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Plante M. Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives. Front Bioeng Biotechnol 2023; 11:1266298. [PMID: 38053845 PMCID: PMC10694798 DOI: 10.3389/fbioe.2023.1266298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.
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Affiliation(s)
- Mirco Plante
- Collège Montmorency, Laval, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
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Wang G, Kong Q, Wang D, Asmi F. Ethical and social insights into synthetic biology: predicting research fronts in the post-COVID-19 era. Front Bioeng Biotechnol 2023; 11:1085797. [PMID: 37274167 PMCID: PMC10235617 DOI: 10.3389/fbioe.2023.1085797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
As a revolutionary biological science and technology, synthetic biology has already spread its influence from natural sciences to humanities and social sciences by introducing biosafety, biosecurity, and ethical issues to society. The current study aims to elaborate the intellectual bases and research front of the synthetic biology field in the sphere of philosophy, ethics, and social sciences, with knowledge mapping and bibliometric methods. The literature records from the Social Sciences Citation Index and Arts & Humanities Citation Index in the Web of Science Core Collection from 1982 to 2021 were collected and analyzed to illustrate the intellectual structure of philosophical, ethical, and social research of synthetic biology. This study profiled the hotspots of research focus on its governance, philosophical and ethical concerns, and relevant technologies. This study offers clues and enlightenment for the stakeholders and researchers to follow the progress of this emerging discipline and technology and to understand the cutting-edge ideas and future form of this field, which takes on greater significance in the post-COVID-19 era.
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Affiliation(s)
| | | | - Dong Wang
- *Correspondence: Dong Wang, ; Fahad Asmi,
| | - Fahad Asmi
- *Correspondence: Dong Wang, ; Fahad Asmi,
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Rees-Garbutt J, Chalkley O, Grierson C, Marucci L. Minimal Genome Design Algorithms Using Whole-Cell Models. Methods Mol Biol 2020; 2189:183-198. [PMID: 33180302 DOI: 10.1007/978-1-0716-0822-7_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Synthetic biologists engineer cells and cellular functions using design-build-test cycles; when the task is to extensively engineer entire genomes, the lack of appropriate design tools and biological knowledge about each gene in a cell can lengthen the process, requiring time-consuming and expensive experimental iterations.Whole-cell models represent a new avenue for genome design; the bacteria Mycoplasma genitalium has the first (and currently only published) whole-cell model which combines 28 cellular submodels and represents the integrated functions of every gene and molecule in a cell.We created two minimal genome design algorithms, GAMA and Minesweeper, that produced 1000s of in silico minimal genomes by running simulations on multiple supercomputers. Here we describe the steps to produce in silico cells with reduced genomes, combining minimisation algorithms with whole-cell model simulations.We foresee that the combination of similar algorithms and whole-cell models could later be used for a broad spectrum of genome design applications across cellular species when appropriate models become available.
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Affiliation(s)
- Joshua Rees-Garbutt
- BrisSynBio, University of Bristol, Bristol, UK.,School of Biological Sciences, University of Bristol, Bristol, UK
| | - Oliver Chalkley
- Department of Engineering Mathematics, University of Bristol, Bristol, UK.,Bristol Centre for Complexity Science, University of Bristol, Bristol, UK
| | - Claire Grierson
- BrisSynBio, University of Bristol, Bristol, UK. .,School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Lucia Marucci
- BrisSynBio, University of Bristol, Bristol, UK. .,Department of Engineering Mathematics, University of Bristol, Bristol, UK. .,School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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Belén Paredes M, Eugenia Sulen M. An overview of synthetic biology. BIONATURA 2020. [DOI: 10.21931/rb/2020.05.01.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Synthetic Biology is the combination of basic sciences with engineering. The aim of Synthetic Biology is to create, design, and redesign biological systems and devices to understand biological processes and to achieve useful and sophisticated functionalities to improve human welfare. When the engineering community took part in the discussion for the definition of Synthetic Biology, the idea of extraction and reassembly of “biological parts” along with the principles of abstraction, modularity, and standardization was introduced. Genetic Engineering is one of the many essential tools for synthetic biology, and even though they share the DNA manipulation basis and approach to intervene in the complexity of molecular biology, they differ in many aspects, and the two terms should not be used interchangeably. Some of the applications that have already been done by Synthetic Biology include the production of 1,4-butanediol (BDO), the antimalarial drug artemisinin, and the anticancer compound taxol. The potential of Synthetic Biology to design new genomes without immediate biological ancestry has raised ontological, political, economic, and ethical concerns based on the possibility that synthetic biology may be intrinsically unethical.
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Landon S, Rees-Garbutt J, Marucci L, Grierson C. Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering. Essays Biochem 2019; 63:267-284. [PMID: 31243142 PMCID: PMC6610458 DOI: 10.1042/ebc20180045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/19/2019] [Accepted: 05/23/2019] [Indexed: 01/04/2023]
Abstract
Producing 'designer cells' with specific functions is potentially feasible in the near future. Recent developments, including whole-cell models, genome design algorithms and gene editing tools, have advanced the possibility of combining biological research and mathematical modelling to further understand and better design cellular processes. In this review, we will explore computational and experimental approaches used for metabolic and genome design. We will highlight the relevance of modelling in this process, and challenges associated with the generation of quantitative predictions about cell behaviour as a whole: although many cellular processes are well understood at the subsystem level, it has proved a hugely complex task to integrate separate components together to model and study an entire cell. We explore these developments, highlighting where computational design algorithms compensate for missing cellular information and underlining where computational models can complement and reduce lab experimentation. We will examine issues and illuminate the next steps for genome engineering.
