Sunday, July 31, 2005

7-7 bombers,who were they?   posted by Razib @ 7/31/2005 01:04:00 PM

Seething Unease Shaped British Bombers' Newfound Zeal.

Related: Profile of Salafi jihadists....

Update: A British Jihadist.

Update II: This part of the article from The Prospect (an interview with a gleeful radical) is interesting:

Taseer: Given that the Koran is incontestable to the letter, and that it is unique because there is no another religion in which there is a text so pure, handed down from God to man, can there be a moderate Muslim?

Butt: No. You've hit the nail on the head. If someone believes that it's the incontestable word of Allah, how can he take a moderate view? We must fight if it is the will of Allah. I don’t want to say that Muslims don’t believe in Allah, but what I will say is that their faith in Allah is weak. They fear man the same way that the Jews feared the pharaoh, who they feared more than Allah and that's why they were afraid to do anything against him, until Moses came and liberated them. The lack of leadership in the Muslim community is simply because they are too afraid to stand up against this so-called undefeatable giant of the United States.

Taseer: Coming back to the youth, are they angry?

Butt: Many are from quite wealthy families, as I am.

Taseer: So you don't see this rise of extremism among British Muslims as rooted in economic disadvantage?

Butt: I think that's a myth, pushed forward by so-called moderate Muslims. If you look at the 19 hijackers on 9/11, which one of them didn't have a degree? Muhammad Atta was an engineer [he was actually an architect and town planner] at the highest level. His Hamburg lecturer said, “I didn't have a student like him.” These people are not deprived or uneducated; they are the peak of society. They've seen everything there is to see and they are rejecting it outright because there is nothing for them. Most of the people I sit with are in fact university students, they come from wealthy families....

The above is why I have mooted the idea of a new historically contextualized view of the Koran as being an option for some "Muslims." Right now this is a discounted view, and so you have to push the argument over to one of interpretation on the next level. If you read the interview above though, note how sly some of the redefinitions of terms of the radical are.

Note: Value added comments appreciated!

Saturday, July 30, 2005

Continuity, or not....   posted by Razib @ 7/30/2005 10:40:00 PM

Dienekes reports on recent extractions of mtDNA from remains in the Iberian peninsula1...not surprisingly (to me at least) there is continuity between the ancient populations and modern ones. This is relevant to debates about replacement of various aspects of the identity of one people by another. In places like Hungary, Spain or France it seems like there was elite replacement of the substrate language and culture (though not alleles). In contrast, in places like Bulgaria or Assam the substrate absorbed the elite. But, a problem crops up when people try and extend these particular cases to the whole world as if they hold true like a scientific law. For example, the recent story that "Britains have changed little since Ice Age" is a bit too neat, and fits into an archealogical bias that is part of the backlash against excessive typological thinking about "nations" before 1950. That is, the English nation were a volk of one tongue and one blood, which replaced the British ethnos in the 6th century, as hinted in Gildas' writings ("The barbarians drive us to the sea"). Rather, the archealogical and historical paradigms now tend to presume that the replacement of the British by the English was one of elite cultural imposition. If you read the old post Celts and Anglo-Saxons you will find that the "truth" as suggested by the genetic data that is emerging in the last 5 years is more complex than either replacement or acculturation.2 Strictly speaking the assertion that the peoples of the United Kingdom are descended from Ice Age Northern Europeans is probably correct, because even if there was an influx of alleles from Germany in the 5th and 6th centuries the two populations were not particularly distinct (well, at least in comparison to "Neolithic farmers" from the "Near East").

Since islands are relatively simple systems (migration is often constrained to choke points) I leave you with a post Japanese origins.

1 - I assume the reference to "Iberians" implies the peoples of the southern half of the peninsula, who in pre-Roman times spoke their own languages unrelated to Celtiberian and possibly distant from the Basque dialects. The people of Tartessos are the most prominent representatives of this cultural complex.

2 - I have read recently that the transition from a Celtic to an Anglo-Saxon peasantry was marked by a shift in the layouts of field and village in much of the east of England. Such changes could be triggered by cultural diffusion, but since the change wasn't functionally that important it suggests to me that there was some replacement of a Celtic peasantry by Germanic settlers who brought their own traditions and customs.

Reader survey....   posted by Razib @ 7/30/2005 05:42:00 PM

This poll is directed at regular readers....

Results from past reader surveys below....

Political Orientation

Far Right 11% 24
Moderate Right 26% 56
Centrist 8% 18
Moderate Left 15% 33
Far Left 3% 6
Libertarian 26% 56
Other 9% 20

Questions about God (sort of)

I believe in a personal God 17% 35
I bellieve in a impersonal God 8% 17
I believe in a supernatural force 8% 16
Am skeptical of supernatural entities 25% 51
Really don't believe in that kind of thing 43% 88

What is your religon?

Protestant 14% 29
Catholic 10% 21
Orthodox 1% 3
Other Christian 2% 5
Jew 4% 9
Muslim 2% 5
Hindu 4% 9
Buddhist 1% 3
Other religion 3% 6
No religion 57% 119

Who are you voting for (if American)

Kerry 33% 54
Bush 26% 43
Nader 3% 5
Libertarian guy 9% 15
Other 5% 9
None 23% 38

Results so far....

How did you find this web site?

Search engine
19% 43

Word of mouth (includes email)
5% 11

6% 13

Steve Sailer
38% 85

Blogroll of a weblog (besides Instapundit or Steve Sailer)
13% 28

A link in a post on another weblog (besides Instapundit or Steve Sailer)
14% 31

Discussion forum
1% 3

Comment of GNXP poster on another weblog
4% 8

222 votes total

Thursday, July 28, 2005

Not genes and not environment   posted by the @ 7/28/2005 10:31:00 PM

On many measures, identical (monozygotic, MZ) twins are not in fact "identical", despite the fact that they share essentially identical DNA and highly similar family environments. Indeed, for some traits, such as personality, all non-genetic effects appear to be of the kind that makes siblings different than one another. Peer socialization is one plausible source of this non-shared environment, but stochastic biological events probably play a role as well.

These stochastic effects are seen prominently in studies of aging in the worm C. elegans. Even when genes and environment are held constant[1], there is considerable variation in lifespan (time of death) within a population. (Almost as much variation in relative lifespan as the human population of the US.) A paper published this week in Nature Genetics (ironic) reports that chance variation in the level of induction of a stress-induced reporter predicts (to some extent) variation in lifespan.

When both genotype and environment are held constant, 'chance' variation in the lifespan of individuals in a population is still quite large. Using isogenic populations of the nematode Caenorhabditis elegans, we show that, on the first day of adult life, chance variation in the level of induction of a green fluorescent protein (GFP) reporter coupled to a promoter from the gene hsp-16.2 predicts as much as a fourfold variation in subsequent survival. The same reporter is also a predictor of ability to withstand a subsequent lethal thermal stress. The level of induction of GFP is not heritable, and GFP expression levels in other reporter constructs are not associated with differences in longevity. HSP-16.2 itself is probably not responsible for the observed differences in survival but instead probably reflects a hidden, heterogeneous, but now quantifiable, physiological state that dictates the ability of an organism to deal with the rigors of living.

The astonishing implication is that similar reporters could be found that predict the chance variation in human lifespan (or other dimensions of human biodiversity).

How did they do this research?

First, they created a strain of worm which fluoresces in response to exposure to high temperatures ("heat shock") (panel "a" below). The "heat-shock gene" hsp-16.2 is expressed when worms are heat shocked. The promoter of hsp-16.2 was joined with the protein coding sequence of green fluorescent protein (GFP) and this construct was integrated into the worm's genome. The intensity of GFP expression (measured by fluorescent intensity) is variable within an isogenic population (panel e). For their experiments, young adult worms were exposed to a heat shock (panel b) and then some time later they the worms were sorted into high, medium and low GFP subpopulations (panels f-h). The level of GFP expression becomes more variable at later times (panels c-d). The GFP expression level is not heritable: the progeny of worms from the high and low groups are indistinguishable when tested for GFP induction.

After sorting into three subpopulations, worms were tested for lifespan (panels a-c) or thermotolerance (i.e., lifespan at high temperature; panels d-f).

Numerous controls follow. The biggest problem for their study is that heat shock is known to cause increased lifespan on its own. They don't claim to have overcome this confounding effect, and so it seems to me that differential GFP expression may actually be a marker for this effect.

1 - C. elegans has two sexes: male and hermaphrodite. Hermaphrodites are self-fertilizing. Selfing allows for the production of genetically homogenous populations (except random mutations). Worms are grown on solid media in Petri dishes ("plates") or in liquid cultures. Worms living on the same plate are essentially experiencing the same environment, but undetected variation may exist between different plates or within different regions of the same plate.

Stem cells....   posted by Razib @ 7/28/2005 09:43:00 PM

Drudge says that Bill Frist will back stem cell research funding.

Battle of the disciplines   posted by Razib @ 7/28/2005 08:24:00 PM

I'm conflicted, Discovering functional relationships: biochemistry versus genetics:

Biochemists and geneticists, represented by Doug and Bill in classic essays, have long debated the merits of their methods. We revisited this issue using genomic data from the budding yeast, Saccharomyces cerevisiae, and found that genetic interactions outperformed protein interactions in predicting functional relationships between genes. However, when combined, these interaction types yielded superior performance, convincing Doug and Bill to call a truce.

I've cut & pasted the text below, it works out in the end.


For more than ten years, Doug, a retired biochemist, and Bill, a retired geneticist, have lived on a hill overlooking a car factory, debating their strategies for reverse engineering a car (see: Doug advocated rolling up his sleeves, getting under the hood and determining how the parts fit together. Bill preferred tying the hands of a different car-factory worker each morning, then relaxing with a cup of coffee and later examining the cars that emerged from the factory.

One day, Doug and Bill strolled over the next hill. In the midst of debate, they encountered Sharyl, a graduate student in computational genomics. Having overheard their debate, she interjected, ‘I don't know much about cars, but I detect an analogy to biochemistry and genetics. I'm trying to discover functional relationships between genes and proteins in yeast and I wonder which of your strategies would work best.’
Differing approaches to determining gene function

To discover functional relationships, Doug would ask, ‘Which proteins physically interact with my favorite protein?’ By contrast, Bill would perturb the DNA sequence of a gene and observe the consequences in vivo, asking ‘What are the genetic interaction partners of my favorite gene?’ In other words, ‘Which genes produce surprising phenotypes if mutated in combination with my favorite gene?’ Sharyl described how the fields of biochemistry and genetics had ‘gone genomic,’ scaling up their classical approaches to discover functional relationships with ever-greater efficiency. Their resulting systematic studies offered a playing field on which to assess Doug and Bill's dilemma. Sharyl then wondered, ‘Which type of interaction – protein or genetic – is better at revealing functional relationships?’ She pulled out her laptop computer and set to work (Figure 1).

Protein versus genetic interactions in predicting functional relationships

Because ‘gene function’ is vaguely defined, Sharyl used the Gene Ontology (GO) vocabulary, which describes gene products in terms of biological process, cellular component and molecular function ( 1 and 2. She defined three measures of functional relatedness for a pair of genes: (i) shared GO biological process (shared process); (ii) shared GO cellular component (shared component); and (iii) shared GO molecular function (shared function). For example, if two genes were assigned to the same GO biological process category, Sharyl considered the gene pair to have a ‘shared process’. To avoid associations between genes in broadly defined categories, she considered only specific GO categories – those to which 200 or fewer genes (out of not, vert, similar6000 total yeast genes) were assigned, including genes assigned to more specific daughter categories. To represent the biochemists, she chose a high-confidence protein-interaction data set based on affinity purification followed by mass spectrometry (APMS) [3]. For the geneticists, she fielded a recent systematic genetic-interaction data set [4] (Tables 1 and 2 in the supplementary data online; Box 1).

Protein and genetic-interaction screens

Synthetic genetic array (SGA) analysis is a high-throughput method that assesses pairs of genes for genetic interaction 4 and 19. A strain carrying a mutated query gene is crossed to an array of not, vert, similar4700 strains, each mutated in a different non-essential yeast gene. The resulting double mutants are then assessed for fitness. Slow growth or lethality relative to each of the single-mutant strains is declared synthetic sickness or lethality. In the SGA data set used here, 159 query genes were crossed to the array, resulting in not, vert, similar730 000 gene pairs tested for genetic interaction. Based on this data set, the genetic network is between two and 54 times more dense than the protein-interaction network.

Affinity purification followed by mass spectrometry (APMS) is used for high-throughput discovery of physical protein interactions. A ‘bait’ protein is precipitated in a complex with its interacting proteins. Members of this ‘pulled-down’ complex are then identified by mass spectrometry. The two large APMS studies in yeast are known as the tandem affinity purification (TAP) [3] and high-throughput mass spectrometric protein complex identification (HMS-PCI) [6] studies. In both studies, the data can be interpreted in two ways. The spoke interpretation defines an interaction between a bait protein and each protein it pulls down. The matrix interpretation, however, counts interactions between all pairs of proteins pulled down by a bait. In the TAP study, bait constructs were integrated into the yeast genome and expression was controlled by an endogenous promoter. In the HMS-PCI study, however, the bait construct was plamid-borne and expression was controlled by a robust exogenous promoter. Thus, the TAP data set is more likely to be physiologically relevant, although the HMS-PCI study could detect interactions between gene products not normally expressed in the condition examined. The TAP and HMS-PCI data sets employed 1167 and 725 baits, respectively. A gene pair was considered assessed for protein interaction, if at least one gene of the pair was a bait and the other was not filtered out as a ‘promiscuous prey’ [6].

Yeast-two-hybrid (Y2H) is a high-throughput method for assessing direct physical interaction between two proteins (although indirect ‘bridged’ interactions can also be detected). Here our Y2H data set consisted of the union of the interactions reported by Uetz et al. [18] and the ‘core’ version (corresponding to interactions detected at least three times) of the data set produced by Ito et al. [17].

To level the playing field, she considered only the 104 409 gene pairs (the ‘arena’) assessed by both approaches and for which both genes in each pair had a GO annotation. In this arena, the number of gene pairs sharing a specific GO process, component or function was 3841, 1803 and 1139, respectively. The arena contained 48 biochemical interactions and 729 genetic interactions, derived primarily from screens involving the 17 genes used both as baits in the protein-interaction screens and as query genes crossed to 4500 mutants in synthetic genetic array (SGA) analysis. Interestingly, there was no overlap between the protein and genetic interactions (Table 3, supplementary data online). A previous related study [5] did not consider whether gene pairs had been assessed for both types of interaction and used literature-derived interaction data, which are subject to inspection bias.

With a few taps on her keyboard, Sharyl let the games begin. Two proteins exhibiting a protein interaction had a shared process, component or function 42% (P=2e-17), 31% (P=2e-15) and 29% (P=1e-16) of the time, respectively. Genetic interactions were uniformly less-accurate indicators of shared function, with corresponding rates of 19% (P=2e-63), 15% (P=2e-66) and 8% (P=2e-28). However, genetic interactions detected gene pairs with shared function with much higher sensitivity (4–6%) than biochemical interactions (0.5–1.2%; Table 4 in the supplementary data online). When considering different physical-interaction data sets 3 and 6 (Box 1), genetic interactions were consistently more sensitive and sometimes more accurate (see Glossary; Table 4, supplementary data online). Thus, it was difficult to declare a clear winner.
Combining genetic and protein interactions with other data

Are genetic interactions combined with other types of evidence more informative than protein interactions combined with other evidence? Rather than considering each type of interaction in isolation, several groups have previously combined heterogeneous data, using machine learning approaches to predict some property of a gene pair or to predict gene function 7, 8, 9, 10, 11 and 12. Therefore, Sharyl combined multiple types of evidence [11] – including co-localization [13], sequence homology [14], correlated mRNA expression 15 and 16 and chromosomal distance (Table 5, supplementary data online) – to predict shared function. She chose a previously described probabilistic-decision tree approach [12] and compared performance with and without the benefit of protein and/or genetic-interaction data. For each of shared process, component, and function and for each choice of input data, she performed cross-validation: she randomized all gene pairs in the arena into four groups, and successively scored each group using a model trained on the remaining three. She then compared the prediction score of each gene pair with its corresponding shared process, function or component status. A plot of true- versus false-positive rates revealed that genetic and protein interactions were comparable at low sensitivities; however, as sensitivity increased, genetic-interaction data enhanced performance more than protein-interaction data. This trend was observed for shared process (Figure 2), component (Figure 1a, supplementary data online) and function (Figure 1b, supplementary data online). Doug, the biochemist, began to despair.

Before Bill could begin to gloat, however, Sharyl showed that genetic- and protein-interaction data together gave markedly better results than either alone, suggesting that each offers distinctly different types of information. Although protein interactions can represent associations between genes in the same complex or physically connected pathway, genetic interactions can additionally reflect relationships between genes in physically non-interacting pathways. She repeated this analysis with another APMS protein-interaction data set [6] and then with the union of two yeast-two-hybrid (Y2H) data sets 17 and 18 (Tables 1 and 3, and Figures 2 and 3 in the supplementary data online), altering the arena appropriately. In each case, genetics beat biochemistry by a slim margin, but the combination of these complementary interaction types outperformed either alone. Sharyl's results convinced Doug and Bill to shake hands and head back over the hill … until new data or new technology call for a rematch.

Eating their own   posted by Razib @ 7/28/2005 07:20:00 PM

Seems like there is some intellectual cannibalism going on over on the Left. The Savage Minds anthropology weblog is being stomped on from all angles of the Progressosphere because they dared to point a sharp object at Jared Diamond. Kerim has the round up. He pointed to us back when Greg & Henry's paper broke and I appreciate that, but my experience on that weblog is that it has a pretty standard liberal slant, so I'm sure this episode of being broadsided by big names in the Progressosphere must be somewhat surreal. Anyway, the original post that started this actually referenced Guns, Germs and Gonads, you know, to show the racist perspective. Also check out Henry Farrell's post. I think I agree with him that Ozma does throw around the term "racist" in a cavalier fashion. Shit gets complicated when you are trying to stay on the politically correct side all the time.

Addendum: Since I've been a bit priggish about concepts, categories and precision recently, I will admit I probably elided over great differences within what I termed the "Progressosphere" because I'm not too political and my own inclinations are pretty orthogonal to the center to Left axis. So yeah, they aren't all Muguloos.

Cajun genetics   posted by Razib @ 7/28/2005 06:25:00 PM

Here is a profile of a researcher who has been on the Cajun beat for a while now. If you are a member of a small relatively homogenous group which has weird diseases and keeps decent records, well, expect more of this sort of thing.

Not a "paradox" at all   posted by Razib @ 7/28/2005 03:21:00 PM

The article, The Christian Paradox is making the rounds. It starts:

Only 40 percent of Americans can name more than four of the Ten Commandments, and a scant half can cite any of the four authors of the Gospels. Twelve percent believe Joan of Arc was Noah's wife...Three quarters of Americans believe the Bible teaches that "God helps those who help themselves." That is, three out of four Americans believe that this uber-American idea, a notion at the core of our current individualist politics and culture, which was in fact uttered by Ben Franklin, actually appears in Holy Scripture.

Perhaps the readers of Harper's believe that Christianity is something you find in the Gospels (sola scriptura writ large), but if you are an unbelieving anthropologist you would say that a religion is lived by the people who profess it, and it is out here, not in there. This is relevant to the thread below where we discuss the future of (North) American Islam. If you are a believer in religion X, you are going to assent to creedal assertions a, b, c..., and the intersection of those assertions help define what a religion is fundamentally. But, if you are not a believer a religion is nothing fundamentally except for what the people who espouse it say it is, and to make that judgement you need to weight various semantical nuances in their proper context, ascertaining the character of a religion is not an act of faith but a cognitive process of category creation.

Apropos of this, in the first chapter of Knowledge, Concepts, and Categories I learned that:
  1. People tend to create concepts or categories with OR conditions more than AND conditions (that is, a loose set of probable characteristics rather than a tightly integrated set of necessary traits).
  2. People are aware of the correlated variables within the concept.
  3. Context matters in how people perceive a category.
  4. Repeated input can result in adaption via inductive reasoning so that the center of gravity of a concept can shift over time.
  5. Not all traits have additive effects (ie; not "linearly separable").
  6. And people tend to attribute essences to a category.

I think the last is a problem in light of public policy disputes because we no longer live in bands of 100 people, we exist in a world where macroscale constructs which exhibit flux and continuity are the norm. 10,000 years ago there might have been 50 Muguloo tribesmen, and you could make pretty robust generalizations of those Muguloos, to the point where a distribution-population way of thinking was unnecessary. Today, you have 12 million Jews, or 1.2 billion Muslims, tens of millions of liberals and conservatives...but we still talk as if they were just a band of Muguloos.1 Additionally, the disjunctive tendency of categories (trait A OR trait B OR trait C) also causes confusions because people disagree about the particulars but never make their axioms explicit so that it is often the norm to just talk past each other. More later....

1 - The closer a category or concept comes to one's own self-reference the more nuanced, precise and qualified one will get about defining it. Muguloos be damned!

Wednesday, July 27, 2005

Play with meiosis   posted by Razib @ 7/27/2005 02:58:00 PM

One of the main reasons this site is around is to make basic genetic knowledge a casual background feature of the data bases of people who would otherwise not know much about this important science (another reason, at least for me, is to dump a lot of historical and non-science data out there to a scientifically literate audience so they can better form models which influence their view of public policy). So in that spirit, check out Using Karyotypes to Predict Genetic Disorders (it has some neat interactive movies, though if you know genetics, don't worry about it, but if you have been skipping the science posts for lack of a basic background, I advise you check out the link). Remember, to the first approximation it all starts out on basic Mendelian principles.

The wild "horse" and other knots   posted by Razib @ 7/27/2005 12:58:00 PM

Przewalski's Horse:

Some authorities believe the Przewalski is a direct ancestor of the modern day domesticated horse. Others contend this is not possible as the Przewalski is a different species having sixty-six chromosomes while the domestic horse carries sixty-four. It is possible to cross the Przewalski with the domestic horse, and the resulting hybrid is fertile; however this offspring has sixty-five chromosomes. When crossed again to the domestic horse, the new generation returns to sixty-four chromosomes and little influence of the Przewalski horse is evident.

