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

March 31, 2012

Post-Neolithic revenge of the foragers

Filed under: anthropology,Culture,Farmers vs. Foragers,History — Razib Khan @ 10:18 am

If I have something to share, why not share it? Over the past few weeks I’ve been ruminating on some of the possible intersections between historical population genetics and anthropology, especially in light of the discussion that I’ve had in the past with Robin Hanson about ‘farmers vs. foragers’. Entering into the record that such a dichotomy is too stark, and only marginally useful (i.e., I think it is important to separate farmers and foragers in to their own sub-classes, as some farmer types may share more with some forager types, and so forth), it may be that after the first wave of the Neolithic expansion the descendants of the foragers “bounced back” in many regions of the world. It does seem that ancient European hunter-gatherers have left modern descendants. They were not totally swamped out. Using autosomal patterns some genome bloggers have inferred the same pattern, and perhaps even a counter-reaction by “Mesolithic” populations which adopted some aspects of the “Neolithic” cultural toolkit.

But here let me come back to the Turks. Are they the descendants of farmers who expanded out of the valleys of eastern ...

December 12, 2011

Out of the agricultural hearths

Filed under: Agriculture,Anthroplogy,anthropology,Genetics,Genomics — Razib Khan @ 2:34 pm

Dienekes has an important post up, The womb of nations: how West Eurasians came to be. He outlines a scenario where a rapid expansion of a farming population has overlain much of Western Eurasia, atop aboriginal substrata. A few years ago you’d have laughed at such a model, mostly due to the authority of archaeologists and phylogeographers relying on mtDNA lineage distributions. No longer. This is not necessarily an orthodoxy, and the details of the model vary, but here is my verbal rendering of the simplest scenario:

1) ~50 thousand years hybridization between Eurasian hominins and “Out of Africa”

2) ~40-10 thousand years before the present, crystallization of the Paleolithic order of human population structure, derived from groups seeded in the original migration

3) ~10 thousand to a few thousand years before the present, the Paleolithic order is replaced and assimilated by farmers expanding from a few hearths

Below the fold is a stylized tree representation of what I have in mind.


October 13, 2011

Australia on fire

Fascinating, Orbital cycles, Australian lake levels, and the arrival of aborigines:

But the other big feature is that the lake-filling events that occurred after 50,000 years ago were much smaller than those which occurred before. Climactically, the conditions 10,000 years ago should have been the same as the conditions 115,000 years ago. But the lake was only a fraction of the size. The authors find no natural causes which can explain this. So they suggest that the aridity starting around 50,000 years ago is related to the reduction in forest and increase in grasslands which occurred at this time. This vegetation change was a result of a huge increase in the frequency of fire in central Australia, which allowed fire-adapted plants to prosper at the expense of moisture-retaining forest. The increase in fire at this time is generally associated with the arrival of the first people on the Australian continent. It is known that of Australia’s megafauna went extinct at this time, but Magee et al. (2004) show that even the tropical rains were effected by human migration, with drastic changes to the continent’s largest river basin.

If you read some of the academic literature on fire ecology you have a hard time not coming to the conclusion that modern humans terraformed the planet Earth! The hallmark of modern H. sapiens seems to be extinction of large organisms, a propensity to go where no hominin has gone before, and copious utilization of the “red flower.”

September 22, 2011

Out of Africa onward to Wallacea


There are two interesting and related papers out today which I want to review really quickly, in particular in relation to the results (as opposed to the guts of the methods). Taken together they do change our perception of how the world was settled by anatomically modern humans, and if the findings are found to be valid via replication (I think this is likely, in at least some parts) I was clearly wrong and misled others in assertions I made earlier on this weblog (more on that later). The first paper is somewhat easier to parse because it is in some ways a follow up on the paper from 2010 which documented admixture into Near Oceanian (Melanesian + Australian Aboriginal) populations from a distant hominin lineage, the Denisovans.

In this paper in The American Journal of Human Genetics they extend their geographic coverage. Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania:

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.


In some ways the result is not too surprising. There’s a rather clear cline of declining Melanesian admixture as one moves west across the Indonesian archipelago. Intriguingly the Denisovan admixture seems restricted on the western boundary to Wallacea, though the story is made more complex by the existence of the Philippines. The latter archipelago was connected to Sundaland during the last Ice Age, not Sahul, or isolated such as the isles of Wallacea.

The more complex aspect of the paper is that Denisovan admixture is not just a function of admixture with Near Oceanians. Obviously the proportion for Polynesians is elegantly explained by this model, because there is a well known cline of admixture amongst various Polynesian groups with Melanesian populations. And as I noted earlier there is also a Melanesian cline in Indonesia. But the story is not neat for the Philippines due to geography and other genetic results.

