What's all this about "open", anyway? (long)
Bryan Bishop
I don't think we've ever gone explicitly over the idea of the
debian/ubuntu social contracts, and how those concepts might be useful
in pursuing our shared interests as diybio grows. From what I saw at
BioBarCamp 2008, where many of us found each other in person, there's
a lot of positive effort and energy being channeled in these
directions, so the very least I can do is document a little bit of it
from all over the web. This is a draft at best, so go easy on me :-).
This email is more like a safari tour through some relevant portions
of the internet that are of interest to diybio and maybe developing
'contracts', so if somebody else wants to write something more
coherent, go ahead- this is more like bibliography material, but also
interesting for those who don't know about these developments. With
some annotation and running commentary :-). I hope others comment on
some of these excerpts.
((At the bottom and very end is the debian and ubuntu social contracts
or codes of conduct for an example, but it's best taken in context
with everything else in this email)). (((This is also re: IP law and
some other recent topics on the list.)))
http://p2pfoundation.net/Open_Source_Biotechnology
http://rsss.anu.edu.au/~janeth/
http://rsss.anu.edu.au/~janeth/OpenSourceBiotechnology27July2005.pdf (thesis)
"""
"Open Source licensing is a style of intellectual property management
that has evolved in the past half-decade out of the Free Software
movement, initiated in the early 1980s in response to restrictive
copyright licensing practices adopted by commercial software
developers. The Open Source approach seeks to preserve ongoing
community access to proprietary software tools without precluding or
discouraging commercial involvement in their development.
"Open Source Biotechnology" refers to the possibility of extending the
principles of commerce-friendly, commons-based peer production
exemplified by Open Source software development to the development of
research tools in biomedical and agricultural biotechnology."
(http://rsss.anu.edu.au/~janeth/)
"""
Janet Hope:
"Since the 1980's, the life sciences have undergone a process of rapid
commercialization. The legal mechanism for this process of
commercialization has been the expansion of intellectual property (IP)
protection to inventions that were previously regarded as
unpatentable. The result has been a literally exponential increase in
applications for biotechnology patents.
These patents not only protect inventions that are valuable as end
products; they also protect early stage inventions and research tools.
Advances in biotechnology require the use of many of the latter, for
which researchers must obtain licenses from patent owners. A good
example is "golden rice", which utilized more than 70 different
patented procedures and processes. To get permission to use all of
these tools, scientists enter into multiple negotiations for each
piece of IP. These mounting transaction costs can retard, and in some
cases completely undermine, their scientific projects. Even if they
are not prevented from pursuing research itself, institutions may find
that the rights of other IP holders prevent them from commercializing
the fruits of their labor.
In biomedicine, there are considerable social costs associated with
working within this expensive proprietary system. These stem from the
fact that such costs are beyond the resources of the smallest
participants, or would-be participants, in the industry. Market forces
will naturally tend to direct efforts by big private sector players to
where there is the most substantial return on investment. This means
research goals are inevitably being narrowed to those that will be
most profitable, though not necessarily most useful. Thus, it is often
not commercially worthwhile for the biomedical industry to devote
significant resources to addressing medical or social needs, such as
drugs for very common diseases like tuberculosis or malaria.
Similarly, in agriculture, breeding strategies will be oriented
towards major crops in developed country markets, not towards finding
genetic traits with characteristics that are useful to poor farmers.
The last few years have also seen a series of mergers and acquisitions
that have dramatically consolidated the industry, with a huge portion
of fundamental research tools ending up in the hands of a tiny number
of big multinationals. This level of industry concentration has
inevitably led to the overpricing of technologies and the exclusion of
innovative start-ups and public sector institutions. This, in turn,
means that smaller firms can't get a foot in the door.
This situation has been described as a "tragedy of the anticommons."
In contrast to the tragedy of the commons, when a public resource is
overused because there is no one owner to regulate it, a tragedy of
the anticommons occurs when a resource is underused because it has
been divided up by a number of owners who may not be willing to agree
or cooperate with one another."
Can Open Source Licensing Work With Biotechnology? (still with Janet Hope)
"""
"When I spoke to Bruce Perens, who helped define the basis for open
source development in his aptly titled document, The Open Source
Definition, he took the view that the open source biotechnology
movement does not aim to create a particular legal framework. Instead,
it is a form of social engineering. There is no question that one
could produce a legally binding open source license in biotechnology
if one wanted to—the real question is whether anyone will use it.
The different proprietary regimes that prevail in the software and
biotechnology contexts are important to consider in answering this
question. Both software code and biotechnology innovations are
protected under a mixture of licensing systems , but the primary one
in software is copyright, whereas in biotechnology it is patents. The
cost of patent protection can be substantial, whereas copyright
protection arises automatically and without cost to the owner. Also,
patent fees are usually at least partly recovered from licensees under
the remuneration clauses in a proprietary license.
Second, standardized licenses appear to be important for keeping
transaction costs low in open source software, but this approach may
be less applicable outside a digital context. Biotechnology
innovations are far more diverse in terms of composition than
software, which is essentially non-physical and instantly
reproducible. Defining rights in living biological materials, given
their capacity for self-replication and mutation, is difficult.
Determining what constitutes an improvement to a licensed biological
technology is also challenging. This aspect would be especially
critical in open source applications. As stated earlier, open source
licenses generally require that improvements to the technology be made
available to the other users. Naturally, this is far more difficult
when the medium is biological matter, as opposed to digital
information.
To explore how open source might translate into the biotechnology
context, it is necessary to characterize it in terms of generalized
principles, as distinct from software-specific features. Although it
is becoming a popular subject of study for people in many disciplines,
no unifying principle has yet emerged as the dominant approach. I have
chosen to view open source development through the lens of a
relatively new theory from the field of innovation management, known
as User Innovation Theory
"""
For those of you who don't know Bruce:
http://en.wikipedia.org/wiki/Bruce_Perens (do I have to remind anyone
that Wikipedia, itself, is licensed under the GFDL?)
"""
Bruce Perens is a computer programmer and advocate in the open source
community. He created the Open Source Definition and published the
first formal announcement and manifesto of open source.[1] He
co-founded the Open Source Initiative with Eric S. Raymond.[2] In
2005, Perens represented Open Source at the United Nations World
Summit on the Information Society, at the invitation of the United
Nations Development Program.[3] He has appeared before national
legislatures and is often quoted in the press, advocating for open
source and the reform of national and international technology policy.
"""
This part is also relevant:
http://rsss.anu.edu.au/~janeth/OSBiotech.html
"""
In the end, the proof for the viability open source biotechnology is
not tied to the ultimate success of open source software. Open source
software is simply the basis for an analogy—the seed of an idea rather
than a rigid formula for success."
(http://www.gene-watch.org/genewatch/articles/18-1Hope.html)
"""
http://p2pfoundation.net/Open_Science_Licenses
http://www.firstmonday.org/issues/issue12_6/burk/index.html
"""
Copyleft–style licensing has also been applied to physical materials,
such as the biological materials made available via the Biological
Innovation for Open Society project or "BIOS" (Boettiger and Burk,
2004). The BIOS project is intended to make publicly available certain
biological research tools and techniques, and to attract contributions
of further research tools. While the project organizers are not
adverse to users of these tools filing patents on discoveries made by
use of the tools, the intention is to preserve public access to the
tools themselves. The danger to such access comes from patenting of
improvements or modifications that users might make to the basic
tools, encumbering the basic tools with proprietary claims.
Internet–based electronic resources offer information about the tools
and their use, and facilitate contact for physical transfer of the
tools, but physical access is conditioned on agreement not to patent
any improvements or modifications to the tools, and to make any such
modifications or improvements available on the same terms. No such
restrictions are placed upon products or discoveries generated by use
of the tools; such products or discoveries can be patented without
limitation.
However, it is critical to recognize that such application of the open
source copyleft model to research data and other resources
contemplates a different intellectual property system — the patent
system — than the copyright system in which the licensing scheme was
developed. This transfer of the open source "copyleft" model from the
legal regime of copyright to that of patent presents several
difficulties. As an initial matter, it is worth observing that the
"open source" designation is something of a misnomer in the patent
context. Patents require as a condition for the grant of exclusive
rights a disclosure of the invention sufficient to allow one of skill
to make and use the claimed invention. As a practical matter, this
disclosure for software this may not always include source code; for
biotechnology, the disclosure typically does include macromolecular
sequence data. But in either case, the disclosure requirements of
patenting should effectuate the goal of the "open source" movement to
publish the technical data necessary to allow tinkering, improvement,
and critique of the invention.
Thus, at least in theory, the patent system already entails a level of
disclosure sufficient to allow the sort of access for tinkering and
improvement envisioned by the open source and free software movement.
But as a practical matter, such tinkering and improvement of the
disclosed invention may be effectively precluded by the exclusive
rights conferred under the patent. As mentioned above, some
jurisdictions provide little or no room in the patent system for
experimental use or reverse engineering. And, even if the details of
an invention are already made accessible in the patent, the use of the
term "open source" in this context may rather signal a philosophical
commitment to "openness" or "free" science paralleling that of the
free software movement.
Transfer of the copyleft licensing model to the patent environment
also raises legal considerations not present in a copyright
environment (Boettiger and Burk, 2004; Feldman, 2005). First, the
nature of the exclusive rights — granted by copyright and by patent —
are quite different. Copyright excludes unauthorized copying and
related activities — activities that are triggered by access to the
protected work. Such access serves as the trigger or activating event
for the copyleft license — copying or adapting the open source code
opens the copyist or adapter to a lawsuit unless the copying or
adapting is done in accordance with the terms of the license. But
patent rights exclude all uses of the claimed invention, even those
conducted independently, without any access to the invention. In such
cases, the infringing act would not serve to channel the infringer
into compliance with the terms of the license, as there would be no
knowledge, let alone manifestation of assent, to the license.
Second, the restrictions on further patenting that are incorporated
into some "open biology" licenses may run afoul of the general public
policy of the patent system. In the United States particularly,
federal statutory and constitutional law encourages patenting, and
licenses deterring patents may be preempted. Additionally, and perhaps
more seriously, patents raise competition law considerations that are
not necessarily present under copyright law. Certain types of patent
licensing arrangements are subject to extra antitrust scrutiny, such
as patent "pools," in which participants cross license one another's
patents, patent "grant–backs," which require licensing of technology
developed with a patented tool back to the patent owner, and patent
"reach–through," which requires payment of royalties to a patent owner
for products developed with a patented tool. Patenting restrictions in
open biology licenses resemble these types of arrangement — for
example, requiring products developed with "open source" biology tools
to be licensed back to others on an "open source" basis — and so may
raise antitrust concerns.
But the greatest obstacle to movement of "copyleft" licenses into
electronic research collaborations may be the social disparity between
the licenses' original open source milieu and that of scientific
research settings (Burk, 2005a). There are marked differences in the
organizational and institutional networks of each community. Despite
the some apparent congruence between the normative expectations in
each community, academic science as currently practiced, particularly
in industrialized nations, has a different and far more complicated
profile than that of the open source community. The scientific
community is older and more institutionally invested, with a decided
organizational structure not present in open source coding.
Despite its profession of "openness," academic science has an
effectively hierarchical organization at the level of individual
laboratories, as well as at the level of professional association.
Graduate and undergraduate training in the sciences also contributes a
distinct social sub–structure to the scientific community.
Additionally, academic science is heavily subsidized by governmental
grants, with the result that funding agencies may have interests and
involvement in the disposition of intellectual property, both at the
level of formal agency objectives and in the biases or preferences of
peer review committees. Other formal institutions, such as
institutional ethics review boards, university technology transfer
offices, and peer–review journal publishers may also play roles not
contemplated by the open source licensing system.
Such normative considerations may complicate the development of
licenses that would ameliorate the legal conflicts issues in
cyberinfrastructure. The success of the copyleft model in software
development is due in no small part to strong buttressing of the
license by the normative expectations of the community. In the broader
scientific context, it is unclear whether the license will have the
same status, the same social meaning, and the same success in a
different community setting.
