Writing in a special Wired series on patent reform, Free Software Foundation founder Richard Stallman proposes to limit the harms that patents do to computers, their users, and free/open development by passing a law that says that running software on a general purpose computer doesn't infringe patents. In Stallman's view, this would cut through a lot of the knottier problems in patent reform, including defining "software patents;" the fact that clever patent lawyers can work around any such definition; the risks from the existing pool of patents that won't expire for decades and so on. Stallman points out that surgeons already have a statutory exemption to patent liability -- performing surgery isn't a patent violation, even if the devices and techniques employed in the operation are found to infringe. Stallman sees this as a precedent that can work to solve the problem. Though it seems to me that it might be easier to define "performing surgery" than "operating a general purpose computer."
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This approach doesn’t entirely invalidate existing computational idea patents, because they would continue to apply to implementations using special-purpose hardware. This is an advantage because it eliminates an argument against the legal validity of the plan. The U.S. passed a law some years ago shielding surgeons from patent lawsuits, so that even if surgical procedures are patented, surgeons are safe. That provides a precedent for this solution.
Software developers and software users need protection from patents. This is the only legislative solution that would provide full protection for all.