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Thursday, January 31, 2008
It's like shark week, only better! Whet your appetite with "High-Resolution Mapping of Crossovers Reveals Extensive Variation in Fine-Scale Recombination Patterns Among Humans", then top it off with "Sequence Variants in the RNF212 Gene Associate with Genomewide Recombination Rate". Enjoy!
Labels: Association, Genetics, Population genetics  The figure to the left is from Signatures of Positive Selection in Genes Associated with Human Skin Pigmentation as Revealed from Analyses of Single Nucleotide Polymorphisms. I thought of this chart when considering the idea that the phenotypic races that we see around us might be relatively new; perhaps an artifact of recent human evolution. Look at "Oceania," those are Bougainville Islanders, from off the coast of Papua New Guinea. In the CEPH-HGDP populations the "South Asians" are from the much lighter skinned northwest fringe of the subcontinent; otherwise, I suspect you would be seeing the South Asian group moving toward the location of the Bougainville Islanders. This is not a surprising finding, earlier studies implied that very dark-skinned populations tended to exhibit a "consensus sequence" due to functional constraint; there's a reason humans are dark-skinned around the equator, and there's only one way to do it. But here's an important point: Bougainville Islanders are closer to East Eurasians than they are to other world populations in terms of ancestry. In other words, the dark-skin and the genes which confer that trait that results in an affinity between Melanesians and Africans in appearance is not a function of relatively recent common descent, but of local adaptation. Similarly, extreme dark-skinned South Asian groups are generally closer to Europeans in terms of ancestry than light-skinned East Asians.This is all pretty common sense when you think about it. But with that said skin color is a very salient trait. The skin is our biggest organ, it's a large part of what others see. Therefore, there is a natural human tendency to classify in colors. If you read the reports from Chinese delegations who were sent to investigate Cambodia they describe the natives as "black." Similarly, according to Mary Lefkowitz the ancient Greeks observed that there were the blacks of Ethiopia and those of Southern India. They also noted that both the Egyptians and North Indians were brown-skinned people ("wheat colored"). But, perhaps importantly, they often distinguished the various peoples by other characteristics (e.g., Ethiopians and Indian hair form). So on the one hand you have an nod to the importance of skin color as a criterion of perception & categorization, and on the other hand an acknowledgment that populations differ in more than color. But in the United States there are peculiar social conditions which result in problematic conflations. As everyone knows, to be very dark-skinned in the United States was identical to being of one race for a greater part of our history. Certainly there was a small Native American population, but they could be discarded from the shaping of social norms because of their low numbers. To have dark-skin was to be of African ancestry. Though there were certainly other distinguishing characteristics between those of African and European ancestry, skin color was the most visible and noticeable. It was used as the main discriminatory trait because that was all that necessary. This still persists in our folk culture when people talk about individuals "being discriminated against because of the color of their skin." Skin color connotes a racial identity. And yet you have groups like South Asians, who overlap with African Americans in complexion, but are not really"black" as we understand it. Steve Sailer has been noting for years the implicit value system highlighted by the reality that the very dark-skinned Vijay Singh is not identified as a black golfer, while the lighter-skinned (and only 1/4 African in ancestry) Tiger Woods is. Of course it doesn't work this way all the time, and South Asians are often identified as black, at least upon first impression. But the more confusing situations can also occur because of the nature of American categorizations. So tight is the correlation of non-white and "black" in the minds of some people that really peculiar characterizations can ensue. For example, in high school I had an acquaintance who would refer to myself & a Cambodian girl as black. That was understandable, we both had brown-skin. But, one day he referred to a Chinese friend of mine as black. This friend was not a dark-skinned, she had a brunette white complexion (not olive). When I queried my acquaintance about the fact that this "black" individual was probably lighter skinned than at least 1/3 of our other classmates (all of whom were white), he simply insisted that she was a "Chinese black." That was about as far as I got, obviously he couldn't express the inchoate associations within his mind between racial identity and skin color. In his world, there were whites and blacks. If someone wasn't white, that entailed that they were black. As is rather clear from the content on this weblog we are getting a good fix on the genetics of pigmentation. Not only do we know the patterns of inheritance via classical pedigree analysis, but we now have a good grasp on which regions of the genome control world-wide variation in melanin content of the skin, eye and hair. We are even beginning to understand when selection began to occur on the loci which control this variation. We have some working hypotheses of why skin color is under functional constraint, and what sort of changes might drive adaptive evolution. But all this is sometimes harder to discuss because the typical American has so many social and psychological associations between skin color and group identity. It isn't just another trait, like bristles on the back of a Drosophila, no, it is the token of one of the most significant sociological phenomena which characterize American society today. Steve will have quite a bit to blog about into the foreseeable future. Note: I suspect that the transposition of genomic knowledge to folk wisdom is easier in societies such as Brazil or India where extant phenotypic variation on this trait exhibits a larger range, much of it within families. Race and color are still very important issues, but the joints around which the perceptions are carved are more flexible and numerous. Labels: Genetics, human biodiversity
