I expect that any trivial software application has many (many) orders of magnitude more patent-vulnerable elements than the most complex commercially produced chemicals.
Software is much more free to include complexity because of the low cost of each element - there's no need to create a physical plant that implements the software.
This makes progress in software much more vulnerable to impedance by patents, because patents cause a greater increase in the relative cost of each element and because there are more elements involved.
And I think if we only allowed patents on "ground breaking" inventions, there would be many fewer patents and much less basis for anti-patent opinions.
It's kind of neat actually; synthetic chemistry in many ways shares its algorithmic and design-oriented nature with software engineering. Rational drug design will only add to the similarities and overlaps going forward.
I think you're possibly understating the problem. The idea that there are "more elements" implies that there are something like ten or a hundred times as many in software as in other industries, but it's worse than that.
The problem is that software uses categories where other industries use instances. Everything is designed as an abstraction on purpose. The result is that patent claim limitations that would be actual limitations in other industries are in software de facto claims of the entire class.
For example, if a claim limitation requires a network connection -- even a specific kind of network connection (e.g. stream sockets or unix domain sockets) -- and you're writing a piece of software intended for use with files on disk, you might think you're safe because you can't infringe that claim. But you're not, because the system calls that work on file descriptors also work on socket descriptors, and socket descriptors can be associated with any supported kind of connection. Your users can run your program and give it the name of a "file" which is really a socket and wham, your software is infringing. The abstractions we use to make things scalable and efficient also cause a combinatorial explosion in the scope of possible infringement.
In the extreme case, general purpose programming tools can in concept infringe any software patent. A user merely needs to type the claim limitations into the source file and the interpreter is happy to infringe. Naturally that case is probably too extreme to find much sympathy in the courts (or they'll come up with something like "substantial non-infringing use"), but the problem is that there is no line. Can we really draw a reasoned distinction between a bash interpreter that allows you to infringe a software patent by typing a twelve line shell script, and a web page that allows you to infringe a software patent with twelve mouse clicks?
It reminds me of this (http://boingboing.net/2012/08/23/civilwar.html) re: DRM. "Make me a general purpose computer that runs all programs except for one program that freaks me out." That's not how computers work. It's not how software works, and it's not how software is designed. You make software to have all the features users want by abstracting everything and making it modular so that anyone can plug in alternatives as they come about. Software patents come in and say "make the software have all possible combinations of features in the world, except this one combination which is covered by these claims." It just doesn't work that way.
Define "ground-breaking".
This is the myth of the patent system: the lone inventor doing dazzling unprecedented work that they can only recoup by being granted a patent. Those people don't exist. You may find one or two, but not enough to justify the overbearing patent system.
The idea of a patent is heavily predicated on one novel advance in an otherwise freely implementable design. But in software that is (or threatens to become) a myth rather than a reality.
Patents no longer serve their original purpose and the current system should be dismantled (though I know it won't be, because the big money is on the side of keeping the broken system).
I'm okay with the idea of something new being created to give protection to intellectual property (on a much shorter timescale, say 2-5 years), but the current patent system is incredibly broken.
Why? Because you want to give them incentives to invest in costly research that wouldn't pay off without a limited monopoly.
But what if research paid off even without such protection? And, more importantly, what if research is not even research at all, let alone costly?
I know little of other industries, but practically none of the recent software patents are a result of costly research, and therefore deserve no protection.
For me the question isn't, 'how do we protect the intellectual property of the people who do research', because the term intellectual property is a legal one that varies massively in time and geography. I would probably be more inclined to ask the question 'how do we make sure that the people who do research get paid really well and are really well resourced', and work from there.
