Noise. I've also heard the "unexplained or un-identified" genes as junk. What we're learning is that there's a lot going on in the junk and there's more to "noise" than things that get in the way and mess up packaged & neat theories & products. I haven't much about biotech developments @ CU recently. No doubt they're wrestling with these issues. Tony
On 7/19/07, Joey Gates <[EMAIL PROTECTED]> wrote: > > Thanks for sharing that. (I was actually going to post it also.) > > Seems amazing that gene theory and application would be based on > reductionist principles... > > I have also read that "90% of the genome is noise. That is, "there is a > lot of DNA that is "in between" genes. Since people don't understand it, > some have called it random "noise"." > > > Tony Del Plato <[EMAIL PROTECTED]> wrote: > BIO-IPR docserver | http://www.grain.org/bio-ipr > ________________________________________________________ > > TITLE: A challenge to gene theory, a tougher look at biotech > AUTHOR: Denise Caruso > PUBLICATION: The New York Times > DATE: 1 July 2007 > URL: http://www.genetics-and-society.org/newsdisp.asp?id=1226 > ________________________________________________________ > > New York Times | July 1, 2007 > > A CHALLENGE TO GENE THEORY, A TOUGHER LOOK AT BIOTECH > > Denise Caruso > > The $73.5 billion global biotech business may soon have to grapple with > a discovery that calls into question the scientific principles on which > it was founded. > > 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. > > Instead, genes appear to operate in a complex network, and interact and > overlap with one another and with other components in ways not yet fully > understood. According to the institute, these findings will challenge > scientists "to rethink some long-held views about what genes are and > what they do." > > Biologists have recorded these network effects for many years in other > organisms. But in the world of science, discoveries often do not become > part of mainstream thought until they are linked to humans. > > With that link now in place, the report is likely to have repercussions > far beyond the laboratory. The presumption that genes operate > independently 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. > > Innovation begets risk, almost by definition. When something is truly > new, only so much can be predicted about how it will play out. > Proponents of a discovery often see and believe only in the benefits it > will deliver. But when it comes to innovations in food and medicine, > belief can be dangerous. Often, new information is discovered that > invalidates the principles -- thus the claims of benefit and, sometimes, > safety -- on which proponents have built their products. > > For example, antibiotics were once considered miracle drugs that, for > the first time in history, greatly reduced the probability that people > would die from common bacterial infections. But doctors did not yet know > that the genetic material responsible for conferring antibiotic > resistance moves easily between different species of bacteria. > Overprescribing antibiotics for virtually every ailment has given rise > to "superbugs" that are now virtually unkillable. > > The principle that gave rise to the biotech industry promised benefits > that were equally compelling. Known as the Central Dogma of molecular > biology, it stated that each gene in living organisms, from humans to > bacteria, carries the information needed to construct one protein. > > Proteins are the cogs and the motors that drive the function of cells > and, ultimately, organisms. In the 1960s, scientists discovered that a > gene that produces one type of protein in one organism would produce a > remarkably similar protein in another. The similarity between the > insulin produced by humans and by pigs is what once made pig insulin a > life-saving treatment for diabetics. > > The scientists who invented recombinant DNA in 1973 built their > innovation on this mechanistic, "one gene, one protein" principle. > > Because donor genes could be associated with specific functions, with > discrete properties and clear boundaries, scientists then believed that > a gene from any organism could fit neatly and predictably into a larger > design -- one that products and companies could be built around, and > that could be protected by intellectual-property laws. > > This presumption, now disputed, is what one molecular biologist calls > "the industrial gene." > > "The industrial gene is one that can be defined, owned, tracked, proven > acceptably safe, proven to have uniform effect, sold and recalled," said > Jack Heinemann, a professor of molecular biology in the School of > Biological Sciences at the University of Canterbury in New Zealand and > director of its Center for Integrated Research in Biosafety. > > In the United States, the Patent and Trademark Office allows genes to be > patented on the basis of this uniform effect or function. In fact, it > defines a gene in these terms, as an ordered sequence of DNA "that > encodes a specific functional product." > > In 2005, a study showed that more than 4,000 human genes had already > been patented in the United States alone. And this is but a small > fraction of the total number of patented plant, animal and microbial > genes. > > In the context of the consortium's findings, this definition now raises > some fundamental questions about the defensibility of those patents. > > If genes are only one component of how a genome