Wednesday, January 30, 2008
I was doing some snooping around due some questions about the HERC2 & eye color papers I mentioned yesterday. Guess what? Earlier this month a Danish group published a similar paper, Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. It's Open Access, so you can read it yourself. The language is a bit more stilted and hurried than the two papers I mentioned yesterday, but the basically independently confirmed the Australian group's specific finding:
In conclusion, we have identified a conserved regulatory element within intron 86 of the HERC2 gene that is perfectly associated with the brown/blue eye color in studied individuals from Denmark, Turkey and Jordan. This element had an inhibitory effect on the OCA2 promoter activity in cell cultures, and the blue and the brown alleles were shown to bind non-identical subsets of nuclear extracts. In total, all these data strongly support a model where the blue eye color in humans is caused by homozygosity of the rs12913832*G allele. Instead of just doing comparative analysis they actually tested the hypothesis in cell culture after preforming linkage & association, and seem to have come out with what you'd expect, the SNP on intron 86 of HERC2 regulates transcription at OCA2. Their Ns were a little small compared to the other two groups, but their inclusion of Middle Eastern individuals was interesting. They imply that it's a common haplotype derived from a single mutational event, presumably recently driven up in frequency by selection. Their conjecture of location and rationale aren't convincing, I'm sure commenters here could offer many more ingenious models based on historical & geographical particulars (I know the reasons proffered overlap with some of mine, but I'm a dude on a blog). I get the impression they haven't heard of Haplotter (look at the references). All that being said, at the rate that papers are being pumped out the golden age of pigmentation genetics may not have a very long shelf life (granted, that's a good thing). By the way, the gene they say has an association with hair color, RABGGTA, has been pegged as being under negative selection. Update: ScienceDaily has a summary up with a most retarded title. Labels: Genetics
Tuesday, January 29, 2008
Two interesting articles out in the PNAS early release feed.
Molecular insights into human daily behavior: Human beings exhibit wide variation in their timing of daily behavior. We and others have suggested previously that such differences might arise because of alterations in the period length of the endogenous human circadian oscillator. Using dermal fibroblast cells from skin biopsies of 28 subjects of early and late chronotype (11 "larks" and 17 "owls"), we have studied the circadian period lengths of these two groups, as well as their ability to phase-shift and entrain to environmental and chemical signals. We find not only period length differences between the two classes, but also significant changes in the amplitude and phase-shifting properties of the circadian oscillator among individuals with identical "normal" period lengths. Mathematical modeling shows that these alterations could also account for the extreme behavioral phenotypes of these subjects. We conclude that human chronotype may be influenced not only by the period length of the circadian oscillator, but also by cellular components that affect its amplitude and phase. In many instances, these changes can be studied at the molecular level in primary dermal cells. Weird. ScienceNow notes some implications: ...raises the possibility of an inexpensive and objective test of a person's "owlness" or "larkness." Such a test would be no small matter, given the prevalence of sleep disorders and the fact that many drugs, including cholesterol medications and chemotherapy, work more effectively if administered at certain points in a person's sleep/wake cycle. Pinpointing individual clock cycles could pave the way for personalized sleep and drug therapies, says Achim Kramer, a Free University chronobiologist who helped design the study. Selectivity of Black Death mortality with respect to preexisting health: Was the mortality associated with the deadliest known epidemic in human history, the Black Death of 1347-1351, selective with respect to preexisting health conditions ("frailty")? Many researchers have assumed that the Black Death was so virulent, and the European population so immunologically naive, that the epidemic killed indiscriminately, irrespective of age, sex, or frailty. If this were true, Black Death cemeteries would provide unbiased cross-sections of demographic and epidemiological conditions in 14th-century Europe. Using skeletal remains from medieval England and Denmark, new methods of paleodemographic age estimation, and a recent multistate model of selective mortality, we test the assumption that the mid-14th-century Black Death killed indiscriminately. Skeletons from the East Smithfield Black Death cemetery in London are compared with normal, nonepidemic cemetery samples from two medieval Danish towns (Viborg and Odense). The results suggest that the Black Death did not kill indiscriminately-that it was, in fact, selective with respect to frailty, although probably not as strongly selective as normal mortality. We've all read Farewell to Alms, so we know the argument that quick die offs can be good for standards of living by relieving some of the Malthusian pressure. Though if you ever took a normal medieval history course you'd probably be told about the premium on labor which emerged after the Black Death due to shortages and its affect on the collapse of the old manorial system (I was). But this data is interesting because it confirms that the most economically productive proportion a society where muscle power might was of essence have increased as a proportion of the population after these sorts of epidemics swept through. Perhaps these are the sorts of shocks that social systems need to shift toward another equilibrium? (I know, morbid) Labels: Behavior Genetics, Economics, History
Yanked out of google analytics, below the fold....
