[chox] Open Source Biotech. Artikel von Keneth Cukier

• From: "Franz Nahrada" <f.nahrada reflex.at>
• Date: Mon, 22 Nov 2004 06:06:58 +0100

Danke an Bala für die Weiterleitung dieses Artikels in Minciu Sodas

source:

[ http://www.cukier.com/writings/opensourcebiotech.html
]http://www.cukier.com/writings/opensourcebiotech.html

Note: This article is the complete text, including references, of a
shorter, edited version that appeared in The Acumen Journal of Life
Sciences, Vol. I, Issue 3. September/October 2003. Online at:
http://acumenjournal.com


Open Source Biotech


Can a non-proprietary approach to intellectual property work in the life
sciences?

 By Kenneth Neil Cukier

 In early 1999, as labs around the world raced to decode the human genome,
Tim Hubbard, the head of human genome analysis group at the Sanger
Institute in Britain, was becoming more and more interested in something
father afield: Open-source software. On the Sanger strategy group's
internal email list, he drew parallels between the open source movement's
philosophy and what the six-nation project was trying to achieve by making
the genome sequence publicly available. While surfing the Net in his
office late one evening in January 2000, he stumbled upon something called
"open content licenses." It offered a way to apply open-source principles
to information, not just computer code. "I realized that there might be
ways to adapt [open source licenses] to something appropriate to the
genome that had legal weight," he recalled. [1] 

With six months to go before the draft of the genome would be completed -
helped along, controversially, by the private-sector company Celera
Genomics - Dr. Hubbard knew he had to act fast. A flurry of emails ensued,
teleconferences hastily called, and lawyers set in motion. The team even
contacted the scraggily father of the free software movement, Richard
Stallman, to get advice. Soon, draft license agreements and implementation
plans were circulated, followed by a round of legal reviews. A "click-wrap
contract" was drawn up so that if a party refined a sequence by mixing the
Human Genome Project's public draft version with extra sequence data, they
would be obliged to release it. "Protecting the sequence from someone
taking it, refining it and then licensing it in a way that locked everyone
in, was the primary objective," says Dr. Hubbard. 

 The result? At the end of February, a little over a month after the crash
initiative began, the Sanger Institute opted not to pursue the open-source
strategy. Genomic data had historically been placed in the public domain
with unrestricted use. Imposing any sort of restriction on it, even in the
form of an open-source license that ensured its non-proprietary nature,
would run counter to that tradition, the group decided. [2] Yet far from a
set-back, the voluminous work of Dr. Hubbard and others represented a
secret triumph. Crucial groundwork had been laid; and a precedent
established, if only ideologically. The issue of applying intellectual
property law to the life sciences would never be the same again.

 
Dr. Hubbard is a far cry from a cyberpunk. Rather, the staid scientist may
well represent the future of the life sciences. As the industry advances,
there is a growing call among researchers to redraw the lines of
intellectual property. [3] Instead of simply learning to live with the
current system, they want to upend it. In addition to graduate degrees,
they're armed with moral arguments, evidence of economic efficiency and a
nascent spirit of solidarity that exceeds the traditional ethos of
cooperation found in the sciences and the academy. And the approach that
is gaining momentum comes from the neighboring industry of information
technology: open-source. Its underlying principles are the communal
development of a technology, complete transparency in how it works, and
the ability to use and improve it freely provided improvements are shared
openly. [4] Where proprietary software's underlying code is forbidden to
be modified (and normally even inspected) by customers, open source
products encourage users to develop it further. The parallel in life
sciences are things like the Human Genome Project that represent a "common
good," says Sir John Sulston, co-recipient of the 2002 Nobel Prize.
"Progress is best in open source," he concludes. [5] 


To be sure, it's still business as usual for today's university
tech-transfer offices, patent lawyers, venture capitalists and
entrepreneurs. They don't oppose open source as much as feel skeptical
about it. Whatever the apparent virtues, the approach is fraught with
serious obstacles - from the professional credentials of scientists and
cost of research, to the rarity of success among projects and uncertain
incentive structure. No biotechnology company currently fears its prized
intellectual property will be rendered worthless by a band of teenagers
with a wet lab in their garage. But that belies a major shift in the
industry. The current intellectual property system for the life sciences
has created a lot of losers, who are bound by increasingly onerous
licensing obligations. [6] On the one hand, these underdogs have an
interest in joining forces. On the other hand, as they develop
intellectual property of their own, some are looking to make it publicly
available in ways that benefit the entire community. The question isn't
whether open source biotech will happen - it is happening now, says Janet
Hope, a lawyer examining the feasibility of open source biotechnology as a
PhD candidate at the Australian National University in Canberra. "There
are lots of areas in the biotech and pharma industries where people are
already doing things that are analogous to open source." [7]

