> ...optimized factories...

> 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.

FWIW, in a past life, I bought (4) 2L Sartorius reactors used for $75k, built out my lab for <$50k and had an operating budget of $450k w/ 2 fully-burdened RAs.

I agree with much else of what you've said. I worked in biosynthetics with some of the Lygos teammates at another company. All-in-all it's not a bad idea, but the development time is _so_ long, especially in yeasts. It's analgous to writing assembly w/o documentation, and debugging takes months per code-change.

What if you added a lot of "error-checking" code that kills the host when it doesn't produce enough of the valuable chemical? I'd guess this is very difficult in practice.

Or also add a competing organism that "triggers" when the concentration of byproduct is too low?

For the first idea, you'd have to have some lethal protein or something that's specifically inhibited by the chemical of interest. Coming up with that might be even harder than the original problem. And even if you could, evolution wouldn't favor cells that produced it, since it confers no advantage. There's an energetic cost to making that protein.

For the second idea, again, evolution ruins everything. The competing organism would do just that - compete.

Because "you get what you select for". Instead of getting more of the chemical, you'll get a host that has hacked and disabled your error checking code.

Why can't you just design organism / insert DNA to make X.

Grow organism in 1,000 little reactors, measure output of X, keep top y% and repeat?

Yield may drop over time, but this way evolution is somewhat on your side.

PS: I don't expect that to work, but I am not sure what the issues are.

Let's say you had such an organism.

Naturally, all the yeast individuals in your population have slight genetic variations. Maybe millions of them. Most have your plasmid to make X.

Due to natural selection, the competing priority—let's call it the "Y" product—is reproducing * surviving as much as possible. The yeast genes that make the yeast reproduce as much as possible and survive as well as possible will eventually be the largest population in your reactor.

So if X doesn't also achieve Y, the only thing that will be left in your reactor is a population that achieves Y.

The worst thing (which is true most of the time) is that achieving X is opposed to Y. Processing some chemical in the media that doesn't translate to food for the organism is wasted metabolic resources. So for most applications you can think of, your X population will die or reproduce away its X genes.

There's nothing you can parameterize to fix this! Like Y will happen regardless of what temperatures you use, or what media you use, or how much oxygen you give the reactor. By virtue of growing something, you're optimizing for Y. Either design X to also achieve Y, or fail. Evolution is opposed to you, not on your side!

In practice today, we don't understand the biological systems design well enough to make X also achieve Y. So what happens is you grow the yeast until you have a population with maximum metabolic efficiency (i.e., maximally achieves Y), and THEN modify the yeast to do X. It dies quickly, and your left with a little bit of product. This works, but it's not viable.

So from my understanding,

bacteria is competing to reproduce the fastest, and the chemical that we want is simply a byproduct of its metabolism or pathway for reproduction

issue is, however, the byproduct has to either be the most efficient factor for reproduction, or else by natural selection it will be removed

my question is, can we use the same techniques found in tree grafting to prevent or delay natural selection, and grow our byproduct?

question - so why does agriculture work? why are we able to grow tomatoes year after year.

is the entropy at the cellular level versus at a plant level so different that the processes are "locked" in place.

does it make more sense to try and grow plants that produce malic-acid tomatoes? sure it might be harder to geow one... but once grown, you can scale it infinitely.

I suspect that it's that you can manually select which tomatoes you want. It's a bit harder to select individual microbes.

So essentially, the difference between the trait you want, X, and the trait that survives, Y, doesn't exist. Every Y is an X, since generations of farmers are the ones manually doing the selection.

that makes a lot of sense. so in case of tomatoes, the survivability of the plant has no correlation with actual survival. it is being engineered by the farmers.

what we really need is a way to select and ensure survival of the yeast that we want.

Alot of companies do exactly that. Using systems like: http://www.tapbiosystems.com/

But it's not cost effective when producing millions of liters.

TAP Biosystems is the manufacturer of what is now called the Sartorius.

Also, if you look carefully at the Lygos website photos, you'll see the Sartorius.

@doctorpangloss's comment is 100% right. I'd add the small problem that behavior in small reactor != behavior in large reactor. Reactor scale-up is somewhat unpredictable and often ends in tears.

Here are two great articles on the challenges of biofuels:

1. The Rise And Fall Of The Company That Was Going To Have Us All Using Biofuels: https://www.fastcompany.com/3000040/rise-and-fall-company-wa...

2. A Biofuel Dream Gone Bad: http://fortune.com/kior-vinod-khosla-clean-tech/

just another iteration of biofuel..

So, Dupont has a production-scale microbial process for 1,3-propanediol. What is the market for malonic acid if Dupont can already go directly to 1,3-propanediol?

http://www.dupont.com/products-and-services/fabrics-fibers-n...

Malonic acid and its derivatives have their own demand as esters and neat acid apart from conversion to 1,3 propanediol. It's possible to catalytically oxidize 1,3 propanediol to malonic acid, so they are somewhat competing in the same space.

The "clean" advantage of these fermentation processes is IMO greater than the "sustainable" part. You could use renewable energy to synthesize all the upstream precursors of traditionally-synthesized malonic acid (e.g. monochloroacetic acid, hydrogen cyanide) from air and seawater and it would be perfectly sustainable. But the intermediate products are hazardous to handle and there's a large waste stream of aqueous salt solutions and organic solvents. Eliminating hazardous intermediates and producing waste streams that can be handled by simple wastewater treatment makes it cheaper to build and operate facilities for these chemicals.

Agreed. Just pointing out that they're going up against an established DuPont process.

Also that process has been around for at least 10 years:

https://www.ncbi.nlm.nih.gov/pubmed/14580573

I met the guy (Charlie Nakamura) who developed the process. It took a hell of a long time to get everything working at useful efficiency, then a fair amount of development to get it working at scale.

Also see others in this space:

Amyris (older synthetic bio company) Zymergen (newer synthetic bio company that seems to be doing some of the same things Lygos wants to do)

Agree- our startup (www.Librede.com) does biosynthesis of cannabinoids in yeast from sugar. Much more environmentally sustainable and economical. Further, the modularity of the cannabinoid synthesis pathways in cannabis allows production of specific cannabinoids by substitution of single enzymes.

I just want to say thank you for making a startup from an idea my friends had in college. For some reason we just never managed to get our shit together to the point of doing this. I can't remember why...