10 - Why is porn legal but prostitution illegal? 9 - IQ comparison site. 8 - Converting between IQ and SAT scores . 7 - Genetics of Hair Color (again). 6 - German penises 'too small for EU condoms'. 5 - Porno Arabica (this is due to Assman over-utilizing our search boxes!) 4 - Pigmentation variation in Europe. 3 - James Watson Tells the Inconvenient Truth: Faces the Consequences. 2 - 10 Questions for Heather Mac Donald. 1 - Intercourse and Intelligence. Hm.... Labels: Blog
Monday, January 28, 2008
A few weeks ago Kambiz of Anthropology.net was mentioning how there's very little mention of gene expression on this weblog. Fair enough, but hey, what about this? And this paper just popped into my RSS today, so check it out, Differential Allelic Expression in the Human Genome: A Robust Approach to Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression:
We describe a new methodology to identify individual differences in the expression of the two copies of one gene. This is achieved by comparing the mRNA level of the two alleles using a heterozygous polymorphism in the transcript as marker. We show that this approach allows an exhaustive survey of cis-acting regulation in the genome: we can identify allelic expression differences due to epigenetic mechanisms of gene regulation (e.g. imprinting or X-inactivation) as well as differences due to the presence of polymorphisms in regulatory elements. The direct comparison of the expression of both alleles nullifies possible trans-acting regulatory effects (that influence equally both alleles) and thus complements the findings from gene expression association studies. Our approach can be easily applied to any cohort of interest for a wide range of studies. It notably allows following-up association signals and testing whether a gene sitting on a particular haplotype is over- or under-expressed; or can be used for screening cancer tissues for aberrant gene expression due to newly arisen mutations or alteration of the methylation patterns. This is a provisional paper, so one assumes there will be some revisions. In any case, cancer is important & all, but this is the kind of stuff I'm interested in (see Discussion): ...We tested 56 genes for association of differential allelic expression patterns observed with a cis-acting regulatory polymorphism using genotypes generated by the HapMap project...For 23 of these genes we identified a region statistically associated with differences in allele expression that could indicate the existence of a regulatory haplotype (i.e., a region of one chromosome likely containing the polymorphism(s) causing the differential cis-regulation). These regions are often tens of kb long, consistent with previous descriptions of the linkage disequilibrium patterns in humans.... Related: Kambiz has a post up on this with a lot more commentary, Identifying Cis-Acting Elements that regulate Human Gene Expression. Also, in Nature, Genome-wide analysis of transcript isoform variation in humans. Labels: Genetics  There are two new papers out in AJHG about eye color variation and genomics. Three Genome-wide Association Studies and a Linkage Analysis Identify HERC2 as a Human Iris Color Gene and A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color. The second paper is an extension of the work of the Australian group which has been elucidating pigmentation relationships around OCA2 for several years now. The first paper is more interesting (to my mind) because it's the first genome-wide association study to focus on this region. I've extracted figure 6a out of the paper, you might recognize the map. I'm not surprised; go to Haplotter and enter in HERC2, it pops out as a region of selection near OCA2 (I first noticed it when checking for OCA2). As for the map, pretty cool huh? As the authors note there's a pretty good correlation between the frequency of the trait and the SNP of interest. The authors point to the north-south cline, but I am curious about the east-west one. Additionally, look at Bulgaria. I've been looking at Slavicization of the Balkans, and this is an interesting data point....Related: Dienekes has a high res map up. Note: Please be careful about taking the phenotypic clines too literally, I am to understand that there was a little extrapolation going on here and there. And of course, standard caveats on representativeness of the samples from each region and all. (Via Assman) Labels: Genetics
Sunday, January 27, 2008
 From Geographic distribution of environmental factors influencing human skin coloration:...The UVR [ultraviolet radiation] data recorded by satellite were combined with environmental variables and data on human skin reflectance in a geographic information system (GIS). These were then analyzed visually and statistically through exploratory data analysis, correlation analysis, principal components analysis, least-squares regression analysis, and nonlinear techniques. The main finding of this study was that the evolution of skin reflectance could be almost fully modeled as a linear effect of UVR in the autumn alone. This linear model needs only minor modification, by the introduction of terms for the maximum amount of UVR, and for summer precipitation and winter precipitation, to account for almost all the variation in skin reflectance..... The map above was generated from the regression analysis. Apparently it has been updated as of 2007 (received the link from a friend). It does look much better than it did in the original paper (which I have read and have a PDF copy of). Do note that the selection of peoples whose reflectance values were plugged into the model obviously matters. But I still think it's interesting the sort of predictions this map produces and how it fits with our intuitions of what the distributions should be, and the knowledge of what they are. Note the equivalent latitudes in Europe and North America, or Australia. Labels: human biodiversity
