When we engineer things, it's one-part-one-function. Living systems are every-part-every-function network graphs with weighted edges that are subject to dynamic reconfiguration.
A cell isn't a computer that runs "code" in the form of DNA, nor is it a "machine" as we understand it. A "structured cloud of probabilistic quantum interactions among molecular nanomachines" is a bit more accurate.
Until we conquer these meta-problems, we won't understand the cell or the genome. I don't think they can be understood classically -- and I don't mean classically in the sense of omitting quantum mechanics. (Though that's true too.) I mean classically in the sense of linear fixed-relationship cause and effect machines.