Related to this, FISH analysis comparing genome organization in the domestic horse (Equus caballus) to that of the Mongolian wild horse (E. przewalskii):

...Previous studies of GTG-banded karyotypes suggested that the chromosomes of both equids were homologous and the difference in chromosome number was due to a Robertsonian event involving two pairs of acrocentric chromosomes in EPR and one pair of metacentric chromosomes in ECA (ECA5). To determine which EPR chromosomes were homologous to ECA5 and to confirm the predicted chromosome homologies based on GTG banding, we constructed a comparative gene map between ECA and EPR by FISH mapping 46 domestic horse-derived BAC clones containing genes previously mapped to ECA chromosomes. The results indicated that all ECA and EPR chromosomes were homologous as predicted by GTG banding, but provide new information in that the EPR acrocentric chromosomes EPR23 and EPR24 were shown to be homologues of the ECA metacentric chromosome ECA5.

Also, Invasive honeysuckle opens door for new hybrid insect species:

The animal family tree may not be filled just with forks, but may also contain knots: hybrid species with two different ancestors rather than one, according to a team of Penn State researchers.

"Hybrid" speciation is pretty common in plants from what I know, but the issues surrounding animals are sketchier....

Related: Breakin' free of biology?

Beyound the omniscient CPU   posted by Razib @ 7/27/2005 12:26:00 PM

In Genesis 6:3 God states "...My spirit shall not always strive with man, for that he also is flesh: yet his days shall be an hundred and twenty years." And yet if you keep reading you note that many people do live beyond 120 year in the Bible. And in the past century people have lived past 120 years. Something is off. In a comment below one individual asserts that "religion - no matter what the denomination is, and always has been a logical absurdity." I believe when viewed as a system of axioms religious beliefs fall flat on their face due to an internal lack of coherency, and yet they persist.

But just because religion fails as a system of formalized knowledge about the world does not mean that we should chalk it up to historical forces (opium of the masses), abstracted psychological yearnings (wish fulfillment) or an inexplicable irrationality (mass hysteria). I have stated that the religious need seems to be rather lacking in my own person, but, two personal points should get across what I want to communicate:

1) I can still repeat Surah Fatihah, the opening passage of the Koran and the preamble to the daily prayers, when called upon to (in a language foreign to me, and without any ability to break the passage into "chunks").
2) When I hear a call to prayer I have a difficult time expressing in words the peculiar chill that runs down my spine.

One must keep in context the following facts:

1) I never really believed.
2) My Islamic education was minimal at best.
3) I have never lived in an area with many Muslims.

If I could "delete" my knowledge of the Surah Fatihah, I surely would if that meant I could free up "space" for something far more interesting. But somehow it persists in my memory.1 Humans often live under the illusion that we govern ourselves fully consciously, but a moment of reflection on what you've done in the past hour would surely disabuse you of that notion if you still hold to it. You might have taken a shower, locked the door or turned the oven off with barely a recollection of the details, these chores have become "instincts." Many aspects of our nature are delegated to subroutines or helper programs, and we don't really have conscious access to what's going on down there. In theory we can issue a chain of commands, but don't expect the help to oblige you if they are of one mind. It recalls an acquaintance of mine who was raised a Born Again Christian, and though a vocal atheist now, he still listens to Christian music. Though he didn't believe in the message, the melodies and themes were familiar to him and still aroused an emotional response that he sought out.

The importance of indepdent cognitive subroutines and emotional associations are just two of the facts that I believe make religion explicable. For whatever reason a minority of any given population tends to dissent from the dominant supernatural narrative of its locale, but unfortunately many of these individuals project their own peculiar psychology on to the rest of the population. I believe a good portion of this minority even verbally assents to the general supernatural narrative but recreates it so that it is intelligible in its own language (ie; theology). I suspect an understanding of religious process is possible, but we need to move beyond assuming that it is either a formal system of thought or that it is at its core irrational, and will never be accessible to systematic inquiry.

1 - Some Muslims would offer this as evidence of the miraculous nature of the Koran, but I could give other examples of things I can't forget that I would like to.

Tuesday, July 26, 2005

Worm's life   posted by Razib @ 7/26/2005 11:11:00 PM

In 1998 the C. elegans genome was complete. Two years later we had the draft of the human genome. The connection between these two events is the "hook" for Andrew Brown's In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite (also author of the The Darwin Wars, which focuses on the life of George Price and his influence on seminal figures in evolutionary biology like J.M. Smith and W.D. Hamilton). I actually didn't find the last part of the book that interesting because the topic has been pretty well done. Who wants anymore anecdotes on the toothy Jim Watson? Rather, the first 150 pages (out of some 200) which chronicled the persistence of the brilliant Sydney Brenner1 and the team of researchers that he gathered around him in the late 1960s and 1970s before the worm was "hot" is an interesting anecdote laced analysis of the sociology and psychology of science. This isn't surprising, Brown has a background as a religion reporter, which showed in The Darwin Wars, and here he goes out of his way to note the quirky socio-religious backgrounds of many of the early wormers (Quakers, Jews and other assorted nonconformists).

There is scientific detail in the book, the simple anatomy of the worm is sketched out (~1000 cells, eukaryotic and multicellular, but not too much!), the benefits of selfing hermaphroditism is highlighted (recessives can be snatched out as one out of four self-crosses are homozygous on the two alleles which produce a non-dominant phenotype) as well as the utility of the rare males in swapping alleles between the lineages. I felt Brown spent way too much time ruminating on Brenner doing Assembly coding back ~1970, it boggles the mind.2 But the meat of the book is the sociology, personality and philosophy. Some of the anecdotes are really bizarre...who would have guessed that the first "picks" were actually toothpicks! The researchers would spend an hour each morning sharpening them and discarding their pile throughout the day. When one of them got the bright idea of sticking a platinum filament to a tong-handle Brenner disapproved, suggesting that brilliance doesn't forbid obstinacy.

But there are also the "big picture" questions. How far can reductionism go? What is the worth of a model organism? Is there any real point in the Human Genome Project beyond the "It was there" aspect? The book only really gives a good answer on the last question, chalking up Sydney Brenner's skepticism of the enterprise to age and ego (Brown was gentler, but that's what he was saying). There are many golden roads, but many dark and thankless ditches in science, and I think the fact that for every winner (as the worm people were) there are innumerable losers. That's how lab science works, it isn't measured in individuals as much as man hours many times (the mapping of the worm nervous system for example seemed to be a chore of herculean tedium). The decisions people make aren't always justifiable, but some of the times their hunches hit paydirt. The good angel on your right shoulder and the bad angel on your left shoulder both give a skewed view of who you are to God on the day of judgement, but summed together they hit the proper mark. Science is filled with good angels and bad angels, and the God of Spinoza judges fairly in the end.

Addendum: Non-science types might find the bitchness of the "fly" (Drosophila) people to the worm people pretty funny. I wonder though, do astrophysicists who study black holes look down on those who model neutron stars???

Update Rikurzhen: Most of the tools are now in place to dissect worm biology from a systems level down to molecules. If there is a logical limitation to reductionism, work on the worm will soon the bumping into it. The genome is complete and feature annotation is greatly simpler in a 100MB genome (worms) than a 3000MB genome (mammals). Reverse genetics using RNAi is ridiculously easy to do (>80% of known genes have been assayed by RNAi for many, many phenotypes). Worms can be grown to population sizes unimaginable for other multicellular model organisms, and many phenotypes can now be assayed with automation. But obviously the most important question is whether this model organism can keep producing new insights into (human) biology. I anticipate that "$1000 genome" sequencing technologies are going to accelerate work on new/existing model organisms just as much as they will human genetics.

1 - Brenner's father was an illiterate. He, on the other hand, matriculated as an undergraduate at the age of 14.

2 - I recall that back in the 1990s the WordPerfect guys were forced to write the app in Assembly so that they could be closer to machine language and optimize performance. Of course, soon enough Word blew them out of the water, partly because Microsoft could push it via its Office Suite, but also because they were coming out with new versions slapped together (I assume) in a human friendly VB IDE at a much faster clip.

Some Musings on Patent Law   posted by TangoMan @ 7/26/2005 11:09:00 PM

In Razib's post Patents, genes and Jews some commentators raised concerns about the patents granted, so I thought I'd expound a bit on this particular issue.

There is a long legal debate underlying the patentability of claims that many critics feel should be classified as being within the Common Heritage of Mankind. I get the sense that many objections that we're going to see on gene patents in the coming years are going to be framed from such a perspective.

We can go back to the 1600's and the writings of Hugo Grotius in Mare Liberum where he wrote about that the ownership of goods that were created by nature for common use should be forbidden and that common use is viable as long as the object can be used without loss to anyone else. He was at the time writing specifically about the laws of the sea, but many in the years that followed took these principles of international law to apply to to other realms, such as outer space and agriculture.

Twenty-five years ago when Diamond vs. Chakrabarty was decided it brought the issue of patents for life forms front and center into conflict with with the principle of Common Heritage. The ruling set about a flurry of debate regarding plant life and how the gene poor but industrial West was robbing the poor, but gene-rich, Third World of their genetic resources with as much as 95% of world food crops originating in the developing world. If you're interested in the views of a defender of Indigenous Peoples who isn't as hysteric as the persecutors of the Human Genome Diversity Project, you might find this page to be of interest. The author doesn't begrudge the right of those scientists who add value to genetic material to profit from their work but champions the position of Indigenous Peoples so that they too may also profit from the seed material that is collected from their territory. He notes, afterall, that:

The developed countries have already realized enormous benefits from their access to Third World genetic materials. This is perhaps most clear in the case of crop plants. Few of the crops that today make the United States an agricultural power are native to North America. European colonizers found Native Americans growing maize, beans, tobacco, and squash; but these crops had been introduced from Central America and the Caribbean. A truly North American meal would consist only of sunflowers, blueberries, cranberries, pecans, and chestnuts.

Northern Europe's original genetic poverty is only slightly less striking: oats, rye, currants, and raspberries constitute the complement of major crops indigenous to that region.The crops that one associates today with the agricultural economies of the developed nations - maize, wheat, soybeans, potatoes, alfalfa, barley, sorghum, tomatoes, cotton, tobacco - have in fact been introduced from their areas of origin in what are now the nations of the Third World. The agricultural development that has undergirded the industrialization of the rich but gene-poor North has been predicated on the collection of genetic materials from the poor but gene-rich South.

Does anyone else see the parallels to the genetic information that is being mined from Jewish, Finnish, and Icelandic peoples with most of the benefits flowing to the researchers? I wouldn't be surprised to see the same arguments flare-up as human gene patents more frequently find their way into the marketplace.

If such a replay does come to pass, it might help to keep in mind how it played out with plant genetics. The effort to redress the situation resulted in a UN Agency, the Food and Agriculture Organization, at it's 22nd biennial meeting in 1983 to come forth with a resolution 8/83 that stated "plant genetic resources are a heritage of mankind and consequently should be available without restriction." This resolution, especially Article 2.1 (a) (v) in the Annex to Resolution 8/83, which read "special genetic stocks (including elite and current breeders’ lines and mutants);" put the FAO Undertaking in direct conflict with Diamond vs. Chakrabarty.

Now politics being what it is, and especially UN-centric politics, I happen to think that the FAO undertaking had more to do with advancing the dead horse of the New International Economic Order than it really did with settling the issues of intellectual property law, the prinicples of CHM and International law.

The developed nations were opposed to the FAO undertaking and its attack on IP law and property rights and their position had three main pillars:

1.) A price can't be assigned to raw germplasm because, while there may contain useful genes, until those genes are evaluated and traits identified, the germplasm is an unknown quantity.

2.) The collection of germplasm doesn't deprive a country of a good or benefit. If utility isn't lost, then there is no claim for compensation.

3.) The FAO undertaking was inconsistent with Intellectual Property rights.

The FAO Undertaking would have had to overturn quite a number of patents, and and for the expired patents, their history and reasoning, such as that found in patent #141072 granted to Louis Pasteur for claiming "yeast, free from organic germs of disease, as an article of manufacture" and precedents established in cases such as Argoudelis, Feldman v. Aunstrup, and a host of other rulings.

What we're seeing with the BRCA2 gene is the gene has existed in certain populations but there was little that could be done medically with regards to its effects until BCRA2 was evaluated and it's traits identified, and therefore it remained an unknown quantity. Myriad Genetics has though their work in identification and evalution brought value to the identification of the gene, therefore the test for the presence of the gene is their intellectual property. The fact that it is targeted predominantly at Jewish populations who provided the "raw material" for study doesn't unfairly target them, nor does it exploit them, for without the research performed by Myriad Genetics the presence, and identification, of BCRA2 within the population wouldn't by itself create any value. The study of Jewish genes doesn't deprive the community of any goods or benefits and as a community they don't lose any utility of those genes, so it's difficult to base a claim of exploitation when a test for BCRA2 is offered to the commmunity.

Patents, genes and Jews   posted by Razib @ 7/26/2005 11:03:00 AM

Slate has an interesting piece up that highlights the controversy with patenting aspects of the BRCA2 gene. Of course the article focuses on the specific case of Jews, but as far as the ultimate issues of intellectual rights relating to genetic sequences and the methods to ascertain their identity, this is the tip of the iceberg. Today we are squabbling over music and film, but in the near future I suspect that we are going to focus less on such trivialities.

Monday, July 25, 2005

Religion in public life   posted by Razib @ 7/25/2005 11:29:00 PM

Randall has a long post up where he highlights a book titled The Impossibility of Religious Freedom, which addresses the legal implications of religious pluralism. There are many complicated issues here, and I simply ask readers to check out the facts for themselves, but not get too caught up in the details. From the introduction:

This book is about the impossibility of religious freedom. Many laws, constitutions, and international treaties today grant legally enforceable rights to those whose religious freedom is infringed. Stories of the conflict between the demands of religion and the demands of law are daily news items all over the world, and take a familiar patterned form. Schoolgirls in France seek permission to wear the hijab to school. Sikhs in Britain seek exemption from motorcycle helmet laws. Muslim women seek civil divorces in India on the same ground as their Hindu and Christian neighbors. The Jehovah's Witnesses seek the right to be a recognized religious organization in Russia and to be exempt from patriotic exercises in Greece....

I have read a fair amount about the Reformation as well as the history of Northern Europe in the 16th and 17th century and I support one of the contentions of the author that something rather peculiar happened in places like England1 and The Netherlands during this period, and the full flower of that process can be found in the United States, a nation that gives expression to Christianities, but no support for one state church. Of course, there isn't a sharp dichotomy between the "Protestant model" and everything else, there is after all a difference between 16th century Spain or 21st century Saudi Arabia and traditional Chinese or Indian attitudes toward pluralism of faith.2 Also, note that one reason I believe Roman Catholicism has been such a success in the United States is that operationally it has become a Protestant religion here, when I listened to Catholics being interviewed on television after the priest scandals talking about how "they cared more about their relationship to Jesus" than "the edicts of the Church" it really struck home. Many Jews also mock the Reform as (in the words of John Stewart) "Christians with curly hair," but again, the introduction of organs and other Protestant motifs and the popularity of personal "spirituality" as opposed to adherence to the norms of halakah suggests to me a definite inward Protestantization of that faith as well. Will Herberg's Protestant-Catholic-Jew triumvirate was possible in large part, I believe, because the latter two were fast renorming themselves to adhere to mainline Protestant mores.

1 - Please note that there were multiple Reformations (including a Catholic one, what is termed the "Counter Reformation"). To say that the Protestant Reformation resulted in the trend toward disestablishmentarianism is to ignore the reality that in much of Germany and Scandinavia Lutheranism was closely identified with the temporal powers that be, that in Geneva and Scotland Calvinism became the state church (with some bumps in the road in the latter case). Rather, the road to disestablishmentarianism was seeded by the intransigence of groups like Baptists, Quakers and other assorted "Free Thinkers" who simply could not or would not submit themselves to the religious establishment and had abandoned any pretense of universal societal salvation. The difference between the Roman Catholic and Protestant models was not their mode or median, that is, as a whole Protestantism was not more or less predisposed to disestablishmentarianism than Roman Catholicism, but there was far greater variation because of the nature of Protestantism. It could be argued that in many parts of the Roman Catholic world the church was more separate from the state than in parts of the Protestant world (ie; Scandinavia), but for every Denmark you had a Holland.

2 - Many Hindus take pride in the fact that religious minorities like Jews and Parsis came to India to escape persecution, and rightfully so.

British Army Music Video   posted by TangoMan @ 7/25/2005 11:01:00 PM

It seems that the lads in Iraq can find some free time to make an absolutely hilarious music video entitled "Is this the way to Armadillo?"

Click here to watch "Is this the way to Armadillo"

UPDATE: Here is the version done by Dutch troops stationed in Afghanistan. Here is the original version that the soldiers are spoofing. Here is the BBC story on how the demand for this video crashed military servers.

Across the gap   posted by Razib @ 7/25/2005 02:32:00 PM


Fitness interactions between loci in the genome, or epistasis, can result in mutations that are individually deleterious but jointly beneficial. Such epistasis gives rise to multiple peaks on the genotypic fitness landscape...Here we develop an analytic expression for Ncrit, the critical population size that defines the boundary between these regimes, which shows that both are likely to operate in nature. Frequent recombination may disrupt high-fitness escape genotypes produced in populations larger than Ncrit before they reach fixation, defining a third regime whose rate again slows with increasing population size. We develop a novel expression for this critical recombination rate, which shows that in large populations the simultaneous fixation of mutations that are beneficial only jointly is unlikely to be disrupted by genetic recombination if their map distance is on the order of the size of single genes. Thus, counterintuitively, mass selection alone offers a biologically realistic resolution to the problem of evolutionary escape from local fitness peaks in natural populations.

Please note I'm not making assertions about the ubiquity of these novel processes. I suspect they play a role in speciation, but I won't wager any guesses beyond that.

The "concept" of a "religion"   posted by Razib @ 7/25/2005 12:51:00 AM

Over at Randy's place a heated discussion about Islam & homosexuality has broken out (via Abiola). One of the issues that (as always) crops up is the "true" Islam vs. Islamism dispute. To which I ask, what is the more birdy bird, a robin or an ostrich? Both are birds by a checklist definition, or a phylogenetic definition, but when posed this question by cognitive scientists, most people assert that the robin is the more exemplar or prototypical "bird." Concepts derive from a host of inputs (induction via examples), a few axioms, a general theory of the concept (ie; often a level of telos, which shouldn't surprise those familiar with evolutionary biology) and the context that the concept is framed within. In other words, most concepts are not derived from a few axioms like the mathematical definition of a triangle. Attempting to use logical methods to falsify someone as a "Muslim" or infer the "natural" implications of being a Muslim are fraught with difficulty because the assumption is that there is a prototypical or ideal Islam that naturally follows from agreed upon axioms. Unfortunately many concepts (most) don't work this way, they are characterized by a continuous distribution about central tendency (or central tendencies if there are multiple exemplars) with variation and outliers. Additionally, context matters, grey hair is generally clustered with white hair, with black hair being the outgroup, but grey clouds and black clouds are clustered together with white clouds being the outgroup.

Of course, aside from ornithologists and hard-core cladists (yes, you GFA) the question of what is a bird is not ontologically significant. But as I noted yesterday, arcane circumlocutions around the unknowable in the garb of logic is a common tendency when you are talking about heartfelt beliefs that are difficult to approach using rationality or empiricism (politics?), but from the attempt at such a feat comes the impression that there is a truist Islam, closer to the ideal as inferred from the axioms of the faith (by learned scholars in the faith). The problem is that language is not expressed through formal logical notation, and squishiness is a feature not a bug. Consider the idea that "there is no compulsion in religion" in Islam. Sayyid Qutb, the evil genius who was the Marx to bin Laden's Lenin agreed with this, for you see, his idea was simply that under and Islamic government everyone could choose to be a Muslim or a dhimmi,1 there was no compulsion, and everyone then had the "freedom" to choose Islam as they should. As Bill O'Reilly would say, "Show me where I'm wrong?"

Recommended: A far more adroit explication of concepts can be found at Chris' blog (I left a lot of stuff implicit obviously, in part because I'm not familiar with this area, it just "makes sense" to me in terms of the religion debates that go on on weblogs), Concepts I: The Classical View, ConceptsII: The Prototypes, Concepts III: The Exemplars, Concepts IV: A Second Revolution and The Importance of Names. If paper is your thang, check out Mind Readings: Introductory Selections on Cognitive Science or Mind: Introduction to Cognitive Science, both have chapters on concepts.

Addendum: Obviously some of the ideas that I hint at about concepts (and categories) have relevance to many socially constructed demarcations with fuzzy boundaries. Longtime readers of this blog might find this from page 102 of Mind Readings amusing: "...sensitivity to correlations of properties with a category enables finger predictions...." Yes Virginia, there is one true reality, and intellectual disciplines are its many faces.

1 - Apostasy is of course not permissible, but one Muslim apologist (see Leaving Islam: Apostates Speak Out) for this position simply said this did not contradict the "no compulsion in religon" edict because apostasy (from Islam) was an act against nature itself, so it really didn't fit the bill. Of course, it all makes rational sense.

Sunday, July 24, 2005

PLOS Genetics is open for business!   posted by Razib @ 7/24/2005 11:38:00 PM

PLOS Genetics is online today! The full interview with Neil Risch is up. Snip that might interest readers:

Clinton, for example, when the first draft of the human genome sequence came out, made a statement about how all people in the world, in terms of their genetic makeup, are 99.9% the same. His intent—to reduce conflict among peoples—is noble. People on the left, anthropologists and sociologists, do the same thing. They use the 99.9% figure as an argument for social equality. But the truth is that people do differ by that remaining 0.1% and that people do cluster according to their ancestry. The problem is that others could use that information to create division.

Expertise, knowledge....   posted by Razib @ 7/24/2005 10:27:00 PM

One of my favorite biblical scholars, Richard Elliott Friedman, is out with a new book, The Bible with Sources Revealed.1 In the introduction he notes:
...Both traditional and radical scholars...have claimed that the hypothesis [the Documentary Hypothesis] has been overthrown, that "hardly anybody believes that anymore,"...The hypothesis that, supposedly, no one believes anymore continues to be the model in which most scholars work. It continues to be taught in courses in major universities and seminaries. And it continues to be outlined in introductory textbooks on biblical studies. The primary arguments for it continue to go undebated-and frequently unmentioned.

