The best mistake I ever made: How a daunting administrative role became the experience of a lifetime| 05/23/2016
Ten years ago, Jay Keasling asked me to take part in Synberc, and I said no.
At the time, Jay was just emerging as a leader of the new research field called synthetic biology. He had just formed the world’s first Synthetic Biology Department at Berkeley Lab, co-organized the Second International Conference on Synthetic Biology (SB2.0), and received a significant grant from the National Science Foundation (NSF) to create the Synthetic Biology Engineering Research Center, or Synberc. I was an administrator at Berkeley Lab and had helped Jay with these and other activities in the early days of this burgeoning field. I distinctly remember the pre-award meeting with NSF at the start of Synberc, and how the NSF went out of its way to impress upon us the crushing administrative and reporting requirements attached to these large and complicated research centers. I felt sorry for the poor sucker who got that job. I told Jay as much, hence my turning down the Synberc opportunity… at least for a day.
Thankfully, I reconsidered, and joining Synberc was the best mistake I ever made. Why? There are three reasons really.
The first is that, as difficult as Synberc was to manage, it exposed me to just about every research administration challenge imaginable. Whether it is reporting, managing subawards, cost sharing, human resources, IT, event planning, government affairs, setting up industry programs, or simply paying bills, NSF Engineering Research Centers like Synberc touch just about every aspect of the university research enterprise. Having run Synberc, I feel have the know-how to administer just about anything in a university setting. And because ERCs are multi-university collaborations, I got to see how other universities approach the same kinds of research administration challenges.
The first year or so, though, I was in something like the fog of war. I had to learn the fundamentals of research administration while simultaneously starting Synberc programs and figuring out how to give NSF all the data it required. As time went on, I built an online data collection and project proposal system to manage the NSF requirements and our internal project selection process. I also learned how best to connect with Synberc investigators, UC Berkeley business offices, and our partner universities. It all began to gel, although the NSF annual reporting was a huge burden that never seemed to get easier.
Meanwhile, Synberc researchers were climbing their own learning curve. In particular, I remember early conversations about whether Synberc ought to take a bottom-up approach (build basic, generally useful biological parts in an open source manner) or a top-down approach (build integrated systems for specific testbed applications). The answer seemed to be something in the middle, and Synberc eventually rallied around projects that would create compelling proofs-of-principle as well as drive the creation of basic parts, tools, and knowledge. It was a fascinating conversation -- one that made me feel like something big was happening.
As the fog of war lifted and the administrative aspects became more routine, I was able to turn my attention elsewhere and take on new challenges. There was a lot to do: The NSF gave us a broad mandate to advance a new field, train a generation of synthetic biologists, and engage diverse groups about the responsible advance of synthetic biology. The opportunities seemed endless. This brings me to the second reason I’m thankful I joined Synberc: with Jay’s encouragement, I was able to go beyond the typical role of research administrator and participate in several intriguing Synberc projects.
For example, I found myself working with researchers in what was called the Human Practices group of Synberc. Researchers like Gaymon Bennett (ASU) were interested in the social dimensions of synthetic biology: how it was defined and framed, who benefited from it, and how organizations like ours shaped its development. In exploring these issues, I helped them write a small, successful proposal to create an interactive website conveying their conceptual view of synthetic biology. Later, I worked with Megan Palmer (Stanford) and Samuel Weiss Evans (Harvard) to develop processes that encouraged researchers to think through the broad potential impacts of their work beyond the bench. These experiences have encouraged me to continually explore how, as a research administrator, I can better orient Synberc’s organizational and research practices toward a mindset of responsibility and public-mindedness.
In another example, one year the NSF nudged Synberc to improve its diversity numbers. Several of us took it as an opportunity to do something meaningful about diversity and inclusion. We first developed a climate survey that sparked a conversation within the entire Synberc community around themes of implicit bias and inclusivity. Soon after, we appointed our first Synberc Diversity Fellow, Sabriya Rosemond (UC Berkeley). This grew into the Expanding Potential program, which I co-founded with Shaila Kotadia (UC Berkeley) to create a more inclusive STEM environment within and beyond Synberc’s borders. Expanding Potential stands as an excellent and effective model program for creating change in diversity and inclusion at many scales. I also helped to create a “Women in Synthetic Biology” resource to encourage gender-balanced conferences in our field that remains in wide use today. All of this taught me a lot about the real issues facing underrepresented students and faculty in STEM and how we might address them.
