I read Noble Savages, Napoleon Chagnon‘s memoir, last week. There isn’t much to say about this book that’s revelatory, but it definitely was a page turner. As far as my personal tastes go there was a little too much autobiography, and not enough science, in Noble Savages. But it’s a long work, so in absolute terms there’s a lot of science to dig into if you want to skim over the personal sections (frankly, I had a hard time keeping all the various tribes and individuals straight). There have been many reviews of Noble Savages since it came out last week. If you haven’t read the profile in The New York Time Magazine, I advise you to do so right now. At Scientific American John Horgan put up a post which illustrates how Chagnon has become a sort of token in the tribal wars between scientists (or scientists and no-scientists). You can see this in two reviews at The New York Times, one which consists of an extended sneer from a professor of cultural anthropology and gender studies, Elizabeth Povinelli, while the second treatment from Nicholas Wade reads almost as a panegyric. Charles C. Mann navigates the middle path in his review, being critical in some instances, but by and large praising the memoir.
Just pre-ordered a Kindle Edition of Napoleon Chagnon‘s new book Noble Savages: My Life Among Two Dangerous Tribes — the Yanomamo and the Anthropologists. I didn’t even know this was coming out next week, but The New York Times Magazine has a piece up, The Indiana Jones of Anthropology, which chronicles the controversial the life & times of Chagnon. My previous posts about cultural anthropology were written with no knowledge about the impending publication of this article, or Napoleon Chagnon’s memoir. But the timing is fortuitous. One complaint by rightfully enraged cultural anthropologists (I didn’t deny that I was attacking their profession in the most extreme terms) is that I didn’t really offer an argument. As I said, the reason is that life is short and I’m not interested in convincing anyone.
But here’s a section of the article above which reflects just what I was alluding to:
In light of my two jeremiads against cultural anthropology, some readers may be curious if I have any positive vision, in the sense of any alternative model. To get a sense of my own orientation, Explaining Culture by Dan Sperber and The Origin and Evolution of Cultures by Peter Richerson and Robert Boyd would be sufficient (Scott Atran’s In Gods We Trust has been highly influential in my thought, but it is a rather dense work whose central topic may not be of interest to everyone). If books are not to your liking, see the resources at the Culture and Cognition Institute. Just to be explicit, an understanding of evolution or genetics is not necessary to gain a first order understanding of the nature of the phenomenon of human culture, but cognition is. When I say cognition, I mean the cognitive revolution and its rivals. An anthropology which binds disparate aggregate social phenomena and explains the variation which we see to any satisfaction must be rooted in what we know of the science of the mind.
My post below on Jared Diamond and his cultural anthropological critics has attracted a fair amount of attention (e.g., see the Twitter re-tweets of the post). But first I’d like to admit that I think it was wrong in its specific thrust. Though I’ve seen Stephen Corry of Survival International referred to as an anthropologist, he’s certainly not an academic. Corry is an explicit and open advocate, as is Jonathan Mazower. The Guardian piece which I linked to also was not entirely clear on this point. In other words, the example in that article was not particularly relevant to my broader thesis. But overall my position remains unchanged, because The Guardian was not presented as evidence, but an illustration of a trend which I have long commented upon. Many of the academics who re-tweeted my post focused on the assertion that “cultural anthropology has gone down an intellectual black hole, beyond the event horizon of comprehension, never to recover.” Those who agree with my position understand exactly why I would say this.
My daughter has four grandparents. Genetically she is a little over 25 percent her paternal grandfather and maternal grandmother, and a little under 25 percent her maternal grandfather and paternal grandmother.* Why? Because she is 50 percent genetically identical by descent with her mother and likewise with her father. This is all rather straightforward. But what about culturally?
With biological heredity we can speak of genes, the substrate by which inheritance occurs. With culture memes have been far less fruitful as anything more than an illustration, as opposed to the basis of a formal system of logic and analysis. Nevertheless, we can describe with relative clarity many aspects of culture as a trait or phenotype. And this is important. Recall that evolutionary process was characterized by Charles Darwin despite lacking a satisfying theory of inheritance.
Note: An update on this post. I want to be clear that I think Jared Diamond is wrong on a lot of details, and many cultural anthropologists are rightly calling him out on that. But, they do a disservice to their message by politicizing their critique, and ascribing malevolence to all those who disagree with their normative presuppositions. Scholarship is hard enough without personalized politicization, and I stand by Jared Diamond’s right to be sincerely wrong without having his character assassinated. As the vehemence of my post suggests the only solution I can see to this ingrained tick among many cultural anthropologists is to drop the pretense of genteel discourse, and blast back at them with all the means at our disposal. Telling them to stick to facts nicely won’t do any good, these are trenchant critics of Social Darwinism who engage in the most bare-knuckle war of all-against-all when given any quarter. Coexistence in the academy is simply not possible with this particular culture, extirpation is the only long term ESS for the rest of us.
