I spent time in this field. In the early 1990s I founded the Project to Label Gene Altered Food. So I met the other key people in the field, and I know the issues. I ended my own campaign when the Department of Agriculture finally agreed on a definition of "organic" food that excluded gene altered varieties.
I totally support Judge Sweet's ruling, without having read the decision. I hope he has written a good decision and the ruling holds up at higher court levels.
The problem with patents is that the patent law clearly prohibits the patenting of obvious ideas and tools and objects in the natural world. So clocks, hammers, wind power and lightening can't be patented, but a specific clock mechanism, hammer with toe nail clipper, specific wind generator and blade and copper lightening rod can be patented.
So what about genes? Humans have several thousand genes on each genome that produce proteins and tens of thousands of others whose function is unknown. Myriad Genetics and others have argued that a specific segment of the human gene can be patented. Myriad found the gene and its connection to a human disease, therefor they claimed a right to have a patent on that specific gene. Trouble is, (1) that specific gene sequence could do many other things, under a variety of developmental circumstances and a patent would restrict other uses of that gene sequence, (2) worse, other researchers could find other ways to identify and isolate that gene that may be useful and important but would be prohibited from doing so because of the Myriad patent.
Genes are part of the natural world, like wind and lightening. How you use them, how you extract them should be patentable, but the genes themselves should not be patented.