I highly encourage you guys to think about adopting something from the
information that the free/open source movement has been providing. For
instance, many heavy-duty projects have something about their
specialization to free and open source materials, or something. For
instance, the debian community has a social policy or 'contract' that
tries to help explicitly define what "open" is--
Which I have copied below. This is something to consider for
DIYbio-nyc, or any other DIYbio group. Work not meeting these criteria
or not following the spirit of the contract would be where it's the
administration's duty to step in and see what's up- although I don't
know how you guys want to handle authority, and it's something I'd
rather avoid, but if you must, it has to be started somehow.
“Social Contract” with the Free Software Community
Debian will remain 100% free
We provide the guidelines that we use to determine if a work is “free”
in the document entitled “The Debian Free Software Guidelines”. We
promise that the Debian system and all its components will be free
according to these guidelines. We will support people who create or
use both free and non-free works on Debian. We will never make the
system require the use of a non-free component.
We will give back to the free software community
When we write new components of the Debian system, we will license
them in a manner consistent with the Debian Free Software Guidelines.
We will make the best system we can, so that free works will be widely
distributed and used. We will communicate things such as bug fixes,
improvements and user requests to the “upstream” authors of works
included in our system.
We will not hide problems
We will keep our entire bug report database open for public view at
all times. Reports that people file online will promptly become
visible to others.
Our priorities are our users and free software
We will be guided by the needs of our users and the free software
community. We will place their interests first in our priorities. We
will support the needs of our users for operation in many different
kinds of computing environments. We will not object to non-free works
that are intended to be used on Debian systems, or attempt to charge a
fee to people who create or use such works. We will allow others to
create distributions containing both the Debian system and other
works, without any fee from us. In furtherance of these goals, we will
provide an integrated system of high-quality materials with no legal
restrictions that would prevent such uses of the system.
Works that do not meet our free software standards
We acknowledge that some of our users require the use of works that do
not conform to the Debian Free Software Guidelines. We have created
“contrib” and “non-free” areas in our archive for these works. The
packages in these areas are not part of the Debian system, although
they have been configured for use with Debian. We encourage CD
manufacturers to read the licenses of the packages in these areas and
determine if they can distribute the packages on their CDs. Thus,
although non-free works are not a part of Debian, we support their use
and provide infrastructure for non-free packages (such as our bug
tracking system and mailing lists).
Now, just imagine saying that for a diybio group, if you're looking to
"incorporate" or "go non-profit" or make something "legal" out of your
band up in NYC. By the way, I typed up some notes on this in a much
more extensive form earlier this year, it might prove useful if you
have no idea what "open" actually means (it's recently become so much
of a buzzword that it's lost meaning)-- not that I'm saying you don't,
it's just a possibility that somebody reading, doesn't:
What's all this about "open", anyway?
That's what I thought originally, until someone (Cory Tobin) corrected
me. See here:
` "For example, in the United States, a patent covers research, except
"purely philosophical" inquiry. A U.S. patent is infringed by any
"making" of the invention, even a making that goes toward development
of a new invention — which may itself become subject of a patent."
[ http://en.wikipedia.org/wiki/Patent ]`
> just for the sake of learning about biology, or furthering knowledge
> without wanting to keep fame and fortune for yourself, then that's
> easy. You just do the work, publish it, and let whoever wants to use
> the knowledge use it. It's only when you start wanting to control the
Nope, apparently they can still legally attack your or something, and
make your life miserable. Unless this isn't true? Can we get some
law-heavyweights in on this? It's my understanding that we're not safe
from the law and lawtrolls. Maybe we need an EFF for DIY.
> commercial use of your work that you run into difficulties. I am
> uneasy at putting too much open-source language into our by-laws.
What? Then why are you in an open source diybio group?
http://groups.google.com/group/diybio/about "A community of
open-source and DIY biology geeks discussing all kinds of amateur
biology, from distributed flashlab science experiements to diy genetic
> When we talk about openness in the group I feel it is more related to
> making sure we don't hide anything we do from the world. That's why we
> are talking to all these reporters.