Sound familiar? No doubt many of you who see it written somewhere that people should "teach the controversy" about evolution wonder, "what controversy?" Some of the readers of this weblog make arguments that teaching Intelligent Design makes political or intellectual sense in some fashion, but few would credit the idea that descent with modification and/or methodological naturalism is under some "debate" in the academy. Nevertheless, I have met many evangelical Christians who want to "argue" the "controversy" with me.

Human beings today are specialists. No one can know everything, and so we appeal to authorities. When someone who is a scientist speaks before your church and tells you that there is a controversy as to the validity of the theory of evolution, who are you to disagree? As I've noted, many of the people who are movers and shakers in the Young Earth Creationist movement are scientists, of a sort. The problem of course is that science is an enormous field of study, and though over time there are many cross-linkages between the disciplines very few people keep up on the literature even within sister fields. In other words, if you a biochemist, you might not know that much about molecular genetics beyond what you learned as an undergraduate (and conversely). If you are an organic chemist you might not know much about biochemisty. A friend of mine who is in graduate school in chemical physics was telling me about how he regularly observes his Ph.D. advisor bullshit about material he has no clue about because it is embarrassing for him to acknowledge that he hasn't kept up on the literature in the subfield of his subfield (that is, the corners of the field that his graduate students are focusing on).

I recall a conversation with a friend of mine who was discussing with me the plausibility of quick response to selection in microevolutionary processes. He hadn't known that I had done a lot of reading in this area of late and so I was up on the literature and the analytic models in circulation, and so when I disagreed with his characterization of plausibilities his comeback was "well, my wife is a veterinarian and she said...." Simply replace "veterinarian" with "doctor" and you have, in my experience, the most common appeal-to-authority I have observed. Since when it relates to specific evolutionary or genetic questions I often do know more about the topic at hand than my M.D. friends I have no problem in brushing aside that appeal to authority, a pro forma deluge of impressive sounding vocabularly usually mollifies the target and we can get back to the normal business of actually exchanging information and progressing in extracting insight via communication. But this sort of interjection is ubiquitous in some fashion. Consider a thread over at the anthropology weblog Savage Minds where a reader noted that she worked in a neurochemistry lab, and while she was there she had no idea who E.O. Wilson was, ergo, the implication was that he can't be very prominent in biology. Of course, Wilson is an entomologist, and one of the world's experts on ants.2 As an organismic biologist it wouldn't surprise me that people in neurochemistry wouldn't talk about him. I also wouldn't expect that R.A. Fisher, Sewall Wright or J.M. Smith would be figures that she was acquainted with, that doesn't mean that they weren't prominent (she later notes that Wilson was someone she heard about in graduate school in anthropology, which makes sense if you think about, that is, someone with a training in ethology and ecology might seem more relevant to people who are working in a higher order complexity field. Ontologically anthropology is reducible to physics on some level, but no one is going to chatter much about Edward Witten). The insight here is that biology is a big field with diverse methodologies and literature ghettos.3

This is a serious problem in many contexts. For example, I have heard from people that a "linguist friend" has assured them that the "Chomskyian model" has been overthrown. I don't have the expertise to judge this assertion. Or, consider our friend Bora Zivkovic who regularly goes around commenting on blogs that "genocentrism" is an old paradigm and that the hot field of inquiry is multi-level selectionism. I happen to think that is a load of crap. But Bora has a lot of cred with many liberal webloggers because he's a liberal, and well, I'm not. Or consider the appeal to the 1982 Lewontin and Sober paper Artifact, Cause and Genic Selection over at Crooked Timber thread on Evolutionary Psychology.

How to resolve this problem? If I was God I would have the NSF fund regular surveys on "Big Questions" within various subfields among NAS scientists, and whatever equivalents exist in other fields. This would be a good pulse check for those of us who aren't in field X and so can't make a gestalt evaluation based on personal review of the literature and knowledge of others who work within that field. Unfortunately, this probably isn't going to happen anytime soon, so what to do? I think there are two short term strategies: 1) try and find a survey within that field to establish the bounds of orthodoxy and heterodoxy, 2) remember that the fine distinctions of knowledge and expertise that you are familiar within your areas of fluency apply elsewhere. There is a reason there is biochemistry, and organic chemistry and cognitive psychology. These modifiers are essential markers which suggest tightly bound disciplines, and even within them there are narrow specialities, so don't expect more than undergraduate level of fluency when they venture outside their ghetto.

Addendum: Of course, you could immerse yourself in the literature of a particular field if you wanted to get firsthand knowledge and sample the zeitgeist, but this isn't a general strategy you can follow because of the finite nature of disposable time for most people.

1 - Not the "whole Bible" as understood in the Christian tradition, but the Pentateuch.

2 - He was also given a professorship at Harvard before James Watson.

3 - I happen to think there is a lot of convergence going on though. A lot of evolutionary biology today uses molecular method.

Wonder....   posted by Razib @ 7/24/2005 01:40:00 PM

Back when I was a kid I used to really enjoy reading books about Voyager, in large part because they were jam-packed with color pictures of the planets. Today you can get a lot of data and images just online...and I don't check it out enough. We take so much for granted, in the 1930s artists sketched out their imaginings of planetary surfaces in pulp science fiction magazines...but today we can look at photos of the surface of Titan! Anyway, here are the Cassini-Huygens Top 10 Science Highlights.

Chasing your own axioms....   posted by Razib @ 7/24/2005 12:43:00 AM

Readers who are somewhat familiar with Islam should check out this comment over at Jason Soon's blog by a Muslim named Amir Butler. It is, in essence, a long apologia for "Salafism." After reading Western Muslims and the Future of Islam much of what he is saying is intelligible to me (and I know a little bit about Islam aside from that too!). Amir Butler is not a dissembler in the most direct fashion, but, he fails to remember that his audience does not share his axioms of belief. This makes a lot of what he says totally irrelevant and incomprehensible. For instance, the Muslim fixation with tawhid, is not something that can really be understandable outside of the religion. It is as interesting to non-Muslims as the details of the Monophysite controversies are to non-Christians (or more realistically, non-Eastern Orthodox and Eastern Christians). After reading Ramadan elucidate tawhid page after page, I felt like I was trying to read Heidegger ramble about Being or Wittgenstein whistle at elementary propositions (round and round we go, but the essence of God we never know!). Since the book was aimed at Muslims it made sense that he went on about tawhid, if Muslims can see that tawhid and Western democracy are compatible, all for the good. But many times when interviewed by non-Muslims the more pious of the believers tend to ramble on about Islamic concepts as if the interviewer really cares beyond trying to figure out a) why some Muslims blow themselves up around non-Muslims b) how non-Muslims can convince them not to do this anymore. As far as Amir Butler goes, I think his typological dodges simply seem like bizarre obfuscations, sociologically it is a plain fact that the most prominent Islamic nutsos have been self-proclaimed Salafis.1 This is the point that one needs to start from, the relationship of "Salafism" to the rest of Sunnism, or its difference from Shiism is really irrelevant, no one would care about Salafism if self-proclaimed Salafis hadn't rammed jets into skyscrapers, most non-Muslims aren't interested in what Islam is, they are interested in what Islam does.

Note: Also, let me add that I'm not one to consider pedantry a sin. But it seems to me that the response by Mr. Butler was totally off-base in the context of the question Jason was posing, how did the Salafi-Sufi split play out in Australia's Muslim community. Instead of a sincere, prosaic and plain response Jason was on the receiving end of theo-babble.

1 - Butler either mistakes, or shades, the details a bit as well. He attempts for example to assert that the Muslim Brotherhood is non-Salafi, after dodging back and forth with quotes to obscure the term Salafi in such a fashion as to make it hard to know if he thinks it's valid. The Brotherhood's ideology is hard to characterize because it is an enormous group (Banna and Qutb were certainly influenced by Salafi thinkers if you don't define them as Salafi), and the two primary groups which carried out the most radical Muslim terrorist acts in Egypt were breakaway factions of the Brotherhood which did explicitly espouse Salafi principles (Egyptian Islamic Jihad and The Islamic Group, Ayman Al-Zawahri is the leader of the first group).

502 errors   posted by Razib @ 7/24/2005 12:33:00 AM

Do many of you get 502 errors for this website?

Saturday, July 23, 2005

Inducing disgust   posted by Razib @ 7/23/2005 09:54:00 PM

In Descarte's Baby the psychologist Paul Bloom puts a mild evolutionary psychological spin on child development and ties it in thematically with the concept of Cartesian dualism as an innate trait of human cognition (I agree with him there, I have to remind myself that my body isn't just a flesh puppet, it is me). There wasn't much new in here, though it was a breezy read, except for the chapter which dealt with digust, and how people use the term. The definition from is:

1. To excite nausea or loathing in; sicken.
2. To offend the taste or moral sense of; repel.

Bloom makes a simple argument that the atomic core of disgust is the aversion to spoilage of meats, and fear of contagion. Rotten meat smells, it is often slimy and has a sickly pallor. Though we are primed to this aversion, it takes time to kick in. Feces fall under one of the main items that are universal objects of disgust, but infants are not repulsed by their own shit. Freud of course made this data point a central aspect of his pseudoscience, but Bloom offers that infants who are relatively immobile when they soil themselves and become exhausted by crying because of their innate revulsion at their state might not be at an advantage. Far better to allow digust to work its magic on someone who can affect change, the parent.

The literature seems to suggest that attitudes toward disgust are time released and tend to crystalize by 5-6 and initiate around 3, the age at which many children start to be averse to their own feces. Bloom hypothesizes that disgust is a default feature that inculcates in us an early aversion to most foods, in particular, meats, because though we are ominivores our digestive tracts are not totally promiscuous. Though we are primed toward pickiness, the particular range of meats we consume is culturally conditioned. Research indicates that the later you transition a child toward "adult" solid foods, the smaller their range of acceptable foods are. In other words, bombarding children with a wide range of foods tends to acculturate them to the items and blocks the disgust response. While a Muslim is disgusted by pork, an East Asian might relish it. The extrapolation of meat disgust toward feces or other biological products is easy, like spoiled meat they smell, are often slimy and are soft to the touch. A disgust response toward someone with low standards of hygiene is likely an extension of the smell factor.

But all the circumstances I am pointing to are more applicable to definition 1. What about 2? A term like disgust is malleable. Something is not just either disgusting or not, and context matters (sex with a fat man is disgusting, sex with a rich fat man is not so disgusting, at least on the check account balance). Disgust is more often used as a metaphor when verbalized, and the metaphor often carries with it an implication of inevitable instinctiveness, like the response toward a pile of feces. But Bloom makes the point that the use of disgust as a metaphor is usually never so clear cut, but rather part of a rhetorical campaign. From page 174: is just not true that we react to cloning in the same way that we do to incest, corpse mutilation, and bestiality. Many people think that human cloning is a bad idea, even a terrible idea, but this is not the same as feeling revulsion. Perhaps you tok the kids to see Arnold Schwarzenegger in the popular movie The Sixty Day? (Arnold goes to clone the family pet, and then, through sinister machinations, he gets cloned!) I would be surprised if Columbia Pictures were to release a popular actions film around the them of bestiality....

Bloom's point is there is a wisdom to repugnance, but outside of the most abstract and detached discussions acts and objects that elicit genuine innate revulsion are not those that you have to make a case for. At this point standard phenomena in the past that would have elicited revulsion are trotted out and shown to now be considered rather banal. Consider black males having sexual intercourse with white females. The standard past denigration of this involved the depicition of black males as beasts, ergo, this was tatamount to bestiality, an act which in the literal sense humans do seem to find offensive (there are the rather numerous legal codes which punish the animal as well as the human, I don't know what that says). Yet today there is a flourishing sub-genre of pornography that deals in black-white sex (often with black males and white females). A portion of the population no doubt still considers this disgusting (that is, if they do not consider pornography as a whole disgusting), but certain social norms have changed. In contrast, the market for bestiality and feces related porn seems rather limited, but the fact that there is a market for such products does clue us in to two important facts: 1) human variation in disgust might still exist, or, 2) disgust can be deadened over time, and coupled with the tendency toward seeking novelty, this can result in very bizarre predilections (I put pregnancy porn and lactation porn into the same bizarro category).

Psychological traits, tendencies and paradigms are part and parcel of many "high brow" discussions because they are part of the intellectual zeitgeist, whether the ideas were transmitted via developmental psychology popularizations picked up in one's feminist book club, or Pinker's latest bestsellar peddled by Barnes & Noble. Something like disgust illustrates that even simple tightly defined traits can't be easily sliced, diced and dichotomized, the way we use language tends to result in our deployment of the ideas as if they were hammers when what is really needed in any dialogue is a knife.

Raw material matters....   posted by Razib @ 7/23/2005 11:45:00 AM

From Sons of the Conquerors: The Rise of the Turkic World:

...The German Turks in my queue for a 1998 workers' charter flight to Berlin seemed a tribe apart from other queues filled with more sophisticated-looking Istanbul businessmen and holiday-makers. They were indeed of different origin, since Turkey had sent village folk to work in Germany, wanting to give industrial training to is rural underclass...The men were short, stock Anatolian types, wearing baggy trousers, clipped beards and gruff expressions, a pre-1980 rural style....

Archeology blog of note....   posted by Razib @ 7/23/2005 01:50:00 AM

Just so you know, I think The Life of Meaning has potential to be the archeological version of what John Hawks is to paleoanthropology or Chris to cognitive psychology. Mark's latest post is titled The War on Trees, which caught my eye in light of this story in The Times that chronicles the expansion of wilderness in much of Europe due to the graying of the populace and the depopulation of the countryside. This waxing of the wild isn't just limited to Europe, here in the United States wolves are on the march again, reflecting both the change in general public attitudes and the diminishing of the rural populace which held the animals at bay with surreptitious hunting. And if you've ever driven through Vermont, you might be shocked to know that one century ago most of the state was farmland, and the rich foliage that characterizes the state today is due to secondary growth as farmlands that were abandoned by Yankees because of competition from fertile large scale operations out in the middle of the country.

Endless forms truncated   posted by Razib @ 7/23/2005 12:04:00 AM

Evolution at Two Levels: Gene and Form, is an article (based on a lecture) given by Sean Carroll, author of Endless Forms Most Beautiful. Evolgen has more. If you haven't read the book, but read this article, save your money (I don't think the first half of the book is worth it for the savvy reader, he spends way too much time on operons)....

Friday, July 22, 2005

The Telegraph poll of British Muslims   posted by Razib @ 7/22/2005 11:40:00 PM

I figured I'd just reformat the poll results from The Telegraph that are making the rounds.

Q: Do you think the bombing attacks in London on July 7 were justified or not?

6% - On the balance justified
11%- On the balance not justified
77%- Not njustified at all
6% - Don't know

Q: Whether or not you think the attacks were justified, do you personally have any sympathy with the feelings and motives of those who carried out the attacks?

13%- Yes, a lot
11%- Yes, a little
16%- No, not much
55%- No, none at all
6% - Don't know

Q: Whether or not you have any sympath with the feelings of those who carreid out the attacks, do you think you understand why some behave in that way?

56%- Yes, I think I can understand
39%- No, I don't understand how anyone could behave like that
4% - Don't know

Q: The Prime Minister has described as 'perverted and poisonous' the ideas that led the London suicide bombers to carry out their attacks. Do you agree or disagree with him that their ideas must have been perverted and poisonous?

58%- Yes, I agree
26%- No, disagree
16%- Don't know

Q: How loyal would you say you personally feel towards Britain?

48%- Very loyal
33%- Fairly loyal
6% - Not very loyal
10%- Not at all loyal
4% - Don't know

Q: Which of these views comes closest to your own?

1% - Western society is decadent and immoral, and Muslims should seek to bring it to an end, if necessary by violence
31%- Western society is decadent and immoral, and Muslims should seek to bring it to an end, but only by non-violent means
56%- Western society may not be perfect, but Muslims should live with and not seek to bring it to an end
11%- Don't know

Q: Do you agree or disagree with this statement? 'British political leaders don't mean it when they talk about equality. They regard the lives of white British people as more valuable than the lives of British Muslims.'

52%- Agree
29%- Disagree
18%- Don't know

Q: If anyone is charged and put on trial in Britain in connection with the bombings on July 7, do you think they will or will not receive a fair trial?

37%- They will
44%- They will not
19%- Don't know

Q: The leaders of Britain's main political parties have said that they respect Islam and want to co-operate with Britain's Muslim communities. In general, do you think Britain's political leaders are sincere or not sincere when they say these things?

33%- Sincere
50%- Not sincere
16%- Don't know

Q: How much responsibility do you think Muslims show now take on for peventing such crimes and bringing to justice those who commit them?

32%- A great deal of responsibility
34%- Some responsibility
10%- Not much
14%- None at all
1% - Don't know

I left the last three poll questions off because I don't think they were that interesting and this post is a bit long. You can find them at the link above. My only comment is that many of these people expressing sympathetic opinions about the terrorists must be grotesquely stupid, since they surely knew that the results would be made public and perhaps generate further animus toward their community as a whole.

Still not afraid...   posted by DavidB @ 7/22/2005 04:35:00 AM

...but getting bloody irritated. I was going to go into London yesterday around midday, switched on the TV to check travel details, and thought it was Groundhog Day.

As I couldn't go yesterday, I was planning to go today (right now!), switched on the TV again, and find a suspected bomber has been shot dead at Stockwell (where coincidentally I used to live). Inevitably, several Tube lines are shut down.

Well, sod it, I'm going anyway. Must return some library books.

I was already vaguely thinking about posting something on the London bombings, but my thoughts at the moment are unprintable.

Meanwhile, there was an interesting report in today's London Times about the discovery of a caterpillar species in Hawaii that eats snails. Evidently a gourmet! I won't provide a link - if you're interested, search Google News for 'caterpillar', 'snails' and 'Hawaii' and you'll find several reports.

More on the landscape....   posted by Razib @ 7/22/2005 12:23:00 AM


...We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.

So the deviation is flipping between positive and negative and deep fitness valleys separate peaks, impeding the exploration of the adaptive landscape. At least that's how I read it....

Related: Through the rugged roads of gene land.

Thursday, July 21, 2005

Brown...or...not   posted by Razib @ 7/21/2005 09:56:00 PM

From The Economist:

...For a new generation of British Muslims, such behaviour represents the stirrings of a new identity whose common denominator is not ethnic origin, but religion....

...Soon after America's invasion of Afghanistan, a poll of British Muslims found that among those over 35, some 30% saw religion as their main source of identity. For those under 35, the figure was 41%.

This is apropos of a thread at the brown-American weblog Sepia Mutiny which sparked a lot of debate over the term "South Asian." "Asian American" was a catchall term formulated by activists in the 1960s to bring together groups who were tied together by common bonds in the United States (though not in Asia). Eventually South Asians (as well as Southeast Asians) were included under the umbrella of that identity. Asian-American activists have used the fact that Buddhism is derived from India, and has a clear relationship to Hinduism, to make a cultural argument for the coherency of the term, though the rise of desi or South Asian speaks to the reality that brown people are a people apart under the umbrella.1 The term "South Asian" seems to be analogous to Asian American in that it takes a real geographic and cultural relation and attempts to crystalize it into something with more concreteness. Obviously, removing brown people from the Indian subcontinent results in a shift in cultural context.2 For individuals of Hindu identity there seems to be a diminution of the importance of caste and ethnic barriers that were salient in the old country, so pan-Indian (brown, South Asian, desi) identitification becomes more relevant.3 But for Muslims, the relaxation of the peculiar constraints of the Indian subcontinent has resulted in the rise of religious identity because of the simultaneous emergence of non-brown ties of affinities (multi-ethnic mosques) and the loosening of a common sense of brownness (for example, dietary acculturation) among the parental generation who were strangers in a strange land. So, for South Asians of Muslim origin, I would argue that pan-brown identification becomes less relevant.4

1 - Brown and yellow don't socialize to a great extent from what I can see, at least to a greater extent than other variables (working in the same lab for example) would make you expect.

2 - Also note that like a bottleneck, the Diaspora is usually characterized by skewed sampling toward particular regions, castes and ethnic groups, so there isn't anything like a recapitulation of the diversity that is found in the motherlands. One reason there aren't tensions between high castes and Dalits in the UK or the USA is that there aren't that many Dalits who emigrate.

3 - I am speaking mostly to the modern West, but Mauritius and Trinidad and Tobogo have had 3-4 generations of people of Indian origin residing in a non-South Asian environment, and the extreme simplification of South Asian caste and ethnic markers is notable. Additionally, geographic distance has a large effect even in these two cases, Mauritius is far more "Indian" than Trinidad because it is still connected was still connected with the Indian ocean trade throughout the 20th century, and some groups, like Ismaili Gujarati Muslim merchants, have still retained a strong connection with South Asia through marriage.

4 - Among South Asian Muslim intellectuals there were always many camps. Some favored a transnational Islamic vision, which denied the importance of their Indianness. Some argued for a Muslim Indian nationalism (this was the original idea behind Pakistan, and to some extent became the grounding for the birth of Bangladesh with the "Indian" being replaced by Bengali). And then there Muslims who were more sensitive about the reconciliation of their Indian and Muslim identities. I would argue that in the West the balance of power between these tendencies has shifted toward the first because for believing Muslims the "push" of society that identifies them physically as Hindu (Indian) is not as strong as the "pull" of common religious feeling. Additionally, with the removal of South Asian environmental context many of the sentimental roots of an Indian Muslim identity, as opposed to just an unmodified Muslim one, disappeared.

Young American   posted by Razib @ 7/21/2005 12:40:00 AM

This post on the demographics of young Americans over at Pearsall's deserves some comments.

Second front - Rise of the GONGO   posted by dobeln @ 7/21/2005 12:06:00 AM

I have previously covered the main front in the struggle against freedom of speech in Europe – hate speech laws. Now it’s time to move on to another, more low-profile phenomenon: The Government Oriented (or "Organized") Non-Governmental Organization, or GONGO for short.

The GONGO is a tax-payer-funded organization, set up by the government to promote a specific policy, or point of view.

Sweden has naturally been at the forefront of this effort to snuff out incorrect thinking. Using organizations such as “Flicka”, “Centrum mot Rasism”, and “Forum Syd”, the government has been able to:

- Criticize magazine publishers who publish incorrect, sexist material. (On huge subway billboards, no less...)

- Fight the menace of racist ice cream.

