Credit: Characterizing the admixed African ancestry of African Americans

My own inclination has been to not get bogged down in the latest race and IQ controversy because I don’t have that much time, and the core readership here is probably not going to get any new information from me, since this is not an area of hot novel research. But that doesn’t mean the rest of the world isn’t talking, and I think perhaps it might be useful for people if I stepped a bit into this discussion between Andrew Sullivan and Ta-Nehisi Coates specifically. My primary concern is that here we have two literary intellectuals arguing about a complex topic which spans the humanities and the sciences. Ta-Nehisi, as one who studies history, feels confident that he can dismiss the utility of racial population structure categorization because as he says, “no coherent, fixed definition of race actually exists.” I am actually more of a history guy than a math guy, not because I love history more than math, but because I am not very good at math. And I’ve even read books such as The Rise and Fall of the Caucasian Race and The History of White People (as well as biographies of older racial theorists, such as Madison Grant). So I am not entirely ignorant of Ta-Nehisi’s bailiwick, but, I think it would be prudent for the hoarders of old texts to become a touch more familiar with the crisp formalities of the natural sciences.

In his posts on this topic Ta-Nehisi repeatedly points to the real diversity in physical type and ancestry among African Americans, despite acknowledging implicitly the shared preponderant history. But today with genomic methods we have a rather better idea of the distribution of ancestry among African Americans. The above plot is from Characterizing the admixed African ancestry of African Americans, a 2009 paper with 94 Africans of diverse geographic origins, 136 African Americans, and 38 European Americans. They looked at 450,000 genetic variants (SNPs) per person (there are somewhat more than 10 million SNPs in the human genome). Obviously individuals and populations exhibit genetic relationships to each other contingent upon the patterns of the variation of base pairs (A, C, G, and T) across the genomes of individuals, but there’s no reasonable way to comprehend this “by eye” when you’re talking about hundreds of thousands of markers. The authors used two simple methods to infer clustering within the data set.

First, you see a PCA plot. This method is one where the independent dimensions of variation within the data set of the markers are pulled out. They are rank ordered in terms of how much variation they can explain (dimension 1 by convention explains the most, dimension 2 explains the second most, and so forth). Each dimension can be thought of has having a value proportional to its explanatory power. Each individual then has a value position on the dimension, dependent on how that individual relates to the others. When you take multiple dimensions and transpose the data geometrically you quickly see population structure fall out of the data set. Notice above that the first dimension of variation (PC1) separates the Europeans from all the African populations. The second dimension of variation (PC2) separates the hunter-gatherer populations of Africa from the agriculturalists. While the Mandenka are from Senegal, the Yoruba are from Nigeria, at opposite ends of what is traditionally termed West Africa. This was the presumed source of most of the African slaves who arrived in the United States. Once these slaves came to the United States some of then had children with white Americans.  It turns out that the average African ancestral contribution to to African Americans is ~80%, with the balance being mostly European (there is some Native American, but not much). In fact this is very close to the estimates which were produced by genealogists. The concordance of these methods is reassuring, since the underlying phenomena is the same.

Notice that on the PCA plot no African American falls in the Mandenka-Yoruba cluster. That is because almost no African American whose ancestors are not recent immigrants from Africa lack white ancestry. This is entirely reasonable when you consider that the vast majority of their ancestors were resident in the colonies before the Revolutionary War. Admixture events would have percolated throughout the genealogical tree in subsequent generations. The African Americans are distributed almost perfectly along a line between the West African populations and the European Americans. Observe that the density seems to decrease as you approach the European American cluster.

Now we can move to the second visualization technique. While the PCA does not posit any hypothesis of population structure (it just “fell out” of the genetic variation due to the shared history of some individuals via their common ancestors), the second method is “model based,” in that the authors posited seven ancestral populations to match the seven populations which African Americans may be derived from. In a way this is rigging the game; if you force the method to squeeze out particular numbers of populations it may act strangely. But in this case we have prior expectations, so this number of populations is not unreasonable. Above each bar plot represents an African American individual, with each fraction of shading an ancestral element. The results from the PCA are reproduced nearly perfectly by this differing method. The average ancestral quantum of African heritage in this sample is ~80%. And, you see more cleanly the variation in European ancestry among African Americans. Less than 10% of African Americans are like Barack Obama, at least 50% (or more) of European ancestry. The African ancestry excludes the hunter-gatherer populations which is reasonable since the slaves were from the Congo in the east (where some were Bantu) as far as Senegal in the west.

The first black head of the NAACP

Ta-Nehisi has used an imagine of Walter White, the first African American head of the NAACP, to illustrate the pliability of the black identity. It certainly shows that there are no fixed definitions of race which are particularly useful. But that is a misconception of biological science, which is rife with exceptions and boundary conditions, and characterized by an instrumental perspective. The data above suggests that self-identified African Americans are characterized by some African ancestry, but over 90% are more than 50% African in ancestry. Walter White, who had five black great great great grandparents and 27 white ones, was almost certainly less than 20% African in ancestry. There are such people even today, but they are not typical, and do not disprove the reality that African Americans are predominantly of African ancestry.

From a scientific perspective in biology there are not ultimate and fundamental taxonomic facts. There are simply useful ideas and concepts to illustrate and explore the objective phenomena of the natural world. The Species Concepts debate shows us this reality well, as even species can be tendentious. But the debate often shakes out along disciplinary lines. Many more ecological scientists seem to be taken by the ecological species concept, while evolutionary geneticists are more keen on the biological species concept. That is because they are choosing the framework most useful for their ends. There is nothing “Post Modern” in this in that it denies reality. Rather, we are disputing the ideas which we use to capture the essence of real phenomena in compact semantic relations suitable for symbolic representation (whether with math or language).

Prior to the modern systematic era of biology humans did attempt to classify themselves. Generally they looked at a few informative features. For example the Chinese referred to both South and Southeast Asians as “black,” not because they thought they were African, but because they had brown or dark brown skins. Similarly, Arab ethnographers differentiated between ruddy peoples to the north, black ones to the south, and black ones to the east (Indians). And so on. This is almost certainly an elaboration of our innate cognitive ‘folk biology.’ By this, I mean that we as humans tend to classify organisms. Why this is adaptive is trivially obvious. When humans meet new organisms which resemble those which they have familiarity with prior, they simply reformulate the novel creatures as variants of the familiar ones. For example the Tasmanian Tiger was no tiger. It was not even a placental mammal. But through convergent evolution it resembled placental carnivores. Analogously, when Europeans first met the straight haired brown skinned native peoples of the New World they termed them “Indians,” a straight haired brown skinned population of the Old World. When they met the very dark and kinky haired peoples of the western Pacific they assumed they were some relation to Africans, and these became “Melanesians” (which means “black islanders”).

A second component of human nature which Coates alludes to is our tendency to cohere into groups with narratives of internal identity set apart from the Other. In the pre-modern world these inter-group cleavages would be marked by accent, dress, and tattoos. In the early modern world they would be correlated with religion or nationality. The dynamic at issue here is that extremely genetically close populations which would be indistinguishable naked had to generate salient cultural markers. In the case of the ancient Hebrews one could argue that circumcision was exactly the sort of marker which would persist even when naked!* This does not mean that there were no detectable genetic differences between adjacent small scale societies; there are after all detectable genetic differences across European villages today. But for particular technical evolutionary reasons (far more within group variance than between group variance in regards to genetics) it is likely that for inter-group competition cultural forces reigned supreme over biology, and were determinative of identity.

