Synthetic Biology, Designing and Building Living Systems
A joint initiative of Leuven.Inc and IMEC
Synthetic Biology is a rapidly emerging technology resulting from a symbiosis of biology, synthetic chemistry and engineering. It originated about seven years ago at several top US universities where biologists, computer scientists and electrical engineers joined forces to create an engineering approach to biology. Its first goal is the systematic design and manufacturing of biological systems of predictable functional behaviour that do not exist as such in nature. Its second goal is the redesign of existing bio systems to get a better understanding of the underlying mechanisms.
Synthetic Biology holds great promise for many emerging technologies of the 21st century such as nanomedicine, systematic synthesis of biopharmaceuticals, sustainable chemical industry, production of hydrogen and bio fuels, smart biosensors for medicine and environment, waste removal,...
The four speakers in this seminar represent the cross-disciplinary aspect: Prof. Piet Herdewijn and Prof. Guido Volckaert will consider the field from the biological side while Prof. Em. Hugo De Man will highlight the engineering aspects and Prof. Markus Schmidt will talk about the safety and ethics of synthetic life.
Programme
* 17h15: Registration participants
* 17h45: Welcome and introduction to Synthetic Biology
Piet Herdewijn (Prof. K.U.Leuven Dep. Pharmaceutical Sciences)
- What is it?
- What is its importance? (convergence technologies)
- Overview of the chemical sector, link to computer sciences, combination diagnostics and therapy.
- Previsions for the future, possibilities, problems
- State of affairs in Belgium, Europe, the world
* 18h15: Nature's tools: Case study
Guido Volckaert (Prof. K.U.Leuven Dep. Biosystems)
* 18h45: Sandwich break
* 19h15: Where biology meets engineering
Hugo De Man (Prof. Em. K.U.Leuven - Senior Fellow IMEC)
- Different methodologies
- Multidisciplinary character
- Converging technologies
* 19h45: Synbiosafe: Safety, security and ethical aspects of Synthetic Biology
Markus Schmidt (Organisation for International Dialogue and Conflict Management, Biosafety Working Group, Vienna, Austria)
* 20h15: Q & A
* 20h45: Closing remarks and drink
Practical details
Date: Thursday January 17, 2008 (17h15-21h00)
Location: IMEC 'Expo', Kapeldreef 75, 3001 Leuven
Abstracts
Welcome and introduction to Synthetic Biology - Prof.Piet Herdewijn
Synthetic Biology has developed from the convergence of knowledge and tools from different disciplines such as engineering, chemistry and biology. It has the aim to construct new devices using biological and synthetic macromolecules as building modules. For a biologist it means a complementary perspective to understand the living world. A chemist is interested to probe the behaviour of molecules and their activity inside living cells. For an engineer, the living world provides a medium for controlling and processing information, materials and energy.
Synthetic Biology already has several accomplishments to its credit such as a diagnostic tool for HIV, the creation of a synthetic genetic system, the use of proteins as interchangeable parts for the production of an antimalaria drug and the engineering of regulatory circuits. However, many scientific and technological hurdles need to be taken to make design processes in Synthetic Biology really rational. More than any other scientific discipline, Synthetic Biology needs to be controlled by strict rules giving the danger of playing around and recombination of genes.
The Synthetic Biology Society is a reality in the USA, and Europe is doing efforts to try to become an important player in the field.
Case study: Nature's tools - Prof.Guido Volckaerts
Proteins are ordinarily synthesized by the cell in the ribosomal system which stepwise decodes the triplets corresponding to the individual amino acids. 61 triplets code for 20 amino acids. This system has been explored for several decades and is now quite well understood. Engineering has allowed to modify it so that some 'non-natural' amino acids can be incorporated as well, or to insert amino acids at one of the three remaining triplets (which normally function as termination signals under natural conditions).
Nature also has a non-ribosomal synthetic machinery which was discovered but much later, and allows to assemble many more ('non-protein') amino acids into peptide chains, thus providing much more product diversity. In addition, also keto-compounds can be assembled into so-called polyketides. Many antibiotic secondary metabolites are synthesized via such biosynthetic pathways. This machinery operates via enzymatic reactions and is organized in a modular fashion.
Understanding this system can provide more tools to engineering of novel compounds displaying 'unnatural' properties. In this presentation, the key elements of this 'lego-ization' process will be highlighted.
