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The relationships and high-level effects are maintained in our body of literature. It's hard to resist wanting to put it all in some sort of megachart, but even the pathway diagrams vastly simplify the real interactions. The reason they don't seem to connect substance and effect is because often the substances are very far removed from effect, or may not lie on a known pathway at all.

It's still very much a "we don't know what we don't know" situation, which is both intimidating and exciting. There's a lot to be done before our models are even adequate, but we at least get to be part of that learning process.