It’s happening again, another issue of Jared Diamond vs. the anthropologists. Part of this is surely personal. Diamond has been trading in glib and gloss for years, and profitably so, in both financial and fame terms. There is also a deep scholarly divide. Diamond’s way of viewing historical development is reminiscent of, if not equivalent to, materialism. That is, external material forces (geography) and broad macro-historical dynamics (the transition across modes of production) loom large in his thinking. In contrast, many cultural anthropologists disagree with this paradigm, and see it as outmoded, old fashioned, and false. Not that I can decrypt what they believe, because clarity is not something that seems to be valued by cultural anthropologists in most domains.
With all the crazy talk about George Church and an adventurous young woman conspiring to bring back Neandertals, I do think it is important to keep in mind that we can bring back an individual with a predominantly Neandertal genome in a very old fashioned manner: controlled breeding. The most humane and viable manner in which you might do this is simply start a religion in a Bene Gesserit fashion where the prophesied Kwisatz Haderach is a Neandertal. Over the generations by selecting individuals within the population (which could draw in converts) enriched for Neandertal ancestry to mate assortatively one could slowly increase the proportion of that ancestral component. The population would become more and more “Neandertal,” probably to the point of being phenotypically distinctive in a dozen generations (even a minority of non-modern human ancestry is probably significant, just as many individuals who are 3/4 European and 1/4 African still exhibit features of their minority heritage). One could apply the same logic to the Denisovans.
Most people in South Asia speak one of two varieties of language, Indo-Aryan and Dravidian. These two are not particularly closely related. Indo-Aryan is an Indo-European language, as is evident in the plethora of obvious cognates with other Indo-European dialects. I have a minimal fluency in Bengali, the easternmost of the Indo-European languages, and quite a bit more fluency with English, one of the most westernmost, and it was evident to me rather early on (e.g., grass vs. gash, man vs. manush, nose vs. nak). In contrast to me Dravidian languages are peculiar because the accent and cadence are clearly South Asian, but they are utterly impenetrable (though there are many loan words into Indo-Aryan from Dravidian).
This morning in Slate I encountered a rather peculiar piece, The Original Jewish Genius: How the Gaon of Vilna helps explain Jewish intellectual achievement. The reason I found this piece peculiar is that it strikes me as something of a rewriting of the conventional historical narrative for anyone who is not what we today term an Orthodox Jew. The Gaon of Vilna may have been a luminescent mind, but a figure such as Moses Mendelssohn, also an Ashkenazi Jew of approximately the same period, is much more the spiritual ancestor of the typical modern Jewish intellectual, who synthesizes their cultural identity within the broader currents dominant in the gentile milieu.
The Gaon of Vilna was the culmination of over 1,000 years of Rabbinal Judaism, an intellectual tradition which had marginal impact on the gentile world, as Christianity and Islam sealed off the Jews from the outside in the centuries after the Babylonian Talmud came into being. The Lithuanian Mitnagdim who looked to the Gaon ultimately became foes of the Jewish Enlightenment, which witnessed the emergence of identified Jews as prominent figures in Western civilization for the first time in 2,000 years (since Josephus and the Jewish courtiers who were familiars with the Julio-Claudians). In short the Gaon of Vilna is rightly a marginal figure from a gentile perspective, no matter his parochial brilliance.
Since John Hawks already hit it I don’t have much to add about the dog-starch-adaptation-paper in Nature, The genomic signature of dog domestication reveals adaptation to a starch-rich diet. I’m impressed at the yield from the sample sizes that they had, but as John alludes to this area of study has huge possibilities. The authors suggest that agriculture catalyzed domestication. That’s fair enough, and carefully stated I’d say, because the Amerindians seem to have brought domestic dogs to the New World long before agriculture. In other words, the “domestication” event was probably a multi-layered affair. Looking through the supporting information it’s obvious that the domestics were almost all Western breeds. As the search for adaptive variants expands to other lineages we might be in for surprises in terms of the signatures of selection as they vary across the dogs.
Over the past decade or so much of the reconstruction of the human genetic past has occurred through inferences generated from variation of extant human beings. In more plain English the patterns of genetic variation of modern populations have been used to map out the patterns of the past. There are serious difficulties with these sorts of inferences. For example you generate a huge number of potential phylogenetic trees and zero in on the “most probable tree” (or, the distribution of trees). But at the end of the day these inferences are only as good as your assumptions.
My attitude toward most cultural anthropologists is similar to Jerry Coyne’s sentiment toward theologians. So I’m going to share two examples of why I have these feelings, without commenting.
