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.