Kavli Futures Symposium Report 2007

 

The Merging of Bio and Nano: Toward Cyborg Cells

June 11-15, 2007, Ilulissat, Greenland 

 

Introduction

Synthetic biology and nanotechnology are two of today’s most powerful and versatile emerging technologies. With their common focus on events at a similar size scale – from a few to a few hundred nanometers – they also offer the potential for synergies that might achieve far more than either technology standing alone. Initiated and organized by Cees Dekker and Paul McEuen, who are affiliated with the Kavli Institute for Nanoscience at Delft and the Kavli Institute at Cornell for Nanoscience, respectively, this meeting was convened to explore such possibilities. In particular, it would ask whether a convergence of synthetic biology and nanotechnology might soon supply new forms of life: living cells that are either partially or wholly synthetic. How close are we to this goal? What are the major obstacles? What might we do with such entities? And what are the dangers and the ethical dilemmas?

Starting with these questions, the discussion extended to broader issues in science, technology and society. Among the topics raised were the problem of defining life, the potential benefits of nanotechnology to cell biology and other life sciences, and the technological challenges that lie ahead in fields such as energy and medicine.

The meeting ended with the drafting of a declaration – the Ilulissat Statement, attached as Appendix III. The Statement sums up the participant’s views on what needs to be done to bring about a convergence of nanotechnology and synthetic biology with maximum benefit to humanity and the planet.

Key terms

Nanotechnology, as used in this report, refers to the attempts to control and manipulate matter on scales ranging from a few nanometres – the size of individual large molecules – to several hundred nanometers, which approaches the size of small whole cells. The biological applications of nanotechnology were of particular interest to the Ilulissat conference. Some that have already been developed include the use of nanoparticles as fluorescent labels for fundamental studies in molecular and cell biology, and the nano-manipulation techniques for studying the properties of individual biomolecules. Scientists look to biology to provide more ideas and components that would lead to new nanotechnological devices and functions.

Synthetic biology is the synthesis of complex, biologically based (or inspired) systems that display functions that do not exist in nature. It applies knowledge from fields such as genetic engineering, protein engineering, metabolic engineering, DNA synthesis and systems biology to enable the design of biological systems (e.g. cells or cell components) in a rational and systematic way. Its potential applications range widely across scientific and engineering disciplines, from medicine. It might, for instance, lead to the engineering of organisms to supply new drugs, or to more efficient production of ethanol and hydrogen.

Themes of the meeting

 

Basic challenges in cell biology

To create synthetic biological systems, it is necessary first to understand fully how natural systems work. One needs to know how each enzyme, organelle and module in a cell works, and how these activities are coordinated in the whole organism. As conference participants noted, science is still far from reaching that level of knowledge. They saw the need for new techniques to probe and visualize cell processes over a range of length and time scales. Other questions identified at Ilullisat included:

  • How important are thermal noise, fluctuations and stochastic variation in the way components function? (In engineering such things are commonly seen as problems; in biology, it may be that they are exploited to good effect.)
  • How does one describe chemical reactivity when it takes place not in a dilute, homogenous solution but in an environment that is well organized on many scales?
  • To what extent can biological processes be understood by looking at single molecules, and when is it necessary to consider the statistical behavior of populations, including the possibility of collective effects?
  • How do nanometer-scale molecules build structures much larger than themselves? How are information flows managed to enable that?
  • How reducible is biology? How much can its processes by explained by general principles of physics? As one participant put it, are the rules of the cell “local,” or are cells entirely governed by global principles analogous to those that govern thermodynamic equilibrium or the stable steady states of dynamical systems?

One point of debate was the question of how much fundamental understanding is needed in order to make practical advances. Some participants argued that it was necessary to have a good grasp of how individual biological components work before trying to understand their collective behaviour. Others said this was not necessary. As one of them said, “We should be capable of making cells before we understand them” (just as engineers were able to make suspension bridges without a theory of quantum gravity).