 
* * *


One thing is for certain: the current system of biotechnology patent law
is the subject of fierce controversy. Patents - essentially
government-granted temporary monopolies for inventions that are novel,
useful and man-made - reward innovation and act as incentives for
investment. But at times, the system can become a serious encumbrance. A
study published last year in the Journal of the American Medical
Association found that 47 percent of geneticists who requested information
of findings from other researchers were rejected at least once. Ten
percent of all requests for information in genetics were denied, leaving a
quarter of researchers unable to replicate published results and forced to
delay their own publications. [8] The current patent law system is a major
culprit. Critics say that categories of research that is currently
patentable shouldn't be encumbered by intellectual property law because
it's a matter of discovery not invention, and thwarts new innovation.
Also, opponents argue that patent awards are overbroad, or simply so
extensive that it makes research for everyone more difficult for the sake
of protecting the financial interests of a single player. The process,
they say, becomes self-perpetuating which masks its true evil: Researchers
are forced to patent new discoveries if only as a means to use that
intellectual property as a negotiating tool to gain access to other's
intellectual property. Some observers go so far as to state that this
"patent thicket" leads to an "anti-commons," whereby the biotech industry
is forced to combine a large number of separately patentable elements to
form a single product, which is cumbersome to achieve, and once the
license fees are stacked up, overwhelms the value of the ultimate product.
[9]

 

At the same time, even the much hailed 1980 Bayh-Dole Act that has done so
much to commercialize federally-funded research has come under its share
of criticism, by transforming academic institutions into ersatz commercial
entities. [10] In July 2003, a number of biotechnology companies including
Amgen, Genetech and Biogen sued Columbia University alleging that the
school improperly obtained a new patent on an earlier invention whose
patent expired in 2000. Universities adopting the hardball tactics of the
private sector is seen in the 1994 patent infringement lawsuit by Johns
Hopkins University against CellPro, over a process of isolating stem cells
from bone marrow, which bankrupt the start-up. [11] Meanwhile, as
materials transfer agreements, a means of free-yet- formal sharing among
institutions, gains ground in academe, it's not clear whether they solve
the problems or symbolize them. 

 

Strikingly, a study in 2002 commissioned by a National Academy of
Science's panel on intellectual property that is used by proponents of the
status quo to refute charges that the current system is broken actually
identifies so many problem areas that its main point gets overshadowed.
[12] The study found that despite an appreciable increase in patents on
research tools, drug discovery and university research hasn't been
substantially impeded. However, it acknowledged that patents have caused
delays in access to tools and genetic diagnostics, as well as restricted
access to foundational discoveries. Ultimately it reports that in certain
cases "research is redirected to areas with more intellectual property
freedom" - the harshest indictment that exists in the sciences. Far from a
model of efficiency, the current intellectual property system is a
testament to the lengths researchers go to circumvent it, mainly by
infringement. Making criminals out of scientists seems a short-sighted
strategy, and where a "research exemption" once existed, it's been
whittled away by the courts. [13] 

 

The result is that a third of private firms and all university or
government labs in the NAS study admitted to using patented research tools
without a license. What is more, commercial patent holders say they
tolerate the academic research infringement "partly because it can
increase the value of the patented technology." [14] Ironically, this
admission - that building upon a technology without constraints increases
rather than diminishes its value - is precisely the underlying precept of
the open source movement. [15] 

 

* * *

 

The life sciences of course isn't the only place where patent law has
become overbearing. Similar concerns, and open source reactions, are
cropping up in the physical sciences and biology generally. But the huge
rush of investment in biotechnology companies has raised the sector's
profile as well as led to an increase in patent applications, which
deepens the magnitude of the problem. Strikingly, the situation seems to
follow a classic pattern of intellectual property for new technologies,
whether it's the railroad, the airplane, broadcast radio or computer
software. Reactions to overcome the problems varied. In the case of
technologies like the pumping engine and iron industry, "collective
invention" took place, akin to today's open source movement. [16] For the
airplane, the US government threatened to expropriate the patents held by
the Wright Brothers and the rival airplane manufacturer Herring-Curtiss
Co. on the grounds of eminent domain since the companies refused to
cross-license; the resulting patent pool ultimately freed the technology.
[17] With radio, squabbles among the patent holders (AT&T, Westinghouse,
GE and, of all things, United Fruit) restrained the technology so much
that in 1919 the government stepped in and created a patent pool called
the Radio Corporation of America, or RCA. In a historical echo, likeminded
patent pools have been suggested for biotechnology. [18]

 

In the information technology sector, the method of commercializing
intellectual property has occasionally been to open it up rather than lock
it up. But it took the industry a long time to get to there, a trail
littered by tears before triumphs. For instance, Sony's Betamax technology
for home videotape recording was superior to the VHS system, but by
refusing to open up its intellectual property to the home entertainment
industry, including potential competitors, the Japanese firm shrunk its
overall market and allowed the VHS system to acquire more users, thus
becoming the dominant standard. A similar history applies to Apple
Computer, which in the 1980s and 90s lurched between licensing its
technology and keeping it in-house, only to watch its market share
shrivel. That is not to say that dismissing intellectual property rights
is the recipe for success. Xerox's Palo Alto Research Center (PARC) is
widely acknowledged to have "fumbled the future" by failing to
strategically license its patent portfolio, which included inventions like
the graphical user interface and mouse that are staples of personal
computing, to the ubiquitous data-networking protocol Ethernet. [19] 

