Except computer behaviour isn't emergent from its structure, it's emergent from its programming which happens after its structure is fully formed. And neural structure changes during its operation, which most computers don't.
They aren't remotely the same thing. Certainly you can simulate this operation of neural structure, but to suggest they are effectively the same is to suggest that cars and mice are effectively the same. They're both just made of matter aren't they?
In order to understand computation it's obviously useful to humans to think in an abstract way about what we're trying to accomplish with a computer, and how. The distinction we draw between computer hardware and computer software is obviously part of that understanding.
That said, programming is "merely" inducing specific alterations to the electrical charge distribution in the hardware of the computer. The computation we ascribe to the computer is the product of the physical changes induced in the structure of the computer by our act of programming it. As far as the physical artifact of the computer is concerned, as opposed to our mental model of it, there is no clear distinction to be made between hardware and software. That doesn't make the distinction we draw in practice an inappropriate metaphor.
No that is completely wrong and it is a common mistake made by people at all levels. The available pathways inside a computer, whether at the CPU level or in memory, or the system bus do not change no matter which program you run (barring exceptional cases of malware which destroy the computer).
What changes when you run a computer program is which pathways turn on and off, and these change based on reading the instruction set, which causes one operational circuit in the CPU to turn on and the results of that operation are stored for the next operation. RAM is simply a series of switches that can be "read" from the bus and passed to parts of the processor.
The only thing that may, arguably, work like that is writing to a storage medium like a hard disk or tape, and even then the circuitry around the medium does not change, just the magnetic or other impression stored on the disk itself.
Neurons are completely different in that they are made up of different connections to other neurons and it is these connections that make up both the storage medium, and the processing medium is what occurs when different neurons fire together.
[edit] The bottom line is that the brain can create new "instructions" on its own by physically rearranging the groupings of neurons. For a computer to do the same requires a new CPU with a different instruction circuit baked into the chip.
