I'd go with #1. Especially considering that there are quantum approaches to protein folding. But nature hasn't really "solved" the problem, it is just doing it

I'd go with #1. Especially considering that there are quantum approaches to protein folding. But nature hasn't really "solved" the problem, it is just doing its thing, but the way it does things is completely different from what our computers do. It is like trying to reproduce a guitar sound using a synthesizer. A guitar solves to problem of sounding like a guitar, but it doesn't mean it is more sophisticated than a synthesizer, in fact, a synthesizer can do much more, it is just that the process by which the guitar makes sounds are hard to simulate.