- Promote Global Jihad, as well as a deeper understanding of (often misunderstood) North Korea and Cuba.

Now however, it appears that the GONGO:s have hit a spot of trouble. It has been revealed that the aforementioned “Centrum mot Rasism”:

- Has done preciously little, except for running up large hotel and restaurant bills.

- Has been taken over by representatives of the ruling Social Democrats and the Greens.

- ...carried out the aforementioned attack on racist ice cream mostly as a ploy to cover up their own inaction.

Only time will tell if this will stem the tide of governmental non-governmental organizations attempting to snuff out incorrect thinking. I sort of doubt it.

Update: Replaced the clunky GNGO with GONGO

The BTNL2 Gene and Sarcoidosis Susceptibility in African Americans and Whites   posted by Razib @ 7/21/2005 12:04:00 AM


...Although rs2076530 was not associated with sarcoidosis in either African American sample, a three-locus haplotype that included rs2076530 was associated with sarcoidosis across all three study samples. Multivariable logistic regression analyses showed that BTNL2 effects are independent of human leukocyte antigen class II genes in whites but may interact antagonistically in African Americans. Our results underscore the complexity of genetic risk for sarcoidosis emanating from the MHC region.

Wednesday, July 20, 2005

On French "Muslims" and apostates....   posted by Razib @ 7/20/2005 08:12:00 PM

A few years ago I told Randall Parker that I was reluctant to really tackle "Islam" because I didn't know enough. I know I post here and there (a lot) on the topic, but mostly they are not thematic or interconnected, just random drive-by jottings strewn across the public-web-space. Of late I've realized I will never know enough (that is, to my satisfaction), certainly I know very little Islamic history, theology and overall thought compared to someone like Thebit, but I know a lot of non-Islamic history that I find Muslims who are fluent in their own traditions tend to be blind to (you can generalize this about most people steeped in their own culture). So in the near future I'll write in a more precise and unequivocal fashion and present a series of posts that have a sequential form (last minute spare-time binge of reading though!). Since I've already admitted that I'm not particularly educated on the topic (I am compared to the median...but that's saying very little)1 I invite informed criticisms of the details of my posts. I say informed because superficial reflections are going to just muddy the waters instead of sharpening the progression of thought.

In any case, I will leave you with a little data from Leaving Islam: Apostates Speak Out

...In 1995 the French daily Liberation conducted a thorough survey. Here are some of its findings:

Thirty percent of those men born in France and both of whose parents were born in Algeria declared themselves to be without any religion. This percentage is higher than the national average: 27 percent of all Frenchmen describes as without any religion. Sixty percent of those men born in France with only one parent born in Algeria declared themselves to be without religion, more than double the national average! The figures for women remain almost unchanged: 30 percent born in France and both of whose parents were born in Algeria said they were without religion. This precentage is even higher than the national average: 20 percent of all Frenchwomen say they are without religion. Fifty-eight percent of women with one parent born in Algeria said they were without any religion, almost three times the national average.6

The notation is: Immigration Supplement, La Libération, Paris, March 22, 1995, p. 5. For context you can check out the France entry over at, but this is a good gauge of French religious attitudes:

In contrast, 85 percent of French object to clergy activism - the strongest opposition of any nation surveyed. France has strict curbs on public religious expression and, according to the poll, 19 percent are atheists. South Korea is the only other nation [surveyed] with that high a percentage of nonbelievers....

Please note that in France there has been a strong association between anti-clericalism, the proletariat and underclass for over a century, with religion (that is, Roman Catholicism) to some extent being a practice of the middle class. The relative secularism of French of North African ancestry and their simultaenous economic deprivation need not be surprising. I would also not put too much stock in the figures for those with one Algerian parent, as one who would outmarry (both Root French and Algerian) is less likely to have traditionalist religious sensibilities. On the number converting to Catholicism:

...In the year 2000, 2,503 adults were baptized, of which 9 percent were of Muslim origin; thus, 225 Muslims apostasized in France alone in 2000.19

The notation is "Les Pentes Croisees du bapteme," Le Figaro, Paris, APril 12, 2000, p. 9. There are various estimates for the number of conversions to Islam, but I saw a quote from a French government official (a minister of some type) last year of "4,000 native French per year" converting to Islam (there are reports that there are 30,000-50,000 converts in all of France, so 4,000 seems like a highbound estimate). Since only ~10% of France's population is Muslim origin (I'm using an estimate at the high end), the rescaled ratio of Muslim → Christian : Christian → Muslim (the religious identities seen in cultural, not confessional terms, in terms of origin) is about 1:2. Of course, since there are many more Christians in absolute terms, the Muslim conversions to Roman Catholicism can almost be ignored. But I highlight Roman Catholicism for a reason: it is possible that there are many more conversions to evangelical Protestant sects among non-religious Muslims than to Roman Catholicism. And unfortunately as my post Profile of Salafi jihadists highlights, North African Islamist radicals are often drawn from the non-religious youth of the Diaspora.

Finally, I want to end with an observation. In the section of the book titled "Testimonies of born Muslims: Murtadd Fitri," here are the countries of origin (or in one case, parental origin) of the apostates:

Iran, Pakistan, Bangladesh, Iran, Iran, Pakistan, Bangladesh, Pakistan, Far East (the author says he was born in a "Buddhist nation," likely Thailand I think), Turkey, Pakistan, Pakistan, Bangladesh, Morocco, Pakistan, Malaysia, Tunisia and India. 6 from Pakistan, 3 from Iran and 3 from Bangladesh. Since the editor is of Pakistani origin the slant is probably a partial reflection of his own social networks, nevertheless, it is sad to see that only two Arabs are on the list since Arabs are, no matter what non-Arabs protest (ie; Mahathir Mohammed's boast a few years back that Southeast Asia was going to move forward and be the face of 21st century Islam), the preeminent nation of the Muslim religion.2

Update: Muslims or people of Muslim origin might be 70% of the prisoners in France.

1 - There are some technical scientific-genetical questions I'm pursuing and exploring that will prevent me, due to time constraints, from ever being fluent enough in Islamic thought to really be totally unself-conscious about commenting.

2 - Certainly Islam is a universalist faith, but my personal experience at mosques was that Arabs always had a certain confident self-assurance that went with knowing they had nothing to prove, they were all The Natural when it came to the worship of Allah, the very language they spoke was the language of heaven (Punjabis would joke that Pashtun was the language of hell).

Metaphors (analogies) we don't live by....   posted by Razib @ 7/20/2005 04:11:00 PM

In many discussions where genes and sociology intersect there is often a group of individuals who will deny that one can truly make non-trivial assertions about genetic effects over the generations, that interactional influences, whether they be gene-to-gene, gene-to-environment, or even more complex feedback loops, make talk of "heritability" null and void. I've talked about epistasis, how R.A. Fisher rejected its relevance as an evolutionary force and its role in his dispute with Sewall Right over the character of the adaptive landscape. By the mid-20th century the orthinologist and systematist Ernst Mayr expressed skepticism toward "Bean Bag Genetics," a paradigm which held that it was acceptable to treat loci as independent agents which each injected their own quanta or fraction to the variance of a particular phenotype (an additive approach). J.B.S. Haldane, an avowed Marxist, came to the defense of the English tradition of mathematical genetics that he and Fisher pioneered in a famous essay where he rebutted Mayr. My point though is not to recap the history of genetics in the 20th century, but to note that a certain stream of thinkers have a habitual tendency when engaging in public policy debates where the issue of heredity comes up to reflexively appeal to interaction and other non-additive factors to subborn the arguments of their opponents in the genetical-social realm, drawing on the same talking points made prominent by Mayr. By emphasizing the non-linear and contextual/contingent factors in the equation they attack the utility of provisional models as a guide toward making decisions. A genetic-environmental produced phenotype is a complex, almost mysterious system, which simply does not brook analysis and decomposition.

Now, let us move to the broader canvas of society as a whole. The law of unintended consequences suggests to us that social systems are filled with unknown contingencies and variables which are simply not transparent to us on first, or second, or third analysis. Some people would argue that social systems are simply irreducible, that model building and attempting to "rationalize" society is a futile endeavour, that actions have wildly unpredictable consequences. On the other hand, there are those who seem to posit a "Bean Bag Sociology," where social good A has implication B, rather than being enmeshed in a nest of interlocking relations which might be disrupted if social good A's state is changed. Let us move this to the realm of specifics. Women were given the right to vote, the South was desegregated and abortion was legalized. I point out policies which progressives tended to favor and conservatives tended to reject to illustrate that in this case the social Left is engaged in a kind of sociological Bean Baggery. In contrast, the more traditional conservatives appeal to custom and tradition because they believe that the organically developed social systems of the past are not simply the reducible sum of their parts (additive), and that "progress" on one issue may have a drastic, non-linear, effect on the society as a whole.

So you have a situation where in two domains of knowledge the parties who demand absolute certainty switch polemics. Of course, I would admit that the analogy is imperfect, genes are a rock-hard theoretical basis for evolutionary biology and the disciplines which draw from it (though I am not offering that the theories themelves are rock-hard, simply asserting that the accused jelly sits upon bedrock), while memes have yet to be properly characterized as anything beyond a metaphor. I will lay my cards on the table and say that I am cautiously optimistic about model building in both situations, though I am not a strict Fisherian in that I think there may be multiple equilibria or peaks on the landscape of genes and society, but even if I was a Fisherian, recall that his theory of evolutionary change via microevolution posited sequential fixations of loci over time, one at a time. Change occurs, simply not through dynamic gene-to-gene interactions, let alone anything like a "genome reorganization." Make of that what you will in the domain of sociology.

QIMR Identifies Genetic Links to IQ   posted by Jemima @ 7/20/2005 01:28:00 PM

QIMR Scientists Identify Genetic Links to Human Intelligence:

The QIMR group, led by Professor Nick Martin, has identified specific locations on Chromosomes 2 and 6 as being highly influential in determining IQ. To do this, they applied multipoint linkage analysis to data from 634 sibling pairs (including non-identical twins) from Australia and the Netherlands who were genetically scanned for the study.

Although earlier twin studies had revealed the existence of genes that dictated human intelligence, usual genetic association methods had not been effective in identifying them. Where association analysis may overlook closely spaced genes that act together to affect a trait, linkage analysis is more sensitive to such combined effects.

Traditional IQ tests are designed to assess abilities across different areas - memory, vocabulary, semantics, symbolic reasoning - collectively grouped into higher orders such as verbal and performance intelligence. The region on Chromosome 2 shows significant links to performance IQ, also overlapping a region associated with autism. The region on Chromosome 6 showed strong links with both full-scale and verbal IQ with a marginal overlap to an area implicated in reading disability and dyslexia.

During the study, where the non-identical twins and other sibling pairs had significant differences in IQ, they also had significant variation in these regions on Chromosomes 2 and 6.

Tuesday, July 19, 2005

Ebonics as a means to increase scholastic achievement for Black students   posted by Alex B. @ 7/19/2005 08:36:00 PM

Article in the San Bernardino News suggesting Ebonics as a way to raise academic achievement for Black students.

There are so many things wrong in that article, I'll stick the two most basic that it is hard to believe I have to state them:

1) I would like to see one, data-backed and independently tested (i.e., subject to peer-review and multiple investigations) theory that posits speaking Ebonics either a) keeps Black students interested in core academics (e.g., math, reading, chemistry) above and beyond the norm or b) has a positive effect on college admissions to mildly selective universities. Note, I didn't say a thing about raising IQ scores, which is really what this whole thing is all about.

2) The article says:
A pilot of the policy, known as the Students Accumulating New Knowledge Optimizing Future Accomplishment Initiative, has been implemented at two city schools.

Have any results been published? Can I have access to the data? Or is this going to be another fraud in the name of social justice.

I searched PsychInfo and the Internet in general (i.e., Google and Google Scholar) and found not one article, much less a peer-reviewed one, with the following key words: "Students Accumulating New Knowledge Optimizing Future Accomplishment Initiative" or "Mary Texeira".

I challenge anyone involved in this project to give citations of where the public can go to review a) their research design, b) their data collection instrumentation, and (if available) c) their analysis.

Until such a time, this effort, to paraphrase KA, will have to be classified as ass.

*Thanks to Scott for the heads up on this article.

Robots and camels   posted by Razib @ 7/19/2005 12:01:00 AM

Robots replace child jockeys in Arab camel race. Don't liberal do-gooders know that families in Bangladesh depend on the remittances sent by the child jockeys?

Update: Just want to make clear, the initial post was meant in mirth. I really didn't know how serious the whole "camel jockey" thing was.

Monday, July 18, 2005

Men, women, math....   posted by Razib @ 7/18/2005 10:44:00 PM

Griffe has a new article up, Sex Differences in Mathematical Aptitude.

Related: Much ado about women & Larry Summers.

C.P. Snow surely failed   posted by Razib @ 7/18/2005 01:24:00 AM

Four Challenges to Postcolonial Theory:

More broadly, I question O’Connor’s disdain for inductive reasoning, generalizations, and conjecture. As anyone who has ever struggled with arguments about literature must know, literary studies has never conformed to the modern ‘scientific method.’ One generates viable arguments and new forms of literary knowledge via routes that are often tangled, using reasoning that may be equal parts inductive and deductive, as well as through through conjectures (that are eventually substantiated), generalizations (that are hopefully true), and partial initial knowledge (that is later filled in). It may drive scientists insane to say it, but a literary critic has to have some sense of what she or he expects to find before writing a question or filing a proposal....
As I've said before, I don't "follow" any particular philospher of science (Popper, Kuhn, Lakatos, etc.), but, as I note in the comments, I assumed that literary folk were familiar with them. When I read that passage I was rather disoriented. It seems to imply that:
  • Inductive reasoning and science are exclusive (someone should have told Dimitri Mendeleev).
  • That generalization and scientific theory are somehow exclusive.
  • That conjecture and hypothesis are not synonyms (or at least intersecting concepts).
  • That scientists propose hypotheses and conduct experiments with little foreknowledge of the range of possibilities.
Reading that passage, I got the strong impression that the author was conflating "science" with mathematical formalism.1 Now, it is true that humanists of the literary bent often get irritated when simple folk of scientific inclination like I misrepresent their discipline through ignorance and inability to grasp the subtle meaning in their "words," but science is in its essence a rather simple method....a method that I see described above, with only minor specific modifications necessary,2 in science testability is a measure of the model against the world, while reproducibility is a measure of the model against your fellow man.

1 - Even my interactions with friends who do graduate work in mathematics does not suggest to me that they are automatons at the service of axioms, inexorably ground down by the "logic" of their work. The finish product is certainly clean, but the process is filled with intuitional leaps and hunches from what I can gather.

2 - It is through testing and reproducibility that we get through the slop of misimpression and error. The problem that I have with many Literary Theorists and other assorted humanistic scholars who employ "Theory" is that I don't get a strong sense that they are studying anything aside from their own circular suppositions. In other words, it resembles pure mathematics, but without formal rigor or felicitous applicability in modeling the universe we see around us. I do not think it necessary that humanists should all strike the perfectly rationalistic pose that some analytic philosophers do, I simply wish, for lack of a precise phrase, that people like Gayatri Chakravorty Spivak would help us engage the world transparently and learn to love life with innocence, rather than being tied down by tangled ropes of faux-verbal unmeaning. If they so often did not have the title "Ph.D." their words would indicate to me that they abominate sincere cognition altogether. They strike me as modern day analogs to the fakirs and ascetics who the Buddha initially sought wisdom from, before realizing that their self-denial and flagellation was futile.

Sunday, July 17, 2005

The paths of polygyny....   posted by Razib @ 7/17/2005 11:19:00 PM

From page 332 of After the Ice: A Global Human History 20,000-5000 BC:

Lloyd Warner argued that warfare and killing within the Murngin was a consequence of their marriage system. This was polygyny, which allowed men to have several wives; most middle-aged Murngin men had at least three. As the number of Murngin men and women were approximately equal, and as women married just before puberty, there were simply too few women for the young men to marry. And so, in Lloyd Warner's words, there was a 'seasonal slaying' of young men who had passed into adolescence.15 This culling of the young and eligible was presumably in the interests of the older members of society who were happy to encourage the younger men to fight.

A week ago I excised the comments of an Islamic scholar who argued that neo-Darwinian gene-centered thinking illustrated why polygyny was a "natural" social arrangement. Not only did he present the ultimate level justification, that successful alleles induce male preference for a great number of sexual partners, he added the proximate realities of male compulsion toward sexual satiation with multiple females. Most proponents of polygyny do not offer the ultimate neo-Darwinian explanation, though generally they present a correct diagnosis of the proximate behavioral biases that males are prone towards. Additionally there is the other justification that polygyny allows all women to enter into marriages, because there is a mysterious excess of females. Truthfully there are cases where this does occur. Mormons explain away Brigham Young's polygynous marriages as good deeds because so many Mormon men were killed during the early years of the community (they have a more difficult time explaining away Joseph Smith's preference for this sort of marriage in utilitarian terms). Muslims have offered similar justifications for Muhammed's many marriages, in addition to the banal one that they were simply a means to an ends of cementing alliances with the various tribes of Arabia. But of course, these are atypical circumstances, so the persistent use of this argument strikes me as rather peculiar.1

But in any case, note that I emphasized that the hypothesis above suggests that warfare is a consequence of the marriage system. Of course, once warfare ensues, an there will be a deficit of older males who are suitable for marriage! So the argument for polygyny as a solution to male shortages is empirically justifiable in the most narrow of readings. That is the problem with many of these sociological models, they need to evaluated over a period of time, and the dynamic interplay of "cause" and "effect" need to be smoked out. One generation of enforced monogamy might leave many females without partners, but the subsequent one will have passed the threshold to a new social equilibrium.

Additionally, as to the ultimate and proximate arguments of the Islamic scholar on the merits of polygyny, I would argue that he is being disingenuous, because I doubt he views neo-Darwinian genic imperatives as the sum of all things. Rather, he sees the edicts of his God as the ultimate Ground of Being. The neo-Darwinian argument is a tool to convince those who do not share his religious convinctions, or believers who doubt the norms of the faith tradition, but it is in the end an secondary consideration, a bullet point rather than a thesis. Similarly, the sexual appetite of males is also not an important consideration, as his religion in other circumstances enjoins a great deal of restraint upon true believers (alcohol, Ramadan, etc.). The circumstances where appetites are restrained or accommodated are based on religious norms, ostensibly derived from God (I have argued many a time that religious norms are socially mediated more than they are transparent inferences from divine edicts, ergo, the modifier). The situations where appetites are constrained or accommodated may shed light on norms, but their constraint or accommodation is contingent upon the axioms of the religion, not on Nature.

Personally, I find ultimate genetic imperatives uncompelling beyond what my intuition suggests (I have had the capacity to produce many copies of my genes which are carried by other bodies for the past 15 years, and yet I have not). As for my proximate biases, they are constrained by my values and long term utilitarian calculations. All sociological models derived from a mix of genetic and environmental parameters will be aproximations, they are rough and ready guides as to the difficulty of a given project (or the possibility of a given project). To illustrate the issues with a more prosaic example, the most efficient (in terms of expenditure of resources) path to build a road between points A and B may take an arc around a mountain, but, because of other constraints one may still have to choose the "suboptimal" route of building a tunnel directly through the barrier. Perhaps the periphery of the mountain is controlled by hostile states. Perhaps the periphery of the mountain is ringed by religiously sacrosanct locations. Or, perhaps the long term savings in fuel by taking the shorter straight line path will recoup the short term costs and dangers of constructing a tunnel (you may object that maintenance will consume the savings!).

All too often people will point to nature and declare, see, it should be as it should be! The Naturalistic Fallacy is one reason that many reasonable people shy away from, in my view, a fuller and richer description of reality. The problem is that people confuse science and engineering. Science refines a model, ideally it is "objective" and individual bias or preference is subtracted from the system. But engineering (social, biological or physical) is contingent upon your specifications and ultimate goals (in the case of social engineering, your values), its methods may derive from science, but its rationale is often2 extra-scientific. Prometheus gave us fire, for good or ill, do with it what you will.

Addendum: Terms like "polygyny" are often an idealized description a far more imprecise reality. For example, the geriatric polygyny practiced by some Aboriginal peoples (the Arunta of Central Australia I believe for example) in practice is characterized by a great deal of toleration for dalliances on the part of the young wives with single young men of the tribe. In a strictly monogamous society, serial monogamy on the part of high status males may result in a shortage of age appropriate mates for young males and older females, in the former case mimicking aspects of polygyny (in most populations there are more males than females born, so until the the late 20s in most modern nations there are more males in any case).

1 - In Why Sex Matters Bobbi S. Low argues that polygyny in regions like Africa is due to high pathogenic load the environment, which puts a premium on genetically "fit" males. Low also uses a populational definition of polygyny, it is defined by a high ratio of male reproductive variance to female reproductive variance (this results in a constant offloading of genetic load).

2 - I say often because the engineering department at NASA is at the service of science. But is it? The reasons given for the manned space program are often scientific, but talk to many scientists and they will assert that it is a waste of money and its actual (as opposed to stated) reason for existence is non-scientific (national pride, emotional considerations and most ironically, jobs for engineers ). Reasons within reasons.

Lustrous Sepharad   posted by Razib @ 7/17/2005 02:10:00 AM

Since I've been doing a lot of reading where "Maghrebi" kept coming up...I decided to see if IMDB had any new pictures of Moroccan Canadian actress Emmanuelle Chriqui (she was Lance Bug-eye-Bass's romantic interest in his flop movie from a few years back). There were some here and there, but I did a little more web searching...and I stumbled on to the fact that her parents are actually Morrocan Jews. A month back some might have wondered if we had it in for Sephardic Jews, with the whole Ashkenazi IQ debate, and the implicit diss on their southern cousins. But if Ms. Chriqui is held as an exemplar, I will offer that Sephardic Jews have a leg up in the T&A factor. For your edification, I have placed an image of Ms. Chriqui below the fold, placed above another of Ms. Natalie Portman, the pearl of Ashkenazi Jewish pulchritude (not work safe, especially in the Arab world!).

