This is a silly forum in which to have a long debate :). I will admit, I mostly agree that the vast majority of software patents should probably be invalid, and that the existing system leaves a lot to be desired.
A couple of important points:
> They are still making innovative products, but they distorted their market power and millions of poor Indian citizen's lives were immeasurably worse off for it.
No, most innovation in new drugs happen in countries with strong patent protection. There is a lot of development outsourced to India, but almost nothing innovative on the development side. That isn't to say India's policy doesn't make sense for them, but they are essentially just stealing from the US and other countries. Imagine if that were true worldwide 20 years ago. Health insurance would be a lot cheaper, yes, but a large percentage of drugs developed in the last 20 years would not exist. It's a trade off that maximizes a longer term return.
> infringement
Yeah, I was just pointing out that a lot of the patent system is designed to protect people who are being infringed by larger entities. Just because it is abused by others doesn't mean it doesn't serve a purpose.
> patents distort markets
Of course they do, but it is not necessarily net negative.
> demonstrated that patents aren't orthogonal
Yes, that is a very long discussion. However, it should be fairly obvious that the software developed by industry and the software available in the open source world is not the same. I would go so far as to say the open source world is an order of magnitude or two smaller than software from for-profit entities. There are different incentives for releasing open source software than starting a business, and patents are designed to make the latter more attractive.
> Patents attempt to produce a monopoly on an idea and prevent anyone else from capitalising on it for decades.
No, patents provide a temporary, licensable monopoly on an implementation. You don't patent the idea of holding paper together, you patent the concrete implementation and manufacture of a paper clip.
More importantly, they require disclosure of that implementation to the rest of the world. I think this gets lost when people talk about removing the patent system. The primary purpose wasn't to encourage invention, but to make sure people disclose it.