WG: Bio-Commons Whitepaper

[Rüdiger Trojok]

Dear Biohackers, tinkerers, Citizens and Bio-Commoners,

in June we had a little workshop on the festival Pixelache in Helsinki on the topic of the Commons (e.g. creative commons).

There, a number of biohackers and citizens from Europe and Asia discussed ways to make the concept of the commons fruitful for the life science.

 

Abstract

With increasing knowledge and technical skill, the sphere in which intentional intervention in nature are possible will further be expanded. Alternative IP regimes such as open-access and open-source could in future help to leverage the cost for research and development in the life sciences, mobilize unused knowledge and become more adaptable to spark new inventions. Citizens proposed a ‘Bio-Commons’ license model to put biological innovation into service to society and at the same time limit the potential misuse of knowledge and material. Taking the antibiotic resistance problem as an example, this whitepaper aims to demonstrate the necessity and feasibility of a Bio-Commons approach. Overuse of the available antibiotics and subsequent evolutionary pressure has led to the development of multi-resistant bacteria. Bacteria are under selective pressure and evolve mechanisms to avoid the antimicrobial effects of the antibiotics. Once developed, the genes for the resistance rapidly spread, and even cross over between different species - a process called horizontal gene transfer. It is therefore necessary to continuously develop new antibiotics to keep up pace with resistant bacteria. The reason for an exacerbation of the antibiotics problem into an antibiotics crisis is a market failure due to a lack of financial incentives for the pharmaceutical industry to develop new drugs like antibiotics with a small profit margin. Citizens thought of three possible scenarios of how to detect antibiotic substances from samples collected in the field. In a citizen science project dubbed ‘Biostrike’, people around the globe could contribute to the solution to the antibiotics problem by raising awareness on the issue. Citizens and Scientists could participate in a global community around Biostrike, collaborating to find new antibiotics. Specialists from all fields of expertise could put together their knowledge to build the tool sets – that is wetware, hardware and software - to enable decentralized research on antibiotics. The Bio-Commons license could make licensing of innovation and discovery easier for researchers and thereby stabilize global collaborations that will help overcome market failure situations as they exist in antibiotics research. A widely accepted regulatory framework would be required to provide legal security and reliability as well as equal, transparent, and fair terms for all participants. Before creating a legal framework for the Bio-Commons, the social relations and assumptions underlying an idea of the Bio-Commons need to be addressed. Opening up the Bio-Commons discussion and introducing democratic decision making will make everybody a stakeholder. To successfully initiate a broader discussion about the underlying principles for the Bio-Commons, a mutually understandable bio-language is needed that adequately describes the biological reality in digital form. The development of this bio-language in turn opens the possibility for responsible research and innovation already at the earliest stages in the development of a new living system. Citizens also looked for technical solutions and defined a number of requirements for software to handle the data generated under a Bio-Commons license. It was thought that the blockchain technology could in future comprise the technical infrastructure for the Bio-Commons.

 

 

Please read the whitepaper and contribute to the development of the idea on github!

https://github.com/Bio-Commons/Bio-Commons

 

 

Best,

Rüdiger

[Nathan McCorkle]

I just scanned the PDF and really have no idea what the point of it
is. Can you summarize what the problem was, what your solution was,
and how that is supposed to be useful in implementation?

Why would a professor scanning molecule libraries want to use this
license? What protections does it afford them? How and/or why is it
better than copyright or patenting? How will it ensure they receive
recognition they already seek? Does it prevent non-commercial usage of
licensed items? What can even be licensed, sequences, data sets, the
act of producing a real thing with such information?

From what I can tell the problem nowadays is development is high-cost,
monetarily and regarding time for human commitment (work), and people
want to ensure that if their work and investment (monetary or
otherwise) eventually results in market success, that they will be
compensated (with money or some other liquid asset) and also that they
will be recognized for their effort. What does your (or the group you
are posting about) idea help in that regard?

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[Dakota Hamill]

Though I wanted to type out a long, eloquent, and detailed message in regards to this, I'm choosing not to right now because I'm to tired to make it eloquent and detailed, though very long it probably would be.