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Affiliation(s)
- Sophie Landon
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
| | - Joshua Rees-Garbutt
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, U.K
| | - Lucia Marucci
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K.
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
| | - Claire Grierson
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K.
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, U.K
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Design Methodologies and the Limits of the Engineering-Dominated Conception of Synthetic Biology. Acta Biotheor 2019; 67:1-18. [PMID: 30121875 DOI: 10.1007/s10441-018-9338-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 08/14/2018] [Indexed: 10/28/2022]
Abstract
Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design and the variability of design methodologies in synthetic biology. I focus on two prominent design methodologies: rational design and directed evolution. Rational design resembles the design methodology of traditional engineering sciences. However, it is often replaced and complemented by the more biologically-inspired method of directed evolution, which models itself on natural evolution. These two approaches take philosophically different stances to the design of biological systems. Rational design aims to make biological systems more machine-like, whereas directed evolution utilizes variation and emergent features of living systems. I provide an analysis of the methodological basis of these design approaches, and highlight important methodological differences between them. By analyzing the respective benefits and limitations of these approaches, I argue against the engineering-dominated conception of synthetic biology and its "methodological monism", where the rational design approach is taken as the default design methodology. Alternative design methodologies, like directed evolution, should be considered as complementary, not competitive, to rational design.
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Abstract
New health technologies are rapidly emerging from various areas of bioscience research, such as gene editing, regenerative medicine and synthetic biology. These technologies raise promising medical possibilities but also a range of ethical considerations. Apart from the issues involved in considering whether novel health technologies can or should become part of mainstream medical treatment once established, the process of research translation to develop such therapies itself entails particular ethical concerns. In this paper I use synthetic biology as an example of a new and largely unexplored area of health technology to consider the ways in which novel health technologies are likely to emerge and the ethical challenges these will present. I argue that such developments require us to rethink conventional attitudes towards clinical research, the roles of doctors/researchers and patients/participants with respect to research, and the relationship between science and society; and that a broader framework is required to address the plurality of stakeholder roles and interests involved in the development of treatments based on novel technologies.
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Designing with living systems in the synthetic yeast project. Nat Commun 2018; 9:2950. [PMID: 30054478 PMCID: PMC6063962 DOI: 10.1038/s41467-018-05332-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/28/2018] [Indexed: 11/08/2022] Open
Abstract
Synthetic biology is challenged by the complexity and the unpredictability of living systems. While one response to this complexity involves simplifying cells to create more fully specified systems, another approach utilizes directed evolution, releasing some control and using unpredictable change to achieve design goals. Here we discuss SCRaMbLE, employed in the synthetic yeast project, as an example of synthetic biology design through working with living systems. SCRaMbLE is a designed tool without being a design tool, harnessing the activities of the yeast rather than relying entirely on scientists’ deliberate choices. We suggest that directed evolution at the level of the whole organism allows scientists and microorganisms to “collaborate” to achieve design goals, suggesting new directions for synthetic biology. Synthetic biology often views the organism as a chassis into which a circuit can be inserted. Here the authors explore the idea of the organism as a core aspect of design, aiding researchers in navigating the genetic space opened up by SCRaMbLE.
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Szymanski EA. Who are the users of synthetic DNA? Using metaphors to activate microorganisms at the center of synthetic biology. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:15. [PMID: 30006902 PMCID: PMC6045561 DOI: 10.1186/s40504-018-0080-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Synthetic biology, a multidisciplinary field involving designing and building with DNA, often designs and builds in microorganisms. The role of these microorganisms tends to be understood through metaphors making the microbial cell like a machine and emphasizing its passivity: cells are described as platforms, chassis, and computers. Here, I point to the efficacy of such metaphors in enacting the microorganism as a particular kind of (non-)participant in the research process, and I suggest the utility of employing metaphors that make microorganisms a different kind of thing-active participants, contributors, and even collaborators in scientific research. This suggestion is worth making, I argue, because enabling the activity of the microorganism generates opportunities for learning from microorganisms in ways that may help explain currently unexplained phenomena in synthetic biology and suggest new experimental directions. Moreover, "activating the microorganism" reorients relationships between human scientists and nonhuman experimental participants away from control over nonhuman creatures and toward respect for and listening to them, generating conditions of possibility for exploring what responsible research means when humans try to be responsible toward and even with creatures across species boundaries.
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Affiliation(s)
- Erika Amethyst Szymanski
- Science, Technology, and Innovation Studies, University of Edinburgh, Edinburgh, UK.
- Chisholm House, High School Yards, Edinburgh, EH1 1LZ, UK.
