It’s not entirely obvious at first, but this article in the New York Times is about the problems with gene patents in a world where one gene does not equal one protein. Now, we’ve known that this model isn’t entirely correct, what with alternative splicing and all. Additionally, the human genome also contains many “genes” which are only transcribed into RNAs, but not translated into proteins. All of this has been pretty much accepted by geneticists for a few years.
But rather than putting all of this in the appropriate context, Denise Caruso muddies the waters by overemphasizing the importance of the recent ENCODE paper. At least, we think she’s writing about ENCODE, but we’re not entirely sure because here’s how she does it:
Last month, a consortium of scientists published findings that challenge the traditional view of how genes function. The exhaustive four-year effort was organized by the United States National Human Genome Research Institute and carried out by 35 groups from 80 organizations around the world. To their surprise, researchers found that the human genome might not be a “tidy collection of independent genes” after all, with each sequence of DNA linked to a single function, such as a predisposition to diabetes or heart disease.
First of all, the recent ENCODE paper was more of a proof a principle than anything else. A mere 1% of the human genome was studied in a intense detail — this was only a pilot project, after all — with more coverage expected in the future. That said, much can be learned from the research reported, especially about DNA sequence evolution and how gene transcription is regulated. But it’s not like there is anything in the paper that would represent a paradigm shift as described by Caruso.
Caruso then riffs off of this misunderstanding of the ENCODE findings by claiming that the validity of patenting genes should be questioned. I won’t be taking a position on gene patents, but I will point out that arguing against gene patenting based on ENCODE represents faulty logic. I say this because one need not even invoke any of the ENCODE results to point out that “genomes are complex” and that it does not make sense to patent a “gene”. The one gene one protein concept has been dead for years, and the non-independence of genes is hardly anything new either.
From here, Caruso goes on to discuss how antibiotics were created prior to biologists developing an understanding of how antibiotic resistance evolves. Somehow, this is related to the ENCODE findings (or gene patenting), as is the subsequent discussion of how recombinant DNA techniques allow us to insert individual genes into organisms. Caruso makes the point that genes which may be patented by different companies could interact in a network. I have no idea whether this is a valid argument against gene patenting, but Caruso does seem to string together a couple of paragraphs that actually contain a reasonable amount of scientific accuracy.
Alas, this could only continue for so long. She goes on to quote Barbara Caulfield, vice president of Affymetrix:
“We’re learning that many diseases are caused not by the action of single genes, but by the interplay among multiple genes,” Ms. Caulfield said. She noted that just before she wrote her article, “scientists announced that they had decoded the genetic structures of one of the most virulent forms of malaria and that it may involve interactions among as many as 500 genes.”
It’s more of the “genes don’t make sense outside of their interaction network” argument against gene patenting (which, I’ll point out once again, I am not taking a side on), but I can’t make heads or tails of the second part of the quote. I think she’s referring to this paper on Plasmodium falciparum protein interaction networks, but it takes a bit of digging to figure out what’s going on. In the end, Caruso’s argument may make sense, but it’s damn near impossible to evaluate it because it’s hidden behind a veil of muddled science and tangential points.
Who is Denise Caruso? Aside from writing the Re:Framing column for the Times, she is also the founder and director of the Hybrid Vigor Institute. Caruso’s institute claims to help with problem solving by encouraging cross-disciplinary collaborations. Just like her writing, however, I can’t figure out what the hell that means. I worry that, despite the fact that she may be drawing upon diverse areas to create novel collaborations, Caruso can’t make the necessary connections to really bring them together. At least, that’s the conclusion one draws from reading her column.