I think in short I've become really quite jaded over the past 4-6 years, starting with the hope that science could be done for all, with everyone chipping in, and taking an equal share of the pie.  I've come to realize that isn't the case.  We don't live in a Utopian society where people do things for the betterment of all, or because its the right thing to do.  It's sad, but it's true.    For a while I thought maybe it'd be noble to take the righteous path and always do the right thing no matter what, even if no one notices, but then I realized, that's how you live your entire life suffering for others, and you die alone and your name is forgotten.

Maybe that will get you through the pearly gates,  but it won't get you jack shit on Earth.  I try to talk myself out of this recent change I've gone through, but I don't see it happening.  

Philosophizing aside, certain people work harder and smarter than others, and as such, they should be rewarded.  If I skip my weekends and weeknights to sit in a lab for no pay, paying for my own consumables, and come up with something, why would or should I ever consider giving up a % ownership of that to anyone else?

Believe me, as someone who has been entirely focused on antibiotic discovery for the past 4-5 years, I'd love for a super awesome crowd sourced experiment to work.  In fact, that's what I was slowly piecing together pieces for for the past 3 years, and I even saw some others launch before me.   That said, in thinking more about it and speaking to others, it became evidently clear that although one could leverage the environmental sampling diversity using multiple people, the actual REAL science would be EXTREMELY difficult to coordinate effectively.  

Albert Schatz was an OG in my mind, and an amazing scientist.  I've read multiple accounts from different parties concerning Streptomycin's discovery, and it sounds like Selman Waksman was an asshole.  A dude like Schatz, slaving away in the basement using simple old school techniques, and discovering Streptomycin, is honestly hero material.  He's a straight G.  Look up Percy Julian if you want to see another badass chemist.  

That said, although my heart says yes to having certain aspects of science be open and certain data figures shared, my mind says no when I know how hard, lonely, and soul sucking science can be at times when you're alone at midnight doing a reaction, and yet people who are "on the project" with you are  out drinking or already in bed.

IP protection, it's current state aside, is there to protect blood sweat and tears, and until I am on a project with people that bleed, sweat, and cry as much as me, I don't think I'd want them to have any of the credit or $ that might come from it.

I've become quite cynical over the years, I guess I'm well on my way to becoming a grumpy synthetic chemist.  

All that aside, the white-paper seems to sound very majestic, noble, and optimistic, but in what ways is it realistic? 

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[Bryan Bishop]

On Tue, Aug 12, 2014 at 8:37 PM, Dakota Hamill <dko...@gmail.com> wrote:

why would or should I ever consider giving up a % ownership of that to anyone else?

Nobody gives up any amount of ownership when they license their work with an open source license. They are still the copyright owners. Licensing your work doesn't dilute your ownership of said work. I am not sure if you are arguing about open source licensing in particular, but I do see some conflation with crowdsourcing (why would it matter where your funding comes from? could be from the boogeyman, etc). Also, likewise for anything that uses a creative commons license; the original authors are still the owners of the copyright itself.

- Bryan
http://heybryan.org/
1 512 203 0507

[Dakota Hamill]

"""""A widely accepted regulatory framework would be required to provide legal security and reliability as well as equal, transparent, and fair terms for all participants. Before creating a legal framework for the Bio-Commons, the social relations and assumptions underlying an idea of the Bio-Commons need to be addressed.""""""

I don't know how to quote stuff in this new crappy gmail format so I just put that up there.

I realized my last email lamented things mildly irrelevant to the discussion at hand, which was after all, this white-paper.

I thought about the questions posed above for a while in regards to crowd sourced drug discovery, mainly, how should potential profits or discoveries be shared? 

The answer: I don't know, but I've been mulling over it for years.

Let me give you a hypothetical.  You get 10,000 people from across europe to screen a bacterial species for inhibition against a target pathogen.  

One person has an isolate that has massive inhibition, something that warrants further investigation.  Let's assume this complete amateur has done everything correctly and they send you the isolated strain. 

You somehow get the money to pay for scaled up fermentation,  MIC testing, bio-assay guided fractionation followed by NMR and LCMS structure elucidation, and it happens to be that a novel structure is found with antibiotic properties.  Moving on, who is going to pay for tox studies and all the other downstream experiments needed to create a drug candidate, exploring things like SAR?  Plenty of things have antibacterial properties, but very few are good drug candidates.  

I thought, perhaps if you had 10,000 people in the project, certain people could select what candidates move forward, and the money raised by selling kits to all those people could pay for structure elucidation and tox studies, etc.

