October 28, 2005

Nicholas Wade on the Hap-Map

The NYT genetics reporter describes the latest on the DNA haplotype study.

Besides the hapmap's potential importance for medicine, it has undoubted significance for understanding the biology of the human genome and its recent evolution. The hapmap team has already identified 14 regions of the genome that show signs of having changed in different ethnic groups under the pressure of natural selection. One of the most striking, though known already from earlier studies, is a DNA region in Europeans that confers lactose tolerance, the unusual ability to digest milk in adulthood. This genetic propensity is known to have arisen among cattle herders of northern Europe some 5,000 years ago.

Other genomic regions bear strong marks of natural selection but contain no known gene, a highly perplexing outcome that suggests, Dr. Altshuler said, that "our current ability to predict the function of DNA is very flawed."

The common variation picked up by the hapmap is much the same in different ethnic groups, because most of it is inherited from the ancestral human population before modern humans are believed to have dispersed from Africa about 50,000 years ago. The four ethnic groups studied so far have yielded four million sites of common variation, from which the total number in the world's population is expected to be 10 million.

The hapmap researchers have found that the Chinese and Japanese genomes are so similar that they can be grouped together for many purposes. The genetic differences between Europeans, East Asians and Africans lie mostly in the relative abundance in each of the common DNA mutations. But the hapmap team has found a handful of fixed differences in the first million mutations it studied - 11 between Europeans and the Yoruba, 21 between Europeans and Asians and 5 between the Yoruba and Asians. The role of these mutations is unknown.

A more marked difference emerged on the X chromosome, which is more highly differentiated between ethnic groups than are the other chromosomes. The reason, Dr. Altshuler said, could arise from the fact that men carry only one X chromosome and so, unlike women, have no backup copy if a gene on their single X is inactivated through mutation. That puts the X chromosome under heavy pressure of natural selection when it is carried by a man, and the different pressures experienced by various ethnic groups may have forced the X chromosome to differentiate more than the other chromosomes.

The hapmap team believe they have created a powerful new tool for exploring the human genome but they advise researchers to be careful about publicizing their work, especially when exploring genetic links to human characteristics that are not medical. "We urge conservatism and restraint in the public dissemination and interpretation of such studies, especially if nonmedical phenotypes are explored," they wrote.

A reader writes:

I will be watching how hapmap awareness propagates, and it is certainly off to a careful start. Too careful maybe, or is this all part of the plan?

For example at wikipedia in the description of the hapmap they include this:

"Another potential concern is that the inclusion of populations based on ancestral geography could result in categories such as " race," which are largely socially constructed, being incorrectly viewed as precise and highly meaningful biological constructs. The project undertook the community consultations to understand community concerns about such issues."

This is simply text taken from the official government Hapmap site. Of course, I could be missing something, as my primitive brain is not good at various social double-think, but "ancestral geography" seems like a peculiar category. Unless of course one's ancestral geography includes places like the US, in which case ancestral geography does not seem like an appropriate thing to base the study on at all. Googling "ancestral geography" in order to get a better grasp of the meaning brought up the official hapmap site as the top page of course. In fact, the page that came up, Guidelines for Referring to the HapMap Populations in Publications and Presentations is very specific in how we are to talk about and describe these people's "ancestral geography".

So I am left confused. Unless the point of the whole thing is that it is okay to say that people with different "ancestral geographies" are indeed different, but it is not okay to say that different "races" are indeed different.

The more I write the more confused I become. I think it is because my brain lacks some key part that allows this to all make sense.

Of course, the U.S. Census Bureau talks about "race" all the time, and explains how it's different from "ethnicity," and indeed insists that every single person in America fill in their race.

My published articles are archived at iSteve.com -- Steve Sailer

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