"""
How likely is it that pharmaceutical companies would go open source?
http://p2pfoundation.net/Open_Source_Biotechnology#How_likely_is_it_that_pharmaceutical_companies_would_go_open_source.3F
"""
2. Established business practice: Pharmaceutical companies rely
heavily on patent positions - whether or not they have a patent on a
particular pharmaceutical product makes a big difference both to the
results of their operations in terms of the economics of selling
drugs, and to the company's valuation on the stock market; and this
translates into a big emphasis on IP, to a degree even in areas that
aren't really related to their proprietary position on their drug
products. In other words, not sharing IP is deeply ingrained. To a
large degree the biotech industry has inherited that culture of not
sharing. The costs of changing established business practice are very
real in terms of organisational structure and providing incentives for
your employees to shift the way they look at things - and so there is
plenty of inertia for large, established companies like the big pharma
companies when it comes to adopting fundamentally new business models
like open source.
"""
"""
1. One established use of open source business strategies in the
software context is to pre-empt the establishment of proprietary
technological standards owned by your rivals. Even though
pharmaceutical companies hate sharing, one thing they hate even more
is being beholden to a single supplier for some critical value driver.
This means they might be prepared to put money into an open source
biotech company that planned to come up with a really critical tool --
say a toxicology tool that would help predict R&D failures before a
drug hit the expensive clinical phase of development. This is a
significant example because currently, exclusive patent positions are
important to biotech start-ups largely as a way to attract capital. So
this kind of support would provide a credible alternative story for
biotech start-ups to tell potential investors and thus could promote
the development of open source strategies in the biotechnology sector.
"""
There's also a quote from Rob Carlson on that page--
http://synthesis.typepad.com/synthesis/2007/03/thoughts_on_ope.html
"""
When I first heard Drew Endy utter the phrase "Open Source Biology",
it was within the broader context of living in Berkeley, trying to
understand the future of biology as technology, and working in an
environment (the then embryonic Molecular Sciences Institute) that
encouraged thinking anything was possible. It was also within the
context of Microsoft's domination of the OS market, the general
technology boom in the San Francisco Bay area, the skyrocketing cost
of drug development coupled to a stagnation of investment return on
those dollars, and the obvious gap in our capabilities in designing
and building biological systems. OSB seemed the right strategy to get
to where I thought we ought to be in the future, which is to create
the ability to tinker effectively, perhaps someday even to engineer
biology, and to employ biology as technology for solving some of the
many problems humans face, and that humans have created.
As in 2000, I remain today most interested in maintaining, and
enhancing, the ability to innovate. In particular, I feel that safe
and secure innovation is likely to be best achieved through
distributed research and through distributed biological manufacturing.
By "Open Biology" I mean access to the tools and skills necessary to
participate in that innovation and distributed economy.
"Open source biology" and "open source biotechnology" are catchy
phrases, but they have little if any content for the moment. As
various non-profits get up and running (e.g., CAMBIA and the BioBrick
Foundation), some of the vagaries will be defined, and at least we
will have some structure to talk about and test in the real world.
When there is a real license a la the GPL, or the Lesser License, and
when it is finally tested in court we will have some sense of how this
will all work out.
I am by no means saying work should stop on OSB, or on figuring out
the licenses, just that I don't understand how it fits into helping
innovation at the moment. A great deal of the innovation we need to
see will not come from academia or existing corporations, but from
people noodling around in their garages or in start-ups yet to be
founded. These are the customers for Biobricks, these are the people
who want the ability to build biological systems without needing an
NIH grant."
"""
Of course, the Biobrick Foundation, iGEM, OpenWetWare, diybio and
other related initiatives have been seeing great growth since Rob
wrote that, so things are changing. :-) And for the agricultural side
of things, check this out:
"Researchers in Australia have devised a method of creating
genetically modified crops that does not infringe on patents held by
big biotechnology companies. The technique will be made available free
to others to use and improve, as long as any improvements are also
available free."
(http://business-times.asia1.com.sg/sub/views/story/0,4574,144880,00.html)
Open Source Biotechnology, from The Economist
http://www.economist.com/displaystory.cfm?story_id=2724420
"""
open-source approaches have emerged in biotechnology already. The
international effort to sequence the human genome, for instance,
resembled an open-source initiative. It placed all the resulting data
into the public domain rather than allow any participant to patent any
of the results. Open source is also flourishing in bioinformatics, the
field in which biology meets information technology. This involves
performing biological research using supercomputers rather than
test-tubes. Within the bioinformatics community, software code and
databases are often swapped on "you share, I share" terms, for the
greater good of all. Evidently the open-source approach works in
biological-research tools and pre-competitive platform technologies.
The question now is whether it will work further downstream, closer to
the patient, where the development costs are greater and the potential
benefits more direct. Open-source research could indeed, it seems,
open up two areas in particular. The first is that of non-patentable
compounds and drugs whose patents have expired. These receive very
little attention from researchers, because there would be no way to
protect (and so profit from) any discovery that was made about their
effectiveness. To give an oft-quoted example, if aspirin cured cancer,
no company would bother to do the trials to prove it, or go through
the rigmarole of regulatory approval, since it could not patent the
discovery. (In fact, it might be possible to apply for a process
patent that covers a new method of treatment, but the broader point
still stands.) Lots of potentially useful drugs could be sitting under
researchers' noses.
The second area where open source might be able to help would be in
developing treatments for diseases that afflict small numbers of
people, such as Parkinson's disease, or are found mainly in poor
countries, such as malaria. In such cases, there simply is not a large
enough market of paying customers to justify the enormous expense of
developing a new drug. America's Orphan Drug Act, which provides
financial incentives to develop drugs for small numbers of patients,
is one approach. But there is still plenty of room for
improvement—which is where the open-source approach might have a
valuable role to play.
"""
Open Bioinformatics Foundation
http://www.open-bio.org/
"""
The Open Bioinformatics Foundation is a non profit, volunteer run
organization focused on supporting open source programming in
bioinformatics. The foundation grew out of the volunteer projects
BioPerl, BioJava and BioPython and was formally incorporated in order
to handle our modest requirements of hardware ownership, domain name
management and funding for conferences and workshops.The Foundation
does not participate directly in the development or structure of the
open source work, but as the members of the foundation are drawn from
the member projects, there is clear commonality of direction and
purpose. Occasionally the O|B|F directors may make announcements about
our direction or purpose (a recent one was on the licensing of
academic software) when the board feels there is a need to clarify
matters, but in general we prefer to remain simply the administrative
support organization for our member projects.
Our main activities are:
Underwriting and supporting the BOSC conferences
Organizing and supporting developer-centric "hackathon" events
Managing our servers, colocation facilities, bank account & other assets
"""
Next up on the list is about open source biology, a big topic that we
last talked about at BioBarCamp 2008:
http://p2pfoundation.net/Open_Source_Biology
which contains a bit of a story of Drew and Rob's involvement from
which I'm excerpting:
"Since we ourselves depend on the information encoded in genetic
material," Endy explains, "we should work together to share genetic
information."
http://www.eastbayexpress.com/2005-03-30/news/steal-this-genome/
"""
They also made a plea on behalf of public safety; there's no way any
federal law can ensure that someone doesn't create an organism that,
as Brent puts it, "liquefies Cincinnati." Rather than trying to keep
secret, for example, the genome of a potential bioterror agent, the
institute crew concluded that it's better to empower as many people as
possible to develop countermeasures such as new drugs and vaccines.
"Consider that the only effective counterterrorism measures on
September 11, 2001 were made by the passengers of Flight 93," Brent
says.
Carlson, Endy, and Brent all agree that the best way to keep tabs on
the potential dangers brewing in labs was to share information. "The
only way the shit doesn't hit the fan is if everybody engineering
biology does so in the open," Endy says. "We're co-opting the idea
from open-source software that 'many eyes lead to few bugs.' In other
words, I don't trust you not to make any mistakes the next time you
program a piece of DNA. You shouldn't trust me."
"""
Rob still contrasting on parallels (or lack thereof) between
biological freedom and software freedom:
http://web.archive.org/web/20010412011122/http://www.intentionalbiology.org/osb.html
"What does 'ownership' mean when property is infinitely reduplicable,
highly malleable, and the surrounding culture has neither coercive
power relationships nor material scarcity economics?" -Eric S Raymond,
Homesteading the Noosphere.
"""
The biohacker community will emerge as DNA manipulation technology
decreases in cost and when the overall technological infrastructure
enables instruments to be assembled in the garage. The Molecular
Sciences Institute has a parallel DNA synthesizer that can synthesize
sufficient DNA to build a human pathogenic virus from scratch in about
a week. Assembled, this machine cost ~$100,000 about 18 months ago. We
estimate the parts could be purchased for ~$10,000 today. A working
DNA synthesizer could be built with relative ease. Synthesizers of
this sort produce ~50 mers, and it is likely that methods to assemble
these short oligos into chromosomes will be perfected relaltively
soon. Hobbyists often spent similar sums on cars, motocycles,
computers, and aquariums. <snip>
It is not that we expect (or desire) open-source biology to share the
various shades of anti-commercial bent which exist in the software
community, but rather that the future of a likely distributed
biological research effort implies significant changes in the way we
view commercial efforts. Rather than send samples through the mail,
sequences will be transferred electronically between researchers and
directly into DNA synthesizers. Biological manufacturing will be
everywhere, making irrelevant standard notions of centralized
production, and the real economy will be of design and infrastructure.
(v.01, Rob Carlson Copyright 2000, 12/10/2000) <snip>
One aspect of hacker culture that is highly relevant to Open-Source
Biology is the general disapproval of "hoarding." The concentration
and segregation of technology and standards by particular actors
(companies, in this instance) is viewed as simply greedy and as
retarding the development and acceptance of improved technology.
The explicit goal of companies is, of course, to make money. However,
when it comes to a technology that can directly influence the
organisms that humans rely on for food and shelter there should be
great concern in the concentration of power by any given organization.
Moreover, the intervening period between when we can genetically alter
organisms and the time when we know what we are doing and can fix
mistakes (that time period is right now) should be made as short as
possible. We should move with all haste to ensure that biological
technology moves as rapidly as possible and is disseminated as widely
as possible.
In Homesteading the Noosphere, Eric Raymond makes the interesting
point that the cracker culture maintains itself in a very different
fashion than the hacker culture, and develops differently as a result.
In the cracker culture, process and programming knowledge is closely
guarded, and Raymond suggests that this impedes the growth of
knowledge. In contrast, "in the hacker community, one's work is one's
statement. The best craftsmanship wins. Thus, the hacker culture's
knowledge base increases rapidly." In other words, the cracker culture
condones a form of 'hoarding' and knowledge disperses slowly as a
result. It is clear that the hacker community is a far better model
for those interested in moving biology forward as quickly as possible.
(v.01, Rob Carlson Copyright 2000, 12/10/2000)
"""
Open Source Drug Discovery program (officially mandated by the govt.
of India, ~$34 million USD)
http://osdd.org/
http://p2pfoundation.net/Open_Source_Drug_Discovery
There's enough news links from the osdd.org front page to get a feel
for their Tuberculosis-oriented program. OSDD is very recent and very
big news for the pharmaceutical sector, I've joined and been
contributing and there's been talk with the manufacturing guys about
how to implement some of the tech they've been thinking up.
http://p2pfoundation.net/Open_Biology
http://www.forbes.com/2007/02/12/novartis-genes-diabetes-research-biz-cz_mh_0212novartis.html
"""
There was a time when drug giants tried to keep leads like that to
themselves in an attempt to gain an advantage over their competitors.
They paid lots of money for the privilege, too. In 1993,
GlaxoSmithKline tied up with Human Genome Sciences to develop drugs
based on genome data. Five years later, Bayer spent $465 million to
get access to the genetic library being assembled by Millennium
Pharmaceuticals. Neither collaboration has led to a marketed drug. But
another requirement of making the leap from genes to drugs is making
the research public--a step that will make it difficult for
researchers elsewhere to patent any of this raw genetic information.
Novartis isn't the only drug firm embracing this "give it away for
free" mentality. Pfizer has promised to make available for free a
swath of genetic information emerging from a three-year collaboration
with the National Institutes of Health."
Also: Open Source methods are increasingly being used as a mechanism
to organise drug discovery. Examples include the Medicines for Malaria
Venture (MMV), the Global Alliance for TB Drug Development (TB
Alliance) and the Institute of One World Health (IOWH).
