Between you the reader and me, this is my take on how things work, rephrasing what’s been said, but in terms of the relationality of things.
Whether we are considering the grand scheme of things material, where we have Relativity, or chopping them up and ending up with Heisenberg’s Uncertainty Principle, we see that everything is related to something other, to everything else. That is not only how events are able to happen, but also what makes it possible for us to know what goes on.
We ourselves, think, using images and words in different languages to express those thoughts not only to others but within ourselves. Who we are and the relationships we are capable of building with what is other is more complex than the relationships that exist between the more basic components of physical creation. Being material, we also participate in those basic interactions. Having also a spiritual nature, while these words on the monitor evoke electrochemical reactions on a material level, their perception and understanding involve a knower who is whole and can choose how to react. We relate perceptually, cognitively, and emotionally giving ourselves to the world, thereby commune with its deepest aspects.
At any level when things relate, there exists a triad of the two entities and the relationship between them, which is defined by what they are. The point of this thread is that that this triad may constitute a new whole, which is a totally different being, with a different way of relating to everything else. That is how the universe is more than a totally mind-blowingly large soup of bosons, and why we exist separate and able to contemplate all that is.
The OP concerns atoms having specific properties. It is assumed that they do exist. Their being being seems different and more than than their constituent particles. Atoms combine to form molecules and molecules combine to form cells, which combine to form organs, which in turn work together as the body. What may be reduced to complex interactions of subatomic particles is the actual experience of reading this post. While there is no denying that what is happening here is occuring within the material universe, that universe contains persons. Person’s relate differently to the world than the atoms which constitute their physical nature.
Between the smallest levels and us here, we have bacteria, plants and animals, with simpler relational naturse than ours, but nonetheless “transcending” the bosons and atoms of which their physical being is formed. The whole of any particular being is formed not only by its constituent parts and their relationships, but by primarily nature of its own being, its particular way of relating to all else that is.
This is what Genesis is getting at, that the creation of the universe happened in step-wise fashion in time, with the new being brought into existence from the old. There was light, separated from darkness, the earth and stars, plants and animals, and ultimately we ourselves, brought forth from the earth. Gravity, electromagnetic, and intranuclear forces make up the relationships that produce the various forms of matter, space and time. Biological entities go beyond this, transforming matter into themselves, maintaining themselves growing, reproducing, and behaving. For us the nature of the relationship we have with the world is the spirit of God. We can know and love, act in the best interests of and give ourselves one each other. We require a free will to do so, and as a consequence can also do evil. It is that spirit that permits us to enter into relation with God, pure and perfect Relationally - Love, who has left His stamp on even the most basic of the world’s constituents.