 

Today, the technology sector has a fairly well-defined mental algorithm
over what sort of intellectual property to make openly available to the
benefit of all and what to keep proprietary and monetize. [20] For
instance, for consumer software, the model is to make client-side, or
end-user, products free so as to achieve a large user base and influence
standards, while selling the server-side software and document authoring
tools. The browser wars between Netscape and Microsoft in the 1990s was
based upon just this premise. Meanwhile, Adobe Systems' Acrobat software
has successfully embodied that business model - and as a result, the US
government electronically published its official documents on that format. 

 

The cost to firms that don't develop dexterous intellectual property
policies can be death by Lilliputians. Consider the genesis of the most
prominent open source movement: The Internet. [21] In the mid 1980s there
were a number of competing data communication protocols that had larger
users bases and were superior in performance - but not in price - to the
Internet Protocol. The technologies, including IBM's Simple Network
Architecture, AT&T's Token Ring and the International Telecommunication
Union's X.25 standard (upon which France Telecom's Minitel system was
based), were closed and did not allow for modification by users. By
contrast, the Internet's technology, shepherded by a group of
decentralized but highly-organized computer engineers from outside of the
major technology vendors, was open in its design process and free to use.
Over time, it supplanted the rival proprietary technologies. 

 

Today, a similar form of battle is being waged for the operating system of
person computers, pitting Microsoft Windows against the open-source Linux
system. Moreover, the means by which the open source movement is fighting
isn't by eliminating intellectual property. [22] Rather, it is by a form
of legal jujitsu that turns the opponent's strength against itself. The
movement uses radical intellectual property licenses, sometimes called
"copyleft" (an antidote to "copyright"), to ensure that the open-source
technology remains non-proprietary and free. For software, things like the
GNU General Public License [23] enables code to be shared but not
corralled; for written material, user-designed licenses via the Creative
Commons ensures the text is openly available but without the risk of being
misappropriated. 

 

The lesson for the life sciences is that just as the information
technology sector had to go through a rough period of transition to figure
out workable models of sharing intellectual property - an evolution that
is still ongoing - so too must biotechnology. The process is incremental,
and probably inevitable. There are powerful economic arguments in its
favor. [24] The open source movement encompasses the classical economists'
spirit of decentralization that is considered essential to progress, with
a relatively new conception of enlightened community-interest, championed
by the New York University legal theorist Yochai Benkler, who considers
open source processes as a peer-based, non-capitalist modes of production
that is likely to expand well beyond software design. [25] There are even
moral imperatives facing the biotechnology industry that propel it in this
direction, namely, the aim to improve and preserve life, which doesn't
exist in information technology. At the same time, the professional
culture of the life sciences and information technology share an
acknowledged desire to change the world. Perhaps fittingly, then, the
first seedlings of an open-source biotech movement are beginning to emerge
in the field that melds both molecular biology and computing:
Bioinformatics. 

 

* * *

 

The duality of wet biology and hot transistors is personified in Tom
Knight at the Massachusetts Institute of Technology. On the ninth floor of
the fabled computer science building at 200 Technology Square in
Cambridge, past a maze of antechambers teeming with dismembered robots and
stray wires and sleek electronics, are doors to his laboratory, emblazoned
with the familiar orange and black BIOHAZARD stickers. It seems
incongruous that DNA synthesizers and freezers filled with test tubes and
Petri dishes should sit comfortably beside hardcore circuit boards, and
Dr. Knight, a computer scientist by background, admits it's not an
ordinary comp lab. It's the epicenter of BioBricks, an attempt to
establish standardized, non-proprietary terms, tools and processes for DNA
work. This, as much as anything, can free the biotech industry from an
ungainly reliance on patented technologies. It's a matter of
interoperability; the life sciences' equivalent of software Application
Programming Interfaces.

 

BioBricks will make it more reliable and less expensive for researchers to
assemble genetic sequences, by using standardized process and
non-proprietary tools that are forever being improved upon by the
community. "The idea of copying one gene from one place to another - that
goes away," Dr. Knight says. "It is a computer science problem." [26] In
such a world, the base pairs that comprise strands of DNA are akin to
digital bits, and just as computers modify those bits from scanner (the
input) to printer (the output), so too will we be able to sequence  and
synthesize DNA. The central tool in both cases is the same - a computer -
so it only makes sense that the same approach to the technology, via open
source methods and practices, emerges in the life sciences as it did in
computing. 

