The article missed some of the other giveaways to Big Pharma. One is a narrowing of the patent obviousness requirement for "me-too" drugs. Claritin (loratidine) is the classic example. Loratidine is a stereoisomer; there's a left handed and a right handed version of the molecule. One has an anti-allergy effect, and the other doesn't seem to do much. (That's very common; biology isn't symmetrical at the molecular level.)

When the patent ran out on Claritin, the manufacturer came out with Clarinex, which contains only the one isomer that does something useful. They then pitched doctors hard to switch their patients to Clarinex, with considerable success.

But the manufacturer lost a patent case, on the grounds that separating the isomers and only keeping the useful one is obvious to anyone skilled in the art.[1] Now that isomer separation is routine, although non-trivial, the FDA requires it as a purification step if the non-useful isomer has any negative effects.[2] You can't claim that a step required by existing regulation is a new invention.

There's a clause in the TPP IP section to reverse that decision.[3] "[US/JP propose; CL/MY/PE/SG/VN/BN/AU/NZ/CA/MX oppose: For greater certainty, a Party may not deny a patent solely on the basis that the product did not result in an enhanced efficacy of the known product when the applicant has set forth distinguishing features establishing that the invention is new, involves an inventive step, and is capable of industrial application.]" That's from last year's draft on Wikileaks; I haven't seen the new draft yet.

Incidentally, the TPP resolves the issue of patentablity for software and business methods: "Subject to the provisions of paragraph 2 and 3 (which relate mostly to plant and animal patents), each Party shall make patents available for any invention, whether a product or process, in all fields of technology, provided that the invention is new, involves an inventive step, and is capable of industrial application." So software and business methods must be made patentable in all TPP-signatory countries. This, again, is from last year's draft. Check the new one once it gets published.

[1] http://www.prnewswire.com/news-releases/schering-plough-lose... [2] http://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInforma... [3] https://wikileaks.org/tpp-ip2/