"""
"""
Robb Carlson argues that since the cost of biological production is
going down, and the risks of unintentional spreading of pathogens is
going to increase, then only further openness can work as security
strategy, as has already been demonstrated in the fruitless attempts
to curtain P2P Filesharing.
"""
On security:
http://www.kurzweilai.net/meme/frame.html?main=/articles/art0614.html?
(Kurzweil wrote "The Singularity is Near")
"""
The real threat from distributed biological technologies lies neither
in their development nor use, per se, but rather that biological
systems may be the subject of accidental or intentional modification
without the knowledge of those who might be harmed. Because this may
include significant human, animal, or plant populations, it behooves
us to maximize our knowledge about what sort of experimentation is
taking place around the world. Unfortunately (though understandably),
the first response to incidents such as the anthrax attacks in the
fall of 2001 is to attempt to improve public safety through means that
paradoxically often limit our capabilities to gather such information.
Some view as an immediate threat the proliferation of technologies
useful in manipulating biological systems: Passionate arguments are
being made that research should be slowed and that some research
should be avoided altogether. "Letting the genie out of the bottle" is
a ubiquitous concern, one that has been loudly voiced in other fields
over the years and is meant to set off alarm bells about biological
research.
A favorite rhetorical device in this discussion is the comparison of
nuclear technologies with biological technologies. Success in limiting
the development and spread of nuclear technologies is taken to mean
similar feats are possible with biological technologies. But this sort
of argument fails to consider the logistical, let alone ethical,
differences between embargoing raw fissionable materials used in
nuclear or radiological weapons and embargoing biological technology
or even biology itself.
Regulation of the development of nuclear weapons has been successful
only because access to raw fissionable materials has, fortunately,
been relatively easy to restrict. However, both the knowledge and
tools necessary to construct rudimentary weapons have for decades been
highly distributed. It is arguable that, with some effort,
construction of a rudimentary nuclear device is within the
capabilities of most physics and engineering college graduates who
have access to a basic machine shop. Building nuclear devices is thus
theoretically quite feasible but physically difficult, even for the
knowledgeable, because the raw materials are simply not available. Yet
the raw stuff of biology has always been readily at hand, and our
schools and industries are now equipping students with the skills to
manipulate biological systems through powerful and distributed
technology. Because skills are already widespread and will only become
more so, altering and reverse engineering biological systems will
become both easier and more common. Regulation can do little to alter
this trend.
If strict regulation held promise of real protection, it would be well
worth considering. But regulation is inherently leaky, and it is more
often a form of management than blanket prohibition. Certainly no
category of crime has ever been eliminated through legal prohibition.
In this light, we must ask how many infringements of potential
regulation of biological technologies we are willing to risk. Further,
will the threat of sanctions such as imprisonment ever be enough to
dissuade infringement? Given the potential damage wrought by misuses
of the technology, we may never be satisfied that such sanctions would
constitute a repayment of debt to society, the fundamental tenet of
our criminal justice system. The damages may always exceed any
punishment meted out to those deemed criminal. These considerations
come down to how we choose to balance the risks and consequences of
infringement against whatever safety may be found in regulation and
attempts at enforcement. More important than this tenuous safety,
however, is the potential danger of enforced ignorance. In the end, we
must decide not whether we are willing to risk damages caused by
biological technology, but whether limiting the general direction of
biological research in the coming years will enable us to deal with
the outcome of mischief or mistake. We must decide if we are willing
to take the risk of being unprepared.
There are currently calls to limit research in the United States on
the basic biology of many pathogens to preempt their use as
bioweapons,22 and the possession and transport of many pathogens was
legislated into criminality by the Patriot Act.23 The main difficulty
with this approach is not that it assumes the basic biology of
pathogens is static—which because of either natural variation or human
intervention it is not—but rather that it assumes we have already
catalogued all possible natural pathogens, that we already know how to
detect and defeat known and unknown pathogens, and that rogue elements
will not be able to learn how to manipulate pathogens and toxins on
their own. These assumptions are demonstrably false. Pathogens ranging
from HIV to M. tuberculosis to P. falciparum (which causes malaria)
have successfully evolved to escape formerly effective treatments. New
human pathogens are constantly emerging, which as in the case of SARS
might be identified quickly but require much longer to develop
treatments against. In the last century governments and independent
organizations alike have developed and used biological weapons.
Restricting our own research will merely leave us less prepared for
the inevitable emergence of new natural and artificial biological
threats. Moreover, it is naive to think we can successfully limit
access to existing pertinent information within our current economic
and political framework.
As is clear from recent efforts to limit peer-to-peer file sharing on
the Internet, in today's environment strict prohibition of information
flow can only be achieved by quarantine—unplugging wires and blocking
wireless transmission. Thwarted by the difficulty of such endeavors,
music conglomerates have resorted to flooding file servers with
corrupted files (camouflage),24 and requesting the legal authority to
engage in preemptive cracking of file trader's computers (sabotage).25
Neither strategy is likely to be a long term solution of controlling
information for the music industry, and similar efforts to regulate
biological technologies are bound to be more difficult still.
Attempting to maintain control of information and instrumentation will
be a futile task in light of the increasingly sophisticated biological
technologies blossoming around the world."
"""
Rob Carlson on what needs to be done for a secure open biology approach
"""
We should focus on three challenges:
1) We should resist the impulse to restrict research and the flow of
information. Ignorance will help no one in the event of an emergent
threat and, given the pace and proliferation of biological
technologies, the likelihood of threats will increase in coming years.
Among the greatest threats we face is that potentially detrimental
work will proceed while we sit on our hands. If we are not ourselves
pushing the boundaries of what is known about how pathogens work or
ways to manipulate them, we are by definition at a disadvantage. Put
simply, it will be much easier to keep track of what is in the wind if
we don't have our heads in the sand.
2) The best way to keep apprised of the activities of both amateurs
and professionals is to establish open networks of researchers,
perhaps modeled on the Open Source Software (OSS) movement, and
potentially sponsored by the government during their embryonic phases.
The Open Source development community thrives on constant
communication and plentiful free advice. This behavior is common
practice for professional biology hackers, and it is already evident
on the Web amongst amateur biology hackers.14 This represents an
opportunity to keep apprised of current research in a distributed
fashion. Anyone trying something new will require advice from peers
and may advertise at least some portion of the results of their work.
As is evident from the ready criticism leveled at miscreants in online
forums frequented by software developers (Slashdot, Kuro5hin, etc.),
people are not afraid to speak out when they feel the work of a
particular person or group is substandard or threatens the public
good. Thus our best potential defense against biological threats is to
create and maintain open networks of researchers at every level,
thereby magnifying the number of eyes and ears keeping track of what
is going on in the world.
3) Because human intelligence gathering is, alas, demonstrably
inadequate for the task at hand, we should develop technology that
enables pervasive environmental monitoring. The best way to detect
biological threats is using biology itself, in the form of genetically
modified organisms. Unlike the production and deployment of chemical
weapons or fissile materials, which can often be monitored with remote
sensing technologies such as aerial and satellite reconnaissance, the
initial indication of biological threats may be only a few cells or
molecules. This small quantity may already be a lethal dose and can be
very hard to detect using physical means. Alternatively, "surveillance
bugs" distributed in the environment could transduce small amounts of
cells or molecules into signals measurable by remote sensing. The
organisms might be modified to reproduce in the presence of certain
signals, to change their schooling or flocking behavior, or to alter
their physical appearance. Candidate "detector platforms" span the
range of bacteria, insects, plants, and animals. Transgenic
zebrafish34 and nematodes35 have already been produced for this
purpose, and there is some progress in producing a generalized system
for detecting arbitrary molecules using signal transduction pathways
in bacteria.
None of these recommended goals will be trivial to accomplish.
Considerable sums have already been spent over the last five decades
to understand biological systems at the molecular level, much of this
in the name of defeating infectious disease. While this effort has
produced considerable advances in diagnosing and treating disease, we
should now redouble our efforts. We have entered an era when the
ability to modify biological systems is becoming widespread in the
absence of an attendant ability to remediate potential mistakes or
mischief. Maintaining safety and security in this context will require
concerted effort, and an immediate, focused governmental R&D
investment would be a good start. Although "bug to drug in twenty four
hours" sounds much flashier than "bug to drug in six to eight weeks,"
the latter is the more realistic timeline to shoot for—even if it is a
decade or more away—and this goal may serve as an organizational focus
for an endeavor organized and sponsored by the government.
"""
Some related links:
http://del.icio.us/mbauwens/Open-Biology
http://www.bios.net/daisy/bios/15
http://www.wired.com/news/medtech/0,1286,66545,00.html
http://www.wired.com/news/medtech/0,1286,66289,00.html
http://www.worldchanging.com/archives/002893.html
http://opensource.mit.edu/papers/rai.pdf (Open and Collaborative
Biomedical Research: Theory and Evidence, Rai Arti.)
and then all of the wonderful open access journals :-) like
http://biomedcentral.com/home/ and PLoS Biology etc.
Then there's also the issue of genomics:
http://p2pfoundation.net/Open_Genomics
http://genomics.org/ and the $0 Genomics Project, plus lots of other tools
http://polonator.org/
"""
To usher in the dawn of truly personalized medicine, and accurately
tease apart the confluence of factors determining human pathology, it
will be necessary (albeit not sufficient) that large numbers of
reliable, high-throughput second-generation sequencers be installed
and operated. We have identified the upfront and recurring cost of
second-generation sequencing as key factors inhibiting their rate of
adoption, and have assiduously sought to drive these as low as
possible. At the same time, throughput, accuracy, and reliability have
been the focus of relentless development efforts.
A key differentiator in our approach to second-generation sequencing
is our embrace of a flexible, open source development model. The
system's operating software is fully documented and freely available
for public download, as are the protocols and reagent sets. All
aspects of the system are fully programmable, with parameters and
sequences accessible and modifiable by its users to improve and extend
the instrument. In addition, all subsystems are highly modular and
easily upgraded and/or retrofitted; as a result, we fully anticipate
that the instrument will evolve and improve over time. We expect a
worldwide user community to develop and flourish, advancing both the
design and the operational specifics of the platform, from which all
users in turn will benefit.
"""
Implications on health reform:
http://www.designcouncil.info/mt/RED/health/
http://p2pfoundation.net/Open_Health
http://p2pfoundation.net/Open_Notebook_Science
http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
"""
To clear up confusion, I will use the term Open Notebook Science,
which has not yet suffered meme mutation. By this I mean that there is
a URL to a laboratory notebook (like this) that is freely available
and indexed on common search engines. It does not necessarily have to
look like a paper notebook but it is essential that all of the
information available to the researchers to make their conclusions is
equally available to the rest of the world. Basically, no insider
information.
"""
IIRC, openwetware.org includes some "open notebooks" on the wiki from
iGEM participants and other research teams.
Also, open access research has been hitting a high note recently.
http://en.wikipedia.org/wiki/Open_access
"""
Open access (OA) or open access publishing is the publication of
material in such a way that it is available to all potential users
without financial or other barriers. An open access publisher is a
publisher producing such material. Many types of material can be
published in this manner: scholarly journals, known specifically as
open access journals, magazines and newsletters, e-text or other
e-books (whether scholarly, literary, or recreational), music, fine
arts, or any product of intellectual activity. In this context,
non-open access distribution is called "toll access" or "subscription
access".