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McLeod C, Nerlich B. Synthetic biology, metaphors and responsibility. LIFE SCIENCES, SOCIETY AND POLICY 2017; 13:13. [PMID: 28849542 PMCID: PMC5573707 DOI: 10.1186/s40504-017-0061-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/08/2017] [Indexed: 05/25/2023]
Abstract
Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The language we use to make a better world matters; words matter; metaphors matter. Words have consequences - ethical, social and legal ones, as well as political and economic ones. They need to be used 'responsibly'. They also need to be studied carefully - this is what we want to do through this editorial and the related thematic collection. In the context of synthetic biology, natural and social scientists have become increasingly interested in metaphors, a wave of interest that we want to exploit and amplify. We want to build on emerging articles and books on synthetic biology, metaphors of life and the ethical and moral implications of such metaphors. This editorial provides a brief introduction to synthetic biology and responsible innovation, as well as a comprehensive review of literature on the social, cultural and ethical impacts of metaphor use in genomics and synthetic biology. Our aim is to stimulate an interdisciplinary and international discussion on the impact that metaphors can have on science, policy and publics in the context of synthetic biology.
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Affiliation(s)
- Carmen McLeod
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK.
| | - Brigitte Nerlich
- School of Sociology and Social Policy, University of Nottingham, Nottingham, UK
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Raimbault B, Cointet JP, Joly PB. Mapping the Emergence of Synthetic Biology. PLoS One 2016; 11:e0161522. [PMID: 27611324 PMCID: PMC5017775 DOI: 10.1371/journal.pone.0161522] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/08/2016] [Indexed: 11/18/2022] Open
Abstract
In this paper, we apply an original scientometric analyses to a corpus comprising synthetic biology (SynBio) publications in Thomson Reuters Web of Science to characterize the emergence of this new scientific field. Three results were drawn from this empirical investigation. First, despite the exponential growth of publications, the study of population level statistics (newcomers proportion, collaboration network structure) shows that SynBio has entered a stabilization process since 2010. Second, the mapping of textual and citational networks shows that SynBio is characterized by high heterogeneity and four different approaches: the central approach, where biobrick engineering is the most widespread; genome engineering; protocell creation; and metabolic engineering. We suggest that synthetic biology acts as an umbrella term allowing for the mobilization of resources, and also serves to relate scientific content and promises of applications. Third, we observed a strong intertwinement between epistemic and socio-economic dynamics. Measuring scientific production and impact and using structural analysis data, we identified a core set of mostly American scientists. Biographical analysis shows that these central and influential scientists act as "boundary spanners," meaning that their importance to the field lies not only in their academic contributions, but also in their capacity to interact with other social spaces that are outside the academic sphere.
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Kendig CE. What is Proof of Concept Research and how does it Generate Epistemic and Ethical Categories for Future Scientific Practice? SCIENCE AND ENGINEERING ETHICS 2016; 22:735-753. [PMID: 26009258 DOI: 10.1007/s11948-015-9654-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 05/14/2015] [Indexed: 06/04/2023]
Abstract
"Proof of concept" is a phrase frequently used in descriptions of research sought in program announcements, in experimental studies, and in the marketing of new technologies. It is often coupled with either a short definition or none at all, its meaning assumed to be fully understood. This is problematic. As a phrase with potential implications for research and technology, its assumed meaning requires some analysis to avoid it becoming a descriptive category that refers to all things scientifically exciting. I provide a short analysis of proof of concept research and offer an example of it within synthetic biology. I suggest that not only are there activities that circumscribe new epistemological categories but there are also associated normative ethical categories or principles linked to the research. I examine these and provide an outline for an alternative ethical account to describe these activities that I refer to as "extended agency ethics". This view is used to explain how the type of research described as proof of concept also provides an attendant proof of principle that is the result of decision-making that extends across practitioners, their tools, techniques, and the problem solving activities of other research groups.
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Affiliation(s)
- Catherine Elizabeth Kendig
- Department of Philosophy and Religion, Missouri Western State University, 4525 Downs Drive, Saint Joseph, MO, 64507, USA.
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15
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Beyond unity: Nurturing diversity in synthetic biology and its publics. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-658-10988-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Qi H, Li BZ, Zhang WQ, Liu D, Yuan YJ. Modularization of genetic elements promotes synthetic metabolic engineering. Biotechnol Adv 2015; 33:1412-9. [DOI: 10.1016/j.biotechadv.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/12/2015] [Accepted: 04/05/2015] [Indexed: 01/24/2023]
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Schmidt M, Meyer A, Cserer A. The Bio:Fiction film festival: Sensing how a debate about synthetic biology might evolve. PUBLIC UNDERSTANDING OF SCIENCE (BRISTOL, ENGLAND) 2015; 24:619-635. [PMID: 24164747 PMCID: PMC4466099 DOI: 10.1177/0963662513503772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Synthetic biology (SB) is a new techno-scientific field surrounded by an aura of hope, hype and fear. Currently it is difficult to predict which way the public debate - and thus the social shaping of technology - is heading. With limited hard evidence at hand, we resort to a strategy that takes into account speculative design and diegetic prototyping, accessing the Bio:Fiction science film festival, and its 52 short films from international independent filmmakers. Our first hypothesis was that these films could be used as an indicator of a public debate to come. The second hypothesis was that SB would most likely not follow the debate around genetic engineering (framing technology as conflict) as assumed by many observers. Instead, we found good evidence for two alternative comparators, namely nanotechnology (technology as progress) and information technology (technology as gadget) as stronger attractors for an upcoming public debate on SB.
