Synthetic Biology - Industrial And Environmental Applications

This is the only book to focus on industrial and environmental applications of synthetic biology, covering 17 of the most promising uses in the areas of biofuel, bioremediation and biomaterials. The contributions are written by experts from academia, non-profit organizations and industry, outlining not only the scientific basics but also the economic, environmental and ethical impact of the new technologies.
This makes it not only suitable as supplementary material for students but also the perfect companion for policy makers and funding agencies, if they are to make informed decisions about synthetic biology.
Largely coordinated by Markus Schmidt, a policy adviser, and the only European to testify in front of the bioethics commission of the Obama administration.

Markus Schmidt has an interdisciplinary background with an education in electronic and biomedical engineering, biology (MSc) and risk research (PhD). His research interests include risk assessment, the science-society interface, and technology assessment (TA) of novel bio-, nano- and converging technologies. Since 2005 he pioneered synthetic biology safety and ELSI research in Europe. See: www.markusschmidt.eu for details.

Lei Pei completed her PhD at the Division of Clinical Bacteriology, Karolinska Institute, Sweden, in 2002. After her PhD she worked at the Division of Infectious Diseases, Department of Medicine, at the Massachusetts General Hospital/Harvard Medical School, Boston, USA, as a Postdoctoral Research Fellow. Between 2005 and 2009 she completed her second postdoc position at the Flanders Institute for Biotechnology, Department of Molecular Biology, Gent University, Belgium. Since 2009 she works with Markus Schmidt as a postdoc on synthetic biology and risk assessment.

Antoine Danchin is a French geneticist known for his research in several fields of biology. Originally he was trained as a mathematician at the Institut Henri Poincare and a physicist at the Ecole Polytechnique. He is the Chairman of the startup AMAbiotics, specialised in metabolic bioremediation and synthetic biology. He was the director of the Department Genomes and Genetics at the Institut Pasteur in Paris where he headed the Genetics of Bacterial Genomes Unit.

Ismail Mahmutoglu is a Chemist as Bauer Umwelt GmbH, a specialist on the remediation of brownfields, and the treatment of waters and gases. He is a spezialist for design and manufactureing of water treatment plants for decontamination, for waste water and for potable water. The range of projects he is dealing with includes complex technical treatment steps with biological treatment steps, but also in situ technologies to improve the underground conditions for the microorganism.

Michel Morange is Professor in molecular biology at the CNRS-ENS (Centre National de la Recherche Scientifique, Centre Cavailles, Ecole normale superieure,), and a specialist in the history of molecular biology. Michel previously studied the history of the molecular revolution, and the post-genomic transformations of biology. Synthetic biology is in the direct continuity of these early works.

Vincent Schachter is Vice-President for Research & Development at Total Gas & Power. Before that he was the director of Systems Biology of the french CEA, where he lead the Computational Systems Biology research group. He holds a PhD in Computer Science from the Ecole Normale Superieure in Paris, and entered bioinformatics through the field of protein interaction network analysis. He has also acquired applied experience with high-throughput experimental data ? protein-protein interactions, sequence, cellular phenotypes ? first as Director of Bioinformatics Research at Hybrigenics SA, a biotech company, and then as Director of Bioinformatics at CEA. He is a co-founder of the BioPathways, Consortium and a participant in the BioPAX standardization effort, and is a referee for several bioinformatics and biology journals.

Mark A. Bedau is an internationally recognized leader in the interdisciplinary study of complex adaptive systems. He co-founded and is currently COO of ProtoLife Srl in Venice, Italy. He also cofounded the European Centre for Living Technology (UNIVE), in Venice, Italy. Professor of Philosophy and Humanities at Reed College, and visiting Professor at the European School of Molecular Medicine (Milan, Italy). He is internationally recognized as a uniquely qualified expert in the philosophical foundations of complex adaptive systems.

Rachel Armstrong is a medical doctor with qualifications in general practice, a multi-media producer, and arts collaborator whose current research explores the possibilities of architectural design to create positive practices and mythologies about new technology. She is collaborating with international scientists and architects to explore cutting-edge, sustainable technologies by developing metabolic materials in an experimental setting.