Saturday, January 26, 2008
The New York Times Magazine has a long piece about replacement of Uganda's native Ankole breed with Holsteins:
"You know, in Uganda, we have to look for survival of the fittest," Mugira said once he finished sorting out the confusion. "These ones, they are the fittest," he went on to say, gesturing toward his Holsteins. In physical terms, there was really no contest between the tough Ankoles and the fussy foreign cattle, which were always hungry and often sick. But the foreigners possessed arguably the single most important adaptive trait for livestock: they made money. Holsteins are lactating behemoths. In an African setting, a good one can produce 20 or 30 times as much milk as an Ankole. Who could complain about over an order of magnitude increase in productivity? Well: If the Ankole cattle are able to mount a comeback, it will be because circumstances have endowed them with a unique set of defenses, both evolutionary and political. Members of President Museveni's ethnic group populate the upper ranks of Uganda's government. Some prominent Bahima have started an organization devoted to preserving Ankoles, under the patronage of a one-eyed army general who spends his free time painting rapturous portraits of cows. One afternoon, at a pricey restaurant in Kampala, I had lunch with the organization's chairman, Samuel Mugasi. Dressed in a dapper gray suit and a French-cuffed pale blue shirt, he told me he was a civil servant and part-time rancher. A lot of people talk as if white tourists in Third World countries are special in the way that they bemoan the passing of quaint "traditions" which they had enjoyed "experiencing," but which the "natives" were happy to get rid of. But this sort of patronizing and instrumental attitude toward the unwashed is universal, it seems to be an attitude correlated with leisured status. Indian Americans and Irish Americans who visit their ancestral "homelands" over the years complain about the destruction of the cultural traditions, i.e, poverty, which made their earlier experiences more "authentic: (luckily for Indian Americans who want to get in touch with their "roots" most of India is still living in authentic squalor and deprivation!). But there's a serious case to be made for preservation of extant genetic variation. The question I have is this: how many individuals of various breeds do you really need to keep around so that diversity is preserved for future utilization? In other words, I understand the logic of adaptive acceleration where large Ne is critical to the production of rare positive mutations; but don't we get to a point of diminishing returns for populations where we're more interested in modal alleles which might be disjoint across breeds? That is, the genetic traits from breed A you want to preserve in case they come in handy are common in breed A, so you don't need that many of breed A around to serve as a reservoir. I just don't see why we need maximal diversity, it seems the sort of variation which is encapsulated by species richness is more important here than proportionally weighted diversity indexes. In any case, as alluded to in the article, maintaining relict populations of dying breeds like this seems like a public good which any prudent government can provide. But another issue with the article is that it doesn't seem like the author is a science writer, so he engages in the fallacy of blending genetics. For example: ...And something else is being obliterated: genes. Each time a farmer crossbreeds his Ankoles, a little of the country's stockpile of adaptive traits disappears. It isn't easy to measure genetic "dilution." What is evident, however, is that the Ankoles possess much worth saving. For instance, their horns, often seen as ornaments, actually disperse excess body heat.I guess it's nice that he put quotes around dilution, but the rest of the article suggests to me that the author hasn't internalized that genetics is discrete, and that information isn't destroyed through cross-breeding. Rather, it seems that a good program of cross-breeding could result in a superior breeds of Holstein optimally suited to the local climate. That's what happened with indigenous African lineages as they hybridized with introduced South Asian ones 2,000 years ago to produce the Ankole according to the article! This sort of piece in a widely circulated publication such as The New York Times Magazine could have been a serious examination of agricultural and quantitative genetics, and just how much we depend on these unsexy sciences to feed the world. As it is, there's a lot of hand-waving scare-mongering.... Labels: Genetics
In classic heritability studies, the variance of some phenotype Y is decomposed (in the simplest model) into the variance attributable to genetic effects, G, and the variance attributable to environment, E, such that Var(Y) = G+E. As the majority of heritability studies are done by geneticists, who are in general more interested in G than in E, the environmental variance is, to them, largely an error term. When thought of this way, it is clear that "environmental variance" can contain effects that, though not genetic, are certainly not "environmental" in any traditional sense.
