The Anti-Patent Beat Goes on at The New York Times

    By Kevin E. Noonan --

The hostility of The New York Times to patents in general (and gene patenting in particular) has been well documented (see "Anti-Patent ('Sullivan?') Malice by The New York Times" and "Science Fiction in The New York Times").  However, until now this bias has been confined to the editorial page, where it at least can be recognized as a particular point of view and subject to public debate.  This Sunday (July 1, 2007), the Times proved that even the purported "paper of record" is not immune to the modern virus of letting its opinion pieces bleed onto the news pages, with an "analysis" on new developments in biological sciences which the author (falsely) asserts places the validity of biotech patents, particularly gene patents, into question (see "A Challenge to Gene Theory, a Tougher Look at Biotech").

The piece, in the "science" section, is by Denise Caruso (at left), a frequent Times contributor and executive director of the Hybrid Vigor Institute, a private think tank putatively dedicated to assessing risk in an interdisciplinary fashion; its biases, and its directors, will become evident shortly.  The subject of the piece is recent evidence that mammalian (including human) genes are not expressed as simply as are the genes of less complicated organisms, such as bacteria and yeast.  These results show that a majority of the DNA sequences studied are transcribed into RNA, including both gene sequences and sequences understood to be non-coding, "junk" DNA, and that these primary transcripts are overlapping, i.e., they start and stop at a more diverse array of sites than previously appreciated (see "What's ENCODE'd in Your Genome Isn't a Simple Collection of Genes").  As the authors explain, "[i]nstead of the traditional view that many genes have one or more alternative transcripts that code for alternative proteins, our data suggest that a given gene may both encode multiple protein products and produce other transcripts that include sequences from both strands and from neighbouring loci (often without encoding a different protein)."  The authors were quick to point out, however, the important caveat that the study was limited to only 1% of the human genome.

No such caution from Ms. Caruso, however.  In her article, she asserts from the very first sentence that these results challenge the scientific principles upon which the biotechnology industry is based.  She claims that this is contrary to "[t]he presumption that genes operate independently [that] has been institutionalized since 1976, when the first biotech company was founded.  In fact, it is the economic and regulatory foundation on which the entire biotechnology industry is built."  She goes on to analogize the biotech industry to the development of antibiotics, with the unknown consequences of "superbugs" resistant to them (ignoring, as only those who disregard history can, the overwhelming countervailing benefit that the antibiotic era conferred on mankind).  She characterizes the ENCODE results as challenging the "central dogma of molecular biology," while actually mischaracterizing what she is describing:  the principle of "one gene, one enzyme" enunciated by Beadle and Tatum in 1941, twelve years before Watson and Crick invented molecular biology and Crick formulated the central dogma.  She then raises explicitly the issue of whether "gene patenting" by the U.S. Patent and Trademark Office is tenable, saying the ENCODE data "now raises some fundamental questions about the defensibility of those patents."

In all of this, she is not only wrong but misses the point of the scientific results.  (Understandable for someone who was an English major at California Polytechnic State University.)  The ENCODE study did not overturn more than 100 years of genetics, mammalian or otherwise.  Genes as a concept and a reality still exist; they can be physically mapped to specific locations in human chromosomes, and mutations and other changes have consequences consistent with their physical reality as discrete genes.  What ENCODE tells us is that expression of these genes in native form in a cell is more complex than previously appreciated.  Regardless, however, the messenger RNA that enters the cytoplasm from the nucleus is exactly the same discrete "gene" (more accurately, protein coding sequence) that it always has been, and which it has always been understood to be.  And it is complementary DNA copies of those mRNAs that have formed the basis for most of the "gene patents" granted in the U.S. and elsewhere.  The reason for this is technical:  it has been known for more than thirty years that the coding sequence of most mammalian "genes" was interrupted by intervening sequences (called "introns" to the coding sequence's "exons") and that the primary transcript from the "gene" was processed in the nucleus to produce messenger RNA.  Even if it has turned out that the biological mechanism is more complicated than that, it hasn't done anything to the usefulness of cloned genes recognized by the Patent Office and industry for the past 30 years.