Both of these parameters are from our deep history as a species characterized by life as hunter-gatherers in bands. The next force is more recent, and historically contingent. As I suggested above non-European and pre-modern peoples had a vague conception of race on the continental scale. The Classical Greeks even distinguished he various brown peoples, the Egyptians and the Indians of the north, and black peoples, the Ethiopians and the Indians of the south. The fact that the initial explorers who arrived in the New World labeled the indigenous people Indians, and not Chinese or Africans, shows an awareness of global diversity (in contrast, the British referred to the Australian Aboriginals as blacks). When the British first arrived in India as supplicants to the Great Mughal they differentiated between the diverse races of the subcontinent. The black and brown natives, and a portion of the elites who were white (West Asian Persians and Turks).

This changed over the centuries, and after 1800 the age of European supremacy and the rise of systematic science produced the sort of racial nationalism which serves as the backdrop to our understanding of race more generally. Whereas the pre-modern folk biological taxonomies were coarse, but generally accurate up to a point, the age of white supremacy produced a somewhat schizophrenic science of precision and exaggeration. By this, I mean that the attempt to be formally scientific resulted in a plethora of categorizations and grades of hierarchy. But, the reality of white supremacy generated a taxonomy of dominion, where all the races of color were aggregated into an amorphous whole. Perhaps these two countervailing tendencies explains the juxtaposition of quasi-fixed racial characters with a bizarrely elastic definition of the Other, the non-white. Few moderns agree with Lothrop Stoddard’s The Rising Tide of Color Against White World-Supremacy, but many implicitly accept the framework of whites and a coalition of “people of color.”

So there you have it. An underlying biological reality which is a reflection of deep history. It may not be real or factual, but it is consistent and coherent. Then there are innate faculties which lead us toward categorization of humans into various kinds, for deeply adaptive purposes. Finally, there are historically contingent events which warp our perception of categories so as to fit into power relations in a straightforward sense. But wait, there’s more!

Diabetes risk higher in African Americans with more African ancestry, link

The biological aspect above focused on ancestry and history. But this is not academic detail. The history of a population affects it genome, and its genome effects the nature of its traits and diseases.  Because of differences across populations statistical geneticists with medical aims routinely restrict their data set to individuals of one population. And, within groups like African Americans which are admixed there is variation in disease risk by genomic fraction. Though an individual with 60 percent African ancestry may feel and say they are no more or no less African American than someone who is 80 percent African in ancestry, there are differences in disease susceptibilities.

There is no Platonic sense where there are perfect categories with ideal uses. Rather, we muddle on, making usage of heuristics and frameworks which are serviceable for the moment. We lose our way when we ignore the multi-textured nature of the issues.

* Though many of the neighboring peoples practiced circumcision, so this is more of an apocryphal illustration than a real instance of functional traits on a cultural level in societies.

I went to the talks about the Myriad case at ASHG, and I have to say it was all law, and no science. The science was confused and laughable. The panelists themselves rolled their eyes and expressed resignation as to the garbled ratiocinations of the judges who reviewed the case. There is a classic “two cultures” problem.

Credit: cavorite

A few years ago I predicted to some friends that ancient DNA would transform our understanding of the human past. The reason being that inferences of population movements via material remains were imprecise at best. We are beginning to see my prediction come to fruit (mind you, the prediction was not a bold or courageous one). A new short communication in Nature Communications, A European population in Minoan Bronze Age Crete, addresses an old and frankly somewhat outdated question: whether the first European literate civilization derived from a transplantation from Egypt, or was autochthonous.

I say that this is a somewhat outdated test because the modern proponent of this theory, Arthur Evans, lived a century ago, when our understanding of pre-Classical antiquity (i.e., the world before 600 BC and literate alphabetic Greek civilization) was sketchy at best. The reality is that ancient Crete, like the ancient Levant, does seem to have been in the greater Egyptian culture sphere of influence, just as ancient Elam (southwest Iran) was a de facto part of the Mesopotamian world. But we know the language of the Elamites, and it was not related to Mesopotamian languages. Just as the Finns have been influenced by their Nordic neighbors, so were the Elamites influenced by their Sumerian neighbors. But their linguistic difference points to fundamentally distinct origins. And so it is with the Minoans. It was already likely from the peculiar nature of Minoan writing, Linear A, that this civilization was not a simple derivation of Egypt. These genetic data just add more evidence.

Over at Nature Ewen Callaway has naturally written up an excellent summation of the relevant points of the paper. First, they used mtDNA. The maternal lineage (mtDNA is copious, so excellent for ancient DNA extraction). They compared their several dozen Minoan era (Bronze Age) samples to other various ancient and modern populations. Even with the modest sample sizes and the mtDNA as the sole line of inference it seems that the authors do a reasonable job of rebutting a North African origin for Minoans. Plenty of modern data imply that for whatever reason the Mediterranean is a formidable barrier, and that populations seem to have hugged the northern and southern coasts as they pushed from the East. The exceptions in later times, for example the migration of the Sea Peoples in the Bronze Age, seem not to have perturbed the underlying genetic substrate. More importantly, as I note above we know far more about the Bronze Age Aegean than Sir Arthur Evans. For example, we know that the mainland populations who seem to have displaced Minoan civlization >1500 BC were Greek speakers! Evans did not know this, and this fact was somewhat of a surprise when Michael Ventris stumbled upon this reality.

Credit: Rosemania

To understand why, one must grasp that we are arguably more culturally conscious of the Athens of the 5th century BC than those Athenians were of the Athens of the 12th century BC. At the end of the Bronze Age there was a great cataclysm in terms of the breakdown of the social and political order. Aegean civilization as it was properly understood was erased, and Greece descended into barbarism. Egypt itself barely managed to hold onto its sense of self in the face of barbarian attacks. While Egypt retrenched the mysterious Hittite Empire of Anatolia collapsed in totality. The only recollection of the Hittites persisting down to the modern era can be found in the Hebrew Bible, where there are references toward satellite Levantine Hittite principalities which limped onward after the fall of the center.

After the collapse of the Myceanean citadel culture which succeeded the Minoans Aegean Greek civilization was rebuilt on fundamentally different foundations. The Greeks forgot the art of writing, and invented their own alphabet after being stimulated by the Phoenicians. The legends of the Trojan War and the broader mythological backdrop of Classical Greek society recalled fragments of the memories of the Bronze Age, but only just fragments. The tales of Agamemnon reflect barbaric Dark Age Greece (1200-800 BC), not the bureaucratized world of the Mycenaeans.

In light of all this it is no surprise that early 20th century scholars posited an exotic origin for the peculiar Minoan-Myceanean civilizations whose material remains they stumbled upon. Many of these were gentlemen who were classically educated, and the coarse and brutal world of Bronze Age Greece was utterly alien to them. Not only that, these scholars would have been surprised that Crete and to a lesser extent the Myceaneans were part of the broader Near Eastern world system, despite being of fundamentally different cultural origin. The reality is that it is somewhat deceptive to label Cretan civilization as European, because Europe is an anachronism.