A simple model would be that Philippine Negrito admixture with the Denisovans is also a function of admixture with Near Oceanians. An event which we have no record of or reason to suspect, but may have occurred. But they did not find evidence for this. To the left is a figure which shows some of the phylogenetic relationships which they report from their analysis of SNP data. First, you see the admixture of Neandertals with all non-Africans. Second, you see the admixture of Denisovans with the very distant common ancestors of the Philippine Negritos and Near Oceanians. Next, you see an admixture of what I term “Western Negritos” (Andaman Islanders + Malaysian Negritos) with the ancestral Near Oceanian population, but not with the Philippine Negritos. Then you see admixture of an East Asian element, probably Austronesian, with various Negrito groups. The distinction between Philippine and Malaysian Negritos from each other is not that surprising if you look at PanAsian Consortium SNP data. It is a nice result though that the Andaman Islanders seem to be related to the Malaysian Negritos. The geography of the Ice Age implies the origin of this group on western mainland Southeast Asia, in close proximity to the domains of the Negritos of southern Thailand and peninsular Malaysia.

Probably the most tantalizing element to me is that the ancestry and genesis of what we term Near Oceanians may be a more complex affair than we had previous thought. This brings me to the next paper, An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia:

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

This figure distills the model down to its essence:

The main technical issue which is straightforward when comparing the previous paper to this one is that here they sequenced a whole genome of an Australian Aboriginal man who lived 100 years ago. So while the previous paper was working with tens of thousands of markers, this paper could play with millions of SNPs (though do recall that the previous paper had a much wider set of populations covered, which isn’t trivial). The top line finding seems to be that Europeans and East Asians are closer to each other than either is to the Australian Aboriginal. I’ve seen this result before. But, a major issue which is resolved here with their methods is that Aboriginals are closer to East Asians than they are to Europeans! This is the major problem I’ve always had with the idea that there were “two waves” of migration Out of Africa. If this was so, why isn’t it that Australian Aboriginals exhibit equal distance from East Asians and Europeans? The answer here is simple: admixture between the two waves, but only amongst those going east.

In other words I was confused by excessive “tree” thinking, and neglected the possibility of admixture. The first paper also hints as a possible candidate source for the admixture event: the same source population of the Western Negritos! From what I can gather this population falls into the “eastern” branch Eurasian humanity. Not quite close to East Asians, but definitely closer to them than West Eurasians. Therefore the affinity of East Asians to Aborigines may be due to this broader global “East Eurasian” heritage, which was injected into the Aboriginal man’s genome at some point in the past. Interestingly the authors found no difference in admixture from Neandertals between the populations, in line with earlier results. This implies to me, though does not prove, that the Aboriginals are a basal outgroup to other non-Africans, who all underwent the same rough admixture dynamic with Neandertals as they pushed out of Africa. Instead of two waves Out of Africa, perhaps two pulses just outside of Africa?

Finally, the fact that the gene flow seems to pre-date the separation of Native Americans from East Eurasians serves as a “peg” on the populating of Australia. The authors conclude that at a minimum we’re talking 15-30,000 years before the present. The distinctiveness of Australian Aboriginal mtDNAs, as well the localization of Denisovan admixture amongst Near Oceanians, in addition to the archaeology, makes me credit this early founding event. The populations of Sahul may have avoided being swamped out by newcomers by and large since their arrival ~50,000 years ago. I will speculate that this may explain their relatively high quantum of “archaic” ancestry. It may be that in pre-agricultural Eurasia there were many groups with higher fractions of Neandertal ancestry on the margins of the wave of anatomically modern human advance, which were only later assimilated by the demographic swell of the farmers.

There’s a lot more one could say, but I’ll leave it to readers….

September 5, 2011

Horses, not people (sort of)

Filed under: Anthroplogy,anthropology,History,Pots not People — Razib Khan @ 2:16 am
I have criticized the “pots not people” paradigm on this weblog before. In short, the idea is that material cultural changes reflected in the archaeological record are an indicator of memetic, not genetic, evolution. So a shift from pottery style X to pottery style Y informs you of an cultural switch. This is not implausible [...]

July 25, 2011

War in Pre-Columbian Sumeria

Filed under: Anthroplogy,anthropology,History,War — Razib Khan @ 11:05 pm

For most of my life I have had an implicit directional view of Holocene human culture. And that direction was toward more social complexity and cultural proteanism. Ancient Egypt traversed ~2,000 years between the Old Kingdom and the fall of the New Kingdom. But it s rather clear that the cultural distance which separated the Egypt of Ramesses and that of Khufu was smaller than the cultural distance which separates that of the Italy of Berlusconi and the Italy of Augustus. Not only is the pace of change more rapid, but the change seems to tend toward complexity and scale. For most of history most humans were primary producers (or consumers as hunter-gatherers). Today primary producers are only a proportion of the labor force (less than 2% in the USA), and there are whole specialized sectors of secondary producers, service workers, as well as professionals whose duty is to “intermediate” between other sectors and smooth the functioning of society. The machine is more complex than it was, and it has gotten more complex faster and faster.

