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

January 31, 2017

New Gene Expression live soon….

Filed under: Uncategorized — Razib Khan @ 1:02 pm

Please be patient. Loading archives so backlog of posts might show up over the next month.

April 10, 2013

My 23andMe affiliate link

Filed under: Uncategorized — Razib Khan @ 1:07 pm

Friends have been asking if I have an affiliate code for 23andMe since I have been promoting it so much over the past few years. Well, I finally got one. Here it is:

Razib’s 23andMe.com affiliate link.

Full URL: http://www.dpbolvw.net/click-7088698-11032058

October 12, 2011

Is publishing your genome unethical?

Filed under: Culture,Personal genomics,Uncategorized — Razib Khan @ 8:49 am

Larry Moran thinks that I had to ask my parents and siblings for permission before publishing my genotype. Interestingly, most of his readers seems to disagree with Larry on this, so I won’t offer my own response in any detail. They’re handling it well enough. I would like to add though that obviously this isn’t a either/or proposition. If my family had a history of a particular genetic disease which was well characterized in terms of causative alleles I might not have published my genotype. As it is, we don’t. So I didn’t see much of a downside. I would also add that in my case It wasn’t possible to have genuine consent in the first place. My mother isn’t much into science, and we don’t share a common first language. There’s really no way that I could have gotten substantive consent, insofar as my mother understood what I was doing.

More broadly though I think it is useful to broach this question and think about it. People do have social responsibilities by and large, and we’re embedded in a broader fabric. This isn’t true in all cases, some people have such horrible relationships with their families (e.g., victims of abuse) that it’s obviously ridiculous to wonder if they should ask their family for consent.

April 7, 2011

The ethnogenesis of brown

Filed under: Uncategorized — Razib Khan @ 10:21 am

Credit: Bollywood Hungama

I should be explicit and lay my cards on the table about what I think properly models the ethnogenesis of brown folk over the past 50,000 years.

1) 40-50% of the ancestry pre-dates the Holocene, ~10,000 years B.P. This element is termed “Ancestral South Indian.” It has a moderately closer relationship to the peoples eastern Eurasia, the New World, and Oceania, than those those of Western Eurasia (when viewing the non-African branches of humanity).

2) Somewhat more than 50% post-dates the Holocene, within the last ~10,000 years, and is intrusive to the subcontinent from the northwest. These are the “Ancestral North Indians,” ANI. They are very close, nearly identical, to the populations of West Eurasia. A reconstruction of the genetic profile of ANI puts them at about the same distance to modern Europeans as the distance between Finns and Italians; not trivial, but on a global scale rather close.

3) The fact that the ANI are so close to West Eurasians, and the ASI a bit closer to East Eurasians, explains the genetic distance measures of South Asians; generally closer to West Eurasians, but shifted toward East Asians.

4) The proportion of ANI/ASI among populations is a function of geography (the ratio increases to the northwest, with ASI nearly disappearing among the non-South Asian Iranian peoples) and caste (“high caste” having more ANI to ASI).

5) There are two subsequent prehistoric events of note. The intrusion of Indo-Europeans from the northwest, and the Mundari speaking people from the northeast. The cultural influence of Indo-Europeans is well known, but the Mundari may have brought rice agriculture to India. Both these groups contribute less than 5% to the ancestry of South Asians, with strong concentrations in the northwest and northeast respectively.

6) Then there are assorted historically attested migrations of and long term residence of groups from the northwest (“Huns” and Muslims) and northeast (Tibeto-Burmans such as the Ahom and Garo). These two groups contribute about ~1% each to the ancestry of South Asians.

Two papers of note:

- Reconstructing Indian population history

- Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture

Finally, a rule-of-thumb is that the more deviated from the expectation the residence of a group in South Asia, the stronger the sex bias of the admixture. So, the ASI are the most female biased ancestrally, and the Muslims the most male biased.

#4 and #5 are the points where my confidence is the lowest in that there is a possibility that the ANI were Indo-Europeans, though I do not believe so personally, and the Munda are indigenous to South Asia. For the record I think the ANI and ASI were both agriculturalists, though the ANI kit was somewhat more successful, and imported from West Asia to a great extent.

February 9, 2011

Genetic variation in three dimensions

Filed under: Genetics,Genomics,Uncategorized — Razib Khan @ 11:31 pm

Preview of a GNXP post which will go up tomorrow. The following is a 3-D plot of the top three components of genetic variation in a data set of Gujaratis, white Europeans (Anglo-Saxon Americans & Tuscans), Chinese, and my parents & a few friends.

February 2, 2011

Diminishing returns of ancestry analysis (for me)

Filed under: Genetics,Uncategorized — Razib Khan @ 12:32 am

Zack has finally started posting results from HAP. To the left you see the results generated at K = 5 from his merged data set with the first 10 HAP members. I am HRP002. Zack is HRP001. Paul G., who is an ethnic Assyrian, is HRP010. Some others have already “outed” themselves, so I could proceed via process of elimination for the other bars. There isn’t anything very surprising here. Zack is 1/4 Egyptian, so he has a rather diverse ancestry. Jatts, who are from Northwest India, are known to have more affinity with populations to the west than those of us from the east or south of the subcontinent. With just that knowledge you can make some educated guesses as to what the “ancestral components” inferred from ADMIXTURE might correspond with in a concrete sense. After submitting to Dodecad and the BGA Project I pretty much know what to expect in relation to me. I’m a rather generic South Asian, except, I have an obvious input of “eastern” ancestry.

This is what Dienekes also found. Aggregating various ancestral components together to be analogous to what Zack produced at K = 5, you get the bar plot below from his runs:

I assume that all ancestry analyses will find that I have a substantial minority of East Eurasian ancestry. I have a similar amount of ancestry which is obviously connected to West Eurasia. And the rest of my ancestry is going to fall into the catchall which is “South Asian,” which Reich et al. in Reconstructing Indian History argued was in fact a compound between a West Eurasian-like population (“Ancestral North Indian,” ANI) and a South Eurasian population (“Ancestral South Indian,” ASI) which was more closely related to East Eurasians than West Eurasians, though distantly so at that (modern West Eurasians are interchangeable with ANI, but ASI do not exist in unadmixed form).

Finally, here’s an analysis of chromosome 1 and its affinities to various reference populations. I’ve labelled myself. No surprises:

I am HRP002 in HAP. DOD075 in Dodecad. IN8 in BGA. I am willing to submit to any of these new grassroots ancestry projects if they want me. But I doubt I’ll find anything too surprising now. They converge upon the same rough proportions (as they should).

I’m at the stage where I want to look more deeply into the details of how long ago the “eastern” admixture occurred. It seems to come down from both parents. If it was very recent there should be some linkage disequilibrium detectable because recombination should not have broken down the allelic associations distinctive to each ethnic group yet (this is noticeable in African Americans). But I am not so sure it is recent anymore, as I’d thought. I suspect a Tibeto-Burman and Munda element were absorbed by Bengali peasants in the course of demographic expansion in what became Bangladesh between 1000 and 1500 A.D., and that ancestry is well distributed across the population now.

