I am quite sure I am missing your point, but just in case...
Why is there a ton of this molecule here? Because it was useful for something bigger, whether a nematode or a pharmaceutical company. There is no other way to account for this particular molecule existing in such quantities given, again, combinatorics.
You might be vaguely gesturing at a weak emergence? (Strong emergence is not a thing.) When you are not a Laplace’s demon, but a bounded embedded agent trying to make accurate predictions, that might be one useful way to abstract your observations to simplify this job. If so, emergence is fully compatible with reductionism.
I am quite sure I am missing your point, but just in case...
You might be vaguely gesturing at a weak emergence? (Strong emergence is not a thing.) When you are not a Laplace’s demon, but a bounded embedded agent trying to make accurate predictions, that might be one useful way to abstract your observations to simplify this job. If so, emergence is fully compatible with reductionism.