This is a accurate model as far as it goes, but of late I have ...

June 18, 2011

Grain, disease, and innovation

I just finished reading a review of the literature since 1984 on the bioarchaeology of the transition to agriculture. Stature and robusticity during the agricultural transition: Evidence from the bioarchaeological record:

The population explosion that followed the Neolithic revolution was initially explained by improved health experiences for agriculturalists. However, empirical studies of societies shifting subsistence from foraging to primary food production have found evidence for deteriorating health from an increase in infectious and dental disease and a rise in nutritional deficiencies. In Paleopathology at the Origins of Agriculture (Cohen and Armelagos, 1984), this trend towards declining health was observed for 19 of 21 societies undergoing the agricultural transformation. The counterintuitive increase in nutritional diseases resulted from seasonal hunger, reliance on single crops deficient in essential nutrients, crop blights, social inequalities, and trade. In this study, we examined the evidence of stature reduction in studies since 1984 to evaluate if the trend towards decreased health after agricultural transitions remains. The trend towards a decrease in adult height and a general reduction of overall health during times of subsistence change remains valid, with the majority of studies finding stature to decline as the reliance on agriculture increased. The impact of agriculture, accompanied ...

May 17, 2011

There was scale and structure before history

Filed under: Anthroplogy,anthropology,Culture — Razib Khan @ 1:56 pm

Until relatively recently the spread of agriculture in Europe, and to some extent the whole world, was pigeon-holed into two maximalist models: cultural or demographic diffusionist. Neither of these models were maximalist in that they denied the impact of culture or demographics in totality, but they tended to be rhetorically brandished in a manner where it was clear which dynamic was the dominant mode of explaining the nature of cultural and genetic variation and their origins. Here are two representative headlines from the BBC:

- Most European males ‘descended from farmers’.

- Genetic roots of Europe, “New DNA evidence suggests that a few hundred Stone Age hunter-gatherers were the ancestors of many modern day northern Europeans.”

For whatever reason archaeologists themselves haven’t been able to resolve these issues. To me it seems that ultimately even if genetics is not determinate or even fundamentally specially insightful, it will at least sharpen the discussions, and move scholars away from arguments of rhetorical excess.

One of the broader issues which I’ve been coming to greater consciousness of is the idea whereby all pre-literate societies were diffuse to the point of being in a state of ...

May 6, 2011

How the “fierce people” came to be

The pith: there are differences between populations on genes which result in “novelty seeking.” These differences can be traced to migration out of Africa, and can’t be explained as an artifact of random genetic drift.

I’m not going to lie, when I first saw the headline “Out of Africa migration selected novelty-seeking genes”, I was a little worried. My immediate assumption was that a new paper on correlations between dopamine receptor genes, behavior genetics, and geographical variation had some out. I was right! But my worry was motivated by the fact that this would just be another in a long line of research which pushed the same result without adding anything new to the body of evidence. Let me be clear: there are decades of very robust evidence that much of the variation in human behavior we see around us is heritable. That the variation in our psychological dispositions, from intelligence to schizophrenia, is substantially explained by who our biological parents are. This is clear when you look at adoption studies which show a strong concordance between biological parents and biological children on many metrics as adults, as opposed ...

April 24, 2011

South Asian endogamy predates the British

Filed under: Anthroplogy,anthropology,Genetics,Genomics,India — Razib Khan @ 10:36 pm

One of the things that happens if you read ethnographically thick books like Nicholas Dirks’ Castes of Mind: Colonialism and the Making of Modern India is that you start to wonder if most castes were simply created by the British and for the British. Granted, even Dirks would not deny the existence of Brahmins prior to the British period, but those who work within his general paradigm might argue that a group like Kayasthas were the product of very recent developments (e.g., the uplift of a non-Brahmin literate group willing to serve Muslim and British rulers). The emergence of genomics complicates this sort narrative, because you can examine relationships and see how plausible they would be given a particular social model.

Zack Ajmal is now at 90 participants in the Harappa Ancestry Project. He’s still undersampling people from the Indo-Gangetic plain between Punjab and Bengal, but that’s not his fault. Hopefully that will change. He posted K = 4 recently for the last 10 participants, but I notice K = 12 in his spreadsheets. So this is what I did:

1) I aligned the ethnic identification information with the K = 12 results.