functions, for example, > will infringement claims be subject to dispute when another crucial > component of the network is claimed by someone else? Might owners of > gene patents also find themselves liable for unintended collateral > damage caused by the network effects of the genes they own? > > And, just as important, will these not-yet-understood components of gene > function tarnish the appeal of the market for biotech investors, who > prefer their intellectual property claims to be unambiguous and > indisputable? > > While no one has yet challenged the legal basis for gene patents, the > biotech industry itself has long since acknowledged the science behind > the question. > > "The genome is enormously complex, and the only thing we can say about > it with certainty is how much more we have left to learn," wrote Barbara > A. Caulfield, executive vice president and general counsel at the > biotech pioneer Affymetrix, in a 2002 article on Law.com called "Why We > Hate Gene Patents." > > "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." > > Even more important than patent laws are safety issues raised by the > consortium's findings. Evidence of a networked genome shatters the > scientific basis for virtually every official risk assessment of today's > commercial biotech products, from genetically engineered crops to > pharmaceuticals. > > "The real worry for us has always been that the commercial agenda for > biotech may be premature, based on what we have long known was an > incomplete understanding of genetics," said Professor Heinemann, who > writes and teaches extensively on biosafety issues. > > "Because gene patents and the genetic engineering process itself are > both defined in terms of genes acting independently," he said, > "regulators may be unaware of the potential impacts arising from these > network effects." > > Yet to date, every attempt to challenge safety claims for biotech > products has been categorically dismissed, or derided as unscientific. A > 2004 round table on the safety of biotech food, sponsored by the Pew > Initiative on Food and Biotechnology, provided a typical example: > > "Both theory and experience confirm the extraordinary predictability and > safety of gene-splicing technology and its products," said Dr. Henry I. > Miller, a fellow at the Hoover Institution who represented the > pro-biotech position. Dr. Miller was the founding director of the Office > of Biotechnology at the Food and Drug Administration, and presided over > the approval of the first biotech food in 1992. > > Now that the consortium's findings have cast the validity of that theory > into question, it may be time for the biotech industry to re-examine the > more subtle effects of its products, and to share what it knows about > them with regulators and other scientists. > > This is not the first time it has been asked to do so. A 2004 editorial > in the journal Nature Genetics beseeched academic and corporate > researchers to start releasing their proprietary data to reviewers, so > it might receive the kind of scrutiny required of credible science. > > According to Professor Heinemann, many biotech companies already conduct > detailed genetic studies of their products that profile the expression > of proteins and other elements. But they are not required to report most > of this data to regulators, so they do not. Thus vast stores of > important research information sit idle. > > "Something that is front and center in the biosafety community in New > Zealand now is whether companies should be required to submit their > gene-profiling data for hazard identification," Professor Heinemann > said. With no such reporting requirements, companies and regulators > alike will continue to "blind themselves to network effects," he said. > > The Nature Genetics editorial, titled "Good Citizenship, or Good > Business?," presented its argument as a choice for the industry to make. > Given the significance of these new findings, it is a distinction > without a difference. > > ________________________________________________________ > > GOING FURTHER (compiled by GRAIN) > > National Human Genome Research Institute, "New findings challenge > established views on human genome - ENCODE research consortium uncovers > surprises related to organization and function of human genetic > blueprint", National Institutes of Health, Bethesda MD, 13 June 2007. > http://www.genome.gov/25521554 > > GRAIN, "Blinded by the gene", Seedling, Barcelona, July 2003. > http://www.grain.org/seedling/?id=239 > > Barbara A. Caulfield, "Why we hate gene patents", IP Worldwide, 30 > December 2002. > http://www.law.com/jsp/article.jsp?id=1039054490790 > > ________________________________________________________ > ABOUT BIO-IPR -- BIO-IPR is an irregular listserver produced by GRAIN. > Its purpose is to circulate news and information about recent > developments in the field of intellectual property rights related to > biodiversity and associated knowledge. BIO-IPR is a strictly > non-commercial and educational service for nonprofit organisations and > individuals active in the struggle against IPRs on life. The views > expressed in each post are those of the indicated author(s). > ARCHIVES -- The full archives are online at http://www.grain.org/bio-ipr. > SUBSCRIPTIONS -- To subscribe or modify your subscription details, > please go to http://www.grain.org/subscribe/bioipr.cfm and either join > or login. 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