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Affiliation(s)
- Markus Schmidt
- Organisation for International Dialogue and Conflict Management IDC, Austria;Biofaction KG, Austria
| | - Angela Meyer
- Organisation for International Dialogue and Conflict Management IDC, Austria
| | - Amelie Cserer
- Organisation for International Dialogue and Conflict Management IDC, Austria;Technische Universität Wien, Austria
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Kaebnick GE, Gusmano MK, Murray TH. The ethics of synthetic biology: next steps and prior questions. Hastings Cent Rep 2015; 44:S4-S26. [PMID: 25418704 DOI: 10.1002/hast.392] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Bensaude-Vincent B. Synthetic Biology As a Replica of Synthetic Chemistry? Uses and Misuses of History. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot_a_00007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
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Douglas CMW, Stemerding D. Challenges for the European governance of synthetic biology for human health. LIFE SCIENCES, SOCIETY AND POLICY 2014; 10:6. [PMID: 26085442 PMCID: PMC4686464 DOI: 10.1186/s40504-014-0006-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 01/08/2014] [Indexed: 06/04/2023]
Abstract
Synthetic biology is a series of scientific and technological practices involved in the application of engineering principles to the design and production of predictable and robust biological systems. While policy discussions abound in this area, emerging technologies like synthetic biology present considerable challenges in the articulation of concrete policy options given that their introduction into society may still be in the distant future. This paper reports on a series of governance workshops that focused on synthetic biology's ethical, legal, and social implications (ELSI) as they pertain to human health, and discusses particular limitations of the ELSI approach that we encountered in our work. In an attempt to avoid policymaking for potential implications of uncertain future applications we instead conclude by proposing tangible forms of anticipatory governance that may be more adequate in addressing the more immediate concerns raised by synthetic biology.
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Affiliation(s)
- Conor MW Douglas
- />Technology Assessment, Rathenau Institute, The Hague, 2593 HW,, The Netherlands
- />Collaborations for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver BC V6T 1Z3,, Canada
| | - Dirk Stemerding
- />Technology Assessment, Rathenau Institute, The Hague, 2593 HW,, The Netherlands
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Abstract
Prototrophic bacteria grow on M-9 minimal salts medium supplemented with glucose (M-9 medium), which is used as a carbon and energy source. Auxotrophs can be generated using a transposome. The commercially available, Tn5-derived transposome used in this protocol consists of a linear segment of DNA containing an R6Kγ replication origin, a gene for kanamycin resistance and two mosaic sequence ends, which serve as transposase binding sites. The transposome, provided as a DNA/transposase protein complex, is introduced by electroporation into the prototrophic strain, Enterobacter sp. YSU, and randomly incorporates itself into this host's genome. Transformants are replica plated onto Luria-Bertani agar plates containing kanamycin, (LB-kan) and onto M-9 medium agar plates containing kanamycin (M-9-kan). The transformants that grow on LB-kan plates but not on M-9-kan plates are considered to be auxotrophs. Purified genomic DNA from an auxotroph is partially digested, ligated and transformed into a pir+ Escherichia coli (E. coli) strain. The R6Kγ replication origin allows the plasmid to replicate in pir+ E. coli strains, and the kanamycin resistance marker allows for plasmid selection. Each transformant possesses a new plasmid containing the transposon flanked by the interrupted chromosomal region. Sanger sequencing and the Basic Local Alignment Search Tool (BLAST) suggest a putative identity of the interrupted gene. There are three advantages to using this transposome mutagenesis strategy. First, it does not rely on the expression of a transposase gene by the host. Second, the transposome is introduced into the target host by electroporation, rather than by conjugation or by transduction and therefore is more efficient. Third, the R6Kγ replication origin makes it easy to identify the mutated gene which is partially recovered in a recombinant plasmid. This technique can be used to investigate the genes involved in other characteristics of Enterobacter sp. YSU or of a wider variety of bacterial strains.
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Affiliation(s)
- Jonathan James Caguiat
- Department of Biological Sciences, Center for Applied Chemical Biology, Youngstown State University;
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Revolution versus evolution?: Understanding scientific and technological diffusion in synthetic biology and their implications for biosecurity policies. BIOSOCIETIES 2014. [DOI: 10.1057/biosoc.2014.31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jovicevic D, Blount BA, Ellis T. Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast. Bioessays 2014; 36:855-60. [PMID: 25048260 DOI: 10.1002/bies.201400086] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A team of US researchers recently reported the design, assembly and in vivo functionality of a synthetic chromosome III (SynIII) for the yeast Saccharomyces cerevisiae. The synthetic chromosome was assembled bottom-up from DNA oligomers by teams of students working over several years with researchers as the first part of an international synthetic yeast genome project. Embedded into the sequence of the synthetic chromosome are multiple design changes that include a novel in-built recombination scheme that can be induced to catalyse intra-chromosomal rearrangements in a variety of different conditions. This system, along with the other synthetic sequence changes, is intended to aid researchers develop a deeper understanding of how genomes function and find new ways to exploit yeast in future biotechnologies. The landmark of the first synthesised designer eukaryote chromosome, and the power of its massively parallel recombination system, provide new perspectives on the future of synthetic biology and genome research.