That's odd. It just sounds like using 'open' as a buzzword rather than
what it's meant for. We have some individuals running around in these
communities who have made a career out of asking (or telling) people
to be careful with what words you use. "Open source" specifically
refers to a special set of standards. "Freedom" too- that's why you
have the people complaining about the mangled uses of libre/gratis.
"Every problem could be solved if everyone would just have learned
latin" (or something).
> As far as committing to anything we create being "open" in the sense
> that it can be used and practised by all, then it intellectually
> limits what we can do. For example, say I want to see what effect a
> gene has on the transcriptome. I put the gene into a commercial
> expression vector from Promega, do a microarray, and report to the
> world which genes are perturbed, giving insight into hitherto unknown
> functions of that protein. I give my results freely to the world. Now
> someone says "Hey, if you are open source, why can't I have some of
> your plasmid with the gene in it to help build a biomachine or a
That's certainly a legitimate question. That's why you shouldn't be
using the concept of "open source" incorrectly- it promotes bogus
thinking like, "everyone should send me biological materials, even
though there's no precedent for this". The issue of bootstrapping of
biological collections of plasmids is a totally different issue than
"open source". Actually it's not totally different but it's
substantially different in the sense that it's not about free or open
source software, it's about materials, and if you want to talk about
free manufacturing of the materials, sure, we can talk about that, but
that's not covered under "open source" really. If you confuse and
mangle the concepts, you run into murky waters like that where people
become unhappy because people were not clear when they communicated.
:-( That's just how group dynamics goes.
> vaccine?" Well, they can't do it without running into Promega's
> patents. Does that mean I shouldn't do the experiment at all? Or I
Are you asking: "if I am planning an experiment that isn't repeatable,
then should I not bother doing it?" Repeatability is very important. I
know we all want to jump the gun and do amazingly awesome iGEM stuff
and synthetic biology, but you have to get the infrastructure there in
the first place .. you have to be able to purify your reagents before
you can use the reagents, unless you want to subject yourself to
Promega, or whoever else you're depending on / relying on. It's sad
but true. But some of us are working on these deep infrastructure
issues, and I think it's a solvable problem, we just have to be more
aware of it.
> have to use an open-source plasmid that may not be as good for my
> purposes just so I can fullfill the "open source" requirement in our
I don't know what an open source plasmid is. Btw, thanks for these
comments- I think it's important we discuss this out loud. Can you
reply to (or cc) the diy...@googlegroups.com list next time as well so
that we can all listen in and participate in this discussion? Thanks!
Okay. We seem to be on the main list now (but not nyc). This is
confusing. Regional groups can be painful.
> I guess I just don't understand what you mean by "Open Source" when
> you apply it to lab work. I have read and reread the definitions you
Okay, so that's progress. What is open source, anyway? "Under Perens'
definition, open source describes a broad general type of software
license that makes source code available to the general public with
relaxed or non-existent copyright restrictions. The principles, as
stated, say absolutely nothing about trademark or patent use and
require absolutely no cooperation to ensure that any common audit or
release regime applies to any derived works. It is an explicit
“feature” of open source that it may put no restrictions on the use or
distribution by any organization or user. It forbids this, in
principle, to guarantee continued access to derived works even by the
major original contributors."
Bruce Perens and Richard Stallman run around the internet as popular
figures who are trying to do some damage control when it comes to free
and open source software, or how people are understanding the
situation- for instance, it's not generally true that all of our
problems are solved, but that's kind of why we're here to begin with-
to explore what's possible while making it happen.
But how does "open source" apply to lab work? Lab work is a very broad
domain. You have reagents, chemicals, compounds, other forms of
materials; you have lab equipment, hardware, machines, fixtures,
supports, physical infrastructure. You have some physical space, too,
and hacker spaces have been taking a stab at how to manage these
shared co-op spaces, or whatever. There are other forms of shared
space- like, renting, but it's not necessarily ideal (I'd rather not
have to pay rent, personally- the Seasteading Institute and SSI need
to get back to work!). And then you have data- and you have people
like Jonathan Gray who are advocating open access science datasets,
and then individuals who are advocating open access literature, and
then you have the Science Commons folks who are trying to get the
semantic web thingy jump-started with data, and so on and so forth.
