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I never quite thought of it that way. The first challenge would be mapping out the computational underpinnings of the simulation. I can't even begin to imagine how that might work, though I bet it would look something like physics.

This is a really interesting concept illustrated on this story: http://lesswrong.com/lw/qk/that_alien_message/

I'm imagining a glider in Conway's game of life trying to find a bug to exploit. What would that even mean?

I imagine the glider will try to figure out how to get around one of the 4 rules thereby changing its live neighbor cell count which in effect changes its evolution through board henceforth.

If those bugs manifest as miracles etc, then there are already plenty of people looking :)

Wonder what the language was to create the simulation, so one could have a more educated go at finding the exploits.