Over the next few years more and more DNA samples will come to light. I will predict that the Mediterranean islands were come to viewed as very specific reservoirs for ancient genetic variation. The mainland seems to have been  subject to folk migrations, but islands were spared (because barbarians from the hinterland lack native skill on the sea?) As more Greek samples come in I suspect that Slavic admixture will be obvious, meaning Create and Cyprus (along with Sardinia)  represent more ‘authentic’ ancient Greek populations.

Note: I highly recommend Michael Wood’s In Search of the Trojan War.

I will state though Kevin’s argument seems to be predicated on the implicit assumption that his interlocutors hold to some sort of Platonic ideal of the most-perfect-human. There’s no such thing obviously, and even those who sympathized with eugenic policies such as W. D. Hamilton rejected this notion at the end of the day. Rather, human traits are evaluated in terms of how they serve the flourishing of individuals and society according to understood values. Intelligence is generally assumed to benefit individuals, and, I believe that it benefits society as well through innovation. Innovation drives the productivity growth which is the foundation of our post-Malthusian age.

And the reality is that this isn’t all about talk. As I’ve mentioned multiple times the frequency of individuals with Down syndrome is reduced by selective abortion. Screens to detect this condition in utero are getting better and better. The sketchy empirical results we do have implies that ~90 percent of couples who receive a “positive” result chose to abort. Should this be against the law? If you take the anti-eugenic argument to its logical conclusion perhaps, because you are making a value judgement on the “quality” of an individual.

Taking an argument to a logical conclusion may give some insight, but generally it is not too useful in practice. We should be careful about taking things their logical conclusion because human affairs aren’t often dictated by logic. The reality is that eugenics in the 21st century will be driven from the “bottom-up,” through individual choice. Market forces and revealed preferences. There will be no ministry of procreation, or social engineering to sculpt the Übermensch. In fact there may be rational reasons to regulate and curtail choice so as to minimize positional bidding on the margin.

On a broader normative note, I am fine with the idea that there are beautiful people and ugly people, smart people and stupid people, nice people and mean people. Some of this is socially constructed, but some of this is not. Kevin makes the accusation of elitism against those academics, such as Steve, who support selection for intelligence. Let me suggest something here: Steve has much to lose in a selfish zero sum sense because he’s already rather assured of intelligent offspring. He’s smart. His wife is smart. Standard quantitative genetics implies that even if they regress to the mean his offspring will be quite bright. There may not be much more juice to squeeze out of that genetic background. It may be very different for a couple with more average endowments. So sorry to turn this upside down, but personal eugenics may in fact be a boon for the ugly, stupid, and psychologically unstable, because it gives them a opportunity to close much of the gap with those who were lucky in the genetic lottery. Some of you may object to terms such as “ugly,” “stupid,” or “psychological unstable.” But people with these issues have to deal with them in their day to day. One can make all the platitudes one wants to make about “inner beauty,” but very few people live by this ideal.

The biggest issue I have with Kevin’s post is that it’s general and over-broad, with a focus on 20th century industrial scale eugenics and genocide. What we’re really going to confront are a myriad of specific cases, and market-driven personal eugenics which has a service sector tinge.

Addendum: It makes sense to be skeptical of the scientific possibilities in the near to medium term.

* Someone attempted to post the following comment:

“I don’t have a great deal of time to engage Kevin right now.” is not the best way to begin an article in which you proceed to do exactly that. It’s disrespectful to both your readers and Kevin: either engage properly or not at all.

1) If you attempt to be my editor I’m going to ban you without warning. Readers don’t make demands of me. If you do so, I’ll ban you.

2) This post was nothing of the kind in terms of being a real response to Kevin’s very wide ranging elucidation of opinions. It took 30 minutes of my time to quickly reiterate some rather simple positions I’ve long stated. That being said, I think it was still useful for someone to outline this position concisely, which is all I could do with my current constraint of marginal time.

I haven’t been able to blog much because of various other responsibilities, but I definitely do feel pent up posting energy. So when I come back I assume that I’ll have a lot of stuff to say. Meanwhile I’m chortling a bit about this bizarre attack on my friend Steve Hsu. Here’s the issue that I always have with this: Steve managed to get tenure as a theoretical physicist. When you’re talking to someone who is an academic theoretical physicist it is generally optimal to not assume a priori that they’re ignorant dullards. Unless that is you want to just engage in empty signalling rhetoric.

Though despite not having concerted time to write, I am tweeting a lot since that requires only minimal lengths of attention. Mostly it’s just repeating the functionality of my Pinboard, though I do comment and what not.

Finally, I keep hearing that the Big Five personality typology is much more scientific than Myers Briggs. So I took a bunch of tests which purport to analyze the Big Five categories.

Extraverted: Very high. Consistent. I was 90-99% on all tests.
Agreeableness: Low. Consistent. Generally in the 15-0% range.
Openness: Medium. This was not very consistent. 40-60% range.
Neuroticism: Erratic. For whatever reason I varied from 20-80% here.
Conscientiousness: Medium. But there was some variation.

Oh, and here’s a list of books I’ve rated for Good Reads.

(via The Festival of Patience)

Cite: :10.1080/00224499.2011.628132

The above figure displays results from males in the General Social Survey who answer yes to the proposition that they’ve watched a pornographic film over the past year. This fact was cited in my post Porn, rape, and a ‘natural experiment’, to disabuse people of the notion that porn consumption has increased radically the past generation. I was aware of this finding, and so generally am careful to focus on the quantity of porn consumed, rather than the social penetration of porn consumption. No matter what the “survey says,” the IT sector is quite aware of the fact that pornographic material is a very high fraction of internet traffic (e.g., more people check Pornhub than BBC).

But I am not sure sure we should trust the GSS results any more at this point. I did some cursory poking around and last month there was a large sample size survey of Dutch youth to investigate the effects of porn consumption, Does Viewing Explain Doing? Assessing the Association Between Sexually Explicit Materials Use and Sexual Behaviors in a Large Sample of Dutch Adolescents and Young Adults:

The study found that 88% of men and 45% of women had consumed SEM ["sexually explicit material"] in the past 12 months. Using hierarchical multiple regression analyses to control for other factors, the association between SEM consumption and a variety of sexual behaviors was found to be significant, accounting for between 0.3% and 4% of the total explained variance in investigated sexual behaviors.

How the sample was collected is important for generalization, so I want to reproduce that part of the method in case you don’t have access:

Data were collected as part of the “Speak up now!” survey, a comprehensive online sexuality study among a large and diverse, self-referred sample of adolescents and young adults in The Netherlands…To be eligible for participation, individuals had to be between 15 and 25 years of age and have had any sexual experience as self-defined, with sex indicated to encompass a broad range of behaviors other than sexual intercourse, including having kissed someone or having engaged in any other type of sexual behavior. Participants were recruited between November 2008 and June 2009 through advertisements in various online and offline youth media and on electronic blackboards at schools. Ads were strategically published to promote the inclusion of lower educated, ethnic minority, and same-sex-attracted young people. The ads invited young people to express their views about sexuality and share their sexual experiences by completing a series of online questionnaires and routed them to the study website that also provided further participant information research details, and referral information for participants wanting to seek counseling.