Lots of different issues here. One of the problems that I have noticed
with the shared hacker spaces stuff is that some people might feel
like they are just bleeding away material resources without anything
coming back to productively work on the shared space- it's like
materials are being lifted off and no new machines are being built, or
any "self-improvement projects" are being done; maybe that's the
uniting principle that needs to be understood? Self-improvement? I
don't know if there is any single uniting principle that you're going
to be able to find like that-- this is hard and needs to be worked
Sometimes what I imagine is that experiments need to be more
repeatable. Imagine taking the entire "context" of an experiment and
being able to encode it in a way that others find useful, and that you
don't have to spend a great deal of time on. This is exactly what has
happened in the free software community- and it's really quite an
amazing experience to be able to use all of this free software of tens
and hundreds of thousands of programmers all at once. And it is all
"compressed" into this one tiny machine- and this is what should be
possible with experiments. An amateur then can set up his own lab as
he pleases, he can participate with friends or if some people don't
like it, then they can freely leave and "fork" all of the same
technology- since it's all free etc. That's what I would like to see
happen. I mean, it's terrible if there are ever disagreements about
the legal aspects of a group or something, but if there are such
disagreements, then people should be able to freely "fork" all of the
technical infrastructure and then carry on. Material-wise, it's a bit
of a different issue: how do you "bootstrap" a pool of philanthropical
materials for others to use and bootstrap from? I don't know- but
freecycle is one way, for instance, and philanthropical bootstrapping
(like, "here's free energy- go forth and do stuff) and abandoned mines
are a few other options.
In computer programming, "forking" is where you take a running program
and can split it up so that it runs on multiple processor cores, or so
that a single core can work on the two different parts at the same
time, so that's where the term comes from. Think of it like mitosis,
maybe. That "mitosis" is what should be protected- and the genome is
what should be improved- but if there's disagreement about this, then
that's absolutely fine and natural, since you can take the entire
genome and copy it and go modify it, augment it, mutate it, shake
things up. That's a really big advantage of all of this technical
> posted, but they all seem to pertain to lab software and schematics
> for equipment, not biomolecules. I really am trying to get what you
Yes, data and materials seem to be treated so far. How should we treat
materials? Should we give them away freely? But to who? And how do we
make more? Are there any prior examples from history of people solving
this problem? And if not, then what ideas can we come up with?
> are saying about the correct use of the term, but for me the meaning
> at the level of exactness you are asking me to "get" is still not
Hopefully this could help?
"Opponents of the spread of the label “open source,” including Richard
Stallman, argue that the requirements and restrictions ensure the
continuation of the effort, and resist attempts to redefine the
labels. He argues also that most supporters of open source are
actually supporters of much more equitable agreements and support
re-integration of derived works and that most contributors do not
intend to release their work to others who can extend it, hide the
extensions, patent those very extensions, and demand royalties or
restrict the use of all other users—all while not violating the open
source principles with respect to the initial code they acquired."
> My understanding is that BioBricks are parts that consist of pieces of
> DNA that have certain functions which we want defined in a manner so
> that folks can splice them together easily to achieve higher level
> function. From my understanding the information concerning the
> characterization (sequence data, how well they function, etc.) of the
> BioBricks is publicly available, but the physical collection is not
The data is available over the internet, without any barriers to
entry, but I don't know what licensing of the data is involved there,
but after briefly visiting the biobrick registry and BBF website, I
can't see anything in particular except a blurb about trademarks, " A
"biobrick" is a type (brand) of standard biological part. The words
"biobricks" and "biobrick" are adjectives, not nouns. The BBF
maintains the "biobrick(s)" trademarks in order to enable and defend
the set of BioBrick™ standard biological parts as an open and
free-to-use collection of standard biological parts."
> freely accessible to anyone who asks. So the open source lies in the
Is this bad? Are they working to make it freely accessible? Do they
send out free kits to interested parties, do they have any funding to
do this, and if they did get funding, would they? I don't know, if
they aren't interested in distributing the materials, maybe it's a
sign that they're not being friendly, or something, so if we had a
'social contract' we would at least have some sort of formal way of
slapping them on a wrist and having legitimate things to complain
about. But it wouldn't be particularly effective :-( Worst case
scenario we have to go synthesize our own biobricks from scratch, or
something .. which might suck immensely.
