ON THE OTHER HAND, THEY GOT LOTS OF GRANT MONEY (via Mike Daley):

Another God That Failed (Tom Bethell, 3/4/2004, The American Spectator)

HUMAN DNA IS A GREAT STRING of four nucleotides, three billion letters long.
Some of these sequences -- the "coding regions" -- are called genes. They control the construction of proteins in the body. But far greater stretches of the same DNA are "non coding regions," and for many years they were called "junk." That was the word scientists used. Junk DNA had no function and could be ignored. These enormous sequences, amounting to 98.5 percent of the whole genome, were dismissed as the accumulated rubbish and detritus left behind by the constant trial and error of evolution.

Now the white-coats are beginning to suspect that they made a mistake. Wayt Gibbs reported in November's Scientific American that "journals and conferences have been buzzing with new evidence," contradicting the old idea that genes "are the sole mainspring of heredity and the complete blueprint of life." Included in this "unseen genome" is the 98.5 percent that had been
"written off as irrelevant." Some scientists now suspect that the key to understanding what makes one person different from the next is, precisely, "hidden within our 'junk' DNA."

Sooner or later this will make its way to the front pages, and we will realize that the genome project was based on a misconception. Some scientists are already arguing that the gene must be rethought and may have to be abandoned in favor of something more fluid. [...]

THE GENE MANIA OF THE LAST generation has had serious consequences. Above all it has led to what is surely the most serious error of modern medical science -- the unproductive 25-year pursuit of the theory that mutations or "spelling errors" in the genome turn normal cells into cancer cells. (Wayt Gibbs also discusses this matter -- more tactfully and politely than I have
here -- in an earlier [July] issue of Scientific American.)

I believe the underlying problem is that government funding, which increasingly dominates medical research, demands that a "political" consensus be substituted for the exploration of rival theories by the normal trial and error of scientific method. Government agencies won't fund rival
theories.

A year ago, the writer Michael Crichton gave a lecture at Caltech in which he explored the harmful transition from science to consensus. His argument was fascinating. The search for extraterrestrial intelligence somehow morphed into nuclear winter, and from there, from "second hand smoke to
global warming." Science and policy have become inextricably mixed, he said. We have seen this most strikingly with AIDS -- turned now into a grossly politicized rationale for the expansion of foreign aid. We have seen it with cancer -- over 100 "oncogenes" have been catalogued, not one of which has been shown to cause cancer. And we have only begun to see it with the Human Genome Project.

Human Genome Project: Help or Hindrance? (Matthew Albright, May 2001, Genewatch)

[T]wo related indicators ––the multiple unexplored functions of the DNA sequences that constitute “the gene” and the definition of the gene itself–– may demand that the United States Patent and Trademark Office examine more closely the “utility” requirement when reviewing gene patents (Ed. Note: see Warren Kaplan’s companion article). In other words, it is hard to award a patent to an inventor who appears to have very little idea of what their invention is or how it functions.

Already, some predict that the number of lawsuits between companies that own patents on specific genes and those that try to conduct further research or explore new uses for those genes will be on the increase. 40,000 genes are not a lot to work with and the patent system does not facilitate sharing of research materials. The outcome of these lawsuits may yet find that general patents on specific genes are too broad and unsupportable in courts of law.

More likely, however, even broader monopolies may be given to those who have already patented genes or will do so soon. The human genome project has made clear that corporations that have already claimed genes as their own have, in fact, laid claim to a higher percentage of the entire human genome than they at first realized. Looking at the four leading private companies who patent genes, about 750 human genes have been patented by them so far and applications for about 20,000 more are pending. In the case that the pending patents are all awarded (which is unlikely, as many will prove to be redundant), those four private companies could own half of the human genome.

Furthermore, as Craig Venter has already indicated, the new fish to catch with patents may be the proteins. The reductionism that we have seen with the now antiquated idea of a single-function gene may simply be reconcentrated on the proteins. Proteomics, the analysis of complete complements of proteins, will take over where genomics has proven inadequate: giving simplistic genetic determinants for human health and behavior.

