For reference only.

The colloquium will take place on September 30, 2011 in the University of Ottawa’s Tabaret Hall, room 112.  The event will begin at 0900, but attendees should arrive at 0830 to sign in.

0830 Sign-In

0900   Opening of colloquium – Purpose, Agenda and Introductions

0915    Johannes Geiselmann (Grenoble) – Synthetic Biology 101

In this opening talk I will try to define “synthetic biology” and illustrate its principles using selected examples. Synthetic biology is an emerging discipline combining approaches from the life sciences, engineering, physical sciences and mathematical modeling. Even though the techniques taken from each discipline are not revolutionized, their combination produced results that go well beyond classical biotechnology or genetic engineering. Using knowledge about the global functioning of an organism, the field of systems biology, we can imagine new biological functions, model the behaviour of the new system, and assemble the corresponding biological parts. These new biological functions can simply be additions to the behavioural repertoire of the host organism that remain almost independent of the host itself. Other modifications rewire the regulatory networks of the target organism and profoundly alter its functioning. Selected examples will illustrate these different levels of engineering of a living organism.

0930    Alexandre Dawid (Grenoble) – From Computer Simulations to Gene Design: the Case of RNA

DNA is maybe the most popular figure and symbol of modern genetics and of our understanding of the intimate mechanisms of life. DNA is known to carry the genetic information, encoded in its two helical strands. This information is transcribed by the cells into another biomolecule, the RNA, which in turn is translated into proteins, which for a long time were believed to be the principal hard workers of the cell. In recent years, however, it was shown that RNA, an a priori mere copy of DNA, carries not only the genetic information but is also able to take a tremendous variety of roles in the cell. RNA is built from 4 elementary building blocks called bases, which bind to each other by defined rules. These rules explain how RNA molecules fold on themselves in complex functional structures. I will present how a computational approach integrating these rules can be used to design synthetic RNA sequences with predefined biological functions.

1000    François Képès (CNRS) – Synthetic Biology and Global Optimization of the Transcriptional Scheme in Microorganisms

Synthetic Biology renews the agenda of biotechnology and sets new ambitions. Paradoxically, it simultaneously attempts at perfecting the industrial character of biotechnology, for instance by emphasizing standardization and re-utilization, and at freeing itself of the historical process of evolution to allow new degrees of creative freedom, for instance by announcing that natural Life as we know it is one form of Life among many. We shall examine how this apparent paradox may be reduced in daily practice.

1030    Break

1100    Mads Kaern (University of Ottawa) – Advancing Genetic Engineering through Synthetic Biology

Synthetic biology has enabled advanced genetic engineering where multiple DNA parts are assembled into arrangements that provide genomes with novel or improved functionalities. In this talk, I describe two initiatives launched to facilitate the engineering of biology, the Registry of Standard Biological Parts and the International Genetically Engineered Machines Competition (iGEM). While the Registry ensures that synthetic biology parts and tools are freely available for innovation, the iGEM provides the training of the next generation of genetic engineers and biotechnology entrepreneurs.

1130    Christina Agapakis (UCLA) – Designing Biologically: Synthetic Biology Devices in an Environmental and Social Context

Synthetic biology aims to turn molecular biology into an engineering practice grounded in design principles in order to better understand and simplify the complexity of biology and apply it to industrially useful processes. In this vision of the future, living cells become the machines of a new industrial revolution, with new technologies bridging the molecular and industrial scale while often ignoring the human, social, and environmental scales. Leaving behind the metaphors of machines and computers and learning from the rich complexity of living cells and the work of artists and designers studying the social implications of biotechnologies, we can find the tools that make biology a good substrate for design and the principles for beneficial engineering at the human scale. Collaborations between engineers, biologists, designers, and artists embracing evolution as a design tool and ecology as a model for robust systems have the potential to lead to useful, environmental, and ethical synthetic biology projects and products.

1200    End of Morning Session

1215    Lunch

 1330    Keynote address
Michele Garfinkel (EMBO and J. Craig Venter Institute) – Synthetic Genomics: Science and Governance

In 2010, scientists at the J. Craig Venter Institute reported the construction of a small bacterial genome that could be transplanted into a related cell, and would ultimately drive the replication of many subsequent generations of bacteria. Among other techniques, the scientists employed a set of DNA construction technologies collectively called synthetic genomics. Focusing on the construction of this genome and the resultant bacterium Mycoplasma mycoides JCVI-syn1.0 to provide examples of the range of scientific and policy issues prompted by research in many areas of biology, including synthetic biology, I will describe efforts at the Institute and by others to evaluate the potential risks and benefits of the use of synthetic genomics technologies. I will discuss both the methodologies and outcomes of several studies aimed at understanding the range of governance concerns, and possible mechanisms for mitigating potential harms while encouraging the development of beneficial applications.

1430    Opening of afternoon session – Agenda and Introductions

1440    Virginie Tournay (Grenoble) – Synthetic Biology: Genetic Engineering Like Any Other?

The knowledge of scientific properties and technical challenges is essential for establishing public policies related to biotechnology. It is therefore necessary to take into account the evolution of scientific paradigms in the construction of legal frameworks in charge of regulating biotechnological products. I propose to discuss the EU directive 2001/18 which provides a legal definition of “genetic modification” in order to clarify technologies whose products are subject to a risk assessment. This presentation shows that the metaphorical force of the central dogma of the “genetic paradigm” leads to a certain kind of GM technologies being on the spotlight by framing their public debates and conditions of acceptance. In this context, the status of synthetic biology remains unclear since the practical organization of this “genetic design” stems from the insertion/synthesis of multiple genetic traits.

1510   Jeremy de Beer (University of Ottawa) – Synthetic Biology: The Case for Free Revealing

Recent empirical, policy and theoretical work on innovation in the life sciences strongly suggest that existing, proprietary, modes of innovation are not only inefficient but are unlikely to lead to health, industrial and environmental breakthroughs. Drawing on work done by the OECD, VALGEN (Value Addition Through Genomics and GE3LS), and the Structural Genomics Consortium, this presentation will focus on models for pre-competitive open innovation/free revealing. Given the convergence of technologies and class of cultural norms, synthetic biology provides an excellent case study through which to explore novel models of innovation.

1540     Jim Thomas (ETC Group, Ottawa) - Whose Industrial Revolution is it Anyway? 

As synthetic biology leaves the academic lab and rapidly scales to a multibillion dollar industry, comfortable debates about ethics will quickly give way to real world fights over the material impact of this industrial revolution on human rights, livelihoods and the environment. With their aggressive focus on creating a ‘new bioeconomy’ of biofuels and bio-based materials, the current clutch of Syn Bio startups (and their Fortune 500 backers) are driving forward an industrial vision that directly attacks the interests of the poor and the ecological support systems of the planet. For civil society the new Syn Bio industry is now becoming synonomous with land grabs, monopoly, ecological destruction, hunger and false technofixes. Every revolution has its winners and losers but so far this particular technological revolution is merely deeping existing global inequalities . In social terms there is really no revolution here at all.

1610    Break

1630    Roundtable Discussion

  • Moderator: Peter Calamai (Carleton)
  • Virginie Tournay (Grenoble)
  • Christina Agapakis (UCLA)
  • Jim Thomas (ETC Group, Ottawa)
  • Geoff Munro (Chief Scientist, Natural Resources Canada)
  • Pierre Charest (Natural Sciences and Engineering Research Council of Canada)

  1715    Adjourn