"""
Also in the news, NIH has been going open access:
http://slashdot.org/article.pl?sid=07/12/27/0219228
http://science.slashdot.org/article.pl?sid=07/11/07/2318208
http://science.slashdot.org/article.pl?sid=04/08/06/1225211&tid=134&tid=103
http://yro.slashdot.org/article.pl?sid=07/03/02/0158208
PLoS is a life-saver, and so are the many, many other open access
preprint archives available through the web. Everyone on this list is
probably familiar with pubmedcentral, or pubget.com, and in general
see these lists-
http://heybryan.org/mediawiki/index.php/List_of_bioinformatics_databases
http://web.archive.org/web/20020206160321/http://gwu.edu/~gprice/science.htm
http://www.freepint.com/gary/direct.htm
http://slashdot.org/comments.pl?sid=239163&cid=19595767
.. there are many, many databases that I have been unable to recall
and cite all at once, so if anyone ever needs to find a paper or look
up some piece of information, there's more open access and free
databases than I can recall, and the proprietary stuff is also
available to almost anybody with a community college library
subscription or otherwise a university enrollment/faculty status.
http://p2pfoundation.net/Openness_in_Science
http://blog.openwetware.org/scienceintheopen/2008/09/30/a-personal-view-of-open-science-part-i/
""" (summarizing)
1. Science is traditionally an open endeavour
2. The internet/web potentially increases the openness
3. This potential is under-used
4. An advocacy movement is needed
"""
So, now for some licensing stuff. For the run down on GNU, the free
software movement, open source licenses, then there's an excellent
video that has been produced called "Revolution OS" and it's available
on Google Video:
http://video.google.com/videosearch?q=revolution+os&emb=0#
(w/ Richard Stallman (RMS), Eric S Raymond (ESR), Linus Torvalds,
Bruce Perens, ...)
http://p2pfoundation.net/Open_Licenses
http://creativecommons.org/
http://sciencecommons.org/
http://en.wikipedia.org/wiki/Science_Commons
"Creative Commons provides free tools that let authors, scientists,
artists, and educators easily mark their creative work with the
freedoms they want it to carry. You can use CC to change your
copyright terms from "All Rights Reserved" to "Some Rights Reserved."
We're a nonprofit organization. Everything we do — including the
software we create — is free."
"Science Commons designs strategies and tools for faster, more
efficient web-enabled scientific research. We identify unnecessary
barriers to research, craft policy guidelines and legal agreements to
lower those barriers, and develop technology to make research, data
and materials easier to find and use. Our goal is to speed the
translation of data into discovery — unlocking the value of research
so more people can benefit from the work scientists are doing."
Quick video on Science Commons:
http://sciencecommons.org/about/science-commons-dylan-video/
And again the "Revolution OS" video:
http://video.google.com/videosearch?q=revolution+os&emb=0#
And there are many more of interest on http://ted.com/ (and its little
(free) brother: http://bilconference.com/ )
And then there's the open manufacturing group that has been exploring
some of these issues, like biotech, but also in terms of machine
shops, kinematic self-replicating machines, advanced automation, etc.,
in terms of open source hardware and shared design initiatives:
http://openmanufacturing.net/
http://groups.google.com/group/openmanufacturing
http://p2pfoundation.net/Product_Hacking for a list of many open
hardware projects. A quick glance shows that there are vehicles,
microprocessors, DNA synthesizers, most of everything from the Maker
community, instructables, etc.
Open Design Foundation
http://www.opendesign.org/
"The mission of the Open Design Foundation is to promote an
alternative method for designing and developing technology, based on
the free exchange of comprehensive design information. The Open Design
Foundation provides the collaborative space to foster open source
physical design, and seeks to strike a balance between the
independence of individual designers and the collective power of
collaboration. The Open Design Foundation hopes that this method will
enable and promote design projects, which are motivated by personal
conviction and passion of designers for the greater benefit of a
global society."
Debian Social Contract
http://www.debian.org/social_contract
http://en.wikipedia.org/wiki/Debian_Social_Contract
Ubuntu Code of Conduct
http://www.ubuntu.com/community/conduct
"""
Ubuntu is an African concept of 'humanity towards others'. It is 'the
belief in a universal bond of sharing that connects all humanity'. The
same ideas are central to the way the Ubuntu community collaborates.
Members of the Ubuntu community need to work together effectively, and
this code of conduct lays down the "ground rules" for our cooperation.
We chose the name Ubuntu for our distribution because we think it
captures perfectly the spirit of the sharing and cooperation that is
at the heart of the open source movement. In the Free Software world,
we collaborate freely on a volunteer basis to build software for
everyone's benefit. We improve on the work of others, which we have
been given freely, and then share our improvements on the same basis.
That collaboration depends on good relationships between developers.
To this end, we've agreed on the following code of conduct to help
define the ways that we think collaboration and cooperation should
work.
If you wish to sign the code of conduct, you can sign the canonical copy online.
"""
Open Source Definition
http://www.opensource.org/docs/definition.php
Summarized, the "open source definition" is generally:
"""
1. Free Redistribution
2. Source Code [how it's done]
3. Derived Works
4. Integrity of The Author's Source Code
5. No Discrimination Against Persons or Groups
6. No Discrimination Against Fields of Endeavor
7. Distribution of License
8. License Must Not Be Specific to a Product
9. License Must Not Restrict Other Software
10. License Must Be Technology-Neutral
"""
Another good book to read on these subjects is Two Bits:
http://twobits.net/about/
"In Two Bits, Christopher M. Kelty investigates the history and
cultural significance of Free Software, revealing the people and
practices that have transformed not only software, but also music,
film, science, and education."
and: "Free Software is a set of practices devoted to the collaborative
creation of software source code that is made openly and freely
available through an unconventional use of copyright law. Kelty shows
how these specific practices have reoriented the relations of power
around the creation, dissemination, and authorization of all kinds of
knowledge after the arrival of the Internet. Two Bits also makes an
important contribution to discussions of public spheres and social
imaginaries by demonstrating how Free Software is a "recursive public"
public organized around the ability to build, modify, and maintain the
very infrastructure that gives it life in the first place."
Alright, that feels like enough for at least one book to elaborate on,
so is probably a good stopping point. And to think that I haven't
included any sources explaining the importance of debian ("$10 billion
worth of work" - for free - over 20,000 free software packages,
apt-get, repositories, etc.), or works like Andreas Lloyd's
anthropological exploration into the ubuntu user community.
bioj...@gmail.com
Do you believe that the patent system should be abolished?
Interesting to note that the patent system is established directly
under Article 1, Section 8 of the Constitution giving "authors and
inventors the exclusive right to their respective writings and
discoveries." Thomas Jefferson was one of the leaders of the patent
office when it was first established, but I was surprised to learn
that he had misgivings about the system.
http://www.earlyamerica.com/review/winter2000/jefferson.html
Most of the great technologies developed in the United States have
been associated with patents - including Morse's telegraph - who tried
to patent every mode of transmitting an EM signal over distance
(see http://www6.miami.edu/ethics/jpsl/archives/all/gene.pdf). I
supposed that would have covered the Internet, had it been granted.
But, you can see, that patent "abuse" is not something hat has
recently been "invented" but has been around for as long as there have
been patents in the US. Bell's telephone, Edison's electric light,
and many other pioneering inventions have been patented.
Is open source based on altruistism or mistrust.
You quoted Drew Endy as saying "I don't trust you not to make any
program a piece of DNA. You shouldn't trust me."
community embrace the same standard. It doesn't have to be all or
nothing. But, rather patent wisely, without over-reaching, share the
royalties, and let academic non-profit researchers use it for true
academic purposes. This idea is not new. I believe that Stanford now
includes a clause in their licenses which reserves rights in the
patented technology for academic purposes.
I wonder, though, if some of the allegations about the adverse effects
of patents are not over-stated. It's very easy to hypothesize that
stacking patent rights will escalate the cost of doing research and
making new discoveries - but where's the evidence? As I recall, there
are not many real examples, just a lot of talk. This is one of the
reason why I established the Mercantile Gene (http://mercantile-
gene.wikidot.com/)
One way in which the courts are policing patents is by re-evaluating
the standards under which inventions can be patented. There are two
recent Federal Circuit cases and a Supreme court case (KSR) that have
raised the patentability bar and limited the type of subject matter
that can be patented. In In re Bilski, the Federal Circuit put a
brake on so-called business method patents.
From Patently-O (http://www.patentlyo.com/patent/2008/10/in-re-
bilski.html)
"The Federal Circuit has affirmed the PTO's Board of Patent Appeals
(BPAI) finding that Bilski's claimed invention (a method of hedging
risks in commodities trading) does not satisfy the patentable subject
matter requirements of 35 U.S.C. § 101. In doing so, the nine-member
majority opinion (penned by Chief Judge Michel) spelled out the
"machine-or-transformation" test as the sole test of subject matter
eligibility for a claimed process."
On Dec 29 2008, 9:06 pm, "Bryan Bishop" <kanz...@gmail.com> wrote:
> Hi all,
>
> I don't think we've ever gone explicitly over the idea of the
> debian/ubuntu social contracts, and how those concepts might be useful
> in pursuing our shared interests as diybio grows. From what I saw at
> BioBarCamp 2008, where many of us found each other in person, there's
> a lot of positive effort and energy being channeled in these
> directions, so the very least I can do is document a little bit of it
> from all over the web. This is a draft at best, so go easy on me :-).
>
> This email is more like a safari tour through some relevant portions
> of the internet that are of interest to diybio and maybe developing
> 'contracts', so if somebody else wants to write something more
> coherent, go ahead- this is more like bibliography material, but also
> interesting for those who don't know about these developments. With
> some annotation and running commentary :-). I hope others comment on
> some of these excerpts.
>
> ((At the bottom and very end is the debian and ubuntu social contracts
> or codes of conduct for an example, but it's best taken in context
> with everything else in this email)). (((This is also re: IP law and
> some other recent topics on the list.)))
>
> http://p2pfoundation.net/Open_Source_Biotechnologyhttp://rsss.anu.edu.au/~janeth/http://rsss.anu.edu.au/~janeth/OpenSourceBiotechnology27July2005.pdf(thesis)
> """
> movement, initiated in the early 1980s in response to restrictive
> copyright licensing practices adopted by commercial software
> discouraging commercial involvement in their development.
>
> "When I spoke to Bruce Perens, who helped define the basis foropen
> source development in his aptly titled document, TheOpenSource
> it is a form of social engineering. There is no question that one
>
> The different proprietary regimes that prevail in the software and
> biotechnology contexts are important to consider in answering this
> question. Both software code and biotechnology innovations are
> protected under a mixture of licensing systems , but the primary one
> in software is copyright, whereas in biotechnology it is patents. The
> cost of patent protection can be substantial, whereas copyright
> protection arises automatically and without cost to the owner. Also,
> patent fees are usually at least partly recovered from licensees under
> the remuneration clauses in a proprietary license.
>
> Second, standardized licenses appear to be important for keeping
> innovations are far more diverse in terms of composition than
> software, which is essentially non-physical and instantly
> reproducible. Defining rights in living biological materials, given
> their capacity for self-replication and mutation, is difficult.
> Determining what constitutes an improvement to a licensed biological
> technology is also challenging. This aspect would be especially
> critical inopensource applications. As stated earlier,opensource
> licenses generally require that improvements to the technology be made
> available to the other users. Naturally, this is far more difficult
> when the medium is biological matter, as opposed to digital
> information.
>
> principles, as distinct from software-specific features. Although it
> is becoming a popular subject of study for people in many disciplines,
> no unifying principle has yet emerged as the dominant approach. I have
> as User Innovation Theory
> """
>
> For those of you who don't know Bruce:http://en.wikipedia.org/wiki/Bruce_Perens (do I have to remind anyone
> that Wikipedia, itself, is licensed under the GFDL?)
> """
> Bruce Perens is a computer programmer and advocate in theopensource
> 2005, Perens representedOpenSource at the United Nations World
> Nations Development Program.[3] He has appeared before national
> legislatures and is often quoted in the press, advocating foropen
> source and the reform of national and international technology policy.
> """
>
> This part is also relevant:http://rsss.anu.edu.au/~janeth/OSBiotech.html
> """
> software is simply the basis for an analogy—the seed of an idea rather
> than a rigid formula for success."
> (http://www.gene-watch.org/genewatch/articles/18-1Hope.html)
> """
>
> Copyleft–style licensing has also been applied to physical materials,
> such as the biological materials made available via the Biological
> biological research tools and techniques, and to attract contributions
> of further research tools. While the project organizers are not
> adverse to users of these tools filing patents on discoveries made by
> use of the tools, the intention is to preserve public access to the
> tools themselves. The danger to such access comes from patenting of
> improvements or modifications that users might make to the basic
> tools, encumbering the basic tools with proprietary claims.
