First, the simplest atom is the hydrogen atom. It is a proton with a single electron "orbiting" it.

The hydrogen atom can also have a neutron closely bound to the proton. (A neutron is a lot like a proton but it does not have a positive charge, it is neutral.) The electron has a negative charge and is attracted to the proton. The word "atom" means, indivisible, but they can be divided into protons,neutrons and electrons. We know they exist because imagining a bunch of things that are basically groups of protons and neutrons with electrons orbiting around them explains so many things. It explains all the chemical reactions that we observe. It explains for example why something that has the properties of a liquid will turn into something that has the properties of a solid when we cool it. (ie water vs ice). The idea explains everything we observe. We know there are protons,neutrons and electrons because we can separate them from each other and study their individual properties and how they interact with each other. Your right we can't see atoms directly but we can infer their existence. But what does it mean to "see" something anyway? When you "see" something it really only means that light is coming from a certain direction. You are really only inferring, for example, the existence of a house in the distance because light is forming an image in the back of your eye. The "idea" of a house explains the image that is on the back of your eye. You don't need light coming directly from something to be able to infer its existence. Atoms didn't begin their existence as atoms. At the moment of the big bang what there where where quarks, electrons and light(photons). As the explosion cooled off the quarks formed in groups of threes to make protons and neutrons. The protons and neutrons began bonding together and then the electrons started orbiting around them. No one knows where the quarks, electrons and photons came from. It is one of the big unanswered questions. I agree they had to come from something even if they are just the "idea" of God. Assuming their is a God, which I do. But then where did God come from? Maybe the question is meaningless. =========== Don't forget to let us know you're reading these answers by picking a best answer or at least saying thanks.