference to such an explanation).

Anytime you see someone supporting their argument with specific numbers in a discussion with no hint at how they were arrived at, your bullshit detector should go off and you should demand an explanation of the method by which those numbers were produced. If upon being pressed your interlocutor cannot or will not adequately explain this (or provide a link or reference to someone else's adequate explanation), an argumentative foul has been comitted; those specific numbers and whatever parts of his argument require them may be disregarded and the offender's credibility reduced as punishment. Call it the lamp post rule.

And if this ever becomes as commonly referenced as Godwin, rememeber, you read it here first.


Wednesday, March 07, 2007

g: A precis   posted by Alex B. @ 3/07/2007 08:35:00 PM


The study of intelligence goes back many millennia, but, as such, it was usually defined as a nebulous construct and it fell more under the domain of philosophy than, say, science. Enter Francis Galton. With his Darwinian ancestry and precocious nature, Galton became fascinated by human variability and spent most of his life pursuing various distributaries from this river (e.g., dactylography, anthropology). Most important to the field of individual differences, was his study of the nature of human cognitive abilities. That is, he was one the first (if not the first) to make a systematic study of human variation in cognitive abilities. In doing so, he developed a cadre of "brass instruments" to measure various aspects of basic human abilities, which, to him, were all related to this underlying, general cognitive ability.

People lay too much stress on apparent specialities, thinking over-rashly that, because a man is devoted to some particular pursuit, he could not possibly have succeeded in anything else. They might as well say that, because a youth had fallen desperately in love with a brunette, he could not possibly have fallen in love with a blonde. He may or may not have more natural liking for the former type of beauty than the latter, but it is more probable a not the affair was mainly or wholly due to a general amorousness of disposition (Galton, 1869, p. 6)

While in his time, his elementary task/sensory discrimination data did not support his hypothesis that they were related to other "common sense" criteria such as education and occupation, later, when Fisherian analysis were applied, Galton was proved to be correct--that is, there were group differences in average scores (Johnson, McClearn, Yuen, Nagoshi, Ahern, & Cole, 1985).

In addition to his interest in elementary tasks, Galton was also interested in more traditional psychometrics. In fact, he convinced the British Association for the Advancement of Science to conduct a survey of mental capacities throughout British schools. William McDougal was appointed to head this up and his student, Sir Cyril Burt, got his initial taste of the field of applied psychometrics from this project (Burt, 1972).


As important as Galton was in developing the underpinnings to modern intelligence research, he was not able to conceive of a way to measure general cognitive ability. Instead, this task was accomplished by engineer-turned-psychologist Charles Spearman (1904). Spearman was able to accomplish this based on two of his mathematical "inventions:" Classical Test Theory (CTT) and Factor Analysis (FA). Neither one of these is particularly easy to explicate via BLOG form, but the bottom line is: (a) CTT allowed for one to find the correlation between two variables, disattenuated by (random) measurement error; and (b) FA allowed for one to extract commonalities in groups of correlations. That is: If variable A, variable B, and variable C are all highly correlated with each other, then they likely have something in common. FA allows one to "get at" the thing (loosely speaking) that they have in common.

For example, if we have the following correlations for A, B, and C, then the last row has the correlations between the variable and the common factor (i.e., factor loadings)


B 0.7

C 0.8 0.75

g loadings

0.864 0.810 0.926

Spearman called that underlying factor general intelligence, and that is still what is meant today when the moniker Spearman's g is used, even though the factor analytic techniques have greatly advanced since Spearman's day.

After Spearman's developments, there was a period of controversy as to (a) whether g existed, (b) if it existed, was it the only factor that could be extracted, and (c) if other factors could be extracted, could g be extracted at the same time? The details of this (needless?) argumentation need not concern this post (for a succinct summary, see Carroll, 1993), with the eventual conclusion being that, given a sufficient diversity of tests, g could be extracted, but other, more primary factors (e.g., Working memory, Long-term memory, Quantitative knowledge) could also be extracted. A picture is given below:

Spearman's g is at the apex, the more primary ability are the circles below, and the tests from which the factors were extracted are represented by the boxes [the circles are used as that is the common way of representing latent variables; likewise, boxes are common way of representing manifest variables]


Around the same time Spearman and his London School contemporaries were doing their work in g theory, the field of intelligence testing was arising--due in large part to Binet and Simon's work in France, Goddard and Terman's work in the US, and Burt's work in the UK. Today, intelligence is often used synonymously with IQ scores, which, outside of differential psychology and psychometrics, is also used synonymously with Spearman's g. They are similar concepts, undoubtedly, but they need distinction.

Intelligence. A nebulous construct at best, it had eluded a century of definition, and, in Arthur Jensen's (1998) own words, "psychologists are incapable of reaching a consensus on its definition" (p. 48) As it cannot be defined, we will not use it any further.

Spearman's g. It is the primary factor extracted from the correlation matrix of a group of variables that all measure some aspect of cognitive ability. That is, it is the part of the covariance that all the variables have in common with each other.

Intelligence Quotient (IQ). An imperfect measure of Spearman's g. That is, in modern IQ tests, IQ scores are the weighted average of performance all the subtests involved. This is sometimes referred to as "intelligence in general" as opposed to "general intelligence" (i.e., Spearman's g), but for general purposes an IQ score can be thought of as rough measure of Spearman's' g, plus some (random) measurement error. Usually these scores are scaled such that most people will have a score between 90 and 110; mental retardation is a serious consideration for people with IQs below 70, as giftedness is a serious consideration for people with IQs greater that 120.

Why All the Fuss?