In particular, the error term must includes simple stochastic noise on any part of the complex mapping from genotype to phenotype. Even at the early points in this map--the genome sequence and gene expression--there is considerable opportunity for random events to greatly affect phenotype. For lack of a better term, I'm going to call noise introduced at this level "genomic noise"; some examples follow: 1. While the genome is sometimes thought of as a constant in all cells from a given individual, that is not the case. Besides mutations, the genomes in some cell types undergo extensive remodeling during development. For example, consider the T and B cells of the immune system. During development, the genes in the immunoglobulin cluster are recombined to create the receptors presented by the cell. This recombination is stochastic-- even from an identical starting spot, the precise combination of genes obtained in independent recombinations can vary greatly. It stands to reason that this genomic noise could, in turn, propogate up to phenotypic variation, and indeed, that is the case-- if you look at identical twins who are discordant for multiple sclerosis (an autoimmune disease), you find that those early recombination events have made them less than identical. 2. Genomic noise is introduced in brain cells, as well, by the random movement of transposable elements and their effects on gene expression. The important studies (or perhaps study, singular; I can't seem to find anything other than the linked paper) here have been done in the mouse, and any phenotypic effect is highly speculative, but as the costs of sequencing drop, it will be possible to study these sorts of somatic changes on a large scale. 3. Moving up a level from genomes to gene expression, it's clear that some variation in levels of gene expression is simply stochastic. But interestingly, recent work has suggested that, though most everyone has two copies of all autosomal genes, a rather large fraction of genes (excluding imprinted ones) are only expressed from one copy, and the choice of copy to express varies from cell to cell. This opens up the possibility of cells or even entire tissues ending up effectively haploid for a given gene. So if you were to have two individuals heterozygous for some phenotypically relevant variant, they could end up with quite different phenotypes depending on the random choice of allele to express (see also G's post on the topic here). I find these sorts of speculations entertaining, and I imagine some of these postulated effects will soon be tested. Until then, just something to keep in mind. Labels: Genetics
Friday, January 25, 2008
The first genome-wide association study on human episodic memory back in 2006 showed an association between the T allele of a gene called KIBRA and better performance on certain list-learning tasks. That study contained two replications in different populations, and the outcome was independently replicated in healthy, elderly folks. Next, another group showed an association between the T allele and very late-onset Alzheimer's. There are some issues with interpreting this study that I certainly didn't think of the first time I read it. Almeida et al. point out that this could be due to 'survivorship bias' wherein the C allele carriers that were gonna get AD got it a lot earlier and left the T allele folks to provide the 'very late-onset' crowd (or at least that's how I interpret survivorship bias).
