Rather than spend ages trying (and failing) to define exactly what makes software patents different from other kinds of patents, I would just declare that software, and abstract mathematical transformations in general, cannot infringe any patent, whether in their inert form, e.g. a program stored on a hard drive or distributed to others as data, or in the act of being evaluated (on a computer or otherwise).
You could still infringe on a patent for something that incorporates software, just not on the basis of using the same or equivalent software. This would eliminate the threat of software patents without creating concerns about unintended consequences for non-software patents.
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