Exploring evolution

The meeting examined the role of evolution as one key to understanding the design of organisms. One line of inquiry dealt with the concept of a “fitness landscape,” an abstract, multi-dimensional space that encompasses the possible characteristics of on organism. It was suggested that micro- and nanofabrication technologies might enable researchers to create structures that house microorganisms in designed fitness landscapes where the stresses and the exchanges between populations are controlled. With such devices coupled to automated systems for genomic analysis of the cell populations, experiments could be conducted on evolution in real time. As one participant noted, such experiments run for several years might provide detailed hard data on evolutionary questions that are difficult to study in the wild.

Energy generation and conversion

Researchers are attempting to make fuels from biomass by using microorganisms to break down the complex, polymeric components of plant cells. However, plants have evolved a battery of defences against this process. Cellulose, the main component of plant cell walls, is already difficult for many organisms to digest, and the resinous ‘cement’ of plant cells, lignin, is even more resistant to degradation. The scientists at Ilulissat discussed the possible use of synthetic biology to overcome this problem by engineering metabolic pathways for digestion of lignocellulosic material. They heard a description of recent work on the engineering of Clostridium bacteria, combining the cellulose-busting properties of C. cellulolyticum (which makes glucose) with the ethanol/butanol-synthesizing capabilities of C. acetobutylicum (which cannot use cellulose. They also considered the possibility of engineering plants for easier digestion by removing lignin-making genes, and of extending the reach of synthetic biology to the production of fuels other than conventional biofuels (e.g. ethanol). They expressed interest, for instance, in exploiting the hydrogen-generating machinery of some organisms to make a zero-carbon fuel.

Cell-based chemical synthesis

The effort to make chemical fuels by re-engineering microorganisms is part of a more general strategy to use synthetic biology for chemical synthesis. The Ilulissat scientists discussed a number of initiatives in this area, including:

  • Research to engineer microbes such as yeast for making the anti-malarial drug artemisinin. This is a natural product, found in an Asian shrub, but it is present in such small amounts that the cost of extracting it is prohibitive. A team led by Jay Keasling, (one of the Ilulissat participants, has made yeast that can generate artemisinic acid, the immediate precursor to artemisinin. It was suggested that the synthesis of drugs might best performed by “minimal organisms” designed from scratch to meet the stringent requirements of the process.
  • The use of live organisms as miniature in vivo drug factories or doctors. (One example is a microbe that has been developed at the University of California at San Francisco to seek out tumor cells and inject them with a lethal drug). Addressing safety questions, one thread of the discussion focused on the use of bacterial viruses (phage) rather than human viruses or bacteria, since these should not be pathogenic or provoke an immune response.
  • Using viruses to to synthesize new materials. A group led by Ilulissat participant Andrea Belcher has developed methods for coating virus particles with surface proteins that recognize and bind to specific inorganic materials, such as those used for semiconductors. This technique seeks to apply the selectivity and nanoscale precision of biological synthesis to the construction of new materials and devices. Other possibilities were raised for viral engineering, such as the use of viruses to transport encoded genetic “assembly instructions” for engineering new organisms, or the creation of viral templates with well defined sizes and shapes for the synthesis of inorganic nanostructures.

Personalized medicine

Ilulissat conferees discussed how nanotechnology might help match drugs to the patients who would benefit from them the most, with the least risk. One approach, being developed by Ilulissat participant Scott Fraser, is to use microscopic optical resonators (devices that respond to specific light-wave frequencies) to detect mRNA or protein molecules that indicate a patient’s sensitivity to particular drugs. It was suggested that such devices might reduce the culling of promising drug candidates that work safely and well, but only for people with a certain genetic profile.

Design of synthetic biology “parts” and platforms

In electronic and mechanical engineering, it is routine to design circuits and functions without the need to worry about the details of components. Will a similar standardization and abstraction emerge in biology, greatly simplifying the task of designing synthetic biological systems?