 

BioBricks is only one of a number of initiatives that have adopted open
source practices. [27] For instance, there are other bioinformatics
projects, such as those overseen by the Open Bioinformatics Foundation,
for tailoring numerous open-source computer languages for life sciences
research. One success in the field is BLAST, the Basic Local Alignment
Search Tool, which has for years been used to find similarities in DNA and
protein sequences. Ensembl, a joint project between the Sanger Institute
and the European Bioinformatics Institute aims to provide a freely
available genome annotation software system, starting with the whole of
the human genome sequence. An extension of this is the distributed
annotation system, or DAS, which is a nascent protocol standard
coordinated by Lincoln Stein, the celebrated champion of open source
bioinformatics based at Cold Spring Harbor Labs in New York. The movement
has for years even had its own annual conferences. [28] Then, there's the
computational-heavy SNP Consortium, a joint public/private sector
initiative to create an open database of single nucleotide polymorphisms
(SNPs), the DNA sequence variations among individuals that are key for new
drug development.

 

Though on the surface the projects seem rather basic, it is precisely
these boring, low-level aspects of modern biotechnology research that are
costly and where cooperation could benefit everyone. "When I'm doing an
analysis, I'm not interested in coding, I'm interested in getting the
results of the analysis," says Ann Loraine, a bioinformatics scientist.
"There are certain computations that every computational biologist does
over and over and over - its great to have open source software that you
can use to execute these mundane tasks." Dr. Loraine developed that ethos
as a student sharing code at the Berkeley Drosophila Genome Project, which
she brought over with her to industry as a researcher at Affymetrix.
Christopher Dagdigian, a board member of the Open Bioinformatics
Foundation, concurs. "It's really boring, really routine, everyone has to
do it, and no one gets a competitive advantage," he says. "Our philosophy
is let everyone agree on a common foundation so we can pursue what
actually interests us."

 

While for the moment, most open-source biotech initiatives spring from
academia or the non-profit sector, one start-up company has pinned its
fortunes on it as a business model. Electric Genetics Corp., based in
South Africa, offers bioinformatics software, validation and support
services. For one product, it co-developed [29] a standard for gene
expression ontologies that the company placed under a free open-source
license to see it widely adopted, in order to swell the market for its
commercial software that best parses the data. "Some people think we are
quite crazy," admits Tania Broveak, the managing director, about the
company's approach. To write software, the company organized a "hackathon"
in 2002 and flew a score of top-notch open-source programmers to South
Africa for a week to write code. Electric Genetics has managed to attract
a slight amount of venture capital backing (about $1.5 million) and
expects to be profitable by mid 2004.

 

Companies like Electric Genetics are rare. If an open source movement in
the life sciences is going to take off, it may not come from the deep
pockets of venture capitalists, who are skittish on how to glean returns
on biotech even when they own all the intellectual property. Instead, it
may be borne of the purse of federal funding agencies, which may see open
source projects as a way to ensure that public monies result in public
goods. [30] Dr. Peter Good, a program director at the NIH's National Human
Genome Research Institute, says that they are particularly sensitive to
the issue when deciding whether to fund grant applications. "We have to
deal with the concern that the software be available to people to use to
build on," he says. "We don't say it has to be, but we encourage open
source."[31] At DARPA, which sponsors an open-source biotechnology project
called BioSPICE that uses software to simulate cell life, administrators
say that although they have no formal position on open-source they found
the approach "useful" and "effective." [32] 

 

However, officials at government funding agencies acknowledge
difficulties. They say they want to keep their options open rather than
favor one sort of method of development and approach to intellectual
property over another. What is more, supporting open-source projects is on
uncertain legal terrain. The Bayh-Dole Act lets universities patent and
profit from federally-funded research; stipulating open-source licenses
may run foul of that. In fact, in one instance a professor at the
University of California-Berkeley, Steven Brenner, had to make special
arrangements with the school before he could participate in an open-source
bioinformatics project and give away his work freely. [33] These concerns
are merely speed-bumps on an inevitable road, believes Roger Brent, the
director of the Molecular Sciences Institute in Berkeley. Putting his
patents where his principles are, Dr. Brent's institute has drafted an
"Open Source Policy" which commits to "[making] reagents and methods
freely available to the research community." [34]

 

On a more fundamental level, the simplest form of open source material is
the publication of research. A number of initiatives exits to link up
databases in standardized, non-proprietary ways that would greatly
increase the availability of scientific data. [35] Also, there are moves
afoot to create non-proprietary peer-reviewed journals, such as the Public
Library of Science. [36] They have an allies in government, as politicians
question why research funded by public monies go to private publishers
rather than the public domain. In the US, Representative Martin Sabo, a
Democrat from Minnesota, recently introduced legislation that would
require federally-funded research be made available to the public. A House
appropriations report requested that the National Library of Medicine
consider the same. [37] Internationally, the Organzation for Economic
Cooperation and Development issued a report in March 2003 arguing for a
"core principle" that "publicly funded research data should be openly
available to the maximum extent possible." [38]

 

Whether the groundswell of open source activity that is emerging will
become a potent force in the life sciences or remains a non-threatening
niche will determined by the degree to which it is able to tackle large
scale projects that would be too complex and expensive for any company to
do individually, and for which the use benefits all. So far, these are
exactly the kinds of projects where open source approaches are taking
hold. But they are so-called "pre-competitive" areas like the Human Genome
Project, the SNP Consortium and bioinformatics. Will it be sustainable for
more sophisticated and lucratively patentable things as the industry
matures?

