The most recent issue of the Journal of Economic Perspectives is focused on the patent issue.
All articles reach similar conclusions to the first (Boldrin and Levine). They have been saying the same thing about patents for over 10 years, so don't expect their careers to be destroyed or whatever other apocalyptic scenarios were discussed above. They are academic economists who have worked for a several strong research departments and feds over the years. They (and others) provide very strong evidence that the current patent system does not help consumers/citizens. That is the purpose of laws governing commerce, correct?
It is highly likely that a perfectly designed and operated patent system would be better than no patent system. Given the reality of humans running things, this is unattainable and no patents are probably better than the current system for consumers. When examining the evidence, this claim appears obviously true (to me at least, but I read the Boldrin/Levine book a decade ago). The NIH and NSF could pick up the slack in funding pharma research, and in other fields, first-mover advantage seems to provide plenty of monopoly profits for innovators.