I’ll put the study’s demographics below. The key for me is that 30% of young male Dutch nationals looked at porn less than once a month, or never. Feel free to find other citations and drop them in the comments. If you don’t have access I’ll check out the descriptive results.

 SEXUALLY EXPLICIT MATERIAL CONSUMPTION OF DUTCH YOUTH

Don’t forget the deep structure in Italy!
Credit: Rita Molnar

Standard apologies that I have had not the marginal time to blog much, but I thought it was important that I least note that Dr. Peter Ralph and Dr. Graham Coop’s paper on identity-by-descent segments and European populations and history is out in its final form in PLoS Biology, The Geography of Recent Genetic Ancestry across Europe. I’ve been familiar with the outlines of these results for about a year now, and to be frank I am still digesting them. The media hype will come and go, with true but to some extent trivial headlines that “all Europeans are related,” but the consequences of these sorts of genetic inquiries into the relatedness of populations are going to be long lasting. At least they should be.

But before I go on about that, if you find the paper itself a bit daunting (though the main body of the text strikes me as eminently readable for a piece of statistical genetics), see Carl Zimmer’s condensation. With this sort of result there is liable to be confusion, so note that Graham Coop has been posting comments on Carl’s blog (and elsewhere, and you can always send him a note on Twitter). Additionally he has a very readable FAQ out. Dr. Coop told me on Twitter that there would even be updates tomorrow as well! In particular one aspect of the paper which I noticed is that most relatively short, but detectable segments (~10 cM), between any two individuals in many nationalities is not going to be evidence of recent genealogical affinities, but deeper historical process.

As for my earlier allusion about this paper: every historian of the Roman Empire interested in demographic and social questions needs to read this sort of work. The reason is the specific result from Italy, which seems to exhibit a lot of deep local population structure. This is in contrast to other European nations, which are relatively homogenized, to the point of being international in the case of Slavic peoples. Despite decades of genetic work on Italians (thanks to L. L. Cavalli-Sforza) this is the first work which highlights this particularity in relation to other Europeans. That is because as Ralph & Coop note other measures of genetic differentiation (e.g., PCA utilizing thick density SNP-chips) tend to pick up deeper time historical and prehistorical events. In contrast Ralph & Coop are focusing upon segments of the genome inherited as a unit from a common ancestor, whose detectable integrity decays rapidly over the generations via recombination. Though this technique of focusing on inherited segments is powerful, it also has a shallow time depth.

I shall quote the authors from their discussion on Italy:

In addition to the very few genetic common ancestors that Italians share both with each other and with other Europeans, we have seen significant modern substructure within Italy (i.e., Figure 2) that predates most of this common ancestry, and estimate that most of the common ancestry shared between Italy and other populations is older than about 2,300 years (Figure S16). Also recall that most populations show no substructure with regards to the number of blocks shared with Italians, implying that the common ancestors other populations share with Italy predate divisions within these other populations. This suggests significant old substructure and large population sizes within Italy, strong enough that different groups within Italy share as little recent common ancestry as other distinct, modern-day countries, substructure that was not homogenized during the migration period. These patterns could also reflect in part geographic isolation within Italy as well as a long history of settlement of Italy from diverse sources.

The latter idea is the classic one the native Italian people were replaced by migrants during the Roman period, especially from the Eastern Mediterranean. Epigraphic and textual evidence as to the proliferation of Greek names in places such as Rome are proffered to support this case. I am skeptical of these data because slaves and the urban proletariat often had low fertility in antiquity, and cities may have been population sinks anyhow. Rather, I suspect that the primary eastern influence on the genetics of modern Italians comes from the era of Greek colonization during Magna Graecia, because despite the urban focus of their civilization the Hellenes did engage in agriculture.

Rather, I lean toward the proposition that Italy was sui generis in continental Europe after the fall of Rome in that despite its regress it maintained local regional identities due to high population densities. The widespread coalescence of genealogies across vast swaths of the other post-Roman domains (Iberia, France, and Britain) may reflect the shattering of the societies and demographic collapse and localized disturbances. The true test of this hypothesis is when these methods expand out to other regions of the world, especially the southern Mediterranean. Egypt and the Levant should exhibit a more Italian pattern, because there was no deep rupture with antiquity in these areas.

There is much more to say about this paper. But I feel that this result from Italy the sore thumb that sticks out and warrants out attention. Ralph & Coop suggest that collaboration with anthropologists and historians is needed. True indeed.

Citation: Ralph P, Coop G (2013) The Geography of Recent Genetic Ancestry across Europe. PLoS Biol 11(5): e1001555. doi:10.1371/journal.pbio.1001555

I’ve mentioned before that many (most?) Muslims are Creationists, broadly understood. According to Pew’s Religious Landscape Survey 42 percent of American Muslims accept that evolution is the best explanation for the origin of human life on earth. This is roughly in line with the American public, if a touch on the Creationist side. The numbers are similar in Turkey. Also, it must be mentioned that unlike most I have some experience with educated (and scientifically trained) Muslims, and can attest to the fact that many are Creationists (my family).

So the results of a new survey of the world’s Muslims by Pew took me aback a bit, in that it reports widespread acceptance of evolution among Muslims.  To add to the plausibility the results for Turkey are in line with previous findings: a bit more of Turkey’s population are Creationist than not. The results for highly secularized European Muslim populations are plausible, though the gap between Albania and Kosovo is somewhat strange. But look at the results for Bangladesh and Lebanon!

I have to admit some skepticism. My concerns are twofold: first, many of these questions may be interpreted differently from society to society, so that comparison may be difficult. This is why I tended to focus on within-region comparisons when ingesting the other survey responses (Pakistan vs. Bangladesh, Lebanon vs. Palestinian territories). Second, I am not sure as to the representativeness of the sample. Do the opinions surveyed actually reflect the broader society? In extremely poor nations like Bangladesh I have difficulty even comprehending how illiterate subsistence farmers would interpret some of these questions, their perceptions of modern abstractions of nationality and identity are generally so inchoate.

There’s also a broader dynamic which needs to be addressed: modernization in many cases leads to greater ‘conservatism’ of belief and practice. Older subsistence farming societies are often tolerant and accepting of diversity of opinion on a macro-social scale because they are fragmented enough that such variation can be accommodated without too much controversy. In contrast, urbanizing societies characterized by upwardly mobile middle classes living cheek by jowl often exhibit simultaneous patterns of secularization and radicalization, with the latter often defined by appeals to a reversion to tradition and proper adherence to formality and ritual (often these are novel constructions and modern interpretations of ancient motifs). Turkey’s Creationism in relation to Bangladesh may simply be due to the relative social advancement of the former in relation to the latter, where broad based mass popular culture has attained a level of power and self-determination to challenge elite narratives. Ultimately the terminal state of this challenge seems to be capitulation and co-option by the elites, but until that moment one is confronted by the reality of dramatic ideological tensions between the elite and aspirant elite factions.