Here’s one last example of being taken in career directions I never expected. As terms like “genetic engineering” become mainstream and the products of engineering biology make their way to the public, synthetic biology has come under scrutiny from skeptics questioning whether researchers are creating dangerous new abilities or playing god. This led me to think about these issues myself and explore how we might better engage the public on questions like: What are the benefits and risks of synthetic biology? Where are the bright red lines we should not cross? How can researchers share their progress and passion for engineering biology without becoming self-interested advocates? And finally, how do we incorporate public input into our national strategy for advancing synthetic biology responsibly and for the greatest public benefit? This led me to develop a public engagement plan and initiate Synberc’s “Conversations about Synthetic Biology” series. I gained a deep appreciation of the challenges of communicating across the expert-layperson divide, and learned much about how we can more authentically engage the people we endeavor to serve.
Beyond the professional experiences and achievements is the third and most important reason why Synberc was the best mistake I ever made: I feel as though I have had a front-row seat at this fascinating moment in biotechnology. The feeling that “something big was happening” never left me, and it has been a privilege to work with some of the best minds in science and engineering. Though I’m not a researcher myself, I know that people like me play an important role in supporting and enabling scientific progress. I also feel responsibility as a citizen and non-scientist to bear witness to what’s going on, share what I see, and encourage others to consider our fast-changing relationship with biotechnology. With something so important as building the future with biology, all of us should participate in the conversation.
Stepping uncertainly into Synberc a decade ago, I could never have imagined what a long, strange and wonderful trip it would be. Yes, it’s like herding cats. Yes, staring at spreadsheets can be a real drag. And yes, every annual report gives me more gray hairs. But if the opportunity arose for ten more years of the same, this time I would jump at it.
co-written with Shaila Kotadia, PhD, Synberc Education, Outreach and Diversity Manager
Too often, scientific meetings consist mainly of male speakers, and synthetic biology is no exception. Recently, a genome engineering conference asked Synberc to become a sponsor. We noticed that the program had an extreme gender imbalance: Only two women at the podium while over 30 men would be speaking. Synberc informed the organizers that we would not support their meeting due in part to the gender inequity. We followed up with a second email detailing our decision and providing practical advice for avoiding a lopsided gender imbalance in the future.
The organizers responded and explained to us the reason for the gender imbalance. In summary, the organizers wanted to bring together leaders in academia and industry that published in Science, Cell and Nature over the past two years to represent the most recent discoveries. They generated a list using these criteria with “no biases” (i.e., no attention to gender, religion, race, and other groups). More females were invited but declined.
While we appreciate the organizers’ attempt to remain neutral, such an approach is flawed in that it perpetuates the underlying biases endemic at those publications, as evidenced by the list of speakers generated. Ignoring gender implicitly endorses existing imbalances. (West et al. have shown gender disparities in scholarly authorship are persistent although decreasing.) Therefore, conference organizers must work proactively to right systemic underlying biases. In addition, generating a program based on authors from the most elite journals ignores many important papers from other journals such as PNAS, ACS Synthetic Biology, Nucleic Acids Research, Nature Biotechnology, and others. Unfortunately, there are no good measures for whether a given journal is diversity balanced, and no guarantee that these journals are any less biased.
Many resources exist to help generate a more balanced podium. These include Synberc’s women at the podium list, a case study from the American Society for Microbiology, and ten simple rules to achieve gender balance at conferences published in PLoS Computational Biology. We too have observed that females are more likely than males to decline a speaking invitation. When these women decline, we use it as an opportunity to ask them to suggest other well qualified non-male speakers. We are pleased that the conference organizers who approached us have committed to utilizing these resources and strategies in the future.
Speaker bias goes beyond the male-female divide: Many underrepresented groups are not fairly represented at scientific meetings. Moreover, gender is not binary, and other gender identities should be represented at the podium as well. The reasons for gender and racial imbalances at the podium may differ, but awareness and preemptive strategies are essential to solving both problems.