Ilulissat participants approached this topic from a number of angles. One was to consider the question of how design methods are themselves designed: Should they be based on ‘rational’ first principles, or should they should use an evolutionary approach to search the possible (and generally immense) design space? There was some consensus that the current understanding of biological systems is inadequate to make completely bottom-up design feasible, so that evolutionary methods will probably be indispensable to some degree. It was noted, however, that evolutionary designs can be very hard to reverse-engineer to figure out how or why they work.

Another line of inquiry concerned the nature of the system “platform” being designed. When a microorganism is redesigned to perform a non-natural functions, it can be embedded in a living or non-living system. One example of the latter, from the research or Ilulissat participant Ehud Shapiro, is “smart drugs” packaged in “logical envelopes” – analogous to computers – that receive information from their environment and process it to deduce an appropriate response. As for living platforms, the conferees examined the idea of a “minimal organism,” with the bare minimum of genes needed to retain viability. They discussed one candidate, explored at the Venter Institute, that might be pared down into a minimal organism. This is the bacteria Mycoplasma genitalium, which has just 485 protein-coding genes.

Making artificial cells and new life forms

Research on Mycoplasma also figured prominently in another area of discussion, about the possibilities of creating artificial cells or organisms. The participants generally agreed that anything warranting the genuine description of ‘artificial life’ is going to come first from a top-down strategy rather than bottom-up: by reconstituting existing cells rather than making them from scratch. As an example of this, they heard about the Venter Institute’s latest work with Mycoplasma “genome transplants,” a process in which one species of the bacteria receives an entirely new genome from a different species. The recipient cells are then able to “boot up” with the new genome and show phenotypic behavior characteristic of the donor species.

The conferees also learned more about the work of Ilulissat participant Petra Schwille, who is synthesizing microenvironments – liquid droplets – that contain the molecules needed to encode and transcribe genetic information. These are created in a microfluidic system, and might ultimately contain elements such as membrane channels and surface recognition groups to allow binding to real cells or assembly into artificial “tissues.”

Complexity and computation

Even the simplest living organisms are enormously complex. One major challenge of synthetic biology is to know just how much of that complexity really needs to be reproduced to create artificial life. Ilulissat participants discussed at least two approaches to this issue. One, embodied in the work of conference participant Bob Hazen and his Harvard colleague Jack Szostak, is to identify how much of the information in a complex system is directed towards attaining its functionality. This method might enable one to estimate the minimum amount of information /complexity required to achieve a given function – or conversely, what functionality can and can’t be obtained from a given complex system.

Another aspect of complexity -- robustness – is the subject of research by Ilulissat participant Hiroaki Kitano. Conferees learned about his attempts to characterize gene networks in terms of the contributions that each of the components makes to the overall robustness (against, in this case, over-expression of genes).

Social and policy concerns

As the Ilulissat participants noted in their concluding statement (see Appendix III), the coming convergence of nanotechnology and synthetic biology has the potential to produce enormous benefits by helping to the “daunting problems of climate change, energy, health, and water resources." It also carries risks, and these were a signficant topic of discussion at the conference. As one participant pointed out, the rapid progress in synthetic biology has lowered the cost of doing harm as well as doing good: The price of an amount of DNA equivalent to the genome of the Ebola virus is about the same as a Volkswagen car, while in three years it will cost about as much as a laptop computer, and in 5-7 years, about that of an iPod.

In their concluding Statement, the scientists at Ilullisat expressed a hope for “protective measures against accidents and abuses of synthetic biology," as well as "a system of best practices … to foster positive uses of the technology and suppress negative ones." One participant proposed setting up an organized professional body that is able to deal with questions of ethics and responsibilities in this area. These issues now are considered largely by isolated groups or individuals on an ad hoc basis.

Intellectual property protection was also a key concern for the Ilulissat group. One of the scientists argued that excessive patenting in the pharmaceutical industry has had an inhibitory effect on biotechnology. For the production of pharmaceuticals from engineered organisms, and probably for synthetic biology in general, he proposed that the patenting be carried out at the high levels (whole organisms, for instance), not at the level of individual components.