But even though I won’t find anything out for myself, the reason HAP and projects like it are useful is that we need better coverage of the world’s variation. There are big coarse questions which we’ve tapped out, but there are still lots of gaps to fill. I’m willing to do my part in that (or, more precisely, at this point I’ve drafted my parents into the role, since they aren’t related and so represent two independent data points for Bengal).

Addendum: I know for many people of European ancestry this sort of thing doesn’t tell them anything new. Not so for me. I always suspected East Asian admixture due to the phenotype of my extended family (and to some extent, me. I did not need to shave regularly until my 20s), but I was always curious as to its extent. Additionally, for the reasons of phenotype I had assumed my mother had very little of such ancestry while my father had a great deal. It turns out that in fact my mother may marginally be more “eastern” than my father.

January 10, 2011

Print vs. web in science

Filed under: Uncategorized — Razib Khan @ 10:26 am

I have some Google Alerts set up relating to human evolution and such, and a few days ago I noticed a spike in articles about the evolution of clothing and lice. Like this: We were all naked until 170,000 years ago. Since I blogged this in September, The naked years, I was confused. Here’s the explanation in USA Today:

The study, in this month’s print edition of Molecular Biology and Evolution, finds that the one louse species began to diverge into two about 170,000 years ago, 70,000 years before humans started migrating to colder climates, which began about 100,000 years ago.

The paper was on the website in early September, but didn’t make it into the print edition until 2011. I have no idea how this sort of stuff works; contrary to perceptions of many I’m not a science writer. Perhaps they blasted a new wave of press releases? Whatever they did, it worked. A huge plume of articles has been welling up over the weekend on the topic.

But it does make me wonder as to the possibility of getting new publicity for “old” science. There are certain papers which are going to make a big splash, no matter what. This is a case where there is a “hook,” but it isn’t a sure thing. And the core of the research on the evolution of lice morphs is a somewhat abstruse statistical method.

September 10, 2010

George C. Williams, (1926-2010)

Filed under: Uncategorized — Razib Khan @ 8:17 am

Jerry Coyne notes that George C. Williams died a few days ago. I’d heard he was ill. Michael Ruse has an obituary up. Williams’ book Adaptation and Natural Selection prefigured Richard Dawkins’ The Selfish Gene.

Update: Please see Carl Zimmer’s reflections and recollections.

September 9, 2010

Daily Data Dump – Thursday

Filed under: Uncategorized — Razib Khan @ 10:48 am

More on The Social Sensitivity Hypothesis. At A Replicated Typo a post which explores a model whereby different morphs emerge which migrate and flourish based on genotype. The “sensitive” and “non-sensitive” tendency is optimized for different ecologies, whereby in high resource zones the sensitives do better. The author expresses a lot of caution, but the awesomeness in the post is that he wrote up the model as a script. Here’s the graphical output (see the post for an explanation):

Gene Discovery Holds Key to Growing Crops in Cold Climates. The agricultural sciences are woefully underexposed. Astronomy feeds the soul, but cow-colleges help feed the stomach.

The Artificial Ape: How Technology Changed the Course of Human Evolution by Timothy Taylor. A mixed review of the book of the same name. It’s probably an unfortunate cognitive bias to construct a one-causal-factor-explains-it-all for “why we’re human” (also, these models sell books, nuance gets by peer review). But our utilization of technology has to be high up on the list “what makes man.” I think there’s a good case that technology is the root of many of the other posited changes. For example, fire is a technology which drives the “cooking model.”

Beware of Greeks Bearing Bonds. Michael Lewis profiles the society that is Greece. In describing the faction and distrust which lay at the heart of Greece I can’t but help but think of inferences from “natural character” as to why the city-states of yore could never unify into a coherent whole, and were conquered by Macedon and Rome in turn. In 1999 according to the Census the per capita income of Greek Americans was $27,400, as opposed to $21,600 for the average American. It seems that if Greece just fired most of their civil servants and replaced them with Finns the nation’s real economic productivity would immediately skyrocket. The main issue is that the Finns would need intensive training on how not to get screwed.

Greatest of All Time. Gaius Appuleius Diocles, a charioteer in 2nd century Rome, may have had lifetime earnings on the order of the equivalent of $15 billion dollars! More precisely, he earned 35,863,120 sesterces over his career, which could have funded the entire Roman army alone for a little over two months, or fed the city of Rome on grain for a year.

September 8, 2010

After the codex

Filed under: Uncategorized — Razib Khan @ 9:18 pm

440px-Köln-Tora-und-Innenansicht-Synagoge-Glockengasse-040Today we’re seeing a transition in the medium of literacy. I’m alluding to the emergence of digital formats, which will transform the physical experience of reading. You’re part of the process right now, unless you’ve printed this out. Of course we have books around, and we will for quite some time. I assume for the most precious elements of our literary collections the physical book will remain preferred until the current generations pass on. But this transition is not the first one. The book, also known as the codex, has been the primary medium of literacy in the Western world (which I will define as from Mesopotamia to the Atlantic) for only ~1/3 of the whole period across which humans have been literate. Before the book, there was the scroll, and before the scroll, there were cuneiform tablets. From Wikipedia:

The Romans used precursors made of reusable wax-covered tablets of wood for taking notes and other informal writings; while codices of parchment or papyrus appear to have been widely used as personal notebooks, for instance in recording copies of letters sent (Cicero Fam. 9.26.1). The pages of such notebooks were commonly washed or scraped for re-use; and consequently writings on codex were considered informal and impermanent.

The first recorded Roman use of the codex for publishing and distributing literary works dates from the late first century AD, when Martial experimented with the format. At that time the scroll was the dominant medium for literary works and would remain dominant for secular works until the fourth century….

I thought of this while perusing Jonah Lehrer’s post, The Future Of Reading, in which he makes reference to the new Stanislas Dehaene book, Reading in the Brain: The Science and Evolution of a Human Invention. Lehrer offers up the argument that sometimes making the process of reading easier may actually result in us not making use of our full-spectrum cognitive resources. I’m skeptical of this argument, though I’d be curious as to what cognitive neuroscientists would make of it. Until then, an amusing reenactment of the travails of those who weren’t quite early adopters of the codex technology:

Image Credit: Willy Horsch, Torah Scroll

Daily Data Dump – Wednesday

Filed under: Uncategorized — Razib Khan @ 9:49 am

Human Meat Just Another Meal for Early Europeans? The argument about cannibalism always goes back and forth. It seems entirely plausible that at some point in our lineage’s history the consumption of conspecifics may not have been shocking, as the human cognitive toolkit had not evolved to the level of sophistication which makes cannibalism cross-culturally abhorrent. Now, you may object that cannibalism has been known among H. sapiens sapiens, but regular cannibalism generally is sanctified in some ritual fashion. The Aztecs for example seem to have consumed the human sacrifices to their gods. Cannibalism without ritual, as often occurred during pre-modern sieges of cities, emerges only in contexts of extreme deprivation.

ReadingLevelByRaceThe REAL ‘Stuff White People Like’. White people are the “hook,” but there’s a lot in this post from OKCupid on the personals profiles of various ethnic groups, as well as religions. To the left is an analysis of profile sophistication in terms of prose by racial group. Asian and Indian males in particular should work on their prose on OKCupid, since they’re strongly disfavored as partners according to OKCupid’s past analysis. Though Latinos and black males aren’t doing much hotter in response rate, so that can’t be the total explanation. Rather, seems like the prose quality is a better reflection of mean years of education by ethnic group in the United States.

