@maggiekb Thanks for the fix; that was very important. And thanks for spending some time on the subject.
To adequately present the position of the SCOTUS, you have to explain their rationale. I think it is incorrect (at least in spirit, see below), but it is not mysterious. They single out cDNA because it is synthetically produced in the lab by human manipulations. Ian Bosdet and Science on Google+ had an excellent Hangout On Air recently to explain this issue (https://plus.google.com/events/cb8gdd8olcclfkcnmp1787uu8a8).
The synthetic origins of cDNA, according to the SCOTUS may render it patentable for the same reason that synthetic drugs (as substances) are patentable. This makes some sense, but ignores the fact that not all cDNA is synthetic, which makes the decision short-sighted (to say the least).
There is also the big picture: people fail to recognize that what is being patented is information. This is not done in a straightforward way (the synthetic cDNA molecule is the disguise here), but that is what's happening. The primary role that nucleic acids play in cells is information storage. Therefore, when you patent genomic DNA, or cDNA, or RNA you are (in effect) patenting information that can be interpreted by the cell (or, since we all share the same genetic code—roughly speaking—information that can be interpreted by biological systems on Earth). I think this is the big problem, not the arbitrary picking of cDNA as a potentially patentable entity.
In fact, imo, the outstanding question is the same here as with the software patents: how (and if) can we patent information?