Credit: USDA

A few years back I was rather fixated on issues of maternal fetal health. In particular I was worried about gestational diabetes in relation to my wife because I come from an ethnic group with an elevated risk for these sorts of problems, and the effect when you are in mixed-race marriages seems to be additive (i.e., unlike some risk factors associated with pregnancies the mother’s ethnicity is not the only relevant variable). This is embedded in the broader suite of metabolic diseases which exhibit ethnic variation. Early work on genome-wide selection in humans yielded the result that there was a strong enrichment for signals of adaption within regions of the genome associated with metabolism, so this should not be that surprising. Humans are a geographically dispersed species that inhabits a wide range of environments, so natural selection would shape the distribution of phenotypes within populations if evolution is a significant historical process (it is).

A paper in last month’s Trends in Genetics highlights more precisely how natural selection would operate in a life history context in specific cases. Many ways to die, one way to arrive: how selection acts through pregnancy:

When considering selective forces shaping human evolution, the importance of pregnancy to fitness should not be underestimated. Although specific mortality factors may only impact upon a fraction of the population, birth is a funnel through which all individuals must pass. Human pregnancy places exceptional energetic, physical, and immunological demands on the mother to accommodate the needs of the fetus, making the woman more vulnerable during this time-period. Here, we examine how metabolic imbalances, infectious diseases, oxygen deficiency, and nutrient levels in pregnancy can exert selective pressures on women and their unborn offspring. Numerous candidate genes under selection are being revealed by next-generation sequencing, providing the opportunity to study further the relationship between selection and pregnancy. This relationship is important to consider to gain insight into recent human adaptations to unique diets and environments worldwide.

The logic is eminently simple if the abstract didn’t make it clear. Adaptations which increase fitness early in life are much more beneficial in an evolutionary sense than adaptations which increase fitness late in life. What might seem like a late life adaptation, menopause, is actually generally interpreted as a means by which females can increase the fitness of their daughter’s offspring. In other words, though the mechanism manifests late in life, the evolutionary target remains younger individuals.

Credit: Hamilton 1966

The figure to the left, from a 1966 paper by W. D. Hamilton, illustrates the change in reproductive value over a lifetime (the curves are based on Taiwanese data, and in this case assume a constant population). The peak is at ~20, and declines down to about zero around age 50. It is therefore no surprise that for women this latter period of life history is when the physiological changes which we label menopause occur, as females trade off their low direct reproductive value for increasing their own descendant’s fitness indirectly through supplementing the resources of their daughters.

In the Trends in Genetics paper the authors focus on gestational diabetes mellitus (GDM), preeclampsia (hypertension in pregnancy), neural tube defects, hypoxia, and various infectious diseases. When it comes to neural tube defects due to folate deficiency (and the inverse, vitamin D deficiency), the work seems an extension of Nina Jablonksi’s model for the origin of variation in skin color. The altitude adaptation issue is probably the most straightforward case, as hypoxia would no doubt lead to higher fetal and maternal mortality. As for infectious diseases, as the authors note there is surprisingly little deep exploration of the effects of endemic illnesses such as influenza. This is an area where populations which have been subject to “mass society” and agriculture for thousands have years are likely very different in substantive ways from those which have been hunter gatherers.

Gestational diabetes and preeclampsia are the diseases of particular interest to me. The broad outlines of the situation are evident in the table below:

The authors note that “insensitivity to salt in the diet is common in Japanese: women consuming the most salt (20.6 g/day) have no more hypertension than those consuming the least (8 g/day)…By comparison, the WHO recommends less than 5 g/day of salt consumption for adult.” To me this seems like an important datum indeed considering how much debate there is in our society about the consumption levels of salt. If you are from a genetic background where risk for hypertension is reduced then you might be leaving a lot of utility on the table if you cut back on salt due to coarse guidelines that are blind to your own individual priors.

In relation to the statistics on gestational diabetes the numbers are rather stark. From studies in British samples one can see that Bangladeshis in particular seem to have a greater likelihood of metabolic diseases than other South Asians. The question here is whether the cause is genetic in a direct and classic sense, or is the risk elevation a complex mix of epigenetics, environment, and conventional genetics. Let me give the authors the floor here:

By comparison, South Central Asians had a much higher incidence of GDM in the NYC cohort (14.3%), with Bangladeshis the highest at 21.2% [19]. Traditionally, Bangladeshis have had high consumption of fish, a low glycemic food; rice, of moderate glycemic index due to little processing; and no dairy 36 and 37. Finally, among African-Americans, the incidence of GDM was intermediate at 4.3%…This is consistent with their admixed ancestry and the mixed consumption of dairy across populations in West Africa, the origin of most US African-Americans.

First, I don’t see much evidence in the data that African Americans have much ancestry derivable from those populations (e.g., Fulani) which consume milk. So I have no idea why this was introduced in the text (there are large data sets of African Americans out there). It seems straightforward that African American non-European ancestry derives from coastal agriculturalists across the broad swath of territory from Senegal down to the Yoruba land in Nigeria. Second, as suggested by Henry Harpending there needs to be more input from anthropologists who study food production before we infer that because South Asians have metabolic disease they must not have been as exposed to as much refined starch as Northern Europeans over evolutionary time scales. Agriculture did not arrive in Scandinavia until ~5,000 years ago, so it isn’t as if one can presume that the whole ~10,000 years of Middle Eastern derived agriculture shaped the Northern European genome (unless Northern Europeans are mostly derived from those original Middle Easterners, which seems unlikely). Second, the widespread cultivation of much of Bengal was relatively recent (last ~3,000 years), but the genetics makes it clear that most of change was not due to adoption of agriculture by hunter-gatherers, but the migration of farmers from the west (some of the genetics though implies a non-trivial admixture from eastern populations; but these were the ones who brought rice). Obligate hunter-gatherers in any case were likely not present in South Asia by this time, as opposed to slash and burn populations which also practiced horticulture.

It is the fact that South Asians tend to have higher rates of diabetes than African Americans, which suggests to me that it isn’t a simple story of agricultural adoption and extent of grain processing (West African agriculture tends to be lower in intensity, and likely more diversified in diet and nutrient content, than South Asian grain societies). If one wants to adhere to a standard genetic narrative then perhaps metabolic disease is a more confounding side effect, with no straightforward relation to food production. Or, it may be time to look at environmental co-variates. Unlike East Asian cuisine the South Asian culinary tradition does allow for rather rich sweets. In pre-modern times these would be rare treats, but today consumption levels are much higher. Because of my awareness of metabolic disease in South Asians I’m rather scolding when I see co-ethnic loading up on treats with refined sugars (South Asians tend toward more obesity than East Asians in any survey I’ve seen in the West or developed non-Western societies such as Singapore). Ultimately I am profoundly skeptical of the idea that South Asians cluster with hunter-gatherers (e.g., Australian Aboriginals have similar problems) because of late adoption of agriculture or diversified diet with lack of processing (milling).

Related: Carl Zimmer has also talked about this paper. Excellent as usual.

Credit: Plp

Update: To be explicit, I’m not claiming that the correlation is causal. Rather, I’m pointing out that the explosion in porn use does not seem to have led to a concomitant explosion in sex crimes, which would have been the prediction by social conservatives and radical feminists if they could have known of the extent of penetration of pornography into culture and private lives over the next 20 years in 1990.

