While talking with a theorist grad student here, I realized that people can have very different standards by which they judge whether a scientific question is solved.
It started with the evolution of sex: I find pretty unsatisfactory the current situation where there are a variety of hypotheses, each with some support in few systems, but nothing that approaches a general explanation across all eukaryotes. To me, the lack of coherence suggests that we really don’t have a handle on what’s going on. The grad student, on the other hand, had no problems with there being a variety of ad-hoc explanations. He pointed out that the natural world is under no obligation to conform to my desire for there to be a single general principle for any particular evolutionary phenomenon.
Then we discussed why so many bacterial genes are carried by phages and plasmids. He may have been half-joking, but it seemed like he thought a problem basically solved if there was a theoretical model he liked that seemed to fit the anecdotal evidence. I tend to think a problem isn’t solved until there’s enough direct testing to make a reasonable person who doesn’t want to believe the explanation go “well… I guess so.”