As presented, one may easily come to the conclusion of, so what? IQ/g sounds like it is another entry in the massive world of psychobabble, along with mental bonds, closure, and life coaching. The fuss is this:

No other variable in the history of psychology has (strongly) predicted such a wide variety of life outcomes.

  • Educational Outcomes (Deary, Strand, Smith, & Fernandes, 2007; Kuncel, Hezlett, & Ones, 2004)

  • Physical Health/Accidents (Gottfredson, 2004; Gottfredson & Deary, 2004).

  • Reaction Time to Cognitive Tasks (Jensen, 2006)

  • Occupation Status (Gottfredson, 1986; Herrnstein & Murray, 1994)

  • Job Success (Schmidt & Hunter, 1998, 2004)

  • Crime (Ellis & Walsh, 2003).

  • Race Differences (Lynn, 2005; Rushton & Jensen, 2005)

  • Sex Differences (Lynn & Irwing, 2004)

  • GDP (Lynn & Vanhanen, 2006)

And this is to just name a few.

If I were to stop here, one might be under the impression that g/IQ are important, but (a) there are other forms of "intelligence"; and (b) that IQ is just a product of the environment and can be raised (almost) at will.

Multiple Intelligences

The theory of Multiple Intelligences (MI) stems from Howard Gardner who (now) posits that g exists, but so do other forms of independent "intelligences" that (equally) predict life success. His other forms are things like interpersonal skills, intrapersonal knowledge, and kinesthetic ability. Since in the 25 years since MI has been around, Gardner has refused to test his hypotheses, it really is not even worth mentioning anymore. Thus, I won't (for some empirical work showing why Gardner is, well, wrong, see Visser, Ashton, & Verson, 2006, under review).

Triarchic Theory of Intelligence

This works stem from the work of Robert Sternberg, and his theory of cognitive ability that, similar to Gardner, posits that g exists, but that there are independent cognitive entities that are useful in life, such as practical intelligence; he even goes so far as to say that these independent entities are better predictors of life outcomes than g. Unfortunately, like Gardner, he doesn't readily submit his theories to much empiricism, and his claims, to date, are unsubstantiated (for an excellent critique, see Gottfredson, 2003).

Stability and Raising g/IQ

If one is under the impression that the environment can have massive influence on g, the logical product of that belief is that massive government programs should be able to raise cognitive abilities. In short, they do not. They produce short-term gains, but the gains do not last long (see, for example, Spitz, 1986, 1992). This is not to say that other things, such as nutritional supplementation, might not be able to increase cognitive performance, but massive environmental programs, at least as implemented in the past 50 years, have not. Moreover, IQ scores measured when one is 10ish are consistent, very consistent, with IQ scores measured almost 70 years later on the same individuals (Deary, Whalley, Lemmon, Crawford & Starr, 2000). That is, despite a life's worth of diversity of experience, your IQ when you are in Middle School is very predictive of your IQ when you retire.

Take Home Message

g is ubiquitous in cognitive tasks, it is stable across time in individuals, and no other variable in the history of psychology has been able to predict so many life outcomes, so well.


Burt, C. L. (1972). Inheritance of general intelligence. American Psychologist, 27, 175–190

Carroll, J.B. (1993) Human cognitive abilities. Cambridge University Press.

Deary, I. J., Whalley, L. J., Lemmon, H., Crawford, J. R., & Starr, J. M. (2000). The stability of individual differences in mental ability from childhood to old age: Follow-up of the 1932 Scottish Mental Survey. Intelligence, 28, 49-55.

Deary, I. J., Strand, S., Smith, P., & Fernandes, C. (2007). Intelligence and educational achievement. Intelligence, 35, 13-21.

Ellis, L., & Walsh, A. (2003). Crime, delinquency, and intelligence: A review of the worldwide literature. In H. Nyborg (Ed.), The scientific study of general intelligence: Tribute to Arthur R. Jensen (pp. 343-365). New York: Pergamon.

Galton, F. (1869). Hereditary genius: An inquiry into its laws and consequences. London: MacMillan

Gottfredson, L. S. (Ed.) (1986). The g factor in employment. Journal of Vocational Behavior, 29 (3). (Special Issue)

Gottfredson, L. S. (2003). Dissecting practical intelligence theory: Its claims and evidence. Intelligence, 31(4), 343-397.

Gottfredson, L. S. (2004). Intelligence: Is it the epidemiologists' elusive "fundamental cause" of social class inequalities in health? Journal of Personality and Social Psychology, 86, 174-199.

Gottfredson, L., & Deary, I. J. (2004). Intelligence predicts health and longevity: but why? Current Directions in Psychological Science, 13, 1-4.

Herrnstein, R. & Murray (1994) The Bell Curve: Intelligence and class structure in american life. New York: Free Pres

Jensen, A. R. (1998). The g factor. Westport, CT: Praeger.

Jensen, A.R. (2006). Clocking the mind: Mental chronometry and individual differences. Oxford: Elsevier.

Johnson, R. C., McClearn, G. E., Yuen, S., Nagoshi, C. T., Ahern, F. M., & Cole, R. E. (1985). Galton’s data a century later. American Psychologist, 40, 875–892

Kuncel, N. R., Hezlett, S. A., & Ones, D. S. (2004). Academic performance, career potential, creativity, and job performance: Can one construct predict them all? Journal of Personality and Social Psychology, 86, 148-161.

Lynn R. (2005). Race differences in intelligence: An evolutionary analysis. Augusta, GA: Washington Summit.

Lynn, R. and Irwing, P. (2004) Sex differences on the Progressive Matrices: a meta-analysis. Intelligence, 32, 481-498.