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Affiliation(s)
- Dejana Jovicevic
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
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Abstract
Theorists analyzing the concept of disease on the basis of the notion of dysfunction consider disease to be dysfunction requiring. More specifically, dysfunction-requiring theories of disease claim that for an individual to be diseased certain biological facts about it must be the case. Disease is not wholly a matter of evaluative attitudes. In this paper, I consider the dysfunction-requiring component of Wakefield's hybrid account of disease in light of the artifactual organisms envisioned by current research in synthetic biology. In particular, I argue that the possibility of artifactual organisms and the case of oncomice and other bred or genetically modified strains of organism constitute a significant objection to Wakefield's etiological account of the dysfunction requirement. I then develop a new alternative understanding of the dysfunction requirement that builds on the organizational theory of function. I conclude that my suggestion is superior to Wakefield's theory because it (a) can accommodate both artifactual and naturally evolved organisms, (b) avoids the possibility of there being a conflict between what an organismic part is supposed to do and the health of the organism, and (c) provides a nonarbitrary and practical way of determining whether dysfunction occurs.
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Affiliation(s)
- Sune Holm
- University of Copenhagen, Copenhagen, Denmark
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Lange O, Binder A, Lahaye T. From dead leaf, to new life:
TAL
effectors as tools for synthetic biology. THE PLANT JOURNAL 2014; 78:753-771. [PMID: 24602153 DOI: 10.1111/tpj.12431] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Orlando Lange
- Department of General Genetics Centre for Plant Molecular Biology Eberhard‐Karls‐University Tübingen Auf der Morgenstelle 32 72076 Tübingen Germany
| | - Andreas Binder
- Genetics Faculty of Biology I University of Munich Großhaderner Straße 2‐4 82152 Martinsried Germany
| | - Thomas Lahaye
- Department of General Genetics Centre for Plant Molecular Biology Eberhard‐Karls‐University Tübingen Auf der Morgenstelle 32 72076 Tübingen Germany
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30
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Lewens T. From bricolage to BioBricks™: Synthetic biology and rational design. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:641-648. [PMID: 23838473 DOI: 10.1016/j.shpsc.2013.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Synthetic biology is often described as a project that applies rational design methods to the organic world. Although humans have influenced organic lineages in many ways, it is nonetheless reasonable to place synthetic biology towards one end of a continuum between purely 'blind' processes of organic modification at one extreme, and wholly rational, design-led processes at the other. An example from evolutionary electronics illustrates some of the constraints imposed by the rational design methodology itself. These constraints reinforce the limitations of the synthetic biology ideal, limitations that are often freely acknowledged by synthetic biology's own practitioners. The synthetic biology methodology reflects a series of constraints imposed on finite human designers who wish, as far as is practicable, to communicate with each other and to intervene in nature in reasonably targeted and well-understood ways. This is better understood as indicative of an underlying awareness of human limitations, rather than as expressive of an objectionable impulse to mastery over nature.
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Affiliation(s)
- Tim Lewens
- University of Cambridge, Department of History and Philosophy of Science, Free School Lane, Cambridge CB2 3RH, UK.
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31
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Schyfter P. How a 'drive to make' shapes synthetic biology. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:632-640. [PMID: 23777680 DOI: 10.1016/j.shpsc.2013.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A commitment to 'making'--creating or producing things--can shape scientific and technological fields in important ways. This article demonstrates this by exploring synthetic biology, a field committed to making use of advanced techniques from molecular biology in order to make with living matter (and for some, to engineer living matter). I describe and analyse how this field's 'drive to make' shapes its organisational, methodological, epistemological, and ontological character. Synthetic biologists' ambition to make helps determine how their field demarcates itself, sets appropriate methods and practices, construes the purpose and character of knowledge, and views the things of the living world. Using empirical data from extensive ethnographic and interview-based research, I discuss the importance of seemingly simple and unimportant commitments-in this case, a focus on the making of things rather than the production of knowledge claims. I conclude by examining the ramifications of this line of research for studies of science and technology.
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Affiliation(s)
- Pablo Schyfter
- Science, Technology and Innovation Studies, The University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh EH1 1LZ, UK.
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32
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Holm S, Powell R. Organism, machine, artifact: The conceptual and normative challenges of synthetic biology. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:627-31. [PMID: 23810468 DOI: 10.1016/j.shpsc.2013.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Synthetic biology is an emerging discipline that aims to apply rational engineering principles in the design and creation of organisms that are exquisitely tailored to human ends. The creation of artificial life raises conceptual, methodological and normative challenges that are ripe for philosophical investigation. This special issue examines the defining concepts and methods of synthetic biology, details the contours of the organism-artifact distinction, situates the products of synthetic biology vis-à-vis this conceptual typology and against historical human manipulation of the living world, and explores the normative implications of these conclusions. In addressing the challenges posed by emerging biotechnologies, new light can be thrown on old problems in the philosophy of biology, such as the nature of the organism, the structure of biological teleology, the utility of engineering metaphors and methods in biological science, and humankind's relationship to nature.
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Affiliation(s)
- Sune Holm
- Philosophy Section, Department of Media, Cognition and Communication, University of Copenhagen, Denmark.