List of Contributors XI
Short CVs of Contributors XIII
Preface XVII
Acknowledgments XIX
Executive Summary XXIMarkus Schmidt
Biofuels XXI
Bioremediation XXII
Biomaterials XXIV
Novel Developments in Synthetic Biology XXV
Introduction 1Markus Schmidt
What Are Synthetic Biology Applications? 1
Which Synthetic Biology Applications Did We Consider? 2
Selecting and Assessing Synthetic Biology Applications 3
The Regulatory Context for Synthetic Biology 4
References 6
1 Biofuels 7Markus Schmidt, Manuel Porcar, Vincent Schachter, Antoine Danchin, and Ismail Mahmutoglu
1.1 Biofuels in General 7
1.1.1 Introduction 7
1.1.2 Economic Potential 8
1.1.3 Environmental Impact 13
1.1.3.1 Land Requirements for Projected Biofuel Use 14
1.1.3.2 Other Environmental Concerns 16
1.1.3.3 Impact of Legislative Decicions 16
1.1.4 Foreseeable Social and Ethical Aspects 17
1.1.4.1 How Could the New SB Application Impact Society at Large? 18
1.2 Ethanol 19
1.2.1 Introduction 19
1.2.2 Economic Potential 20
1.2.3 Environmental Impact 21
1.2.4 Foreseeable Social and Ethical Aspects 24
1.2.4.1 Could the Application Change Social Interactions? 26
1.2.4.2 Producing Countries, Rich Countries? 26
1.3 Non-ethanol Fuels 27
1.3.1 Introduction 27
1.3.2 Economic Potential 31
1.3.3 Environmental Impact 32
1.3.4 Foreseeable Social and Ethical Aspects 33
1.3.4.1 Impact on Social Interaction 34
1.4 Algae-based Fuels 35
1.4.1 Introduction 35
1.4.2 Economic Potential 37
1.4.3 Environmental Impact 41
1.4.4 Foreseeable Social and Ethical Aspects 42
1.4.4.1 Could the Application Change Social Interactions? 42
1.5 Hydrogen Production 43
1.5.1 Introduction 43
1.5.2 Economic Potential 46
1.5.2.1 Cost Comparison with Gasoline for Transport Fuels 46
1.5.3 Environmental Impact 49
1.5.3.1 Environmental Concerns 51
1.5.4 Foreseeable Social and Ethical Aspects 51
1.5.4.1 Could the Application Change Social Interactions? If Yes, in Which Way? 52
1.6 Microbial Fuel Cells and Bio-photovoltaics 52
1.6.1 Introduction 52
1.6.2 Economic Potential 56
1.6.3 Environmental Impact 56
1.6.4 Foreseeable Social and Ethical Aspects 59
1.7 Recommendations for Biofuels 59
References 61
2 Bioremediation 67Ismail Mahmutoglu, Lei Pei, Manuel Porcar, Rachel Armstrong, and Mark Bedau
2.1 Bioremediation in General 67
2.1.1 Introduction 67
2.1.2 Economic Potential 68
2.1.3 Environmental Impact 69
2.1.4 Foreseeable Social and Ethical Aspects 70
2.2 Detection of Environmental Pollutants (Biosensors) 70
2.2.1 Introduction 70
2.2.2 Economic Potential 73
2.2.3 Environmental Impact 74
2.2.4 Foreseeable Social and Ethical Aspects 76
2.3 Water Treatment 77
2.3.1 Introduction 77
2.3.2 Economic Potential 78
2.3.3 Environmental Impact 78
2.3.4 Foreseeable Social and Ethical Aspects 79
2.4 Water Desalination with Biomembranes 79
2.4.1 Introduction 79
2.4.2 Economic Potential 80
2.4.3 Environmental Impact 81
2.4.4 Foreseeable Social and Ethical Aspects 81
2.5 Soil and Groundwater Decontamination 82
2.5.1 Introduction 82
2.5.2 Economic Potential 83
2.5.3 Environmental Impact 84
2.5.4 Foreseeable Social and Ethical Aspects 85
2.6 Solid Waste Treatment 85
2.6.1 Introduction 85
2.6.2 Economic Potential 87
2.6.3 Environmental Impact 87
2.6.4 Foreseeable Social and Ethical Aspects 87
2.7 CO2 Recapturing 89
2.7.1 Introduction 89
2.7.2 Economic Potential 92
2.7.2.1 How Is Carbon Traded? 93
2.7.3 Environmental Impact 95
2.7.4 Foreseeable Social and Ethical Aspects 96
2.8 Recommendations for Bioremediation 98
References 99
Further Reading 101