Saturday, July 16, 2005

Profile of Salafi jihadists....   posted by Razib @ 7/16/2005 08:37:00 PM

This morning I saw a post over at ParaPundit where Randall Parker quoted Marc Sageman, my ubiquitous source for the factoid about the overrepresentation of technical (scientists, engineers, etc.) types in Al Qaeda. As it happens, I had a copy of Sageman's book, Understanding Terror Networks, on hand, and I decided to read it today. If you are interested in understanding the Al Qaeda network from a scholarly angle, read this book! It is less than 200 pages long, and the text is not even particularly small, the prose is social science dense, but not opaque or jargonistic (there are Arabic terms throughout, but they are precisely defined prior to use). In particular, you should read chapter 3, "The Muhjahedin," which is a ethnography of the world "Salafist terror network." This is the data that serves as the core of this book, and no matter your political beliefs it is genuine empirical red meat to bite into. Sageman explains that he made choices about data selection, he focused on those who were involved in worldwide Islamic terrorism driven by purely religious-Salafist motives. This means that localized Islamic terrorists (Hamas) and secular terrorists from Muslim nations (Al Aqsa Brigades) are not included in his sample. Below, I have copied the essential tables from the aforementioned chapter, but it is important to note that Sageman provides a lot of context and framing, so if you don't have time to read the book, just read chapter 3, it'll take you a half an hour at B&N or Borders.

First, you have to understand that Sagemen broke up his sample by region and amalgamated them into four primary clusters:
  • The Central Staff (Al Qaeda command & control)
  • Core Arabs (those activists from the central Arab region)
  • Maghreb Arabs (those from North Africa and the North African Diaspora)
  • Southeast Asians (mostly Indonesians)
Though there are individuals of other Muslim nationalities within the sample, it is dominated by Arabs and Southeast Asians, with a heavy skew toward Egyptians in "The Central Staff."

I'm having a hard time getting blogger not to format my tables and so mess everything up, so here is where I put them.

Here are the general trends that Sageman highlights:
  • Salafist radicals are not impoverished and uneducated. In fact, the Central Staff + Core Arabs, who are the main actors, are extremely privileged and well educated (even by Western standards, but they are off the charts in the context of their nations of origin). The Maghreb Arabs, many of whom were actually raised in relatively (though not in absolute terms) deprived circumstances in France are much less affluent and well educated than the dominant personalities in Al Qaeda. The Southeast Asians tend to derive from the pesantrans (the Southeast Asian version of madrassas) of Indonesia, and are associated with one or two relatively top-down organizations.
  • A relatively secular background was the norm for the Maghrebis, many of whom Sageman notes grew up in France with little Islamic education. In contrast, the Arabs and Southeast Asians tended to have a more thorough Islamic background, even if they were not "green diaper" babies. Sageman notes that removing the Maghrebis from the equation though does make a difference and makes the "green diaper baby" thesis more defensible. In addition, many of the central players in Al Qaeda do come from a Salafist cultural milieu, and most radical Salafist terrorists will be familiar with Islamic concepts at the very least. These are not died-in-the-wool-atheists who find God.
  • Out of the sample of 117 where Sageman had information about childhood religious values, 9 were Christian. This is a frequency of converts far higher than in the Muslim population worldwide.
  • 78% of the terrorists joined the Salafist jihadi movement away from their country of origin, whether in the West or in another Muslim nation.
  • There was a tendency toward underemployment and perceptions of relative deprivation (ie; Arab French resentment toward the majority population). In the case of those from affluent families in the Middle East, the underemployment is probably partially an artifiact of the fact that they tend to join the Salafist terror movements in their early 20s, just as they are finishing their educations, and likely do not ever enter "normal" society and instead focus on jihadi activism.

Sageman dismisses the standard Freudian explanations offered as the motivations behind terroristic behavior, and rebuts the stereotype that these individuals are frought with psychopathologies. In fact, 80% were also married men, and few engaged in criminal activites as their vocation (the exception was among some of the Maghrebis and converts from Christianity, the latter of which tended to skew toward lower class origins). Sageman's thesis is pretty simple, in the later chapters he sketches out the importance of networks effects, friendships, bonding, clique formation, etc. He tends to reject excessive focus on ideology as the driving factor, though it is clearly a necessary factor to crystalize the path of the lives of these men. The author simple reminds readers that there is a wide ranging literature which suggests that individuals who join radical groups tend to overemphasize the ideological reasons for their joining, and underemphasize the personal life context and in particular the influence of peer groups and family. In other words, Salafist radicals did not have a lurking disease-of-the-mind which religious fundamentalism could coopt, rather, they were a self-selected group of individuals who must be understood in the context of their social universe, and in many ways they were rather banal personalities.

In any case, since I recommended that you read the book, I'm not going to go on much further, but I will offer that some might quibble with Sageman's terminology. He uses the term "Salafist jihadi" very precisely, as he distinguishes them from more traditional Salafists, and fundamentalists of other stripes. Additionally, I believe he makes some minor doctrinal errors and elides over disputes and debates in terms of Islamic sectarian typology without indicating to the reader of the issues undernearth the surface, but, I think these errors don't really detract from the ethnographic data and the network based analytic model he deploys. I suspect that a full fleshing out of the nuances of Salafi vs. Wahabbi vs. Deobandi vs. Tablighi, etc. etc. would have weighed the book down a great deal (the categories are not always exclusive and equivalent in the way he tends to frame them).

One important thing though, Sageman goes to great lengths to suggest that the Salafi worldwide jihadis are a very peculiar, self-selected and abberant group in the context of Islamic radicals. He points to the origin of the core of Al Qaeda in one of two Egyptian Islamic terrorist groups, a Cairo based organization which he claims exhibited a tendency toward being less rooted within their social context, and so more prone toward abstraction and vague ideological goals. In contrast, the rival of the group that was absorbed by Al Qaeda was also radical, and moved in the same circles (a faction was responsible for the Luxor massacre), but this movement never warmed to the idea of worldwide jihad. Sageman offers that the reason is that this group was more closely connected with the milieu of Upper Egypt, and so it was grounded in a way that the Cairo branch was not in the social environment and restraints eventually pulled it back from the path that Al Qaeda took (it is now in ceasefire with the Egyptian state and has rejected violence as ineffectual).1

Addendum: The reason I am happy to leave comments on on this blog is that I see this as a way to engage with intelligent readers who are moving through knowledge-space with me, scaling various factual mountains and ascending upward so we can gain the best vantage point of the world below us. This means that I expect people to actually read the tables I copied and pasted if they want to offer comments! My commentary is just fat, the tables are the muscle and bone.

1 - Though the Upper Egyptian group was also drawn from "scientists and engineers" as well, the individuals probably had the same psychology, but their predispositions resulted in a disparate life path because of their social context.

Language, genes, etc.   posted by Razib @ 7/16/2005 09:47:00 AM

Luigi Cavalli-Sforza's magnum opus The History and Geography of Genes opened the flood gates in terms of a series of popular books which attempted to glean the movements of peoples by the examination of data from their genes (of late, usually matrilineally transmitted mitochondrial DNA and patrilineally transmitted Y chromosomal sequences). Of course, there is the ever present problem that different genes might have different histories, that selection confounds our inferences, and many of the models make gross simplifying assumptions (ie; no admixture, etc.). In Beyond languagese I highlighted the issues that crop up with the nomenclature used when referring to various language groups, as the names themselves often confuse those who attempt to interpret them transparently.1 The problem with language also crops up in historical genetics, as people want to revert back to the early 20th century tendency to fix on to a particular language group a distinctive genetic history. Cavalli-Sforza is I think responsible for this tendency, because many people were drawn to the section of his book where he addresses this question, and illustrates the concordance between gene and language trees with graphs.

So, getting to the point, there has been some recent work that indicates that the peoples of Madagascar are predominantly Asian, specifically derived from Borneo, on their male genetic line (Y) and African on their female genetic line (mtDNA). The authors of the paper make a big deal about this, but 1) I thought this was assumed from previous studies, if not as definitively, 2) you can find similar asymmetries across the New World. One issue that the authors find surprising is the contrast with the genetic data as far as the language as Malagasy seems almost wholly Asian. Well, again I think the New World example should indicate to us that this can happen, and has happened many a time in the past (non-Indo-European substratum are strewn across Europe via place names and other localized terms). And today I stumble upon this:

...Wood and colleagues tested 40 populations across the continent for associations between genetic, linguistic and geographical distances. Examining Y chromosomes and mtDNA revealed that gene flow patterns have been different for men and women historically: language appears to be passed from father to child, and women may have mixed between populations more than men....

I doubt we will ever find a One True General Answer to these sorts of question, though we may begin to establish an overall preponderance and a knowledge of local patterns. I for one am really curious as to how the languae of the Magyars managed to establish itself as dominant upon the Danube plain (there seems little genetic differentiation from neighboring populations, though that might be due to high levels of genetic exchange after Christianization circa 1000, and so an obscuring the original admixture dynamics).

Related: "Racial Diversity."

1 - One time I mentioned to a friend that 40% of the words in Greek (like the ones with ending in nth) seem to be "Mediterranean." By this I meant a catchall term I have seen used to simply clump all the pre-Indo-European dialects that dominated Greece before the arrival of Greek speakers. But my friend interpreted the term directly and responded, "Well, that makes sense, since Greeks are 'Mediterranean' and Greek is a 'Mediterranean' language."

Friday, July 15, 2005

Is the "afterlife" a human universal?   posted by Razib @ 7/15/2005 11:08:00 PM

In Frank Tipler's The Physics of Immortality : Modern Cosmology, God and the Resurrection of the Dead he makes a really strange case for the existence of God (I'm not going to try to summarize it). Nevertheless, one of his points is that religion needs science to buttress itself against erosion among the educated. I happen to think that to the first aproximation is wrong, but, one data point that Tipler grasped on to was that scientists in the United States expressed far less belief in life after death in the 1990s than they did in the early 20th century (suggesting the corrosive impact of science was taking its toll). Unfortunately for Tipler's case, it is undermined by the fact that their rates of God belief remained about the same.

I am one who has gone on the record that I think that belief in a supernatural deity is probably a human cognitive bias, overreach of the agency detection mechanism. How it manifests itself (and how frequently) in society is shaped by the "environment" (however you define it). On the other hand, as to the question of the afterlife, I don't think it is necessarily a cognitive bias, at least in the form that Westerners generally conceive of it, that is, heavenly immortality. No matter the theological nuances I can perceive the same general characteristics of the deity in most religions, "high" and "low." On the other hand, most ancient Greeks did not go to the Fields of Elysium, Gilgamesh's true immortality was attained through the memory of his fame, while to be a bit simplistic, one disagreemant between the Sadduccees and Pharisees was whether there actually was an immortal soul (sheol seems more like the underworld of the Greeks and Mesopotamians than heaven).

I think Tipler's problem was that he was comparing two very different concepts. "God" is a rather intuitive one. Frankly, aside from religious professionals the people most engaged with, and aware of, the God of the philosophers as elaborated by theologians are usually atheists! Certainly most religious people sincerely believe in creedal formulas, but I've said many times I don't think these are really substantive assertions because I don't think most people know the philosophical details, nor do I think the philosophical details express much more than word games which spawn a niche for religious professionals and the institutions they create. In contrast, I suspect that the Christian-Muslim-Jewish broad sense idea of eternally blissful afterlife (derived from Zoroastrianism) is something that needs to be learned.1 "Beliefs about death" are listed among the human universals, but my impression from the anthropological and historical literature is that these beliefs are generally not positive ones, and often rather vague and incoherent (perhaps because thoughts of death are not emotionally attractive). Roughly speaking, modern ideas about the afterlife (belief which tends to score lower in frequency than "God" in surveys) derive from institutional religions, and supersede the dark imaginings of our intuition. In contrast, institutional religions simply add some nuance (or gibberish, depending on your perspective) to our intuitive beliefs about God.2

Which all relates back to the poll results (taken by Leuba in the early 20th century and Larson and Witham in the late 20th century), belief in the afterlife has eroded among scientists to a greater extend than belief in God because the former is a reflective wish, while the latter is a natural belief.

Related: Reflections on the "God Module."

1 - Hindu and Buddhist beliefs differ in the details, but in the end I think they offer the same general relatively "positive" outlooks in comparison to "tribal" religions.

2 - This is not to say that positive beliefs about the afterlife are not here to stay, rather, I am simply suggesting that if H. sapiens reverted to hunter-gatherer bands, eternal bliss in the glory of the Lord might be forgotten without the indoctrination by professionals and their attendant institutions, but belief in the Lord would not.

Ancient DNA....   posted by Razib @ 7/15/2005 10:18:00 PM

Dienekes links to two recent papers, one indicates that a pre-Mongoloid substrate existed in Thailand ~30,000 years B.P. through inspection of fossil morphology, while extracted mtDNA shows similarities to the non-Malay Semang peoples of the interior of Malaysia, another article confirms the ancient status of many Native American lineages through comparison with a 10,300 sequence of mtDNA.

"Third culture" summer reading list....   posted by Razib @ 7/15/2005 10:09:00 PM

Thought this summer reading list might interest some. I've read 9 out of the 40 books listed, with a few in the "pending" category (own 'em, will get to 'em).

Administrative note on the Science Fiction weblog   posted by Razib @ 7/15/2005 09:53:00 PM

The Movable Type issues are gone, but I am going to stay with Blogger for now because I am skeptical about the future support for the old free version of MT that ran this site (this blog is too big for the licensing conditions for the current gratis service, and the number of authors is way too high to be economical). But, I have left everything intact and switched the link back to the old Science Fiction Weblog so that people with privs over there can keep posting with MT.

Which lives matter?   posted by Razib @ 7/15/2005 09:01:00 PM

In a follow up of my earlier post:

"We know that the killing of innocents is forbidden," Dr. Waheed said. "But we don't see two classes of blood; the blood of Iraqis is just as important to us as English blood."
(source: Anger Burns on the Fringe of Britain's Muslims)

I have serious problems with how State Confucianism played itself out over the 2,000 years of its dominance as the central idea of the Chinese nation-empire, but, its convinction that there are grades of loyalty and fidelity (rejecting Moism), starting with family and extending out toward the state, and its rejection of abstract legalistic principle in favor of humanistic adjudication (denying Legalism), resulted in a remarkably robust system. Similarly, the modern nation-state rests on the conviction that individuals within a circumscribed geographical space are bound together to a greater extent than those outside the "magic circle" of citizenship (by blood, history, culture, conviction, war, etc.). This is not absolute, and loyalty to the nation-state coexists with loyalty to family and god(s) as well as a basic level of fellow feeling with the rest of humanity. The grades of loyalty are always applicable in the context of those outside the magic circle of citizenship, in the United States conservative Christians have been aggressive in bringing to light the persecutions of their coreligionists in Sudan and China, while secular liberals have focused on the repression in Tibet.

Nevertheless, I do think there are issues that need to be addressed with Muslims in particular. In the short-term there is the flair up of violence, but in the long term, there is the issue that there are 1 billion Muslims, scattered across dozens of countries. If Indian Americans, or Chinese Americans, or Jewish Americans do have "dual loyalties," the range of foreign policy questions where this is relevant is rather constrained because there are only two China's (PRC and ROC) and one India or Israel. On the other hand, the geography of the Dar-al-Islam is rather expansive and the number of nation-states with conflicts, potential conflicts and international grievances numerous. Regardless of whether there are fundamental issues with how Muslim minorities relate to the non-Muslim majority (and implicitly, the non-Muslim nation-state), there is the structural issue of the geopolitics of the Muslim world which are simply inescapable. Of course, as one can see with Christians, this structural issue can be obviated....

Addendum: I am not going address the implicit hypocrisy of the individual whose quotation I excised, as I doubt he sheds tears or spends much time thinking of the travails of Nigerian Christians in Kano, Roman Catholics in Vietnam, Buddhists in Tibet.

Correction on MC1R....   posted by Razib @ 7/15/2005 08:08:00 PM

I misreported Heather Norton's presentation in the post below. I emailed her a few questions, and she responded:

Actually, my data do not show that Europeans and East Asians have different MC1R alleles, but rather that they appear to be different for two alleles in the genes TYR and MATP. I didn't see strong differences between Europeans and East Asians at the two MC1R SNPs that I stated that I had presented them at a conference in Europe. The conference was in fact at the Annual Association of Physical Anthropologists Meeting in Milwaukee, Wisconsin earlier this year.

...I'm in the process of writing up the results of the work that I presented at the AAPA meeting for publication I am not prepared to discuss them fully right now, but I can tell you that I think that MC1R is often attribted a larger role in pigmentation regulation than perhaps it really has. In no way can I disupte that MC1R sequence variation is highly constrained, especially populations living in regions of high UVR (like West Africans), and I do believe that this is because certain MC1R mutations lead to lighter skin, which would be maladaptive in these regions. However, pigmentation is a complex trait that is under the control of many genes, and I think that while MC1R might explain a lot of the variation in skin and hair pigmentation phenotypes that we see among different European populations it is not so great at explaining variation at more global level. In other words, I believe that there are a number of other genes that may play just as important a role, if not a greater role, than MC1R in explaining these differences (and of course, I'm saying this because of my some of my results do indicate that other genes are involved). I think that one reason why MC1R is often cited in discussions of pigmentation differences is because it is a short gene (only 1 exon ~ 1kb in length) and so is very easy to sequence. Also, some MC1R alleles have very easily visible effects on phenotype (these would be the strong RHC alleles), which of course makes things easier. So, I'm not knocking MC1R, I think it's a very important gene and I think that it's great that it's been so well-studied. However, I don't think it tells the whole story about global
human pigmentation variation....

She can't answer my direct questions right now because there is a paper pending publication. Here is her abstract from the presentation:

Using measures of locus-specific differentiation to find genes underlying traits subject to recent genetic adaptation: a test case using skin pigmentation.

H. Norton1, R. Kittles2, C. Bonilla2, J. Akey3, M. Shriver1. 1Department of Anthropology, Penn State University, 2College of Medicine and Public Health, Ohio State University, 3Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA.

A number of DNA sequence-based statistics are available to identify signatures of natural selection. However, sequencing large numbers of individuals across multiple genes can be costly and time consuming. An alternate method that uses allele frequency data has received less attention, but may be more efficient for large screening studies. This method is based on the idea that demographic events affect loci across the genome equally, while adaptation affects individual genes and nearby markers. We have applied the locus-specific pairwise FST (lspFST) to survey seven pigmentation candidate genes from six geographically diverse populations. Using the allele frequencies at these genes, we calculated the lspFST statistic and compared it to an empirical distribution based on 11,078 SNPs analyzed in the same populations. With this comparison we are able to take into consideration the demographic histories of the populations and calculate likelihoods of the data given neutral evolution. Several pigmentation candidate genes show evidence of non-neutral patterns of differentiation. Interestingly, population differentiation at pigmentation
candidate SNPs was observed both for populations differing in pigmentation phenotype (ASIP and OCA2), as well as for populations similar in pigmentation phenotype (TYR). Additionally, SNPs in MATP show high levels of European-specific population differentiation. These results suggest a strong role for natural (and/or sexual) selection in shaping human pigmentation variation. Patterns of allele frequency and lspFST variation at TYR and MATP between Europeans and East Asians raise the possibility that natural selection may have acted on different alleles to produce a similar adaptive phenotype in these populations.

Where "folk biology" fails....   posted by Razib @ 7/15/2005 12:35:00 PM

Reading After the Ice: A Global Human History 20,000-5000 BC by Steve Mithen I came across this interesting fact: ~12,000 years ago the peoples of Western Asia were selectively hunting male gazelle. They clearly understood enough about animal reproduction (perhaps extrapolated from human patterns) that female mammals were the rate limiting step in the perpetuation of a species, so males were to some extent a superfluous element aside from the necessary reservoir needed for fertilization.1 But, these same people did not have a model of selective breeding which would allow them to anticipate the response of the character of the gazelle population to their preference for culling large males: the smaller males were the only ones who remained to mate with the females, so there was strong directional pressure for many generations toward less meaty gazelles! (the same process is occurring with the Asian elephant, as only males have tusks, and the less tusked males are most likely to survive to reproduce. If tusk size is a proxy for genetical health this might result in a mutational meltdown in the future)

Related: As the essay Folk Biology and the Anthropology of Science states explicitly, "folk biology" is most closely related to Systematics.

1 - Here is some information on why 50:50 sex ratios persist, though note that for most species reproductive skew is greater for males so that fewer of them pass on genes to the next generation than females.

Thursday, July 14, 2005

East Asian origins?   posted by Razib @ 7/14/2005 04:21:00 PM

Y-Chromosome Evidence of Southern Origin of the East Asian–Specific Haplogroup O3-M122:

...Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred ∼25,000–30,000 years ago, consistent with the fossil records of modern humans in East Asia.

Take it all with a grain of salt, in light of possible revisions in the "Standard Model" of modern human origins, but a date of 25-30,000 years BP isn't that much earlier than the coalescence points some bandy about for New World lineages.

On a related note, I added a new weblog to the blogroll that deals in East Asian genetics, Quetzalcoatl.

Model rising....(?)   posted by Razib @ 7/14/2005 06:03:00 AM

Eric Trinkaus says: conjunction with the emerging chronology of the earliest modern humans, the paleontological data indicate an assimilation model for modern human origins, in which the earliest modern humans emerged in eastern Africa, dispersed briefly into southwestern Asia, and then subsequently spread into the remainder of Africa and southern Asia, eventually into higher latitude Eurasia. The earliest modern humans outside of the core area of eastern Africa can be understood only if a variable degree of admixture with regional groups of late archaic humans occurred....