2) I removed relatives and those who ...

March 18, 2011

Foragers to farmers: a tale of collective action?

Filed under: Anthroplogy,anthropology,Culture,Farming,Neolithic Revolution — Razib Khan @ 12:46 am

The economist Samuel Bowles recently had a paper out in PNAS which caught my attention, Cultivation of cereals by the first farmers was not more productive than foraging. This naturally begs the question: why did farming conquer foraging as a lifestyle? First, let’s look at the abstract:

Did foragers become farmers because cultivation of crops was simply a better way to make a living? If so, what is arguably the greatest ever revolution in human livelihoods is readily explained. To answer the question, I estimate the caloric returns per hour of labor devoted to foraging wild species and cultivating the cereals exploited by the first farmers, using data on foragers and land-abundant hand-tool farmers in the ethnographic and historical record, as well as archaeological evidence. A convincing answer must account not only for the work of foraging and cultivation but also for storage, processing, and other indirect labor, and for the costs associated with the delayed nature of agricultural production and the greater exposure to risk of those whose livelihoods depended on a few cultivars rather than a larger number of wild species. Notwithstanding the considerable uncertainty to which these estimates inevitably are subject, the evidence is inconsistent with ...

February 8, 2011

Why Some Like It Hot: Food, Genes, and Cultural Diversity

Link to review: Slow and diverse food.

February 4, 2011

Empires of the Word: A Language History of the World

Link to review: Empires of the Word & anti-Babel

February 3, 2011

Pandora’s Seed: The Unforeseen Cost of Civilization

Link to review: Pandora’s Seed: The Unforeseen Cost of Civilization

Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present

Link to review: Who’s the barbarian now? Empires of the Silk Road

Dragon Bone Hill: An Ice-Age Saga of Homo erectus

Link to review: Dragon’s Battles

Mother Nature: Maternal Instincts and How They Shape the Human Species

Link to review: Mother Nature: a complicated and morally ambivalent tale

Mother Nature: Maternal Instincts and How They Shape the Human Species

Link to review: Mother Nature: a complicated and morally ambivalent tale

December 14, 2010

To classify humanity is not that hard

snpskinIn my post below I quoted my interview L. L. Cavalli-Sforza because I think it gets to the heart of some confusions which have emerged since the finding that most variation on any given locus is found within populations, rather than between them. The standard figure is that 85% of genetic variance is within continental races, and 15% is between them. You can see some Fst values on Wikipedia to get an intuition. Concretely, at a given locus X in population 1 the frequency of allele A may be 40%, while in population 2 it may be 45%. Obviously the populations differ, but the small difference is not going to be very informative of population substructure when most of the difference is within populations.

But there are loci which are much more informative. Interestingly, one controls variation on a trait which you are familiar with, skin color (unless you happen to lack vision). A large fraction (on the order of 25-40%) of the between population variance in the complexion of Africans and Europeans can be predicted by substitution on one SNP in the gene SLC24A5. The substitution has a major phenotypic effect, and, exhibits a great deal of between population variation. One variant is nearly fixed in Europeans, and another is nearly fixed in Africans. In other words the component of genetic variance on this trait that is between population is nearly 100%, not 15%. This illustrates that the 15% value was an average across the genome, and in fact there are significant differences on the genetic level which can be ancestrally informative. You can take this to the next level: increase the number of ancestrally informative markers to obtain a fine-grained picture of population structure. In the illustration above the top panel shows the frequencies at the SNP mentioned earlier on SLC24A5. The second panel shows variation at another SNP controlling skin color, SLC45A2. This second SNP is useful in separating South and Central Asians from Europeans and Middle Easterners, if not perfectly so. In other words, the more markers you have, the better your resolution of inter-population difference. This is why I found the following comment very interesting:

Razib’s final concession (that genetic variation exists) is revealing because I think that’s as far as the argument can really be taken. It’s a bit of a strawman, in that people who argue that race is entirely a social construct don’t actually deny that human genetic variation exists. What they deny is that there are non-arbitrary and mutually exclusive categories into which humans can be resolved. This is, I think, the point being made by the “Race by Fingerprints” etc. rhetorical device cited earlier.

In other words, it may be possible for any particular phenotypic trait or genetic locus to be resolved into a strictly cladistic system but humans, being an amalgam of such traits and locii, defy such resoution. So while the study of human genetic variation does, indeed, have “instrumental utility” the concept of biological races is, itself, an arcahic relic.