Two studies have come out in the past few months. One replicates the effect of the T allele on memory with a little smaller effect size than before. The second fails to find any effect at all. One experiment in this latter report was an exact replication of the 2006 memory study with a population of European origin (German vs. Swiss. That shouldn't matter should it?).I don't know how to explain the failure to replicate, but it is duly noted. Perhaps it really really matters how well you vet your cohort. For instance (from Almeida and co again): We did not find evidence in support of our original hypothesis that CC carriers would be at greater risk of MCI (ed: Mild Cognitive Impairment) (although we did observe a trend in that direction), nor were we able to show any evidence of an effect of the gene on the memory scores of older people with MCI. These results suggest that the effect size of the T→C polymorphism decreases with increasing impairment of episodic memory, and that the KIBRA gene plays all but a limited role after scoresfall below a certain threshold, as is the case in MCI. I don't think there is any evidence that the cohort that failed to replicate had especially bad memory, but I'm not an expert in human memory assessment. A few more molecular details below: Kibra had an especially good tie-in to memory because in yeast two-hybrid studies it binds to PKM zeta which is established as a key player in maintenance of several types of memory and synaptic plasticity in a completely separate literature. The molecular situation is foggy as well though. We don't have any published assessment of the function or localization of endogenous Kibra protein in neurons. In fact, most of the molecular work has been done with an overexpressed GFP fusion protein. The group that discovered Kibra reports that it is a 125-kDa protein with specialized "WW" protein interaction domains at one end, while the group that reported the Kibra-memory association used a custom antibody to detect human Kibra protein and identified a 100-kDa truncated protein. One final issue is that the memory-SNP (and all SNPs in linkage disequilibrium) in human Kibra is intronic, which means we have no straightforward prediction as to how it might alter protein function. Papassotiropoulos et al.(2006) could not find a difference in the total amount of Kibra protein in human brain tissue with different alleles. Either we have to predict that the SNP produces an expression change that they couldn't detect or that the SNP alters splicing such that the protein sequence changes but the size doesn't.
Reza Aslan and Rod Dreher had a disagreement about the general concept of "Clash of Civilizations" on the latest bloggingheads.tv. I think people who actually read Samuel Huntington's original book would feel that the caricature of his thesis is a bit unfair; granted, such macro-scale typologies invite criticism, and there were some embarrassing factual errors. But Aslan himself himself is coming back with Platonic seeming typologies (e.g., "Arab culture") while at the same time ridiculing the whole enterprise.1 The reality is that the human mind is geared toward these clear and distinct types, despite the fact that reality exhibits continuity. I am, for example, always surprised at the alliances of convenience which confound our expectations based on higher-level categories. For example, the Abbasid caliphs & the Carolingians engaged communications in the interests of forging common cause against the Byzantines, prefiguring the later French alliance with the Ottomans against the Hapbsurgs. This is a case where it seems geographic parameters overruled the historically contingent cultural affinities between various states (during the time of Charlemagne the Latin and Greek churches were not even in schism!). The Umayyads of Spain similarly attempted to act in concert with the Byzantines against the rising Muslim powers of North Africa who were pushing into southern Italy and challenging their status as the paramount Islamic power in the western Mediterranean. And in the last case, cities such as Amalfi long served as federates in the North African Muslim cause against other Italian Christians for decades, enabling the endemic depredations of the Muslims upon their co-religionists in exchange for a cut of the plunder and strategic alliance. In China the Hui (or Dungans), the Chinese speaking Muslims, were used by the Manchus to conquer & suppress the Turkic speaking Muslims of Xinjiang toward the interests of consolidating the hold of the Chinese Empire upon these marginal regions. And in a peculiar case, rebellions of the Hui against their non-Muslim rulers predicated on religious differences tended to succeed only when Muslim preachers embedded within their sermons metaphors and analogies drawn from common Chinese (often Daoist) mythology! And yet, you often see this:
