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You might have missed the point. What the article says is that you can't get a patent for revealing the secrets of nature. Rather, patents are awarded for solving some need in our human society. An algorithm that proves a fundamental fact of mathematics can't be patented, but an algorithm that lets you use electronics to heterodyne cell phone frequencies can; the former is a revelation about the natural world, the latter is a practical application that solves a specific problem. I'm not a lawyer, but that is my best understanding of what was said in the cited article.

First and foremost, patents should not be lottery tickets. To patent something, and then be passive and not use the patent, and wait for someone else to use it so they can be sued -- that turns the concept of patents 180 degrees around from the intention of intellectual property. This happened to RIM; they built a successful company, then, after all the work had been done, they got sued. The purpose of patents is very specifically to encourage an inventor to bring an idea into production. Without patents, an inventor tends to keep things secret, which discourages production. With patents, an inventor must fully disclose everything, in return for which he gets an intellectual property right. The law exists not for the benefit of the inventor, but for the benefit of society. Society benefits because the item is in production, and because the methods are published and others can inovate and improve on what has been published. But if the thing doesn't go into production, or if the producer fails to keep it in production, then I wish the law would say that there can be no patent infringement. Trademark law has this -- "use it or lose it," but not so for patents. In my opinion, patent law should have a "use it or lose it" proviso.

This, of course, is in addition to the changes needed to adapt patent law to the world of software. Currently, software patents mostly serve a cause that is 180 degrees the reverse of the intention of why patent law exists. Currently, software patents are used to block innovation, rather than encourage it. The result is that society suffers, rather than benefits.