Summary

The Ilulissat meeting was organized to stimulate discussions, not come up with definitive answers. But the discussions did sound common themes such as these:

  • Nanotechnology and synthetic biology have plenty to offer one another. At this stage, nano is primarily a fertile source of new techniques for probing the biomolecular world. But it might ultimately provide new parts and suggest design principles. Molecular biology is already a source of inspiration and components for nanoscience, and may in the future offer ways of organizing matter and information flows in a hierarchical manner over many length scales.
  • There is still much that we do not know about how cells work, in terms of the logic, the spatial and temporal organization, the design principles, or even the details of how many individual molecular components function.
  • As a consequence, the idea of de novo design of an ‘artificial living cell’ is probably not practical.
  • By the same token, we still have much to learn about evolution: about what determines the behavior and history of groups of organisms, and how evolution has shaped organismal design.
  • The nature of the environment and context is crucial to any discussion about what constitutes life.
  • There are roles for both rational and evolutionary approaches to design of complex systems, although it is hard to generalize about their relative roles.
  • Energy and medicine will be two of the key drivers toward a convergence of nanotechnology and synthetic biology. The creation of new materials is also an important (and often related) objective.

For the official presentation of the conferees’ views on the future of synthetic biology and nanotechnology, see “The Ilulissat Statement,” Appendix III.

Appendix I

List of Participants

Appendix II

Expenditure of Funds

Appendix III

The Ilulissat Statement

Appendix IV

Final Round Table

Appendix V

Articles Written from the Meeting (compiled Summer, 2007)

 

Appendix I

LIST OF PARTICIPANTS

  • Robert Austin, Princeton University, Princeton, USA
  • Angela Belcher, Massachusetts Institute of Technology, Cambridge, USA
  • David Bensimon, Ecole Normale Superieure, Paris, France
  • Steven Chu, Lawrence Berkeley National Laboratory, Berkeley, USA
  • Cees Dekker, Delft University of Technology, Delft, The Netherlands
  • Freeman Dyson, Institute for Advanced Study, Princeton, USA
  • Drew Endy, Massachusetts Institute of Technology, Cambridge, USA
  • Scott Fraser, California Institute of Technology, Pasadena, USA
  • John Glass, J. Craig Venter Institute, Rockville, USA
  • Robert Hazen, Carnegie Institution of Washington, Washington, USA
  • Joe Howard, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
  • Jay Keasling, University of California at Berkeley, Berkeley, USA
  • Hiroaki Kitano, The Systems Biology Institute, and Sony Computer Science Laboratories, Japan
  • Paul McEuen, Cornell University, Ithaca, USA
  • Petra Schwille, TU Dresden, Dresden, Germany
  • Ehud Shapiro, Weizman Institute of Science, Rehovot, Israel
  • Julie Theriot, Stanford University, Stanford, USA

Writer in attendance

  • Philip Ball, Nature, London, United Kingdom

Appendix II

EXPENDITURE OF FUNDS

The Kavli Foundation supported the Kavli Futures Symposium, Ilulissat, with a grant of 40,000. Matching funds were supplied by the Kavli Institute at Cornell and the Kavli Institute of Nanoscience at Delft.

Expenses:
Travel: $49,954.71
Postage: $192.20
Lodging, Food, Excursions: $25,311.00
Total: $75,457.91

Kavli Foundation grant $40,000
Kavli Institute at Cornell: $17,728.96
Kavli Institute of Nanoscience, Delft: $17,728.95

Appendix III

THE ILULISSAT STATEMENT
Synthesizing the Future: A vision for the convergence of synthetic biology and nanotechnology

 

This document expresses the views that emerged from the Kavli Futures Symposium ‘The merging of bio and nano: towards cyborg cells’, 11-15 June 2007, Ilulissat, Greenland.

Approximately fifty years ago, two revolutions began. The invention of the transistor and the integrated circuit paved the way for the modern information society. At the same time, Watson and Crick unlocked the structure of the double helix of DNA, exposing the language of life with stunning clarity. The electronics revolution has changed the way we live and work, while the genetic revolution has transformed the way we think about life and medical science.