Omar, the Kurds claim, was once an inconsequential deputy to the now-deceased terrorist chieftain Abu Musab al-Zarqawi. Omar disputed this characterization. By his own telling, he accomplished prodigies of terror against the pro-American Kurdish forces in the northern provinces of Iraq. "You are worse than the Americans," he told his Kurdish interrogator. "You are the enemy of the Muslim nation. You are enemies of God." The interrogator-I will not name him here, for reasons that will become apparent in a moment-sat sturdily opposite Omar, absorbing his invective for several minutes, absentmindedly paging through a copy of the Koran. It is true that may Islamist Arabs have an operational tendency to conflate the "Muslim nation" with the "Arab nation," but, I do not think one can deny the internationalist tendencies of a particular tendency with Islam. Reza Aslan in the diavlog with Rod asserts the multiplicity of identities which individuals tend to have. Cultural anthropologists also tend to make this claim. It seems an obviously true claim. But, the problem to me is that Aslan (and cultural anthropologists) take this complexity and use it as a cudgel against any attempt to construct general trends or patterns of relations (outside of their own preferred narratives!). There are sociological and historical analyses of the manner in which people identify; for example, middle class Bengali speaking Muslims before the partition, and under British rule, tended to coalesce around their identity as Muslims who were marginalized by the Hindu elite of Calcutta. After independence under Pakistan Bengali speaking Muslims were dominated by a non-Bengali speaking Muslim elite; whereas before they were marginalized as mussulmans, now they were marginalized as crypto-Hindu kala Bengalis. In my own family this has manifested in a generational difference; my mother noted that her parents, especially her father who was often the only Muslim physician among his colleagues (he was born in 1896), was extremely attached to the idea of Pakistan. In contrast, her own generation experienced little discrimination from Hindus, who were by that period a minority out of power, as opposed to Urdu-speaking immigrants from India ("Biharis") who would engage in attempts to assert naked dominance in public such as forcing Bengalis out of seats on a bus if all spots were already taken (and yelling loudly in Urdu, which the bus driver might not understand, when they were denied what they wanted). Context matters. Most of us get that. Obviously we use them as heuristics in our day to day life (among a bunch of white Americans I suppose I'm the "brown guy," and among a bunch of non-American brown guys I'm "the American"). Rather, people should engage in more scholarship to map out how how these identities apply in particular contexts and what their long-term effects are. For example, it is trivially easy to find alliances across the religious chasm for states during the medieval period; but it might be interesting to see how much deviation from expectation based purely on real-politik there was over the centuries. I think that the sincere Christian religiosity of Louis IX of France did have geopolitical consequences which could not be inferred from pure calculation of interest. It may be that though most state-action can not be derived from civilizational adherence (after, most conflict is intra-civilizational), the deviations from expectation can be, and those deviations might be particularly significant hinges of history. Finally, I think that though broad social and historical studies are essential, we need to explore the psychology of identity in more detail. There is a difference between what people say, and what people do. I suspect many Syrian Muslims would avow more affinity to a South Asian Muslim than to a Christian, at least to the South Asian Muslim. But I also suspect that racial prejudice and to a lesser extent Arab chauvinism strongly shape realized choices, and in reality association with a Syrian Christian might actually be more likely (this doesn't take into account variables such as food, where local geography and culture matters a great deal). Ultimately, these questions of identity are empirical, and it would be nice if people spent less time arguing and more time collecting data and analyzing it. 1 - Do Syrian Christians, Arabs of Khuzistan in Iran and the Arabs of Morocco truly have in common with each other than each does with an Armenian Christian of Syria, a Persian from Fars and a Berber from the Rif? Labels: culture
Thursday, January 24, 2008
I've been posting a fair amount on the transition from hunter-gatherer to farmer in northern Europe lately. Though I'm obviously interested in historical scholarship in and of itself, my focus on this period has been triggered by the spate of recent papers on selection within the last 10,000 years or so. It seems that the overwhelming shift of humans from hunter-gathering toward agricultural lifestyles within the period between 10,000 and 2,000 years ago had to have had a major impact on evolutionary pressures; just as fire might have hundreds of thousands (or millions) of years in the past. The amylase and lactase persistence stories are pretty straightforward derivations of the change in lifestyle; different food inputs will result in different optimal digestive propensities. Then there are pretty obvious second order concerns; farming societies are usually characterized by more individuals per unit area because less land is needed to support one person.1 The implications of this for disease are clear from the dependence of endemic diseases on particular density thresholds. Additionally, the domestication of herbivores also likely cranked up the rate of production of new diseases as pathogens crossed the species barrier. Finally, there are more nebulous possibilities such as various in alleles which are known to have behavioral correlates, such as DRD4, and their possible relationship to a local human ecology.
