This is more technical than my usual pieces; please bear with me and remember I'm still not a lawyer, just doing my best.
The decision last month in Mayo v Prometheus was either good or bad, depending on which side you stand for. Organizations such as the (generally liberal) ACLU, the (generally libertarian) Cato Institute, and the (generally non-politically aligned) AMA were all pleased by the ruling in Mayo's favor. Biotech/pharma companies were dismayed. But there's a third group, nominally neutral in this particular dispute, who have to deal with its consequences: the patent examiners who have to decide what they should and should not allow as patents and the applicants (and their attorneys) who have to construct patent applications, draw defensible claims, and secure the patents that the SCOTUS decision should enable.
To the dismay of this third group the majority decision, written by Justice Breyer, is causing more confusion than clarity, as has happened with several recent SCOTUS patent decisions. Greg Aharonian's PATNEWS published a letter this month from an anonymous group of examiners in the USPTO's "biotech Art Groups" - the people responsible for making judgments of patent applications in light of this decision. And they are not happy people.
It seems that Breyer's opinion confuses 35 U.S.C. 101 and 35 U.S.C. 103. That's two key sections of US patent law covering the requirements for an invention to be patentable. See the Wikipedia entry for a mostly non-legalese discussion. The actual (sparse) legal language can be found at sites such as Cornell's Legal Information Institute.
Taken as a whole, a non-patenting outsider doesn't care about these distinctions. Either something is or is not covered by a patent and it doesn't matter why unless you plan to challenge the patent somehow. But the people who are involved in practicing the law care a great deal about these distinctions. An invention may be rejected on 101 grounds or, separately, on 103 grounds. Challenges to patents, or to specific patent claims, can be brought under different sections of the law, and there are different requirements in each of these cases
And let's not forget that none of these things is free. Patent examiners always have more work to do than they can handle; if they reject wrongly and have to re-examine then they've taken away time that could have been used to examine another patent, which harms them and the long queue of waiting applicants. Patent applicants have to pay lawyers, court costs, their own time, etc., none of which are cheap. Getting 101/103 wrong can cost a lot of money, so it really matters if Breyer's opinion has messed this up.
Specifically, the patent examiners say:
[T]he decision never says what the natural laws are in the claims or how the claims are simply an application of the natural laws. The starting material and product are not naturally occurring. How are we to justify saying something is or isn't simply an application of a natural law?
The point of novelty in the patents (Applicants' discovery) seems to be that a therapeutic amount of the drug is one that produces an amount of the metabolite in claim 1 in the blood within the range recited in claim 1. [...] Determining this indicator (metabolite range) may or may not be an invention. But that determination is better treated under 103.
We don't know what the PTO can do with this decision, because no examiner thinks like the Supremes.
The 101/103 distinction revolves around what is eligible to be patented with 101 criteria supposed to govern novelty and usefulness versus 103 criteria governing (non)obviousness. That is, even if you've come up with something new and useful, if the invention was obvious you still may not be able to get a patent on it. What Breyer's opinion seems to be doing is stating that Prometheus's patent is invalid in part because of the use of "natural laws" (which might be read as a 101 objection) and in part because the result (of reading the metabolite level) is obvious - to a person skilled in the art, remember.
But if natural law applications fail for obviousness reasons then... um, what's the point of having 101 and 103 be separate? The examiner writing above seems to be making the point that the Supreme Court majority is written as if by a layperson who doesn't care about the 101/103 distinctions, but has to be treated as law of the land by patent examiners who care very much about this.
No wonder they're tearing their hair out.
(Excerpts and quotes above taken from PATNEWS by kind permission of Greg Aharonian of Internet Patent News Service and publisher of PATNEWS. The newsletter itself has no online site, but you can subscribe at http://bustpatents.com/)