[open-science] Fwd: Compilation of material on open science and open biology

Jonathan Gray jonathan.gray at okfn.org
Tue Mar 3 16:28:32 GMT 2009


Michel Bauwens asked me to forward this on his behalf. All material
below is also available at:

  http://p2pfoundation.net/Category:Science

Warm regards,

-- 
Jonathan Gray

Community Coordinator
The Open Knowledge Foundation
http://www.okfn.org


---------- Forwarded message ----------
Great rundown of material, with a lot of usage from the material collated on
the p2pfoundation wiki.

By Bryan Bishop:

Bryan Bishop    View
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 More options Dec 30 2008, 9:06 am     From: *"Bryan Bishop"
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Date: *Mon, 29 Dec 2008 20:06:09 -0600*
Local: *Tues, Dec 30 2008 9:06 am *
Subject: *What's all this about "open", anyway? (long)*
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 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_Biotechnology
http://rsss.anu.edu.au/~janeth/ <http://rsss.anu.edu.au/%7Ejaneth/>
http://rsss.anu.edu.au/~janeth/OpenSourceBiotechnology27July2005.pdf<http://rsss.anu.edu.au/%7Ejaneth/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/ <http://rsss.anu.edu.au/%7Ejaneth/>)
"""

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<http://rsss.anu.edu.au/%7Ejaneth/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_t...<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.intentionalbiolo...<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...<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-scien...<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&t...<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/scie...<http://web.archive.org/web/20020206160321/http://gwu.edu/%7Egprice/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-vi...<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.
- Bryan
http://heybryan.org/
1 512 203 0507

--
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