The misunderstanding
I understand why no one within this patent system (lawyers, judges, patent clerks, patentees) wants anything to really change. It’s not that no one understands software, because there are definitely people within this process that are software experts.

For those in the process that don’t understand software, it’s reasonable for them to want to see patents as the correct form of legal protections. From the outside, software serves a function. It looks like a machine, and machines are patentable. Looking at the process by which software is made, it looks like just that: a process.

This is not the way we should be thinking about software, however. To put it in software terms, it is harmful. To understand why this is not the way to regulate software, we will need a few metaphors, and we’ll need to change copyright law a little bit. These are not impossible things, however, as the U.S. Copyright Office often takes public comment on copyright issues.

I’ve briefed them before. You can, too. Check out their site and see when they’re looking for comments.

First, however, we must understand why patents exist.

The patent system
The patent system exists for one reason: to save technology from the dustbin of history. Back in the 1600s, if someone invented a new method of making horseshoes, it was in their own best interest to keep that method secret. If someone else discovered the secret method, the originator could be ruined and had no recourse to prove he had thought of it first.

The patent office was created to preserve that information. In exchange for a temporary monopoly on the invention, society is availed of the secret behind what makes that invention work. Thus, inventions that move humanity forward are not lost to history when their creators die. In terms of the game Civilization, you could call the patent the time period between when you start researching a technology, and the time when it becomes a national asset: the alphabet, gunpowder, or the steam engine.

Without a patent system, if someone discovers how to make gunpowder and takes that secret to their grave, your society is going to be overrun with foreign invaders using muskets.

Thus, Eli Whitney did not go to his grave holding the secret of the cotton gin in his cold dead fingers. Society was able to continue to benefit from his invention after he had passed away because he was not hiding the technology from history to save his advantage in the marketplace.