Thanks for the feedback,
Danstan,
The only way I've been able to figure out to run selections is to save the selection to a temporary file and run the temporary file. Alan suggested saving the file in /temp/somthing.do, rather than in the current working directory. I think that makes sense and will give it a bid. I looked at the R bundle's implementation of running a selection, and as best I could tell (not very well, granted) it relies on some AppleScript that Stata doesn't recognize. Simply stealing the R implementation was my first instinct, but I couldn't get it to work (which doesn't mean, it can't work, just that I couldn't get it to work).
Alan,
Thanks for the suggestions, I think I'll probably use both of them,
Tim