What does the sentence mean?

Solution 1:

Context is important here:

If a piece of steel or a piece of salt, consisting of atoms one next to the other, can have such interesting properties; if water—which is nothing but these little blobs, mile upon mile of the same thing over the earth—can form waves and foam, and make rushing noises and strange patterns as it runs over cement; if all of this, all the life of a stream of water, can be nothing but a pile of atoms, how much more is possible? If instead of arranging the atoms in some definite pattern, again and again repeated, on and on, or even forming little lumps of complexity like the odor of violets, we make an arrangement which is always different from place to place, with different kinds of atoms arranged in many ways, continually changing, not repeating, how much more marvelously is it possible that this thing might behave? Is it possible that that “thing” walking back and forth in front of you, talking to you, is a great glob of these atoms in a very complex arrangement, such that the sheer complexity of it staggers the imagination as to what it can do? When we say we are a pile of atoms, we do not mean we are merely a pile of atoms, because a pile of atoms which is not repeated from one to the other might well have the possibilities which you see before you in the mirror.

Emergent properties of even simple systems can be remarkably complex, as a complexly arranged pile of atoms, our emergent properties may be even more amazing than water patterns.

Solution 2:

When we say we are a pile of atoms, we do not mean we are merely a pile of atoms, because a pile of atoms which is not repeated from one to the other might well have the possibilities which you see before you in the mirror.

What he means is that human beings are different from bars of gold, even though both are "piles of atoms" because a bar of gold is just the same structure repeated over and over while a human being is not a simple, repeated pattern.

A human being is a "pile of atoms", but unlike most uninteresting piles of atoms, human beings have complex, non-repeating structure. That's what you see when you look in the mirror, not the pile of atoms but the structure.