Recently National Geographic did a cover article on science skepticism. The article discussed the specious claims linking vaccines to autism, or denying evolution or the moon landing, and examined the collective psychological reasons behind such anti-scientific thinking. Among the supposedly specious claims on the cover was "Genetically modified foods are evil". I was struck by the fact that, while the other claims were issues of refutable fact (evolution and the moon landing either did or did not happen, vaccines either can or can't lead to autism), this claim on transgenics was a value judgment. In other words, something that can't be confirmed or refuted, and really has little to do with scientific or anti-scientific though processes. I was dismayed to see NG enter the fray of popular media polemics and industrial transgenic pushers by lumping in a totally different kind of statement with other patently absurd denials of fact.
This article comments on the NG treatment, though it focuses on the supposed lack of scientific consensus around the safety of transgenic foods.
I tend to agree more with this article, which argues that a pretty robust scientific consensus has formed on the immediate safety of eating genetically engineered food (at least the Roundup Ready and Bt soy and corn that comprises most of our current GE food consumption).
At the same time, this second author hints at my major concern; that genetic engineering is profoundly and fundamentally different from the conventional breeding work that has been carried on by humans since the dawn of agriculture, and streamlined in the 20th century. I think it is perfectly valid for society to collectively decide (and thus for individuals to advocate for such decision) that genetic engineering is a technology that we have ethical objections to, and thus that it should be avoided as much as possible except in clear cases where it can be shown to have a real societal benefit. Glow-in-the-dark pet fish would not meet this criterion, while synthetic insulin clearly would. Glyphosate-resistant crops might or might not.
The bottom line is that science and technology exist in a social, economic, and political milieu, and it is perfectly valid to guide and regulate them according to this milieu. Many potential lines in medical research are forbidden by ethical concerns--certain types of human or animal testing, stem-cell work, etc. Some societies have decided to limit or strictly circumscribe the use and study of nuclear energy. Certain industrial technologies that would negatively impact workers or small producers are discouraged by legislation (for instance Colombia's policy of reserving panela production to small farmers as a way of promoting rural livelihoods and preventing mass banditry and insurgency of displaced farmers). We should all probably put strict controls on self-replicating technologies of global impact, such as nanotechnology or geoengineering.
I would argue that, because of its self-replicating and inevitable potential of transgenes to spread throughout the entire gene pool for a given species, genetic engineering should be another such technology that we strictly regulate. Just as bison conservationists try to maintain at least a reserve population of "pure" bison, that is bison that have never been crossed with domestic cattle genes, society should strive to maintain plant and animal populations free of transgenes. There's nothing inherently bad about the cattle genes, and in fact domestic cattle are very close genetically to bison (that's why they can interbreed). But I think most people can agree on the inherent value of purity in the natural world--full-blood bison, natural areas free from invasives, seas without man-made chemicals, food without petroleum-derived additives.
You could argue that everything under the sun is in fact natural, and thus that such emphasis on "purity" is misplaced. A cow is not inherently better or worse than a bison. One plant species is not inherently superior to another. Indeed, even man-made plastics or anything else extracted from petroleum is ultimately "natural", in that petroleum is ultimately derived from plants and animals that lived millions of years ago. But I think that such justifications would ring hollow to most people, and reasonably so. We all know the difference between a wild animal population and a domesticated species, or an intact ecosystem versus one degraded by invasives or synthetic chemicals.
On this basis I would argue for keeping transgenes out of our natural and managed ecosystems, to the extent possible. Having a Bt gene present in native Mesoamerican corn and its relatives will not kill any people, and it might not even alter the local insect populations that much. But something will be lost, just as it would be if there were some heavy metal or organic solvent or invasive plant added by humankind to those Mesoamerican ecosystems.