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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/sy

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.)
- xkcd-sucks 12y ago
  Given that "reverse-engineering" DNA is trivial compared to "reverse-engineering" small molecules or reverse-engineering software, do you have an opinion on what constitutes non-"open source" DNA?
  - jjoonathan 12y ago
    Just because Ken Dill declared victory on the protein folding problem [1] doesn't mean it's going to become trivial any time in the next few decades... EDIT: after checking the paper, it looks like he qualified himself far better than I remembered. Maybe I was thinking of a different paper? In any case the lower-left part of the last page is a good partial list of reasons why reverse engineering DNA is not trivial. [1] http://web.iitd.ac.in/~nkurur/2012-13/IIsem/cyl110/protfoldprob50.pdf http://web.iitd.ac.in/~nkurur/2012-13/IIsem/cyl110/protfoldp...

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.)
xkcd-sucks 12y ago
Given that "reverse-engineering" DNA is trivial compared to "reverse-engineering" small molecules or reverse-engineering software, do you have an opinion on what constitutes non-"open source" DNA?
- jjoonathan 12y ago
  Just because Ken Dill declared victory on the protein folding problem [1] doesn't mean it's going to become trivial any time in the next few decades... EDIT: after checking the paper, it looks like he qualified himself far better than I remembered. Maybe I was thinking of a different paper? In any case the lower-left part of the last page is a good partial list of reasons why reverse engineering DNA is not trivial. [1] http://web.iitd.ac.in/~nkurur/2012-13/IIsem/cyl110/protfoldprob50.pdf http://web.iitd.ac.in/~nkurur/2012-13/IIsem/cyl110/protfoldp...