Bruce Perens is active in the fight against software patenting in Europe, where software patents are granted but not yet entirely enforcible. He also works for reform of the patent system in the United States and worldwide.
Primary to his concern is the conflict between software patenting and Open Source. Software patenting is generally hostile to Open Source, because patent holders require a royalty payment that isn't possible for developers who distribute their software at no charge.
There are also many other reasons that the software patenting system is broken and actually works to discourage innovation.
In the United States, the Bayh-Dole Act made it clear that it was legal to for a university to patent publicly-funded research and sell the patent to a private company that would hold it as a monopoly. This, unfortunately, creates some injustice and economic inefficiency. The injustice is that the taxpayers who funded the research may be the targets of lawsuits based on the research patents. There is also the problem that this uses public funding to lock out areas of development to Open Source through patenting, and thus works against the interest of the general public who would use that software.
Dissemination of research results through patenting is inefficient for software in comparison to other commodities like pharmaceuticals. It might take a Billion dollar project to commercialize a pharmaceutical, and a patent monopoly might be the only way to provide a monetary incentive for a company to invest that money. In contrast, software can be produced by individuals, small industry, and Open Source teams, none of which require a large capitalization. Thus, it is not economically efficient for publicly-developed software algorithms to be monopolized through patents. It would be more efficient to allow all possible entities to use these algorithms. This would guarantee that a number of different entities would implement the algorithm, and it would be more likely that one of the implementations would be a successful product. Patenting of software often results in the algorithm being locked up in a failing and then bankrupt company, since most companies do fail. The eventual fate of such a patent would probably be purchase from the bankruptcy court by one of the patent troll companies for use in lawsuits against companies that make real products.