Totally stupid that one can patent an organism. By this logic, a dog breeder who makes a new crossbreed should be able to patent that dog. If the Court has any common sense (and they most certainly don't, see 'racial entitlements' as evidence [or Citizen's United, or Bush v. Gore, or...you get my point]), they'll put an end to this. Indians should try to patent corn and see how far they get.
It is totally stupid, but I don't think that's ever going to be a successful legal argument. Patents are there to do a stupid thing, keeping anyone but the patent holder from using an idea that many other than the patent holder could get good use out of, in order to encourage people to develop patentable ideas. The way to argue against it is not to point out that the patents are stupid, it's to point out that they don't achieve their goal. We never got any traction arguing against software patents on the grounds that an algorithm is a mathematical object, no matter how strongly many of us felt that software patents were stupid for that reason, but we are finally, too slowly and without being able kill off the notion that patent holders deserve any consideration at all yet, making some progress on the grounds that they actually impede what they were meant to encourage. Likewise, I think the only way for farmers to defeat the patenting of organisms will be to fund, or maybe even participate in, the development of GMOs of their own, maybe through a trade organization. Then they get unencumbered seeds, and any conflicts with Monsanto pile up as evidence that encumbered organisms impede progress.