The original question seems to be:

Why are our atoms arranged in such a way that we ask why they are?

In other words, why are we "wired" to ask why?

I don't think that the answers given here so far have really answered the "why" question but have detailed "how".

The simplistic answer to "why", given here by Bill D, is that the arrangement was designed by a superior sentient being, but we are then left to question why such a being would be sentient when it does not have the same basic design (brain cells, neurons, etc.) that its sentient creations do. The reason I call "God made it so" the simplistic answer is that it's the answer people give when they really don't want to explore the causes of things in a reasoning way.

Interestingly, we could not even ask the question about atom-arrangement if those before us had not already discovered the existence of atoms as a result of asking "why?" and exploring the causes of things in a reasonable way, instead of adopting the Dark-Age "don't question God" attitude.

So my answer to SPB-Cooperator's original question is: we don't know yet, but we should keep asking.