> Internet–based electronic resources offer information about the tools
> and their use, and facilitate contact for physical transfer of the
> tools, but physical access is conditioned on agreement not to patent
> any improvements or modifications to the tools, and to make any such
> modifications or improvements available on the same terms. No such
> restrictions are placed upon products or discoveries generated by use
> of the tools; such products or discoveries can be patented without
> limitation.
>
> However, it is critical to recognize that such application of theopen
> source copyleft model to research data and other resources
> contemplates a different intellectual property system — the patent
> system — than the copyright system in which the licensing scheme was
> difficulties. As an initial matter, it is worth observing that the
> rights a disclosure of the invention sufficient to allow one of skill
> to make and use the claimed invention. As a practical matter, this
> disclosure for software this may not always include source code; for
> biotechnology, the disclosure typically does include macromolecular
> sequence data. But in either case, the disclosure requirements of
> and critique of the invention.
>
> Thus, at least in theory, the patent system already entails a level of
> disclosure sufficient to allow the sort of access for tinkering and
> disclosed invention may be effectively precluded by the exclusive
> rights conferred under the patent. As mentioned above, some
> jurisdictions provide little or no room in the patent system for
> experimental use or reverse engineering. And, even if the details of
> an invention are already made accessible in the patent, the use of the
> free software movement.
>
> Transfer of the copyleft licensing model to the patent environment
> also raises legal considerations not present in a copyright
> environment (Boettiger and Burk, 2004; Feldman, 2005). First, the
> nature of the exclusive rights — granted by copyright and by patent —
> are quite different. Copyright excludes unauthorized copying and
> related activities — activities that are triggered by access to the
> protected work. Such access serves as the trigger or activating event
> adapting is done in accordance with the terms of the license. But
> patent rights exclude all uses of the claimed invention, even those
> conducted independently, without any access to the invention. In such
> cases, the infringing act would not serve to channel the infringer
> into compliance with the terms of the license, as there would be no
> knowledge, let alone manifestation of assent, to the license.
>
> Second, the restrictions on further patenting that are incorporated
> federal statutory and constitutional law encourages patenting, and
> licenses deterring patents may be preempted. Additionally, and perhaps
> more seriously, patents raise competition law considerations that are
> not necessarily present under copyright law. Certain types of patent
> licensing arrangements are subject to extra antitrust scrutiny, such
> as patent "pools," in which participants cross license one another's
> patents, patent "grant–backs," which require licensing of technology
> developed with a patented tool back to the patent owner, and patent
> "reach–through," which requires payment of royalties to a patent owner
> example, requiring products developed with "opensource" biology tools
> to be licensed back to others on an "opensource" basis — and so may
>
> But the greatest obstacle to movement of "copyleft" licenses into
> electronic research collaborations may be the social disparity between
> organizational and institutional networks of each community. Despite
> the some apparent congruence between the normative expectations in
> each community, academic science as currently practiced, particularly
> in industrialized nations, has a different and far more complicated
> Despite its profession of "openness," academic science has an
> effectively hierarchical organization at the level of individual
> laboratories, as well as at the level of professional association.
>
> Graduate and undergraduate training in the sciences also contributes a
> distinct social sub–structure to the scientific community.
> Additionally, academic science is heavily subsidized by governmental
> grants, with the result that funding agencies may have interests and
> involvement in the disposition of intellectual property, both at the
> level of formal agency objectives and in the biases or preferences of
> peer review committees. Other formal institutions, such as
> institutional ethics review boards, university technology transfer
> offices, and peer–review journal publishers may also play roles not
> Such normative considerations may complicate the development of
> licenses that would ameliorate the legal conflicts issues in
> cyberinfrastructure. The success of the copyleft model in software
> development is due in no small part to strong buttressing of the
> license by the normative expectations of the community. In the broader
> scientific context, it is unclear whether the license will have the
> same status, the same social meaning, and the same success in a
> different community setting.
> """
>
> 2. Established business practice: Pharmaceutical companies rely
> heavily on patent positions - whether or not they have a patent on a
> particular pharmaceutical product makes a big difference both to the
> results of their operations in terms of the economics of selling
> drugs, and to the company's valuation on the stock market; and this
> translates into a big emphasis on IP, to a degree even in areas that
> aren't really related to their proprietary position on their drug
> products. In other words, not sharing IP is deeply ingrained. To a
> large degree the biotech industry has inherited that culture of not
> sharing. The costs of changing established business practice are very
> real in terms of organisational structure and providing incentives for
> your employees to shift the way they look at things - and so there is
> plenty of inertia for large, established companies like the big pharma
> companies when it comes to adopting fundamentally new business models
> likeopensource.
> """
>
> """
> technological standards owned by your rivals. Even though
> pharmaceutical companies hate sharing, one thing they hate even more
> is being beholden to a single supplier for some critical value driver.
> This means they might be prepared to put money into anopensource
> biotech company that planned to come up with a really critical tool --
> say a toxicology tool that would help predict R&D failures before a
> drug hit the expensive clinical phase of development. This is a
> significant example because currently, exclusive patent positions are
> important to biotech start-ups largely as a way to attract capital. So
> this kind of support would provide a credible alternative story for
> biotech start-ups to tell potential investors and thus could promote
> """
>
> There's also a quote from Rob Carlson on that page--http://synthesis.typepad.com/synthesis/2007/03/thoughts_on_ope.html
> """
> When I first heard Drew Endy utter the phrase "OpenSource Biology",
> understand the future of biology as technology, and working in an
> environment (the then embryonic Molecular Sciences Institute) that
> encouraged thinking anything was possible. It was also within the
> context of Microsoft's domination of the OS market, the general
> technology boom in the San Francisco Bay area, the skyrocketing cost
> of drug development coupled to a stagnation of investment return on
> those dollars, and the obvious gap in our capabilities in designing
> and building biological systems. OSB seemed the right strategy to get
> to where I thought we ought to be in the future, which is to create
> the ability to tinker effectively, perhaps someday even to engineer
> biology, and to employ biology as technology for solving some of the
> many problems humans face, and that humans have created.
>
> As in 2000, I remain today most interested in maintaining, and
> enhancing, the ability to innovate. In particular, I feel that safe
> and secure innovation is likely to be best achieved through
> distributed research and through distributed biological manufacturing.
>
> international effort to sequence the human genome, for instance,
> performing biological research using supercomputers rather than
> test-tubes. Within the bioinformatics community, software code and
> databases are often swapped on "you share, I share" terms, for the
> The question now is whether it will work further downstream, closer to
> the patient, where the development costs are greater and the potential
> little attention from researchers, because there would be no way to
> protect (and so profit from) any discovery that was made about their
> effectiveness. To give an oft-quoted example, if aspirin cured cancer,
> no company would bother to do the trials to prove it, or go through
> the rigmarole of regulatory approval, since it could not patent the
> discovery. (In fact, it might be possible to apply for a process
> patent that covers a new method of treatment, but the broader point
> still stands.) Lots of potentially useful drugs could be sitting under
> researchers' noses.
>
> people, such as Parkinson's disease, or are found mainly in poor
> countries, such as malaria. In such cases, there simply is not a large
> enough market of paying customers to justify the enormous expense of
> developing a new drug. America's Orphan Drug Act, which provides
> financial incentives to develop drugs for small numbers of patients,
> is one approach. But there is still plenty of room for
> TheOpenBioinformatics Foundation is a non profit, volunteer run
> organization focused on supportingopensource programming in
> BioPerl, BioJava and BioPython and was formally incorporated in order
> to handle our modest requirements of hardware ownership, domain name
> management and funding for conferences and workshops.The Foundation
> purpose. Occasionally the O|B|F directors may make announcements about
> our direction or purpose (a recent one was on the licensing of
> academic software) when the board feels there is a need to clarify
> matters, but in general we prefer to remain simply the administrative
> support organization for our member projects.
>
> Our main activities are:
> Underwriting and supporting the BOSC conferences
> Organizing and supporting developer-centric "hackathon" events
> Managing our servers, colocation facilities, bank account & other assets
> """
>
>
> http://p2pfoundation.net/Open_Source_Biology
> which contains a bit of a story of Drew and Rob's involvement from
> which I'm excerpting:
>
> "Since we ourselves depend on the information encoded in genetic
> material," Endy explains, "we should work together to share genetic
> information."
>
> http://www.eastbayexpress.com/2005-03-30/news/steal-this-genome/
> """
> They also made a plea on behalf of public safety; there's no way any
> federal law can ensure that someone doesn't create an organism that,
> as Brent puts it, "liquefies Cincinnati." Rather than trying to keep
> secret, for example, the genome of a potential bioterror agent, the
> institute crew concluded that it's better to empower as many people as
> possible to develop countermeasures such as new drugs and vaccines.
> "Consider that the only effective counterterrorism measures on
> September 11, 2001 were made by the passengers of Flight 93," Brent
> says.
>
> Carlson, Endy, and Brent all agree that the best way to keep tabs on
> the potential dangers brewing in labs was to share information. "The
> only way the shit doesn't hit the fan is if everybody engineering
> fromopen-source software that 'many eyes lead to few bugs.' In other
> program a piece of DNA. You shouldn't trust me."
> """
>
> Rob still contrasting on parallels (or lack thereof) between
> "What does 'ownership' mean when property is infinitely reduplicable,
> highly malleable, and the surrounding culture has neither coercive
> power relationships nor material scarcity economics?" -Eric S Raymond,
> Homesteading the Noosphere.
>
> """
> The biohacker community will emerge as DNA manipulation technology
> decreases in cost and when the overall technological infrastructure
> enables instruments to be assembled in the garage. The Molecular
> Sciences Institute has a parallel DNA synthesizer that can synthesize
> sufficient DNA to build a human pathogenic virus from scratch in about
> a week. Assembled, this machine cost ~$100,000 about 18 months ago. We
> estimate the parts could be purchased for ~$10,000 today. A working
> DNA synthesizer could be built with relative ease. Synthesizers of
> this sort produce ~50 mers, and it is likely that methods to assemble
> these short oligos into chromosomes will be perfected relaltively
> soon. Hobbyists often spent similar sums on cars, motocycles,
> computers, and aquariums. <snip>
>
> of India, ~$34 million USD)http://osdd.org/http://p2pfoundation.net/Open_Source_Drug_Discovery
> There's enough news links from the osdd.org front page to get a feel
> for their Tuberculosis-oriented program. OSDD is very recent and very
> big news for the pharmaceutical sector, I've joined and been
> contributing and there's been talk with the manufacturing guys about
> how to implement some of the tech they've been thinking up.
>
> There was a time when drug giants tried to keep leads like that to
> themselves in an attempt to gain an advantage over their competitors.
> They paid lots of money for the privilege, too. In 1993,
> GlaxoSmithKline tied up with Human Genome Sciences to develop drugs
> based on genome data. Five years later, Bayer spent $465 million to
> get access to the genetic library being assembled by Millennium
> Pharmaceuticals. Neither collaboration has led to a marketed drug. But
> another requirement of making the leap from genes to drugs is making
> the research public--a step that will make it difficult for
> researchers elsewhere to patent any of this raw genetic information.
> Novartis isn't the only drug firm embracing this "give it away for
> free" mentality. Pfizer has promised to make available for free a
> swath of genetic information emerging from a three-year collaboration
> with the National Institutes of Health."
>
> We should focus on three challenges:
> 1) We should resist the impulse to restrict research and the flow of
> information. Ignorance will help no one in the event of an emergent
> threat and, given the pace and proliferation of biological
> technologies, the likelihood of threats will increase in coming years.
> Among the greatest threats we face is that potentially detrimental
> work will proceed while we sit on our hands. If we are not ourselves
> pushing the boundaries of what is known about how pathogens work or
> ways to manipulate them, we are by definition at a disadvantage. Put
> simply, it will be much easier to keep track of what is in the wind if
> we don't have our heads in the sand.
>
> 2) The best way to keep apprised of the activities of both amateurs
> perhaps modeled on theOpenSource Software (OSS) movement, and
> practice for professional biology hackers, and it is already evident
> on the Web amongst amateur biology hackers.14 This represents an
> opportunity to keep apprised of current research in a distributed
> fashion. Anyone trying something new will require advice from peers
> and may advertise at least some portion of the results of their work.