In order for the biotech industry to survive at all ––at the very least it has yet to break even financially–– the reductionist and determinist ideals must be maintained in their marketing. Easily definable, single-function units of biological material are necessary for making any real money. It is hard to market genes and proteins if molecular biology is continually described as a hornets’ nest of undecipherable relationships.

In the end, the results of sequencing the human genome may not affect gene patenting one way or another. Gene patenting will continue to depend on the lawyers, the biotech industry’s public relations, and the economic powers that be, who will all put their own spin on research data. Scientific results – no matter how humbling -- can never be politically neutral.

Defying Genomania: a review of It Ain't Necessarily So: The Dream of the Human Genome and Other Illusions. Richard Lewontin and The Triple Helix: Gene, Organism and Environment. Richard Lewontin (Robert Dorit, American Scientist)

[A]s Lewontin's books make clear, with the success of the Human Genome Project, the era of naive reductionism—the very perspective that promoted an almost exclusive emphasis on genome sequencing over the past decade—may take its final bow.

For the past three decades, molecular biology has been a phenomenally productive branch of the natural sciences. Successes have come in part from a commitment to the notion that complex organisms can best be understood by examining their parts. The advent of DNA sequencing promised to reduce life to its simplest components, the units of inherited information. Decoding the sequence of DNA (soon rechristened "the master molecule") seemed to promise the resolution of the most recalcitrant problems in biology. Yet as soon as significant amounts of sequence began to accumulate, it became obvious that things were not as simple as we might have hoped. My molecular biologist colleagues have voiced their frustration and bewilderment at discovering just how unintuitive, disorganized and plain inefficient genomes have turned out to be (an outcome less surprising to evolutionary biologists). Nonetheless, despite this messiness, molecular biologists have kept the faith—at least in public—by arguing that the sequence was incomplete, with key bits missing, or was the wrong kind of sequence. Those excuses no longer hold.

The completion of the Human Genome Project means we will soon have to confront the fact that, fascinating and useful as the complete genome of a complex eukaryote is, sheer information will not resolve the central questions in human biology. Personally, I find it comforting to think that our mission as biologists goes beyond the tedious accumulation of sequence (sequencing being one of the more numbing activities in our profession). After all, it confirms that the difficult problems in our field are conceptual—more data are always welcome, but not in lieu of thought.

For some time now, Lewontin has been warning that the pieces of the human puzzle will not all simply fall into place when the sequencing is done. The Triple Helix and It Ain't Necessarily So take clear and direct aim at the way much of biology is now being done. Lewontin's claim is radical and convincingly argued: The world is complicated, and the current way we approach that world is in subtle ways defective. These essays make clear that the problem has never been insufficient data, but rather insufficient understanding of that data, and specifically of the relationship between parts and whole in living systems.

Much has been written about the tension in biology between holistic and atomistic perspectives. Unfortunately, critiques of reductionism have often suffered from a certain romantic longing for a more mysterious, less explainable world. Lewontin will have none of it. From the outset, these books make clear that a commitment to material explanation is not negotiable, nor is it automatically a vote for the reductionist approach. Lewontin makes a riveting case for the interactionist perspective, based on the notion that living systems arise at the intersection of multiple weak forces. That postulate carries with it profound ontological implications: No single force, factor or source of data is likely to explain fully the world as we see it. Equally important, if the interaction of many weak forces dominates outcomes in living systems, we cannot learn much by isolating a single factor and studying it intensively, since in so doing we obscure the very interactions that we wish to understand. Lewontin's version of the uncertainty principle is that the emphasis of reductionist biology on parts, on holding everything constant while we tweak a single variable, destroys precisely what we need to examine.

Gotta love Mr. Lewontin's faith that the problem lies in the naivety, not the reductionism.

Posted by Orrin Judd at March 4, 2004 7:55 AM