I would find your claim to be slightly outlandish. Even if we assume that you could simulate anything known to humankind with software, you would still need to invent a thing to properly simulate it.
I'm not claiming I could INVENT any machine with a software process. Only that one could take any patent granted for a machine, and build a total software simulation for the described machine. By the judges' logic in this ruling, the software simulation of the machine is unpatentable. But what's the difference if the machine is implemented with atoms instead of bits?