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National Research Council (US) Board on Research Data and Information; Uhlir PF, editor. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington (DC): National Academies Press (US); 2011.

Cover of Designing the Microbial Research Commons

Designing the Microbial Research Commons: Proceedings of an International Symposium.

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20Microbial Commons: Governing Complex Knowledge Assets46


University of Waterloo, Canada

In talking about the governance of the microbial commons, I will apply a strategic level of analysis and a knowledge perspective. I would like to leave you with three messages:

First, biological knowledge structures are evolving, not only in terms of complexity, but also in terms of their value for future discovery and commercialization. We need to understand what belongs in the commons from a dynamic perspective. What might not have belonged in the commons yesterday may belong in the commons today.

Second, we need to understand clearly the motivation of participants in any commons. It is not just a matter of public sector participants. When my colleagues and I from the University of Waterloo and Wilfrid Laurier University studied 39 open-source initiatives developed after the completion of the Human Genome Project, we found that in many cases private-sector participants were involved, and a few actually catalyzed the formation of those initiatives. We need to understand both the positive and negative consequences of this participation.

Third, we should document these lessons from the commons so that they can be transferred across disciplines and even across markets, as we see researchers from different areas seeking to enter this domain, looking to participate in the commons that are being proposed as well as their own internal commons.

Commencing with the knowledge perspective, the Human Genome Project advanced the view that biological information operates on multiple hierarchical levels and that information is processed in complex networks. It is no longer sufficient to look at just the genomic and proteomic levels. We need to understand the interactions among genes and proteins—how to modulate systems, minimize malfunctions, and optimize for positive functions. From a knowledge perspective, then, biological information has become complementary. Downstream product development relies strongly on upstream research inputs. Furthermore, there is high applicability across biological systems and for our purposes microbial systems.47

Complicating the matter from an intellectual property perspective is that patents can exist at any level of the hierarchy of the research process and, depending on the breadth of those patents they can greatly influence the incentive for follow-on researchers to examine or use elements of such systems. Too broad a patent can inhibit the incentive of users to look at the underlying knowledge assets. So we need to find solutions to manage those incentives, both for first innovators and for follow-on incremental innovators. The proposal of the commons and the liability regime from this symposium is one possible solution.

Turning to motivation, we do need to understand the incentives for participating in the commons. As noted above, our research on 39 initiatives found strong involvement from private-sector participants. There are six classes of incentives:

  1. The development of a collegial reputation as a reward for working in open science. This is no longer restricted to public-sector participants; private-sector participants want to signal their quality as allies, particularly for downstream product development. Beyond catalyzation of several initiatives in our study by private sector participants, the recent open donation of compounds and continued creation of open source discovery initiatives by several multi-national pharmaceutical organizations such as GSK, Pfizer, Eli Lilly, and Merck, provide evidence of this need to signal quality and openness to further collaboration for downstream development.
  2. To generate general reciprocity obligations. I mentioned the complexities and the complementarity between knowledge assets. Both public and private sector participants may want to create reciprocal obligations signaling that they are willing to contribute to the commons so that in the future they can access other external knowledge assets. The creation of open patent pools with multiple contributors can signal this reciprocal obligation assuming equitable contributions and fair access terms.
  3. To influence adoption of a technology or a technology standard through increased diffusion of knowledge. We saw this in our research with the microarray providers participating in the biotech commons in order to influence adoption of their technology as a standard. However, we must note that there may be positive or negative consequences when you influence the adoption of a premature or insufficient technological standard.
  4. To improve the aggregate performance of an industry in order to increase safety or regulation associated with that industry as we discussed yesterday with reference to microbiological materials and outputs.
  5. To preempt rivals. We clearly saw this after the mapping of the human genome, when 10 of the world’s largest pharmaceutical companies came together and formed the Single Nucleotide Polymorphism (SNP) Consortium to ensure that rivals would not encroach on this territory and build patent fences around critical areas necessary for future product development.
  6. To share the risk associated with knowledge production. It is important to examine not only the issue of shared implementation from open-source software development and fair access to technology or biotechnology development, but also the way in which a commons serves to enable collaborative knowledge production. For example, in the pharmaceutical industry, the complexities associated with drug discovery are very intense. The risks are frequently too high and many pipelines for new products are currently empty. The commons can provide the incentive to share the risk for collaborative knowledge production where there are complexities associated with new knowledge and its association to products.

