If you had some time and computing power (not even all that much, in the large scale of things), you could simulate perfectly how a human grows from an embryo to an adult, or how an entire human brain processes some incoming signal, and yet this wouldn't give you the understanding to design a human or human brain from scratch.

You call this a "scale problem" as if there's some scalable way such as an algorithm to resolve arbitrary scientific questions and we simply haven't done it, but of course no such algorithm exists, which is why there's plenty of science that's still not settled.