[law]

I was referring to business method patents, not software patents. Art. 52 paragraph 3 clarifies what's in paragraph 2:

(3) Paragraph 2 shall exclude the patentability of the subject-matter or activities referred to therein only to the extent to which a European patent application or European patent relates to such subject‑matter or activities as such (emphasis added)

This is where I imagine much of the confusion lies. My interpretation combined with a brief search on google seems to indicate that software could make its way into patentable subject matter if it's a subset of a larger system, but not if its the sole "invention" claimed in the patent.

In other words, if you have a hardware device running embedded software, you could patent the device, including in it "programs for computers." Thus, Art 52 doesn't mean that all inventions including computer software are, as a matter of law, not patentable.