As I noted below, the comment doesn’t make sense. Here is a PCA of world populations using 250,000 markers:

lotsofmarkers

The relationships between individuals is hypothesis-free. That is, the two largest components of variance in the data just happen to produce clusters which neatly map onto geographic realities. If you think about this a little weird, it makes total sense: populations share a history of intermarriage, so over time they will develop population-specific distinctiveness. It may be true that most of the variance is between populations, but it is not difficult at all to discriminate populations, or generate clusters which are not arbitrary as a function of geography or social identity.

There are relationships which do not match intuition. Or at least intuition as it crystallized during the period of the rise of modern taxonomic science. The various phenotypically “black” peoples of the world, Africans, Melanesians, and some South Asians, do not cluster together. Rather, all non-Africans are separated from Africans by the largest component of variance within the data set. The traits used to make inferences of taxonomy in “folk biology” and early scientific attempts to generate a systematic tree of life in relation to the human races were not necessarily representative of total genome variation, which captures the evolutionary history of a population with greater accuracy and precision.

And obviously you don’t need 250,000 markers, let alone all ~3 billion base pairs in the human genome, to distinguish on the level of continental races/populations. A paper in 2002 laid out the parameters. δ is a measure of between population difference on genes.

sig1
sig2

From the paper:

…we can estimate that about 120 unselected SNPs or 20 highly selected SNPs can distinguish group CA from NA, AA from AS and AA from NA. A few hundred random SNPs are required to separate CA from AA, CA from AS and AS from NA, or about 40 highly selected loci. STRP loci are more powerful and have higher effective δ values because they have multiple alleles. Table 3 reveals that fewer than 100 random STRPs, or about 30 highly selected loci, can distinguish the major racial groups. As expected, differentiating Caucasians and Hispanic Americans, who are admixed but mostly of Caucasian ancestry, is more difficult and requires a few hundred random STRPs or about 50 highly selected loci. These results also indicate that many hundreds of markers or more would be required to accurately differentiate more closely related groups, for example populations within the same racial category.

The paper was written in 2002. Since then much has changed. Here is an image from a post from last summer:

village1

People within European villages tend to be relatively closely related. Again, it is totally reasonable that given enough markers you could assign individuals to different villages with a high confidence. Concretely, person X may show up in the pedigree of individuals from village 1 ~100 times at a given generation, while the same person may show up in the pedigree of individuals from village 2 ~10 times at a given generation. This isn’t rocket science, the basic logic as to why populations shake out based on geography and endogamy patterns is pretty obvious when you think about it.

At about the same time as the above work, A. W. F. Edwards, a statistical geneticist, published a paper titled Lewontin’s Fallacy which took direct aim at the misunderstand of the human Fst statistic and its relevance for classification. Here is Edwards answering why he wrote the article in 2002 (my co-blogger at GNXP, David B, is doing the questioning):

4. Your recent article on ‘Lewontin’s Fallacy’ criticises the claim that human geographical races have no biological meaning. As the article itself points out, it could have been written at any time in the last 30 years. So why did it take so long – and have you had any reactions from Lewontin or his supporters? [David B's question -R]

I can only speak for myself as to why it took me so long. Others closer to the field will have to explain why the penny did not drop earlier, but the principal cause must be the huge gap in communication that exists between anthropology, especially social anthropology, on the one hand, and the humdrum world of population and statistical genetics on the other. When someone like Lewontin bridges the gap, bearing from genetics a message which the other side wants to hear, it spreads fast – on that side. But there was no feedback. Others might have noticed Lewontin’s 1972 paper but I had stopped working in human and population genetics in 1968 on moving to Cambridge because I could not get any support (so I settled down to writing books instead). In the 1990s I began to pick up the message about only 15% of human genetic variation being between, as opposed to within, populations with its non-sequitur that classification was nigh impossible, and started asking my population-genetics colleagues where it came from. Most had not heard of it, and those that had did not know its source. I regret now that in my paper I did not acknowledge the influence of my brother John, Professor of Genetics in Oxford, because he was independently worrying over the question, inventing the phrase ‘the death of phylogeny’ which spurred me on.

Eventually the argument turned up unchallenged in Nature and the New Scientist and I was able to locate its origin. I only started writing about it after lunch one day in Caius during which I had tried to explain the fallacy across the table to a chemist, a physicist, a physiologist and an experimental psychologist – all Fellows of the Royal Society – and found myself faltering. I like to write to clear my mind. Then I met Adam Wilkins, the editor of BioEssays, and he urged me to work my notes up into a paper.

