For someone like myself that has no scientific background I am in awe of the minds of those who have worked out how these things and others have come about. The thing is though, although we may know how, we don't know why atoms or molecules formed. Either it is by random chance or by a designer. Neither can be proved so choosing either option requires a leap of faith.
Ah, the ever-present false dichotomy of the religious mind!
What makes you think that the question of why atoms etc formed is even a legitimate question? It presupposes the action of an intelligence.
If these things formed simply due to the properties of the universe (as seems to actually be the case), the why question is either meaningless or equivalent to the how question.
In any case, you have left out the "we don't know just now" option.
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