If you're referring to the apples redness analogy, here's my thoughts on it. There's indeed no redness to be found in constituent parts of the apple, but there's still a relevant causal connection between those parts properties and the emergent quality of the whole, the redness. So you can't just disregard that connection because you found no redness at that level, something other than the macro property on the micro level caused the macro property. The parts are demonstrably relevant here. The same is true for the main problem.

I don't think philosophy can just ignore science anymore.

The point with the molecules it that after acknowledgeing the whole emerges from parts you casually say the parts are irrelevant. And now you're ignoring what the guy said of it.

Yes I'm aware. And why is preserving this system important?

I have one question. Why is preserving moral responsibility so important?