I have had no adverse reaction to it at all, but plenty of plaudits from geneticists, many of whom told me that they too had been perplexed. Perhaps the communication gap is still too large, or just possibly the point has been taken. After all, Fisher made it in 1925 in Statistical Methods which was written for biologists so it is hardly new. [my emphasis -R]

Richard Dawkins repeated Edward’s argument in The Ancestor’s Tale. You can read Edward’s full essay online. Also see p-ter’s lucid exposition at GNXP.

discblogsSo far I’ve been talking mostly about genes. But in terms of classification there isn’t anything magical about genes. Biological anthropologists using more robust morphometric traits have discerned an “Out of Africa” movement, just as geneticists have. You have above five individuals. All of them have dark hair and dark eyes. There’s total overlap on those traits. And yet I’m pretty sure you can assign their rough population identity to each. Why? Because humans take a look at correlated clusters of traits in assigning population identity intuitively. Some traits are more salient, such as skin color, but early geographers understood that East Asians and Europeans were different populations despite similarity of light complexion. The ancient Greeks understood that Indians and Ethiopians were different groups despite their similar complexions, because they differed on other informative traits.

Let’s bring it back down to earth. Population structure exists. Phylogenetic analyses of humans are trivial in their difficulty. They track geography rather closely, at least before the age of mass migration. Additionally, they tend to follow endogamous social groups, such as Ashkenazi Jews. A South Asian is going to be more genetically related to a South Asian than they are to an African. There are many cosmetic differences between populations. But there are also less cosmetic differences which are very important. You can even assign different regions of a chromosome to different ancestral components.

Where does this leave us? Ultimately, it’s about the “R-word.” “Race is a myth.” Or, as PBS stated, an illusion. Here’s some of the precis of the PBS documentary:

Everyone can tell a Nubian from a Norwegian, so why not divide people into different races? That’s the question explored in “The Difference Between Us,” the first hour of the series. This episode shows that despite what we’ve always believed, the world’s peoples simply don’t come bundled into distinct biological groups. We begin by following a dozen students, including Black athletes and Asian string players, who sequence and compare their own DNA to see who is more genetically similar. The results surprise the students and the viewer, when they discover their closest genetic matches are as likely to be with people from other “races” as their own.

Much of the program is devoted to understanding why. We look at several scientific discoveries that illustrate why humans cannot be subdivided into races and how there isn’t a single characteristic, trait – or even one gene - that can be used to distinguish all members of one race from all members of another.

Modern humans – all of us – emerged in Africa about 150,000 to 200,000 years ago. Bands of humans began migrating out of Africa only about 70,000 years ago. As we spread across the globe, populations continually bumped into one another and mixed their mates and genes. As a species, we’re simply too young and too intermixed to have evolved into separate races or subspecies.

So what about the obvious physical differences we see between people? A closer look helps us understand patterns of human variation:

  • In a virtual “walk” from the equator to northern Europe, we see that visual characteristics vary gradually and continuously from one population to the next. There are no boundaries, so how can we draw a line between where one race ends and another begins?
  • We also learn that most traits – whether skin color, hair texture or blood group – are influenced by separate genes and thus inherited independently one from the other. Having one trait does not necessarily imply the existence of others. Racial profiling is as inaccurate on the genetic level as it is on the New Jersey Turnpike.
  • We also learn that many of our visual characteristics, like different skin colors, appear to have evolved recently, after we left Africa, but the traits we care about – intelligence, musical ability, physical aptitude – are much older, and thus common to all populations. Geneticists have discovered that 85% of all genetic variants can be found within any local population, regardless of whether they’re Poles, Hmong or Fulani. Skin color really is only skin deep. Beneath the skin, we are one of the most similar of all species.

Certainly a few gene forms are more common in some populations than others, such as those controlling skin color and inherited diseases like Tay Sachs and sickle cell. But are these markers of “race?” They reflect ancestry, but as our DNA experiment shows us, that’s not the same thing as race. The mutation that causes sickle cell, we learn, was passed on because it conferred resistance to malaria. It is found among people whose ancestors came from parts of the world where malaria was common: central and western Africa, Turkey, India, Greece, Sicily and even Portugal – but not southern Africa.

This documentary came out in 2003. In late 2005 scientists discovered the role that SLC24A5 plays in skin color. It is the second most ancestrally informative locus typed so far to differentiate Europeans and Africans. It actually does come close to being a single gene which differentiates two populations! It is true that human populations have mixed. I probably have ancestors who were resident in China and Northern Europe within the last 1,000 years. That’s the way genealogy works. All Eurasians may be able to find a genealogical line of ancestry back to Genghis Khan (though not necessarily distinctive genes attributable to him). But that does not negate the fact that some of your ancestors show up in your pedigree orders of magnitude more than others of your ancestors. The vast majority of my ancestors within the last 1,000 years were South Asian, though a substantial minority were Southeast Asian. The question of our youth as a species and its relation to our differentiation into races and subspecies is an empirical matter, not an a priori one determined by a fixed number of years. Since races and subspecies are fuzzy characteristics they’re easy to refute, just pick the definition which is refutable. I have no idea how they adduce that traits like intelligence, musical ability, and physical aptitude, are that much older than the “Out of Africa” migration. Humans have been getting much more gracile over the last 10,000 years as a whole, while I don’t know how one can know about the musical abilities of anatomically modern humans in Africa 200,000 years. These traits are quantitative, and based on standing genetic variation, so the architecture is qualitatively different from that of skin color (though in 2003 we didn’t know the architecture of skin color, the confusion is explainable).

