I'm puzzled by what's happening on page 9 of that PDF.
Ok, I quickly browsed through it, but a chemical reaction where two identical molecules react into those same molecules plus another molecule? How can this be possible?
I'm not up to speed on all of the things that computational biology is up to. But IIRC there are some metabolic pathways that cascade into producing a lot of whatever it is the organism is trying to produce. Which sounds kind of like what you're describing.