> As is evident from the ready criticism leveled at miscreants in online
> forums frequented by software developers (Slashdot, Kuro5hin, etc.),
> people are not afraid to speak out when they feel the work of a
> particular person or group is substandard or threatens the public
> good. Thus our best potential defense against biological threats is to
> Then there's also the issue of genomics:
>
> To usher in the dawn of truly personalized medicine, and accurately
> tease apart the confluence of factors determining human pathology, it
> will be necessary (albeit not sufficient) that large numbers of
> reliable, high-throughput second-generation sequencers be installed
> and operated. We have identified the upfront and recurring cost of
> second-generation sequencing as key factors inhibiting their rate of
> adoption, and have assiduously sought to drive these as low as
> possible. At the same time, throughput, accuracy, and reliability have
> been the focus of relentless development efforts.
>
> A key differentiator in our approach to second-generation sequencing
> for public download, as are the protocols and reagent sets. All
> aspects of the system are fully programmable, with parameters and
> sequences accessible and modifiable by its users to improve and extend
> the instrument. In addition, all subsystems are highly modular and
> easily upgraded and/or retrofitted; as a result, we fully anticipate
> that the instrument will evolve and improve over time. We expect a
> worldwide user community to develop and flourish, advancing both the
> design and the operational specifics of the platform, from which all
> users in turn will benefit.
> """
>
> Implications on health reform:http://www.designcouncil.info/mt/RED/health/http://p2pfoundation.net/Open_Health
>
> """
> To clear up confusion, I will use the termOpenNotebook Science,
> a URL to a laboratory notebook (like this) that is freely available
> and indexed on common search engines. It does not necessarily have to
> look like a paper notebook but it is essential that all of the
> information available to the researchers to make their conclusions is
> equally available to the rest of the world. Basically, no insider
> information.
> """
>
> """Openaccess (OA) oropenaccess publishing is the publication of
> arts, or any product of intellectual activity. In this context,
> access".
> """
>
> Also in the news, NIH has been goingopenaccess:http://slashdot.org/article.pl?sid=07/12/27/0219228http://science.slashdot.org/article.pl?sid=07/11/07/2318208http://science.slashdot.org/article.pl?sid=04/08/06/1225211&tid=134&t...http://yro.slashdot.org/article.pl?sid=07/03/02/0158208
> PLoS is a life-saver, and so are the many, many otheropenaccess
> preprint archives available through the web. Everyone on this list is
> probably familiar with pubmedcentral, or pubget.com, and in general
> and cite all at once, so if anyone ever needs to find a paper or look
> available to almost anybody with a community college library
> subscription or otherwise a university enrollment/faculty status.
>
> 1. Science is traditionally anopenendeavour
> 2. The internet/web potentially increases the openness
> 3. This potential is under-used
> 4. An advocacy movement is needed
> """
>
> So, now for some licensing stuff. For the run down on GNU, the free
> on Google Video:http://video.google.com/videosearch?q=revolution+os&emb=0#
> (w/ Richard Stallman (RMS), Eric S Raymond (ESR), Linus Torvalds,
> Bruce Perens, ...)
>
> http://p2pfoundation.net/Open_Licenses
>
> "Creative Commons provides free tools that let authors, scientists,
> artists, and educators easily mark their creative work with the
> freedoms they want it to carry. You can use CC to change your
> copyright terms from "All Rights Reserved" to "Some Rights Reserved."
> We're a nonprofit organization. Everything we do — including the
> software we create — is free."
>
> "Science Commons designs strategies and tools for faster, more
> efficient web-enabled scientific research. We identify unnecessary
> barriers to research, craft policy guidelines and legal agreements to
> lower those barriers, and develop technology to make research, data
> and materials easier to find and use. Our goal is to speed the
> translation of data into discovery — unlocking the value of research
> so more people can benefit from the work scientists are doing."
>
> Quick video on Science Commons:http://sciencecommons.org/about/science-commons-dylan-video/
> And again the "Revolution OS" video:http://video.google.com/videosearch?q=revolution+os&emb=0#
> (free) brother:http://bilconference.com/)
>
> And then there's theopenmanufacturing group that has been exploring
> shops, kinematic self-replicating machines, advanced automation, etc.,
> microprocessors, DNA synthesizers, most of everything from the Maker
> community, instructables, etc.
>
> OpenDesign Foundationhttp://www.opendesign.org/
> the free exchange of comprehensive design information. TheOpenDesign
> Foundation provides the collaborative space to fosteropensource
> physical design, and seeks to strike a balance between the
> independence of individual designers and the collective power of
> conviction and passion of designers for the greater benefit of a
> global society."
>
> Debian Social Contracthttp://www.debian.org/social_contracthttp://en.wikipedia.org/wiki/Debian_Social_Contract
>
> """
> Ubuntu is an African concept of 'humanity towards others'. It is 'the
> belief in a universal bond of sharing that connects all humanity'. The
> same ideas are central to the way the Ubuntu community collaborates.
> Members of the Ubuntu community need to work together effectively, and
> this code of conduct lays down the "ground rules" for our cooperation.
>
> We chose the name Ubuntu for our distribution because we think it
> captures perfectly the spirit of the sharing and cooperation that is
> everyone's benefit. We improve on the work of others, which we have
> been given freely, and then share our improvements on the same basis.
>
> That collaboration depends on good relationships between developers.
> To this end, we've agreed on the following code of conduct to help
> define the ways that we think collaboration and cooperation should
> work.
>
> If you wish to sign the code of conduct, you can sign the canonical copy online.
> """
>
> OpenSource Definitionhttp://www.opensource.org/docs/definition.php
>
> 1 512 203 0507
Jim H
Thanks for the write up. You are correct: tossing the patent system
out in entirety probably wouldn't be a good idea.
Particularly relevant to bioscience IP is the Bayh-Dole Act. Passed
into law in only 1980, it gives it gave US universities, small
businesses and non-profits intellectual property control of their
inventions and other intellectual property that resulted from
government funded research. This is taking its toll in terms of human
suffering and stifling scientific research and translational
development.
I believe the intent of the Constitutional protection is to limit the
ability of government to "steal" from inventors. Since taxpayers
provide the NIH budget, I do not believe "inventors" paid with my tax
money should "own" these inventions. Neither should the government.
The people own these inventions.
There is nothing in the Constitution about establishment of the NIH,
so the Founding Fathers could not have envisioned the power government
plays in providing cutting edge research and the amount of our GDP
going into research today. Give back to us what we have already paid
for and make this Open for others to use, commercialze, develop and
improve for the benefit of mankind.
O Jan 2, 5:38 pm, "bioju...@gmail.com" <bioju...@gmail.com> wrote:
> Thanks for the Safari tour. Interesting ideas.
> Do you believe that the patent system should be abolished?
>
> Interesting to note that the patent system is established directly
> under Article 1, Section 8 of the Constitution giving "authors and
> inventors the exclusive right to their respective writings and
> discoveries." Thomas Jefferson was one of the leaders of the patent
> office when it was first established, but I was surprised to learn
> Most of the great technologies developed in the United States have
> been associated with patents - including Morse's telegraph - who tried
> to patent every mode of transmitting an EM signal over distance
>
> read more »
Nick Taylor
For what it's worth, for the last 8 years I've been on a mailing list which has been frenetically debating this issue with regards music and film...
... and it has gotten precisely nowhere. The same arguments have revolved etc... shifted slightly, but not much.
You can't control digital replication. You especially can't control it using law - which is basically trying to legislate against an environmental condition, and you especially can't control it using American law in a world thoroughly offended by the tone-deaf arrogance of the last 8 years.
People (and by that I mean corporations) will try of course, and trying will do more damage than not - just as they have done with music/film.
Personally I think bio patents should be treated with the same contempt that software patents are. Unenforceable, immoral, and utterly detrimental to progress.
It's attempting to create a fake scarcity in an arena that is inherently abundant.
Scrap em.
So um... there's my 2c.
Guido D. Núñez-Mujica
how do you explain the Golden Rice case, biojuris? Intellectual
property needs to be reshaped and inventions should be open to
modification and use instead of do nothing in boxes in universities.
bioj...@gmail.com
You raise interesting points about the Bayh-Dole Act.
Why should tax funded research be transformed into private property?
I'd like to see an economic analysis of this, which I'm sure has been
done.
Look at the Stanford example. Some of the basic gene cloning
technologies were invented and patented at Stanford - creating a
stream of revenue for Stanford to .... well, what did they do with the
royalties collected from the cloning vector patents? I know they
spent money on getting more patents, but what else??
You say: "Give back to us what we have already paid for and make this
benefit of mankind."
incentive to "commercialize" and "develop" by providing limited
periods of exclusivity to the patent owner. The benefits to humankind
accrue as the result of the commercialization and development.
Without the patent incentive, would companies have been willing to pay
HGS, Incyte, etc., big dollars to peek inside their databases? The
dollars paid to HGS are pumped into the human economy because:
The dollar is like a blood cell flowing through the human economy ...
tax dollars into companies ... company dollars into research, into
salaries, into bonuses and stock options ... salary and bonus dollars
into
consumer goods, like cars, computers ... consumer spending dollars
into ... China .... China dollars into US bonds .... US bond dollars
bailing out companies ....
You're right: the founding fathers did not envision a federal
government amassing so much power. That's the reason why the Bill of
Rights was not included in the original constitution. Many believed
it was unneccessary because the feds were not intended to wield so
much power over people's lives. That was supposed to be reserved for
state governments.
>
> read more »- Hide quoted text -
>
> - Show quoted text -
bioj...@gmail.com
According to a recent Science report, Golden rice is still just a
promise because "Well organized opposition and a thicket of
regulations on transgenic crops have prevented the plant from
appearing on Asian farms ..."
Also, in that same article, it reports that important contributions
were made by Syngenta when it got involved in Golden rice, replacing
one of the pathway genes with another gene that permitted the GM rice
to produce 23 times more beta carotene in its seeds, than the
originally developed strain.
"Dubock [at Syngenta] helped work out a deal in which Syngenta could
develop golden rice commercially, but farmers in developing countries
who make less than $10,000 a year could get it for free."
See:
Tough Lessons From Golden Rice
Enserink
Science 25 April 2008: 468-471
DOI: 10.1126/science.320.5875.468
Another point: the way the electronic industry has addressed stacking
patents is by patent pools. A pool of patents necessary to utilize a
technology are pooled - and licensed as a pool in one-shot ...
reducing transaction costs and making it easier to play in the game.
See http://en.wikipedia.org/wiki/Patent_pool
On Jan 2, 10:04 pm, "Guido D. Núñez-Mujica"
Joseph Jackson
bibliography I compiled here http://freedomofscience.org/?page_id=10
I didn't quite finish it and never tracked down links to all the
papers as some are not easy to find and I'd be violating copyright
(which I am happy to do but just took to long to find "pirated"
versions and upload).
Bryan, I have gotten quite behind during the holiday period but I will
catch up and send you my list of people/organizaitons relevant to Open
Science. We should compile a master list and get some type of
database. An open science mailing list was launched in November but
it doesn't capture the info the way I'd like to see it--eg a
compilation with everybody tagged by interest and capabilities (syn
bio/diy bio/open data/stem cells/patent law, and every combination
thereof). Right now people are on many mailing lists and FriendFeed;
I'll do my best to scrape this. Also happy birthday tomorrow.
Bayh-Dole is truly an insidious piece of legislation and a form of
high-way robbery. Last year I attended an interesting seminar at
Berkley with CIRM and the Harvard Stem Cell Institute. The meeting
was convened to consider the proposal below--to create an
institutional clearinghouse/patent pool among the major players in
stem cell research. Skim the paper if you want--perhaps 15 minutes.
http://freedomofscience.org/wp-content/uploads/2008/07/stem-cell-rd-clearinghouse-consortium.pdf
Basically, this group would use an attenuated form of Open Source
licensing among members of the group. They are copying PIPRA, a non-
profit IP clearinghouse which was set up in 2002 to facilitate IP
sharing between the major land grant universities facing problems in
bioagriculture.
To really make things move, we'd need the consortium to bundle the IP
and license it conveniently and cheaply to entrepreneurs. It wasn't
clear that CIRM and Harvard were going to act quickly to enact such a
plan (typical).
