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From a physics perspective I bet you have two things happening:

1. These molecules are moving around a lot. The kinetic energy of molecules at room or body temperature gives them impressive velocity relative to their scale, and they're also rotating altogether and internally.

2. Compatible molecules are like magnetic keys and locks. They attract each other and the forces align with meeting points. The same way that proteins fold spontaneously.

So the remaining part is getting concentrations appropriate for what you want to happen - and that's a matter of signaling molecules and "automatic" cell responses to changes in equilibrium. It's a really chaotic system and it's a wonder it works at all.

I imagine that's also one reason life is imprecise, i.e. no two individuals are alike even with identical genes. There's a lot of extra "entropy" introduced by that mess of a soup.



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