This should not surprise readers. John foreshadowed these comments, and I'm sure he'll have more to say later. Henry has been pointing out the differences between a few neutral markers (Y and mtDNA) and various functional loci for years in terms of the picture they present of the human past. Greg has been pushing the 2s hypothesis recently. These models imply that we have to rework the "Human Species Concept" a bit. Additionally, if there are ancient alleles from "archaics" which have introgressed into a predominantly neo-African worldwide human population, that might explain some of the incredible human adaptational flexibility. Where as before a pure African replacement model envisages the development of localized races out of the variational genetic background of a small founder population of East Africans within the last 100,000 years, this model can leverage the genetic background of the entire extent homonid population of the Old World. For instance, I have already pointed out some groups in the southern hemisphere seem to be rather dark for their latitude. The hypothesis I offered was that perhaps MC1R, the locus at the heart of skin color regulation, jumped from northern Eurasian archaics but could not cross the fitness valley of Southeast Asia over to Australia.1 While the southern moderns swept past ancient homonid populations who were tropically adapted just as they were, the northerners encountered peoples with hundreds of thousands and possibly millions of years of different adaptationally relevant alleles. Heather Norton at Penn State has already done research which suggests that East Eurasians and West Eurasians have different variants for the MC1R locus which controls melanin production and so results in lighter skin color outside the tropics (unpublished, though presented at a conference in Europe). So if the replacement model is correct the African populations brought different variants to the north and directional selection fixed alternative alleles (or the mutation emerged in situ within a particular geographic zone, which would fit in with the thesis of relaxation of functional constraint outside of the tropics). The assimilation model implies that the local Eurasian archaics had long independent existences and different alleles might have been dominant at the antipodes of the World Island. As a point of comparison the phenotypic variation of the Native Americans is on subjective grounds often evaluated to have been rather narrow for the wide latitudes and habitats that they inhabited, so it does not seem that 10,000 years (lowbound) is enough time for the "full range" of human coloration to manifest itself out of the genetic background. One obvious expalantion is that founder effect severely limited the genetic variation of the New World populations from which selection could work, but note that the original East African expansion event is often hypothesized to have been an almost explosive demographic event, likely going through several bottlenecks.

Via Dienekes.

Related: What's your s?

1 - The main issue I might have with this is that there seem to have been migrations into Australia within the last 10,000 years. But nevertheless these populations would still have to squeeze through the high UV regions of the tropics. And though Julian O'Dea has pointed out that Tasmania is at the latitude of Corsica, my impression is that Napoleon wasn't that swarthy (he certainly thought of himself as white, as illustrated by his declaration that he was "for the whites" in Haiti because "he was white").

Species concepts   posted by Razib @ 7/14/2005 02:51:00 AM

Since we mysteriously tend to show up rather high on some science related google queries, I have decided to copy many of the "species concepts" found in Coyne and Orr's Speciation below (adapted from table 1.1 on page 27). Google does have a list of sites with a lot of information, but none of them strike the balance of brevity and thoroughness I would like. I think a familiarity with the general outlines of the "Species Controversy" can also help people grapple with within-species population substructure. Obviously species exist, right? But drawing hard and fast lines based on deterministic axioms aren't as easy as you might think, good enough for government work, but definately nothing that could ever quench physics-envy.

First, the Biological Species Concept - Species are groups of interbreeding natural populations that are reproductively isolated from other such groups (Mayr 1995).

Genotypic Cluster Species Concept - A species is a [morphologically or genetically] distinguishable group of individuals that has few or no intermediates when in contact with other such clusters (Mallet 1995).

Recognition Species Concept - A species is the most inclusive population of individual biparental organisms which shares common fertilization system (Patterson 1985).

Cohesion Species Concept - A species is the most inclusive population of individuals having the potential for phenotypic cohesion through instrinsic cohesion mechanisms (Templeton 1989).

Ecological Species Concept - A species is a lineage (or a closely related set of lineages) which occupies an adaptive zone minimally different from that of any other lineage in its range and which evolves separately from all lineages outside its range (Van Valen 1976).

Evolutionary Species Concept - A species is a single lineage of ancestral descendent populations or organisms which maintains its identity from other such lineages which has its own evolutionary tendencies and historical fate (Wiley 1978, modified from Simpson, 1961)

Phylogenetic Species Concept 1 - A phylogenetic species is an irreducible (basal) cluster of organisms that is diagnosably distinct from other such clusters, and within which there is a paternal pattern of ancestry and descent (Cracraft 1989).

Phylogenetic Species Concept 2 - A species is the smallest [exclusive] monophyletic group of common ancestry (de Queiroz and Donoghue 1988).

Phylogenetic Species Concept 3 - A species is a basal, exclusive group of organisms, all of whose genes coalesce more recently with each other than with those of any organisms outside the group, and that contains no exclusive group with it (Baum and Donoghue 1995; Shaw 1998).

Personally, the "Species Controversy" is not that interesting to me, my attitude toward species is strictly ends-based, that is, what does the "concept" species convey to you in terms of information, framing a basis for further research and contributing to model building? Coyne and Orr take the same general approach from what I can gather. It seems that some of the species concepts, especially the phylogenetic ones, are favored by biologists whose sole focus is Sytematics. But for all its problems the Biological Species Concept seems the more useful for day to day research in most areas, and helps guide us along the path to the Most Perfect System of the World. I am really more interested in the dynamics of alleles in gene space, and "species" are simply one verbal description of that space. On the adaptive landscape that I have spoken of recently the boundaries between species can be thought of as very deep trenches, or even untraversable "holes" which separate the fitness peaks which correspond to the species.

Wednesday, July 13, 2005

All lives are not equal in our eyes (duh....)   posted by Razib @ 7/13/2005 11:21:00 PM

Listening to the BBC (and reading a few articles) I hear some British Muslims griping that the bombings are an inevitable response to British foreign policy and they note that dozens of Iraqis often die in one day. Oh, but did I mention that soldiers are chowing down on vagina roast in the Congo? Sometimes when I get tired of comment threads where Muslims and Jews are arguing as if killings in the Middle East are of world-shattering proportions, or when Muslims and Hindus get into online shouting matches over the regular brown-on-brown-riot-fests, I simply to point to the bloody wound that is Africa. Usually I am ignored, as the conversations blissfully sail on toward their inevitable Godwinian-MAD denouement. Not that I care particularly much about Africa or Africans, I get much more disconcerted when my computer crashes and I am about to lose precious files or when I find out that I can't get George R. R. Martin's latest book "early" by purchasing the English copy from,1 but, I don't really care about foreign Muslims or Hindus or Indonesians to a greater extent than Africans.

Now, I am willing to grant that for Muslims or Hindus that what happens to their co-religionists matters to them, they have a sense of affinity which I lack. I even grant that Muslims or Hindus or any other group (Jews for one) can and should argue for the interests of their fellows if their values, principles and common feeling so dictates, but, those of us who lack such fellow feeling beyond common basal humanity (something I concede I was shorted on by God when he got down to shaping me from gold-dust) for those in distant lands should simply point to Africa, for if humanitarian concerns are foremost than that is where our sentiment should lay. Otherwise, let the rest of the world keep eating cake, for even that small boon is something Africans are still too often denied. Of course, because of our lack of intensity over our apathy those of us unconcerned about the body-count of Jew vs. Arab or Hindu vs. Muslim will lose these battles, Africans will keep starving while the Gaza Strip will continue to have some of the world's highest birth rates because of UN aid, but at least we might prod the communally self-interested from off their moral high horse and force them to grub through the mud of naked group ego to grasp onto the public monies and resources.

P.S. Of course I care more about British deaths than Iraqi deaths. I have a lot more in common with British people than Iraqi people, and one of my co-bloggers is British. Personal interests matter a great deal, even for the pathologically narcissistic.

1 - I measure concern by the time expended and elevated physiological response that a given situation or information elicits in me. For example, a few years ago I had a roommate who had a really bad case of the flu, and frankly, this elicited in me a far stronger emotional response of concern than the killings of tens of thousands that were simulteanously going on in the Ivory Coast. Now, if millions were being killed in the Ivory Coast, I think the concern would have matched that of my friend with the flu, so I figure 1 million Ivorians = 1 close friend.

Engineer Atta   posted by Razib @ 7/13/2005 10:20:00 PM

From Perfect Soldiers:

[page 15-16]
...It's hard to overemphasize the respect accorded to engineers in much of the Middle East...Within the engineering department, the highest-scoring students were assigned to the architecture program...for the first time in his life, Amir [Mohammed Atta] did not excel. Architecture, more than most creative disciplines, is a blend of the utterly pragmatic-what type of glass do you specify to keep heat out and let light in?-and the artistic-in what vocabulary should a house speak? Amir shone at the analytical subjects....

"He was a very clever person in mathematics, physical structures, less good in design and the more artistic aspects...In the third year, when we studied soils, street plans, and steel, something more concrete, he would recognize him more as an engineer than an architect....
[page 5]
"The jihad for God's cause is hard for the infidels, because our religion has ordered us to cut their throats and that we kill their heirs is a hard thing...God the merciful has created the hell for the infidels as he created the paradise for the believers....
[page 33]
...He did what he was told and did it...with extraordinary single-mindedness. Although already a trained architect and a prospective city planner, Amir-in four years at the company-never once offerred an opinion of the plans he was asked to illustrated. He was assigned to make maps; he made maps.
I have spoken before of norms of reaction, that is, the differential expression of phenotype given the same genotype in a variety of "environments." More later....

Tuesday, July 12, 2005

Do you believe it?   posted by Razib @ 7/12/2005 01:30:00 AM

That additive genetic variance1 can increase after a founder event because various alleles can fix onto the genetic background and subtract epistatic effects which would normally cancel out? This is important since response to selection ~ additive genetic variance * selection coefficient. Researcher dissents/critiques welcome.

Update: Consider epistatic effects which cancel out over the genetic background because the deviation is sometimes positive and negative (Fisher would be proud). A founder event could move some loci to fixation, which frees up some of the other loci2 to work their additive variational magic. A rugged and fitness constrained landscape is now transformed into a clean and conical Fisherian geometry. Do you think this sort of process is evolutionarily relevant?

1 - The variance crucial for microevolutionary process, as in the breeder's equation.

2 - Which were previously hooked into pairwise fitness deviating epistatic interactions.

Sunday, July 10, 2005

Islamic Terrorists Recruiting At British Universities   posted by Razib @ 7/10/2005 03:09:00 PM

Over at ParaPundit.

From dossier 2:

...The ICM poll published in the Guardien on 15 March 2004 recorded 13% of British Muslims as thinking that further terrorist attacks on the USA would be justified.

...a minority of Muslims defend terrorism (up to 13%). A minority do not feel loyal to Britain (up to 26%)....

...By and large most young extremists fall into one of two groups: well educated undergraduates or with degrees and technical professional qualifications in engineering or IT; or under-achievers with few or no qualifications, and often a criminal background....

From dossier 3: Muslims were far more likely than young Christians to regard religon as important to their self-identity (74% against 18%). The figures for young Sikhs and Hindus were also Hind (63% and 62%)....

From dossier 4:

...Active citizenship: Participation of Muslims is around three quarters the rate of all faith communities as a whole. Young Muslims are least likely to participate, compared with all faith groups. Muslims are least likely of all faith groups to engage in volunteering....


Religion-Unemployed-Economically active-Economically inactive

No religion-6.1-75.2-24.8


Whether Muslims need to integrate

Date of poll-Yes-About right-No-Other

Guardian ICM June 2002-41-33-17-9
Guardian ICM June 2004-33-28-26-13

These numbers don't look pretty. I don't see any grounds for complacency. 1 in 10 British Muslims are hostile to the idea of Albion, to the nation of Albion. This is far more concerning than the lack of civic participation or relative economic lack of performance, but there isn't even that upside.

Update: I found it:

Al Qaeda’s members are not the Palestinian fourteen-year- olds we see on the news, but join the jihad at the average age of 26. Three-quarters were professionals or semi- professionals. They are engineers, architects, and civil engineers, mostly scientists. Very few humanities are represented, and quite surprisingly very few had any background in religion. The natural sciences predominate. Bin Laden himself is a civil engineer, Zawahiri is a physician, Mohammed Atta was, of course, an architect; and a few members are military, such as Mohammed Ibrahim Makawi, who is supposedly the head of the military committee.

Look, I come from a family predominantly (in the last 2 generations) of scientists, doctors and engineers. I love science and admire engineering. But this is just the plain truth, and it doesn't surprise me, I've run into way too many dumb-ass science people when it comes to politics and religion, and have experienced bizarro jeremiads from Muslim engineers.

P.S.: For the atheists and secularists out there, perhaps we should reconsider the large scale movement of peoples who have a pre-gelded view of their religious duties into the post-Christian West.

Beyond languagese   posted by Razib @ 7/10/2005 12:46:00 PM

I am not one of those individuals who thinks that language absolutely frames out thought processes, that we can't escape it and that it determines our very perception of reality.1 But, language can confuse, which is why I demand some level of semantic precision from people who participate in discussions on this weblog. Nevertheless, sometimes language is something that simply has to be taken for what it is, and the awkwardness it causes can not be avoided.

One area where this is important is that of historical linguistics, because the terms are often confusing and there is no overall system for nomenclature, at least for older terms that are still central to the discourse (say like in organic chemistry). For example, the names of some branches of the Indo-European languages have strong geographical connotations. "Iranian" speakers live in Iran (roughly speaking, the historical Persia) and Indo-Aryan speakers reside in the Indian subcontinent. But these appellations cause problems when one speaks of the ancient Scythians, who ranged on the Black Sea Steppe, or their successors, the Sarmatians, who eventually settled upon Hungarian plains. Both are often classified as "Iranian" because of the features of their language. But the term elicits in the mind of the target audience outside of linguistics the geographical term, so many assume that the Scythians and Sarmatians swept out of Persia via the Central Asian steppe or up through the trans-Caucasian plains. An even more vexing issue is that of "Indo"-Aryans. Several decades ago an Indo-Aryan group was found to have settled in the kingdom of the Mitanni, roughly the upper regions of the Euphrates now within the borders of Syria. There were terms within the predominantly Hurrian language of the Mitanni, which was non-Indo-European (and not Semitic either, it was one of the many hard-to-classify languages which existed prior to the recent expansion of both the aforementioned language groups), which were clearly Indo-Aryan. For example the number terms that defined the laps a chariot made were derived from Indo-Aryan numbers. Additionally the gods sometimes referred to within the treaties were Indo-Aryan. The key point is that the linguistic clues suggested an Indo-Aryan association, not an Iranian one. When you explain this to a lay audience often the first response is that someone how a group of Aryans traversed Persia from their homeland in the upper Indus valley and settled in Syria. But there are problems with this hypothesis, because the linguistic fragments show no evidence of familiarity with terms that are distinctive to Indo-Aryan due to the encountering of objects and creatures local to India. To top it off, the Mitanni dialect exhibits archaisms that suggest it predates the Sanskrit variant of Indo-Aryan found in the Rig Veda. This is plausible since the Mitanni tablets date from 1600-1500 BCE, and at this point the Indo-Aryan dialect was likely used for ritual or formalistic purposes and so preserved a more ancient manner of speech.2 The Rig Veda was certainly fixed after 1500 BCE, though before 1000 BCE, and its language was a living tongue which was still evolving.

The "solution" to this mystery is rather simple, it seems likely that both the Iranian and Indian Aryans derived from what is termed the Andronovo Cultural Complex, which existed in the late Bronze Age around the Caspian steppe and further east into northern Central Asia. When the original Indo-Iranians dispersed from this region it is likely that they spread out in multiple directions, and there was already some differentiation between the "Indo"-Aryan and Iranian tribes prior to this dispersal.3 Some of the Indo-Aryan groups settled in India, and gave rise to the languages spoke by 3/4 of modern Indians. Others seem to have become absorbed into the milieu of the Middle Eastern cultures, disappearing from history. The Iranian speaking groups eventually dominated the Persia plateau as well as the Central Asian river valleys, but, some of them also migrated to the steppes to the north of the Black Sea and further west. Because linguistic distributions are a palimpsest these patterns and migrations have been obscured by the spread of Turkic languages in Central Asia (with Tajik and a few other Iranian languages as holdouts), breaking the continuity between the southern and northwestern Iranian tongues (Ossetian is a relict in the Caucasus of the western Iranian dialects). The extinction of all Indo-Aryan dialects outside of India also has resulted in the fact that that clade of the Indo-European languages is modified by the term Indo, when prior to the historical period its distribution was possibly far less geographically constrained.4

The same caution extends to many terms which have geographical origins, the classification of "Italic," Latin and its derivates + all the Indo-European non-Latin languages (Umbrian, Oscan, etc.). Or "Iberian" for the extinct language of the Tartessians of southern Spain, which might have a relationship with other dead languages of Western Europe or North Africa.

I have placed a small map for illustrative purposes below the fold.

1 - Philosophically this was a view espoused to some extent by the later Wittgenstein and championed today by many "Post-Modernists." I believe that modern cognitive science has falsified this view.

2 - The preservation of Mitanni Indo-Aryans terms relating to horsemanship is not surprising since it is hypothesized that Indo-Europeans introduced many elements of horse culture into the Middle East. As a point of comparison, Latin was preserved in Byzantine culture the longest in the military and the legal profession, two areas where Western Roman culture could compete with the Greeks.

3 - This idea of pre-dispersal differences and identities for various groups is a neat solution to why the Tocharians, the Indo-Europeans who settled along the northern rim of the Tarim basin in modern Turkestan (it seems likely that the southern rim of the basin had an Indo-Iranian population) are classed with the "western" centum clades of Indo-European, Celtic, Italic and Germanic, as opposed to the "eastern" satem groups, Greek, Armenian, Balto-Slavic and Indo-Iranian. Though some scholars dispute the salience of the
centum-satem distinction, other points of evidence do suggest that there was an association of the pre-Tocharian tribes with groups that later founded the western branches of the Indo-European language family (in particular the Celtic branch). This association likely occurred in the Proto-Indo-European homeland, possibly the grasslands of southeastern Europe and north-central Asia.

4 - One model holds that in fact the Persian plateau was dominated by Indo-Aryans, and the Iranians were latecomers who divided the continuity of Indo-Aryan groups which settled in India, Persia and the Middle East. It is interesting to note that the archaic Indo-Iranian languages, Sanskrit and Avestan, tend to exhibit an inversion of some terms, for example Indo-Aryan daeva has positive divine associations, but in Iranian it is a negative term (hence, devil). The same inversion is found in the term asura, a race of anti-gods in Indian mythos, but on the side of the good God in Iranian tradition.

The Flynn Effect: Flynn, Lynn… or Vernon?   posted by DavidB @ 7/10/2005 03:06:00 AM

The ‘Flynn Effect’ is the name generally given to the long-term trend for average scores on IQ tests to increase. Recently some writers have begun to refer instead to the ‘Lynn-Flynn Effect’. So is this new usage desirable?

To recap a little history, in 1984 James R. Flynn, a New Zealand political scientist, published a long paper [1] showing that there had been large increases in mean IQ scores in the USA between 1932 and 1978. In 1987 he published a further major paper [2] showing that the same trend could be observed in more than a dozen other developed countries. These two papers have stimulated a great deal of research and discussion, including at least one book [3].

In 1994 Herrnstein and Murray’s The Bell Curve [4] discussed the rising trend in IQ and said as follows: ‘We call it “the Flynn Effect” because of psychologist [sic] James Flynn’s pivotal role in focussing attention on it, but the phenomenon itself was noticed in the 1930s when testers began to notice that IQ scores often rose with every successive year after a test was first standardised’. Herrnstein and Murray’s term ‘the Flynn Effect’ has been generally adopted, for example by Arthur Jensen [5], who says ‘This upward trend in the population’s mean test scores has been aptly dubbed the “Flynn Effect”.’

So where does Lynn come in?

Richard Lynn of the University of Ulster is one of many psychologists who have worked on the Flynn Effect since Flynn’s original paper, but those who refer to the ‘Lynn-Flynn’ Effect evidently mean more than this. The first reference I have seen to ‘Lynn-Flynn’ is in a paper of 1999 by J. P. Rushton [6], where he says ‘The rise in IQ phenomenon might be better named the “Lynn-Flynn effect” because it was actually the Lynn (1982) paper in Nature that first identified the trend in recent times (among the Japanese)’. Rushton says that he had made the same suggestion in a book review in 1997. Rushton’s suggestion does not seem to have been widely followed by other psychologists ( I got no hits for the search phrase ‘Lynn-Flynn’ on Google Scholar), but it has been picked up by some internet commentators. For example, Steve Sailer said in August 2004 that ‘This phenomenon was first noticed in the 1940s, but Lynn was one of the first researchers to call lasting attention to it. Later, New Zealand political scientist James Flynn did important work on the subject. It is now usually called the Lynn-Flynn Effect or simply (and somewhat unfairly to Lynn) the Flynn Effect'. The clear implication here, as in Rushton’s paper, is that Lynn identified the ‘effect’ before Flynn.

Lynn’s own website list of his publications includes only two papers before 1984. The one Rushton refers to is a paper of 1982 in Nature. Curiously, the publication details for this paper on Lynn’s website are actually those of a later discussion [7]: I give the correct details for the paper itself below [8]. I have read Lynn’s 1982 paper and in my view it is far from justifying the claim that Lynn anticipates Flynn. As its title suggests, the purpose of Lynn’s paper is to show that IQ has increased in Japan relative to the USA. It compares Japanese IQ scores with American scores on the same tests, shows that the gap between them has increased by about 7 points, and concludes that ‘over the course of a generation the mean IQ in Japan has risen by ~7 IQ points’. This implies that American IQ was static over the same period. Lynn goes on to suggest that improved health and nutrition in Japan may be responsible. But this is only one of many ad hoc observations about rising IQ which have been made sporadically since the 1930s. There is nothing in Lynn’s paper to suggest awareness of a large, widespread, long-term trend, which is the key point of the Flynn Effect. Indeed, it suggests the contrary, because if Lynn had been aware of such a general trend his paper would surely have taken account of it. Notably, he would have had to consider the likelihood that IQ had risen in the USA, and not just in Japan, between the dates of the various tests. Flynn himself commented on Lynn’s paper and gave evidence of rising IQ in the USA in a letter to Nature in 1983 [9]. In his reply [7] Lynn described Flynn’s claim of rising American IQ as ‘more contentious’, and only grudgingly accepted it. Any suggestion that Lynn anticipated the Flynn Effect as we now understand it - a trend found throughout the developed world - can therefore be dismissed.

So unless anyone can produce better evidence for Lynn’s priority, I see no good reason to change the established terminology of the ‘Flynn Effect’. But even if we were to accept Lynn’s work on Japan as a full recognition of the Flynn Effect, before conceding priority to Lynn it would be necessary to show that Lynn’s 1982 paper preceded Flynn. This might seem obvious: 1982 precedes 1984. But this assumes that Flynn’s famous paper of 1984 was his first work on the subject. This is not the case. As already mentioned, Flynn commented on the subject in 1983. This is still after Lynn’s paper. But Flynn’s letter also says that ‘the evidence for American IQ gains has been published in detail elsewhere’, and gives a reference to a paper of his own in the Bulletin of the British Psychological Society for 1982 [10]. I have not seen this paper (the journal is not as widely available as the British Journal of Psychology), but I see no reason to doubt Flynn’s description. Barring the minutiae of publication dates within the same year, the papers of Lynn and Flynn were effectively simultaneous, and the claim that Lynn anticipated Flynn collapses.