Where biology meets engineering - Hugo De Man (Prof. Em. K.U.Leuven - Senior Fellow IMEC)
Synthetic biology (SynBio) is not a 'discovery science' but rather an engineering approach to biology with the intention to design and build living systems not normally present in nature and with a well intended functionality. As such it is perhaps the most impressive example of the trend towards converging bio-nano technologies. SynBio can lead to new, highly innovative, industrial and economic activities in the area of healthcare, production of hydrogen and biofuels, pollutant and toxic material detection and clean-up and numerous others.
In this talk we will pay attention to the great similarities between the evolution of microelectronics and SynBio. It looks like SynBio is today where microelectronics was in the early seventies. In those days microelectronics came about by a joint effort of physicists, chemists, material scientists and electronics engineers. Its exponential growth is based on a methodological approach to the hierarchical synthesis of highly complex functionality based on the interaction of billions of transistors at the nanometer scale. Managing such complexity is based on the availability of a library of well characterized parts and their communication and on a design methodology that is formalized in extensive computer aided design tools from software to atoms. Synthetic biology follows exactly this same approach where building blocks are genes, proteins and cells, communication is exchange of proteins and networks are hierarchical compositions of chemical, genetic and metabolic pathways. The technology tools are DNA sequencing and synthesis as well as genetic modification. Computer libraries of biological parts, such as the 'open wetware' library BIOBRICKTM are becoming available and CAD tools for gene simulation such as BIOSPICE, VIRTUAL CELL, E-CELL are now in the public domain. The first operational 'biological circuits' have been designed and many applications such as the cheap production of anti-malaria drugs and synthesis of ethanol from cellulose are emerging. So there is a great similarity to the exciting first years of integrated circuits and SynBio even has an equivalent to Moore's law called Carlson's law! In this talk we will discuss about these similarities but also about the differences and the grand challenges of the SynBio field. Also the impact on educating engineers and scientists for the era of converging technologies as well as opportunities for the Flanders will be discussed. Is Europe ready for another exploding technology?
Synbiosafe: Safety, security and ethical aspects of Synthetic Biology - Dr. Markus Schmidt (Organisation for International Dialogue and Conflict Management, Biosafety Working Group, Vienna, Austria)
Genetic engineering is old hat, the latest approach is synthetic biology (SB) that fills the gap between molecular biology, IT, engineering technologies, synthetic chemistry, and nanotechnology. Synthetic biologists may use artificial molecules to reproduce emergent behaviour from natural biology, with the goal of creating artificial life or seek interchangeable biological parts to assemble them into systems that function in a manner not found in nature. In Europe this new interdisciplinary research field has gained momentum, resulting in over a dozen European research projects funded by the EC-FP6-NEST programme and as reflected in the recently held international conferences, e.g. the SB 3.0 in Zurich. While progress is being made in Europe regarding the natural science and technological development in SB, until now, ethical, safety and security aspects have not yet been researched in as systematic way that would allow for conclusive assessments. At the same time, concerns about potential risks are being raised and there are first signs of a public debate. Given former experience in the societal aspects of various biotechnologies, a foresighted technology assessment is necessary for SB, which is based on in-depth and well-presented analyses not yet available. In order to start filling this gap the NEST project SYNBIOSAFE carried out a fact-finding mission and is currently analysing potential challenges regarding ethics, safety and security. The fact-finding exercise included a survey among practicing European Synthetic Biologists regarding definition of SB (what makes SB different from conventional biotechnology); ethical issues (e.g. creation of artificial living systems, interaction between 'natural' and synthetic life forms, similarity of ethical issues compared to earlier technology debates); safety issues (e.g. unintended potential negative effects for health, agriculture or the environment, robustness of the biosafety framework for potential future environmental releases, contribution to improve current biosafety problems); security issues (e.g. awareness of major biosecurity events and guidelines of relevance to SB); but also questions on regulation (e.g. how should SB be regulated); and perception (how will SB be perceived by the public and non-scientific stakeholders). A first glance at the results of our survey suggests that (1) European SB scientists rarely see fundamentally new ethical issues involved, (2) that a well founded scientific risk assessment is lacking to assess safety implications, (3) that the biosecurity awareness is rather limited, (4) that there is a need for international regulations in contrast to self regulation, and (5) that most of the time a proactive communication strategy with the public is endorsed. These results are discussed to further stimulate a community discussion in Europe and to contribute to an agenda setting for future safety, ethical and security activities in SB.