We urge all individuals to carefully consider who they invite to speak at meetings. Highlighting the excellent work of underrepresented people gives support to diverse audiences, ultimately leading to a broader and more diverse talent pool. To create a more diverse community, we must recognize our own unconscious biases, be proactive in our approaches, and change our behaviors to be more inclusive.
Submitted to the Inter Academy Panel on May 23, 2014.
Professor ter Meulen,
We respond on behalf of the Synthetic Biology Engineering Research Center, an NSF-supported research consortium. Since 2006, Synberc has helped shape the field of synthetic biology, developed foundational technologies, educated emerging leaders, and promoted the responsible development of the field.
Synberc supports the Inter Academy Panel’s recent statement on realizing the potential of synthetic biology. In particular:
1. We endorse IAP recommendations on the relationship between foundational advances and practical applications. Much more foundational research is still needed to understand the biological and genomic underpinnings of synthetic biology that will allow us to address a broad range of challenges. We must continue to develop sound principles for assembling biological systems across different contexts, construct libraries of well-characterized components, and create the tools to design, build and test biological systems. Importantly, we must also develop the tools and technologies to provide policymakers and the public with the information needed to make science-based policy decisions about risk and uncertainty of real-world applications.
2. We agree with the need to systematically prepare researchers to address the full spectrum of effects of synthetic biology. The next generation of biotechnologists will require not only extraordinary technical foundations, but also serious education on ethical, legal, societal and environmental issues, if the field is to develop justly. Synberc’s Policy & Practices program is working to that end by putting into practice systems to influence the selection and conduct of projects within Synberc. It also leads efforts with our public agencies and company partners to develop policies on governance and risk. Within Synberc-supported iGEM, the Policy & Practices program is helping to cultivate an ethos of responsibility and care among young synthetic biologists. The lessons learned within these efforts can and should be applied within other, broader contexts.
3. We must expand the international dialogue to include diverse academic and public participants. Directing the research toward tangible social goods will require an active process involving academics across many disciplines, industry practitioners, funding agencies, as well as the workers, consumers, families, and patients who we hope to benefit. The field will develop justly only if practitioners listen carefully and respond to public concerns about improving regulations and sharing benefits. Scientists and non-scientists alike must be clear about the ethical issues created by synthetic biology, as well as the critical human needs that this biotechnology can help to address.
4. We endorse the IAP call for a global policy and framework to support responsible science. Funding for the U.S.-based Synberc consortium is scheduled to come to a close at a time when it’s more important than ever to strengthen educational programs, support foundational research, and create inclusive venues on an international scale. We believe now is the time to expand this model into a larger and more inclusive organization to advance scientific and social progress. We would ask the major U.S. funding agencies (NSF, NIH, DOE, DARPA, and others) and their international counterparts to join with existing technologists, industrial partners, and civil society in committing to fund a long-term internationally coordinated program. The organization would serve as the primary conduit to coordinate international efforts and include an iterative roadmapping process to focus on global and topical issues important to and inclusive of both scientists and the public. The exact contours of this organization are to be determined, but models could include the Computing Community Consortium (www.ccc.org), the International Technology Roadmap for Semiconductors (www.itrs.net), and the International Society for Stem Cell Research (http://www.isscr.org/).
We appreciate the IAP’s statement on realizing the global potential of synthetic biology. There is an undeniable need for a coordinated ecosystem of people and institutions if we are to responsibly advance this open and distributed technology for maximum public benefit. We look forward to working with members of the IAP and many, many others to sustain, promote and grow that ecosystem.
Jay D. Keasling (Director), UC Berkeley
J. Christopher Anderson, UC Berkeley
Adam Arkin , UC Berkeley
George Church, Harvard Medical School
Tanja Kortemme, UC San Francisco
Natalie Kuldell, MIT
Wendell Lim, UC San Francisco
Susan Marqusee, UC Berkeley
Kenneth Oye, MIT
Megan Palmer, Stanford University
Kristala Jones Prather, MIT
Pamela Silver, Harvard Medical School
Christopher Voigt, MIT
Ron Weiss, MIT
There seems to be a lot of commotion in the synthetic biology community these days about how to organize our research community at the national level. This is definitely true within Synberc, where our Sustainability Project has been critically assessing what is needed to responsibly advance the field.