The old concept of “race” as outlined by anthropologists in the early 20th century, and accepted broadly, was often unclear, ad hoc, and not empirical. Over the past generation by way of refuting the concept of race people are wont to make unclear, ad hoc, and non-empirical, assertions. The reason that scholars discuss race and refute it is to eliminate confusions and misconceptions from the public, but their presentation has produced more confusions and misconceptions. The idea that human phylogeny is impossible is in the air, I have heard it from many intelligent people. I have no idea why people would be skeptical of it, the way it is presented by many scholars makes the implication clear that phylogeny is impossible, that differences are trivial. Both these are false impressions. I do not believe that the fact that mixed-race people’s real problems obtaining organs with the appropriate tissue match is a trivial affair. Human genetic differences have plenty of concrete impacts which are not socially constructed.

Personally I have no problem with abandoning the word race and all the baggage which that entails. But there’s no reason to throw the baby out with the bathwater here. In the “post-genomic” era human population substructure is taken for granted. The outlines of the history of our species, and its various branches, are getting clearer and clearer. There’s no point in replacing old rubbish with new rubbish. We have the possibility for clear and useful thought, if we choose to grasp it.

December 13, 2010

To study humankind, AAA responds

This morning I received an email from the communication director of the American Anthropology Association. The contents are on the web:

AAA Responds to Public Controversy Over Science in Anthropology

Some recent media coverage, including an article in the New York Times, has portrayed anthropology as divided between those who practice it as a science and those who do not, and has given the mistaken impression that the American Anthropological Association (AAA) Executive Board believes that science no longer has a place in anthropology. On the contrary, the Executive Board recognizes and endorses the crucial place of the scientific method in much anthropological research. To clarify its position the Executive Board is publicly releasing the document “What Is Anthropology?” that was, together with the new Long-Range Plan, approved at the AAA’s annual meeting last month.

The “What Is Anthropology?” statement says, “to understand the full sweep and complexity of cultures across all of human history, anthropology draws and builds upon knowledge from the social and biological sciences as well as the humanities and physical sciences. A central concern of anthropologists is the application of knowledge to the solution of human problems.” Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.

Changes to the AAA’s Long Range Plan have been taken out of context and blown out of proportion in recent media coverage. In approving the changes, it was never the Board’s intention to signal a break with the scientific foundations of anthropology – as the “What is Anthropology?” document approved at the same meeting demonstrates. Further, the long range plan constitutes a planning document which is pending comments from the AAA membership before it is finalized.

Anthropologists have made some of their most powerful contributions to the public understanding of humankind when scientific and humanistic perspectives are fused. A case in point in the AAA’s $4.5 million exhibit, “RACE: Are We So Different?” The exhibit, and its associated website at www.understandingRACE.org, was developed by a team of anthropologists drawing on knowledge from the social and biological sciences and humanities. Science lays bare popular myths that races are distinct biological entities and that sickle cell, for example, is an African-American disease. Knowledge derived from the humanities helps to explain why “race” became such a powerful social concept despite its lack of scientific grounding. The widely acclaimed exhibit “shows the critical power of anthropology when its diverse traditions of knowledge are harnessed together,” said Leith Mullings, AAA’s President-Elect and the Chair of the newly constituted Long-Range Planning Committee.


Up until the last paragraph this is an anodyne statement. Who could disagree with: “Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.” But the explosion of anger from biologically and scientifically oriented anthropologists on the web is drawn from a deeper layer of lived experience. On a raw level many of them feel that some factions in cultural anthropology are obscurantists who are fluent in rhetoric which they utilize in power-plays and politics. There are anthropologists who do deny the deep insights of the scientific method in illuminating reality. In fact, they reject the naive realism at the heart of science as it is practiced. For them science is a swear-word, and connotes an affinity with oppression and all the negative abstractions in fashion at a given time (e.g., patriarchy, heternormativity, capitalism, Eurocentrism, etc.). Of course as I note above scientific anthropologists are not given to tolerating the verbal circumlocutions and incantations of their non-scientific colleagues with much grace themselves. There is a deep cultural chasm, and these sorts of arguments over words in obscure institutional documents are only triggers for a persistent roiling debate.