Furthermore, it is important to understand the incentives to participate as well as to be able to predict when participants may exit from any commons. Here the concept of transition point is of value. The transition point is defined as the point in discovery research when researchers come to believe that unilateral gains from private management of knowledge including appropriation activities are greater than shared gains from open or shared knowledge with the subsequent outcome exit from the commons. Therefore, from a strategic perspective, we need to look at when appropriation will take place— when materials will be removed and no longer deposited.

Because the value of knowledge is changing, we are uncertain at any point what value today’s knowledge will have in terms of discovery and product development. A commons can reduce that uncertainty and make it less likely that premature mistakes will be made— specifically through the enclosure of knowledge, such as occurred with the gene races.

In our research, we sought to analyze 39 open-source initiatives developed after the mapping of the Human Genome Project. We looked at the structure and characteristics of the knowledge at stake. What was being produced? How could you classify or characterize that knowledge? What rules were established to govern both data and materials and for downstream appropriation strategies?

Overall, we have learned the following:

  • Participation rules existed in the majority of cases. Consortia had established entry rules, with screening by executive or steering committees. Often commitment policies, membership fees, or large upfront research payments were established or required to enable both cooperation and research.
  • Knowledge access policies exist. In the majority of cases, information is released not only to members, but also to the public at large. There were a few initiatives that were somewhat more closed, which shared information only with members that had made upfront monetary commitments.
  • There were rules to manage both data and materials. The decision whether to deposit data into an open or a closed repository depended on the knowledge access policy. Where knowledge dissemination was open, peer-reviewed publications and deposit into databases permitted not only the release of data but encouraged the validation of the data or deposits. In the majority of cases, consortia advocated the use of nonexclusive royalty-free licenses for noncommercial use of materials and discovery tools.
  • The consortia generally avoided issues related to commercial use and product development. It was assumed that this would be handled at the individual transaction level.
  • It was absolutely important to create transparency with regard to motivation. In this case, upfront commitments could provide that clarity i.e. monetary support, human capital support, or open donations of knowledge-based assets. Motivation for participation given the objectives established by the initiative clearly had an impact upon knowledge dissemination and access as we discovered when comparing the open initiatives to the more closed initiatives in our sample.

How do we apply these observations to the microbial commons? We have limitless capabilities for applying microbial knowledge to the energy and environmental sectors, in the development of alternative biofuels, the generation of biodiesel, and bioremediation. We need to approach this knowledge from a whole systems perspective, however. Hence, we should look at communities of interacting microbes.

Research and applications require integration and analysis of data to discern patterns of communities of microbes. The continued sharing of microbial information will be critical, as will linking literature, databases, and user communities. This is important not only for collaborative discovery, but also for the validation of the data and the results. In addition, given the sophisticated nature of the visualization data that is emerging today, we need to enable the joint representation and standardization of the data. Some of the governance mechanisms we might need to consider are the timing of data deposits, access and use, exemption clauses for noncommercial use, transfer of management from depositors to collective organizations, and commercial use clauses.

Several open access journals, databases, and supporting tools were discussed in this symposium yesterday. I want to add that it is not just a matter of the data, but we also need to have a supporting tool infrastructure in order to create queries to gain benefits from that data and pursue further discovery. For example, the Global Biodiversity Information Facility (GBIF) is an information-based infrastructure for connecting users to a globally distributed network of databases. Here, we use the notion of linking knowledge assets from an information technology infrastructure perspective.

The incentive to share microbial data is also manifested in the private sector. The Helicos BioSciences Corporation has opened up its microbial datasets, as well as a query tool. What is their motivation? We discussed disincentives yesterday, but what would be the incentive in this case? Most likely it is to showcase their genetic analysis system—an attempt to encourage the adoption of their system by displaying the value and the sophisticated nature of their data.

In yesterday’s talks, we discussed the linking of both materials and information in biological resource centers. The goal is to promote common access to biological resources and information services—we see that StrainInfo is providing electronic access to the information about biological materials in repositories.

BioBricks is quite interesting from a materials management perspective. It was developed as a nonprofit foundation by the Massachusetts Institute of Technology, Harvard, and the University of California, San Francisco. With BioBricks we are moving into what I consider the convergence paradigms, as now it is necessary to manage the complexities associated with synthetic biology. BioBricks makes DNA parts available to the public free of charge via MIT’s registry of standard biological parts. This is a collection of approximately 3,200 genetic parts that can be mixed and matched to build synthetic biology devices and systems. The commercial or other uses of these parts are unencumbered—without the assertion of any property rights held by the contributor over users of the contributed materials. However, novel materials and applications produced using BioBricks contributed parts may be considered for protection via conventional property rights.