 

* * *

 

Far geographically from Tim Hubbard at the Sanger Institute in Britain,
and far ideologically from Tom Knight at MIT, is Lita Nelson, whose office
is just down the road from Dr. Knight's in a modern red brick building on
campus. Dr. Nelson directs MIT's patent transfer office. Rather than a law
degree, hers is a PhD in organic chemistry. Her work has earned her
respect among intellectual property lawyers, and world renowned among
other universities that are keen to emulate MIT's successes. In a ricochet
Rorschach test-like conversation, she was asked three words to start:
"Open Source Biotech?" She stopped short, smiled wide and shot back "I
don't know what it means!" The term is so broad, she says, it's
meaningless. Similarly, she believes trying to adapt intellectual property
approaches for different classes of technology, such as processes versus
products, would be impossible. "One man's infrastructure is another man's
product or biotech company." she says. Patents provide an incentive to
invest; open-source negates this. Many firms won't want access to a tool
if it can't have it exclusively. 

 

Free software and journal articles are small change compared with the
immensity of the life sciences industry and the problem of hindered
innovation. Scientists, lawyers, and businesspeople are divided on whether
open source may apply to designing diagnostic tools and drug therapies due
to a lack of economic incentive to fund research and regulatory
compliance. For instance, the venture capitalist Brook Byers, a principle
at Kleiner Perkins Caufield & Byers, which has backed a number of
important biotechnology firms, says open source processes may work for
platform technologies like the human genome project but may not be
successful for applications that spring from it, which is better suited to
proprietary, commercial models. 

 

Moreover, the life sciences sector doesn't resemble the information
technology industry at all - there is no single nasty incumbent with which
to rally against, nor are there obvious places where one can give away a
product and make it up on services. [39] Likewise, the open source
software movement itself is new and relatively unproven. And Linux, its
champion test-case, is an operating system - as foundational a technology
as is possible, and one whose cost might legitimately drop to nil had the
market not devolved into a near monopoly situation. 

 

Janet Hope at the Australia National University believes many arguments
against open source biotechnology set a false standard that it shouldn't
have to surmount. "Open source is a type of business strategy but it is
rarely the sole strategy," she says. More moderate expectations are
appropriate. Open source will crop up in places where it fits, and won't
elsewhere. But critics who proclaim it inherently impossible, Ms. Hope
contends, miss the point - it's already happening in small pockets of the
industry, providing a symbolic proof-of-concept that may resonate more
widely. It's gaining widespread support. In July, scores of senior
scientists and intellectual property experts wrote an open letter the
Kamil Idris, the director general of the World Intellectual Property
Organization, calling on the UN body to consider adapting its intellectual
property regulations to account for open source approaches. [40] Although
WIPO waffled, first agreeing to convene a meeting on the topic, then later
declaring the issue verboten after the US Patent and Trademark Office
nixed the idea from pressure by commercial software companies, the
groundswell has clearly begun.

 

At its essence, the issue centers on what a patent actually means. Awarded
by governments, it is not so much an exclusionary right as it is a
preventative asset; it marks the domain for an actionable claim for
damages in cases where it is infringed, and the patent holder exercises
its protections. This point is most crucial, because if governments set
the terms under which a patent may exist, it can also modify how its
protections can be exercised. This has long been a staple of intellectual
property law. For instance, US-funded research enables the government to
use the resulting technology on a royalty free basis. In the case of the
Bayh-Dole Act, the government has "march-in" rights to take control of a
patent it does not believe it being sufficiently exploited. [41] More
broadly, the US and its contractors can't be prohibited from using
patented technology as a matter of law [42] (such as when the government
threatened to strip the Wright Brothers of their airplane patents on the
eve of World War I). That's why, for example, US defense contractors never
worry about infringing any of the thousands of patents that go into
building a military aircraft; if they do, the sole recourse is to seek
damages at the Court of Federal Claims. There, the patent holder can't get
an injunction to prevent the technology from being used, and the damages
can only be reasonable, not, say, trebled.

 

That approach - based on the legal doctrines of sovereign immunity and
eminent domain  [43] - makes perfect sense when the critical challenges to
a nation is security. Yet the current concept of national interest has
expanded to include the realm of health as well. As such, it would be
reasonable for the National Institutes of Health to exercise the same
powers, according to Robert Blackburn, a vice president and chief patent
counsel for Chiron Corp. [44] The policy may free up patented technology
without even being called into use, since the threat of lawful
infringement may induce patent holders to license more readily. [45] Mr.
Blackburn's goal isn't to bring down the patent system as much as preserve
it. "Before you go to the length of overhauling the intellectual property
system that has adopted new technologies over and over again, you should
explore all the potential remedies that exist in the current system," he
says.