Lynn, R. & Vanhanen, T. (2006). IQ and global inequality.
Atlanta, GA: Washington Summit.

Rushton, J. P., & Jensen, A. R. (2005). Thirty years of research on race differences in cognitive ability. Psychology, Public Policy, and Law, 11, 235-294.

Schmidt, F. L., & Hunter, J. (1998). The validity and utility of selection methods in personnel psychology practical and theoretical implications of 85 years of research findings. Psychological Bulletin, 124, 262-274.

Schmidt, F. L., & Hunter, J. (2004). General mental ability in the world of work: Occupational attainment and job performance. Journal of Personality and Social Psychology, 86, 162-173.

Spearman, C. E. (1904). “General intelligence”: Objectively defined and measured. American Journal of Psychology, 15, 201–292.

Spitz, H. H. (1986). The raising of intelligence: A selected history of attempts to raise retarded intelligence. Lawrence Erlbaum Associates.

Spitz, H. H. (1992). Does the Carolina Abecedarian Early Intervention Project prevent sociocultural mental retardation? Intelligence, 16, 225-237

Visser, B.A., Ashton, M.C., & Verson, P.A. (under review). Self-estimated general and "multiple" intelligence(s): Accuracy, sex differences, and personality.

Visser, B.A., Ashton, M.C., & Verson, P.A. (2006). Beyond g: putting Multiple Intelligences theory to the test. Intelligence, 34, 487-502.

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GNXP Chat   posted by Razib @ 3/07/2007 06:45:00 PM

I've installed a AJAX chat app, here

I don't know if it will last. A few ground rules:

1) Don't be too stupid...I'm interested in seeing if people have intelligent things to say ;-)

2) Please select distinctive nicknames (if you have a regular handle here, use it)

I've placed the chat as a link to the right (below the RSS icon). This is AJAX, so IE & Firefox are best, etc. etc.

The main reason I added this today is that some of the comment threads basically turn into 2-person chats back and forth. If something like that is going on, it might be good to have an option of "let's take this to chat." More productive for everyone.


March Cell Podcast   posted by amnestic @ 3/07/2007 03:17:00 PM

Cell's new issue is accompanied by a podcast (mp3). Let's hope they start cranking them out regularly. We have interviews with Francis Collins (about knockout mice, not Goddity God God) and Greg Hannon (about piRNAs, ~30 nucleotide regulatory RNAs in mouse nutz). And some other guy (David Fisher) talks about sun tanning and p53, but I never heard of him.


African IQs   posted by DavidB @ 3/07/2007 11:14:00 AM

lwka's excellent post below mentions (among other things) the low reported IQ in African countries.

When this came up on a previous occasion the question was raised whether mean IQ's of 70 or even lower for Africans were compatible with a 'black' mean IQ of 85 in the United States, after taking account of the mixed African and European ancestry of American blacks.

At that time I did a few sums and started writing a post, but never quite finished it. But I have dusted it off and posted it below the fold, as it still seems relevant.

First, some assumptions:

- for the sake of this discussion, I assume that all group differences are wholly genetic in origin. Of course, I don't believe this, and I'm not sure that anyone does.

- I assume that the observed mean IQ of white Americans, on current (2000-ish) norms, is 100, and that of 'black' Americans is 85

- I started by assuming that, on average, 'black' Americans have 20% white ancestry. However, having done all the calculations on this basis and written up the results, I found that a figure of 25% is also sometimes used (e.g. by Jensen). This seems rather high, (see the figures in Sandra Scarr's Race, Social Class and Individual Differences in IQ), but I have repeated the calculations on this basis as an alternative. Rather than present two sets of workings, I have just inserted the key alternative results in square brackets. Whether on the 20% or 25% basis, I assume that the white ancestry of 'blacks' is genetically representative of the white American population.

Needless to say, all of these assumptions could be discussed at length.

With these assumptions, if all genetic effects are strictly additive, with no dominance or epistasis, then the mean IQ of an unmixed 'black' population would be X, where .8X + .2(100) = 85, which gives the value X = 81.25 [or 80 on the alternative 25% basis]. This is the easy bit!

But it is unlikely that all the genes affecting IQ are purely additive. To consider the possible effects of dominance, let us assume that all genes affecting IQ have two alleles, H (High) and L (Low), with H dominant. To take the most extreme assumption for gene frequencies, maximising the effect of dominance in differentiating a 'pure' black population from a black-white mixture, let us assume that the white population is entirely homozygous for the dominant H, while the ancestral black population is entirely homozygous for the recessive L. The US mixed 'black' population would therefore have a gene frequency at each locus of 80% L and 20% H. In Hardy-Weinberg equilibrium this gives genotype frequencies of .64LL, .32HL, and .04HH. The phenotypic value of each locus in the US 'black' population would therefore be .64X + (.32 + .04)100 = 85, where X is the unknown phenotypic value of the 'pure' black population. This gives X = 76.56 [or 73.2 on the 25% basis].

This is not a realistic assumption for gene frequencies, since if it applied to all loci the 'pure' populations would be genetically uniform, which is obviously not the case. To consider a more plausible model for gene frequencies, suppose the frequency of H is 60% in the white population and 30% in a pure black population, so that the frequency of L is 40% in the white population and 70% in a pure black population (since the frequency of H + L must be 100% for each population.) For the US 'black' population the frequencies are therefore (.8 x 30%) + (.2 x 60%) = 36% for H, and 64% for L. The Hardy-Weinberg genotype frequencies for the white population are 36%HH, 48%HL, and 16%LL and for the US 'black' population (approx) 13%HH, 46%HL, and 41%LL. If we designate the phenotypic value of HH and HL as X (not to be confused with the previous X!) and of LL as Y, we get two equations as follows:

(.36 + .48)X + .16Y = 100
(.13 + .46)X + .41Y = 85

Solving these equations gives (approx) X = 109.6 and Y = 49.6 [or 110.4 and 45.4 on the 25% basis].

