The most recent edition of
New Scientist (or maybe it was Scientific American, at this precise moment in time I'm not certain) Discover¹ magazine carried a story which mentioned a researcher who was "simulating the tobacco mosaic virus in unprecedented detail to find out how it reproduces".
Um, no he wasn't. Pardon me, but I'm going to be a little bit pedantic here.: There's a difference betweem simulation and modelling, and they're not interchangeable. Specifically, you cannot find out how something works by simulating it, because to accurately simulate it, you have to know how it works. What he's doing is modelling the virus, and tuning his model until it matches as closely as possible the behavior of the real tobacco mosaic virus, then trying to draw inferences from the model about how the real virus does what it does. This can be a valid technique, if you then take the mechanisms that you believe from your model to exist and check to see whether they do in fact exist, and work the way your model seems to indicate, in the real world.
But you can't use a simulation to figure out a mechanism, because you can't simulate an unknown mechanism. You can only simulate what you already know.
OK, before anyone says it, "What about space-combat simulation games that simulate technologies we don't have yet? How can that be a known mechanism?" Answer: That's not simulating an unknown. That's simulating something where the game designers sat down and said, "OK, we're going to have this technology in the game, and it's going to work like this." It's still a "known" mechanism ... it's just a made-up known mechanism, defined for the purposes of the simulation to work in a certain way.
 My memory came through eventually.