Founder here; working on software that exploits the full potential of engineered microbes; we're using them to make therapeutics, plastics, materials, etc. happy to answer any questions.
When I was studying chemical engineering in university, I tried to get faculty interested in engineering yogurt-producing bacteria (like L. bulgaricus) to produce Vitamin A (or an equivalent retinoid or carotenoid): a "golden yogurt" scheme like Vitamin A producing golden rice [1]. But, they weren't having any of it.
This could be useful for the 670,000 children who die [2] and 250,000 to 500,000 children who go blind from Vitamin A deficiency [unsourced].
The yogurt could be produced from dairy and plant stock (which is presumably easier for subsistence farmers to procure).
I had the good fortune of switching careers into software, so I don't have the wherewithal to do this myself.
If you happen to have time, I think you could produce pretty good results from engineering a Vitamin A producing strain.
Where do you guys stand on "open source" synthetic biology (like BioBricks or OpenWetWare)? Will we see any source from you guys, whether it be of the von Neumann or the Crick variety?
What safeguards are you putting in place to not repeat the Klebsiella planticola debacle [0].
What is the possibility of an engineered organism escaping into the environment and over producing a beneficial substance, insulin, acetaminophen, Lysergic acid, etc.
Any plans to make this available to others who are looking for novel pathways for other (non-microbe) applications? Specifically there are a few chemicals we want to express in plants.
this sounds amazing! aside from the organics-only requirement (which makes sense to me), what other limitations are there on what you can make? or is everything basically open given a long enough search?
Really cool. Question: Assuming that your algorithms will become known or can be replicated, how do you think about your defensibility? What is proprietary here that improves via network effects? How does the licensing model work and what are some comparable (old school/current) companies?
Defensibility for us: microbes we build, and the platform they form. Our software-driven engineering is significantly faster than the state-of-the-art: human's looking at metabolic maps. People will start building on top of our initial microbes and improving them. These initial microbes form the "platform" from which to enable more bioproduction apps.
There is already a lot of competition here (which is not necessarily a bad thing)...will be interested to see how 20n can differentiate and or add value upon what already exists.
Indeed! We love this community [1]. We started 20n with DARPA's help, in part to gather more steam around the accuracy of software predictions tools within synthetic biology. You seem to have worked on these tools, and so must know the pain of convincing wet-lab scientists to follow up on the sw predictions.
Paracetamol, both for academics and to pharma, was a non-biosynthesizable molecule. But once we had the prediction, we were able to go to the lab to construct the microbe pretty easily.
In the end, the tool is the start of the process. We are investing significant resources in constructing the microbes. Over the coarse of the next two year, hopefully you will find some novel molecules in the ones we move to bioproduction.
[1] Have to! We are part of it. :) We know most of them, and they probably know us.
Cool! I almost went into a lab studying polyketide synthase enzymes. How heavily do they feature in your pathways? Is their modularity overstated/understated?
(I fully intend to stalk you on google scholar after I get back to the things I really ought to be working on right now...)
Hah! Oh PKS-es! Megasynthases (PKS, NRPS, FAS) do not currently feature very heavily in our algorithms, but their modeling is certainly within our intended algorithmic expansion plans. As for whether they are understated/overstated, my cofounder can sit you down for hours and speak about them, but you have probably moved on!
ps: Googling me will lead you to program synthesis: programs that program programs :) which is another curiosity that you may or may not want to dive into. You will find a lot more biology from my cofounder. google scholar: chris anderson synthetic biology.
Question: could these be tailored for end-users? So instead a prescription a patient could be sent home with a jar of pickles that synthesized their medication as they fermented? I could see that disrupting the pharmaceutical industry (if dosage could be controlled).
This is really interesting - this field is new to me, but is there existing research available that shows that this works for large scale chemical production or will this be something that you'll be working on inventing?
Optimizing for large scale production is indeed what most of the field works on. There have been many success stories: an anti-malarial drug through yeast (Artemisinin by Amyris+Sanofi), a plastic precursor through bacteria (1,4-BDO by Genomatica+DuPont), and more.
What they are missing is the whole spectrum of what could be made biologically. We will create microbes for the most valuable chemicals and then partner with existing optimization companies that have industrial fermenters running. Think beer fermentation, just instead of the alcohol yeast, you use our yeast.
Really interesting, but the article doesn't explain why someone would want to grow chemicals using microbes instead of synthesizing them through chemistry. Is it cheaper?
Yes. When going after non-trivial chemicals the economics work out, and is cheaper when scaled up. The process essentially repurposes beer fermentation. The usual benefits of biological production: carbon-negative, and not using any toxic catalysts or producing waste products hold as well. Consider the molecule, paracetamol/acetaminophen/Tylenol [1], that we created a microbe for: The US alone produces 35000+ tonnes of it, all currently coming from petro-routes. It would be nicer to get it the same way we get beer, if we could.