Nick, I largely share your sentiments, but we can't complacently
assume that it is possible to ignore these patents in the way that we
can willfully infringe copyright. This is precisely my complaint
against Free Culture/Creative Commons--this battle seems essentially
won at this point--the technology of file sharing is not going away
and it is a matter of time before the rest of the system finally
adjusts to reality. On the other hand, the science/patent issues are
a matter of life and death, literally, and yet we have no popular
movement demanding that citizens/consumers receive the benefits they
have already paid for.
Every time that Thailand or Brazil threatens to issue a compulsory
license or actually does so--the PHRMA lobby successfully paints this
as "stealing" their patent; this is manifestly false, as a patent is a
right granted by a government at its discretion. When a company fails
to practice the invention in a way that benefits the public (in these
cases refusing to price HIV drugs affordably) the government has every
right, under international trade law, to take action to see that the
invention is used.
The problem today is that until the technological balance of power
shifts, corporations and other entities indeed can control and stifle
scientific knowledge/knowhow, and technology. A big part of DIY bio
is to accelerate the capability of individuals and small groups to do
more for themselves. Open Source legal tools can also be a part of
supporting this--especially in pre-empting existing powers from
establishing a chokehold. The problem is that it is costly to obtain
a patent and who is going to pay for this purely as a defensive tool?
Yet defensive publishing is not enough on its own--stuff gets through
all the time despite "prior art" PIPRA and the Stem Cell consortium
mentioned above already have resources and are using their IP as a
bargaining chip in a global game.
If we had a group of pro bono attorneys and a community to create and
defend essential "Free Biotechnologies" (Free not as in price but in
the ability to use them) things could start to change. The BIOS
initiative sort of tried this with backing from Rockefeller
Foundation. I spent 10 months there and witnessed problems
firsthand. Still, this sort of approach could be viable, given a
critical mass of participants and the right technology platforms.
Leslie
common at the time; namely, that federally-funded inventions made at
universities were not being patented and the vast majority,
particularly in the biomedical areas, were therefore not being
developed and brought to market. Essentially, in biotech what is not
patented is dedicated to the public. That does not work for getting
new advances the significant capital invenstments needed to get them
through clinical trials and otehrwise to market. For research tools,
there is great debate. Some companies, for example Affymetrix, are
founded on a base of hundreds of research tool patents, in that case
related to Genechips and their manufacture. Those patents, and the
high fees to license them when licenses are even available, have
blocked many other companies from offering products, such as medical
diagnostics, that utilize that technology. The shareholders of
Affymetrix have seen the value of their company skyrocket. It is
possible to putchase some Genechip technology for reseearch use from
licensed third party providers, with the license cost built into the
cost of the product. However, the use of these tools is definitely
stifled by the Affymetrix death-grip on the patents that cover the
basic technology, some of which based on inventions made at federally-
funded universities (pretty much all are) and thus covered under Bayh-
Dole.
>
> read more »- Hide quoted text -
Bryan Bishop
> Do you believe that the patent system should be abolished?
Maybe. I do think that "something has to give" way to something new
and better. I also think it is important to revise what it means to
'patent' some new technology. At this point, there is so much
confusion between individual players in the system that we have to
have middlemen and things are confusing.
> Interesting to note that the patent system is established directly
> under Article 1, Section 8 of the Constitution giving "authors and
> inventors the exclusive right to their respective writings and
> discoveries." Thomas Jefferson was one of the leaders of the patent
Isn't that ambiguous though? "Exclusive right" hardly begins to
address the multititude of possibilities that we know now are
possible- for instance, the ability to copy information greatly
changes the nature of "Exclusive Right" since you don't really 'steal'
the information in the first place.
> Most of the great technologies developed in the United States have
> been associated with patents - including Morse's telegraph - who tried
> to patent every mode of transmitting an EM signal over distance
> (see http://www6.miami.edu/ethics/jpsl/archives/all/gene.pdf). I
> supposed that would have covered the Internet, had it been granted.
That's maybe only because that's what people have been told to do, not
knowing that other options exist.
> But, you can see, that patent "abuse" is not something hat has
> recently been "invented" but has been around for as long as there have
> been patents in the US. Bell's telephone, Edison's electric light,
> and many other pioneering inventions have been patented.
I am not even sure if the natural state of affairs of patents is
sufficient here. I do agree that there is abuse at the moment, yes.
> Is open source based on altruistism or mistrust.
> You quoted Drew Endy as saying "I don't trust you not to make any
> mistakes the next time you
> program a piece of DNA. You shouldn't trust me."
The mistrust-arguments are kind of like icing on the argument cake.
Open source originated as a way to point out that free software can
still be made to work within businesses (okay, and it happens to work
for nonprofit people, amateurs, etc. as well). There's a certain sense
of "mistrust" of authorities, but this is more of the healthy kind.
It's the same feeling you get when you realize that all of your
proprietary software, your life-force of your company or even your
home computer network, is completely unalterable by you :-(.
> If it's in part motivated by altruism - then why shouldn't the patent
> community embrace the same standard. It doesn't have to be all or
No idea, it's very hard to convince so many people of doing anything
in particular, and that's why I don't presently have recommendations
about reforming the entire patent system or whatever.
> nothing. But, rather patent wisely, without over-reaching, share the
> royalties, and let academic non-profit researchers use it for true
> academic purposes. This idea is not new. I believe that Stanford now
Yes, but even within those restrictions I wonder if the system can
still be gamed and used detrimentally.
> I wonder, though, if some of the allegations about the adverse effects
> of patents are not over-stated. It's very easy to hypothesize that
> stacking patent rights will escalate the cost of doing research and
> making new discoveries - but where's the evidence? As I recall, there
> are not many real examples, just a lot of talk. This is one of the
> reason why I established the Mercantile Gene (http://mercantile-
> gene.wikidot.com/)
Most of the evidence is locked away up in the offices of corporate
lawyers. I've heard many examples on this mailing list and as well
from engineers; the semiconductor industry is bloodthirsty for
patents, any new circuit you design- you betcha that it's going to be
patented.
- Bryan
bioj...@gmail.com
> lawyers.
I agree. Patent licenses terms are closely guarded. However, there
is a way to determine whether a patent is licensed. Under the US
patent statute, a product must be "marked" with the patent number for
certain patent infringement remedies to take effect.
This means when biotech patents are sold, like enzymes, drugs, seeds,
etc., - prudent companies mark the product - such as the package
insert, operating manuals, etc. - with the patent number. Mining
package inserts is a way to learn more about the gene/biotech
licensome.
On Jan 3, 12:18 pm, "Bryan Bishop" <kanz...@gmail.com> wrote:
> > Do you believe that the patent system should be abolished?
>
> Maybe. I do think that "something has to give" way to something new
> and better. I also think it is important to revise what it means to
> 'patent' some new technology. At this point, there is so much
> confusion between individual players in the system that we have to
> have middlemen and things are confusing.
>
> > Interesting to note that the patent system is established directly
> > under Article 1, Section 8 of the Constitution giving "authors and
> > inventors the exclusive right to their respective writings and
> > discoveries." Thomas Jefferson was one of the leaders of the patent
>
> Isn't that ambiguous though? "Exclusive right" hardly begins to
> address the multititude of possibilities that we know now are
> possible- for instance, the ability to copy information greatly
> changes the nature of "Exclusive Right" since you don't really 'steal'
> the information in the first place.
>
> > Most of the great technologies developed in the United States have
> > been associated with patents - including Morse's telegraph - who tried
> > to patent every mode of transmitting an EM signal over distance
> 1 512 203 0507
Ramu
With respect to the statement "Give back to us what we have already
and improve for the
system benefits. But I feel this explanation misses an interesting
point. What happens during this process of commercial and development
is that wealth gets concentrated in selected sectors of the commuity,
while what is actually intended is a more spread-out flow of benefit
to the participants in the system. For example, we belong to a
organization, that has all kinds of staff - housekeeping, support,
innovative, creative etc. If one of the staff members comes up with an
invention that gets commercialized then should the benefit not be
shared in proportionate amount to other staff also? My own impression
is affirmative in that they should also benefit proportionately
because any invention these days do not happen in isolation. It
happens as part of system. So, the improvement of mankind would mean
we should be conscious and work out a system that would benefit one
and all connected with that invention and commerce and not just a
selected set of people. Mankind or better Humankind in my
understanding is accrual of benefit in a more spread out fashion.
With Kind Regards
Ramachandran
Scientist IGIB
Ramu
Well, I appreciate your careful observation and I fully respect. But I
am not agreeing with your conclusion. You seem to suggest to abondon
the patent concept altogether because they are not enforceable. This
is like saying "if at all you place a fence, then do it well so no one
will be able to penetrate". We may like to be reminded that creativity
in negative way is done with as much force as creativity in positive
way and therefore there will be no end to chasing on enforcement as
there will be no end on breakers. In my view it is OK to have these
instruments, but taking your suggestion in a bit toned down way, we
may not place too much emphasis on these instruments. I heard that
some companies do this duplication within their own house under a
different name and release this duplicate in the market after some
time gap from the original release. This means that they go along with
the tide and try get benefit from that also. Similar and other re-use
strategies may eventually discourage duplication malpractise because
their value will go down. Careful pricing and accessibility in the
market can also help. Or one can say, "you pay price X then you get
warranty for 2 years but if you pay price Y then you get warranty for
1 year, where X>Y" and so on. The consumers will still buy from
original company because they are giving certified warranty and they
will buy that product, which can be affordable by them.
With Kind Regards
Ramachandran
Scientist, IGIB
Nick Taylor
Hello, happy New Year from Sunny New Zealand, where it is (needless to say), raining cats and dogs.
Ok.. I also said that bio-patents were immoral and utterly detrimental to progress, and that they are attempting to create a fake scarcity in an arena that is inherently abundant.
If you're not familiar with the arguments against software patents, cast your eye over these:
http://www.gnu.org/philosophy/fighting-software-patents.html
http://www.nosoftwarepatents.com/en/m/basics/webshop.html
These are just the first few that turned up on google etc.
Bio-patents like software-patents are little more than a gold-rush to "own" what is essentially the alphabet of a new language. It is in my most humble of opinions, absolutely disgusting.
Any argument that attempts to frame this around the notion that the benefactors/participants are "consumers" is fundamentally flawed. We aren't consumers, we're people, and at this point about a billion of us are living out of cardboard boxes.
We already have wealth concentrated in so few hands that it is literally killing us. We absolutely do not need an artificially created situation where ownership of knowledge is corporatised as well.
You've heard perhaps,that one of the first laws created during the American occupation of Iraq was one that forbade Iraqi farmers from saving seed from their own crops to replant next season (thousands of years of human tradition going out the window with a single flourish of someone else's pen)?
http://www.grain.org/articles/?id=6
You really want a world where Monsanto owns the food chain?
A large part of the promise of DIY bio is to break this would-be oligarchy.
All the best
Nick
Joseph Jackson
software patents but you don't have to even use this strategy to show
the failure of patents in this area--from an economic standpoint--the
system fails in the terms that its own proponents use to defend it--
the economic effects are intolerable and unnecessary. This is why I
invoked a consumer/patient perspective--Ralph Nader has famously
championed the rights of the consumer for decades in other
industries. One of his disciples, economist Jamie Love, has spent 20
years working on these issues in BIO/PHARMA and has tried to get a
medical innovation prize fund created to replace exclusive phrma
licensing as the standard mechanism for financing drug R&D.
http://www.keionline.org/index.php?option=com_content&task=view&id=4&Itemid=1
Politically, it is unlikely this legislation can get through the PHRMA
lobby's campaign of economic disinformation, but the proposals are
sound.
On Bayh-Dole, the best evidence now indicates this act has been a
total joke. After close to 30 years, only a few universities have
ever broken even, much less earned income for their licensing. It has
been a typical lottery distribution with tons of universities spawning
money losing offices of tech transfer, while Stanford, MIT, U CAL
bring in 60% of the revenues. The most successful example of
university licensing, the Cohen-Boyer patents on recombinant DNA,
which launched the biotech industry, are the COMPLETE OPPOSITE of the
logic underlying Bayh-Dole. As Lita Nelson, former head of MIT tech
transfer explains--
. http://books.nap.edu/openbook.php?record_id=5758&page=40
“This case has three key elements. First, the technology was
inexpensive and easy to use; from a purely technical standpoint, there
were only minimal impediments to widespread dissemination. Second,
there were no alternative technologies. Third, the technology was
critical and of broad importance to research in molecular biology.