In a 'pure' black population with gene frequencies of 30% H and 70% L, and Hardy-Weinberg genotype frequencies, these results give a mean phenotypic value for the population of almost exactly 80 [78.5 on the 25% basis], as compared with 81.25 [80 on the 25% basis] if there is no dominance. It will be seen that in this model the effect of dominance in differentiating 'pure' from 'mixed' black population is not very great.

These are in principle the values for a single locus. In the absence of epistasis, the mean value for the genome as a whole is simply the mean value of all relevant loci.

Epistasis, by definition, means that the phenotypic value of the genome varies according to the particular combination of genes at different loci. Essentially the only limit on possible epistatic effects is the ingenuity of the model-maker. As a general rule, epistasis is less important than dominance, so my gut feeling is that epistasis, on any plausible model, is unlikely to make much difference to the conclusions above. If anyone disagrees, let them set out a plausible model in which it does make a difference. Note that if high white IQ is due to favourable epistatic gene combinations, these are very likely to be broken up in a 'black' population with only 20% or 25% white ancestry, so that in this respect the difference between a 'pure' black population and the US 'black' population would probably be small.

Departures from Hardy-Weinberg equilibrium would also be a complication. Assortative mating within the US 'black' community for traits deriving from white ancestry, such as skin colour or IQ (assuming that this is genetic), would tend to increase the proportion of homozygotes above the Hardy-Weinberg expected levels. This would reduce the overall phenotypic contribution of white ancestry, since the same number of dominant H genes would be distributed among fewer individuals than in Hardy-Weinberg equilibrium. In effect, one of the dominant genes is 'wasted' in a homozygote. On the other hand, first generation black-white hybrids would have a higher proportion of heterozygotes than the rest of the 'black' population. One prediction of a purely genetic model assuming dominance for high-IQ genes is that the IQ of first-generation mixed-race individuals would be closer to the white mean IQ. But this would presumably affect only a small proportion of the 'black' population as a whole.

I haven't bothered calculating the effects on the assumption that the genes for low IQ are dominant. Obviously in that case the 'mixed' black population would be closer to the 'pure' black population.

The general conclusion is, I think, that on hereditarian assumptions about the nature of the black-white IQ difference in the US, the genetic IQ of a 'pure' black population cannot be much below 75 and is more likely around 80. (Note that this is by present-day norms. Due to the Flynn Effect, a present-day score of 80 would have corresponded to about 100 when IQ tests were first established.) This is higher than the mean IQ (often below 70) sometimes reported for black African countries from which the black ancestry of 'black' Americans is derived. Of course, one could in principle argue that the Africans who were taken to the US were above average in genetic IQ (relative to other Africans), but this is hardly likely. Alternatively, one could argue that 'black' Americans have improved their genetic IQ, and/or that African genetic IQ has deteriorated, in the 250 years or so since the slaves arrived in America. Neither hypothesis seems plausible.

It would therefore be difficult to consistently maintain a purely hereditarian view of both the black-white difference in the US and the low measured IQ of black Africans. I am not sure that anyone has actually take this position, but it may still be worth pointing out the difficulties.


Tuesday, March 06, 2007

Validity of national IQ   posted by the @ 3/06/2007 08:11:00 PM

In IQ and the Wealth of Nations (2002; IQatWoN) and IQ and Global Inequality (2006; IQGI), Richard Lynn and Tatu Vanhanen (L&V) present measurements and estimates of average national IQ (national IQ). In IQatWoN, L&V argue that national IQ predicts per-capita GDP (sup Fig 1). In IQGI, L&V argue that national IQ predicts quality of life measures (sup Fig 2). A common criticism of both works is to question the validity of national IQ. This criticism is motivated in part by the very low scores reported for countries in sub-Saharan African. A look at the distribution of national IQ is instructive (Fig 1).

Figure 1. The distribution of national IQ values (192 countries from IQGI).

L&V address the issue of validity by comparison of national IQ values with international test scores in math and science such as TIMSS and PISA. IQGI presents data from 10 different tests, with different scoring scales, in the form of 3 tables. To get a better grasp on the question of the validity of national IQ, I reanalyzed the test score data from IQGI. For better comparison, I renormalized each set of test scores relative to the maximum test score for each assessment. This is an imperfect but sufficient technique. An unweighted average of the available test score data was used to calculate a composite national test score for the set of 62 countries for which at least 1 test score was available (Fig 2).

Figure 2. The association between national test scores and national IQ for 62 nations.

National test scores are available for a limited range of national IQ scores, with few test scores available for countries with national IQs below the mid 80s. I interpret this to mean that for countries with national IQs below ~85, the test score data is insufficient to inform the question of validity. However, for the available scores (i.e., mostly above ~85), the relationship between national IQ and national test scores is very strong (see Sup Table 1).

The validity of sub-80 national IQs is addressed in part by the finding that IQ correlates with GDP and QHC (Sup Figs 1,2) throughout the observed range of IQ.

Update: Although there are only four values, the sub-80 national IQs are outliers, all with positive residuals. While this is hardly informative, it trends in the direction of casting doubt on the validity of sub-80 national IQ values.

Supplemental Figure 1. National IQ correlates with GDP per-capita (192 countries from IQGI).

