4 ms·

Founder here; working on software that exploits the full potential of engineered microbes; we're using them to make therapeutics, plastics, materials, etc. happ

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.

durkie 12y ago
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?
- saurabh20n 12y ago
  Many limitations! Constructing the designs (i.e., going from data->dna->cells) takes time and is expensive: we pay vendors for the construction. So we have to restrict our software to output designs that yield the most novel products, with the least change to the biology of the microbe. Most of the time changes do nothing! But if our models are accurate enough, the engineering can be predictable. We are continuously improving our models -- from more data mining, and from feedback from experiments. That said, what our algorithm predicts right now is still a huge space (5000-10000 products). That is the tree image in the article. For context, the chemical industry centers around 70,000 products.
- avmich 12y ago
  I don't see why certain inorganic substances (like e.g. HOOH) can't be made?
monocasa 12y ago
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?
- graphene 12y ago
  The software project from their research group that sounds a lot like what this startup is doing seems to have been made unavailable: http://act.berkeley.edu/synthesizer http://act.berkeley.edu/synthesizer even though it's still linked from http://andersonlab.qb3.berkeley.edu/#/software http://andersonlab.qb3.berkeley.edu/#/software Shame, but understandable.
  - saurabh20n 12y ago
    Completely understand your sentiment. I have been releasing software as open source for 10+ years -- all of my 7 years of program synthesis PhD sw is available as open source. With 20n, we had to tread more carefully. As monocasa implied, open source here means either code, or dna data. While code stays on the computing platform, dna's platform is every living entity. Lets assume you could predict precisely what a piece of DNA will do -- we are not there yet, but will be at some time in the future. Are you advocating that all of that should be freely available? There are lots of benefits to open source and we understand a lot of it in the context of code, but IMHO, we will need to discuss more before we fully comprehend what it means to open source dna. There are tons of opportunities, e.g., enabling bioproduction, and hopefully the beneficial nature of that (cheaper/carbon negative/environmentally-friendly) will be the leading argument in the conversation than anything else.
    - graphene 12y ago
      Thanks for your comment. As I said, it's understandable for your company to keep its software proprietary, after all Google for example, while a supporter of and contributor to open source, does not open source critical components of its business either. On the wetware side, there is of course a similar incentive to keep the genetic sequences that result from your work private, in addition to perhaps ethical concerns regarding the dissemination of arbitrary DNA. As a fellow software guy considering going into drug development research though, I do wonder: Given your mentioned open source credentials, it's probably plausible that you are at least sceptical about software patents? If so, what is your opinion on patents on drug molecules and DNA sequences? I'm struggling a bit with this since the only way to a big exit seems to involve protecting any findings as IP (because of the costs of the regulatory process), but I'm not sure I'd want my work to be patent-walled. Do you know what you would do if you are one day faced with the choice of whether or not to patent one of your molecules or sequences, knowing that not doing so would have significant adverse financial effects on your company? (This all may sound somewhat critical, but I'm really just curious. My email is in my profile if you prefer to respond privately.)
walsh-cloonagh 12y ago
Hey Mr. Shrivastava, 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/ http://www.goldenrice.org/ [2] http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(07)61690-0/abstract 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 http://link.springer.com/article/10.1007/s12602-013-9133-3
technotony 12y ago
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.
- saurabh20n 12y ago
  Hi glowing plants :) Indeed. We like our simple to manipulate (relatively speaking) microbes, but would be happy to see what avenues there are in other customer domains.
sitkack 12y ago
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. [0] http://www.cracked.com/article_18503_how-biotech-company-almost-killed-world-with-booze.html http://www.cracked.com/article_18503_how-biotech-company-alm...

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.

durkie 12y ago

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?

saurabh20n 12y ago
Many limitations! Constructing the designs (i.e., going from data->dna->cells) takes time and is expensive: we pay vendors for the construction. So we have to restrict our software to output designs that yield the most novel products, with the least change to the biology of the microbe. Most of the time changes do nothing! But if our models are accurate enough, the engineering can be predictable. We are continuously improving our models -- from more data mining, and from feedback from experiments. That said, what our algorithm predicts right now is still a huge space (5000-10000 products). That is the tree image in the article. For context, the chemical industry centers around 70,000 products.
avmich 12y ago
I don't see why certain inorganic substances (like e.g. HOOH) can't be made?

monocasa 12y ago

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?

graphene 12y ago
The software project from their research group that sounds a lot like what this startup is doing seems to have been made unavailable: http://act.berkeley.edu/synthesizer http://act.berkeley.edu/synthesizer even though it's still linked from http://andersonlab.qb3.berkeley.edu/#/software http://andersonlab.qb3.berkeley.edu/#/software Shame, but understandable.
- saurabh20n 12y ago
  Completely understand your sentiment. I have been releasing software as open source for 10+ years -- all of my 7 years of program synthesis PhD sw is available as open source. With 20n, we had to tread more carefully. As monocasa implied, open source here means either code, or dna data. While code stays on the computing platform, dna's platform is every living entity. Lets assume you could predict precisely what a piece of DNA will do -- we are not there yet, but will be at some time in the future. Are you advocating that all of that should be freely available? There are lots of benefits to open source and we understand a lot of it in the context of code, but IMHO, we will need to discuss more before we fully comprehend what it means to open source dna. There are tons of opportunities, e.g., enabling bioproduction, and hopefully the beneficial nature of that (cheaper/carbon negative/environmentally-friendly) will be the leading argument in the conversation than anything else.
  - graphene 12y ago
    Thanks for your comment. As I said, it's understandable for your company to keep its software proprietary, after all Google for example, while a supporter of and contributor to open source, does not open source critical components of its business either. On the wetware side, there is of course a similar incentive to keep the genetic sequences that result from your work private, in addition to perhaps ethical concerns regarding the dissemination of arbitrary DNA. As a fellow software guy considering going into drug development research though, I do wonder: Given your mentioned open source credentials, it's probably plausible that you are at least sceptical about software patents? If so, what is your opinion on patents on drug molecules and DNA sequences? I'm struggling a bit with this since the only way to a big exit seems to involve protecting any findings as IP (because of the costs of the regulatory process), but I'm not sure I'd want my work to be patent-walled. Do you know what you would do if you are one day faced with the choice of whether or not to patent one of your molecules or sequences, knowing that not doing so would have significant adverse financial effects on your company? (This all may sound somewhat critical, but I'm really just curious. My email is in my profile if you prefer to respond privately.)

walsh-cloonagh 12y ago

Hey Mr. Shrivastava, 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/ http://www.goldenrice.org/ [2] http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(07)61690-0/abstract 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 http://link.springer.com/article/10.1007/s12602-013-9133-3

technotony 12y ago

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.

saurabh20n 12y ago
Hi glowing plants :) Indeed. We like our simple to manipulate (relatively speaking) microbes, but would be happy to see what avenues there are in other customer domains.

sitkack 12y ago

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. [0] http://www.cracked.com/article_18503_how-biotech-company-almost-killed-world-with-booze.html http://www.cracked.com/article_18503_how-biotech-company-alm...