> fact that if I want to I can call up a DNA synthesis company, tell
> them the specifications (DNA sequence) of a BioBrick, and have them
> make it for me and I can use it without running into patent hassles?
I don't know- to my knowledge, nobody is checking patents like that
yet, and I hope they don't (ever). And if they do, somebody should
come talk to me about setting up a free DNA synthesis website, or
> Now, if DIYbio NYC is calling itself "open source", does this means
> that EVERY project HAS to be done COMPLETELY with stuff (both
> materials and techniques) that's not covered by patent? For example we
> would never be able to use PCR for anything, because Roche still hold
> the valid patent.
Sucks, doesn't it. I hope that they won't come trolling around and
stepping on our parade. There needs to be some mechanisms that we
won't be killed if somebody does trample on our parade. EFF is one
mechanism that the internet community has, I guess. But anyway, your
other question: should all projects be completely distributed with
instructions as well as physical materials? I think what fenn, myself,
Tito, and many of us here are thinking of is the idea of making kits,
and selling those kits, where the physical kit would have materials,
but by no means is it a requirement that you purchase a kit, or
something. But who gets the money from selling these kits? Bringing
money into things messes everything up. Does it go to the people who
packaged it into a kit (the technical data)? The person who patented
the idea 70 years ago? Straight to DIYbio for "self-improvement" and
grants given out to run projects? Or do you want to just give away
free kits with free materials? That would be neat, but for how long
can you keep that up?
> As far as your comment "What? Then why are you in an open source
> diybio group?" Here is my reply:
> I thought that open source was just ONE goal of the DIYbio movement
> not the ONLY goal. If the "open source" criteria is going to
> drastically restrict what the NYC group can do scientifically, then I
It doesn't restrict what you can do- it restricts what others can do,
the idea is to "forbid [putting restrictions on the use or
distribution [of projects, etc.] by any organization or user], in
principle, to guarantee continued access to derived works even by the
major original contributors."
> am uneasy with it being a go/no go criterion for all potential
> projects. However, if it is ONE of our goals to contribute to the open
> source movement, for example by depositing DNA from any useful part we
> design in the BioBricks collection, I think we can legitimately be
> part of the main DIYbio group. By the way, my day job is working in
> biotech, not open source. Just because that's how I make my living, am
> I to be banned from posting in this group? One can support movements
> at many committment levels.
No, nobody is talking about banning, or anything- please don't
misunderstand all of this- this is just to try to bring some issues
out into the open, to help move discussion along, and better define
what we're up to.
> Lastly, I went over what I wrote several times, and I can't figure out
> where you got the idea that I am promoting the designing of
> "unrepeatable experiments". Way to wave a red cape in front of a
> snorting, pawing, biotech geeks' nose, LOL.
Uh. Let's say you use some "virtually impossible to acquire part" in
order to make your experiment work. And then you release the
experiment. And then nobody can get that part. That's unrepeatable. In
particular you mentioned something about promega plasmids, or
something, and it costs some money to access them. Overall, you'll get
significantly more kudos if you're using some homebrew DNA synthesis
technique and then homebrew plasmid synthesis technique :-p which we
don't have yet. but just saying- having reliances on really
significant barriers to entry just isn't cool when it comes to DIY.
But is anyone going to listen to that? i.e., what happens if some mean
evil corporation doesn't respect this page on openwetware? I know that
what I am doing is "law fearmongering", but it's just something I'm
wondering about- it's just like people throwing up custom licenses on
projects, and then how developers have to show them that it's not such
a smart idea to do that (i.e., it's not necessarily going to hold its
weight when it needs to, or something).
> I was right, in that their intention is their sequences are free to use,
> even as parts of patentable commercial inventions, so long as the patents
> covering the invention do not restrict the use of the part for others in any
Yes, but isn't this going to create license incompatibility issues
with other projects?
Yes, good stuff.
> As far as actually giving materials away, that costs time and money. People
> often share things freely, but nobody should be forced into producing
> plasmids for with world if they don't have the resources.