Supplemental Figure 2. National IQ correlates with a L&V's quality-of-life index (QHC; 192 countries from IQGI).

Supplemental Table 1. Correlation matrix for national IQ (IQ), national test score (Test), L&V's quality of life index (QHC) and log per-capita GDP (logGPD) for 62 countries.
r QHC logGDP IQ Test
QHC 1 0.898936 0.7933265 0.7803476
logGDP 0.898936 1 0.760138 0.7565582
IQ 0.7933265 0.760138 1 0.9008035
Test 0.7803476 0.7565582 0.9008035 1

Related papers:
* Earl Hunt and Werner Wittmann, National intelligence and national prosperity, Intelligence, In Press --examines PISA scores
* Richard Lynn and Jaan Mikk, National differences in intelligence and educational attainment, Intelligence, Volume 35, Issue 2, March-April 2007, Pages 115-121. --examines TIMSS scores

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Tracking the ivory trade with DNA   posted by p-ter @ 3/06/2007 04:48:00 PM

A new paper in PNAS (open access) uses DNA isolated from seized ivory to investigate where elephant poaching is occurring. It's an interesting idea, but for me the idea itself takes a back seat to the clever statistical framework in which it's implemented. The analysis of DNA data is getting more and more sophisticated; this is an excellent example of that phenomenon.

The paper starts with very little data-- 37 tusks from this ivory seizure along with a database of DNA samples of elephants from all over Africa. Traditional methods would treat each of the 37 tusks independently, but the authors want to consider the possibliity that all came from a single area as well as the possiblity that all are from disparate parts of the continent (the two possiblities have different implications for law enforcement). So they create a grid on all of Africa (actually, just the subset containing the elephant range) and randomly split the grid into polygons, considering each polygon as equally likely to be part of area where elephants were poached. This gives them a prior distribution for the origin of the poached elephants.

They then use their data and the existing database to estimate the posterior distribution for that origin using Markov chain Monte Carlo. They provide evidence that this method works very well at distinguishing the two possiblities (a single origin of the elephants or a disparate collection), an advertisement for Bayseian methods and their ability to get as much information as possible from limited data. As can be seen in the figure, all the elephants seem to come from an area centered around Zambia. This has had some consequences:
The seizure immediately followed Zambia's application to CITES for a one-off sale of their ivory stockpiles at COP12 (Conference of the Parties). That application maintained that only 135 elephants were known to have been illegally killed in Zambia during the previous 10 years, woefully shy of the 3,000-6,500 elephants we estimate to have been killed in Zambia surrounding the seizure, let alone during that entire 10-year period. Subsequent to being informed of our findings, the Zambian government replaced its director of wildlife and began imposing significantly harsher sentences for convicted ivory traffickers in its courts.

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Monday, March 05, 2007

The bearableness of beta....   posted by Razib @ 3/05/2007 11:09:00 PM

'Wingman' -- How Buddies Help Alpha Males Get The Girl:
...often than other males, but not necessarily at the same territory where they were betas. Even when the local alpha slot was empty, some betas moved to be helpers elsewhere rather than take over the vacant position.

"Without being an alpha, there's essentially no chance for these males to reproduce," says DuVal. "My results suggest that betas could actually benefit from staying betas for a while, for example by gaining courtship skills during a sort of apprenticeship or by forming alliances with other males who later act as their betas."

These results contrast with those from studies of other birds with cooperative courtship displays: wild turkeys strut cooperatively with close relatives, and ruffs (a shorebird) form alliances of males that often both mate while they are partners. These contrasts are interesting because they show that similar behavior can result from very different social and selective environments....

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Mendel's Garden   posted by Razib @ 3/05/2007 10:08:00 PM

The current Mendel's Garden just went up over at "sperm competition" Matt's place.

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Future archaeogenetic possibilities....   posted by Razib @ 3/05/2007 09:38:00 PM

In The Classical World by Robin Lane Fox the author contends that the extant evidence suggests that Greek colonies were mainly a male affair,1 and that subsequent generations arose from the union of these men with local women. Over at my other weblog I discuss the issues of cultural vs. biological group selection, and the fact that though each parent contributes 1/2 of your genome, they need not contribute 1/2 of your cultural outlook & orientation. I invite those acquainted with the literature on Magna Graecia to chime in, though Fox being a classicist himself, I am skeptical that his contention is without any support.

1 - And lower class and/or toublesome males at that.

Invasion of the ants   posted by p-ter @ 3/05/2007 05:02:00 PM

John Hawks has a great post on the invasion of fire ants and Argentinean ants in the US. I'd quote it, but it's worth reading the whole thing.

Sunday, March 04, 2007

Super-bugs and evolution   posted by p-ter @ 3/04/2007 05:20:00 PM

I'm generally skeptical of claims that "Big Pharma" and shadowy government figures are somehow colluding against us, but this story definitely makes me a little uncomfortable:
The government is on track to approve a new antibiotic to treat a pneumonia-like disease in cattle, despite warnings from health groups and a majority of the agency's own expert advisers that the decision will be dangerous for people.

The drug, called cefquinome, belongs to a class of highly potent antibiotics that are among medicine's last defenses against several serious human infections. No drug from that class has been approved in the United States for use in animals.

The American Medical Association and about a dozen other health groups warned the Food and Drug Administration that giving cefquinome to animals would probably speed the emergence of microbes resistant to that important class of antibiotics, as has happened with other drugs.
It's obvious that wide-scale use of a new antibiotic will ramp up the frequency of resistant bacteria; these are basic evolutionary principles at work.