I am almost literally one of the last of the generation of young men for whom the quest for pornography was an adventure. One could say that I had the misfortune of my adolescence overlapping almost perfectly with the last few years prior to the ‘pornographic singularity.’ I speak here of the internet, circa 1995 and later. Prior to this era of the ‘pornographic explosion’ one often had to rely upon a lax or absentee father of a friend, from whom the porn was ‘borrowed,’ and then returned with the owner none the wiser. My youngest brother, who is 15 years my junior, would no doubt find my escapades as a 15 year old bizarre in the extreme (though I believe I did not view video pornography until I was 16). In fact, I recall realizing that something radical had occurred when visiting my family and observing my brother, who was 8 at the time, deleting porn spam from his Hotmail account. Porn as nuisance rather than treasure would have amazed my adolescent self.

It seems plausible that the generation after 1995 has witnessed levels of aggregate porn consumption orders of magnitude greater than that before 1995. This is a massive natural social experiment. As with any social experiment you have anecdata-driven ‘moral panic’ pieces in the press which don’t seem to align well with what you see in the world at large. Mo Costandi pointed me today to one such piece about porn ‘re-wiring’ the brains of young boys and making them sexually dysfunctional. Standard stuff. On Twitter I pointed out to Mo semi-seriously that actually crime had declined since widespread pornographic consumption in the mid-1990s. Quite reasonably Mo inquired specifically about sex crimes. Fair enough. As it happens the FBI has records of ‘forcible rapes’ reported to the police in the USA going back to 1960.

Here they are in absolute numbers:

And now standardized by the populations of the decennial Census (and per 1,000,000):

The problem, from what I can see, is that the only young males who talk at length about their porn consumption to professionals and the media are those who have problems with that consumption. In contrast, for most men the consumption of porn isn’t a major issue, it’s just part of their life, or not, depending on the situation, and at most it comes up in a humorous manner. Additionally, my own suspicion is that the perversity of online pornography is driven by the fact that perverts are disproportionately represented among the small minority of men who pay for porn in this day and age.

On a more scientific note, some of the fears of porn destroying the male ability and inclination to have sex with women* could be alleviated if people were more aware of the concept of an alief. One can illustrate the relationship of an alief to sex rather easily. Imagine that you, a heterosexual male (if you aren’t a heterosexual male, just put yourself in that individual’s position), meet a very attractive woman at a party, and kiss her and touch her breasts. You are likely rather aroused and excited at this point. You then reach down and feel a penis. Now you are probably quite turned off. Can you appreciate that you were excited literally the moment before? Would you wish to repeat the experience of initial pleasure, and then shock?

The key takeaway is that a major part of the pleasure of an experience is the broader contextual framework in which the pleasure is occurring. Kissing a woman is preferable for a heterosexual man not just because a woman has smooth skin, and attractive facial features, but because the target of their affections is a woman. If that woman turns out to be a very feminine “ladyboy,” then all the pleasure disappears, even if in an objective and reductionist sense nothing has changed about the previous experiences (if you want a deeper exploration of this topic, I recommend Paul Bloom’s How Pleasure Works: The New Science of Why We Like What We Like).

Obviously sex is a somewhat mechanical operation for many males. Ergo, the ease with which males can relieve themselves with masturbation. But you can’t just transpose the mechanics of consuming pornography to the mechanics of sex with a real woman. Porn exists to facilitate masturbation, but so does your hand. Ultimately a woman is preferable to your hand because a woman is a woman, and your hand is just your hand.**

In other words, the modern male, porn-consuming though he might be, still generally prefers sex with real live women. We’re born that way.

* From what I can tell pornography has more mainstream acceptance in the gay male community. And yet to my knowledge gay males are no less interested in sex than straight males.

** I’m stripping away the reality that sex within a relationship is more than arousal and climax, but an essential part of the relationship being more than just a friendship.

Nature Genetics (2013) doi:10.1038/ng.2615

No time to comment extensively, but check out The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan (open access). The paper and the ScienceDaily press release allude to some phylogenetic confusion as to the relationship of turtles to other reptilian lineages, but my own superficial knowledge of this area left me rather unsurprised by this tree. What am I missing? Though reading the Wikipedia entry it seems that spotty marker coverage has produced a lot of controversy. What’s more striking to me is that so many terrestrial vertebrate lineage seem to have emerged over a relatively short period of time. Though presumably this may simply be an artifact of the reality that most lineages go extinct so we’re only left with relatively deep branching patterns. Someone who knows fossils can chime in.

The basic axis of the debate is simple enough. Observers, such as Andrew Sullivan, point out that Muhammad’s life was characterized by a level of directed violence due to this actions which has no analog in the life of Jesus. As Muslims view Muhammad as the perfect man, worthy of emulation, the logic would be that a violent man would result in a violent religion. As Islam is probably the most violent religion today (though yes, Christians commit the most violence because of the simple fact that the United States is a superpower; but Christianity is not particularly relevant to the rationale), the logic is eminently plausible. Conversely, Jesus’ life was one of passivity in the face of violence. Therefore, any violence in the history of Christianity is in contravention to the basic spirit of the religion.

There are two primary issues, one relatively concrete, and another more abstract but fundamental. The concrete one is that it is trite but true to state that Muhammad was his own Constantine. That is, he was not simply a spiritual teacher, but also a temporal ruler. More broadly, while Christianity became an imperial religion, Islam was born an imperial religion. This makes comparisons between the early years of the faiths difficult, because one could argue that Islam recapitulated in 40 years (going from an persecuted sect to the imperial ideology) what took Christianity 400 years! Since founding texts and canons tend to crystallize in the early phase of a religion’s life cycle it stands to reason that their character would be shaped by their local historical-social context. The project of St. Ambrose and St. Augustine in the late 4th and early 5th centuries was in large part to refashion Christianity from a counter-cultural cult whose base consisted of the urban lower middle class to a universal imperial religion suitable for aristocratic patronage and adherence (see: Through the Eye of the Needle). During the Protestant Reformation, and down to the Second Great Awakening, this turn toward the elites has been asserted by radical Christians of a “primitive” bent to have been an error, at variance from the fundamental core of the faith (see: Restorationism)). That may be true, but until the Enlightenment the general outline of the Christian relationship to the political order was exactly the one promoted by St. Augustine and his heirs in the 5th century. That was Christianity. For non-believers what Christianity should have been is irrelevant. What Christianity was and is is the primary concern.

In other words, what Dreher, Sullivan, and many others see as the cause of social and cultural phenomena may actually be the product of that phenomena in the first place (e.g., the oppressive and Machiavellian aspects of Muhammad and the early Muslim community being a function of the fact that early Islam had to deal with almost immediate profane temporal power). Jesus may have been born in a violent Roman Empire, and ultimately the subject of violent acts from the Roman authorities and his enemies among other Jews, but he was heir to a relatively non-violent tradition among the Pharisees (what became Talmudic Judaism and later Orthodox Judaism) which eventually achieved near total acceptance among Jews* after the defeat of Simon bar Kokhba. It is famously pointed out by many that many of the more conciliatory Surahs promulgated by Muhammad date to the period when the Muslim community was weak, while the more hegemonic ones were when the community was hegemonic. This goes to the point that specific context influences the weight of values which are expressed at the founding of a religion. The early Christians and Jews lived under a Roman dominion which was far more powerful than the tribes of pre-Islamic Arabia, and there was no realistic possibility that they could overturn the pagan order (as evidenced by the outcomes of the quixotic Jewish revolts of the 1st and 2nd century, which totally obliterated Jewish militancy).

