I'm currently reading Brian Greene's The Elegant Universe and have also picked up his other book - The Fabric of the Cosmos. In The elegant universe Brian makes up an interesting point that empty space is not really empty. This is according to string theory. Now I may be completely wrong, but lets consider the assumption that empty space is not really empty.
Now there are several analogies to explain the composition of an atom. One favorite analogy says that the atomic nucleus can be considered to be the size of a football placed in the center of a football field, with the electrons moving just outside this field. That's a lot of space! Assuming that empty space is not really empty, what does this atomic space consist of?