I've speculated in the past that our current relative immunity from bacterial infections could be short-lived and that death from them will return to being a basic part of the human condition (as it has been for most of human existence. Penicillin wasn't produced on an industrial scale until something like 70 years ago). If we play the arms race with bacteria, we're eventually going to lose-- the required investment to get the next big antibiotic will eventually get too high. The one thing we have going for us is that we understand the basics of evolution-- that is, we can predict how a population of bacteria will respond to the next antibiotic, and we have an idea of the population dynamics at work as resistance spreads. I have the feeling that somehow this information could be used to defuse the "arms race" (it can definitely slow it down, as the advisory bodies in this article are well aware), but I'm not sure how...


Fair & balanced   posted by Razib @ 3/04/2007 02:40:00 PM

So I've been using google reader to collect the "news" stories which deal with "genetics & evolution" and "human evolution" over the past few weeks. A substantial minority of the former results have been of a Creationist bent, and between 1/3 and 1/2 of the latter have been Creationist columns and opinions. For me, this is a minor irritation (and the reason I last unsubscribed from the "human evolution" query). But if I were a Creationist I am pretty sure that the large number of "news" articles pushing anti-evolutionism would reinforce the position that evolution is a "theory in crisis." Do no evil?


Saturday, March 03, 2007

Why do people believe in God?   posted by Razib @ 3/03/2007 11:10:00 PM

The New York Times Magazine has a long piece which profiles the various naturalistic hypotheses which explain the origin of religious belief. The usual suspects show up. Scott Atran, author of In Gods We Trust looms large, while Justin L. Barrett, who I interviewed last year, also gets some face time. The author of the piece tries to establish a rough dichotomy between adaptationists and non-adaptationists, with the cognitively oriented scientists in the latter camp, and more conventional functionalists in the former. For the purposes of an article in The New York Times Magazine this is acceptable, it adds a necessary element of dramatic tension, but this is a gross oversimplification. Additionally, it should be noted that individuals such as Steven Pinker who are often perceived as adaptationist in their conception of cognitive function support Atran and the non-adaptionists on this question.

One thing that both these groups can agree upon, even if you take the dichotomy at face value, is that religion needs to conceived of as more than a plain set of axioms which serve as the blueprint for behavior and belief. I've been blogging about religion for a while now because I think it is an interesting and significant social phenomenon which touches upon our lives, whether we believe or not. If you talk about foreign policy in the Middle East, for example, it is imperative that you know the general sectarian landscape, as well as the psychological salience of religious identity on a deep level, and the ramifications that might have in how humans behave and act. As a congenitally irreligious person this process of understanding has been a scientific and scholarly one, I don't have recourse to introspection informed by my own religious sensibilities since I generally lack one.

Over time I have started to hold some assumptions as givens as I develop my ideas, otherwise each post would continue to grow in length as I elucidate the theoretical and empirical framework in which I am working within. This is one reason I do express some irritation with those in the comment boxes who are plainly talking out of their ass and repeating intuitions & convential wisdom which they've had nailed down since their bullshit sessions in their freshmen year at university. Life is short and I don't have much patience for mind-farting, even if you think it smells oh so nice. I am not interested in religion because I think that such talk will give me insight into the deep nature of the universe, rather, people are killing themselves in the name of an entity that seems manifestly implausible to me, and that requires some explaining. An explanation can be generated by a precise formulation of the problem at hand and patient data collection. Most discussions about religion are neither precise nor do they trade much in facts. Consider this comment on one of my posts:
Could you please break this statement down for me? On a day to day level, to practising Muslims, how exactly does Islam not promote peace? In what ways do the five pillars cause violence? Shahadah, praying, zakat, Hajj (if possible), and fasting during Ramadan, to most Muslims, this is what Islam consists of. To the dissapointment of most "Islamist ideolouges", I would actually argue that the average Muslim doesn't view Islam as some sort of political movement. At least not yet,and definitely not at the abstrract level that Islamists would desire.

Regular readers will anticipate my irritation with these sort of comments: they tend to imply that "Islam" (or any religion) is something which exists out there, prior to and apart from human belief or practice. "Islam is the 5 pillars..." or "Islam is peace." One of the most common problems with religion are the word games which people into. For example, "You believe in love, and god is love, so you believe in god, and so you aren't an atheist...." This is all fine & dandy, but these word games don't really explain much about the world in my opinion, and I'm not invested in the word atheist or theist. Similarly, I don't care what most Muslims think Islam is, or what the accepted majority of Muslims believe the pillars of the faith are, because such things are prior ideals whose implications in the real world are not always clear. Religion is for me a posterior phenomenon, it characterizes the beliefs and practices of a collection of human beings who avow an affinity for a particular word as a group marker, and these beliefs and practices have a focus upon supernatural concepts which violate some ofour banal and prosaic intuitions about how the world works. There is no "real" Islam, or "real" Christianity, there is simply the distribution of beliefs and practices of a number of individuals which exhibit ranges, variances and central tendencies. The average believer is then important, but sometimes minority practices are also important. Most Muslims are not terrorist nutballs, but my own interest is disproportionately toward the terrorist nutballs since their behaviors might result in my death or discomfort, or that of those who I care for. In contrast, I am less interested in the briefs of elite religious professionals which exhibit little relation to the world as it is (e.g., theological) because I doubt that there is relevance to these beliefs for non-believers (and even for the majority of believers I believe the relevance of theology is symbolic, a group marker).

