You have to know something about the history of crystals that have been found naturally. I can't think of any absolute criterion. Natural gemstones have defects and inclusions that aren't (usually) found in synthetic stones. But some makers of synthetic emeralds have been getting prices higher than natural stones.
But crystals do not require a program to form, except the one I posted the image of. The question is, did it ever form naturally?
Since it's hard to tell that's evidence of design.