What about the (widespread) practice of mutation breeding? [1] Blasting seeds with X-rays and gamma rays in an attempt to generate new cultivars is a genetic wrecking ball compared to performing genetic engineering.
Conventional breeding has given us plenty of Oopses. The modern kiwifruit, whose progenitor (the smaller and less tasty Chinese gooseberry) may have been safely snacked upon by many folks who would today suffer a lethal allergic reaction after eating a kiwi. In the 1980s, a mutant variety of zucchini began producing enough cucurbitacin toxin to hospitalize a number of people. [2]
> If such transfers have occurred in nature for a long, long time, then it's safe to say that nature has created pathways that are safe. Our pathways are new.
We're still playing by nature's fundamental biological rules, and nature has had hundreds of millions of years to develop resiliency inside that same framework. One example: bacterial mechanisms to mitigate the damage from undesirable horizontal gene transfers by recognizing and deactivating to foreign genetic material: [3]
> I'm making a Talebian argument here. Nature is a VERY complex system. When we mess with it, we make incremental visible gains, and run the risk of large, invisible losses.
I think "incremental" is a bit of an understatement if we can, for example, feed tens of millions of humans in parts of the world where conventional crops cannot (yet?) provide reliable and sufficient nutrition, a critical step in reducing poverty.
Having said all this, I think crop monoculture is a serious problem, but I think it's an issue that needs to be solved through sound policy, not just through science.
[1] http://en.wikipedia.org/wiki/Mutation_breeding
[2] http://books.google.ca/books?id=Jcq1wTe_93UC&lpg=PP1&...