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Bryson symbolizes the atom as a fly in a cathedral to help the reader conceptualize the vast amount of empty space that each atom contains. If the cathedral is the size of the whole atom, everything except the space that the fly (nucleus) takes up is empty, meaning the atom is almost entirely comprised of empty space. Once again, this new discovery that atoms contain mostly empty space triggers even more questions (say, about why atoms don’t implode), which underscores that the more scientists find out about the world, the less it turns out they actually know.