I'll let alone the fact that your definition of "software patents" is flawed. Let me address your other points.

> There are so many conclusive arguments against software patents that the result is overdetermined.

Or, also known as "being in an echo chamber".

> Black boxes are never patentable.

The concepts of a Person of Ordinary Skill and Doctrine of Equivalents is not "black boxes". Are you saying all the so-called "bad" patents you've seen were things you couldn't implement by reading them?

>1. Computer programmers are overwhelmingly against software patents.

Echo chamber. The vast majority of developers barely know what a patent is. Many others think they're a point of pride, and that's where all these software patents are coming from. The rest are just really vocal.

> For the first time in my life I see educated people advocating the abolition of the entire patent system, even at the cost of life saving drugs, just to get patents out of computer software

"Educated" does not mean "well-informed", and it does not mean they know anything about patents. Economists are still having trouble quantifying the benefits and harms of patents, let alone software patents, so I'm guessing your "educated people" are basing their opinions on personal biases rather than evidence.

> Programmers hate patents in their industry by something like ten or twenty to one.

Wow, this echo chamber seems to have reached resonance. Here's a statistic closer to the truth: 99% of people complaining about patents don't know jack about how patents work and simply regurgitate what they tech media tells them, and tech media is not only clueless, it's deliberately misleading.

> 2. Software patents are harmful to innovation. They created almost all the modern patent trolling crisis. They shutdown startups and innovative projects and block open source.

Studies [1, 2], albeit with only publicly available data, have found no empirical evidence of a "modern patent trolling crisis", and I have heard of more small companies being ripped off by big guys (see i4i) than being shut down by patent trolls. On the other hand, I can list some studies that find "software" patents are no worse than other types of patents [3, 4, 5], and can actually be pretty useful for startups. [6, 7].

> 3. Software is math and both math and mental processes are SCOTUS identified ineligible subject matter.

"Machines are made of metals which occur in nature, which are SCOTUS identified ineligible subject matter."

> 4. The quality of software patents we see is uniformly bad...

I'm genuinely curious: how do you judge the quality of a patent?

> 5. When we bought our computers, ever since the first general purpose computers in the 1940s, we have done so expecting to run programs on them. Using a machine for its expected and customary use is not subject to any patents beyond the patents on the machine itself.

"When we first mined metals, we have done so expecting to make things out of them. Using a metal for its expected and customary use is not subject to patents beyond the patents on the metal itself."

1. http://www.gao.gov/assets/660/657103.pdf

2. http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1396319

3. http://papers.ssrn.com/sol3/papers.cfm?abstract_id=970083

4. http://papers.ssrn.com/sol3/papers.cfm?abstract_id=650921

5. http://papers.ssrn.com/sol3/papers.cfm?abstract_id=999098

6. http://papers.ssrn.com/sol3/papers.cfm?abstract_id=510103

7. http://papers.ssrn.com/sol3/papers.cfm?abstract_id=989592