Being Attractive Brings Advantages: The Case of Parrot Species in Captivity. “We repeatedly confirmed significant, positive association between the perceived beauty and the size of worldwide zoo population. Moreover, the range size and body size appeared to be significant predictors of zoo population size.” Now you understand cats!

Primed for Reading. Richard Boyd reviews Stanislas Dehaene’s Reading in the Brain: The Science and Evolution of a Human Invention. I enjoyed Dehaene’s The Number Sense: How the Mind Creates Mathematics, so no doubt this will soon be in “in the stack.”

I was wrong about veganism. Let them eat meat – but farm it properly. To assert one is wrong is heroic. People who are wrong always go up in my estimation, because everyone is often wrong, but the human reflex is to deny error. That being said, it seems like the author of the article is reviewing a pro-pig manifesto. The plenitude of pigs in China, a region often at the Malthusian limit, is a good clue as to the animal’s efficiency at converting offal into meat.

September 7, 2010

Daily Data Dump – Tuesday

Filed under: Uncategorized — Razib Khan @ 11:41 am

Big brains attributed to mother’s care. Interesting that the correlation between various characteristics and brain size is highly sensitive to the taxa you include in your scatter plot. Marsupials seem to be substantially different from placental mammals, while primates are different from placentals as a whole. Throwing all the mammalian taxa into the analysis results in maternal care being a robust predictor, but that conclusion seems less interesting than the contingencies of the residuals.

First Irish Genome Sequenced. The paper is open access, and can be found on the Genome Biology website. Nothing too surprising, though interesting to note that they uncovered ~10% more SNPs by performing a deeper read of one individual’s genome. This sort of thing is breathing down HapMap3’s neck, and that’s a good thing for the accumulation of human knowledge.

Young Japanese Seek Second, and Third, Jobs. This quote struck me: “The Japanese economy is not just stagnant, it’s in retreat,” he said. “When people believe the future is going to be better than the present, they are happy. But if they think that the future holds no hope, then they become unhappy. It’s that unhappiness that people are trying to negate with side jobs.” In the human past the future was not necessarily seen as bright. With a world wide demographic transition Japan’s cultural trends may presage what is to come. That being said, it isn’t as if the Japanese are stuck in the Malthusian trap. They just lack the sort of dynamism which youth bulges bring.

Whewell’s Ghost. A new history of science weblog. Some familiar names are contributors. I’ll be watching.

More on Phoneme Inventory Size and Demography. Follow up to Phoneme Inventory Size and Demography. I agree with the caution about throwing too many statistical techniques at this sort of question at this stage of the game.

Genetic differences within European populations

Filed under: Uncategorized — Razib Khan @ 2:15 am

genmap3One of the more popular posts on this weblog (going by StumbleUpon and search engine referrers) focuses on genetic variation in Europe as a function of geography. In some ways the results are common sense; populations closer to each other are more genetically related. Why not? Historically people have married their neighbors and so gene flow is often well modeled as isolation by distance. The scientific rationale for these studies is to smoke out population stratification in medical genetics research programs which attempt to find associations between genes and particular diseases. By population stratification I mean the fact that different populations will naturally have different gene frequencies, and if those populations exhibit different frequencies of the disease/trait under investigation then one may have to deal with spurious correlations. If, for example, your study population includes many people of African and European descent, presumably cautious researchers would immediately by aware of this problem and attempt to take it into account. But what about populations which are genetically closer, or whose genetic difference may not be so well manifest in physical characteristics which might clue you in to the issue of stratification?

ResearchBlogging.orgThat’s why the sorts of results which might seem common sense in the aggregate are useful. One can ask questions as to the genetic closeness of Irish and English, or Irish and Spanish, in a rigorous sense. In the United States research programs which are constrained to white cases and controls may hide population stratification because of the ethnic diversity of the American population. A primary motivation for studies of Jewish genetics are the cluster of “Jewish diseases” which are common within that population. In our age it is fashionable to focus on what binds us together as a species, but genetic differences matter a great deal. Ask the parents of multiracial children who require bone marrow transplants.

A new paper in Human Heredity examines a large sample of five European populations, and goes over the between population allele frequency differences with a fine tooth comb. Genetic Differences between Five European Populations:

We sought to examine the magnitude of the differences in SNP allele frequencies between five European populations (Scotland, Ireland, Sweden, Bulgaria and Portugal) and to identify the loci with the greatest differences…We found 40,593 SNPs which are genome-wide significantly…The largest differences clustered in gene ontology categories for immunity and pigmentation. Some of the top loci span genes that have already been reported as highly stratified: genes for hair color and pigmentation (HERC2, EXOC2, IRF4), the LCT gene, genes involved in NAD metabolism, and in immunity (HLA and the Toll-like receptor genes TLR10, TLR1, TLR6). However, several genes have not previously been reported as stratified within European populations, indicating that they might also have provided selective advantages: several zinc finger genes, two genes involved in glutathione synthesis or function, and most intriguingly, FOXP2, implicated in speech development. Conclusion: Our analysis demonstrates that many SNPs show genome-wide significant differences within European populations and the magnitude of the differences correlate with the geographical distance. At least some of these differences are due to the selective advantage of polymorphisms within these loci

They looked at ~350,000 SNPs across the five populations. The sample sizes were pretty large: 1,129 individuals from Bulgaria, 1,142 from Ireland, 656 from Scotland, 620 from Sweden, and 563 from Portugal. In the supplements they had a figure where they displayed the genetic variation on the two largest principal components for their sample and color-coded by region of origin. Next to this they transposed the PCA onto a map of Europe.


This confirms previous findings that the largest component of variation in Europe is north-south (at least evaluating to the west of a particular geographical cutoff), with a secondary east-west dimension. But the focus of the paper wasn’t really phylogenetic relationships between the populations as such, but the patterns of genetic differences across them. Table 1 shows the population to population differences in SNPs. Rescaled here means that the results were rescaled for sample size, which differed between populations, along with the value after a Bonferroni correction.


The pairwise differences are what you’d expect from the PCA. Most of the between population difference is probably due to history; populations random walk into their own gene frequencies through isolation by distance. But there’s more to the story than that, as is clear in table 2.


As noted by the authors genes in specific categories or classes are overrepresented among those with large between population differences. In particular, they focus on genes related to immune function and pigmentation. The reason for variation on the former is relatively straightforward, research on patterns of natural selection in the human genome have long pinpointed loci implicated in immune function as having been particularly shaped by this evolutionary genetic parameter, no doubt because disease resistance has a major impact on reproductive fitness. Additionally, it seems likely that immune related function is constantly being buffeted by selection because of the prominence of frequency dependent dynamics. As for pigmentation, it has also shown up as a major target of natural selection in many of the more recent papers, and it’s a trait whose genetic architecture we have a reasonably good grasp of now.  They also found that the NAD synthetase 1 gene was stratified. They note that this impacts metabolism and has been found to have a relationship to the disease pellagra. Loci related to diet also seem to be disproportionately affected by natural selection, and that stands to reason as the shift to agriculture was relatively recent and many populations may still be going through transients (e.g., gluten sensitivity). The densities and diets of European populations even today vary a great deal. Italy is about an order of magnitude more dense in population than Sweden, and this has likely been the case for many millennia due to differences in primary agricultural productivity. Finally, the authors observe that FOXP2 is also stratified. This is the famous “language gene,” which regularly makes press every few years. The short of it is that FOXP2 seems to be involved in complex vocalization, and been subject to selection in tetrapod lineages where vocal ability is pronounced (birds, humans, etc.). They don’t make much of the variation in the paper, but it seemed warranted to note that the gene had popped up in their tests.