Nobody is forcing you to do things.
> With regard to my Promega analogy, Promega is a well-known biotech supplier.
> A standard plasmid I looked up in their website is $96. If this amount is a
> barrier to some groups, and the NYC group can raise the money, I don't think
> the NYC group's activities should be limited by the other groups.
I don't think you understood what I wrote. How would anything I have
said mean anything about *other* groups limiting *NYC's* activity? I
Ah, neat. I wasn't aware of the BBF-legal list. I'll be sure to listen
in from now on.
> I think the latest development is that they are working on not a patent- or
> copyright-licensing system, but a formal legal agreement (agreement in this
> case is special and means some kind of formal legal thing that I don't
This legal agreement would be specifically about biobricks, right?
Just to make things clear.
> There were some interesting discussions later in on in the BBF-Legal
> archives about "Bootstrapping an Open Parts Collection"
> It seems very related to the discussion we are having here.
Yes, it does, thanks for the reference, maybe I'll integrate some of
those messages into the FAQ. Very nice to know about, Mac.
> In conclusion, I believe that "open" part licensing is an area of active
> research and development by the BBF and I encourage anyone interested to
> contact le...@biobricks.org. We should try to work together with them
> before reinventing the legal rights to sharing the wheel, so to speak.
> Bryan, could you summarize your main point for the sake of posterity in one
> or two sentences?
Not really. I'm yammering on about multiple issues here. First, it's
nice to be able to take the work of BBF and Gingo Bioworks and run
with it- but it's important to note that that's all legal legwork for
biobricks, and not necessarily the more general issues in open source
diybio or open source hardware/labware, which are different kinds of
parts (not genetic biobrick parts, namely). Secondly, the license
compatibility issues (for splicing together all sorts of projects) are
another item worth investigating- maybe Fish & Richardson will
approach OSI and FSF and EFF and talk about those issues, if they are
serious about this. It would be awesome if they would sponsor the
legal legwork to help us improve the open source hardware status quo,
after the work that kind of went downhill with Bruce Perens and so on-
on a license that I presently forget the name of. The other issues are
related to diybio regional organizations- such as a "social contract"
for how to evaluate whether or not projects are truly deserving to be
under the diybio brand, or whether or not they are actually "free" or
"open source", so that we can use our words instead of just yelling at
each other when somebody does something wrong .. like not providing
information on their project that they claim to be open, etc., but
also for other issues like Ellen was mentioning re: somebody coming up
and asking to "give me teh goods" (make me plasmids because you say
you're open)- these things need to be more fully fleshed out, even if
there are plans to one day in the future use materials to make free
stuff, structure doesn't just magically appear in the mean time.
No. Here is what I said:
> > Lastly, I went over what I wrote several times, and I can't figure out
> > where you got the idea that I am promoting the designing of
> > "unrepeatable experiments". Way to wave a red cape in front of a
> > snorting, pawing, biotech geeks' nose, LOL.
> Uh. Let's say you use some "virtually impossible to acquire part" in
> order to make your experiment work. And then you release the
> experiment. And then nobody can get that part. That's unrepeatable. In
> particular you mentioned something about promega plasmids, or
> something, and it costs some money to access them. Overall, you'll get
> significantly more kudos if you're using some homebrew DNA synthesis
> technique and then homebrew plasmid synthesis technique :-p which we
> don't have yet. but just saying- having reliances on really
> significant barriers to entry just isn't cool when it comes to DIY.
I was talking about "repeatability", not "open". It doesn't matter
that it conforms to some spirit or not, the point is that it's
unrepeatable, and so why would you bother? That's not science.
> And as far as sharing actual material, I was talking about the BioBricks and
> iGEM. They limit access to their material because they want to ensure their
> effort in providing it is not just being
> wasted on a group that has no real possibility of contributing.
Yes, but the biobricks legal 'stuff' is talking about something else
entirely (the licensing of parts as open source), not their actual
distribution, like what you've been talking about or worrying about or
something. I think that warrants another discussion, or something,
which was the entire point of me replying to your thread about
'scheduling' agenda items. But anyway.. that seems to be a lost point