I have had the exact same looking things embedded in some of my stones. I can only figure that they are some kind of parasite. That's only a guess, but hey....."white rice" thingies are paraiste egg sacks, so I would reckon these things might be too, or actual parasites. I don't see how they would be the beginnings of stone formations as we all know they start out as crystals.

I had a lot of these little black things after my first flush and nothing after my second. I read somewhere that the gallbladder also has sand like gravel in it which comes out with a flush. Mine looked like black sea sand.