: Your senses, obviously. Our senses are limited; but we can make tools that help us see beyond our natural capabilities.
: Does a person born blind have a concept of the colour 'red'? - unlikely; but does that mean that there is no such thing as 'red'? Of course not. The fact that humans cannot see atoms does not mean that they do not exist; we build a tool to help us see them, just as we build a tool to help the blind see.
: As far as we can tell using our limited senses and equipment, atoms exist; we are confident in this to make our day-to-day lives dependent on this science; computing, plastics, nuclear power, genetics, chemistry - all are dependent on the atomic theory.
: Of course, we can never be sure that anything exists; but I'm going continue breathing in oxygen atoms; I trust the atomic theory enough to risk my life on it.
: (As do you, although you may not realise it.)
If I'm following you correctly, here's is where I take my next step and put it into faith.
I am staking my eternal life on it, just as my physical life is staked upon the existence of atoms. I believe that atoms exist -- I also believe that God exists. And in my mind the existence of God is a completly logical extension of the results I observe in looking at the physical world.
As you said, we can't "prove" anything, per se. I see physical results of God. Others are free to interpret them as natural results of evolutionary processes. Both of us are staking our eternal destiny upon them.