 

It's an elegant legal hack that may free up public-funded research, the
very programs that are eyeing open source approaches anyway. Arti Rai at
Duke Law School likes it because it applies to patents that may not be
covered under the Bayh-Dole march-in rights. "But a lot of research is in
private organizations," notes Rochelle Dreyfuss, a law professor at New
York University, who believes it doesn't go far enough. Yet the most
powerful aspect of the proposal is what it symbolizes: Even industry
lawyers most in support of the current patent regime are calling for
reforms. 

 

Such legal maneuvering may become besides the point, and the reason is
found back with Tim Hubbard at the Sanger Institute, surfing the Net
instead of peering into a microscope. His work between 1999 and 2000 on
open source licenses for the Human Genome Project, although never used,
didn't lie fallow - it supplied the critical groundwork for researchers,
lawyers and officials to directly build upon. The fruits of Dr. Hubbard's
efforts will be resurrected this fall in an unprecedented approach for the
life sciences - an open source contract for access to data on the
haplotype map of the human genome, or HapMap. Licensees agree not to use
the data in any way that will restrict the access of others, and will only
share the data obtained with others who have accepted the same license. It
serves to block "parasitic patents" by industry, which could otherwise
combine the HapMap's public data with a smidgeon of their own and patent
the haplotype, explains Mark Guyer, the director of the division of
extramural research at the National Human Genome Research Institute. 

 

Beyond the tradition of standing on the shoulders of giants, which has
always been the staple of scientific advancement, open source processes
are emerging in the life sciences because of a patent system that allows
bad-faith players to prosper. This may be the most important reason it
will take hold, just as it did in information technology against
Microsoft. "The bottom line," says Dr. Hubbard, "is that public domain
projects are using proactive mechanisms to prevent their generosity from
being misused."

 

________________

 

 


NOTES


 

1. Interview and email correspondence; July 2003.

 

2. Sir John Sulston, with Georgina Ferry. 2002. The Common Thread: A Story
of Science, Politics, Ethics and the Human Genome. Joseph Henry Press
(National Academy Press). Washington, DC. October 2002

 

3. Burk, Dan. 2001. "Open Source Genomics." Boston University Journal of 
Science and Technology Law. Vol. 8, Issue 1. (Symposium on Bioinformatics
and Intellectual Property Law. Boston, Mass. April 27, 2001. Online at:
http://www.bu.edu/law/scitech/OLJ8-1.htm 

 

4. Bruce Perens. 1999. "The Open Source Definition." Open Sources: Voices
from  the Open Source Revolution, edited by C. DiBona, S. Ockman and M.
Stone. O'Reilly. Online at:
http://www.oreilly.com/catalog/opensources/book/perens.html 

 

5. Interview (unpublished) with journalist Duff McDonald, July 2003. 

 

6. The Royal Society. 2003. "Keeping science open: the effects of
intellectual property policy on the conduct of science." The Royal
Society. April 2003. Online at: http://www.royalsoc.ac.uk/policy/ 

 

7. Interview, July 2003. For more information, see: Janet  Hope. 2003.
Open Source Biotechnology Project (Online working draft of PhD
dissertation). Law Program, Research School of Social  Sciences,
Australian National University (Canberra). Online at:
http://rsss.anu.edu.au/~janeth/home.html 

 

8. Eric G. Campbell, Brian R. Clarridge, Manjusha Gokhale, Lauren
Birenbaum,  Stephen Hilgartner, Neil A. Holtzman, and David Blumenthal.
2002. Data  Withholding in Academic Genetics: Evidence from a National
Survey. Journal  of the American Medical Association 287 (4):473 - 479.
Abstract online at: http://jama.ama-assn.org/cgi/content/abstract/287/4/473

 

9. Heller, M. A. and R. S. Eisenberg1998. "Can Patents Deter Innovation?
The Anticommons in Biomedical Research." Science 280 [1 May]:698-701.
Online at: http://www.sciencemag.org/cgi/content/full/280/5364/698  See
also: Eisenberg, R .S. 2001. "Bargaining over the Transfer of Proprietary
Research Tools: Is This Market Failing or Emerging?" in R. C. Dreyfuss, D.
L. Zimmerman, and H. First, eds. Expanding the Boundaries of Intellectual
Property: Innovation Policy for the Knowledge Society Oxford. Oxford
University Press, pp. 223-250. 