That being said, attention to details is important. The farming lifestyle in Denmark is very different from the farming lifestyle on the North China plain. In Farewell to Alms Greg Clark made a few general claims derived from assumptions which I think are pretty easy to refute. For example: ...Chinese adults, despite their very long history of settled agriculture and the variety of climate zones within China, generally lack the ability to absorb lactase, suggesting that milk was never a large part of the Chinese diet, and that by implication Chinese living standards were generally low in the preindustrial era. Clark assumes that cattle culture is a sign of local wealth, and that the gene-culture co-evolutionary process was driven by economic parameters. The reality is of course that there are ecological considerations; the distribution of cattle culture in Africa is the clearest example, but it seems likely that it was an issue elsewhere. I'm reading A Concise Economic History of the World, and the author notes before the Romans cattle raising and slash & burn farming were the norm in Gaul. With the spread of the Roman empire two-course rotation was introduced, but the thick clay rich soil of northern Europe did not yield easily to the Mediterranean plow. A more powerful heavy wheeled eventually did open up northwest Europe to intense three-course rotation, and resulted in very high population densities and the flourishing of the manorial system by the peak of the Medieval Climate Optimum. That being said, the manorial system did not spread to the Celtic Fringe or most of Scandinavia because the cereal based system was less optimal in extremely moist or cool climates; there a cattle based form of agriculture remained dominant not because of the wealth of the Irish or Norwegians, rather the local ecology placed constraints on the options they could follow. The point of all this is that the spread of agriculture to northern Europe 8,000 years ago did not mean that the hunter-gatherer with his bow immediately became the medieval peasant on his plow, so some of my presentation comes rather close to implying this. No doubt the shift was across a continuous range, and the local configuration was subject to historical contingency and ecological constraint. I do hold that it is likely that endemic disease became much more significant with the rise of agricultural communities, but we should be cautious about projecting from the extremely productive period before the modern era, when better technology (plow, horse collar, etc.) and diversified crops combined to drive the Malthusian limit very high indeed. With that in mind, I'd like to point to a dissertation that Paul found where there are some interest results being reported:
I'll you digest this, but, do keep in mind that histories of populations and particular genes do not always align. A major problem in modeling the past seems to be a disregard for this distinction. Demic diffusion may not be necessarily the substantial replacement of ancestral genome content. Rather, long distance colonies from southern Europe might have brought both a new lifestyle and new genes. Most of their cultural and genetic distinctiveness might have been swamped out, but a few extremely salient elements may have remained and become dominant. 1 - There are exceptions, such as the coastal Pacific Northwest where a dense and affluent society grew up around the abundance of salmon. Labels: History
Via Dienekes, a new paper, A spatial analysis of genetic structure of human populations in China reveals distinct difference between maternal and paternal lineages:
Analyses of archeological, anatomical, linguistic, and genetic data suggested consistently the presence of a significant boundary between the populations of north and south in China. However, the exact location and the strength of this boundary have remained controversial. In this study, we systematically explored the spatial genetic structure and the boundary of north-south division of human populations using mtDNA data in 91 populations and Y-chromosome data in 143 populations. Our results highlight a distinct difference between spatial genetic structures of maternal and paternal lineages. A substantial genetic differentiation between northern and southern populations is the characteristic of maternal structure, with a significant uninterrupted genetic boundary extending approximately along the Huai River and Qin Mountains north to Yangtze River. On the paternal side, however, no obvious genetic differentiation between northern and southern populations is revealed.  The simplest model here is that north Chinese Han males spread over the country and intermarried with southern females. That explains the distinction between northern and southern lineages. But, I think it is important to be specific about the anthropological details which manifested on the local level. The Han are traditionally a patrlineal and patrilocal people. My understanding is that patrilineality and the "clan system" is more extreme in the south than the north. Additionally, going back to the Warring States period before the rise of the Imperial Chinese system scholar-officials would move from state to state in search of employment, power and prestige. On a larger scale there is the historical reality that several times in Chinese history Han ethnic dominance has retreated from the north China plain to a southern redoubt. The subsequent expulsion of barbarians from north China was then accompanied by the migration of long established southern lineages to northern power centers. So one might assume that these southern lineages were originally derived from the north, but after a while it might get difficult to sort out who was who (north & south). Of course the historical record might simply reflect the shifts in elites who remained in power on top of a relatively static ethnic situation in the north, while the south went through a general long term trend of sinicization which accelerated during periods of barbarian rule in the north when the gentry supplemented the local Han base. Finally, do note that south China is geographically far more fragmented than north China, and we know in other contexts this has a long term effect on mating patterns and dynamics. I am also interested why the Mandarin dialects managed to take over southwest China (see map) but not southeast China.Genetically this sex-based distinction seems to confirmed by repeated studies. But, that being said, remember that in the early 1990s Cavalli-Sfroza reported in The History and Geography of Human Genes that north Chinese were genetically closer to Japanese and Koreans and south Chinese with southeast Asians when looking at traditional autosomal loci. It is historically attested that groups like the Thai and Vietnamese have origins within what is now south China (the Thai still have ethnic relations within China proper). Ethographic analysis also suggests the Cantonese, for example, preserve customs which are clearly descended from local traditions which pre-date a Han identity for the people in the region. It would be nice to have a STRUCTURE based analysis address these questions..... Note: Most of the Overseas Chinese are from the south. Especially Fujian. The older Chinese communities in the United States tend to be Cantonese.
I'm sure you have been waiting with bated breath (not!) for the final part of these notes. Part 1 is |
