It was recently reported on this list that Bill Gould thinks that programs
should not need comments. I disagree; it's often hard to remember why a
particular line/variable/condition was needed when reading code written
some months back. Too much computing (eg APL, web-authoring, anything by
** Corp) is write-only code.
On the other hand, for an interpreted language there may be a noticeable
hit on performance if comments are included in, say, an inner loop.
You might try throwing the most monstrous data set you have at your program
and see if the comments really make a significant difference or not. If
they do, then placing the comments just outside the loop might be one way
of addressing the problem.