3 Biomaterials 103Lei Pei, Rachel Armstrong, Antoine Danchin, and Manuel Porcar
3.1 Biomaterials in General 103
3.1.1 Introduction 103
3.1.2 Economic Potential 104
3.1.3 Environmental Impact 106
3.1.4 Foreseeable Social and Ethical Aspects 107
3.2 Biopolymers/Plastics 108
3.2.1 Introduction 108
3.2.2 Economic Potential 111
3.2.3 Environmental Impact 113
3.2.4 Foreseeable Social and Ethical Aspects 115
3.3 Bulk Chemical Production 117
3.3.1 Introduction 117
3.3.2 Economic Potential 120
3.3.3 Environmental Impact 123
3.3.4 Foreseeable Social and Ethical Aspects 124
3.4 Fine Chemical Production 126
3.4.1 Introduction 126
3.4.1.1 Vitamins and Pharmaceuticals 128
3.4.2 Economic Potential 129
3.4.3 Environmental Impact 131
3.4.4 Foreseeable Social and Ethical Aspects 133
3.5 Cellulosomes 134
3.5.1 Introduction 134
3.5.2 Economic Potential 136
3.5.3 Environmental Impact 137
3.5.4 Foreseeable Social and Ethical Aspects 138
3.6 Recommendations for Biomaterials 139
References 140
Further Reading 143
4 Other Developments in Synthetic Biology 145Rachel Armstrong, Markus Schmidt, and Mark Bedau
4.1 Protocells 145
4.1.1 Introduction 145
4.1.2 Economic Potential 147
4.1.3 Environmental Impact 147
4.1.4 Foreseeable Social and Ethical Aspects 149
4.2 Xenobiology 150
4.2.1 Introduction 150
4.2.2 Economic Potential 151
4.2.3 Environmental Impact 152
4.2.4 Foreseeable Social and Ethical Aspect 154
4.3 Recommendations for Protocells and Xenobiology 154
References 155
Further Reading 156
5 Regulatory Frameworks for Synthetic Biology 157Lei Pei, Shlomiya Bar-Yam, Jennifer Byers-Corbin, Rocco Casagrande, Florentine Eichler, Allen Lin, Martin Österreicher, Pernilla C. Regardh, Ralph D. Turlington, Kenneth A. Oye, Helge Torgersen, Zheng-Jun Guan, Wei Wei, and Markus Schmidt
5.1 United States of America 157
5.1.1 Introduction 157
5.1.2 United States Federal Regulations and Guidelines 158
5.1.2.1 National Institutes of Health: Guidelines for Research Involving Recombinant DNA Molecules 158
5.1.2.2 Environmental Protection Agency, US Department of Agriculture and Food and Drug Administration 164
5.1.2.3 USDA Animal and Plant Heath Inspection Service 167
5.1.2.4 Food and Drug Administration 169
5.1.2.5 Department of Commerce Regulations 170
5.1.2.6 Select Agent Rules 172
5.1.2.7 Screening Guidance for Providers of Synthetic Double-Stranded DNA 175
5.1.3 International Conventions and Agreements 176
5.1.3.1 The Convention on Biological Diversity 176
5.1.3.2 The Cartagena Protocol on Biosafety and the Nagoya-Kuala Lumpar Supplementary Protocol on Liability 177
5.1.3.3 The Biological Weapons Convention 178
5.1.3.4 The Australia Group Guidelines 179
5.1.4 Conclusions: Current Coverage and Future Considerations 181
5.1.4.1 Current Coverage 181
5.1.4.2 Future Prospects 183
5.2 Europe 185
5.2.1 Introduction 185
5.2.1.1 Synthetic Biology as a Novel Science and Engineering Field 186
5.2.1.2 Synthetic Biology versus Genetic Engineering 189
5.2.2 Existing Regulations 190
5.2.2.1 European Union 190
5.2.2.2 Examples of National Regulations 195
5.2.2.3 Austria 196
5.2.2.4 Germany 198
5.2.2.5 United Kingdom 201
5.2.2.6 Switzerland 203
5.2.3 Options for Adapting and Improving Regulations 205
5.2.4 Outlook 209
5.3 China 210
5.3.1 Introduction 210
5.3.2 General Provisions 211
5.3.3 Biosecurity and Dual Use 217
5.3.4 Options for Adapting and Improving Regulations 218
5.3.5 Outlook 219
References 220
Further Reading 226
Annex A List of Biofuel Companies 227
Annex B List of Bioremediation Companies 229
Index 231