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***academic conception of patents, in which inventions are always assumed to be clearly defined and non-obvious***
Look at *empirical* research, perhaps by Mark Lemley, Kimberly Moore, Dan Burk and a few others. I think Carl Shapiro and Robert Merges have done some work too. I can send you some links when I have more time.
***At least in the realm of software and business method patents, companies have long since dropped any pretext that their "inventions" are genuinely novel discoveries.***
Perhaps some, but I'm not sure who they are.
How much can you really tell by claim construction alone? If two parties aren't in dispute, they'll license. If they go to litigation, they'll witness an evolved role on patent policy for court interpretation and reexamination at the USPTO. Court interpretation and USPTO re-examination decide how and to what extent a patent is enforced, if at all. Hopefully some of the lessons learned recently will integrate into good patent reform laws.
There is certainly a disconnect between the academic literature and the real world. While its good to take preventative measures for a possible dire situation such as the one Tim writes of, I'd say lets see how things develop. Professor Merges voiced similar view in a 2003 publication where he addressed fears surrounding business method and software patents: "A funny thing happened on the way to the demise of the software industry. It never happened." http://papers.ssrn.com/sol3/papers.cfm?abstract....
Take your pick. Every significant software company has a rewards program for engineers who file patents- and they make it very clear to those engineers internally that it doesn't matter how negligible or insignificant the 'discovery' is, as long as there is even the smallest option the lawyers can twist the wording into something patentable. The goal is very explicitly quantity and not quality. The cheap companies give you a t-shirt ('I filed a patent!') and a gift certificate; more generous companies add extra options. Again, this is all just for contacting the lawyers- if the patent application is actually successful, most companies then add more incentives.
(I'm sort of surprised that the Times didn't point out how these sorts of things, in an industry like Wall Street, almost inevitably turn out- the large players come to a standstill, cross-license, and then sue everyone small or up and coming.)