If that's the case, then I thought, how should you reward those people?

Should all 10,000 get a "share" in the antibiotic profits if it ever moves forward in testing?  Should the 1 person that discovered it be solely credited, but still receive 1/10,000th of the share?  

What if i just bought a kit and didn't do jack shit with it, basically, I bought a lottery ticket without contributing, or if I did contribute, I just falsified the diameter of the ring of inhibition. 

Now what if the people in charge of this operation get an offer from a drug company to sign over this compound and all work associated with it to them for X amount of $?  Who is to say someone wouldn't sell out?  How would you establish a hierarchy where that wouldn't happen?  Say I'm running the show and I bust my ass doing all the structure elucidation, shouldn't I get more than 1,10,000th of a share?  How much should I get?

How do you make sure to not give one company a monopoly control over the drug and its license so that they don't jack the price up?  (If you sell to them, and everyone who participated gets a share, that already exists, it's called a company)

How do you make sure you don't give every company the ability to produce the drug with an open license, such that there is to much competition and not enough profit to give incentive to produce on an industrial scale?

This isn't penicillin and WWII, and there is a reason antibiotics aren't drug companies blockbusters.

I thought crowd source drug discovery would revolutionize how drugs are discovered, then I actually swallowed the truth and not some fantasy, and I realized people with a LOT more money and a LOT more knowledge than you or me are attempting to discover new drugs each day, and if they aren't coming up with anything, what the fuck am I/we going to do?

Obviously that's a terrible reason not to try something, because I do believe in the power of collective thought and effort, but I've since slightly shifted from blindly screening isolates to something more targeted.  In the end, "crowd-sourcing" is nothing more than raising capital for a company which just appears on the outside to be for some noble or shared cause, when in reality, you want to sell a product, get a return, and share that return with shareholders (people who donated to your campaign).

 So basically, it's creating a company without having to give equity away, which is why I feel bad doing that.

[Andreas Stuermer]

"and I realized people with a LOT more money and a LOT more knowledge than you or me are attempting to discover new drugs each day, and if they aren't coming up with anything, what the fuck am I/we going to do?"

That's true, but you can get a luck shot and find one thing that just noone els has investigated before... 

Btw, a lot of goods thought, to which I have no definitive answer :/

--

---------------

http://diyspartanbiotech.files.wordpress.com/2014/03/genetic-engineering-and-synbio-for-beginners-v1.pdf

[John Griessen]

On 08/12/2014 08:37 PM, Dakota Hamill wrote:
> why would or should I ever consider giving up a % ownership of that to anyone else?

No good reason. You're not even being too cynical AFAICS.

I think of projects to crowd source as stepping stones mostly.
Unlike in free-open software, hardware has such high effort levels and costs to
replicate, that freely giving it away can trap you in not recovering your expenses.
So, the free-publishing model I see is crowd-fund stepping stones or building blocks
that are licensed to work with proprietary parts, then earn money, then open some of the
proprietary parts when you see fit in their product life cycle so others can use those
as building blocks also along with the crowd-funded building blocks.

Anything else may be naive from what we've seen over the past 5 years with the reprap
developer founding makerbot, then closing off some areas he'd claimed would stay open before.
I've not seen much of any open experiments in genetic biology -- mostly just things like
beekeeping recipes. The projects on experiment.com formerly microryza.com seemed not to include
genetics.

Genetic engineering has the promise of cornucopias and mega earning potential, so it must be
attracting those who demand compensation more than not. It's also easy to agree that there
is more up front work before getting to sales in genetic engineering than in beekeeping, so
we see more simple stuff -- like I am working on -- generic equipment for lab work that
doesn't even have much original intellectual property for lawyers to wrangle with, just
the "obvious to a practitioner" kind of improvements that are not even being delivered
by the usual equipment suspects today.

[John Griessen]

On 08/12/2014 09:19 PM, Dakota Hamill wrote:
> if they aren't coming up with anything, what the fuck am I/we going to do?
>
> Obviously that's a terrible reason not to try something, because I do believe in the power of collective thought and effort,

I've never had a collective thought ever. Sounds like telepathy.

I haven't gotten much help asking for collaboration in the past 5 yrs either.

All the potential internet collaborators that pop up quickly with lots of talk seem to dissipate into
just hot air when it comes to scheduling activities...

