> Feed them sugar & water, and out pops specialty chemicals.
Even if your culture contains microbes that produce the specialty chemical you're interested in, natural selection in the reactor favors the populations that use the least sugar and water and multiply the most. In other words, reactors are very good at growing microbes: surprise! They're quite bad at selecting for much else.
Just doing what you described is called the Evolvenator. That discovery described how to build and test the microbe, but not necessarily how to design it.
There's a fix: what if we make the interesting chemical a side effect of the kind of more efficient metabolism that's expressed by the highest-surviving population in your culture? In other words, the microbes that multiply the most make the interesting stuff by accident, usually as a consequence of the media in their reactor and a small tweak to their genetic code.
It turns out that designing a chemical pathway that is metabolically superior to a natural one and as a side effect, produces an economically valuable product, is crazy hard. It is usually harder than designing an industrial process to manufacture the economically valuable product in the first place.
That's why the article mentions that these other biotech firms "specialize" in making certain kinds of chemicals. In reality, they experiment with maybe two targets a year, and they land one that works out of 10.
You'd be wrong to judge them on their hit rate: rather, I'm just pointing out how there isn't some kind of "optimization" magic to discover efficient chemical pathways. It's incredibly hard research! And I'm always surprised (though pretty delighted) that VC finds its way to these people, because VC avoids actual science projects like the plague.
PS: The $13 million will buy things like the Sartorius bio reactor, a $1 million up front + $1-2 million a year machine capable of running automated experiments on yeast cultures in bioreactors. If you're in the business of making pickaxes instead of trying to strike gold, clearly you should make a better bioreactor. If you agree, just e-mail me.