For all of the hullabaloo, there’s very little actual organizing going on at the national level. The field has defaulted into a “communities of practice” mode, where smaller groups of practitioners of a particular interest or expertise naturally come together to share information and experience, and have an opportunity to develop themselves personally and professionally, or to advance a particular agenda.
Here are some specific examples of how the synthetic biology community has self-organized:
- iGEM - The “world’s premiere synbio competition” but also an important testbed for educating synthetic biologists, creating a shared database of parts, and for learning how to screen projects for safety/security concerns. Probably the most successful effort to organize the synbio community not just in the US but worldwide.
- SynBioBeta - A recent but highly successful effort led by one organizing dynamo (John Cumbers, Santa Clara University/NASA Ames) that is bringing together small start-up companies and other entrepreneurially minded interests to foster the “synthetic biology start-up ecosystem.”
- BioBricks Foundation - An early pioneer in trying to bring together the synthetic biology community in more or less the mode of a professional society. BBF runs the SBX.0 International Conference Series, which is the synbio community’s primary conference. BBF has also led a call for technical comments that led to the development of a BioBricks Public Agreement (BPA) to enable easier sharing of biological parts.
- The DIYbio 'movement' is a good example of how citizen scientists and enthusiasts are organizing themselves at the very local levels -- the DIYbio community has not yet developed a strong guild at the national level, but the potential appears to be there.
- Synberc - The US’s first and largest single effort to bring together leading researchers and universities to establish the scientific and engineering foundations of synthetic biology. It too was generated at the grassroots level by a group of like-minded researchers, rather than by a national fiat.
One more important way in which the community is organizing itself: A crop of synthetic biology centers has blossomed at individual universities:
- UCSF Systems and Synthetic Biology Center
- Synthetic Biology Center at MIT (SBC@MIT)
- Synthetic Biology Institute at UC Berkeley
- BU Center of Synthetic Biology (new!)
- UW Center for Synthetic Biology
- And others I apologize for not mentioning
The formation of these centers suggest that the community is hungry for organizational entities that last over many years and help researchers from diverse backgrounds come together to pursue shared research aims.
Zooming back out to the national level, the basis set of leaders in synthetic biology are often recombined in different ways to address different problems in different contexts. For example, many of the experts involved in a NAS study on technical roadmaps are likely to be seen at another study on the ethical, legal and social ramifications of synthetic biology. The basis set of leaders is slowing growing outward as the field identifies new opportunities/challenges and becomes aware of and comfortable with others from different research communities. As with any highly multidisciplinary endeavor, the challenge for our community is to enable and encourage diverse practitioners with shared goals to come together to solve problems we cannot solve independently.
In the UK, the scientific community has had better success in organizing itself at the national level, especially through the UK Roadmap process. One might argue about the practical value of the technology and society roadmap that such efforts produce, but the roadmap itself is probably not as important as bringing together new assemblages of scientists, policymakers, funders, and other stakeholders to think about the opportunities and challenges of synthetic biology from many perspectives. The report accompanying the roadmap has a number of important insights (IMHO) and did seem to result in the national synergy in synbio that the UK is now experiencing.
Given the current status of organizing in the US and the need to develop a more coordinated framework, one might consider something like a spoke-and-hub model for getting there. In a sense, this is what Synberc is. The universities are bound together loosely by Synberc. The colleges and their investigators are free to pursue independent projects and even engage in cooperative competition, yet they can leverage Synberc infrastructure for thinking about "problems of the commons". These include strategic roadmapping, responsible innovation, education and workforce development, industry liaison (e.g., creating a one-stop shop for industry members to interact with leaders of the field), addressing intellectual property concerns, metrology and standards, communications & advocacy (enabling the community to speak with a common voice), and simply building community through regular symposia and workshops. Given the proliferation of “communities of practice” across the U.S. in synthetic biology, an elastic organization may be the only kind that can accommodate such a wide range of researchers and organizations.
On July 13, 2013 the U.S. Supreme Court issued their decision in Association for Molecular Pathology v. Myriad Genetics, Inc. Naturally, this decision has sparked much discussion amongst the synthetic biology research community. What does this decision mean with regard to the patentability of synthetic constructs created from natural DNA sequences? Does this decision mean that the information contained within DNA sequences is patentable? And, ultimately, how will this decision affect innovation in synthetic biology?
