Synthetic biology startup Lygos raises $13M to make cleaner chemicals

> 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.

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Honestly, tomatoes are really efficient as is. They grow huge amounts of fruit per acre; they grow in preposterous conditions, like people's windowsills, greenhouses, fields across the world, etc. I don't mean to pick on your particular choice of example, but you really got to get into the weeds to really understand the efficiencies of agriculture.

Indeed, there's consensus that the greatest threat to agricultural efficiency are all the weaknesses of a highly-engineered monoculture. Imagine the devastation of the Florida orange harvest a few years ago due to frost, but due to a single weed.

> a cell is basically a huge finite state machine

There is a huge amount of research to create an "algebra" of synthetic biology, which is really fascinating stuff. You'd love it! You're right that a lot of what you're describing is inevitable, but there's a huge grind to get there, solving engineering problems totally orthogonal to the theoretical biology of it all.

The fact is, even with a perfectly engineered tomato, it's hard to beat the low cost of dirt+sun.

Photosynthesis is actually fairly efficient.

As for the whole cells-are-state-machiines, while that's technically true, the state vector has a trillion parameters.

Where do you suppose sugar comes from?