But if we must hunt for ‘anticipators’ of Flynn, there is a better candidate than Lynn. In 1979 Philip E. Vernon, a distinguished British psychologist, who had been studying IQ since the 1940s, wrote that ‘A similar increase [to the widespread long-term increase in body height] has undoubtedly taken place in intelligence… There is good reason to believe that the average intelligence of the human race will continue to rise as education improves in underdeveloped countries; and that, even in western countries, further gains may occur…’ [11, p. 207] This statement is both earlier and more general than Lynn’s 1982 remarks, so if there is to be any change in usage I would suggest the ‘Flynn-Vernon’ effect as a more appropriate term. But it remains true, as Herrnstein and Murray put it, that Flynn was ‘pivotal’ in drawing attention to the phenomenon, and it was Flynn who did most of the work necessary to document it. I therefore think that the ‘Flynn Effect’ is still the best designation.

There is one proviso. Lynn is well known for the hypothesis that improved nutrition, especially in early childhood, is the main reason for the rising trend of IQ scores, not least because the phenomenon is found in quite young children, before schooling can have affected it. If Lynn is ever proved right (which in my view is quite possible), then it would be appropriate for Lynn and Flynn to share the credit for the ‘effect’: Flynn for identifying the trend, and Lynn for identifying its cause.

David B

[1] James R. Flynn (1984): The mean IQ of Americans: massive gains 1932 to 1978. Psychological Bulletin, 95, 29-51.
[2] James R. Flynn (1987): Massive gains in 14 nations: what IQ tests really measure. Psychological Bulletin, 101, 171-91.
[3} Ulric Neisser (ed.) (1998): The Rising Curve.
[4] R. Herrnstein and C. Murray (1994): The Bell Curve.
[5] Arthur Jensen (1998): The g Factor.
[6] J. P. Rushton (1999): ‘Secular gains in IQ (etc)’, Personality and Individual Differences, 26, 381-9.
[7] IQ in Japan and the United States: ‘Matters arising’, Nature (1983), 306, 291-2.
[8] Richard Lynn (1982): ‘IQ in Japan and the United States shows a growing disparity’, Nature, 297, 222-3.
[9] James R. Flynn (1983): ‘Now the great augmentation of the American IQ’, Nature, 301, 655.
[10] James R. Flynn (1982): Bulletin of the British Psychological Society, 35, 411.
[11] Philip E. Vernon (1979): Intelligence: Heredity and Environment.

Saturday, July 09, 2005

Deepest Syria....   posted by Razib @ 7/09/2005 08:24:00 PM

The Enigma of Damascus is a long piece in The New York Times Magazine on the regime of Bashar al-Assad. They probably did a little bit of Photoshopping, but this image of Assad and his British-born (Syrian ethnicity) wife makes them look pretty Western, and Asma Assad's tousled "honey colored" hair and slightly parted lips with a come hither glance seems aimed at the Babes of Lebanon crowd (this picture suggests that she's a somewhat less attractive version of Mary Kay Letourneau) .

I have talked about Syria now and then partly because I've long had an interest in the sects that dot the Middle East, from explicitly non-Muslim ones like the Yazidis of Kurdistan to splinter Islamic groups like the Alawites (Assad's group). It is a peculiarity that the profusion of Muslim sects blossoms near the heart of the Dar-al-Islam,1 though many of these groups have survived in the face of persecution on the part of the Sunni orthodoxy through dissimulation and retreat to isolated locales. The Alawites come out of a somewhat murky milieu on the traditional borders between Byzantium and the Caliphate where Christians of various sects and heretical Muslims took refuge and synthesized disparate traditions (after the Turkic conquest of Anatolia the focus of power was still in the west of the peninsula, leaving heterodoxy space to the east). Because of the tradition of dissimulation whereby one hides one's truth beliefs there is difficulty in pinning down what exactly the Alawites believe (you will see a great deal of variance in the source materials), but it seems plausible that if you tallied "characters" and constructed a cladogram it would be difficult to place them unambiguously in either the Christian or Muslim clade. Though within the past few years they have become identified as Shia Muslims, usually this is seen as a politically expedient catchall for non-Sunnis (I think Mormon:Christian is a good analogy for Alawite:Muslim). Across the border in Turkey as many as one out of five individuals are "Alevi," which is the Turkic form of the Alawite sect. Again, because of dissimulation Turkey is generally reported as a 99% Sunni nation when in fact there is a large religious minority which is hostile to Sunni orthodoxy (thanks to centuries of persecution and libels by Ottoman authorities). And just like the Alawites in Syria the Alevis in Turkey tend to support the secular regime because of their past history of persecution at the hands of religious Sunnis. In an interesting historical point, the religiously ambiguous milieu of eastern Anatolia was the source of the Sufi movement which catapulted the young Shah Ismail to the conquest of Iran in the 16th century. Once the nation was under his control Ismail and his successors converted the whole region to Twelver Shiism, which in recent years has become the ideological bedrock on which the Islamic regime of Iran rests. So, it is I think somewhat ironical that the distant cousins of the Alawites, who in many ways enforce the mostly religiously liberal of the Arab regimes, were historically crucial in the foundation of a Twelver Shia culture in Iran which serves as the inspiration for a narrow Islamic state. My point in fleshing out these obscure details is that I worry that such nuance, which I think is important, will be lost in the next few years as Syria becomes our possible next target. Iraqi Christians flee to Syria precisely because the Alawites, though "Muslims," are less likely to be hostile because of the traditional similarities between the two groups. From the article:

French were debating how to carve up their League of Nations mandate in the region, a group of Alawite notables urged that their northern mountainous redoubt not be annexed to Syria, which would surely be dominated by Muslims. "The spirit of hatred and fanaticism imbedded in the hearts of the Arab Muslims against everything that is non-Muslim has been perpetually nurtured by the Islamic religion,"....

Such facts are intelligible only against the religiously complex background of the Syrian borderlands, where the line between kufir and believer was more obscure and subjective than elsewhere.

Finally, I would like to add one observation about democratization in the Middle East. Over the past few months I have been reading a fair amount of European national histories, because sometimes I feel there are holes in my knowledge base. So far I have read about England and Scandinavia. What strikes me is the gradual nature of democratization in these nations. The "Left" tended to shift from conservative Whigs, to classically liberal "National Liberals" or Liberals, finally to the culmination of Social Democracy with the attainment of universal suffrage. Those who argue for the democratization of Arab states should keep in mind that here you have a situation where you are shifting from extreme despotism to universal suffrage in a matter of years. Say what you will about the dysfunctions of Arab culture, and they are manifold, but I am skeptical that any culture is robust enough to make such a sharp political transition with grace. I think it is clear that in the Most Perfect World Assad and his wife (who is a Sunni by background) would like Syria to be a liberal democracy, but I also suspect that if suffrage were to become universal tomorrow the Christians of Iraq who have resettled in Damascus would flee to Lebanon at the first opportunity, and the Alawites and other sects would join them. There are all too many Sunnis who yearn to breathe that they can blot out the kufir from their lives.2

1 - The further you move west (past the Suez) or east (past Pakistan) the higher the frequency of Sunni Muslims. I think in Asia this might be a function of the fact that there are still many non-Muslim groups so that there hasn't been the emergence of a frankly quasi-Muslim identity which religious minorities can take refuge in in the face of persecution from the Islamic majority (even in Iran the Bahai drew their support in part from Zoroastrian converts, and initially that religion perceived itself as a reformist Twelver Shiism). The case of the Maghreb is harder to explain because there is a long history of heterodoxy in that region of the world, and its uniform Sunnism is a relatively new development.

2 - And I do not deny that some of their resentment is richly justified, just as I believe the fears of the Alawites and Christians based on historical precedent are also justified. These are not black and white issues and none of the choices is wholly satisfactory, rather, they dictated by one's priority of principles.

Prigs who like 6th grade math   posted by Razib @ 7/09/2005 07:17:00 PM

Over the past few days I've been commenting a lot over at ParaPundit and Sepia Mutiny. I have been a bit of a pest, but I've really started to agitate for more "6th grade math"1 in public policy discussions. Over at Sepia some individuals seem to live in terror of hate crimes because of Islamist bombings. As someone who has spent their whole life in regions where the lowbound frequency of whites is 90%, and more often 99%, I really don't see a Rosewood happening anytime in the near future. In contrast, over at Randall's blog I've made myself a thorn in the side of some by demanding precise numbers for various assertions (I usually know the numbers beforehand and am aware that it would take 15-30 seconds to cough them up using google or wikipedia). In general I tend to agree with Randall's readers on many points...but I get irritateted by the tendency to couch observations impressionistically, and also engage in hyperbole for effect. As far as I'm concerned, this only undermines your case and adds distortion into models that might have utility for public policy. For a specific example, one reader asserted "and reliable projections point to an actual non-White majority by mid-century." Using the UK Census site I back-of-the-enveloped that the absolute number of whites in Great Britain would have to drop by 20 million individuals in 2 generations, assuming the relatively high rate of immigration and non-native total fertility rate remaining constant, for this contention to be defensible. Why is this relevant? After Randy posted his piece debunking the more extreme claims about the Islamicization of France many liberals were jubilant, as far as they were concerned there was no problem to worry about because Randy's analysis had thrown cold water on the more dire demographic "projections."2 I think such a response is wrong-headed and premature, but in the current climate of hyperbole and imprecise formulation of hypotheses, it is entirely all too easy.3

PS: Being a negative pest is a lot easier than putting forward a positive model. I'll put up in the near future....

1 - Steve has generated a large body of work that basically applies arithmetical principles to polling data. It's ludicrous that mainstream journalists can't remember the math they were supposed to learn in 6th grade for the life of them when their "sources" feed them garbage, but that's the way of the world.

2 - Projections are in quotes because they were usually verbal assertions. Sometimes a number would be thrown in for effect, "4,000 Frenchmen are converting to Islam per year," but totally without context and often with little relevance.

3 - Randall points out that a proportion of Muslims on the order of 10-20% of a electorate has consequences. I think the 10-20% is far more plausible than a Muslim majority. This number is something you can use when you look at other nations as "case studies" (India and Singapore are two nations in this range). Unfortunately, I do not see this sort of precision most of the time.

Roman skepticism   posted by Razib @ 7/09/2005 02:03:00 PM

It seems a Cardinal of the Roman Catholic Church has been reading Intelligent Design talking points. This has many individuals worried, both Catholic and non-Catholic, as the Church's general stance in favor of common descent has been a valuable arrow in the arsenal of those who wish to move beyond the conception that evolutionary theory, broadly speaking, excludes theism.1 For me the key point to hone in on is that the Cardinal states that evolution is purely a process of "of random variation and natural selection." The emphasis on the perceived "random" aspect of evolutionary theory is something that many critics like to linger upon because it is a clear philosophical wedge that can be used to peel away theists who believe in a personal Creator. But it is a philosophical issue in the end, and I am confident that Roman Catholic theologians can uphold the Kantian division between the two realms (the means are irrelevant to me as I am not a believer, I have faith in Jesuitical cleverness). An important point to remember though is that natural selection is not random, and I suspect that Stephen Jay Gould's quip that if you rewound the clock of life and allowed evolution to proceed once more that the diversity of the world would flower in a wholly unrecognizable form is probably a minority view among evolutionary biologists.2 Certainly there would be significant differences, but the convergent evolution of similar body forms among various groups of animals tells us that there are canals of development and adaptation strewn across nature's palette (though to be frank, I do not believe that intelligence and sentience is one of those inevitable canals3).

Related: Benedict XVI and evolution.

1 - The Cardinal does not reject common descent.

2 - Orthodox Neo-Darwinians will likely grant that selection leaves the mark of adaptations that seem "designed" for a particular function. The key point though is that once you scratch beyond the surface and examine the evidence of sub-optimality and developmental constraint due to phylogenetic history it is more difficult to hold to the assertion that the Most Perfect Creation implies a Most Perfect Creator.

3 - See Life's Solution : Inevitable Humans in a Lonely Universe by the paleontologist (and theist) Simon Conway Morris for an alternative viewpoint.

Friday, July 08, 2005

Through the rugged roads of gene land   posted by Razib @ 7/08/2005 10:51:00 PM

Several years back David wrote about Sewall Wright's Shifting Balance Theory. If you know much about the history of mathematical genetics you know that R.A. Fisher and Wright's disputes over the importance of population substructure, genetic drift and the adaptive landscape was a simmering pot looming in the background of the emergence of the Modern Synthesis. One of the points that Fisher and Wright clashed over was the relative evolutionary importance of epistasis. I want to emphasize the evolutionary importance, because of course R.A. Fisher did not reject mechanistic epistasis as a background feature of a specie's genetic architecture, rather he was skeptical of its relevance as a driver of evolution. It was the average effect of a single allele against a genetic background which resulted in phenotypic adaptation according to Fisher. Each beneficial mutation would be driven by directional selection toward fixation, while the vast majority of mutations would be purified from the genetic background. In contrast, Wright conceived of an evolutionary landscape where epistatic interactions across loci would result in isolated adaptive peaks cordoned off by depressed regions of reduced fitness. This pluralistic scenario would result in balancing selection that would maintain more variation within the genetic background than in Fisher's model. Then in the late 1960s the Lewontin and Hubby papers reported such high levels of allozyme polymorphism that both the "Classical" (Fisher) and "Balancing" (Wright) schools of the Modern Synthesis were sent scrambling.1 The elucidation of The Neutral Theory of gene substitution by Mootoo Kimura explained away the relative lack of fixation on the molecular level, heterozygosity and polymorphism were simply the transitory states of the dynamic system where neutral alleles were progressively substituted for each other by random walk genetic forces. Nevertheless, after reading Speciation my mind wandered back to the possibilities inherent in epistasis, coadapted gene complexes, supergenes and all the assorted detritus that remains after you remove Fisher's additive genetic effects.

With my questions in hand I decided to dive into Epistasis and the Evolutionary Process, an anthology of recent research on the issue of epistasis and its relationship to evolution.2 My first hurlde was that I had to move beyond my reflexive mechanistic/molecular view of epistasis. To me, epistasis, the interaction between two or more loci on the genome, was always accompanied by an image of molecular products entering into scripted regulatory dances with each other. This is of course ubiquitious in eukaryotic organisms, interlocking cascades of regulation and the precipitous acceleration of combinatorical possibility explains how manifold complexity can emerge from a relatively small number of genes. It was peculiar for me to realize that epistasis on a population genetic level can occur between loci in different individuals when fitness is the dependent variable. Consider maternal effects, an interaction the between genotype of the mother and the genotype of the offspring which shapes the final offspring phenotype, mediated by the uterine environment. Or the variation in fitness of individuals in disparate social groups of conspecifics. The point is that epistasis means many things, and unmodified it is lacking in precision (please note that there is obviously overlap with norm of reaction if other genes are considered the "environment" in which a given gene expresses a phenotype).

The first two chapters of Epistasis and the Evolutionary Process are a rough and ready introduction to the paradigm that the researchers who contributed the 16 chapters of the book are working within. Obviously they think epistasis is important in evolutionary genetics, but, they do not necessarily hew to the view that the Shifting Balance is the most accurate model in which epistatic processes are necessarily relevant. Though the book is filled with equations there is repeated reference to one particular evocative graphical metaphor, that of the wrinkled and rugged surface of the adaptive landscape. Geometrically speaking, at any given time, the Fisherian landscape is conceived of as a constant slope. Contrastingly the epistatic landscape is characterized by relatively flat "canals" and arcs that represent the nonlinear fitness and phenotypic effects that are the hallmark of epistasis (though over a small enough area curved epistatic surfaces can become flat additive ones!). More plainly an adaptive landscape characterize by widespread epistatic effects would be rugged, while that characterized by staid additive effects would be gently sloping. With this visual metaphor the smorgasbord of dancing definitions floats before your eyes, mechanistic epistasis is the direct interaction of genetic products across loci, statistical epistasis is what remains after additive, dominance and environmental variation are accounted for, additive genetic mechanisms can have epistatic statistical effects, while epistatic genetic mechanisms can have additive statistical effects!

I have read most of the chapters (after chapter 2 you can skip around due to tightly constrained topicality as opposed to sequential contingency), but I want to simply introduce a few definitions and get to the "epistatic explanation of sex."

Here is the list of "terms" from chapter 2 (Table B2.1):3

For deleterious mutations:
Synergistic - Negative fitness deviation, double mutant less fit than predicted by additive effects of single mutants.
Diminishing returns - Positive fitness deviation, double mutant more fit than predicated by additive effects of single mutants, but still less fit than a single mutant.
Compensatory - Positve fitness deviation, double mutant more fit than single mutant, less fit than wild type.
Supercompensatory - Positve fitness deviation, double mutant more fit than wild type.

For advantageous mutations (these mutations increase the s):
Synergistic - Positive fitness deviation, double mutant more fit than predicted by additive effects.
Diminishing returns - Negative fitness deviation, double mutant less fit than predicted by additive effects, but still more fit than a single mutant.
Decompensatory - Negative fitness deviation, double mutant less fit than single mutant.

(please plug in various s values into the equation listed in notation 3 to get a more intuitive feel if the jumble above is confusing)

For synthetic mutations, where one allele masks the other:
Synthetic deleterious - Negative fitness deviation, double mutant less fit than single mutant and wild type (both the latter are equal fitness).
Synthetic advantageous - Positive fitness deviation, double mutant more fit than single mutant and wild type (both the latter are equal fitness).

Obviously this alphabet soup of definitions is not unrelated to other concepts in genetics. "Synthetic" mutations induce dominant or recessive phenotypes, depending on what vantage point you approach from. Additionally, keep in mind that one locus may have various epistatic interactions with numerous other loci, so in one context it might increase fitness, and another context decrease fitness, depending on what other alleles are present. The authors argue in fact that this variance of epistasis implies that geneticists must look "beyond the average" of the genetic background (a la Fisher) because the mean effect of a locus in reference to epistatic interactions obscures context dependent information (the mean epistatic effect might be a deviation of zero, but if there is a great deal of variance in that deviation over time, space and individuals, that is clearly relevant).

Since I am a bit overlong at this point I wish to hit a few quick points and gloss over the important connection (possibly) between negative epistasis and sex (particularly recombination). First, in reference to mutational load some analytic models imply that low epistatic variance combined with synergistic epistasis can purge mutations. Others in reference to Muller's Ratchet imply that synergistic epistasis can amplify deleterious effects (so allowing selection to purge the mutation and halt possible substitution). Additionally, variance of epistatic effects and the flipping of the sign of deviation can switch double mutants into a net positive (Synergistic → Supercompensatory). And of course epistasis can be crucial in the formation of coadapted gene complexes which throw up fitness valleys that eventually result in speciation.4

But, to sex. The basic idea is that mild negative epistasis builds up negative linkage disequilibrium (because extreme, that is double mutant, gene combinations are disfavored) which only recombination can break apart so as to generate variation which selection can work with (favorable, but extreme, genotypes are generated). Too much epistasis is problematic because the generation of less fit genotypes from recombination reducing linkage disequilibria can have too great a fitness short term fitness hit. Additionally, the variation of epistasis as a function of time can be incorporated into the "Red Queen" hypothesis put forward by William Hamilton, with a series of epistatic oscillations playing the starring role given to frequency dependence.

I will have more to say on various chapters later, though if you are curious about a "human payoff" I suggest chapter 3 by Alan Templeton. Some of the medically salient traits Templeton highlights are often discussed on the Epistasis Blog, I suggest you check it out.

Jason Wolf's website has several papers related to the topics above in PDF form.

1 - Though I admire Richard Dawkins I do feel that in some ways his fidelity to the rhetoric of Classical Selectionism is a bit much sometimes and his attempts to simply coopt Neutral Theory or Punctuated Equilibria by slight of verbal redefinition ("We believed that all along!") is a bit lame, though perhaps not as inexecusable as the more extreme pronouncements from Neutral Theory champions or S.J. Gould's initial "revolution" against "Ultra-Darwinianism" (and yes, flirtation with Saltationism).

2 - This book is searchable, and after the first two chapters all the others are rather stand alone, so, if something interests you it is entirely possible to read up on a topic without ponying up a red cent.

3 - The authors present a simple two-locus model for illustrative purposes. The fitness, Wab, of a double mutant haplotype is (1 + sa)*(1 + sb) + ε, where ε is the epistatic deviation and the s is the selection coefficient. Note also the "additive effects" are actually multiplicative, so that if the s for each mutation was 0.2, with no epistasis the fitness would be 0.64, 0.8*0.8.

4 - For the record, I tend to believe that allopatric speciation is the norm. I don't think alleles random walk in frequency through gene space and just "lock" at some point into a new complex and speciate sympatrically.

Polygyny in Britain...and Darwin in the service of Allah?   posted by Razib @ 7/08/2005 09:22:00 PM

This two part radio program surveys the state of polygyny (Muslim) in Britain (and to a lesser extent Pakistan). The show is broken up into a "positive" and "negative" segment. There is also a script you can read if you don't have a high speed connection. This to me was one of the most interesting assertions in light of the anti-evolutionism that seems prevelant among some Muslims:

AHR: Whatever view you take of orthodox neo-Darwinism, you have to recognise that it is always part of the survival strategy for ancient human communities to maximise the transmission of one's genetic material. And if a woman has many husbands, she doesn't produce any more children than she does if she chose just one husband. But if a man has a plurality of wives, then he can maximise the spread of his genetic material, and it's all very Darwinian and it actually does make sense as a strategy. And I do think that's the kind of default setting of the emotional make up of men and women, although of course there are many variations and it shouldn't really be regarded as an irrevocable norm. But I think that generally most of us are like that.

AHR = Abdal-Hakim Murad, I'm a bit surprised that a lecturer in Islamic Studies is familiar with Robert Trivers, but so be it.1 I only wish he would keep in mind the naturalistic fallacy.

1 - He distinguishes between microevolution and standard Neo-Darwinian "orthodoxy," but seems be a bit confused as to the general paradigm which currently does suggest that modern humans have a common ancestry.

