Software Patents result from an extension of the "Business Process" form of patents. The idea was that if you invented or discoverred a new process for building something, it was the process, not the machine which implemented the process which was new. For example, if you invent a process which turns lead into gold that does not require magic or nuclear bombardment, that process would be patentable and any device which used that process would need a license. This is why the supreme court has not yet struck down software patents. There is an underlying reason to the patents and broad decision would be "making law" instead of just interpreting it.
The root problem is the difference between an invention and an innovation. Inventions are suppose to be something new, something which did not result from simply modifying something that came before. Inventions can be patented. Innovations are suppose to be a new and useful modification that improves on what came before, a natural growth of the technology. Innovations are not suppose to be patentable. The problem is that much of this is blurred. Since most inventions now result from combining and modifying older technologies, where does it cease to be innovation and become invention?
With software, the problem is even more troublesome. As a programmer, most of the software out there results from ideas bouncing around in numerous people's heads, based on ideas which have been bouncing around the industry for decades. There is "prior art" for almost everything. Everything in software is derived and assembled from bits and pieces that came from all over. What this means is that the vast majority of software is innovative, sometimes even highly innovative, but rare would be the piece that was truly inventive.
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