The technology was developed in universities through publicly funded
research. The strategy used to protect the value of the intellectual
property was to make licenses inexpensive and attach minimal riders.
The tremendous volume of sales made the patents very lucrative.”
“The Cohen-Boyer patent is considered by many to be the classic model
of technology transfer envisaged by supporters of the Bayh-Dole Act,
which was intended to stimulate transfer of university-developed
technology into the commercial sector. Ironically, it presents a
different model of technology than that presumed by advocates of the
Bayh-Dole act (for discussion, see chapter 3). Lita Nelsen, director
of the Technology Licensing Office at the Massachusetts Institute of
Technology (MIT), noted that the premise of the Bayh-Dole Act is that
exclusivity is used to induce development and that universities should
protect their intellectual property because without that protection,
if everybody owns it, nobody invests in it. ''The most-successful
patent in university licensing, in the entire history of university
licensing, is the Cohen-Boyer pattern which is just the reverse.” It
is a nonexclusive license. It provides no incentive, just a small tax
in the form of royalties on the exploitation of the technology.
“The decision to negotiate nonexclusive, rather than exclusive,
licenses was critical to the industry. If the technology had been
licensed exclusively to one company and the entire recombinant DNA
industry had been controlled by one company, the industry might never
have developed. Alternatively, major pharmaceutical firms might have
been motivated to commit their resources to challenging the validity
of the patent.”
From another important paper:
http://www.essentialmedicine.org/wordpress/wp-content/uploads/2008/11/uaem-white-paper-on-indian-bd-act.pdf
"For example, the patented technologies underlying recombinant DNA
were important innovations for biotechnology and generated large
licensing revenues for
Stanford, University of California, Columbia University, and City of
Hope Medical Center,
but patenting was not necessary for commercialization of these
research technologies.23 The
technologies were rapidly adopted by industry even though each was
licensed nonexclusively
to multiple companies, meaning that the exclusivity incentive and
accompanying
monopoly pricing were not necessary to encourage development of these
research tools.24
These rare successes in licensing brought in hundreds of millions for
the institutions who
executed them, yet because the licenses were not necessary to promote
commercialization,
they constituted an unnecessary expense for downstream researchers. As
the manager of
recombinant DNA licensing at Stanford put it, ““[W]hether we licensed
it or not, commercialization of recombinant DNA was going forward…a
nonexclusive licensing program, at its heart, is really a tax…But it's
always nice to say ‘technology transfer.’” 25
Such a “tax” acts as a deterrent to innovation. Aggressive profit-
seeking by public
institutions can exacerbate the problem, as has been the case with the
excessive licensing
fees that University of Wisconsin charges for patents on embryonic
stem cell lines. These
basic research platforms and others like them would be widely used in
the absence of cost prohibitive
intellectual property protection
WORSE still, other countries have copied this flawed model. Look what
India is doing, following our folly. http://www.uaem.org/
"Despite appeals from Universities Allied for Essential Medicines
(UAEM), and other public interest groups, the Indian government has
refused to modify a secretly drafted legislation that would govern the
patenting of the results of publicly funded-research including
publicly-funded medical research. As it currently stands, the Bill
will harm access to medicines and impede the ability of scientists to
conduct innovative research due to a lack of measures to protect the
public interest.
The Indian government made only cosmetic changes to the legislation:
the Bill still removes publicly-funded innovations from the public
sphere and permits monopoly pricing on publicly-funded products
without any effective safeguards to protect the public interest. The
legislation is modeled on the US Bayh-Dole Act which has led to a
proliferation of patenting activity and the creation of patent
thickets. These create barriers to new innovative research and fail to
protect the interests of American taxpayers who end up subsidizing the
discovery of medicines they are often then unable to afford."
Let's clear up something about the Constitution--it also counted
slaves as 3/5ths of a person. Our entire country was founded on a
bogus system of property that ultimately helped lead to its near
implosion from 1860--1865. Not only was this morally disgusting, but
as a property system it FAILED. Freely chosen labor, which we still
don't have today under our essentially wage-slave economic system, but
which we approximate better than in the 19th century, is more
productive and requires less monitoring costs than slavery. Given,
time, the patent system will arguably go the same route. Congress
"may" allow an exclusive right--the patent office is a bureaucratic
creature, dependent on congressional budgeting for its power. All the
incentives for the office are perversely aligned, as it is one of the
only ones that "earns" money for the government, and it does so by
having its examiners process as many patents as they can, inevitably
leading to approval of poor quality applications.
Since the 1980's, exponential increasing of patenting in software and
biotech has occurred because of a few cases of JUDGE MADE LAW that
expanded patenting into new subject matter; nothing that the founders
anticipated or congress deliberated. If we were to abolish our patent
system (a political impossibility until the avian flu pandemic
probably decimates world population) it would not require anything so
drastic as a constitutional amendment. I hear this all the time from
people who don't seem to understand how the govt works--the oft
invoked clause of the constitution ALLOWS but does not REQUIRE govt to
grant exclusive rights. Certainly nothing in the constitution
anticipated the dysfunctional system of "intellectual property" we
have today, epitomized by Bayh-Dole and the Sonny-Bono copyright
extension act (perpetual copyright).
Everyone on this list who wants to really understand the history and
horrific economic harm of patents (and copyright) must read the
groundbreaking book by economists Boldrine and Levine, Against
Intellectual Monopoly. http://levine.sscnet.ucla.edu/general/intellectual/againstfinal.htm
In fact, I would urge everyone to read this book at least 3 times
because you will have spent so many years hearing myths about "IP" it
can take that much to overcome the brainwashing and start to think
clearly.
bioj...@gmail.com
reading.
What is the economic model for Open Source in the software industry?
Excuse my ignorance, but having been nothing but an IP attorney for
the past 20 years, I could use some re-education! In biology terms:
if licensing fees serve as a food/energy source, then what replaces it
in the food chain when all becomes Open? Where do the animals get
their food?
On Jan 4, 11:59 am, Joseph Jackson <joseph.jack...@gmail.com> wrote:
> Nick I concur with your moral arguments about the effects of bio and
> software patents but you don't have to even use this strategy to show
> the failure of patents in this area--from an economic standpoint--the
> system fails in the terms that its own proponents use to defend it--
> the economic effects are intolerable and unnecessary. This is why I
> invoked a consumer/patient perspective--Ralph Nader has famously
> championed the rights of the consumer for decades in other
> industries. One of his disciples, economist Jamie Love, has spent 20
> years working on these issues in BIO/PHARMA and has tried to get a
> medical innovation prize fund created to replace exclusive phrma
> licensing as the standard mechanism for financing drug R&D.
>
Bryan Bishop
> What is the economic model for Open Source in the software industry?
> Excuse my ignorance, but having been nothing but an IP attorney for
> the past 20 years, I could use some re-education! In biology terms:
> if licensing fees serve as a food/energy source, then what replaces it
> in the food chain when all becomes Open? Where do the animals get
> their food?
The most popular economic model in the software industry is the
'service model'. Inhouse programmers contribute to some open source
project, and then wealth is built via providing services like
configuration, customization, technical support, contracted work
(i.e., "hey, this isn't a part of the system yet, can you guys go do
this?), etc.
You might like to read Bruce on this subject-
http://perens.com/Articles/Economic.html
And this is a good resource:
http://p2pfoundation.net/Open_Source_Business_Models
TOC:
1 Open Source Business Models: why they make sense
1.1 Source
1.2 Problems with the older model of IP rents
1.3 Advantages of the new model of engaging outsiders
2 Characteristics of the new Open Source Business Models
2.1 Maximising use value
2.2 Building a user community
2.3 Creating Common Platforms
3 Typology of Business Models
3.1 1. support seller
3.2 2. Loss leader/market positioner
3.3 3. Widget frosting
3.4 4. Accessorising
3.5 5. Service enabler
3.6 6. sell it, free it
3.7 7. Brand licensing
3.8 8. Research tool franchising
4 Typology of Licensing Strategies for Businesses
4.1 The Optimization Strategy
4.2 The Dual License Strategy
4.2.1 Free Core, Added-Value on Top
4.3 The Consulting Strategy
4.4 The Subscription Strategy
4.5 The Patronage Strategy
4.6 The Hosted Strategy
4.7 The Embedded Strategy
5 Competitive Strategies
5.1 Freedom in Pricing
5.2 Support as Marketing
5.3 New Products
5.4 Capacity
5.5 Service
5.6 Signaling
5.7 Conclusion
6 Sustainability Criteria
7 More Information
- Bryan
Guido D. Núñez-Mujica
Right does not change the other fact that a lot of IP have made more
difficult its development.
According to Wikipedia:
"Beyer and Potrykus made use of 70 Intellectual Property rights
belonging to 32 different companies and universities in the making of
golden rice. They needed to establish free licences for all of these
so that Syngenta and humanitarian partners in the project could use
golden rice in breeding programs and to develop new crops.[14]"
Do we really need this kind of red tape in projects that could improve
billions of lives? It would be awful if I had to apply for a license
every time I solve a differential equation for my thesis or use a
"For" loop, and it would be time consuming and tiresome. Somebody
would benefit from it, but we all lose.
And I really think that your analogy of food=licenses is deeply wrong.
Food=ingenuity. To me, considering the fact that Pharma companies
spend more on marketing than on R&D, the fact that they tell us that
if we do not pay what they ask (like with HIV drugs as Ritonavir, when
Abbot raised its cost _SEVEN TIMES_ in 2003) is nothing but a modern
mob threat. We protect you as long as you pay to us.
Yes, R&D is really expensive. Yes, people must be allowed to profit
from their work. But, how much is "fair"? Are Pharma Companies a new
Humpty Dumpty and therefore fair is what they say is fair? How many
more have to die? How much more money must be spent by free market
loving America that is not allowed to choose cheaper equivalent drugs
from abroad?
Joseph Jackson
look like for Open Source Biotech, indeed there will not be any one
model. Andrew Hessel, also on this list, is launching the first ever
Open Source Cancer therapeutic company--more details will emerge when
he gets going.
It is critical to understand that the "biotech industry" did not
really ever come up with a sustainable business model. In 30 years,
approximately 6 companies ever became profitable--with revenues
concentrated among Genentech and Amgen. The other 1400 or so
companies burned cash and if lucky, were bought out by big PHRAMA. We
are approaching an era of radical change in biological technologies--
genomics and synthetic biology, along with stem cells, bring a new
paradigm of personalized cures and regenerative medicine, not
blockbuster "treatments" (drugs that huge numbers of the population
have to take on a chronic, longterm basis).
PHRMA's pipeline has run dry, and everyone realizes we are at the end
of an era. We needs lots of thinking about how to replace the old
innovation system. Prize funds, direct government investment in R&D
(since the taxpayer already funds such a huge amount, this is really
more about the NIH and Universities actually using non-exclusive and
socially responsible licensing), even microfinance for science, are
possible.
New models need to think specifically about the challenges of
different sectors--Vaccines vs Stem Cells vs Gene Therapy. Within
each area, all technologies are not created equal. A "suite" of open
source enabling technologies can accelerate progress. Open Source
immunological adjuvants, for example, would be a great boon to vaccine
design and production world wide; yet today, the strategy is slap as
many patents around them (see avian flu case) as possible--this just
drags the whole field down.
Bryan Bishop
> Biojuris, right now we don't know exactly what the business model will
> look like for Open Source Biotech, indeed there will not be any one
> model. Andrew Hessel, also on this list, is launching the first ever
> Open Source Cancer therapeutic company--more details will emerge when
> he gets going.
Another item worth adding to the list or bibliography is this one-
http://c4ss.org/wp-content/uploads/2009/01/industrialpolicycarson0109.pdf
.. which I just scooped from the open manufacturing list this morning.
Less about business and more about doing stuff on your own.
Srinivasan Ramachandran
Delhi 110 007, India
Tel: 2766-6156
Fax:2766-7471
Nick Taylor
Sorry, I thought I'd done that in the last email.
Nick