For more comprehesive coverage info see http://www.forbes.com/sites/danielfisher/2013/06/13/supreme-...
A crucial point is the cDNA is patentable, which still makes very little sense.
If an algae produces molecule A, one can determine its structure and (in theory) synthesize it in a lab. Both will be structurally identical. Of course, if the chemist wants to add X or Y moieties to the original algal molecule, he can. One could also determine the source of a certain molecule (bio vs. lab) by looking at the different isotopes in each molecule.
(In theory because some syntheses are practically extremely difficult.)
The same does not hold true in the US, thanks to Bridgman Art Library vs. Corel
"Bridgeman Art Library v. Corel Corp., 36 F. Supp. 2d 191 (S.D.N.Y. 1999), was a decision by the United States District Court for the Southern District of New York, which ruled that exact photographic copies of public domain images could not be protected by copyright in the United States because the copies lack originality. Even if accurate reproductions require a great deal of skill, experience and effort, the key element for copyrightability under U.S. law is that copyrighted material must show sufficient originality."
http://en.wikipedia.org/wiki/Bridgeman_Art_Library_v._Corel_....
Of course, this is one ruling by one court. It could be challenged. In the meantime, it looks like the SCOTUS has taken the view that copies can be yours, even if the original isn't.
The practical difference is that the originals are in the genetic makeup of billions and circulating freely, whereas notable paintings tend to be unique and tightly controlled.
Making cDNA is a standard kit, on order from any number of vendors, and is a standard molecular biology technique.
So basically, the Supreme Court, or at least Justice Clarence Thomas, is completely clueless.
Ease is not the question by which a patent is judged. When you do a PCR reaction, introns or not, you are creating a NEW molecule that didn't exist before. Period. If the judges are claiming that the "information content" is what counts, then that goes against the molecule-patenting precedent - it's really the "molecular identity" which should count.
Now, my preference is to not allow patenting - at all - but to be consistent with the existing patenting landscape, they should have allowed the myriad patents (except for the "method" of comparing a patient sequence with the reference sequence) to pass.
You are completely right that the biological molecules could be considered identical to small chemical molecules, and that trivial chemical manufacturing steps could be patented; I do not do synthesis but all the synthetic organic chemists I know are pursuing incredibly complex and difficult procedures that are not on the same playing field as any PCR reaction, and I did not know that simple and straightforward techniques could be patented (which would seem to be counter to the "person skilled in the art" bar that's commonly used for patents, but I am not a synthetic chemist).
However, and I may be completely out of line, I think that the most important thing with patent law is to go for maximum utility as opposed to maximum consistency. Patent law is legal invention intended to maximize innovation and advancement, there is no underlying need for consistency in different realms. The biological and chemical realms have completely different monetization strategies, and it would make sense for the IP realms to be different, just as there are completely different standards for patents of composition, methods and systems. If somebody is using cDNA of a particular gene as a therapy and selling that compound, I could see that being patentable. However, I can't see patents of cDNA for diagnostic purposes being patentable; there the cDNA patent blocks any innovation on the interesting part, the analysis of information.
Furthermore, what constitutes a "trivial chemical manufacturing step" is not really appropriate for a legal decision. Even if step 12 in the synthesis is obvious, is it trivial to decide to use a 500 L batch fed reactor with piping radius X, with a copper pipe, and chiller unit Z for step 12? But in the molecule patents, the steps to synthesis are not necessarily relevant. All that is claimed is the structure of the molecule.
"all the synthetic organic chemists I know are pursuing incredibly complex and difficult procedures"
Keep in mind that the pursuit of complex and difficult procedures (or, really, the molecules that lead to them) is the essential purpose of synthetic organic chemistry in academia, and industrial chemistry is a very, very different beast. Those easy reactions that you learned in your intro ochem class textbook (SNs, Es, Aryl substitutions, halogenations, nitrations, carbonyl chemistry...) it's really those reactions that dominate industrial chemistry - for several reasons - they don't require exotic conditions (extreme cold, extreme hot) - they aren't super exothermic - that's a huge problem when you scale to 500 L you don't want your reaction chamber to turn into a bomb - they have been around for decades so optimization techniques are well characterized - they have been around for decades so regulatory approval is simpler.
But all of this is moot, because the patenting of a molecule doesn't generally hing on the process.
Consider - if you had a Drexler-like nanomachine that could 3d-print a molecular structure on demand, such that chemistry would essentially become "kit-ified" in the same way that molecular biology is, should then chemical patents then be invalidated?
"Patent law is legal invention intended to maximize innovation and advancement, there is no underlying need for consistency in different realms. The biological and chemical realms have completely different monetization strategies, and it would make sense for the IP realms to be different, just as there are completely different standards for patents of composition, methods and systems."
That is generally supposed to be for congress to decide, not the courts.