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I used to hear somewhat-reasonable cynicism over this, that the drug companies could just make some minor change (add more sugar) and repatent it. Did this ever work, and does it no longer apply?
If not they will release a better version of the drug that they had been sitting on for just such an occasion.
Well, it wouldn't stop generic versions of the old version of the drug. And if they couldn't demonstrate increased effectivity of the new drug compared to the old one, why would anyone buy the new one?
While the changes are often less trivial than "adding more sugar" the drug companies have been using their ability to modify drugs slightly to extend patent life. This essentially got them through the last 10 years in many cases. But for most of the big money making drugs, they're out of options. It's interesting to me (having worked for 8 years in pharma R&D) how little the general public and news media have been reporting on the slowly unfolding total meltdown of big pharma. They have been shedding jobs and down-sizing for quite some time. The whole drug business is in complete shambles with lousy R&D productivity and very little good news on the horizon. This is one of the main reasons I left the industry.
"Twenty drug approvals in the United States this year, and others in the next few years, will help replace the revenue"

They make that statement at the end of the article in an almost offhand way, but no analysis I have seen for any of the big pharmas shows them anywhere near to replacing lost revenue from the near-term patent expirations. We are in a period of the fewest approvals for new drugs than almost any time since the beginning of the FDA (and similar regulatory agencies around the world). The industry is in bad shape, and there seems to be no relief for the lack of R&D productivity any time soon.

Wait, wait... aren't patents supposed to encourage R&D? The monopoly rent from a patent is supposedly the only way to encourage firms to do R&D, to innovate rather than copy.

And aren't patents getting stronger based on case law? The i4i vs Microsoft thing re-affirmed quite a strict standard as to patent validity. I know it's nothing compared to how copyrights are being made stronger and stronger, but still, patents are being made stronger.

Shouldn't we be seeing more innovation on that basis? There's a general trend towards strong "intellectual property" protections, and Big Pharma has been the industry pushing that kind of thing pretty hard.

So where's the real problem? Big Pharma R&D not working, FDA getting irrational about approvals, Big Pharma coasting for the past N years? Biology research has hit the limits of what it can do?