if we're defining a miracle as the occurrence of an extremely improbable event, putting the existence of atoms into this category doesn't make a whole lot of sense to me given the fact that just about every single thing in the universe is made of atoms and that physics is a pretty well understood science by this point. you would have to figure out how to compare the odds of atoms existing to the odds of atoms not existing in the universe, which is pretty much impossible to determine.
a better example of a miracle by this definition would be if a stone statue that were made of atoms waved at you. atoms are everywhere, however the chances of every single randomly colliding atom in the statue's arm moving in exactly the same direction at the exact same time for the stone to physically move and appear to be waving at you are extremely, extremely slim. thus, were one to observe this they might be quick to label it a "miracle" since it is such an improbable event that it would appear not to follow the laws of science at all. it is also improbable in a way that we can calculate pretty easily with some knowledge of the behavior of atoms (they randomly collide), the behavior of stone (it doesn't move) and how often on average stone waves at people (never, as far as we know). however, as a lady of science i stay away from the word "miracle" anyway and prefer to think in terms of probabilities anyway so it's all sort of lost on me.
jace and/or friendly mod i would really prefer if you took that image down, thanks.