"Where I disagree with Jonathan is on what’s known as “business-method” patents: one-click ordering, per-employee pricing. I’m having trouble seeing the benefit to society in granting patents on something that could never possibly be done secretly."

That I think should always be the type of reasoning involved. It's not the whole story (some things that couldn't be done in private would still stay uninvited if patents didn't exist) I can't get my head around IP moralising. The bottom line is that patents are intended to be an instrument to encourage innovation to the benefit of society.

I really think there is no sane way out of all this. We tend to act as if there must be some hard definition that will include all novel innovations that wouldn't be worth developing in a patent-less world and exclude those obvious derivative things that would be invented anyway and really need to be freely built upon. There probably isn't such a definition. Even if we do find some complex and inelegant way of mostly accomplishing that it wont last forever.

Making a morality around that seems absurd.