Tuesday, June 26, 2007

It's all in the clusters

Nicholas Wade in the Times on genetic clustering, differential selection and race. See here for previous discussion of a metric on the space of genomes and the scientific meaning of race.

I hear the voice of physicist turned evolutionary biologist Greg Cochran in Wade's writing :-)

Wade: Historians [and social scientists!] often assume that they need pay no attention to human evolution because the process ground to a halt in the distant past. That assumption is looking less and less secure in light of new findings based on decoding human DNA.

People have continued to evolve since leaving the ancestral homeland in northeastern Africa some 50,000 years ago, both through the random process known as genetic drift and through natural selection. The genome bears many fingerprints in places where natural selection has recently remolded the human clay, researchers have found, as people in the various continents adapted to new diseases, climates, diets and, perhaps, behavioral demands. ...

Cochran: There is something new under the sun — us.

Thucydides said that human nature was unchanging and thus predictable — but he was probably wrong. If you consider natural selection operating in fast-changing human environments, such stasis is most unlikely. We know of a number of cases in which there has been rapid adaptive change in humans; for example, most of the malaria-defense mutations such as sickle cell are recent, just a few thousand years old. The lactase mutation that lets most adult Europeans digest ice cream is not much older.

There is no magic principle that restricts human evolutionary change to disease defenses and dietary adaptations: everything is up for grabs. Genes affecting personality, reproductive strategies, cognition, are all able to change significantly over few-millennia time scales if the environment favors such change — and this includes the new environments we have made for ourselves, things like new ways of making a living and new social structures. I would be astonished if the mix of personality types favored among hunter-gatherers is "exactly" the same as that favored among peasant farmers ruled by a Pharaoh. In fact they might be fairly different.

(Larger version here.)

From Dienekes:

A new article in BMC Genomics discusses the issue of predicting continental origin using randomly selected markers. The pdf is freely available.

One of the arguments of those who deny the existence of biological races is that their reality is subjective. Some extremists have argued that race is totally socially constructed; this is, however, disproven by the fact that socially constructed race is correlated with physical characteristics. Thus, rather than being separated from biology, the social phenomenon of race is rooted in biology.

A different argument holds that race is correlated with biology, but the differences are "skin-deep", i.e., involve only superficial, visible, (and by some strange logic unimportant) characteristics. According to the proponents of this view, the idea of biological race places an undue emphasis on a set of traits: it is a result of the subjective choice of a set of traits as race-defining. Thus, the commonly recognized races of traditional physical anthropology are discounted as subjective organizations of the biological data: we could just as simply speak of a "lactose-intolerant race" according to this view.

In forensic science and admixture analysis scientists often discover and use polymorphisms which exhibit large inter-population differences. Decoding DNA isn't free, thus, it makes sense to use the most informative, most "biased" markers when one is trying to discover the origin of a biological sample. For example, if Africans have 55% of gene version A and 45% of gene version B, and Europeans have 53% of A and 47% of B, it makes little sense to type this particular gene, since it cannot really tell us whether a sample is European or African. A gene where Africans have 90% of A while Europeans have 5%of A would be much more useful. Race skeptics claim, as with the physical anthropological data, that to privilege such carefully chosen genes is to stress the differences between groups; the implication is that in randomly chosen genes these differences are minor.

The new paper is one of many (you can click on the Clusters label to find more) recent papers that have discovered that no matter what genetic markers you choose: SNPs, STRs, no matter how you choose them: randomly or based on their "informativeness", it is relatively easy to classify DNA into the correct continental origin. Depending on the marker types (e.g., indel vs. microsatellite), and their informativeness (roughly the distribution differences between populations), one may require more or less markers to achieve a high degree of accuracy. But, the conclusion is the same: after a certain number of markers, you always succeed in classifying individuals according to continental origin.

Thus, the emergent pattern of variation is not at all subjectively constructed: it does not deal specifically with visible traits (randomly chosen markers could influence any trait, or none at all), nor does it privilege markers exhibiting large population differences. The structuring of humanity into more or less disjoint groups is not a subjective choice: it emerges naturally from the genomic composition of humans, irrespective of how you study this composition. Rather than proving that race is skin-deep, non-existent, or unimportant, modern genetic science is both proving that it is in fact existent, but also sets the foundation for the study of its true importance, which is probably somewhere in between the indifference of the sociologists and the hyperbole of the racists.


Anonymous said...

I found Dienekes extended comment on the existence/non-existence of races to be somewhat disingenuous. "Race" has many meanings, not the least of which is the one related to it as a social construct. While it is true that genetic markers are able to pinpoint continental origin, this is not what most people think of when they think of races. Most people think of skin pigmentation or other external markers.

I would claim that instead of the straw man Dienekes props up for demolition, most people think of race as both a social and biological construct all wrapped into one. There is a long history in science of talking of races as it was a biological construct when in fact it referred to external markers such as skin color (pigmentation been known as one of the most mutable of genes in all animals).

Our modern understanding is much more nuanced than this as demonstrated by this recent BBC story on the continental origin of prominent Brazilians. As the article points out, people that may seem of African heritage (because of their skin color and features) are sometimes mostly of European descent.

The common usage of race in society is mostly subjective since it is based on external markers. As the BBC story points out, just because a "black" person may be of European origin, that does not stop them from being harassed by policemen.

To use these new scientific findings on our common genetic heritage to pretend and our imply that our historical use of race was right all along and is not just "skin-deep" is just ludicrous. Racists of times past did not test genetically to see if their classifications were correct.

Steve Hsu said...


"While it is true that genetic markers are able to pinpoint continental origin, this is not what most people think of when they think of races. Most people think of skin pigmentation or other external markers."

I think many people are more sophisticated than this, especially in populations (e.g., Brazil) where there has been a lot of recent population mixing.

"To use these new scientific findings on our common genetic heritage to pretend and our imply that our historical use of race was right all along and is not just "skin-deep" is just ludicrous."

That is not the real interest of scientists here. The interesting question is to what degree evolution led to divergent selection in isolated populations. That's a deep question whose study should not be prevented by political correctness.

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