As for the last paragraph, it illustrates the selectivity of a discipline which attempts to contextualize, and often has a skeptical relationship toward a positive framework. I believe that race is a social construct. The Hispanic identity, which consists of people of indigenous Amerindian, European, and African ancestry, and all their combinations, has been racialized. The Islamic identity has also been racialized. Benjamin Franklin stupidly contended that only the English and Saxons were true whites, with all other Europeans, including Nordics, being swarthy.

But just because a construct has a social element does not mean it has only a social construct. Because of the Left-liberal anti-racist egalitarian bias of anthropology, the academy in general, and the dominant narrative of Western society as a whole, there is a strong tendency to assert flatly that “race does not exist” as a biological concept. There is no interrogation of the concept of race except to refute its utility. This is not a case of agnostic skepticism washing away illusions, but a case of skepticism applied in a fashion to obtain a clear and distinct objective result which corresponds to reality. When it comes to race many become naive realists who accept that biological concepts can be falsified or verified in a simple and straightforward fashion. There is all of a sudden one Way of Knowing which presents us with indubitable truths.

Here is L. L. Cavalli-Sforza (my question in italics):

7) Question #3 hinted at the powerful social impact your work has had in reshaping how we view the natural history of our species. One of the most contentious issues of the 20th, and no doubt of the unfolding 21st century, is that of race. In 1972 Richard Lewontin offered his famous observation that 85% of the variation across human populations was within populations and 15% was between them. Regardless of whether this level of substructure is of note of not, your own work on migrations, admixtures and waves of advance depicts patterns of demographic and genetic interconnectedness, and so refutes typological conceptions of race. Nevertheless, recently A.W.F. Edwards, a fellow student of R.A. Fisher, has argued that Richard Lewontin’s argument neglects the importance of differences of correlation structure across the genome between populations and focuses on variance only across a single locus. Edwards’ argument about the informativeness of correlation structure, and therefore the statistical salience of between-population differences, was echoed by Richard Dawkins in his most recent book. Considering the social import of the question of interpopulational differences as well as the esoteric nature of the mathematical arguments, what do you believe the “take home” message of this should be for the general public?

Edwards and Lewontin are both right. Lewontin said that the between populations fraction of variance is very small in humans, and this is true, as it should be on the basis of present knowledge from archeology and genetics alike, that the human species is very young. It has in fact been shown later that it is one of the smallest among mammals. Lewontin probably hoped, for political reasons, that it is TRIVIALLY small, and he has never shown to my knowledge any interest for evolutionary trees, at least of humans, so he did not care about their reconstruction. In essence, Edwards has objected that it is NOT trivially small, because it is enough for reconstructing the tree of human evolution, as we did, and he is obviously right.

L. L. Cavalli-Sforza contends that between population genetic variation is not trivially small. This is clear from the fact that one can discern village-to-village genetic distinctions in Europe. Human variation exists, and it is not trivial. It is useful for phylogenetics, significantly impacts salient phenotypes, and, risks for particular diseases. The social construction of race has real biological raw materials. At one end, the transformation of white European converts to Islam through changes in personal appearance into de facto “People of Color” are matters of social construction in totality. In contrast, the blackness of a Dinka from Sudan is a matter of biological categorization. The categorization of Egyptian Arabs with obvious African admixture as “white” in the US Census is a matter of social construction due to bureaucratic contingency, and illustrates the intersection of biological reality and social fluidity. It is well known that when foreign Arabs with obvious black admixture visited the American South there was often a debate as to whether they were subject to segregation, illustrating the tensions between social norms (which would have coded them as black), bureaucratic function (which coded them as non-black usually), and biological reality (where they were an amalgam of a minor black African component with a dominant white Arab component).

Of course it is true that on any given trait variation can span populations. But even in the case given above, of sickle cell, the correlations with ancestry and population are striking. A lower boundary value is that 75% of sickle cell suffers are of mostly African ancestry, despite only 15% of the world’s population being of mostly African ancestry. These statistics refute a platonic model of race, but they do not refute the population-thinking which is at the heart of much of modern biology, pure and applied.

All that said, the word “race” is fraught with a lot of historical baggage. Therefore to study population wide variation you need to focus on “fine-scale population structure” and what not. This trend would be something of interest for cultural anthropologists of science to study. Race is just a word. Even a term as widely accept as species exhibits a fair amount of flexibility on the margins. But the underlying biological patterns, and the instrumental utility of those patterns, can not be denied.

Addendum: I often use “human” or “humankind” where earlier norms would be to use “man” or “mankind.” My main rationale is I don’t want annoying comments objecting to the term. The concept which I’m pointing to is the same no matter the pointer, and so I don’t mind changing it to facilitate my intent to communicate clearly and without undue extraneous baggage.

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