For many years US software patents were stopped without stopping patents altogether. And the law is the same now as it was then, as I just detailed in an essay: http://ourdoings.com/ourdoings-startup/2011-07-28 Feel free to submit the essay to HN if you think it clears things up.

EDIT: Timothy Lee pointed to his article from a couple years ago that covers the same topic in more detail: http://arstechnica.com/tech-policy/news/2009/01/resurrecting...