Open Biology

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Open Biology

Putting biological research, such as genome research, in the public domain.

See also our entry on Open Source Biotechnology

Example

From an article in Forbes at 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." (http://www.forbes.com/2007/02/12/novartis-genes-diabetes-research-biz-cz_mh_0212novartis.html?)


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).


Discussion

How Open Biology differs from Open Source Biology

Rob Carlson believes the concept of Open Source Biology or Open Source Biotechnology has no real meaning [1]:

"the analogy between software and biology just doesn't go far enough. Biology isn't software, and DNA isn't code. As I study the historical development of railroads, electricity, aviation, computer hardware, computer software, and of the availability of computation itself (distributed, to desktop, and back to distributed; or ARPANet to Microsoft Office to Google Apps), I am still trying to sort out what lessons can be applied to biological technologies. I have only limited conclusions about how any such lessons will help us plan for the future of biology.

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." (http://synthesis.typepad.com/synthesis/2007/03/thoughts_on_ope.html)


Security advantages of an open biology approach

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.

Rob Carlson [2]:

"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." (http://www.kurzweilai.net/meme/frame.html?main=/articles/art0614.html?)


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." (http://www.kurzweilai.net/meme/frame.html?main=/articles/art0614.html?)

More Information

  1. See our tag on Open Biology at http://del.icio.us/mbauwens/Open-Biology
  2. Biological Innovation for Open Society, at http://www.bios.net/daisy/bios/15 ; overview of 'Open Biology' developments, at http://www.wired.com/news/medtech/0,1286,66545,00.html;
  3. "BIOS will soon launch an open-source platform that promises to free up rights to patented DNA sequences and the methods needed to manipulate biological material. See http://www.wired.com/news/medtech/0,1286,66289,00.html?
  4. This article explains why Open Biology is a good idea, also for security reasons, at http://www.worldchanging.com/archives/002893.html
  5. The Open Lab initiative, http://bioinformatics.org
  6. Essay: Open and Collaborative Biomedical Research: Theory and Evidence. Rai Arti.
  7. 195 peer reviewed Open Access Journals in Biology and Medicine published here: http://www.biomedcentral.com/home/