There might be additional market forces that make a microbial fermentation attractive: e.g., in the case of the anti-malarial drug artemisinin, fluctuation in supply of the plant Artemisia annua, the price of the drug varied between $120-$1200/kg, and Amyris and Sanofi moved it to yeast based production for creating a steady supply [2]. That route was critical for the supply of the drug to African countries.
For many of the requests we get, chemical synthesis is not economically feasible to take the chemical to market, and bioproduction might be the only route. The fact that we suggest routes that work well for the planet is a good side-effect. :)
[+] [-] saurabh20n|11 years ago|reply
[+] [-] walsh-cloonagh|11 years ago|reply
When I was studying chemical engineering in university, I tried to get faculty interested in engineering yogurt-producing bacteria (like L. bulgaricus) to produce Vitamin A (or an equivalent retinoid or carotenoid): a "golden yogurt" scheme like Vitamin A producing golden rice [1]. But, they weren't having any of it.
This could be useful for the 670,000 children who die [2] and 250,000 to 500,000 children who go blind from Vitamin A deficiency [unsourced].
The yogurt could be produced from dairy and plant stock (which is presumably easier for subsistence farmers to procure).
I had the good fortune of switching careers into software, so I don't have the wherewithal to do this myself.
If you happen to have time, I think you could produce pretty good results from engineering a Vitamin A producing strain.
[1] http://www.goldenrice.org/ [2] http://www.thelancet.com/journals/lancet/article/PIIS0140-67...
These guys are working on a more ambitious scheme to engineer bacteria to produce vitamin A in intestines: http://link.springer.com/article/10.1007/s12602-013-9133-3
[+] [-] monocasa|11 years ago|reply
[+] [-] sitkack|11 years ago|reply
What is the possibility of an engineered organism escaping into the environment and over producing a beneficial substance, insulin, acetaminophen, Lysergic acid, etc.
[0] http://www.cracked.com/article_18503_how-biotech-company-alm...
[+] [-] technotony|11 years ago|reply
[+] [-] durkie|11 years ago|reply
[+] [-] unknown|11 years ago|reply
[deleted]
[+] [-] levlandau|11 years ago|reply
[+] [-] saurabh20n|11 years ago|reply
[+] [-] red_dazzler|11 years ago|reply
http://www.nature.com/nrmicro/journal/v10/n3/fig_tab/nrmicro... http://www.ncbi.nlm.nih.gov/pubmed/25080239 http://www.biomedcentral.com/1752-0509/5/122 http://www.ncbi.nlm.nih.gov/pubmed/24642060
[+] [-] saurabh20n|11 years ago|reply
Paracetamol, both for academics and to pharma, was a non-biosynthesizable molecule. But once we had the prediction, we were able to go to the lab to construct the microbe pretty easily.
In the end, the tool is the start of the process. We are investing significant resources in constructing the microbes. Over the coarse of the next two year, hopefully you will find some novel molecules in the ones we move to bioproduction.
[1] Have to! We are part of it. :) We know most of them, and they probably know us.
[+] [-] jjoonathan|11 years ago|reply
(I fully intend to stalk you on google scholar after I get back to the things I really ought to be working on right now...)
[+] [-] saurabh20n|11 years ago|reply
ps: Googling me will lead you to program synthesis: programs that program programs :) which is another curiosity that you may or may not want to dive into. You will find a lot more biology from my cofounder. google scholar: chris anderson synthetic biology.
[+] [-] blacksmith_tb|11 years ago|reply
[+] [-] aareet|11 years ago|reply
[+] [-] saurabh20n|11 years ago|reply
What they are missing is the whole spectrum of what could be made biologically. We will create microbes for the most valuable chemicals and then partner with existing optimization companies that have industrial fermenters running. Think beer fermentation, just instead of the alcohol yeast, you use our yeast.
[+] [-] foobarqux|11 years ago|reply
[+] [-] saurabh20n|11 years ago|reply
There might be additional market forces that make a microbial fermentation attractive: e.g., in the case of the anti-malarial drug artemisinin, fluctuation in supply of the plant Artemisia annua, the price of the drug varied between $120-$1200/kg, and Amyris and Sanofi moved it to yeast based production for creating a steady supply [2]. That route was critical for the supply of the drug to African countries.
For many of the requests we get, chemical synthesis is not economically feasible to take the chemical to market, and bioproduction might be the only route. The fact that we suggest routes that work well for the planet is a good side-effect. :)
[1] http://en.wikipedia.org/wiki/Paracetamol#Synthesis
[2] http://en.wikipedia.org/wiki/Artemisinin#Synthesis_in_engine...
[+] [-] cing|11 years ago|reply
[+] [-] prenschler|11 years ago|reply
[+] [-] saurabh20n|11 years ago|reply