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33
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Holm S. Organism and artifact: Proper functions in Paley organisms. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:706-713. [PMID: 23792090 DOI: 10.1016/j.shpsc.2013.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this paper I assess the explanatory powers of theories of function in the context of products that may result from synthetic biology. The aim is not to develop a new theory of functions, but to assess existing theories of function in relation to a new kind of biological and artifactual entity that might be produced in the not-too-distant future by means of synthetic biology. The paper thus investigates how to conceive of the functional nature of living systems that are not the result of evolution by natural selection, or instantly generated by cosmic coincidence, but which are products of intelligent design. The paper argues that the aetiological theory of proper functions in organisms and artifacts is inadequate as an account of proper functions in such 'Paley organisms' and defends an alternative organisational approach. The paper ends by considering the implications of the discussion of biological function for questions about the interests and moral status of non-sentient organisms.
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Affiliation(s)
- Sune Holm
- Dept. of Media, Cognition and Communication (Philosophy Section), Copenhagen University, Karen Blixens Vej 4, 2300 S, Denmark.
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36
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Calvert J. Engineering Biology and Society: Reflections on Synthetic Biology. SCIENCE TECHNOLOGY AND SOCIETY 2013. [DOI: 10.1177/0971721813498501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Synthetic biology, according to some definitions, is the attempt to make biology into an engineering discipline. I ask what is meant by this objective, which seems to have excited and energised many people and encouraged them to start working in the field. I show how synthetic biologists make a point of distinguishing their work from previous genetic ‘engineering’, which is described as bespoke and artisan. I examine synthetic biologists’ accounts of the differences between biology and engineering, which often oppose comprehension to construction. I argue that synthetic biology, like other branches of engineering, aims to meet recognised needs, and to make the world more manipulable and controllable. But there are tensions within the field—some synthetic biologists have reservations about the extent to which biology can be engineered, and ask whether it is necessary to develop a new type of engineering when working with living systems. After exploring these debates, I turn to some of the broader consequences of making biology easier to engineer, particularly the deskilling and democratisation of the technology. I end by arguing that because synthetic biologists are skilled at bringing together both technical and social forces, they are appropriately described as ‘heterogeneous engineers’.
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Affiliation(s)
- Jane Calvert
- Jane Calvert, Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons’ Hall, Edinburgh, EH1 1LZ, UK
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37
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Meyer A, Cserer A, Schmidt M. Frankenstein 2.0.: Identifying and characterising synthetic biology engineers in science fiction films. LIFE SCIENCES, SOCIETY AND POLICY 2013; 9:9. [PMCID: PMC4513001 DOI: 10.1186/2195-7819-9-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 08/14/2013] [Indexed: 07/24/2023]
Abstract
Synthetic biology (SB) has emerged as one of the newest and promising areas of bio-technology. Issues typically associated to SB, notably in the media, like the idea of artificial life creation and “real” engineering of life also appear in many popular films. Drawing upon the analysis of 48 films, the article discusses how scientists applying technologies that can be related to SB are represented in these movies. It hereby discusses that traditional clichés of scientists in general tend to be sublated by new stereotypical characterizations. These reflect real trends in bio-technological research such as SB, especially the increased relationship between science and industry. Frankenstein 2.0. looks less like the old, genius yet mad scientist, and follows a more entrepreneurial than academic spirit.
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Affiliation(s)
- Angela Meyer
- />Organisation for International Dialogue and Conflict Management (IDC), Vienna, Austria
| | - Amelie Cserer
- />Organisation for International Dialogue and Conflict Management (IDC), Vienna, Austria
| | - Markus Schmidt
- />Organisation for International Dialogue and Conflict Management (IDC), Vienna, Austria
- />Biofaction KG, Vienna, Austria
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38
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Kelle A. Beyond patchwork precaution in the dual-use governance of synthetic biology. SCIENCE AND ENGINEERING ETHICS 2013; 19:1121-39. [PMID: 22535577 PMCID: PMC3735959 DOI: 10.1007/s11948-012-9365-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/12/2012] [Indexed: 05/31/2023]
Abstract
The emergence of synthetic biology holds the potential of a major breakthrough in the life sciences by transforming biology into a predictive science. The dual-use characteristics of similar breakthroughs during the twentieth century have led to the application of benignly intended research in e.g. virology, bacteriology and aerobiology in offensive biological weapons programmes. Against this background the article raises the question whether the precautionary governance of synthetic biology can aid in preventing this techno-science witnessing the same fate? In order to address this question, this paper proceeds in four steps: it firstly introduces the emerging techno-science of synthetic biology and presents some of its potential beneficial applications. It secondly analyses contributions to the bioethical discourse on synthetic biology as well as precautionary reasoning and its application to life science research in general and synthetic biology more specifically. The paper then identifies manifestations of a moderate precautionary principle in the emerging synthetic biology dual-use governance discourse. Using a dual-use governance matrix as heuristic device to analyse some of the proposed measures, it concludes that the identified measures can best be described as "patchwork precaution" and that a more systematic approach to construct a web of dual-use precaution for synthetic biology is needed in order to guard more effectively against the field's future misuse for harmful applications.
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Affiliation(s)
- Alexander Kelle
- Department of Politics, Languages and International Studies, University of Bath, Bath, BA2 7AY, UK.