The authors freely admit that their findings are provisional:

Our paper focuses on the top 11 loci and suggests plausible mechanisms for most of them. However, the total number of genome-wide significant SNPs is 150,000 and the top hits clustered in several GO categories. We cannot judge which ones are due to the effects of selection or to other mechanisms. We present a full list of genes with the best and median p values for SNPs within them (separately for the full sample and for controls only), so that others can make use of this information in future studies…

Citation: Moskvina V, Smith M, Ivanov D, Blackwood D, Stclair D, Hultman C, Toncheva D, Gill M, Corvin A, O’Dushlaine C, Morris DW, Wray NR, Sullivan P, Pato C, Pato MT, Sklar P, Purcell S, Holmans P, O’Donovan MC, Owen MJ, & Kirov G (2010). Genetic Differences between Five European Populations. Human heredity, 70 (2), 141-149 PMID: 20616560

September 6, 2010

Daily Data Dump – Monday

Filed under: Uncategorized — Razib Khan @ 11:06 am

Happy Labor Day!

Price’s First Equation. An in-depth review of the Price Equation. First installment of several.

DNA fingerprinting pioneer discovers role of key genetic catalyst for human diversity. The strange behavior of PRDM9 could be thought of as a factor in the second term of the Price Equation.

Resentment Simmers in Western Chinese Region. “It used to be that state-owned enterprises had Han-only hiring policies, but these days they are more subtle,” said Ilham Tohti, a Uighur economist who studies the job market in Xinjiang. “They reject you after you’ve gone in for the interview and they’ve seen your face.” This indicates that straightforward racism is a problem here. Many Uighurs, including Ilham Tohti, do not have a conventional East Asian appearance. One way to check for racism is to note if Hui are treated any differently. Though Muslim, Hui don’t look much different from the Han (after generations of intermarriage the Hui are genetically no different than the Han of their region, though there is a residual proportion of West and Central Asian genes within them).

Accepted Notion of Mars as Lifeless Is Challenged. Sometimes physical scientists need to chill out in the aspersions they cast toward social scientists. It’s kind of bizarre that people are still arguing about the interpretation of these results.

Housing Woes Bring New Cry: Let Market Fall. This is a intergenerational issue. Because of that I’d bet that the government won’t allow “shock therapy.” Politicians’ first rule: don’t piss off old people.

In the lands of the living God

Filed under: Uncategorized — Razib Khan @ 1:44 am

The-Tenth-ParallelOn the face of it Eliza Griswold’s The Tenth Parallel: Dispatches from the Fault Line Between Christianity and Islam is a book whose content is summed up accurately by the title. The author recounts her experiences in various African and Asian lands which straddle the tenth parallel north of the equator: Nigeria, Sudan, Somalia, Indonesia, Malaysia, and the Philippines. It is a story told through personal narrative, the author’s, and the numerous people who are themselves embedded in larger forces welling up from below and descending from above. One can accurately describe The Tenth Parallel as a travelogue. But it is also a time machine, as Griswold surveys worlds which are a clear simulacrum of those which we know only through works of history; empires of faith, the lands of God’s platoons. As such, The Tenth Parallel is also a narrative which describes an alien world of ideas, outside of our conventional categories and classes. Many of the preconceptions and expectations which we bring to the table are “not even wrong” in the lands Griswold traverses, and what has been learned must sometimes be unlearned. This is not Newtonian Mechanics, where a cold and objective eye surveys the terrain and reports back positions and trajectories across space and time. An awareness of the author’s viewpoint is critical, while the viewpoint of her sources are plain. Finally, your own presuppositions and experiences as a reader shape the ultimate “take home” message which Eliza Griswold stitches together across her disparate sojourns.

eliza-newAs for the author, she is informs you about the details of her background repeatedly. Judging a book by its “cover” you see a young white Christian woman tasked to report on the turmoil in the lands of black and brown folk, many of whom are not Christian themselves, and many of whom are ardently Christian. But Griswold’s vantage point is more nuanced, she is the daughter of Frank Griswold, a prominent cleric in the Episcopal Church of America, who was a participant in the consecration of Gene Robinson, the first openly gay bishop in the Anglican Communion. This event has come close to rending asunder the Anglican Communion, of which the second largest district is covered by the Church of Nigeria (though arguably Nigeria has more practicing Anglicans than Britain, the largest district). In many ways in terms of core values I suspect that Muslims and Christians in Nigeria share more with each other than they do with Eliza Griswold. Her meetings with Franklin Graham, son of Billy Graham, always seem fraught with tension because it is as if Eliza Griswold’s very being serves as a witness for the liberal mainline Protestant tradition in the face of the muscular and unsubtle evangelical Protestant Christianity she observes all around her. The author’s own subjective viewpoint as a liberal Christian (at a minimum culturally, she published no precise statement of faith) interweaves with the story she tells much more subtly in most contexts than it does when she engages with Graham and his coterie. It is as if they bring with them an awareness of American culture wars and to some extent force Griswold to play her part. The author’s peculiar perspective is always there and should never be forgotten. It does not take much reading between the lines to infer that Eliza Griswold is not sympathetic to the methods of Western evangelical Protestants who believe it is their Great Commission to bring the whole world to their own faith. This is not a conclusion which is “wrong” or “right” in a conventional sense, but derived from a set of values, which the reader may or may not share.

1040The bigger canvas on which The Tenth Parallel is painted is is the idea of the 10/40 Window. This is the broad swath of the World Island between the tenth and fortieth parallels north latitude. These are the lands of Islam, Hinduism, Buddhism, and traditional Chinese religion. The vast majority of the world’s non-Christians reside in this zone, and in the past generation Western evangelicals have focused their efforts on spreading their message from Morocco to China. All of the specific conflicts explored in The Tenth Parallel can be viewed through a 10/40 lens, though Griswold is obviously surveying the world of Islam more specifically.

The author emphasizes that the conflict between Islam and Christianity in these lands is often an old one, and she illustrates this point by retelling the story of the first age of global muscular evangelical Christianity, that of the late 19th and early 20th centuries. But even that is simply a later episode of a millennial story. Globalization is often conceived of in terms of economic factors of production moving across borders, but in the pre-modern world it was more often ideas which spanned political units of organization. The expense of moving goods and services across civilizational boundaries meant that such international commerce was restricted to high-value luxuries. But ideas could flow easily because they were theoretically weightless for each marginal unit of meme.

