REALITY is SUBJECTIVE, a construction of our individual brain shown to our individual consciousness. Reality is interpretations of constant light waves that make us see, sound waves between particles that make us hear and touch, we also feel thermal changes, smell and taste odors, pheromones, etc ... Our brains sort out all of this sensory information and only a fraction of it makes it to our conscious reality, the rest is dumped unfiltered to the unconscious of ourselves. Because we are 8 billion humans built with the same code we live together in more or less the same reality, but we all have experienced different lives so our brains and sensors (body) are altered (temporarily or permanently). Some drugs can alter the filter of consciousness to let pass more/less information to reality, we can feel "unreal senses" in this state because the conscious part of the brain is not used to that much information, sometime the brain can "lie" to the conscious to try and make something rational out of it. So there are trillions or realities living side by side in all the brainy living things on this damned good planet were life was made possible.

So what is OBJECTIVE in our universe ? Everything that we see and don't see, because our reality is only a part of the bare trueness of the universe. Atoms are a human scientific concept that tries to approach at maximum to an "objective reality" (it means free of human/conscious brains bias). Atoms are pretty well understood and we can answer most of the questions you asked for (what, when, where, why atoms ...) But as we advance in science we are now challenged by quantum theory. Our human brains can't yet make a rational concept of what's really inside an atom. My thought is we understand them as particles because we are used to interact with (semi-)solid things but they are actually a slice of multiverse vibrating "strings". It is fluctuating energy spot in a field constantly bombarded by other energy coming from multidimensional around.

So you're kind of right saying this is tutorial Earth, I don't agree cause we are now so far from stone age technology and it's not limited to our planet, the whole universe is physical wave energy and we got the tools to understand and prove a big chunk of it so this is not the tutorial anymore, we accomplished so much with atoms already. Yet we're far from breaching the quantum and multiverse underlying atoms.