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39
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Ruiz-Mirazo K, Moreno A. Synthetic Biology: Challenging Life in Order to Grasp, Use, or Extend It. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13752-013-0129-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Left to their own devices: Post-ELSI, ethical equipment and the International Genetically Engineered Machine (iGEM) Competition. BIOSOCIETIES 2013; 8:311-335. [PMID: 24159360 PMCID: PMC3772706 DOI: 10.1057/biosoc.2013.13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, we evaluate a novel method for post-ELSI (ethical, legal and social implications) collaboration, drawing on 'human practices' (HP) to develop a form of reflexive ethical equipment that we termed 'sociotechnical circuits'. We draw on a case study of working collaboratively in the International Genetically Engineered Machine Competition (iGEM) and relate this to the parts-based agenda of synthetic biology. We use qualitative methods to explore the experience of undergraduate students in the Competition, focussing on the 2010 University of Sheffield team. We examine how teams work collaboratively across disciplines to produce novel microorganisms. The Competition involves a HP component and we examine the way in which this has been narrowly defined within the ELSI framework. We argue that this is a much impoverished style of HP when compared with its original articulation as the development of 'ethical equipment'. Inspired by this more theoretically rich HP framework, we explore the relations established between team members and how these were shaped by the norms, materials and practices of the Competition. We highlight the importance of care in the context of post-ELSI collaborations and report on the implications of our case study for such efforts and for the relation of the social sciences to the life sciences more generally.
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41
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Güttinger S. Creating parts that allow for rational design: synthetic biology and the problem of context-sensitivity. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:199-207. [PMID: 23578488 DOI: 10.1016/j.shpsc.2013.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins' account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology.
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Affiliation(s)
- Stephan Güttinger
- Centre for Philosophy of Natural and Social Science, Lakatos Building, London School of Economics and Political Science, Houghton Street, London WC2A 2AE, United Kingdom.
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42
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Gramelsberger G, Knuuttila T, Gelfert A. Philosophical perspectives on synthetic biology. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:119-121. [PMID: 23566940 DOI: 10.1016/j.shpsc.2013.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Gabriele Gramelsberger
- Freie Universität Berlin, Institute of Philosophy, Habelschwerdter Allee 30, 14195 Berlin, Germany.
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43
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Kastenhofer K. Two sides of the same coin? The (techno)epistemic cultures of systems and synthetic biology. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:130-140. [PMID: 23582486 DOI: 10.1016/j.shpsc.2013.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Systems and synthetic biology both emerged around the turn of this century as labels for new research approaches. Although their disciplinary status as well as their relation to each other is rarely discussed in depth, now and again the idea is invoked that both approaches represent 'two sides of the same coin'. The following paper focuses on this general notion and compares it with empirical findings concerning the epistemic cultures prevalent in the two contexts. Drawing on interviews with researchers from both fields, on participatory observation in conferences and courses and on documentary analysis, this paper delineates differences and similarities, incompatibilities and blurred boundaries. By reconstructing systems and synthetic biology's epistemic cultures, this paper argues that they represent two 'communities of vision', encompassing heterogeneous practices. Understanding the relation of the respective visions of understanding nature and engineering life is seen as indispensible for the characterisation of (techno)science in more general terms. Depending on the conceptualisation of understanding and construction (or: science and engineering), related practices such as in silico modelling for enhancing understanding or enabling engineering can either be seen as incommensurable or 'two sides of one coin'.
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Affiliation(s)
- Karen Kastenhofer
- Research Centre for Biotechnology, Society, and the Environment (FSP BIOGUM), University of Hamburg, Austria.
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44
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Gramelsberger G. The simulation approach in synthetic biology. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:150-157. [PMID: 23582487 DOI: 10.1016/j.shpsc.2013.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Synthetic biology and systems biology are often highlighted as antagonistic strategies for dealing with the overwhelming complexity of biology (engineering versus understanding; tinkering in the lab versus modelling in the computer). However, a closer view of contemporary engineering methods (inextricably interwoven with mathematical modelling and simulation) and of the situation in biology (inextricably confronted with the intrinsic complexity of biomolecular environments) demonstrates that tinkering in the lab is increasingly supported by rational design methods. In other words: Synthetic biology and systems biology are merged by the use of computational techniques. These computational techniques are needed because the intrinsic complexity of biomolecular environments (stochasticity, non-linearities, system-level organization, evolution, independence, etc.) require advanced concepts of bio bricks and devices. A philosophical investigation of the history and nature of bio parts and devices reveals that these objects are imitating generic objects of engineering (switches, gates, oscillators, sensors, etc.), but the well-known design principles of generic objects are not sufficient for complex environments like cells. Therefore, the rational design methods have to be used to create more advanced generic objects, which are not only generic in their use, but also adaptive in their behavior. Case studies will show how simulation-based rational design methods are used to identify adequate parameters for synthesized designs (stability analyses), to improve lab experiments by 'looking through noise' (estimation of hidden variables and parameters), and to replace laborious and time-consuming post hoc tweaking in the lab by in-silico guidance (in-silico variation of bio brick properties). The overall aim of these developments, as will be argued in the discussion, is to achieve adaptive-generic instrumentality for bio parts and devices and thus increasingly merging systems and synthetic biology.
