The human genome ten years on (part 2) – it ain’t necessarily so

June 14, 2010 • 11:14 am

by Greg Mayer

In a post a couple of months ago, Matthew took note of the tenth anniversary of the completion of the draft human genome, noting that Nature had published a retrospective.  Matthew rightfully took issue with the dreadful “blueprint” metaphor for the genome, but also concisely noted the meager medical results:

…despite all the hype, the contribution of the genome to human health has been pretty negligible. In other words, from a purely medical point of view, there isn’t much to celebrate.

In yesterday’s New York Times, Nicholas Wade provides a journalistic analysis, and confirms that the results so far are disappointing. Money quote:

…the primary goal of the $3 billion Human Genome Project — to ferret out the genetic roots of common diseases like cancer and Alzheimer’s and then generate treatments — remains largely elusive. Indeed, after 10 years of effort, geneticists are almost back to square one in knowing where to look for the roots of common disease.

This does not come as much of a surprise when you realize that most diseases are not genetically caused (in any straightforward reading of the word caused); that even when there is a genetic basis, the genetics are apt to be complex; and that even when simple, identification of a gene does not lead readily to a cure. These issues were raised most presciently by Dick Lewontin, especially in an essay-review (subscription required) he wrote for The New York Review of Books in 1992. Dick decried scientists’ selling the genome project to governments on the basis of its health benefits, while in fact the project would primarily advance disciplinary (and, in some cases, financial) interests. Endorsing Dick’s genetic arguments, I wrote the following in 2000, at the time of the announcement by Bill Clinton and Tony Blair:

Few diseases are caused by a “gene.” Most diseases, in fact, are caused by the invasion of the body by another organism (bacteria, viruses, protozoa). Our susceptibility and resistance to disease may often have a genetic basis, but these too are usually the result of multiple genes in interaction with the environment. Even when a disease does have a singular genetic cause, finding the gene does not necessarily lead easily to treatment or prevention (e.g. cystic fibrosis).

Last year, over at Mermaid’s Tale (in a post I noted here at WEIT), Ken Weiss put it succinctly (he also discusses Wade’s new NYT article here):

…most common diseases have little to do with genetic variation in any sensible way.

The genome project has provided much useful scientific information. As Wade notes, “For biologists, the genome has yielded one insightful surprise after another.” But that’s not why the project was done. Bill Clinton said it would lead to treatments for “most, if not all, human diseases”; Francis Collins said we’d have genetic diagnosis of diseases within ten years. The genome project’s architects oversold it’s medical (not to mention philosophical) benefits, and now scientists (or at least genome scientists) will lose credibility because of it. Harold Varmus is quoted by Wade as saying “Genomics is a way to do science, not medicine.” If only that had been said louder, and earlier, and by more people.

[PZ and some others are taking Wade to task for saying “humans… [are] higher on the evolutionary scale”. While this is an inopportune use of the scala naturae, it’s part of one paragraph (which does make the interesting point that genome size, as measured by number of protein coding genes, does not vary very widely among metazoans), and does not detract at all from the main thrust of the article.]

The bitterness goes way back

August 17, 2009 • 8:54 am

by Greg Mayer

In a soon to be published paper in the Royal Society’s Biology Letters (abstract only), Carles Lalueza-Fox of Universitat Pompeu Fabra ( website in Catalan!) in Barcelona and colleagues report that they have sequenced the gene TAS2R38 from a Neanderthal man (press coverage by the BBC and NY Times). The ability to sequence genes from fossil material is remarkable enough in itself, but this study has particular interest, and not just because it was done on one of our fossil relatives.  Variation in the gene they sequenced is responsible for the polymorphism in modern man for the ability to perceive bitter tastes (some people can tast bitter, some can’t). Determining the frequency of the two forms (or alleles) of the gene is a classic high school biology exercise, carried out by seeing who can taste the bitter chemical PTC.  People who have either one or two copies (humans are diploid, so most genes are present in each individual’s genome in two copies) of the taster allele can taste bitter; those with two copies of the non-taster allele cannot. Today, the two alleles are about equally frequent, so that about 25% of people have two taster alleles (i.e. they are homozygous for the taster allele), about 50% have one taster and one non-taster (they are heterozygotes), and 25% are homozygous for the non-taster allele.

The Neanderthal they sequenced was a heterozygote, and thus could taste bitter (and also [with sample of only 1, mind you] had the same allele frequencies as we do). The polymorphism thus goes back somewhere on the order of 40,000 years. But Neanderthals split from the lineage leading to modern humans on the order of 300,000 years ago, with little or no subsequent interbreeding. So the polymorphism probably goes back even further, predating the modern Homo sapiens/Neanderthal split. Although an exciting find, this is not a record for the antiquity of a modern polymorphism: some are known to predate the human/chimp split (abstract only), and that’s millions of years ago.