Prior to the rise of Islam there was a Buddhist Age in Asia. From the south of India, to Transoxiana, to Japan, Buddhists traveled via the Silk Road. The monk Kumārajīva, who was instrumental in translating many Buddhist texts into Chinese, was reputedly the son of an Indian Brahmin and a Tocharian princess, a native of the Silk Road city of Kucha. In the 7th century the young Anglo-Saxon Christian Church was headed by an Archbishop of Canterbury, Theodore of Tarsus, who was born in Anatolia, lived under Persian rule, and finally fled the Islamic conquests. The Christians of South India have a long history of communion and connection with Middle Eastern Christianity, first the Persian Church, and later the Syrian Orthodox Church. The current phase of religious globalization is far less of a departure from the norm than the current age of mass migration, economic specialization, and the movement of commodities and manufactured goods.

In fact the ultimate roots of the story in The Tenth Parallel go back to the Axial Age, over 2,000 years ago, with the emergence of what we used to term “higher religions,” forms of supernatural belief which are embedded in institutions, have philosophical scaffolding, and are formalized and flexible enough to move across tribal boundaries in a coherent manner so as to maintain their integrity of identity. That is, religious ideas don’t simply transfer across groups, religious systems do. In our more sensitive age these are referred to as world religions, or organized religion. Christianity, Islam and Buddhism are exemplars. In the past Judaism, Hinduism and Zoroastrianism all had variants which transcended tribal boundaries, though these are traditions which have more or less re-tribalized themselves of late. These tribe-transcending religious systems have served to smooth the paths of travelers who could appeal to the solidarity of belief and practice across differences of ethnicity or geographical origin. The lives of Ibn Battuta and Xuanzang both attest to this. Without the charity and hospitality of co-religionists they would never have been able to complete their treks. But what brings us together can also divide, and the boundaries between world religions are often fraught with misunderstanding and incommensurability of religious foundations. Quantitative historian Peter Turchin terms the regions where world religions meet “meta-ethnic frontiers.”

Clash_of_Civilizations_mapMeta-ethnic frontiers are a touchy subject today. “Right thinking people” tend to dismiss the importance of the concept, it being too associated with Samuel P. Huntington’s The Clash of Civilizations. They reject the idea of the clash of civilizations, and assume that the book which gave rise to the term aligns with their preconceptions of the central argument. Most of the criticisms of Samuel Huntington’s work, imperfect and yet thought provoking, are of a kind where I strongly suspect that the critic hasn’t read the original, but rather is engaging nth hand expositions of the thesis. Many of the enthusiastic exponents of the clash thesis also have clearly not read Huntington’s work, which warns against neoconservative enthusiasms and suggests the necessity of a practical modus vivendi in a multipolar world riven with fissures of values. Macrohistory is generally slotted into one’s ideological preference, in large part because the principals in the discussion aren’t genuinely interested in academic issues but are looking for rhetorical devices. Academics can themselves get caught up in the game. Consider, Historian challenges assumptions about religious conflicts:

Associate professor of history Brian Catlos has spent years researching how Christians, Muslims, and Jews interact.

“Where my research and data leads, though not intentionally, is to debunk the notion of a conflict of civilizations–a conflict between groups of people who identify themselves as Christians, Jews, or Muslims and who articulate their struggle as a result of ideology and national identity,” said Catlos. “Rather what’s really behind history and contemporary human affairs is the interest of relatively small groups who often interact without regard to ideologies, national, or religious boundaries.”

Catlos observed that engaging in this type of historical research is his way of testing common assertions that there is a fundamental and irresolvable conflict between Christian and Muslim, or Jewish and Muslim, cultures. He points out that throughout history, there has been a widespread phenomenon of elites interacting with whoever will serve them best.

Such grand “common assertions” are propounded by people who are stupid. The stupidity can at the root be due to ideological preference (i.e., they know that reality varies with their ideology, but they ignore reality), ignorance, or simple lack of cognitive ability which would allow for the ability to construct models with greater subtly and nuance. It’s just as ridiculous as the inverted narratives which presuppose that religious conflicts are simply aberrations against a long history of interfaith amity. The “interfaith” movement as we understand it today is to a great extent a product of a historical moment. In particular, its roots lay in the ecumenical strand within liberal Protestantism, which eventually expanded to Christianity more generally, and finally to all world religions.

map-konfBrian Catlos’ book, The Victors and the Vanquished: Christians and Muslims of Catalonia and Aragon, 1050-1300, does refute a simple narrative of religious conflict, but, I do not believe it refutes a complex narrative of religious conflict. It is plainly wrong to assert that in every case a Muslim sides with a Muslim, and a Christian sides with a Christian. Reality is not carved out of such stark simplicities, else all scholarly endeavors would have transformed themselves into physics. There are exceptions even in cases where meta-ethnic solidarity was in clear evidence. In 1683 the Habsburg monarchy managed to obtain the support of many of the German princes who owed notional fealty to them and the crown of Poland in their battle against the Ottomans. Much of the rest of Christian European sentiment was on the side of the Hapsburgs, a fact which is notable because of the relatively recency of the Thirty Years War between Catholics and Protestants in Germany. This set of conflicts had polarized elite opinion on the continent and in the British Isles. But by the 1680s the tide had turned and Europe wearied of internecine divides in the face of the Ottoman attack. The unanimity was such that France was vilified in some circles because of its tacit alliance with the Ottomans, despite the fact that the French relationship with the Ottomans stretched back centuries. This was to a very large extent a religious war in the minds of many despite the fact that it could also be interpreted in a more conventional framework of how geopolitical conflicts emerge out of structural parameters.

But there were Christians who traveled with the advancing Ottomans to batter themselves against the walls of Christendom. When it came to the Eastern Orthodox, who had long been Ottoman subjects, and had little necessary affinity for Western Christianity, this may seem somewhat unsurprising. But there were Protestants who fought for the Ottomans. Protestants such as Thököly Imre fomented the conflict, and supported the Ottomans, against their fellow Christians. But the historical context of this alliance makes it entirely comprehensible why these Protestants had little fellow feeling for their Roman Catholic brethren. For decades the Austrian Habsburgs had persecuted Protestants and slowly re-Catholicized their domains by means soft and hard (on the soft side, inducements so that prominent Protestant families would return to the Roman fold, on the hard side a choice between expulsion or conversion in the towns). A grand Christian front against Islam was all well and good in the abstract, but for Hungarian Protestants their proximate existence as a people was dependent on a Muslim shield against their aspirant overlords, who they knew would have reimposed Catholicism upon them. The present day religious map of Hungary reflects these historical accidents. Culturally about ~25% of Hungarians are of Protestant origin, and they are concentrated in the eastern regions of the Magyar lands which were not re-Catholicized because they were under Ottoman hegemony. In contrast, what was Royal Hungary, became overwhelmingly Catholic thanks to the success of the Hapsburgs and their confederates in grinding down the Protestant majority to triviality.

scatterWhat is important is not to deny systematic biases and long term trends when you average out the seemingly random set of alliances which emerge between peoples and individuals based on immediate contingencies. It could be that in most cases alliances between polities don’t line up neatly on civilizational or confessional lines, but, over centuries non-trivial systematic biases matter. They matter insofar as the Reconquesta succeeded despite the infighting between Christian potentates. The rivalries were put aside at the battle of Las Navas de Tolosa. Over most of Iberia’s history in these centuries because of geographical proximity it may have been that most of the conflict was between Muslims and Muslims, Christians and Christians. But when evaluating on a civilizational scale if these lower level conflicts “average out,” then the systematic biases which track meta-ethnic identities can be highly significant. In the course of a few years it is ridiculous to speak in civilizational terms, but in the course of centuries it is precisely the boundaries of civilizations which wax and wane.

