I understand that using real time frame elapses (which should vary between 16-17ms on average) are provided by a lot of frameworks. GetTimeElapsedSinceLastFrame, and it gives you the wall clock time.

But should we use this information in basic physics simulation? It looks to me to be a bad idea.

Say there is a slight lag on the machine, for whatever reason (say a virus scanner starts up). The calculations all jump, and there is no need for this. Why not use a virtual second and ignore wall clock time? For gameplay on the level of Commander Keen, shouldn't you always use the virtual second and not real-time? (Besides stopwatch timing for race games) I don't see a need to use real time and not a fixed 16ms time step.