It's not about the atoms. Atoms are eternal, and that's obvious. It's about what arises from the atoms, the different combinations and complexities that emerge from their interactions.
I've got a trilobite around my neck. Elrathia kingi fluttered in Cambrian oceans half a billion years ago. This is a shape, a formation of atoms, which has remained constant for 1/2 of multicellular history, and 1/9th of Earth's total history. You could undermine it, sure, by saying that all atoms have existed since the dawn of time. You could say that the carbon, calcium, and silicon atoms in the fossil are indistinguishable from other carbon, calcium, and silicon atoms in other places, and you'd be right, except. . . You disregard that they are in other places! The different spatial arrangements of atoms give rise to patterns within patterns, which humans then look at and become inspired by.
Reductionism gives you a view into the world separated into bare parts. Personally, I find that a perspective involving all stages of complexity to be more rewarding. Reductionism is a fine, perhaps ideal starting point, but it shouldn't be your end point. That's death.
Also, from your explanation, I'm not seeing how recycling of atoms shows how time is a fabrication. Don't the alternating positions of atoms, the consequential movement that you witness in everyday life show that there is flow going on?




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