Do you think that this is not true of other engineering disciplines? For instance, can an auto maker build a new car without infringing tons of patents? What about robot makers? Airplane manufacturers? Do you believe that nothing that e.g. SpaceX (or your favorite innovation shop) is working on is worthy of patent protection?

> Do you think this is the way property rights and software ought to work together?

This consequence is clearly horrible. However, let's say there was an innovative physical device (with no software) at play instead. Then we'd say that's exactly how property rights work. We'd presumably be happy that in a few years the rest of society would have access to the device without paying the monopoly rates. The point is the monopoly is an incentive that helps an inventor take an idea from concept to useful product. If the idea had value by itself, we could use my idea for a cancer cure and be free of it tomorrow. (Unfortunately, I am missing the useful -- patentable --parts of the cure.)

What specifically is so different about software that would make it unique among engineering pursuits as the only one unworthy of patent protection?

I do think the degree to which software builds on itself is different than in other engineering disciplines, but I'm afraid I don't have evidence to back it up. The closest I can get in the time I've got this morning: consider the amount of (compiled) code Dell ships on a $500 PC and compare that to a $500 mechanical device like a bicycle. I can imagine doing the research to figure out whether the bicycle infringes any patents. With the PC, I can't imagine how it would be possible. You'd have to understand how all of every program shipped on the PC works; I doubt that there is anyone alive who has even read more than half of the code in any single modern operating system. You'd need a team of programmer/lawyers and the source code from every vendor who ships code on the PC.

From there, I'd say that a system where an inventor can't assess whether their invention is infringing without an effort comparable to the amount of work needed to create the invention is a bad system.

The first counterargument to your position is that it's not based on any guiding principle, but rather the degree of overlap among innovations. That makes it difficult to specify, and hardly seems like reason enough alone to ban software patents. There may be a case for banning software patents, but it seems like the argument would need to be less subjective.

The second counterargument to your position is that you're comparing apples and oranges, on the basis of retail cost. The Dell PC is near the cutting edge of its field, while pretty much everything in the bicycle would have been invented before patents were invented. A better comparison would be the Dell's software vs. a mechanical system developed by Kiva for making their warehouse robots more effective (or a propulsion engineer at SpaceX making some cool rocket stuff). Mechanical engineers pushing the envelope are in the same position as software engineers.

Besides, isn't some of this transitive? If I can make something (unpatentable) in software, but I can build a (patentable) device to perform the same function, what difference makes the software embodiment less worthy? Surely with different incentives the patent system would be flooded with patents on single-use mechanical devices to take the place of the software patent flood we have today.

I can agree with you that the implementation of the current system is a mess, but I'm not sure that translates directly to the case for invalidating software patents. I'm not sure whether software should be patentable or not, I just have yet to hear a compelling case against the principle of software patents vs. other types of patents.