However, the purpose of patents is to promote progress by motivating people to invent. So what matters is the input to the process, i.e. the human activity that eventually leads to a working machine.
The patent system was designed for human activities that involve so much time and effort that people might not do them without an additional incentive, i.e. temporary monopoly. Picture 18th-century mechanical engineering. Building several different designs of a machine to see which works best would be a monumental task. It would be much easier to search the patent database and find something someone else invented, and cheaper to license it from them.
Imagine for a moment what would happen if you gave everyone a machine such that you could simply drop a diagram of a mechanical invention into it, and out the other end comes a working implementation. That would totally change the game. Invention would require much less effort. Everyone would be doing it without consulting the patent database, and the huge influx of inventors would overwhelm the patent office, making it impossible to find which inventions in the flood of incoming applications are novel and nonobvious.
This is what happened with software. Millions of people have these magic machines on their desks and in their backpacks and briefcases. No patent incentive is needed, just as none is needed for mathematics.
The argument, then, is that patents on software are A) unnecessary to encourage innovation and B) actively discourage innovation. The argument for A) is that plenty of software development happened prior to it being patentable, few software developers or startups consider patentability when creating new products, software itself is well covered by trade secret and copyright protection, and the patents themselves contribute basically nothing to the world's store of knowledge about software. The argument for B) is that most software patent suits are complete BS and are launched either by trolls or in an anti-competitive manner rather than as a result of any sort of actual "theft," any piece of software could potentially infringe on hundreds of patents, patents themselves tend to cover "inventions" that anyone else solving a similar problem would come up with, and that patents themselves thus tend to either discourage people from even trying new ventures, out of fear of being sued, or serve to drain resources from companies that actually produce products, tying up resources that could actually be used for innovation. It's also worth noting that the 17/20 year term of a software patent is completely out of whack with the pace of innovation in software.
So you can try to split hairs around saying that some software patents (say those around non-obvious compression schemes) are legitimate, but I'd guess that something close to 99.95% of software patents are trivial/silly/should never have been granted, so in this case I'd argue that's totally worth throwing out that 0.05% of "good" patents in order to ensure that we get rid of the other 99.95% of them. I'd rather see that happen than try to defend that 0.05% and end up keeping even 5% of the current amount of BS patents.
Everybody believed that it does work without actually examining the evidence for the other industries.
Where is that evidence? The US seems to be innovating quite a bit in the software area compared to other countries.
And on the other hand, how often have you heard or read about programmers and companies worrying about unknowingly infringing on software patents, about companies getting sued by other companies that turn whole fields of software into minefields, or about developers or companies that couldn't (afford to) implement the best known algorithm for an application, because someone else had been granted a monopoly on using that algorithm.
At least in the US, you can't create a start up and just create a knock-off of an existing product: you are forced to innovate because of software patent laws. This is probably why the US is striving while countries that don't have such laws such as Chine hardly innovate at all.
I'd also argue that it's mainly copyright law and trademarks that prevents the kind of product piracy that is prevalent in certain countries with a less developed legal system, at least with regard to software products.
That's not what I'm arguing. All I'm saying is that given the fact that US is one of the most innovative countries in the software area, the burden of proof is on those who claim that the software patent system is broken.