Isn't that a paradox and a conundrum that some atoms combined in such a way that different substances could be created that would be the building stones of living organisms and those atoms would be self-aware that they exist and that they are just atoms?
The problem is that you concede that atoms are not living in and of themselves, yet you seek to bestow properties of the living, i.e. conciousness, onto the atoms. Of course it'll be a paradox. If I say that a duck is not living, and then say that it flies, then it will be paradoxical. The truth is, atoms themselves aren't looking at each other or commanding body parts. The smallest unit of life that does these kinds of regulatory functions is the organelle, which is composed of millions of atoms in a certain configuration. After that, life is simply cause and effect.
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