Synthetic Biology is a rapidly emerging technology resulting from a symbiosis of biology, synthetic chemistry and engineering. It originated about seven years ago at several top US universities where biologists, computer scientists and electrical engineers joined forces to create an engineering approach to biology. Its first goal is the systematic design and manufacturing of biological systems of predictable functional behaviour that do not exist as such in nature. Its second goal is the redesign of existing bio systems to get a better understanding of the underlying mechanisms.
Synthetic Biology holds great promise for many emerging technologies of the 21st century such as nanomedicine, systematic synthesis of biopharmaceuticals, sustainable chemical industry, production of hydrogen and bio fuels, smart biosensors for medicine and environment, waste removal,...
The four speakers in this seminar represent the cross-disciplinary aspect: Prof. Piet Herdewijn and Prof. Guido Volckaert will consider the field from the biological side while Prof. Em. Hugo De Man will highlight the engineering aspects and Prof. Markus Schmidt will talk about the safety and ethics of synthetic life.
Programme
* 17h15: Registration participants
* 17h45: Welcome and introduction to Synthetic Biology
Piet Herdewijn (Prof. K.U.Leuven Dep. Pharmaceutical Sciences)
- What is it?
- What is its importance? (convergence technologies)
- Overview of the chemical sector, link to computer sciences, combination diagnostics and therapy.
- Previsions for the future, possibilities, problems
- State of affairs in Belgium, Europe, the world
* 18h15: Nature's tools: Case study
Guido Volckaert (Prof. K.U.Leuven Dep. Biosystems)
* 18h45: Sandwich break
* 19h15: Where biology meets engineering
Hugo De Man (Prof. Em. K.U.Leuven - Senior Fellow IMEC)
- Different methodologies
- Multidisciplinary character
- Converging technologies
* 19h45: Synbiosafe: Safety, security and ethical aspects of Synthetic Biology
Markus Schmidt (Organisation for International Dialogue and Conflict Management, Biosafety Working Group, Vienna, Austria)
* 20h15: Q & A
* 20h45: Closing remarks and drink
Practical details
Date: Thursday January 17, 2008 (17h15-21h00)
Location: IMEC 'Expo', Kapeldreef 75, 3001 Leuven
Abstracts
Welcome and introduction to Synthetic Biology - Prof.Piet Herdewijn
Synthetic Biology has developed from the convergence of knowledge and tools from different disciplines such as engineering, chemistry and biology. It has the aim to construct new devices using biological and synthetic macromolecules as building modules. For a biologist it means a complementary perspective to understand the living world. A chemist is interested to probe the behaviour of molecules and their activity inside living cells. For an engineer, the living world provides a medium for controlling and processing information, materials and energy.
Synthetic Biology already has several accomplishments to its credit such as a diagnostic tool for HIV, the creation of a synthetic genetic system, the use of proteins as interchangeable parts for the production of an antimalaria drug and the engineering of regulatory circuits. However, many scientific and technological hurdles need to be taken to make design processes in Synthetic Biology really rational. More than any other scientific discipline, Synthetic Biology needs to be controlled by strict rules giving the danger of playing around and recombination of genes.
The Synthetic Biology Society is a reality in the USA, and Europe is doing efforts to try to become an important player in the field.
Case study: Nature's tools - Prof.Guido Volckaerts
Proteins are ordinarily synthesized by the cell in the ribosomal system which stepwise decodes the triplets corresponding to the individual amino acids. 61 triplets code for 20 amino acids. This system has been explored for several decades and is now quite well understood. Engineering has allowed to modify it so that some 'non-natural' amino acids can be incorporated as well, or to insert amino acids at one of the three remaining triplets (which normally function as termination signals under natural conditions).
Nature also has a non-ribosomal synthetic machinery which was discovered but much later, and allows to assemble many more ('non-protein') amino acids into peptide chains, thus providing much more product diversity. In addition, also keto-compounds can be assembled into so-called polyketides. Many antibiotic secondary metabolites are synthesized via such biosynthetic pathways. This machinery operates via enzymatic reactions and is organized in a modular fashion.
Understanding this system can provide more tools to engineering of novel compounds displaying 'unnatural' properties. In this presentation, the key elements of this 'lego-ization' process will be highlighted.