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Affiliation(s)
- Gabriele Gramelsberger
- Freie Universität Berlin, Institute of Philosophy, Habelschwerdter Allee 30, 14195 Berlin, Germany.
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45
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Gelfert A. Synthetic biology between technoscience and thing knowledge. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:141-149. [PMID: 23562606 DOI: 10.1016/j.shpsc.2013.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Synthetic biology presents a challenge to traditional accounts of biology: Whereas traditional biology emphasizes the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future of homogeneous, humanly engineered biological systems that may be combined in modular fashion. The present paper approaches this challenge from the perspective of the epistemology of technoscience. In particular, it is argued that synthetic-biological artifacts lend themselves to an analysis in terms of what has been called 'thing knowledge'. As such, they should neither be regarded as the simple outcome of applying theoretical knowledge and engineering principles to specific technological problems, nor should they be treated as mere sources of new evidence in the general pursuit of scientific understanding. Instead, synthetic-biological artifacts should be viewed as partly autonomous research objects which, qua their material-biological constitution, embody knowledge about the natural world-knowledge that, in turn, can be accessed via continuous experimental interrogation.
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Affiliation(s)
- Axel Gelfert
- Department of Philosophy, National University of Singapore, 3 Arts Link, 117570 Singapore, Singapore.
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46
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Oftedal G, Parkkinen VP. Synthetic biology and genetic causation. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:208-216. [PMID: 23591049 DOI: 10.1016/j.shpsc.2013.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Synthetic biology research is often described in terms of programming cells through the introduction of synthetic genes. Genetic material is seemingly attributed with a high level of causal responsibility. We discuss genetic causation in synthetic biology and distinguish three gene concepts differing in their assumptions of genetic control. We argue that synthetic biology generally employs a difference-making approach to establishing genetic causes, and that this approach does not commit to a specific notion of genetic program or genetic control. Still, we suggest that a strong program concept of genetic material can be used as a successful heuristic in certain areas of synthetic biology. Its application requires control of causal context, and may stand in need of a modular decomposition of the target system. We relate different modularity concepts to the discussion of genetic causation and point to possible advantages of and important limitations to seeking modularity in synthetic biology systems.
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Affiliation(s)
- Gry Oftedal
- Philosophical Foundations for Systems Biology (PSBio), Department of Philosophy, Classics, History of Arts and Ideas, University of Oslo, Box 1020 Blindern, 0315 Oslo, Norway.
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47
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Designing de novo: interdisciplinary debates in synthetic biology. SYSTEMS AND SYNTHETIC BIOLOGY 2013; 7:41-50. [PMID: 24432141 DOI: 10.1007/s11693-013-9106-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/27/2013] [Accepted: 03/30/2013] [Indexed: 12/11/2022]
Abstract
Synthetic biology is often presented as a promissory field that ambitions to produce novelty by design. The ultimate promise is the production of living systems that will perform new and desired functions in predictable ways. Nevertheless, realizing promises of novelty has not proven to be a straightforward endeavour. This paper provides an overview of, and explores the existing debates on, the possibility of designing living systems de novo as they appear in interdisciplinary talks between engineering and biological views within the field of synthetic biology. To broaden such interdisciplinary debates, we include the views from the social sciences and the humanities and we point to some fundamental sources of disagreement within the field. Different views co-exist, sometimes as controversial tensions, but sometimes also pointing to integration in the form of intermediate positions. As the field is emerging, multiple choices are possible. They will inform alternative trajectories in synthetic biology and will certainly shape its future. What direction is best is to be decided in reflexive and socially robust ways.
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Deplazes-Zemp A. The conception of life in synthetic biology. SCIENCE AND ENGINEERING ETHICS 2012; 18:757-774. [PMID: 21484320 DOI: 10.1007/s11948-011-9269-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 03/28/2011] [Indexed: 05/30/2023]
Abstract
The phrase 'synthetic biology' is used to describe a set of different scientific and technological disciplines, which share the objective to design and produce new life forms. This essay addresses the following questions: What conception of life stands behind this ambitious objective? In what relation does this conception of life stand to that of traditional biology and biotechnology? And, could such a conception of life raise ethical concerns? Three different observations that provide useful indications for the conception of life in synthetic biology will be discussed in detail: 1. Synthetic biologists focus on different features of living organisms in order to design new life forms, 2. Synthetic biologists want to contribute to the understanding of life, and 3. Synthetic biologists want to modify life through a rational design, which implies the notions of utilising, minimising/optimising, varying and overcoming life. These observations indicate a tight connection between science and technology, a focus on selected aspects of life, a production-oriented approach to life, and a design-oriented understanding of life. It will be argued that through this conception of life synthetic biologists present life in a different light. This conception of life will be illustrated by the metaphor of a toolbox. According to the notion of life as a toolbox, the different features of living organisms are perceived as various rationally designed instruments that can be used for the production of the living organism itself or secondary products made by the organism. According to certain ethical positions this conception of life might raise ethical concerns related to the status of the organism, the motives of the scientists and the role of technology in our society.
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Affiliation(s)
- Anna Deplazes-Zemp
- University of Zurich, IBME, Pestalozzistr. 24, 8032, Zurich, Switzerland.
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