I think crowd funding is great, and it happens for short term goals and deliverables, and then you're back
to toiling alone mostly to generate advances to tech or science. Teams that work together seem to need
job/money glue to hold together. So the plan needs to be to get to a money level where you can hire
engineers and scientists if you have a big involved research goal. I'm going to get there
by crowd-funded lab gear. It will be open. Someone else can be making it four or ten years from now.

[Bryan Bishop]

On Wed, Aug 13, 2014 at 8:04 AM, John Griessen <jo...@industromatic.com> wrote:

Anything else may be naive from what we've seen over the past 5 years with the reprap
developer founding makerbot, then closing off some areas he'd claimed would stay open before.

Anything that was originally licensed as open source is still licensed as such. They might not be distributing those copies any more, but that doesn't mean they can retroactively revoke those licenses (unless it was in the terms, which IIRC it was not). People were upset that they did not want to continue on that path, but open source is not something that should be able to infect an organization and force it to never do anything else. Although to be fair there were many claims about how very derivative of reprap their product continued to be....

[John Griessen]

On 08/13/2014 09:04 AM, Bryan Bishop wrote:
> Anything that was originally licensed as open source is still licensed as such.

Sure, but Makerbot, like many, is a case of a company dominated developer group.
Reprap seems to be going along OK. Makerbot is no longer a source of a ready to use
physical building block for further development, since it is partly closed license now,
so its a set back from the idea of "loads of collaboration with developments building in complexity".
Sparkfun and Adafruit pretty much define "open hardware" today -- that is to say, mostly break out boards
rather than complex machinery.

I was just pointing out that the field of
open hardware is maturing, that some of the promoters really don't expect a community
of any size to develop around their offerings -- one can infer that from the calculated structure
of their company style, product offerings, licenses. Initially publishing few details of a
planned "open hardware" product is the main clue to the style. The other is a forum or an e-list
announcement, then little traffic, so little community. I believe if a company makes small effort
to enlist participation, an imagined community does not virtualize, much less materialize.

Any plan to get more communities to form needs to consider license, compensation,
legal/patents, and practical collaboration. The smaller the technical hurdles, the
easier it is to get a community to coalesce, and some talking it up seems necessary.

[Nathan McCorkle]

So never any response from the O.P....

[Jonathan Cline]

Hundreds of software dudes working really hard on linux for the past 20 years created a system which allowed Google and Samsung to step in and reap gazillions of dollars selling android cell phones, or IBM to step in and reap gazillions of dollars selling services, while the original software dudes get nada, regardless of license, even though linux uses a harmful viral license.

Hundreds of iGem students working really hard on synbio prototypical projects for the past several years created scientific or business ideas which allowed overs to step in and reap funding or startups directly related to or verbatim copied from these ideas while the original students get nada.


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################


 

[Ruediger Trojok]

Hey everyone
thanks for commenting. i am sorry for not responding to the discussion.
I tried publishing in O'reilly Biocoder, but they couldnt fit the whitepaper concept into their format ...
The question is too complex though for lossless compression into old school publication types
and with new internet communication i do not see the reason for that, either.
Anyway, I was quite busy on developing the project behind the scenes.
Early next year i will launch a new website with a dedicated track for the biocommons discussion.
All your critique and points will be taken up into that.
Please stay tuned.

Best,
Rüdiger

[biopeer]

As a co-creator of the Bio-Commons project I agree that a thoroughly discussion is needed.
Also we might want to take inspiration and share law analysis that are happening in the digital fabrication field.
There, a very deep discussion is happening on developing new types of licences that are meant to protect the intellectual assets while guaranteeing the commoning of production.
It's a very broad topic with many issue to be nailed down, however I see a growing interest raising up around this discussion and in the near future I guess many will jump in it by providing their points of view, approaches and eventually solutions.

Cheers
Eugenio Battaglia

[Jonathan Cline]

On 12/15/14 6:28 AM, Ruediger Trojok wrote:
> Hey everyone
> thanks for commenting. i am sorry for not responding to the discussion.
> I tried publishing in O'reilly Biocoder, but they couldnt fit the
> whitepaper concept into their format ...
> The question is too complex though for lossless compression into old
> school publication types

That is a very odd statement. If you can't condense the thesis into:
a) a two sentence elevator pitch;
b) a one hundred word column;
c) a 2,000 word essay;
then, there is something wrong.