These intergenerational ebbs and flows of affinity, ideology and identity, are at the heart of Eliza Griswold’s narrative. In the early 20th century black Africa was operationally a “pagan” continent. Muslims and Christians were thin on the ground, generally restricted to narrow elites. The vast populace still adhered to their traditional tribal religions. As an example, Senegal, which is ~90% Muslim today, was probably only minority Muslim in 1900. Though it has arguably been part of the Dar-ul-Islam for a thousand years the peoples to the south of the Senegal river were only lightly touched by Islamic civilization. In the 20th century modernization, the rise of mass culture and communication, has produced a much deeper Islamicization in African societies where organized religion had previously been a feature of narrow urban elites. But as Eliza Griswold notes the Muslims were not the only ones at the march in Africa. European Christians saw in the “Dark Continent” a treasure trove of souls to be won, so that today Africa is split between Muslims and Christians, with Sub-Saharan Africa being majority Christian. Only in enclaves in coastal West African nations does traditional religion manifest in the public sphere, organizing itself as Vodun. Elsewhere the God of Abraham reigns supreme.

Religion_distribution_Africa_cropAfrica’s adherence to world religions has resulted in the believers aligning themselves with international concerns. Griswold points to this when observing that the religiously split city of Kaduna has Christian neighborhoods with the names Haifa, Jerusalem, and Television, while the Muslim neighborhoods are Baghdad and Afghanistan. What has Kaduna to do with Jerusalem? In concrete terms not much, but symbolically a great deal, and for humans symbolism has concrete consequences. The story Griswold tells throughout The Tenth Parallel is the integration of local concerns and tensions with global dynamics. In Nigeria Islam is closely connected to the Hausa and Fulani identities, while many of the southern ethnic groups are staunchly Christian (though many of the Yoruba have converted to Islam as well). Islam has a long history in Nigeria’s north, and clearly the southerners associate it with the past depredations of Muslim states. In Islamic law it is not legal for Muslims to enslave Muslims (though there are a fair number of “work arounds”), so the fact that West African Muslims were on the border of the Dar-ul-Islam meant that they had a ready export to the rest of the Muslim world in the form of black slaves. Long before Europeans were purchasing Africans “sold down the river,” African Muslims were selling slaves across the Sahara. With the rise to dominance of Christianity in southern Nigeria there was now an organized rival to Islam as meta-ethnic identity. A meta-ethnic frontier had come into being in central Nigeria.

In the Philippines, Malaysia Indonesia and Sudan, Griswold observes repeatedly the intricate dance between ethnicity, history, and religion. In both Indonesia and Malaysia non-Muslim ethnic minorities adhere to Christianity as a way to preserve their distinctive identity and particular history in the face of the assimilative power of the dominant Islamic culture of maritime Southeast Asia. Though outside the purview of The Tenth Parallel the same dynamic is operative in non-Muslim mainland Southeast Asia. Karens in Burma, Montongards in Vietnam, and Hmong in northern Thailand, view adherence to the Buddhism of the ethnic majority of these nations as a step toward assimilation and loss of ethnic identity. Though Christianity is just as alien in nature to the shamanic spiritual traditions of these peoples as Buddhism, it serves as a distinctive ethnic marker in regions where affiliation to the two religions tracks ethnicity perfectly. And, it also allies the Christian minorities with a powerful civilizational international.

In eastern Indonesia the Christian Ambonese, converted during the period of Dutch rule before Islam had swept so far east, were often partisans of the colonial regime against the efforts of the predominantly Muslim independenc movement. The case of the Ambonese points to a general resentment of the majority culture in many regions impacted by European colonialism. It seems plausible that without European involvement many of the “hill tribes” of eastern India and Southeast Asia would eventually have been assimilated into the ethno-religious mainstream, as many of their predecessors had been. In the process though they would have lost their identity, the cost of social harmony being conformity and homogenization. Whether the perpetuation of ethno-cultural distinctiveness through the alignment of particular groups with different meta-ethnic world religious identities is good or bad is strongly conditioned upon your own specific viewpoint. But in The Tenth Parallel Eliza Griswold shows that from Africa to Southeast Asia the general dynamic is similar. The cleavages shake out in a familiar form, despite the local origins of the conflicts.

800px-Taj_Mahal,_Agra,_IndiaOf course despite the subtitle there’s more to religious conflict than that between religions. There is also the conflict within religions. Eliza Griswold’s clear discomfort with the image which evangelical Protestants were projecting to the Muslim world of Christianity is an instance of that. But so is the strife which emerges within and across the sects of Islam. The standard model posits the rise of a Fundamentalist Islam at war with local Sufi traditions. There is a great deal to this story, as far as it goes. But there is a precision and clarity with Fundamentalist Islam, which is really often world normative Islam shifted toward a Saudi Salafi tinge, which does not exist with “moderate Islam” or “Sufi Islam.” By its very nature locally inflected Islam is diverse, and can’t be bracketed under a catchall term on any substantive grounds except to point to its negation of Salafi or reformist Islam. The rise of internationalist Salafi Islams is another case of cultural globalization, and its roots go back centuries. Several hundred years ago many regions of the Islamic world, confronting European powers on the rise, or declining Islamic orders such as that of the Ottomans, entered into a period of reform which gave birth to fundamentalisms of various flavors. The Deobandi movement in India, the Wahhabis of Arabia, and the Fulani jihad may all be considered instantiations of a broader international pattern. Pushing against this were a diverse array of local Islams, many of which lacked the coherency of the reformists who claimed to be bringing Islam back to its first principles. The success of the local Islams varied. In Arabia the Wahhabis allied with the House of Saud and eventually rode the latter’s victories to religious supremacy in most of the peninsula. The Wahhabi ascendancy has been marked by a physical destruction of monuments to rival Islamic traditions, as well as the despised position of Shia within the kingdom. In South Asia the fundamentalist reformists have not swept all before them, as the numerical preponderance of other traditions attests to, though arguably in in Pakistan they have influence out of proportion to their numbers. In Indonesia and Malaysia the fundamentalists are a small minority among the Muslim majority, which varies in its adherence to world normative Islam in any case.