 

10. Berg, Pail. 2003. "Bayh-Dole 23" (version 8). Unpublished update of
remarks presented at the conference Bayh-Dole at 23: Balancing Academic
Values With Commercial Ambition at the Howard Hughes Medical Institute on
May 28, 2003. Online at:
http://www.practicingsafescience.org/conference2003/present.html

 

11. Avital Bar- Shalom and Robert Cook-Deegan. 2002. "Patents and
Innovation in Cancer Therapies: Lessons from CellPro." Milbank Quarterly.
December 2002. Abstract online at: http://www.milbank.org/800402.html 

 

12. John P. Walsh, Ashish Arora, and Wesley M. Cohen. 2002. "Research Tool
Patenting and Licensing and Biomedical Innovation." Study paper for US
National Academy of Science (Science, Technology and Economic Policy
Board). Washington, DC. December 11, 2002. Online at:
http://www.heinz.cmu.edu/wpapers/download.jsp?id=2003- 2

 

13. See the recent US Circuit Court decision in Madey v. Duke University;
Ruling online at:
http://www.ll.georgetown.edu/federal/judicial/fed/opinions/01opinions/01-1567.html


 

14. John P. Walsh, Ashish Arora, and Wesley M. Cohen. 2003. "Working
Through the Patent Problem." Science, vol. 299. 14 February 2003. Online
at: www.uic.edu/~jwalsh/WalshetalScience.pdf . The "working solutions"
include "licensing, inventing around patents, going offshore, the
development and use of public databases and research tools, court
challenges, and simply using the technology without a license (i.e.,
infringement)." Essentially, a molecular biologistÕs version of a slave
revolt.

 

15. Raymond, Eric S. 2001. The Cathedral and the Bazaar: Musings on Linux
and  Open Source by an Accidental Revolutionary. O'Reilly. 2001. (Initial
version of the essay in 1999.) Online at: 
http://www.catb.org/~esr/writings/cathedral-bazaar/cathedral-bazaar/ 

 

16. Nuvolari, Alessandro. 2003. "Open Source Software Development: Some
Historical Perspectives." Eindhoven University of Technology; Centre for
Innovation Studies. Jan. 2003. Online at:
http://opensource.mit.edu/papers/nuvolari.pdf 

 

17. Seth Shulman. 2002. "Unlocking The Sky: Glenn Hammond Curtiss and the
Race to Invent the Airplane." HarperCollins. 2002. See also: Joel I.
Klein. 1997. "Cross-Licensing and Antitrust Law." Address to the American
Intellectual Property Law Association. (Representing the US Department of
Justice.) San Antonio, Texas. May 2, 1997. Online at:
http://www.apeccp.org.tw/doc/USA/Policy/speech/1123.htm 

 

18. David B. Resnik. 2003. "A Biotechnology Patent Pool: An Idea Whose
Time Has Come?" PSL Journal. Vol 3, Jan 2003. Online at:
www.psljournal.com/archives/papers/biotechPatent.cfm 

 

19. Douglas K. Smith, Robert C. Alexander. 1988. "Fumbling the Future: How
Xerox Invented, Then Ignored, the First Personal Computer."  New York.
William Morrow & Co. 1988.

 

20. Joel West. 2003. "How Open Is Open Enough? Melding Proprietary And
Open Source Platform Strategies." Research Policy 32. 2003. Online at:
www.cob.sjsu.edu/west_j/Papers/West2003a.pdf 

 

21. Kenneth Neil Cukier. 1999. "Internet Governance and the Ancien
Regime." The Swiss Review of Political Science. University of Zurich.
Spring, 1999.

 

22. Henry W. Chesbrough. 2003. "The Era of Open Innovation." MIT Sloan
Management Review. Spring 2003. Apparently the publication has not heeded
Professor Chesbrough's wisdom; only the abstract is online, at:
http://smr.mit.edu/past/2003/smr4435.html

 

23. The GPL has never been legally tested but will be in the case of SCO
v. IBM, over alleged patents to the Linux operating system. It is seen as
a litmus test for the intellectual property viability of open source
movements in general.

 

24. As a model of innovation, see: Lawrence Lessig. "The Future of Ideas:
The Fate of the Commons in a Connected World." Random House; 2001; Web
site: http://the-future-of-ideas.com  On the incentives of contributors,
see: J. Lerner and J. Tirole. 2000. "The Simple Economics of Open Source,"
NBER working paper No. W7600. National Bureau of Economic Research.
Cambridge, Mass. March 2000. Online at:
http://papers.nber.org/papers/w7600.

 

25. Yochai Benkler. 2002. Coase's Penguin, or, Linux and The Nature of
the  Firm . 112 Yale Law Journal. Winter 2002-03. Available at:
http://www.law.nyu.edu/benklery/   See also: Benkler. 2000. "A Political
Economy of the Public Domain: Markets in Information Goods vs. The
Marketplace of Ideas," in Expanding the Bound of Intellectual Property:
Innovation Policy for the Knowledge Society (R. Dreyfuss, D. Zimmerman, H.
First eds.). Oxford. 2000.

 

26. Interview, July 2003 at MIT

 

27. For a list of open source-like biotechnology initiatives, see chart
along with this article in The Acumen Journal of Life Sciences, online at:
http://acumenjournal.com.

