Here’s why economists hate software patents http://www.washingtonpost.com/blogs/the-switch/wp/2013/07/31/heres-why-economists-hate-software-pate...

So far, the arguments of these economists hasn’t made much of an impression on the lawyers who run the patent system. When I asked Paul Michel, the recently-retired chief judge of the nation’s top patent court, whether he favored abolishing software patents, he rejected the idea, arguing that “broad categories treated pejoratively are going to lead us toward bad solutions.” Doug Lichtman, a law professor at UCLA, once told me that a rule against patents on software would be an “odd way to divide the world up.” Instead, legal scholars tend to advocate more esoteric changes to patent doctrine to deal with the problems in the software industry. But there’s something to be said for the straightforward approach favored by many economists.

The Washington Post probably just asked the wrong lawyers. There's nothing weird in making a special case for patents. Acutally, under patent law (in Europe and in the US) there are many elements under which the law can make differences between different types of innovation (making innovation happen and marketing it in software is entirely different than in pharmaceutical drugs, for instance). There are legal standards in patent law, such as the "person having ordinary skill in the art" (in French, “l'homme du métier”) which can be used to make such differenciations. Actually, it's already used, see “Is Patent Law Technology-Specific?”  https://papers.ssrn.com/sol3/papers.cfm?abstract_id=349761 The problem is, it's not used properly… (see the paper, in the US some courts view programming as mere “clerical” tasks and think the real innovation happens beforehand…)