But this brings me to the more fundamental issue. Theology and texts have far less power over shaping a religion’s lived experience than intellectuals would like to credit. This is a difficult issue to approach, because even believers who are vague on peculiarities of the details of theology (i.e., nearly all of them!) nevertheless espouse that theology as true. Very few Christians that I have spoken to actually understand the substance of the elements of the Athanasian Creed, though they accept it on faith. Similarly, very few Sunni Muslims could explain with any level of coherency why al-Ghazali‘s refutation of the Hellenistic tendency within early Islam shaped their own theology (if they are Sunni it by definition does!). Conversely, very few Shia could explain why their own tradition retains within its intellectual toolkit the esoteric Hellenistic philosophy which the Sunni have rejected. That’s because almost no believers actually make recourse to their own religion’s intellectual toolkit.

This is the hard part for many intellectuals, religious or irreligious, to understand. For intellectuals ideas have consequences, and they shape their lives. Their religious world view is naturally inflected by this. And most importantly they confuse their own comprehension of religious life, the profession of creeds rationally understand and mystical reflection viscerally experienced, with modal religiosity. This has important consequences, because intellectuals write, and writing is permanent. It echoes down through the ages. Therefore our understanding of the broad scope of religious history is naturally shaped by how intellectuals view religion. In a superficial sense the history of religion is the history of theology, because theology is so amenable to preservation.

To give a concrete example of the confusions that false theoretical commitments can entail, one can model the Reformation as being caused in a necessary and sufficient fashion by Martin Luther’s famous 95 theses. And yet what of radicals such as John Wycliffe and Jan Huss? Arguably Catharism was theologically and institutionally more radical than any Christian mass movement before the 19th century (the Munster Rebellion failed, abortive attempts before Mormonism to reshape Christianity’s Nicene root never took). An excessively materialist reduction of the Reformation is that the arrival of the printing press meant that the Roman Catholic church’s ideological monopoly was no longer enforceable. This seems entirely too pat. Not only that, but though the Reformation resulted in greater ideological diversity at the institutional level, the pre-Tridentine Renaissance Church was quite theologically diverse (this was one of the major criticisms of the “reformers”!). A more thorough understanding of the forces, inevitable and contingent, which led to the outbreak of Europe’s religious fracture in the 16th century surely has to include the diverse social and culture forces shaping people at the time, as well the specific personality of Martin Luther and his confederates.

And yet though Luther’s personality may have had some effect on the initial shape of the Reformation, it seems that to some extent a reordering of the Renaissance Church was inevitable, and if not Luther, then someone else. In other words personalities and ideas are necessary, but the Reformation was frankly not rate limited in terms of theology. There are always many ideas floating around suitable for selection. Theological innovation can not operate on the historical scale without much broader social forces which enable it to flourish (e.g., Hungarian Unitarianism, which has Italian intellectual roots, owes it existence to the patronage of a prince). And importantly the institutional Protestant movements themselves imposed severe checks as excessive theological innovation once intellectuals began to turn against the historic traditions of ancient Christian church (e.g., the Trinity, which is not derivable sola scriptura in any obvious sense).

Ultimately my own personal revelation on these issues occurred in the mid-aughts. Though I have always been skeptical of God, and an explicit and self-conscious atheist from childhood on, I found religious beliefs peculiar and difficult to comprehend in any intuitive sense. This led me early on to reading the source texts and scriptures, as well as theological commentaries (e.g., Summa Theologica, and I’ve read the whole of the Hebrew Bible and New Testament multiple times, and Genesis dozens). In this way I felt I understood on some deep level why people were religious. But I was wrong. When I read Scott Atran’s In Gods We Trust it opened up a whole landscape of cognitive anthropology which explained with much greater accuracy the paradoxes of religious belief and behavior with which I was confronted. The key insight of cognitive scientists is that for the vast majority of human beings religion is about psychological intuition and social identification, and not theology. A deductive theory of religion derived from axioms of creed fails in large part because there is no evidence that the vast majority of religious believers have internalized the sophisticated aspects of their theologies and scriptures in any deep and substantive sense. To give a concrete example, Sri Lankan Buddhists, Hindus, and Muslims can give explicit explanations to at least a rudimentary level as to the differences of their respective religious beliefs. But when prompted to explain their understanding of the supernatural in a manner which was unscripted, and which was not amenable to a fall back upon indoctrinated verbal formulas, their conceptions of god(s) were fundamentally the same! (see: Theological Incorrectness). The superficiality of theological system building is also evident in the fact that when confronted with radicalism derived from the logic of shared axioms during the Reformation prominent Protestant thinkers fell back upon tradition and revelation to defend the common creeds inherited from the early Roman church.

And that is why one should always been cautious of taking theology, textual analysis, and intellectualism too seriously when it comes to religion. Mathematicians can derive proofs from logical analysis. Those proofs are invariant across individuals and subcultures. They are true in a fundamental sense. Though natural science attempts to validate and refine theories and formal models which are robust, it fails when there is no empirical check upon the model building. Outside of pure math our powers of ratiocination are overwhelmed by subjective decisions along the chain of propositions. Separate theologians and have them derive from first principles, and there will be no similarity in their final inferences about the nature of God and the universe. Elite theological conformity is a function of social conformity, not the power of intellectual rigor. When isolation is imposed upon a community of religious believers for any given period of time they are almost always defined by a rapid shift toward heterodoxy, as they lose contact with the broader elite consensus (see: Dao of Muhammad as an example of how strongly an alien milieu can totally transform a familiar religious group unless that subculture remains in contact with the broader community).

Theology is not a cause of any great robustness on the macro scale. Nor does it explain much of micro scale behavior. Where does that leave us to be “serious” about religion? As Noah Millman stated it requires a deep program of empirical analysis and research of massive multi-disciplinary scope. Almost no one is interested in such a program from what I have seen. In my post below several readers ask why I think Islam is inherently violent. After reading this I think you now understand I don’t think this at all, I don’t think Islam is inherently anything. When it comes to religious phenomena I am very much a nominalist. One could say that I’m a nominalist when it comes to the species concept, and I am, but species have much more clear and distinct bounded phenomenological structure than religion does. Rather, when I say that Islamic extremists are qualitatively not like Christian extremists, I am making a descriptive and empirical observation, without much theoretical baggage. My interlocutors have a difficult time comprehending this because to be frank I don’t expect many of them to have thought about religious phenomena in more than a superficial fashion in ideologically motivated arguments. Or, more often, ideologically motivated quorums of consensus.

