So if you look at the [Big Picture of the metabolic pathways in humans](http://biochemical-pathways.com/#/map/1)... what do you have?
Fuzzily defined, extraordinarily complex tangle with feed back loops all over the place, some going through that amazing tangle of the brain.
If you were to translate this into a mathematical model and look at it from a purely mathematical perspective (even if you omit the parts involving the brain).
It's a highly non-linear system of Partial Differential Equation's with many variables and a bunch of fuzzily measured constants.
And then you compare it with a really really simple setup like, say, [3 bodies acting under gravity](https://en.wikipedia.org/wiki/Three-body_problem). You know, something almost as simple as it gets.
Way way way simpler than the metabolic pathways in humanity.
And we know from a purely mathematical point of view.... that except for a very very tiny set of special cases, we haven't clue what will happen with the 3 body problem.
So yes, the article is spot on.
In terms of individual chemical reactions, we have some ideas.
In terms of dietary advice to individuals or populations... We floundering and should admit it.