I've pondered the question of "cooking" the rock as opposed to boiling the stuff on the stove to get rid of bubble algae. Here's my reasoning for boiling it instead of "cooking" it...
"Cooking" the rock kills the algae, but in the case of bubble algae, once the bubbles have been killed due to lack of light, there is every expectation that many, if not most, of the bubbles will have released spores into the "cooking" water. Of course, when you "cook" rock, you also do water changes, rock swishing, some scrubbing, and siphoning out all crud on a regular basis. However, no matter what you do during the "cooking" phase (that will last for months), you will never remove all the spores released by the dead bubble algae. Once the dormant bubble algae spores are again introduced to light, they will grow.
Boiled bubble algae will also release spores, but during the boiling process in untreated tapwater containing, in our case, chloramine, the spores will all be killed.
I don't know how sound this reasoning is. If you can find holes in it anywhere, please let me know.
On the other hand, we have been removing rock from our tank on a (too) regular basis to remove bubble algae. Our removal method is to chip away a bit of rock surrounding the bubble algae so that it does not break, thereby not releasing any spores. It's working okay, except I think often when we introduce a new frag or snails or something from a tank that has bubble algae in it, we get a fresh batch all over again. Very frustrating