And yet how much should we make of this division within Islam, or those within Christianity? In both Malaysia and Indonesia the governments encourage conversion to Islam by the remaining groups not aligned with a world religion. Despite her conflicts with fundamentalists in her own religion Eliza Griswold did in the end agree to pray with Franklin Graham. There are wheels within wheels. Focusing on one specific wheel, one layer of the dynamic, does not deny that that wheel and dynamic may be nested within others, and that others may be nested within it. The frictions and conflicts on the tenth parallel play out on multiple hierarchical levels. Individuals have their own interests, as do ethnic groups, and finally meta-ethnic groups. Modern Westerners tend to have a methodological individualistic bias, and so reduce group actions to an aggregate of the material incentives and preferences of groups of individuals. This is far too pat and simple. But how to define interests and a meta-ethnic group, a religion, can be easily problematized. As I noted above it is highly likely that the Nigerians killing each other over ethno-religious differences share much more in values and outlook with each other than they do with Westerners. But human conflict often hinges on symbolic markers and issues. One can muse in the vein of “War, what is it good for?”, but at the end of the day war is. Similarly, as an atheist I do not believe that there is a God in fact, but the fact of the beliefs of others that God is is highly consequential. It is less important what the real Islam or Christianity is, than what Islam or Christianity is for the people at any specific place and time. By and large in a world characterized by economic growth driven by non-zero sum interactions violent physical conflict produces absolute losers on all sides. But the heuristics and biases research tells us that quite often people care less about the height of the hill than their own peak position atop it. What Eliza Griswold documents in The Tenth Parallel is of great interest precisely because it puts the spotlight on the individual psychology of people who are caught up in eternal macrohistorical dynamics, processes which we’ve only begun to see as destructive for the aims of greater human wealth and health in the last few centuries.

Addendum: I believe that anyone who finds The Tenth Parallel of interest would benefit from reading some of Philip Jenkins and Peter Turchin’s works.

Image Credit: Wikimedia, Antonin Kratochvil

September 5, 2010

More school, more work

Filed under: Uncategorized — Razib Khan @ 11:11 am

Tomorrow is Labor Day in the USA. I was actually shocked to realize last week that the USA has a higher unemployment rate than many European nations. I grew up in the 1990s when we were conditioned to assume that Europe would always have higher structural unemployment for a variety of reasons. In any case, I decided to look at some employment-related data in Google Public Data Explorer. Below on the x-axis are the employment rates for a selected number of nations over time, and on the y-axis the employment rates for the 15-24 age group. The employment rate in the first case is simply the proportion in the age range 15-64 who are in employment. Note the change in the relationship of the two values over time. I’ve highlighted the USA, the Netherlands, Sweden, Greece, and Mexico, to show you their movement across the grid.

Let’s limit the x-axis to women only:

I think what you’re obviously seeing are two general trends: women entering the labor market and the transition from the single-income household to the two-income household, as well as a balance in the younger age brackets through the fact that many more youth are pursuing higher education. So the y-axis is more stable, as the shift toward females in the labor market is balanced by a higher proportion going to university. The changes in some nations like the Netherlands are really striking.

September 4, 2010

Open Thread, September 4th, 2010

Filed under: Uncategorized — Razib Khan @ 9:53 am

If you’re American, you should be at a barbecue or something! So what podcasts do you listen to? The main talk show I listen to is Tom Ashbrook’s.

September 3, 2010

Katz, 9-3-2010

Filed under: Uncategorized — Razib Khan @ 11:06 am



Daily Data Dump – Friday

Filed under: Uncategorized — Razib Khan @ 10:31 am

Have a good Labor Day weekend!

Catholics and the Evolving Cosmos. And yet 35% of American Roman Catholics are Creationists according to the GSS.

23andMe kits at some discount, with a subscription to the “personal genome service” for at least 3 months. Normal complete edition is about $500, with the discount it’s about $300 + 3 X $5 = $315. The personal genome service doesn’t look like much value-add from what I can tell, just a way to get extra money out of you. I assume they’ve calculated that $5 is a small enough amount that many people won’t unsubscribe after 3 months.

Capsaicin Can Act as Co-Carcinogen, Study Finds; Chili Pepper Component Linked to Skin Cancer. The problem is with topical creams. I keep track of this stuff because I eat a lot of spicy food. On the balance it seems that it does more good than bad, so I’m pretty chilled out, so to speak.

Insight Offered Into Superstitious Behavior Thinking about death makes people less superstitious? Can you think of a better explanation of what’s going on here?

How Bankruptcy Can Rescue Students from the Debt Trap. Yeah, I think this should be an option. The median undergrad is graduating with around a little north of $20,000 in debt, but there are people way up the scale. It’s a skewed distribution. Too many people think of student loans as “free money.” Actually, it’s someone’s money. In fact, it’s your money, whether through direct federal loans and subsidizations, or through the big pool of capital drawing on pension and mutual funds.

European man, Y chromosomes & tea leaves

Filed under: Uncategorized — Razib Khan @ 3:00 am

Sydney_opera_house_side_viewSometimes in applied fields artistic license is constrained by the necessity of function to particular creative channels. Architecture comes to mind, at least before innovative technologies produced lighter and stronger materials, freeing up form from its straitjacket (whether this was a positive development is a matter of taste). But there’s only so much you can do with your palette when your palette is limited. This can be a bug, or it can be a feature. Science is not art, but in some ways at its heart it’s a story about the universe. The story can be in words or math, no matter, ultimately it’s the human attempt to map nature and make its subtle patterns comprehensible to us in plainer fashion. Some of the human biases in our quest are transparent. Why is there anthropology? A whole discipline devoted to the study of mankind and his nearest biological kin. We don’t peruse the patters with an objective and uninterested eye. We’re shaped by our presuppositions, as well as the constraints of the methods, and the results we have before us. The emergence of a theoretical evolutionary biology in the decades before the molecular revolution after World War II may have been in part simply a function of the fact that there were only so many results one could squeeze out of classical evolutionary genetic techniques, which relied on tracking only a limited set of phenotypes due to large effect mutations in breeding populations. With the rise of molecular evolution you saw the crystallization of theoretical frameworks, such as the neutral theory, to explain the burst of novel results.

ResearchBlogging.orgAround the year 2000 something similar happened in historical population genetics. The analysis of mtDNA lineages, passed from mother to daughter, had matured, and techniques for typing the Y chromosome had started to catch up, so that a symmetry between the sexes could arise. “Mitochondrial Eve” was now paired with “Y chromosomal Adam.” Though mtDNA and Y lineages were only two direct lines of ancestry, because there was no recombination across much of their sequence it was easy to analyze them within the context of coalescent theory. In contrast, the genealogy of autosomal regions of the genome were confounded by recombination, which mixed & matched the variation in a manner which made reconstruction of past history far more difficult. So we had the technology to extract the genetic variation from mtDNA and the Y chromosome, and, we knew how to model their evolution. The two together produced a genetic time machine.

spencer_wells_00aThe result was a swelling of papers utilizing uniparental markers. You can see the chronology to some extent at the frequency of postings at Stanford’s Human Population Genetics Laboratory online repository. Another byproduct was the emergence of public intellectuals who filled the need which arose to interpret and communicate the findings to a lay audience. Four books are emblematic of the era, Bryan Sykes’ The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry, Spencer Wells’ The Journey of Man: A Genetic Odyssey, Stephen Oppenheimer’s The Real Eve: Modern Man’s Journey Out of Africa, and Steven Olson’s Mapping Human History: Genes, Race, and Our Common Origins. As a professional journalist Olson’s treatment was the odd one out, as much reportage as a personal interpretation. In contrast, Sykes, Wells, and Oppenheimer were making scholarly cases from their own vantage point. Oppenheimer and Wells also paired their books with television documentaries. Wells continues to remain in the public eye, he’s become a new sort of intellectual entrepreneur with the The Genographic Project. The age of uniparental markers then spawned careers and truisms. For example, the patterns of variation of mtDNA and Y chromosomes resulted in the consensus that ~75% of the ancestors of modern Europeans are descended from Paleolithic hunter-gatherers. The proportion of the ancestry contributed by Neolithic farmers decreased from southeast to northwest, converging upon zero in the far reaches of the British Isles and Norden.

