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?
You are treating atoms too simply, as just static, independent entities, when in fact (almost) all atoms are interacting with other atoms in some way. An isolated carbon atom is different from an ionized carbon atom which is different from a carbon atom combined with four hydrogen atoms in a methane molecule, etc, etc,: these carbon atoms are in distinctly different states, or at least their outer electron shells (which is what really matters in what you are discussing) are in different configurations and different energy levels. Even more important, you are ignoring that all these atoms (or, more precisely, their outer shell electrons) interact with light - specifically with photons, the 'atoms' of light, and these interactions form the basis of how the atoms give substance to substance, i. e., what larger scale forms and interactions various combinations of atoms give rise to.
Your opening post is constituted from 26 letters (the 'atoms' of our language). This post is constituted from 26 letters. How can a simple, ignorant set of letters be cognizant of another simple set of letters? Yet, my post is a direct response to yours and is shaped by - even quotes - yours. This is possible, and very understandable, when one recognizes the rules by which letters interact to form words, sentences, and statements of concepts.
So, photons of light from some glowing source strike the outer shell of electrons of the outer layer of atoms in your hand; some are absorbed but some bounce off (as a function of the energy states of those electrons, which is governed by their interactions with neighboring atoms) and some of those strike your eye and are focused onto your retina (again as a result of the optical properties of the atoms in your eyes components which are governed by their states). These photons trigger the release of weakly bound electrons in certain molecules - photoreceptor pigments - in your retinal cells which then travel to nerve endings and start a cascade of well understood and documented electro-chemical interactions in your nerve cells that result in the impression of 'seeing' your hand. The fine details of how we then recognize the hand, remember the hand, and think about the hand are far from being currently understood, but this is a field of very intense and productive research that is producing significant insights into the various processes of our minds.
But I suspect that you will have no more interest in this post than you have shown in CS's reference in message 7 that could start you on a better founded understanding of the issues associated with concepts of thought and consciousness. You appear to be a neo-mysterian: you have found something that strikes you as weird and you are infatuated with its weirdness. That has brought you to a full stop as far as really exploring what has been discovered about the brain and consciousness, how knowledgeable researchers are investigating various aspects of this field and the conceptual frameworks the have found, and anything else that might detract from your beloved position that the mind is unfathomable. In case I am wrong, I would also suggest that you go to Amazon.com and search under the subject 'mind' or 'consciousness'. You will find a great many titles that you can get from your library - I particularly recommend those of Steven Pinker and Richard Rostack(Sp?).
One thing that you will discover is that researchers in this field try to avoid the terms 'conscious' and 'consciousness' as coming with too much baggage and prior misconceptions. Consciousness has become a word like the words flogiston, contagion, and god in designating more our level of ignorance than any definitive concept.
Another thought: I just put my digital camera in from of a mirror and set the self timer. Does the picture it took of itself make the camera self-aware? Is the resultant pattern of electric charges now imprinted on its memory card any less abstract, cognitive, or "conscious" than my thoughts about my hand?
Hopefully, what I have written has helped you to see the light. And yes, we are pretty much puppets on the ends of strings.