 

28. E.g. the 4th Annual Bioinformatics Open Source Conference in 2003
(see: http://news.open-bio.org) as well as the O'Reilly Life Science
Informatics Conference 2004, which marks its third year (see:
www.oreilly.com).

 

29. Co-developed with SANBI, the South African National Bioinformatics
Institute.

 

30. The Wellcome Trust issued a report after a meeting in January 2003 on
the responsibility of funding agencies, researchers and industry in
sharing intellectual property of "community resources" in the sciences. It
called on agencies to "require, as a condition for funding, free and
unrestricted data release." See: "Sharing Data from Large-Scale Biological
Research Projects: A System of Tripartite Responsibilities." 2003.
Wellcome Trust. Oneline at: www.ebi.ac.uk/microarray/General/News/
Prepubl_data_release_6986.pdf 

 

31. Interview, August 2003.

 

32. Telephone and email interview with DARPA officials, August 2003. 

 

33. Interview with Dr. Brenner's colleagues, August 2003. Also, see:
Justin Hibbard. 2002. "The open-source debate enters the genomics arena.
Should publicly funded software be free?" Red Herring. February 25, 2002.
Online at: www.redherring.com/insider/2[PHONE NUMBER REMOVED]/1805.htm 

 

34. Molecular Sciences Institute. "Open Source Policy (draft)" MSI.
Berkeley, CA. Undated. Online at:
http://www.molsci.org/Dispatch?action-WebdocWidget:4866-detail=1 

 

35. Cf: the Biomedical Informatics Research Network BRIN, funded by the
National Institute of Health. Online at: http://www.nbirn.net 

 

36. The Creative Commons copyright license is already used for PubMed
Central, a digital library for research and journal publications being
developed by the National Center for Biotechnology Information at the U.S.
National Library of Medicine. The group plans to initiate a "Science
Commons" program in 2003, due in part to demands in the biotechnology
community to find alternatives to traditional intellectual property
approaches. Interview with Glenn Otis Brown, executive director of
Creative Commons, July 2003. 

 

37. US House of Representatives (2003). Report 108-188. Departments of
Labor, Health and Human Services, and Education, and Related Agencies
Appropriation Bill, 2004. Online at:
http://www.access.gpo.gov/congress/legislation/04appro.html 

 

38. OECD. 2003. "Promoting Access to Public Research Data for Scientific,
Economic and Social Development." Organization for Economic Cooperation
and Development. Final Report. March 2003. Online at:
http://dataaccess.ucsd.edu/FinalReport.htm. 

 

39. James Boyle. 2001. "The Second Enclosure Movement and the Construction
of the Public Domain." Discussion paper at the Conference on the Public
Domain. Duke University School of Law, Durham, NC. November 9-11,  2001.
Online at: http://www.law.duke.edu/pd/papers/boyle.pdf 

 

40. Declan Butler. 2003. "Drive for patent-free innovation gathers pace."
Nature. Vol. 424. 10 July 2003. Letter online at:
http://www.cptech.org/ip/wipo/kamil-idris-7july2003.pdf 

 

41. Rai, Arti Kaur  and Eisenberg, Rebecca  S. 2002. "Bayh-Dole Reform and
the Progress of Biomedicine." Law and Contemporary Problems, Vol. 66, No.
1; Nov 23, 2002. Online at: http://ssrn.com/abstract=348343 

 

42. US Code, title 28, section 1498, which covers patents "used or
manufactured by or for the United States without license." The code is
online at:
http://caselaw.lp.findlaw.com/casecode/uscodes/28/parts/iv/chapters/91/sections/se
ction_1498.html 

 

43. Eugene Volokh. 2000. "Sovereign Immunity and Intellectual Property."
Southern California Law Review 1161 (2000). Online at:
http://www1.law.ucla.edu/~volokh/sovimm.htm

 

44. Telephone and email interviews, July-August 2003. Mr. Blackburn is
examining the approach in a forthcoming paper; initial thoughts were
stated at the Biotechnology Industry Organization's annual conference BIO
in June 2003.See: Ronald Bailey. 2003. "BIO2003: Reporter's Notebook."
Reason online. Washington, DC. June 25, 2003. Online at:
http://reason.com/rb/rb062503.shtml 

 

45. The idea was raised years ago in an NIH report which quickly dismissed
it. See: National Institutes of Health. 1998. "Report of the National
Institutes of Health; Working Group on Research Tools."Presented to the
Advisory Committee to the Director. Washington, DC. June 4, 1998. Online
at: http://www.nih.gov/news/researchtools/ 

 

_____________________

 Copyright 2003 Kenneth Neil Cukier.

 Note: This work may be freely copied and distributed provided that the
author and title is cited, as well as indicating that it is a pre-edited
version of an article that appeared in The Acumen Journal of Life
Sciences. If questions, please email the author at: [ kn cukier.com
]kn cukier.com 

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