On the contrary. Since software source code is (at a fundamental level) math, it is purely informational in nature. One of the goals of the patent system in the first place was so that information would be shared rather than kept secret. The patent holder makes the information public, and in exchange he is granted a temporary monopoly over the physical manifestation of the information. But not the information itself.
This makes it really strange then when you attempt to patent a software algorithm. What is the physical part? Am I allowed to make a book containing original descriptions of patented algorithms? How is that different from sharing code on the web?
Patenting software algorithms is akin to patenting speech itself, which is protected under the first amendment. So I think the "math" thing does matter. A lot.
I just don't believe most software patent fit the description of an algorithm. The real problem with them is they are patents for idea an not for implementation as an algorithm might be considered.
When Amazon patented A 1 click button. They were not talking about an algorithm, they were talking about the idea of having a button which purchases the object I want with 1 click. Implementation of this is wide, this patent tells me nothing of what the process behind the patent should be. If it did then you could get around it. That's the fundamental issue with those patents as you've pointed out. I can't figure out what is or isn't an implementation of this patent because no real useful implementation instruction was given.
On the other hand The Marching Cube algorithm patent does fit what you are talking about, the is instruction on how to implement the algorithm and those kind of patents have some issue for sure too. The claim against it was that it's a completely obvious way to solve the problem. There are alternatives to this algorithm such as the (http://en.wikipedia.org/wiki/Marching_Tetrahedrons) which is just redoing the same thing another way, so it's at least better to me than the 1 click patent.
Software patents in general are wrong, I'm not arguing against that but saying all software patents do is patent algorithms is not strong enough an attack in my view. When people will look at it they will see putting multiple algorithms together to solve a problem in a non obvious way is in a way no different then putting a bunch of smaller components together to create a new device. I don't believe patenting either really helps promote innovation. (I'm pretty much anti all patents).
This makes it really strange then when you attempt to patent a software algorithm. What is the physical part? Am I allowed to make a book containing original descriptions of patented algorithms? How is that different from sharing code on the web?
Patenting software algorithms is akin to patenting speech itself, which is protected under the first amendment. So I think the "math" thing does matter. A lot.