PBO: I took the AP course (college-level- at least, if I do well I’ll get college credits for it), and we learned a great deal about how evolution is behind so much of biology.
First off: evolution doesn’t mean one thing necessarily turns into another- it can also be something more complex developing from something simpler. This is why bacteria will never turn into a virus- they are two entirely different types of organisms, to use your example (viruses are arguably not even living).
Second: You’re spot-on about how MRSA developed, and this is where it gets murky, as what makes two different groups different species as opposed to differently mutated groups of the same species is whether the two groups are able to mate, and viruses reproduce by infecting cells, which doesn’t require mating. However, I’m pretty sure MRSA is a different species from what preceded it. (Help, anyone?)
Your example with the goats doesn’t really work, because the reason why there are no spotted goats is not necessarily because you don’t want spotted goats- it may be because there is a factor selecting against goats in general and one random goat (which has reproduced) has a random genetic mutation to help it survive this selection, so that it and its offspring can now survive. If this happens enough times, and you suddenly brought back one of those original spotted goats (Idunno, maybe they’ll be able to clone from fossils, whatever), if there are enough mutations that their genetic pools are exclusive, that is the creation of a new derivative species.
This can, of course, happen with multiple mutations, leading to multiple species developing alongside each other (as in the case of Darwin’s finches).