But a third innovation contemporaneous with these was the discovery by Miller and Urey that amino acids may be synthesized in conditions thought to exist on the early Earth. This gave us tantalizing hints that we could create life from scratch. That prospect on the one hand, and the ability to manipulate genetic information using the tools of biotechnology on the other, are now combined in the emerging discipline of synthetic biology. How we shape and implement this revolution will have profound effects for humanity in the next fifty years.

It was also almost fifty years ago that the proposal was made by Feynman of engineering matter at the atomic scale – the first intimation of the now burgeoning field of nanotechnology. Since the nanoscale is also the natural scale on which living cells organize matter, we are now seeing a convergence in which molecular biology offers inspiration and components to nanotechnology, while nanotechnology has provided new tools and techniques for probing the fundamental processes of cell biology. Synthetic biology looks sure to profit from this trend.

It is useful to divide synthetic biology, like computer technology, into two parts: hardware and software. The hardware – the molecular machinery of synthetic biology – is rapidly progressing. The ability to sequence and manufacture DNA is growing exponentially, with costs dropping by a factor of two every two years. The construction of arbitrary genetic sequences comparable to the genome size of simple organisms is now possible. Turning these artificial genomes into functioning single-cell factories is probably only a matter of time. On the hardware side of synthetic biology, the train is leaving the station. All we need to do is stoke the engine (by supporting foundational research in synthetic biology technology) and tell the train where to go.

Less clear are the design rules for this remarkable new technology—the software. We have decoded the letters in which life’s instructions are written, and we now understand many of the words – the genes. But we have come to realize that the language is highly complex and context-dependent: meaning comes not from linear strings of words but from networks of interconnections, with its own entwined grammar. For this reason, the ability to write new stories is currently beyond our ability – although we are starting to master simple couplets. Understanding the relative merits of rational design and evolutionary trial-and-error in this endeavor is a major challenge that will take years if not decades. This task will have fundamental significance, helping us to better understand the web of life as expressed in both the genetic code and the complex ecology of living organisms. It will also have practical significance, allowing us to construct synthetic cells that achieve their applied goals (see below) while creating as few problems as possible for the world around them.

These are not merely academic issues. The early twenty first century is a time of tremendous promise and tremendous peril. We face daunting problems of climate change, energy, health, and water resources. Synthetic biology offer solutions to these issues: microorganisms that convert plant matter to fuels or that synthesize new drugs or target and destroy rogue cells in the body. As with any powerful technology, the promise comes with risk. We need to develop protective measures against accidents and abuses of synthetic biology. A system of best practices must be established to foster positive uses of the technology and suppress negative ones. The risks are real, but the potential benefits are truly extraordinary.

Because of the pressing needs and the unique opportunity that now exists from technology convergence, we strongly encourage research on two broad fronts:

Foundational Research
1. Support the development of hardware platforms for synthetic biology.
2. Support fundamental research exploring the software of life, including its interaction with the environment.
3. Support nanotechnology research to assist in the manufacture of synthetic life and its interfacing with the external world.

Societal Impacts and Applications
4. Support programs directed to address the most pressing applications, including energy and health care.
5. Support the establishment of a professional organization that will engage with the broader society to maximize the benefits, minimize the risks, and oversee the ethics of synthetic life.
6. Develop a flexible and sensible approach to ownership, sharing of knowledge, and regulation, that takes into account the needs of all stakeholders.

Fifty years from now, synthetic biology will be as pervasive and transformative as is electronics today. And as with that technology, the applications and impacts are impossible to predict in the field’s nascent stages. Nevertheless, the decisions we make now will have enormous impact on the shape of this future.

The people listed below, participants at the Kavli Futures Symposium ‘The merging of bio and nano: towards cyborg cells’, 11-15 June 2007, Ilulissat, Greenland, agree with the above statement.

