This is where I'm confused. How can they patent what occurs in nature, whether rare or not?
Right now, I’m not sure they can, but this is “new news”, as the law has been recently changed.
“Until recently, natural biological substances themselves could be patented (apart from any associated process or usage) in the United States if they were sufficiently “isolated” from their naturally occurring states.
“Prominent historical examples of such patents on isolated products of nature include adrenaline, insulin, vitamin B12, and gene patents.
“However, the US Supreme Court ruled in 2013 that mere isolation by itself is not sufficient for something to be deemed inventive subject matter.”
http://en.wikipedia.org/wiki/Biological_patents_in_the_United_States
But this being said, the question is how much GM is needed to establish a patent. I suspect that just inserting an otherwise benign substance, like a “glow in the dark” gene, a popular GM addition, that does not otherwise affect its function, might be enough.