First, here’s a transcript of This American Life’s Doppelgänger:
The above map shows the population coverage for the Geno 2.0 SNP-chip, put out by the Genographic Project. Their paper outlining the utility and rationale by the chip is now out on arXiv. I saw this map last summer, when Spencer Wells hosted a webinar on the launch of Geno 2.0, and it was the aspect which really jumped out at me. The number of markers that they have on this chip is modest, only >100,000 on the autosome, with a few tens of thousands more on the X, Y, and mtDNA. In contrast, the Axiom® Genome-Wide Human Origins 1 Array Plate being used by Patterson et al. has ~600,000 SNPs. But as is clear by the map above Geno 2.0 is ascertained in many more populations that the other comparable chips (Human Origins 1 Array uses 12 populations). It’s obvious that if you are only catching variation on a few populations, all the extra million markers may not give you much bang for the buck (not to mention the biases that that may introduce in your population genetic and phylogenetic inferences).
A few days ago I suggested that Dr. Daniel MacArthur might have South Asian ancestry. Now, when confronted with surprise the best option is to stick with your prior assumption, unless that surprise is powerful enough for you to “update” your model. After a few days of further analysis I will update: I do think Dan MacArthur has South Asian ancestry. Dienekes dug further, and noticed that there are hallmarks of “Ancestral South Indian” ancestry along the first 2/3 or so of chromosome 10. Now, you do have to remember that this genomic region is only half South Asian. The other half is European.
But in any case, one question that some people brought up: perhaps MacArthur has Romani heritage? I’m skeptical of this partly because:
1) there weren’t that many Romani in Britain in the 19th century
2) The British Romani are already very highly admixed
One of the primary concerns/questions I had about Luca Pagani’s paper on the genetic origin of Ethiopians is that he found that their West Eurasian ancestor was closer to Levantine than Arabian. I was confused by this because on model-based clustering (e.g., Admixture) when you push down to a fine level of granularity you always see that the Ethiopians cluster with the Yemenis for their non-African ancestry. More precisely, Yemeni Jews are often ~100% component X, which ~50% of the ancestry of Ethiopians.
From what I recall Pagani et al. used haplotype windows which they assigned to Eurasian or African ancestral components, and they compared these to the populations related to the putative ancestral groups. Because Pagani et al. used blocks of the genome, rather than just on specific genotypes, I weight their finding more strongly. But I wanted to double check with TreeMix if the finding in Admixture was peculiar.
So again, I took a ~150,000 SNP set ran it on TreeMix with migration = 5.
Again, you see that the gene flow to the Ethiopians is coming from a position on the tree rather close to Yemenite Jews. One model which may explain this, and still align with Pagani’s findings, is that Arabians themselves are a synthetic population. A “pure” Yemenite Jew may have ancient admixture of African affinity beneath an intrusive element from the north. The parallelism between Ethiopia and Arabia in this model is clear, with the major difference being magnitude of the source population admixture (greater in Arabia), as well as some differences of the target population.
This again reiterates us to be careful of trust first-blush summaries.
As a follow up to my post from yesterday, I decided to run TreeMix on a data set I happened to have had on hand (see Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data for more on TreeMix). Basically I wanted to display a tree with, and without, gene flow.
The technical details are straightforward. I LD pruned ~550,000 SNPs down to ~150,000. I ran TreeMix without and with migration parameters with the Bantu Kenya population being the root. Finally, when I did turn on the migration parameter I set it for 5. You can see the results below.
Most of the flows are pretty expected. The West Eurasian flow from the Turks to the Uygurs makes sense, because there is a large West Asian component to what the Uygurs have (from East Iranians?). The Chuvash are a Turkic group with minor, but significant, Turkic component. The HGDP Russian sample does have some East Eurasian ancestry. And the Moroccans also have African ancestry. But your guess is as good as mine with the Bantu flow in. These are I think Kenya, so it might be trying to interpret Nilotic admixture as generalized Eurasian.
A minor note: installing TreeMix and generating the appropriate files from pedigree format is not to difficult. But you might have confusion in how to generate the pedigree input file. You do it like so in PLINK:
./plink --noweb --bfile YourFile --freq --within YourGroupNamesFile --out YourOutPutFile
It’s the last you want to put into TreeMix’s python conversion script. The YourGroupNamesFile is basically the .fam file with an extra column, the population names for each individual.
I mentioned this in passing on my post on ASHG 2012, but it seems useful to make explicit. For the past few years there has been word of research pointing to connections between the Khoisan and the Cushitic people of Ethiopia. To a great extent in the paper which is forthcoming there is the likely answer to the question of who lived in East Africa before the Bantu, and before the most recent back-migration of West Eurasians. On one level I’m confused as to why this has to be something of a mystery, because the most recent genetic evidence suggests a admixture on the order of 2-3,000 years before the past.* If the admixture was so recent we should find many of the “first people,” no? As it is, we don’t. I think these groups, and perhaps the Sandawe, are the closest we’ll get.