Ms. Caruso also raises the specter of safety in her piece:  if "we" really don't understand how this all works, isn't it (couldn't it) be dangerous?  The answer, for the most part, is "no," and answer is backed up by long experience.  At the dawn of the biotechnology age, its foremost practitioners (who didn't need think tank policy wonks to raise the issue for them) met at Asilomar in California and came up with physical and biological safety standards that were later implemented in large part by the National Institutes of Health.  In the ensuing years, it became evident that most of these precautions were unnecessary, since genes transferred by researchers from organism to organism didn't cause any health or other issues nor pose any threat to humans.  Today, there are neither safety issues nor technical issues for most industrial biotechnology.  Despite the misapplication of the ENCODE results by Ms. Caruso, most industrial genes (for erythropoietin, or tissue plasminogen activator, or any number of antibodies) work just like the traditional model says they should.  This is not surprising, since for recombinant protein production the genes are engineered to work in a culture of isolated cells.  For bacterial cell embodiments of this technology the ENCODE results are inapplicable, and for mammalian cell embodiments they are irrelevant.  It cannot be emphasized enough, in view of the misinformation in Ms. Caruso's piece, that the ENCODE results are directed (and limited) to native expression of native genes, not recombinant ones.  And for transgenic plants and animals, experience teaches that there simply is no "gene transfer" from the transgenic organism to humans, just as native tomato or other genes do not transit the species barrier as they transit our digestive tracts.

While no doubt useful for selling newspapers, the problem with "analyses" such as this one are two-fold (at least).  First, they are based on at best a faulty understanding of the science behind the headlines, written for and consumed by a public with little (perhaps less) understanding of the facts.  Second, they are dishonest, since they are written as if they were dispassionate when in fact they are biased.  A look behind the curtain of the Hybrid Vigor Institute shows that Ms. Caruso started the Institute after a stint with the Electronic Frontier Foundation, an anti-patent, "free information" group representing the interests of the IT community.  For a variety of reasons (some civil libertarian but many economic), this group is against patenting (and copyright, for that matter).  While it is easy to dress these views up as being in favor of "freedom," they are really in favor of economic exploitation without compensation for the innovators.  While this stance may be both attractive and viable for industries where investment in new technology can be a computer and a bright computer science major (or high school student), very different economics attach to the biotechnology industry (see "Could Creating a U.S. 'Utility Model' Patent Fulfill the 'Need' for Patent Law Reform?"), which is why most biotech representatives support patent protection.  Ms. Caruso found one of the few biotech naysayers in Barbara Caulfield (at left) from Affymetrix, who is quoted in the piece, ostensibly in support of the "problems" with gene patenting.  (In fairness, Ms. Caulfield's own bias is evident in her article, "Why We Hate Gene Patents" on Law.com.)  In reality, Ms. Caulfield's anti-patent bias has the same genesis as that of the IT industry:  since the company wants to sell its gene chips that comprise thousands of gene-specific sequences, patent owners of these sequences constitute a "patent thicket" requiring licenses that the company would rather not be forced to obtain.  On the biotechnology side, Ms. Caruso has been involved in studies of the risks of xenotransplantation and pandemic infections (subjects traversed thoroughly by others, including Laurie Garrett in "The Coming Plague: Newly Emerging Diseases in a World Out of Balance").

Ms. Caruso's bias is also evident in the content of her book, "Intervention: Confronting the Real Risks of Genetic Engineering and Life on a Biotech Planet."  It is characterized this way on amazon.com:

INTERVENTION challenges two of the most sacred tenets of modern society, innovation and technology, from the perspective of the unique risks they present.  Using genetic engineering as its model, it paints a vivid picture of the scientific uncertainties that biotech risk evaluations dismiss or ignore, and lays bare the power and money conflicts between academia, industry and regulators that have sped these risky innovations to the market.  Intervention champions an alternative method for assessing the risks of technology, developed by the world's top risk experts, that can eliminate such conflicts, help regain public trust in science and government, and drive research and development toward more useful, safer products.

Whether Luddite or technology Cassandra, Ms. Caruso's public and published career attest to her bias against technology, seeing it as posing a risk to be assessed (preferably not by those with the best understanding of the potential - and potential difficulties - of that technology) rather than an opportunity to be exploited.

Ms. Caruso is entitled to her bias and her opinions, of course.  What is troubling is that those opinions are based on a flawed and incorrect understanding of the facts.  It is even more troubling that The New York Times would accept those opinions, and those misunderstood facts, at face value, and then print them as if they were not opinions but were themselves facts.  This sort of irresponsibility to its reading public is as good a reason as any for the precipitous decline in the level and tenor of public debate at this time in this country.