Where biology meets engineering - Hugo De Man (Prof. Em. K.U.Leuven - Senior Fellow IMEC)
Synthetic biology (SynBio) is not a 'discovery science' but rather an engineering approach to biology with the intention to design and build living systems not normally present in nature and with a well intended functionality. As such it is perhaps the most impressive example of the trend towards converging bio-nano technologies. SynBio can lead to new, highly innovative, industrial and economic activities in the area of healthcare, production of hydrogen and biofuels, pollutant and toxic material detection and clean-up and numerous others.
In this talk we will pay attention to the great similarities between the evolution of microelectronics and SynBio. It looks like SynBio is today where microelectronics was in the early seventies. In those days microelectronics came about by a joint effort of physicists, chemists, material scientists and electronics engineers. Its exponential growth is based on a methodological approach to the hierarchical synthesis of highly complex functionality based on the interaction of billions of transistors at the nanometer scale. Managing such complexity is based on the availability of a library of well characterized parts and their communication and on a design methodology that is formalized in extensive computer aided design tools from software to atoms. Synthetic biology follows exactly this same approach where building blocks are genes, proteins and cells, communication is exchange of proteins and networks are hierarchical compositions of chemical, genetic and metabolic pathways. The technology tools are DNA sequencing and synthesis as well as genetic modification. Computer libraries of biological parts, such as the 'open wetware' library BIOBRICKTM are becoming available and CAD tools for gene simulation such as BIOSPICE, VIRTUAL CELL, E-CELL are now in the public domain. The first operational 'biological circuits' have been designed and many applications such as the cheap production of anti-malaria drugs and synthesis of ethanol from cellulose are emerging. So there is a great similarity to the exciting first years of integrated circuits and SynBio even has an equivalent to Moore's law called Carlson's law! In this talk we will discuss about these similarities but also about the differences and the grand challenges of the SynBio field. Also the impact on educating engineers and scientists for the era of converging technologies as well as opportunities for the Flanders will be discussed. Is Europe ready for another exploding technology?
Synbiosafe: Safety, security and ethical aspects of Synthetic Biology - Dr. Markus Schmidt (Organisation for International Dialogue and Conflict Management, Biosafety Working Group, Vienna, Austria)
Genetic engineering is old hat, the latest approach is synthetic biology (SB) that fills the gap between molecular biology, IT, engineering technologies, synthetic chemistry, and nanotechnology. Synthetic biologists may use artificial molecules to reproduce emergent behaviour from natural biology, with the goal of creating artificial life or seek interchangeable biological parts to assemble them into systems that function in a manner not found in nature. In Europe this new interdisciplinary research field has gained momentum, resulting in over a dozen European research projects funded by the EC-FP6-NEST programme and as reflected in the recently held international conferences, e.g. the SB 3.0 in Zurich. While progress is being made in Europe regarding the natural science and technological development in SB, until now, ethical, safety and security aspects have not yet been researched in as systematic way that would allow for conclusive assessments. At the same time, concerns about potential risks are being raised and there are first signs of a public debate. Given former experience in the societal aspects of various biotechnologies, a foresighted technology assessment is necessary for SB, which is based on in-depth and well-presented analyses not yet available. In order to start filling this gap the NEST project SYNBIOSAFE carried out a fact-finding mission and is currently analysing potential challenges regarding ethics, safety and security. The fact-finding exercise included a survey among practicing European Synthetic Biologists regarding definition of SB (what makes SB different from conventional biotechnology); ethical issues (e.g. creation of artificial living systems, interaction between 'natural' and synthetic life forms, similarity of ethical issues compared to earlier technology debates); safety issues (e.g. unintended potential negative effects for health, agriculture or the environment, robustness of the biosafety framework for potential future environmental releases, contribution to improve current biosafety problems); security issues (e.g. awareness of major biosecurity events and guidelines of relevance to SB); but also questions on regulation (e.g. how should SB be regulated); and perception (how will SB be perceived by the public and non-scientific stakeholders). A first glance at the results of our survey suggests that (1) European SB scientists rarely see fundamentally new ethical issues involved, (2) that a well founded scientific risk assessment is lacking to assess safety implications, (3) that the biosecurity awareness is rather limited, (4) that there is a need for international regulations in contrast to self regulation, and (5) that most of the time a proactive communication strategy with the public is endorsed. These results are discussed to further stimulate a community discussion in Europe and to contribute to an agenda setting for future safety, ethical and security activities in SB.
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