It is important to keep in mind that the court limited their decision to only one inquiry under U.S. patent law: Does isolated DNA or cDNA constitute patentable subject matter under 35 USC 101? The short answer is: NO for isolated DNA based on natural sequences, and MAYBE for cDNA molecules - see end of first paragraph, page 17.
The court specifically expressed no opinion whether cDNA satisfies the other requirements for patentability such as novelty (35 USC 102), non-obviousness (35 USC 103), and enablement/definiteness (35 USC 112) - see footnote 9.
As is typical of U.S. Supreme Court decisions, the full impact will be become more apparent as the lower courts interpret this decision in subsequent cases. While we may not yet have answers to all of our questions, we do have more certainty today than we did before.
What we know for sure is that this decision renders invalid any claim with the structure “isolated DNA having SEQ ID NO: 1”
Synthetic biology is often referred to as "the field of the future," the foundation of a "third industrial revolution" that will change the way we produce fuels, materials, medicines, as well as the way we produce knowledge of biological systems. But while the self-consciously revolutionary language of synthetic biology declares a change of the industrial status quo, the metaphors we rely on are explicit references to the successful revolutions of past industrial technologies.
The term synthetic biology echoes the successes of synthetic chemistry, while the guiding concept of standardization in genetic components is modeled on 19th century standardization of interchangeable parts. Industrial metaphors mix further as we climb the abstraction hierarchy; genetic parts are assembled to fit into a cellular chassis, creating logic gates and circuits that can compute biological information, leading to the control of cellular factories.
These metaphors help us to understand how an industrial revolution might emerge from a biology lab, showing a possible path from ideas to industry. Like the "horseless carriage," perhaps the analogies of living cells to computers give us a sense of familiarity with a technology whose potential we have not yet fully grasped. Industrial metaphors have long played a role in how we understand biology and the human body, from Fritz Kahn’s 1927 paintings of “Man as Industrial Palace” to analogies between brains and computers. By referencing the products and methods of previous industrial revolutions, synthetic biology aims not only to aid understanding but also to demonstrate the future potential of the field. These metaphors draw the projected lines of Moore's exponential increase as strands of DNA, imagining analogous and expanding industries based on carbon and sunlight rather than silicon and fossil fuels.
How will this revolutionary transition happen? What conditions are necessary to foster such a change? As synthetic biology is largely still a laboratory rather than industrial enterprise, perhaps Thomas Kuhn's The Structure of Scientific Revolutions, can provide a useful framework for understanding the structure of the promised techno-scientific-industrial revolution of synthetic biology. Based on his analysis of the history of chemistry and physics, Kuhn argues that the evolution of scientific knowledge proceeds by punctuated equilibrium — periods of "normal science" interrupted by scientific revolutions, paradigm shifts that change the nature of the questions being asked and the "puzzles" being solved. Paradigms shift after the accumulated weight of unexpected results becomes too large, when facts that don’t fit the model begin to open new questions and when the "failure of existing rules is the prelude to a search for new ones."
Some of the failures of modern industry are explicit starting points for synthetic biology projects, like engineered bacteria that can sense or consume industrial pollutants, but norevolution can address all the failures of the paradigms that came before. For scientific revolutions, Kuhn writes, "To be accepted as paradigm, a theory must seem better than its competitors, but it need not, and in fact never does, explain all the facts with which it can be confronted." What problems can synthetic biology solve and what problems are missed, outside of the paradigmatic umbrella of biotechnology? What new problems might arise with a biology-based industrial revolution?
These are difficult and important questions with no clear answer, questions that we ask ourselves when we talk about risk, implications, and outcomes of new technologies. But perhaps there is a deeper question that emerges when we look at synthetic biology through a Kuhnian lens: by working to solve the problems of current industry, replacing or cleaning up after polluting chemical factories with microscopic cellular factories, are we simply replicating the old paradigm with a biological tint? Are we talking revolution while just solving puzzles?
Industrial metaphors for biological systems are being inverted, but the industrial paradigm remains: “Man as Industrial Palace” becomes “Industrial Palace in a Cell.” How can a biologically driven industry change these metaphors, change the way we make things and the way we do things that takes biology on its own terms, that changes the paradigm through which we see the world?