On many specific issues I agree with Rod Dreher a great deal when it comes to Islam. I do think too many Muslims and their liberal fellow travelers attempt to squelch justified critique of the religion by making accusations of bigotry (I’m on the receiving end regularly). Obviously I disagree with that. But, where I part with Rod is his “theory of religion.” As a religious believer with a deep intellectual predisposition I doubt Rod Dreher and I will be able to agree on the primal point at issue. Not only do I believe that the theologies of all religion are false, but I believe that they’re predominantly just intellectual foam generated from the churning of broader social and historical forces. Some segments of the priestly class will always find institutional politics exhausting, mystical experience out of their character, and legal commentaries excessively mundane. These will be drawn to philosophical dimension of religious phenomena. Which is fine as far as it goes, but too often there is an unfortunate tendency toward reducing religion to just this narrow dimension. But I have minimal confidence that most people will accept that the Christianity church has little to do with Jesus and that Islam has little to do with Muhammad. And yet I think that’s the truth of it….

Addendum: I don’t write these posts often to clarify my viewpoints because I’ve written them before. Here’s one from 2006. Between then and now I have no sense that people have bothered to actually read and understand the phenomena which they have such passionate and confident views of.

* Naturally Hellenistic Jews went even further in reconciling themselves with Roman power, by assimilating into Greco-Roman culture more thoroughly.

German woman, product of Mid-Neolithic?
Source: Siebbi

Yesterday I pointed to a paper which was interesting enough, but didn’t pass the smell test in relation to other evidence we have (at least in my opinion!). A primary concern was the fact that uniparental (male and female lineages) show a peculiar distribution of variation in comparison to autosomal genetic variation (i.e., the vast majority of the genome) in the case of Europe (genome-wide analysis suggest more of Europe’s variation is partitioned north-south, but Y and mtDNA results often imply an east-west split). But a secondary concern I had was that I felt the models were a bit too stylized. In particular following Cavalli-Sforza and Ammerman the authors concluded that demic diffusion better fits their results of genetic variation in Europe (as opposed to continuity of Paleolithic hunter-gatherers). This is likely correct, but these are not the only two models.

A paper out in Nature Communications, using analysis of the phylogenetics of whole ancient mitchondrial genomes, outlines my primary concern when it comes to the models being tested, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans:

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

In other words, the mitochondrial genomic landscape of Europeans not only exhibits discontinuity with Paleolithic populations (though ~10% of Europeans, including my father-in-law, carry the U5 mtDNA haplogroup, which does seem to date to the Ice Age), but also with the “First Farmers.” In the case of this paper the focus is on Central Europe and Germany, and haplogroup H, which is modal across Europe (my wife and daughter are H1). That’s because they’ve already done work on this region and these mtDNA genotypes (see: Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities).

Probably the most arresting figure is the panel to the left. Here you have the authors perform a Procrustes analysis where they compared genetic variation of populations to geographic variation. For Europe what is striking (but unsurprising) is the correspondence between the two dimensions. What is noteworthy are the exceptions. The LBK, Germany’s first farming society (ergo, by definition early Neolithic), and the BBC, a late Neolithic culture with putative origins in Spain (this is disputed) do not align with Central Europe. Rather, LBK is shifted toward the Near East, and BBC toward Spain. The former result recapitulates what they discovered earlier. But, The “Middle Neolithic” samples are overlain upon Central Europe! This is why the authors argue that there was a disruption between the LBK and Middle Neolithic cultures (Rossen [4625–4250 BC], Schoningen [4100–3950 BC], Baalberge [3950–3400 BC] and Salzmunde [3400–3025 BC]).

Of course that’s not the end of the story. BBC arrived in the late Neolithic, presumably from Southwest Europe, and also made contributions. The mitochondrial genomic landscape of Central Europe did not freeze in the Middle Neolithic, but, it can be argued that this was a major “phase transition,” just as the shift between the Paleolithic and Neolithic was a major disruption. This is a radical change from the orthodoxy of the early 2000s. Then it was common to assert that the extant haplogroups in the Old World achieved their current distributions between the Last Glacial Maximum and the expansion in the wake of the Holocene warming. These data, along with many other points of evidence imply that in fact contemporary genomic variation is more a function of dynamics particular to the Holocene, the last 10,000 years, rather than the Ice Age.

Going back to the title of the post my contention here is that a stylized demic diffusion scneario with a wave-of-advance as one population expands into another does not model what has occurred in Europe over the past ~10,000 years. Before 2010 the argument was between those who argued that the diffusion was modest in its genetic impact, and those who argued that it wasn’t modest. But ultimately they were arguing over the margins. These results imply that diffusionary processes are not sufficient to characterize the nature of demographic turnover. Rather, there were repeated eruptions, replacements, and admixtures. It is cliche to refer to phyologeographic and archaeogenetic excavations as pealing back a palimpsest, but this actually gets to the reality that the elements of the object under study are more discrete than one might assume.

Let us posit for example an imaginary history which might explain these data.

1 – The “First Farmers” (LBK) establish nucleated settlements isolated from the hunter-gatherers, who recede and are marginalized

2 – A later culture of “Second Farmers” organized around military principles overturns the ascendancy of the “First Farmers.” Additionally, this second wave is a hybrid population, which emerged out of the synthesis of the nucleated first wave and the hunter-gatherer substrate.

3 – Finally, a subsequent series of prehistoric populations interject themselves onto the historical scene, though only inflecting the genomic landscape characterized by step 2. Like the second group these are themselves populations with diverse origins in prehistory, a syntheses of various geographical and tribal strands.

Though isolation by distance and clinal variation is important in this narrative, these dynamics are actually requilibrations after the exogenous shocks of demographic eruptions (note, a reader of this weblog outlined this model years ago in a more primitive form). Agriculture, and agricultural mass societies, were sociological shocks of a massive order, which resulted in protean shifts in the institutional and cultural fabric of diverse peoples. Like early stage innovation and business growth the “Neolithic sector” may have been characterized by rapid growth and high rates of “firm” extinction. Ultimately a series of consolidations and merges resulted in a new more stable order, as the industry entered a “mature phase.” What we term civilization.

Is that a true story? Perhaps not in the details. But I think it’s a truer story than the tales that were on offer in the early 2000s.

Addendum: It is important to note that discontinuity seems a likely story for the Y chromosomes as well (male lineages).

Citation: doi:10.1038/ncomms2656

But there’s a bigger problem. The authors find that ~80% of Spanish ancestry is “Paleolithic” and ~100% of that of Southeast Europeans is “Neolithic.” I don’t have a problem with these figures so much, except that autosomal DNA generally implies the major genetic cline in Europe is north-south, not east-west! By this, I mean that there is more variation between Poland and Greece, than Greece and Spain, and Spain and England, than Spain and Greece. At least on the whole genome scale. But this tends not to be the case when you look at Y chromosomes, for example. There’s an east-west split. Why? I have no idea, but the fact of this contradiction exists should make you cautious.

Finally, I have to throw in that it seems that this model is focused on one expansion of farmers into Europe. Though reading structure plots can be like reading tea-leaves, I think it is important to enter into the record that this may not be correct, and there may have been multiple agricultural expansions. If so, I wonder about the validity of the inferences if the assumptions are faulty. These are all things one has to consider when one tries to gauge the plausibility of abstruse statistical papers like this dependent on silico

Citation: Rasteiro R, Chikhi L (2013) Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data. PLoS ONE 8(4): e60944. doi:10.1371/journal.pone.0060944