What are the ethics surrounding the genetic manipulation of animals and crops?

In the modern scientific era we have come to a turning point where we understand the genetic makeup of a variety of organisms well enough that we can actually manipulate the genes of these animals without the need for selective breeding. Companies such as Monsanto have fronted this drive for the use of genetic modification on our food supply for such benefits as frost resistance, pesticide resistance, or even toxicity to pest animals. All this sounds great on the surface, but when you look deeper you will realize the costs for this practice far outweigh the benefits for society.
The first and perhaps most blatant ethical dilemma is that Monsanto and other gene modifying companies are patenting their efforts as “intellectual property” and this also includes all organisms that are cross bred with the original modified plants and animals. They use this leverage to put farmers into debt around the world, and they treat the keeping of seed as the theft of their intellectual property. This often results in lengthy legal battles in which the farmers are dragged through the courts for years on end, up against the brick wall of these mega-corporation’s resources. In India farmers are actually committing suicide to remove the financial constraint on their families. If these companies were indeed doing such research for the benefit of mankind, an ethically astute position, surely they wouldn’t be subjecting farmers to such horrendous treatment.
The modification of these genes involves the use of animals (human and non-human) as laboratory guinea pigs. The genes for the manipulation of both animal and plants are derived from other organisms, mostly animals. They will take the DNA from animals with desirable traits in a lab which have been imported from all across the world. They then shoot the genes using a particle gun into a single cell of the host organism, in a petri dish. The new genes then spread to the other cells in the organism like cancer. The result, you get bananas crossed with rat DNA, tomatoes crossed with seal DNA, and anything else you can imagine. They have even dreamt up a way to make plants grow with pesticide already inside the plant, so you don’t have to spray them, any insect or small animal that eats it will have its stomach explode.
I think it goes without saying that this is an extremely unethical business, and it deserves proper criticism. Yet even people who seem to have a vested interest in this issue don’t bat an eyelash when Obama appoints Monsanto’s ex- VP to be senior advisor to the FDA.