R1bmapThis inference was made in large part based upon the contemporary patterns of genetic variation, by assigning modern haplogroups to putative ancient populations. To the left is a map of the frequency of haplogroup R1b, which is the most common Y chromosomal lineage in western Europe. The frequency is highest among the Basques, who were presumed to be the most pristine reservoir of the genetic substratum of Paleolithic Europe. The conception here was that the Basques were clearly indigenous to Iberia, they were already there before the arrival of outsiders such as the Celts, Phoenicians, and finally Romans (this has influenced modern Basque nationalism to some extent). Their non-Indo-European language was assumed to be a relic of many dialects which once existed before Indo-European swept over them. Using R1b, and other haplogroups at high frequency among the “indigenous peoples” of Europe, historical geneticists pegged the ancestral quanta of hypothetical prehistoric groups using these putative indigenes as modern references. But the inferences rested on assumptions, assumptions which couldn’t be directly tested. Until that is another methodological revolution arrived on the scene: the extraction of ancient DNA! These new waves of results, which came to the fore in the latter 2000s, have unsettled our preconceptions. It now seems that the past was likely more complex than we’d presumed, and the palimpsest of human genetic variation over time may have obscured and clouded our understanding of the map of what once was.

More recently some researches have gone back and looked at the variation within the R1b haplogroup, specifically the subclade which is very common in Western Europe, R1b1b2, and concluded that in fact it was most diverse in the eastern Mediterranean.  The most plausible inference to be made from this was that the R1b1b2 originated to the east, and spread to the west, rising in frequency due to genetic drift as populations went through bottlenecks and then rapidly expanded in size. Additionally, the last common ancestor of these lineages was on the order of ~10,000 years ago. This naturally upends the model which geneticists were confidently pushing forward in the early 2000s, shutting the door on debates as to the provenance of modern Europeans and their relationship to Ice Age hunter-gatherers. A follow up paper rebutted this new claim as to the origin and expansion of R1b1b2. What had been a stable and conventional area of historical population genetics has now been thrown into tumult, and researchers are looking more closely at the uniparental lineages which had had their time in the sun. Or so it seemed.

So with that background, a paper in The European Journal of Human Genetics steps into the “R1b controversy,” leaning to the side of those who argue for its origin more recently among Neolithic farmers. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe:

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past 10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

There’s aren’t incredibly novel techniques of analyses here. Rather, the confusion around R1b1b2 has prompted researchers to expand their population coverage and resequence the markers around the haplogroup. These phylogenetic trees are constructed by genealogies which are separated by mutational steps, with steps of daughter mutations down a particular branch and distinguishing various derived clades. The terminology can kind of get confusing, but R1b1b2 is equivalent to the M269 branch in this study. What they did was analyze the phylogenetic relationships of the branches of R1b1b2 and it sister clades, and plot their frequencies as a function of geography. Below are a set of figures which show the frequencies of various clades across Europe. The last figure has several panels because they’re all subclades, and of somewhat less interest to the big picture. The first figure has the various branches, so you can see how they relate before browsing the maps.

M269 is really the one to focus on. It and its daughter branches are at the heart of the Paleolithic vs. Neolithic controversy. Compare the phylogenetic tree in the first image, and the distributions of the allele frequencies in the subsequent images. The Western European variants seem to be daughter branches from an ancestral variant which is found in Anatolia or thereabouts. The authors also confirm the coalescence back to the last common ancestor  ~10,000 years ago, though the methods have a bias toward inflating the value, so that’s an upper bound. They also used PCA analysis show how the haplogroup variation exhibited cluster patterns. The first panel has the haplogroups, with PC 1 separating the ancestral R1b variant from the daughters, and the second PC separating each daughter branch. The second panel inputs the various fractions of R1b haplogroups in populations. There’s an obvious recapitulation of the geographical map in the distribution of haplogroups.


What’s the moral of this story? I’m not going to get into the correlations they adduce between various archaeological groups and genetic lineages. That got us into trouble earlier as I implied. I don’t think the fine-grained results are solid enough that we should be taking that sort of interpretation too seriously. Rather, it’s telling us what we don’t know, and what we shouldn’t be clear on. I lean toward the proposition that R1b1b2 was brought by Neolithic farmers at this point, the paper which refuted that finding leaned strong on samples from Sardinia, which I suspect are more than not atypical and not representative (Sardinia tends to be an outlier on genetic plots because of its island isolation). But my confidence is hardly even modest at this point. There’s a lot we don’t know.

Stonehenge_back_wideHistory begins in Sumeria with the written word ~5,000 years ago. But as history dawns agriculture was still new to Norden and the fringes of the Baltic and British Isles. By the time what the ancients called Thule came into some focus, after the fall of the Roman Empire, much had passed beyond our line of sight. The original geneticists and archaeologists who attempted to synthesize their disciplines and construct a plausible model of how Europeans and Europe in its linguistic, genetic, and cultural variation, came to be, followed the principle of parsimony. Cavalli-Sofrza, Ammerman, and Renfrew presented us with a model where Paleolithic Europeans, who hunted & gathered, and spoke non-Indo-European languages, were slowly replaced culturally, linguistically, and partially genetically, by Indo-Europeans who brought farming from the Middle East. This was the “demic diffusion” hypothesis. I don’t think anyone accepts this as likely at this point, at least in its total simplicity of explanatory power. We need to reconsider whether the Basques can even serve as models for Paleolithic European man anymore! It may be that the Basques themselves are culturally and genetically intrusive, bringing their language and folkways along Mediterranean shores with agriculture, eventually marginalizing the thin numbers of hunter-gatherers beyond the limes of their “civilization.” Additionally, we have to remember that there was history before history, that what we term prehistory is rich with many developments which are preserved only vaguely and in the mists of oral tradition (though that tradition rapidly decays in fidelity). The more recent expansion of the Bantu and Austronesian languages do not benefit from copious records, because they spread with preliterate societies. The expansion of Turkic and Indo-Iranian dialects can only be perceived in the outlines because these peoples were on the fringes of societies where writing was part of their culture. Europe’s shift to agriculture occurred over thousands of years, and those thousands of years were all preliterate. Stonehenge and the megaliths were constructed by societies which we can comprehend only through their most robust monuments. The stones speak to a complexity which genetics can not resolve. Sometimes admitting that you don’t know is an answer in and of itself.

Citation: Myres NM, Rootsi S, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Pshenichnov A, Yunusbayev B, Balanovsky O, Balanovska E, Rudan P, Baldovic M, Herrera RJ, Chiaroni J, Di Cristofaro J, Villems R, Kivisild T, & Underhill PA (2010). A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. European journal of human genetics : EJHG PMID: 20736979

Image Credit: Frédéric Vincent, Matthew Field, National Geographic, Wikimedia

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