And yet, we've had plenty of software patents which have held up in court and caused significant damage to companies which were found to be infringing, and many more which have backed off due to fear of the same.

Mathematical facts aren't patentable. That much has been established. Perhaps a "pure" algorithm isn't patentable; but all software patents start out with something like "a general purpose computer which...", tying it to hardware and making it patentable. Good luck implementing that algorithm without a general purpose computer.

For instance, the i4i patent is a patent purely on an algorithm, and Microsoft lost that case and had to remove the feature from its software: http://en.swpat.org/wiki/I4i_v._Microsoft . I'm not sure how you can square that with algorithms not being patentable.

No problem, just find a way to implement the algorithm which doesn't violate at least one of at least 121 "fast fourier transform" pattents and you're all set (http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sec...). Just repeat that process for every algorithm you might want to implement and you'll have no problem writing software.

The "Marching Cubes"[1] algorithm got patented ages ago and the patent was enforced. Some clever people had to come up with a similar solution called "Marching Tetrahedrons" to work around the patent.

[1]http://en.wikipedia.org/wiki/Marching_cubes

That's why they patent the idea of having a general purpose computer do the math. And no, they don't care if the novel part isn't patentable subject matter and the patentable subject matter has already been invented. That's a pretty well-established dodge, except insofar as the recent Supreme Court decisions impact it.

The key phrase is "supposed to be"; "are not supposed to be patentable" does not imply "are not patented" in a system where patent examiners usually have very little idea what they're actually warding patents for and legal fees for challenging invalid patents are prohibitively high.

Where did ya here that? My favorite algorithm is patented: http://en.wikipedia.org/wiki/Scale-invariant_feature_transfo...

As a famous American statesman once put it: "Justice Marshall has made his decision - now let him enforce it."

It's commonly supposed that the Supreme Court could void these illegal patents - could dissolve this entire illegal industry - with a swish of their shiny polyester robes. Actually they already tried that, in Flook. Jedi mind tricks, which in the end is all the Court really has, worked about as well on Andrew Jackson.

I think this explains the disappointing result of Bilski. If you are supposed to have a magic power which in reality doesn't exist, make every excuse to avoid using it. You may still be suspected of impotence, but at least the suspicion is not confirmed.

Unfortunately there isn't really a solution to the patent problem that's compatible with the rule of law, mostly because the rule of law was so long ago abandoned for the rule of lawyers. Perhaps Andrew Jackson could round them all up and march them to Oklahoma - or at least, Marshall, Texas.