Publication is imminent at this point (of this, I was assured), so I’m going to just state the likely candidate population (or at least one of them): the Sanye, who speak a Cushitic language with possible Khoisan influences. There really isn’t that much information on these people, which is why when I first heard about the preliminary results a few years back and looked around for Khoisan-like populations in Kenya I wasn’t sure I’d hit upon the right group. But at ASHG I saw some STRUCTURE plots with the correct populations, and the Sanye were one of them. I would have liked to see something like TreeMix, but the STRUCTURE results were of a quality that I could accept that these populations were not being well modeled by the variation which dominated their data set. Though Cushitic in language the Sanye had far less of the West Eurasian element present among other Cushitic speaking populations of the Horn of Africa. Neither were their African ancestral components quite like that of the Nilotic or Bantu populations. The clustering algorithm was having a “hard time” making sense of them (it seemed to wanted to model them as linear combinations of more familiar groups, but was doing a bad job of it).
Here is an interesting article on these groups: Little known tribe that census forgot. Like the Sandawe this is a population which seems to have been hunter-gatherers very recently, and to some extent still engage in this lifestyle. In this way I think they are fundamentally different from Indian tribal populations, who are often held up to be the “first people” of the subcontinent. More and more it seems that the tribes of India are less the descendants of the original inhabitants of the subcontinent, at least when compared to the typical Indian peasant, and more simply those segments of the Indian population which were marginalized and pushed into less productive territory. Over time they naturally diverged culturally because of their isolation, but the difference was not primal. In contrast, groups like the Sanye and Sandawe may have mixed to a great extent with their neighbors (and lost their language like the Pygmies), but evidence of full featured hunting & gathering lifestyles implies a sort of direct cultural continuity with the landscape of eastern Africa before the arrival of farmers and pastoralists from the west and north.
* I understand some readers refuse to accept the likelihood of these results because of other lines of information. I am just relaying the results of the geneticists. I am not interested in re-litigating prior discussions on this. We’ll probably have a resolution soon enough.
A new press release is circulating on the paper which I blogged a few months ago, Ancient Admixture in Human History. Unlike the paper, the title of the press release is misleading, and unfortunately I notice that people are circulating it, and probably misunderstanding what is going on. Here’s the title and first paragraph:
Native Americans and Northern Europeans More Closely Related Than Previously Thought
Released: 11/30/2012 2:00 PM EST
Source: Genetics Society of America
Newswise — BETHESDA, MD – November 30, 2012 — Using genetic analyses, scientists have discovered that Northern European populations—including British, Scandinavians, French, and some Eastern Europeans—descend from a mixture of two very different ancestral populations, and one of these populations is related to Native Americans. This discovery helps fill gaps in scientific understanding of both Native American and Northern European ancestry, while providing an explanation for some genetic similarities among what would otherwise seem to be very divergent groups. This research was published in the November 2012 issue of the Genetics Society of America’s journal GENETICS
The reality is ta Native Americans and Northern Europeans are not more “closely related” genetically than they were before this paper. There has been no great change to standard genetic distance measures or phylogeographic understanding of human genetic variation. A measure of relatedness is to a great extent a summary of historical and genealogical processes, and as such it collapses a great deal of disparate elements together into one description. What the paper in Genetics outlined was the excavation of specific historically contingent processes which result in the summaries of relatedness which we are presented with, whether they be principal component analysis, Fst, or model-based clustering.
What I’m getting at can be easily illustrated by a concrete example. To the left is a 23andMe chromosome 1 “ancestry painting” of two individuals. On the left is me, and the right is a friend. The orange represents “Asian ancestry,” and the blue represents “European” ancestry. We are both ~50% of both ancestral components. This is a correct summary of our ancestry, as far as it goes. But you need some more information. My friend has a Chinese father and a European mother. In contrast, I am South Asian, and the end product of an ancient admixture event. You can’t tell that from a simple recitation of ancestral quanta. But it is clear when you look at the distribution of ancestry on the chromosomes. My components have been mixed and matched by recombination, because there have been many generations between the original admixture and myself. In contrast, my friend has not had any recombination events between his ancestral components, because he is the first generation of that combination.
So what the paper publicized in the press release does is present methods to reconstruct exactly how patterns of relatedness came to be, rather than reiterating well understood patterns of relatedness. With the rise of whole-genome sequencing and more powerful computational resources to reconstruct genealogies we’ll be seeing much more of this to come in the future, so it is important that people are not misled as to the details of the implications.
A month ago I posted Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology, in response to James Fallows at At 5% Neanderthal, You Are an Outlier. Fallows has now put up a follow up, The Neanderthal Defense Committee Swings Into Action, where he links to my response post. This prompted the original archaeologist in question to reach out to me via email. I am posting the letter, with their permission, below.