I've also been following some of the discussion on Twitter, and the overrall theme for Nilay seems to be to ask for a citation for any claim he doesn't agree with, e.g. the fairly uncontroversial claim that any non-trivial piece of software will infringe many patents.
1. Patents encourage R&D. The relevant criticism here is to ask: does this incentive outweight the costs of the patent system as a whole? (These costs are many. They include: any friction on innovation generally; the costs of running the patent office; patent application; patent litigation; defense against patent litigation; patent portfolio acquisition; the opportunity cost of all these people spending all this money, time, energy, and brain power on patents.)
2. Disclosure. Relevant criticism: is it in fact that likely that interested parties wouldn't be able to independently develop a given innovation without the patent system? It seems fairly uncontroversial to say that, as it is, a company will only apply for a patent if they think the patent protection will actually last longer than any protection they would get from trade secrecy. I.e. if a company really thought trade secrecy would keep an innovation out of the hands of their competitors for longer than a patent would, they just wouldn't patent it and keep it as a trade secret instead. So almost by definition this is pretty clearly false.
3. High fixed cost, low marginal cost innovations don't have enough incentive. This seems like the strongest argument for patent on some things, but I have yet to see any strong citations to research that isn't done by or paid for by pharmaceutical companies. It's an empirical claim that needs to be tested, and it seems to me that the burden of proof is on the proponents of patent law, not opponents to disprove it.
4. Designing around patents leads to more innovation. This seems like a fairly obvious case of introducing artificial inefficiency. Sure, you might get some unrelated and unexpected benefits from all of this incidental research that you're forcing, but it seems pretty obvious that this is going to be a net friction on overall innovation.
More on 2.; for the purpose of disclosing knowledge, patents are typically somewhere between 10 and 1000x less useful than a good scientific paper. And the content of the innovative parts of most scientific papers are not covered by patents. Open source software is another thing that makes software patents useless for the purpose of disclosure; the value it could bring to society is hugely inferior to the value achieved by open source software + academic publications, and the cost is hugely superior. In itself, that should be enough to forbid software patents, especially because there are at the same time proven efficient ways to protect computer programs.
It's not that nobody has told Nilay why the patent system is broken, I'm sure a lot of people have, and he's read many articles on it, too. It's just that he doesn't want to hear that side. I've listened to his last podcast with Joshua, and he'll completely shut down to anything that doesn't agree with his views on patents. From what I've seen he thinks he's right that the patent system isn't broken and there isn't anything anyone can tell him that will disprove it. I doubt writing another article on this will change his mind, but I suppose it could be useful to the people who started agreeing with him after reading his post.
"Making your product free does not make it impossible to compete with you." And the evidence the writer cites is third party Twitter clients. Um, right.
Now, the quoted statement started out as a dismissal of Gruber's remark that it's hypocritical to accept Google's anticompetitive dumping but complain about Microsoft et al using patents. A more intellectually honest approach would be to say BOTH are wrong. I could accept that.
Well, I'm not making a moral argument. I did imply that it was "a slightly shady business practice". Clearly, Google is using money from its search business to fund OS development, and to undercut competitors. I do have a bit of a problem with that.
But I don't think it's as problematic as using patents to go after your competition. Like I said, offering something for free makes it harder to compete with you, but not impossible. Lots of companies compete with free alternatives. Twitter clearly isn't the only example. Desktop operating systems, word processors, text editors, pick whichever example you prefer.
Owning the right patents, on the other hand, can make it impossible for others to compete with you (e.g. what's happening to HTC right now).