Robert Austin
Princeton University, Princeton, USA
Philip Ball

Nature, London, United Kingdom<
Angela Belcher
Massachusetts Institute of Technology, Cambridge, USA
David Bensimon
Ecole Normale Superieure, Paris, France
Steven Chu
Lawrence Berkeley National Laboratory, Berkeley, USA
Cees Dekker
Delft University of Technology, Delft, The Netherlands
Freeman Dyson
Institute for Advanced Study, Princeton, USA
Drew Endy
Massachusetts Institute of Technology, Cambridge, USA
Scott Fraser
California Institute of Technology, Pasadena, USA
John Glass
J. Craig Venter Institute, Rockville, USA
Robert Hazen
Carnegie Institution of Washington, Washington, USA
Joe Howard
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
Jay Keasling
University of California at Berkeley, Berkeley, USA
Hiroaki Kitano
The Systems Biology Institute, and Sony Computer Science Laboratories, Japan
Paul McEuen
Cornell University, Ithaca, USA
Petra Schwille
TU Dresden, Dresden, Germany
Ehud Shapiro
Weizman Institute of Science, Rehovot, Israel
Julie Theriot
Stanford University, Stanford, USA

 

 Appendix IV

FINAL ROUND TABLE

At the end of the meeting, the participants were asked each to specify which question, issue or objective they considered to be the single most important in this area, and also which idea or objective currently being considered that they felt would not pan out. Here are the responses (in arbitrary order of participants). (Note that Ehud Shapiro had to leave early.)

The Big Question

  • Bob Austin: Is the response of collections of single cells to other cells different from what a single cell does?
  • John Glass: Can life be made using component chemicals?
  • Jay Keasling: We need a microorganism that will produce fuel from biomass.
  • David Bensimon: How does evolution work?
  • Angela Belcher: We need biological processes for making fuels
  • Petra Schwille: Can we make a self-replicating system from ‘minimal’ components?
  • Paul McEuen: Can we make artificial organelles from inorganic components?
  • Cees Dekker: Can we develop a bottom-up biology?
  • Drew Endy: We need therapies or vaccines against infectious agents that are fully encoded in information and can be manufactured locally.
  • Hiroaki Kitano: We need to create complex systems from a distributed approach. And can we ‘terraform’ planetary environments?
  • Julie Theriot: We need to develop fine spatial control of bio/synthetic systems.
  • Scott Fraser: We need to improve methods of interfacing and readout.
  • Steve Chu: We need to figure out how the ribosome works.
  • Joe Howard: How do organisms measure the size of things?
  • Bob Hazen: We need to make self-replicating chemical systems – but not necessarily ‘living cells’ from scratch.

The False Trail

  • Bob Austin: Moore’s Law and digital computers are overhyped.
  • John Glass: Personalized medicine.
  • Jay Keasling: The problems foreseen for creating a valuable and safe synthetic biology won’t materialize if we put enough effort into avoiding or overcoming them.
  • David Bensimon: The artificial creation of life from scratch.
  • Angela Belcher: The necessary educational system is not being supported.
  • Petra Schwille: We won’t create artificial life from scratch.
  • Freeman Dyson: The minimal genome.
  • Paul McEuen: Energy generation will remain inorganic.
  • Cees Dekker: Systems biology.
  • Drew Endy: There will be more active participation in the development of technologies.
  • Julie Theriot: Personalized medicine.
  • Scott Fraser: Pure ‘design’ solutions to an organism or biological circuit.
  • Steve Chu: The biomimetic part of the energy problem won’t work.
  • Joe Howard: Systems biology.
  • Bob Hazen: We will find no clear evidence for life on Mars.

Appendix V

Articles Written from the Meeting

(Compiled Summer, 2007. All are authored by Philip Ball; copies available upon request)

  • “Designs for life” (News and Views), Nature 448, 32-33 (5 July 2007).
  • “Meanings of life” (Editorial), Nature 447, 1031-1032 (28 June 2007).
  • “The patent threat to designer biology,” Nature online news (22 June 2007).
  • Opinion: The Crucible, Chemistry World 4(7), 36 (July 2007).
  • “Licking lignin”, Nature Materials 6, 553 (August 2007).
  • “Life, but not as we know it”, Prospect 137 (August 2007).