Beyond the issues of data and materials management, we must also deal with the changing value of knowledge, and we find the commons model being used to manage downstream assets. One example of the latter is the Eco-Patent Commons. This is a project by the World Business Council for Sustainable Development whose mission is to manage a collection of patents pledged for unencumbered uses—even for proprietary purposes in products, processes, and composition of matter—that are directed towards environmentally friendly applications. As of 2008, 100 eco-friendly patents had been pledged by private-sector participants, ranging from manufacturing processes to compounds useful in waste management. What is the motivation there? Perhaps the participants recognize that, in dealing with premature technologies, they need to assure that there will be interoperability between technologies that develop downstream. The AlgOS Initiative is very premature and not particularly coherent yet, but I thought it was worthwhile to mention. It is an open-source initiative seeking ways to produce biodiesel from algae. The group is attempting to aggregate research inputs from a variety of experts in order to arrive at a full-cycle design for biodiesel production from algae, allowing for modification based on the open source software GNU General Public License approach, in which modifications are permitted as long as one complies with the requirements to pass on the source code to any recipients of one’s modifications, to provide them the same freedom to modify it, and to provide notice of those terms of the license.

Finally, in parallel with these other efforts, stakeholders are discussing so-called “green” licensing. Such licensing is directed towards developing countries that are looking to develop green technologies. An international licensing mechanism is under discussion that would have developing countries pay a fee in order to access this technology, while at the same time protecting the innovating firms. It will be interesting to see what form they choose for their fee mechanism. The underlying goal is to allow countries at different stages of development to be able to access the same technology.

Clearly, as knowledge characteristics change, the governance structures may need to change with them. Early on, for example, some experts suggested that data would not be deposited in the commons. Today, there is a question whether tools—pharmaceutical tools or biological tools—should be placed into the commons. Table 20-1 summarizes various examples from the microbial commons, looking at their characteristics and at the various governance strategies that are currently being employed.

TABLE 20-1. Governing the Microbial Commons.

TABLE 20-1

Governing the Microbial Commons.

To summarize the pragmatic outcomes, managing knowledge assets has become critical, not only in the systems paradigm, but in the convergence paradigm. Here we see biological sciences, chemical sciences, physical sciences and information sciences increasingly coming together to address the complexities of health product technology, nanotechnology, green technology and energy based technology development. We need to determine what really belongs in the commons and what governance strategies are most appropriate so that researchers in multiple markets can pursue product development opportunities. These goals imply certain policies. The need for greater transparency of motives during knowledge production suggests that there should be an establishment of and commitment to rules regarding knowledge production. Different conventions regarding knowledge dissemination and appropriation imply the need to establish early in a research project what should be disseminated and in what format. Here, our research provides some indication of the commonality of rules for both knowledge production and dissemination. Follow-up research also looks closely at the transition point and its application to varied knowledge assets.

The National Research Council report A New Biology for the 21st Century (2009) advocates large teams converging and varied disciplines working together, whether that is promoted through federal policy or other means. We need to keep in mind that as scientists, information technology professionals, and other experts work together, they each have differing conventions regarding knowledge dissemination and appropriation. Some of them may find value in pure disembodied knowledge. Others may find value and appropriate embodied knowledge with the final goal marketable product development. We need to bring together these disciplines under a common framework, which is what a structured commons can offer to them. Extending our analysis and understanding of knowledge based activities to the convergence paradigm should lend insight into how best to structure a commons with varied disciplinary participants. Consequently, it will be important to analyze new case studies involving open-source innovation that targets the energy and environment sectors in order to look at evolving models of innovation. What types of participants are in those sectors pursuing those models? How do they handle the increased complexities as knowledge assets converge and are increasingly linked together and as new rules and perceptions of value emerge?

Finally, it would be valuable to create a repository of governance strategies for knowledge assets as is currently being undertaken by the BioEndeavor Initiative (, including any licensing templates or tools, so that we can apply those across commons, across disciplines, and across markets. As new markets choose to develop their own commons, they can have the benefits of the lessons we have learned about managing knowledge based assets and the development of open access journals, open data networks, and the supporting IT infrastructure.



See Allarakhia M, Wensley A. Systems biology: melting the boundaries in drug discovery research [Internet]. In: A Unifying Discipline for Melting the Boundaries Technology Management: Portland, OR, USA: [date unknown] p. 262–274.[cited 2011 Aug 15] Available from: http://ieeexplore​.ieee​.org/lpdocs/epic03/wrapper​.htm?arnumber=1509700.

Copyright © 2011, National Academy of Sciences.
Bookshelf ID: NBK92719


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