How does "Science prove that the miracles of the Bible did not happen" ?

[Doubting Thomas]

The real element of debate would be science doubting miracles or giving alternate explanations that do not include an all powerful God, not disproving them. 

Check out the thread where we're currently discussing the "miracle" at Fatima, where the sun supposedly danced in the sky.  The alternative (and more rational and likely) explanation was that it was caused by ocular effects of staring at the sun for a while, mass hysteria, and possibly also thermal waves in the atmosphere.

Of course, this kind of disproves any sort of miracle.

Oh and when it comes to debating miracles, science, or things like "creation science," a handy guide is that the more you have to invoke magic, the less likely your explanation is true.