A simple challenge for atheists

[Jenny A]

Imagine an alternate universe which contains a single hydrogen atom. (Lets not include dark matter or other forces in the discussion for the purpose of simplicity.) You could replace the atom with a proton, a neutron, a sub-atomic particle, or a string. The point is, it's real. It can be measured.

Now where did this hydrogen atom come from?
Was it just always there?
Did it spontaneously appear, ie. magically?
Did someone create it?

How did it come into being?

I have several answers to this little hypothetical.

First the existence of a single atom presents no evidence for anything except that atom's existence. From it's existence you can infer that either it always existed, or that it was created by something (which either is outside this alternative universe or has since, like Elvis, left the building), or that it spontaneously popped into existence. Actually, you could consider other possibilities such as that the alternative universe once had a great deal more matter and that everything else has since leaked out. Or that the atom used to exist somewhere else and has leaked into your alternate universe.

But where I presume you want to get to is that the atom couldn't have always existed, therefore god must have made that little atom. That isn't really a solution because then you have to explain whether god always existed or just popped into existence. The conundrum is exactly the same, except that at least we know (for purposes of your hypothetical anyway) that the atom exists. You're asking us to solve one conundrum with a bigger more complex conundrum.

Worse yet, god, even if he existed still doesn't answer the question. If in the beginning there was nothing but god, what did god make the atom out of?

What you are really saying is we don't know, therefore god. But nothing makes god the obvious answer unless you presuppose god. And if I don't get to presuppose the atom, you don't get to presuppose god.

The difference between you and I, is I'm not uncomfortable with we don't know as an answer. Absent real evidence, we don't know is often the best, if not the most comfortable, answer. It has the additional benefit of spurring us on to find a real answer. If your answer is god, you've explained nothing and stopped looking for an explanation.