Diamond days on TV....   posted by Razib @ 7/08/2005 07:21:00 PM

John Hawks notes that Guns, Germs and Steel is now turning into a PBS special. Looks like Diamond is making for a Sagan, trying to jump from being well know amongst the >1 standard deviation set to transitioning into a cultural icon. In any case, I echo many of John's concerns about GSS's thesis, the more we know about the arc of the development of past societies, the more we know we didn't know and don't know. Wish I could say otherwise....

Cross-talk on "Intelligent Design"   posted by Razib @ 7/08/2005 05:58:00 PM

One thing that came up in the survey of conservatives in The New Republic is the confusion over terms like "Intelligent Design." An acquaintance of mine who has a background in phylogenetics and molecular evolution subjected me to a long tirade on "Intelligent Design," in the midst of which I realized he was actually rebutting Youth Earth Creationism. Does this matter? On the first aproximation it didn't, because I tended to understand where he was coming from, but the truth of the matter is that very few biologists give much thought to irreducible complexity, let alone search algorithms. And the truth of it is that very few proponents of "Intelligent Design" care about these topics either.

"Intelligent design" is simply a verbal token which means different things to different people. Theorists within this narrow and marginal field themselves are not in total agreemant. William Dembski focuses on "No Free Lunch Theorems" while Michael Behe highlights "irreducible complexity" (basically taking the "how could the eye couldn't evolve argument" to the molecular and cytological level). Ultimately these thinkers are waging a battle against what Phillip Johnson terms "methodological naturalism," a stance toward science generally accepted by the majority of practioners within the field which was defined and elucidated at Wheaton, America's premier Christian evangelical institution. Add to this the clear reality that men like Dembski are motivated in large part by what seems religious, as much as scientific considerations, and you get a situation where there are multiple meanings ascribed to "Intelligent Design" from various antagonists in the debate.

So here I will reiterate what I think "Intelligent Design," or its predecessor, "Creationism," is all about. Many lay persons of faith seem to posit a dichotomy between Intelligent Design and evolutionary theory, and assume that Intelligent Design is wholly coterminus with religion. There is, therefore, a knee-jerk tendency to be "open" to "alternatives" (roughly speaking, Intelligent Design alternatives, not Native American Creation myths) because of the identification of Intelligent Design with religion. But, I think the identification only holds for a particular conception of religion. The fact that a Catholic theologian can thoroughly reject Intelligent Design should be a clue to this reality. I hold that Intelligent Design is an outgrowth of a particular trend in Protestantism which seeks to sanctify every aspect of human life, to suffuse it with religious meaning and intent, in a very direct manner. This mode of thought is not limited to religious movements that come out of the Protestant Reformation, one reason Intelligent Design is so popular with Islamic thinkers is that (as we all know) there are strong movements within the Muslim community which seek to regulate all of human existence. Similarly, Hindu thinkers who come out of the fundamentalist-modernist mold, that is, a reconstructed Hinduism "purified" of post-Vedic accretions, attempt to glean evidence of nuclear technology in their own religious mythos. In a non-religious context Marxist scientists have also attempted "Communist science," toward the aim of absorbing all of human life into one materialist system of the world.

I am not saying that intellectual proponents of Intelligent Design believe they are doing any such thing, I am implying that the root cognitive impulse to make all aspects of life intelligible through a central system is what is at the heart of the new more high brow attacks on methodological naturalism (and yes, Daniel Dennett and to a far lesser extent Richard Dawkins do the same thing with "Darwinism"). Additionally, I am also making the case that the popular supporters of Intelligent Design do not understand this (the need to rationally systemetize all of life tends to be most urgent in the congitive elite of any given subculture, but that cognitive elite tends to wield influence far beyond its weight of numbers), rather, their support of the movement is based on a misconception of science as a bundle of facts with which they disagree (that is, a bundle of facts which nullify the God hypothesis) rather than a mode of gleaning information about the world and making it intelligible in prosaic natural models (a method which does falsify some God hypotheses,1 but is structurally unable to grapple with other God hypotheses and render any verdict).

1 - Some axiomatic God hypotheses are logically incoherent. Some empirical God hypotheses seem to be falsifiable (there are still people walking about who claim to be incarnations of God and give the impression that they have extraordinary powers).

Back to the past...or not?   posted by Razib @ 7/08/2005 04:50:00 PM

Rolling Stone has an interesting profile of hip young Christian evangelical virgins in Williamsburg (a trendy arty neighborhood across the river from the East Village). Seeing as how the writer works for Rolling Stone he has a hard time moving beyond the "freak show" mindset, and no doubt there are some misrepresentations going on here of the individuals profiled in the piece.

What struck me is the feeling that the "virgin rebels" who are to a great extent part and parcel of "mainstream" culture (rock music, all night raves, etc.) and simultaneously back-to-the-past rebels might be in specific ways a very new phenomenon which slots into a predictable pattern of generic responses to given circumstances. Let me be specific, one of the young Christians states on the record that "he has friends who had enjoyed anal sex and still call themselves virgins." Call me a freak, but in my circles getting shit-on-your-dick (sorry about being explicit, but I want to keep it real) is a step or two beyond normal intercourse. Something is seriously ass-backwards (sorry) when this is a preparatory act. As I said, the freak show aspect prevents the author of the article from exploring distinctions within the virgin rebel camp, after all, you have one expositor of purity lecturing on how to purge sexual thoughts from wet dreams, while many of the young twenty-somethings seem to have an anything-but-vaginal-intercourse philosophy. But, my impression is that anal sex as an alternative to vaginal intercourse is attested in Latin America and the Middle East, and other "traditional" cultures which put a premium on legalistic virginity. My personal interactions with Christian evangelical friends suggests to me that the example of sodomy-as-the-lesser-sin is a symptom of a problem that crops in personalized evangelical practice in the United States.

I also think that contra the perception that these youth are going back to premodern virtuous norms, in many ways they are blazing into rather new social territory. My logic is that many of these virgins expect to be chaste deep into their twenties, or even further (if you are curious, A.C. Green finally lost his virginity). In many past soceities this is rather old not to be married, and my experience on a personal level is that many of my Mormon and evangelical friends married rather young, so "waiting" wasn't a test of years. Granted, in many societies late marriage (if ever) was normal for the lower orders of society because of the lack of resources to support young families. But these individuals often did not expect to spend years in pre-intercourse chastity in romantic relationships with others (any premarital coitus for women is likely to have been in exploitative circumstances).

Many "conservatives" often accuse the cultural Left of pushing social experiments that destabilize society, but though there is great truth in this, many of the responses of various strands of the evangelical counter-culture are also rather ahistorical exercises in taking principles to their logical conclusions. Rather than espousing chastity, I suspect a more humane and pragmatic course for advocates of traditional values would be to encourage early marriage. Of course, early marriage often leads to early divorce.1 Nature's God offers no easy solutions.

Addendum: Control-f "born-again virgin." I can give props to real virgins who have the fortitude to stick by their guns, but jack-asses who use the term "virgin" as a self-description after dipping their stick in the honey jar first really get on my nerves. Hey, I'm not a thief, I just stole a lot of stuff when I was younger! Sorry, I'm not a Christian, Jesus don't wash away some sins in my book.

1 - Though early divorce is not a problem in many religious Jewish communities...but the key here is community. The article notes the importance of group reinforcement of norms as being crucial to maintaining sexual purity, especially for males, but this is simply very difficult to keep up for long periods of time outside of a few subcultures in this nation.

GNXP update....   posted by Razib @ 7/08/2005 03:21:00 PM

I'm sure you are sick and tired of these technical notes. But, you are not wasting your time configuring blogware, so spare me. I am going to try out Blogger now, but I might switch to Word Press with caching plugins if this doesn't work out (already installed). Frankly, I'd use Word Press but I'm sick of wasting my time editing templates.

Thursday, July 07, 2005

Ancient finds in Saudi Arabia?   posted by Razib @ 7/07/2005 05:00:00 PM

Stone Age Artifacts, Carvings Discovered

The Ministry of Education announced yesterday discoveries showing the existence of Stone Age settlements in western and central Saudi Arabia. The discoveries near Wadi Fatimah in the Western Region and Wadi Saffaqah in the Central Region include stone carvings and other artifacts. According to a statement by the antiquities and museums department of the ministry, the findings are estimated to date back to 750,000 B.C.

I'm skeptical about the 750,000 B.C. date...but the important point is the possibility of "carvings" and what not, since it is considered indicative of "symbolic thinking." Another note is that in many ways western Arabia can be biogeographically considered part of Africa, and during interglacial optimums a great deal of African fauna, including homonids, likely pushed their way into the southern periphery of Eurasia. Finally, the fact that these finds are on the homeground of a Salafi-Wahhabi ideological state shows the schizophenria that modernity tends to elicit is ostentatiously 'traditional' soceities.

The New Republic's survey of conservative views on evolution   posted by Arcane @ 7/07/2005 03:27:00 PM

The New Republic has posted a fascinating informal survey of conservative opinion leader's views toward evolution. I was rather surprised to see that most, contrary to conventional left-of-center stereotypes about conservatives, believe in evolution, although how strongly they do varies pretty widely. The neoconservatives, such as Charles Krauthammer and David Brooks, are pretty pro-evolution, while the paleoconservatives, such as Pat Buchanan and Tucker Carlson (maybe it's unfair to label him a paleocon, but his beliefs are increasingly similar to those espoused by paleocons, possibly due to hanging out with Robert Novak a bit too much), are generally anti-evolution. Many of those who are generally supportive of evolution appear to be somewhat obsessed with "teaching both sides" in public schools, which leads some of them to lean towards some positions espoused by IDers. However, it appears that few understand the positions of the ID crowd, which is troublesome.

The main problem with this little survey is that it ignored various opinion leaders from the "Religious Right" wing of the Republican Party. Next time they should ignore hardcore paleocons like Buchanan and instead divert their energies to surveying the "Religious Right" instead, since most of the hardcore paleocons have abandoned the Republicans for the Constitution Party or various insane groupings (great link for information about minor parties) to the right of the GOP.

Since the article requires an account with The New Republic, I reproduce the article in its entirety on the extended entry.

Update from Razib: PZ Meyers has some harsh things to say, understood of course, since these are conservatives (haven't you seen their devil horns?). But...I wish more liberals would admit that many of them mouth off about evolution without knowing jack about the topic. Ignorance knows no politics....

Evolutionary War
by Ben Adler

Later this summer, the Kansas State Board of Education is widely expected to change its state science standards to cast doubt on evolution. The new standards will likely emphasize the unsolved problems in evolutionary theory's explanatory power, like gaps in the fossil record, that are the favorite hobbyhorses of creationists and advocates of "intelligent design." Intelligent design posits that certain biological mechanisms and the nature of DNA itself are too complex to have evolved--and therefore suggest the hand of an original designer. Advocates of intelligent design, including several of the witnesses who testified at the Kansas board's hearings that began in May, say that evolution and the origin of species are unsettled topics and that students should understand and debate different points of view. In the scientific community, however, the debate is one-sided. The 120,000-member American Association for the Advancement of Science (AAAS) passed a resolution in 2002 declaring intelligent design a "philosophical or theological concept" that should not be taught in science classes. Indeed, the AAAS boycotted the Kansas hearings to avoid conferring legitimacy on intelligent design proponents who testified.

Pressure to temper the teaching of evolution in public schools has come overwhelmingly from conservatives; the Kansas board's re-examination of its evolution standards resulted from Republican gains last November that put an anti-evolution conservative majority on the board. So we were curious: How do leading conservative thinkers and pundits feel about evolution and intelligent design? We asked them. Here's what they said.

A few notes about the interviews: All were conducted via phone except where otherwise noted. The interviews are not presented in a chronological question-and-answer format. Instead, we've grouped each person's thoughts on particular subjects into subcategories, which are identified in italics, splicing these statements together with ellipses where necessary. Those interviewed spoke only for themselves.

William Kristol, The Weekly Standard

Whether he personally believes in evolution: "I don't discuss personal opinions. ... I'm familiar with what's obviously true about it as well as what's problematic. ... I'm not a scientist. ... It's like me asking you whether you believe in the Big Bang."

How evolution should be taught in public schools: "I managed to have my children go through the Fairfax, Virginia schools without ever looking at one of their science textbooks."

Grover Norquist, Americans for Tax Reform

Whether he personally believes in evolution: "I've never understood how an eye evolves."

What he thinks of intelligent design: "Put me down for the intelligent design people."

How evolution should be taught in public schools: "The real problem here is that you shouldn't have government-run schools. ... Given that we have to spend all our time crushing the capital gains tax I don't have much time for this issue."

David Frum, American Enterprise Institute and National Review

Whether he personally believes in evolution: "I do believe in evolution."

What he thinks of intelligent design: "If intelligent design means that evolution occurs under some divine guidance, I believe that."

How evolution should be taught in public schools: "I don't believe that anything that offends nine-tenths of the American public should be taught in public schools. ... Christianity is the faith of nine-tenths of the American public. ... I don't believe that public schools should embark on teaching anything that offends Christian principle."

Stephen Moore, Free Enterprise Fund

Whether he personally believes in evolution: "I believe in parts of it but I think there are holes in the evolutionary theory."

What he thinks of intelligent design: "I generally agree with said critique."

Whether intelligent design or a similar critique should be taught in public schools: "I think people should be taught ... that there are various theories about how man was created."

Whether schools should leave open the possibility that man was created by God in his present form: "Of course, yes, definitely."

Jonah Goldberg, National Review

Whether he personally believes in evolution: "Sure."

What he thinks of intelligent design: "I think it's interesting. ... I think it's wrong. I think it's God-in-the-gaps theorizing. But I'm not hostile to it the way other people are because I don't, while I think evolution is real, I don't think any specific--there are a lot of unknowns left in evolution theory and criticizing evolution from different areas doesn't really bother me, just as long as you're not going to say the world was created in six days or something."

How evolution should be taught in public schools: "I don't think you should teach religious conclusions as science and I don't think you should teach science as religion. ... I see nothing [wrong] with having teachers pay some attention to the sensitivities of other people in the room. I think if that means you're more careful about some issues than others that's fine. People are careful about race and gender; I don't see why all of a sudden we can't be diplomatic on these issues when it comes to religion."

Charles Krauthammer, The Washington Post

Whether he personally believes in evolution: "Of course."

What he thinks of intelligent design: "At most, interesting."

Whether intelligent design should be taught in public schools: "The idea that [intelligent design] should be taught as a competing theory to evolution is ridiculous. ... The entire structure of modern biology, and every branch of it [is] built around evolution and to teach anything but evolution would be a tremendous disservice to scientific education. If you wanna have one lecture at the end of your year on evolutionary biology, on intelligent design as a way to understand evolution, that's fine. But the idea that there are these two competing scientific schools is ridiculous."

William Buckley, National Review

Whether he personally believes in evolution: "Yes."

What he thinks of intelligent design: "I'd have to write that down. ... I'd have to say something more carefully than I can over the telephone. I'm a Christian."

Whether schools should raise the possibility that the original genetic code was written by an intelligent designer: "Well, surely, yeah, absolutely."

Whether schools should raise the possibility--but not in biology classes--that man was created by God in his present form? : "Yes, sure, absolutely."

Which classes that should be discussed in: "History, etymology."

John Tierney, The New York Times (via email)

Whether he personally believes in evolution: "I believe that the theory of evolution has great explanatory powers."

What he thinks of intelligent design: "I haven't really studied the arguments for intelligent design, so I'm loath to say much about it except that I'm skeptical."

James Taranto, The Wall Street Journal

Whether he personally believes in evolution: "Yes."

What he thinks of intelligent design: "I could not speak fluently on the subject but I know what the basic argument is."

Whether schools should teach intelligent design or similar critiques of evolution in biology classes: "I guess I would say they probably shouldn't be taught in biology classes; they probably should be taught in philosophy classes if there is such a thing. It seems to me, and again I don't speak with any authority on this, that the hypothesis ... that the universe is somehow inherently intelligent is not a scientific hypothesis. Because how do you prove it or disprove it? And really the question is how do you disprove it, because a scientific hypothesis has to be capable of being falsified. So while there may be holes in Darwinian theory, while there's obviously a lot we don't know, and perhaps Darwinian theory could be wrong altogether, I think whether or not the universe is designed is just a question outside the realm of science."

How evolution should be taught in public schools: "It probably should be taught, if it's going to be taught, in a more thoroughgoing way, a more rigorous way that explains what a scientific theory is. ... You know, my general impression is that high school instruction in general is not all that rigorous. ... I think one possible way of solving this problem is by--if you can't teach it in a rigorous way, if the schools aren't up to that, and if it's going to be a political hot potato in the way it is, and we have schools that are politically run, one possible solution might be just take it out of the curriculum altogether. I'm not necessarily advocating that, but I think it's something that policy makers might think about. I'd rather see it taught in a rigorous and serious way, but as a realistic matter that may be expecting too much of our government schools."

Norman Podhoretz, Commentary (via email)

Whether he personally believes in evolution: "It's impossible to answer that question with a simple yes or no."

Richard Brookhiser, National Review

Whether he personally believes in evolution: "Yes."

What he thinks of intelligent design: "It doesn't seem like good science to me."

Whether intelligent design should be taught in public schools: "No."

Pat Buchanan, The American Conservative

Whether he personally believes in evolution: "Do I believe in absolute evolution? No. I don't believe that evolution can explain the creation of matter. ... Do I believe in Darwinian evolution? The answer is no."

What he thinks of intelligent design: "Do I believe in a Darwinian evolutionary process which can be inspired by a creator? Yeah, that's a real possibility. I don't believe evolution can explain the creation of matter. I don't believe it can explain the intelligent design in the universe. I just don't believe it can explain the tremendous complexity of the human being when you get down to DNA and you get down to atomic particles, and molecules, atomic particles, subatomic particles, which we're only beginning to understand right now. I think to say it all happened by accident or by chance or simply evolved, I just don't believe it."

How evolution should be taught in public schools: "Evolution [has] been so powerful a theory in Western history in the nineteenth and twentieth centuries and often a malevolent force--it's been used by non-Christians and anti-Christians to justify polices which have been horrendous. I do believe that every American student should be introduced to the idea and its effects on society. But I don't think it ought to be taught as fact. It ought to be taught as theory. ... How do you answer a kid who says, 'Where did we all come from?' Do you say, 'We all evolved'? I think that's a theory. ... Now the biblical story of creation should be taught to children, not as dogma but every child should know first of all the famous biblical stories because they have had a tremendous influence as well. ... I don't think it should be taught as religion to kids who don't wanna learn it. ... I think in biology that honest teachers gotta say, 'Look the universe exhibits, betrays the idea that there is a first mover, that there is intelligent design.' ... You should leave the teaching of religion to a voluntary classes in my judgment and only those who wish to attend."

Tucker Carlson, MSNBC

Whether he personally believes in evolution: "I think God's responsible for the existence of the universe and everything in it. ... I think God is probably clever enough to think up evolution. ... It's plausible to me that God designed evolution; I don't know why that's outside the realm. It's not in my view."

On the possibility that God created man in his present form: "I don't know if He created man in his present form. ... I don't discount it at all. I don't know the answer. I would put it this way: The one thing I feel confident saying I'm certain of is that God created everything there is."
On the possibility that man evolved from a common ancestor with apes: "I don't know. It wouldn't rock my world if it were true. It doesn't sound proved to me. But, yeah I'm willing to believe it, sure."

How evolution should be taught in public schools: "I don't have a problem with public schools or any schools teaching evolution. I guess I would have a problem if a school or a science teacher asserted that we know how life began, because we don't so far as I know, do we? ... If science teachers are teaching that we know things that in fact we don't know, then I'm against that. That's a lie. But if they are merely describing the state of knowledge in 2005 then I don't have problem with that. If they are saying, 'Most scientists believe this,' and most scientists believe it, then it's an accurate statement. What bothers me is the suggestion that we know things we don't know. That's just another form of religion it seems to me."

Ramesh Ponnuru, National Review

Whether he personally believes in evolution: "Yes."

What he thinks of intelligent design: "To the extent that I am familiar with it, and that's not very much, I guess what I think is this: The intelligent designers are correct insofar as they are reacting against a view of evolution which holds that it can't have been guided by God in any way--can't even have sort of been set in motion by God to achieve particular results and that no step in the process is guided by God. But they seem to give too little attention to the possibility that God could have set up an evolutionary process."

Whether intelligent design should be taught in public schools: "I guess my own inclination would be to teach evolution in the public schools. I don't think that you ought to make a federal case out of it though."

David Brooks, The New York Times (via email)

Whether he personally believes in evolution: "I believe in the theory of evolution."

What he thinks of intelligent design: "I've never really studied the issue or learned much about ID, so I'm afraid I couldn't add anything intelligent to the discussion."

Ben Adler is a reporter-researcher at TNR.

Epigenetics and Neanderthal genomes....   posted by Razib @ 7/07/2005 01:21:00 AM

As usual, John Hawks summarizes and expands on recent stories about the possible sequencing of the Neanderthal genome and the epigenetics of "identical" twins so well all I can really add is to link and plead that you go and "read the whole thing." There are only two things I feel like saying:

  • The possibility that you could have a Neanderthal-human "chimera" is good fodder for near future science fiction.

  • Epigenetics is one of those topics that the public should know about, but the whole Nature vs. Nurture dichotomy just swallows it up.

Wednesday, July 06, 2005

Ashkenazi women to pay more for BRCA tests   posted by Canton @ 7/06/2005 11:40:00 PM

This news article on New Scientist references a patent awarded on July 1 for a specific mutation of the BRCA breast cancer gene that mostly affects Ashkenazi Jews. Note the strange legal twist where supplimentary royalty fees are only due for testing if you fess up to knowing your Ashenazi ancestry...

Myriad Genetics of Salt Lake City won a European patent on 1 July covering a specific mutation in the BRCA2 gene, which increases the risk of breast cancer. The mutation is found in 1 in 100 women of Ashkenazi Jewish descent. The ruling means that doctors offering tests for BRCA2 mutations are now legally obliged to ask women if they are Ashkenazi Jews. If they say they are, doctors must pay a licence fee to Myriad. No fee is due if a patient says she does not know.

"We believe there is something fundamentally wrong if one ethnic group can be singled out by patenting," says Gert Matthijs of the Catholic University of Leuven (KUL) in Belgium, a member of the European Society of Human Genetics. "It means that someone is exploring the limits of what is acceptable legally and ethically."