I emphasize the various dimensions of religion because a part of the problem that comes with discussing scholars who study the topic is that they are addressing different levels of organization. The article emphasizes three primary camps:

1) Cognitive anthropologists who believe that religion is a cultural byproduct of the necessary architecture of our minds (i.e., non-adaptationists)

2) Group selectionists who tend to take a functionalist tack in regards to religious beliefs and institutions

3) Behavioral scientists which utilize game theory and its related disciplines in analyzing the "rational" import of religious belief

An astute reader can probably guess that a major issue here is that group 1 is addressing a different level of religion than group 2 or 3. Specifically, functionalists who are looking at religion through the lens of broad cultural institutions and mass society, bound by common confession of faith and ritual. In Darwin's Cathedral David S. Wilson lays out his argument using various examples, e.g., the Calvinist religion, or water temples in Bali. One problem is that functionalist explanations often do not hold up to closer analysis, as illustrated by my co-blogger David B's analysis of the Nuer conquest of the Dinka (a canonical example of the superiority of one cultural complex over another). Additionally, the functionalists often have an issue in regards to accepting the explanations of peoples whom they are studying without peeling back the cognitive layers. Modern psychology makes clear that humans are natural fabulists, and we concoct rationales promiscuously and unconsciously, even when they are clearly false or implausible. One reason many tribal people give for shifting toward a world religion, or altering their practice, is that it is simply economically more efficient. For example in East Java slametan is a ritual feast which is ubiquitous as way to cement relationships, mark important festivals and show one's status and generosity. Some conversions to more "orthodox" Islam are justified by the fact that this form of Islam, shorn of Javanese cultural accretions, is simply cheaper and not as wasteful, as slametan is no longer necessary. The exact same reason is given by pagans who convert to Christianity other parts of Southeast Asia, the cost of a ritual feast is obviated by conversion to a religion which bans the practice. In these situations Christianity and a less culturally mediated form of Islam are presented as more rational by the converts, and anthropologists who study these peoples do see them abandoning expensive feasts. But, life isn't always so simple, and the bequests by wealthy Christians or Muslims made to houses of worship or charities shows that wealth signaling continues via other methods. 1,500 years ago in Europe the conversion of pagans to Christianity resulted in a similar abandonment of traditional ritual be replaced by the Saints Calendar. Of course religions do differ, and it is notable that the worshipers of philosophically girded faiths seem to withstand the test of time against those cults which focus on the worship of cult statuary endowed with large penises or the heads of animals. Yet I think that it is more complex than simply assuming that more "primitive" religions by their nature were what resulted in lesser cultural fitness, rather, one could assert that a common causal component is at work in the rise of expansionist and aggressive states and the religions which they champion.

In contrast to Wilson game theorists and those who come out of economics tend to focus on the individual utility of religion. But, this utility is scaffolded in a group level context. Just as co-ethnics may start credit cooperatives, so co-religionists in a foreign land pass a currency of trust bound together by a communal god to whom they owe fealty. Jewish & Jain merchants are classic examples of this, small religious minorities who enter into businesses which require a high level of trust to smooth transactions. It is no surprise that the diamond business in Antwerp is controlled by religious Jews as a particular caste of Jains. The article frames these strategies as adaptationist, and they are, as religious adherence maintains and reinforces belonging to the social group upon which one depends. Recall that in the pre-modern time individuals did not live as an island, that their lives were defined by, and contingent upon, communal ties of trust and cooperation. This form of adaptationism is not as thoroughly functionalist as David S. Wilson's models, such as the water temple, because group solidarity can be engendered by a wide range of beliefs. The nature of the god matters less than the common and universal aspect of that god.

Finally, there is the byproduct school. One analogy I've used for this idea is that just as a car's engine generates heat, so a mind's function generates religion (and art). One can reduce the heat that the engine turning it off, which is clearly not feasible. But, the byproduct heat can also be put to use (to warm up passengers). The various components of the engine, as outlined in the article, are:

* Agent detection
* Causal reasoning
* Theory of mind

There are almost certainly more. The cognitive anthropologist's basic model is that in a the typical human being these cognitive tools interact in a manner which produces byproduct phenomena, religion being a prime one. This is why they reject a simple adaptionist narrative for religion: belief per se is not what is being selected for, but the various propensities and competencies which make that belief highly likely to emerge. The distributed nature of the characters which give rise to religion is, I believe, the reason that atheists exist: each element above (and more) exhibit variation within the population, and so a small proportion always exist who are highly likely to find supernatural beliefs uncompelling because of the architecture of their minds. If, for example, you are weak on agency detection and causal reasoning a simple teleological argument for the existence of god might seem extremely inscrutable. Similarly, an autistic individual who has difficulty forming models of the minds of flesh & blood humans around them might find it nearly impossible to comprehend on a gestalt level the possibility that a noncorporeal entity which they have never seen exists out there and wishes to have a special personal relationship with all humans. Engines are after all designed and constructed differently, and so the amount of heat which they generate might vary (as might their performance at various tasks).*

And yet as I said: the heat of an engine can be put to good use, it is energy, even if a somewhat chaotic and uncontrolled form. This is why the dichotomy between adaptationist and non-adaptationist views is problematic. A "strong form" adaptationist model is, to my mind, implausible. Powerful directional selective forces exhaust variation as all the alleles become fixed, and though atheists are in a majority, it seems that religious zeal, interest and propensity does exhibit variation through all societies. This implies that the underlying components still exhibit variation. Nevertheless, it is clear that religious beliefs can yield a utilitarian value, behavioral economists have shown that highly zealous individuals may defy "rational" expectation. As human culture has become progressively more complex the niches have proliferated, and frequency dependent selection and the importance of mixed behavioral strategies in complex societies may likely play roles in perpetuating variation in belief and practice. In a society where the vast majority are religious it maybe that a "free rider" atheist minority can always make a living simply because the religious majority can rationally assume everyone will be altruistic based on common godly belief. In other words, a form of the Hawk and Dove game might be at work. Similarly, group level selective effects might come to bear and co-opt religious belief, even if that beliefs initial origins had nothing to do with increased fitness.