Within synthetic biology, programs that I’ve been involved with such as Synthetic Aesthetics and the Synthetic Biology Leadership Excellence Accelerator Program (LEAP)--sponsored by Synberc's Practices thrust--are efforts to integrate new questions, metaphors, and paradigms into the research goals and visions of synthetic biologists. Synthetic Aesthetics joins artists and designers with scientists and engineers to consider not just implications of the products of synthetic biology but to reconsider what those products might be—the metaphors that we use to understand and design nature. LEAP has different but complementary goals, bringing together scientists and engineers in academia and industry with experts from policy, ethics, economics, and law and providing a space to creatively consider what it would mean for synthetic biology to work in the public interest.
Both programs encourage those involved with synthetic biology to think beyond existing paradigms, both in science and industry. Conversations like these may help us to push beyond the industrial metaphors that we depend on when we talk about the potential of synthetic biology, providing us with new paradigms that can be truly revolutionary.
Tune into Christina's regular blog at Scientific American.
It’s a particularly exciting time for synthetic biology and for developments in intellectual property law. Advances in the engineering of biology are deepening our understanding of how biological systems work and leading to new applications that could help promote human health and preserve the environment. At the same time, tremendous advances in patent law are changing the way in which innovators seek protection for their intellectual property rights.
The sweeping reforms to U.S. patent law brought about by the Leahy-Smith America Invents Act have created new opportunities and challenges for the synthetic biology research community. On March 16th of this year the U.S. transitioned to a “first-inventor-to-file” priority system for patents, which is more aligned with the patent laws of other countries and will impact the strategic choices made by synthetic biology researchers seeking patent protection for their inventions.
Other exciting changes to U.S. patent law include crowdsourcing the examination of patent applications as well as broadening public participation in the post-grant review of issued patents. These changes open up new possibilities for the synthetic biology research community to engage with the U.S. patent system and help ensure that patent protection is awarded only for inventions that truly merit a 20-year grant of monopoly rights.
Court decisions affecting the interpretation of patent laws also may impact innovation in synthetic biology. One case currently before the U.S. Supreme Court – Association for Molecular Pathology v. Myriad Genetics, Inc. – addresses the patentability of isolated DNA and cDNA molecules. While the Myriad case specifically focuses on DNA derived from human genes, the decision could shed light on the patentability of synthetic DNA derived from natural sources. Oral arguments for the Myriad case are scheduled to take place on April 15th.
Another case currently before the U.S. Supreme Court – Bowman v. Monsanto, Inc. – examines whether patent holders can enforce their patent rights on the products of self-replicating technologies after an authorized sale. The Bowman case is specifically looking at seeds from genetically modified plants, but self-replicating technologies abound in synthetic biology and the decision could impact the commercial development of useful products and constructive applications of synthetic biology. Oral arguments for the Bowman case were held on February 19th and a decision is expected by June.
Here at Synberc, we are focusing on how property rights can best be applied and adapted to promote innovation in synthetic biology. We’re conducting a survey of the enabling technologies of synthetic biology so that we and others can systematically investigate the property rights associated with these technologies. We’re also developing a portfolio of options that will explore possible legislative changes as well as policy initiatives and community actions to more effectively work within the existing patent-based legal framework. We anticipate these options will not present a complete solution for all the property rights issues encountered in the emerging field of synthetic biology, but instead will serve to inform and contribute to broader discussions about the optimal use of property rights to promote innovation in synthetic biology and biotechnology, more generally.
Linda Kahl, Ph.D., J.D.
Legal Scholar, Synberc
Hello and welcome to our blog! Here you'll find informative opinion pieces about a range of issues in the field of synthetic biolgy, researcher profiles, and helpful resources in the form of both videos and text. Please join us here each week for commentary created by and for members of our community.
Stay tuned for Linda Kahl's blog next week, where she discusses U.S. patent law reform and current U.S. Supreme Court cases that may impact the ways in which DNA might be patented, as well as whether patent holders can enforce their patent rights on the products of self-replicating technologies after an authorized sale.
Also on deck is a blog from Christina Agapakis on the impact of Synberc's Leadership Excellence Accelerator Program.
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