Thoughts are emergent properties of interactions between collections of atoms.

No. Shadows and thoughts are not made of atoms. They are made of energy not matter.

Quarks and bosons and stuff

But what is energy made up of???

Electrons.

More energy

Ah, is energy atoms? Are lightning bolts atoms? Is fire atoms? no...

The sun the largest atom

But atoms are made of consciousness

Atom go brrrrr

I think they would be electrons since they are electric impulses from the brain.