Why does this matter? First, I believe it is important to put into their place doctrinal elements in religious systems. They do have importance, but for too many they become the root and ends of all religion. Too many atheists who accept this line waste their time engaging in debate precisely because they believe that falsifying doctrine, or showing its incoherency, will result in disbelief. The problem with this idea is that the body of evidence is growing that doctrine exhibits a very weak hold on the mind, and theological details are generally incomprehensible to most humans aside from notional attachments (e.g., Christians and Muslims know the basic outlines of the theological differences which define their faiths, but, the identity of being part of the faith and a personal understanding of god is far more important on a day to day level than the nuances of tawhid or Substance and Natures). Second, if religion is a natural phenomenon that opens the window for future engineering. Consider the role of Southern white Protestant Christianity in cementing the orthodoxies of its day, or the influence of evangelicals in northern abolitionism. Religious spirit is an important factor in amplifying the magnitude of any social vector, for good or ill. If you can't kill the tiger, learn to ride it so that you may drive your enemies before you.

* I believe that this quantitative genetic model explains why atheism varies between societies over time and space: the distribution of belief exhibits a norm of reaction in disparate environments.

Related: Theological Incorrectness. Why Religion. The gods of the cognitive scientists. Reflections on the "God Module." "Hard-wired" for God. Innate atheism and variation between societies. Atheism, Heresy and Hesychasm. Modes of Religion.

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Nit-picking   posted by p-ter @ 3/03/2007 03:05:00 PM

An article in the Journal of the American Medical Association last year made the case for reconsidering studying the genetics of traits like smoking, arguing that the benefits or such research are limited, at best. I don't totally disagree with the points they make, but statements like this just never should have made it past reviewers:
[I]ncreasingly popular genome-wide association studies have thus far demonstrated only modest success (ie, logarithmic odds [LOD] score of 2.7 for smoking dependence in identifying influential candidate genes. What is the likelihood that further studies will ultimately lead to a gene variant (or gene variants) with both overwhelming influence and ability to affect significant changes in behavior commensurate with community-based interventions?
The study they cite is, of course, not a genome-wide association study, but rather a genome-wide linkage study. The two are not that same thing, and if this reflects a deeper misunderstaning of the different approaches used to map variation underlying traits in humans (as opposed to a simple brain freeze), the authors really have no idea what "the likelihood that further studies will ultimately lead to a gene" is, nor did they bother to think about their question very seriously.

Their article elicited a response, and the response to the response includes this gem:
In response to Dr Bierut and colleagues, the central motivation of our Commentary was not to curtail research funding, and we hope that a careful reading will dissuade others from this interpretation. Rather, we argued for wise use of public resources.
Ah, right, of course. Funny how that non-call for curtailing funding included this:
Genetics studies should be acknowledged as currently unlikely to lead to improved lung cancer prevention compared with the proven, non-genetic-based strategies for smoking cessation outlined above. Even as an interim measure, genetic testing should be secondary in funding and emphasis to universal measures to decrease smoking. And given the obvious dangers of tobacco and the associated imperative to eliminate it, research undertaken purely to unravel mechanisms of tobacco-related cancer is difficult to justify, unless the research can be shown to provide insight into fundamental cancer pathophysiology


Friday, March 02, 2007

Brother and sister who have kids   posted by Razib @ 3/02/2007 10:01:00 AM

Read the story here. Note that they were raised apart (proximate & ultimate issues here). It's the most watched video on CNN. Only in Germany (luridly reported by the Brits)....

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Thursday, March 01, 2007

Dig facial hair?   posted by p-ter @ 3/01/2007 05:54:00 PM

Nature this week has a news feature on research done by Angela Christiano into the genetics of various hair-related phenotypes:
[F]or Christiano, hair is not just an adornment. It is a filament that binds together her appearance, her family, her personal life and her work. Descended from two generations of hairdressers, she came to appreciate hair's true importance when her own locks began to fall out in an episode of alopecia areata. Working at Columbia, she immediately shifted the focus of her research from skin disease to hunting down the genes that underlie human hair disorders, such as an atavistic condition in which people sprout thick hair all over their faces. Her scientific work may even end up with a cosmetic use, saving men and women with normal but nevertheless unwanted hair from shaving, waxing and depilation.
I'd never heard of any of the disorders mentioned in the article, but the references are fascinating. There's the alopecias (a type of which is shown in the bottom picture), one of which is caused by a recessive mutation in a transcription factor. Then there's hypotrichosis, in which hair can grow, but breaks off near the head. This disorder seems to be caused by mutation in a gene encoding for cell adhesion. She also discovered the gene that causes a rare disorder in which the affected individuals have no nails on their fingers or toes.

As for the hairy-faced individual in the top picture, the causal mutation is currently unknown, though it seems to be an X-linked recessive trait:
One of Christiano's most intractable puzzles is in her "Mexican hair people", who have thick, 'terminal' hair all over their faces rather than the finer 'vellus' hair, which is normal. Christiano and her team have spent more than five years studying one of the only reported cases of a family with this disorder - called hypertrichosis4. But although they sequenced 82 genes in the relevant region of the X chromosome and every snippet of microRNA, they could not find a causative mutation. Some kind of genetic trickery could be afoot: perhaps a mutated RNA outside the protein-coding genes is failing to regulate a gene on another chromosome.