Monday 27 October to Tuesday 28 October 2008
Conference
Savoy Place, London WC2
Rapporteur: Emma Frow
In the second ESRC Genomics Network annual conference held in London (27–28 October), one of the parallel sessions focused on synthetic biology. Titled ‘Biology as Engineering,’ the speakers in this session explored the relationship between engineering and biology from several perspectives.
DAN NICHOLSON (University of Exeter) traced ideas of mechanistic biology from Descartes to the present day, showing how the links between engineering and biology stretch back a long way. He considered some of the tensions between engineering-led and biology-led approaches to synthetic biology. In this context, Dan discussed the oft-cited Feynman quotation: “What I cannot create, I do not understand,” cautioning that a biologically oriented approach might not see constructing a biological system as equivalent to understanding it.
ALEX POWELL (University of Exeter) discussed ideas of ‘mechanism’ in engineering and biology, and considered whether computational analogies and concepts of mechanism are useful for synthetic biology. He suggested that the idea of mechanism focuses on the intersection between structure and function. Alex identified a tension in synthetic biology between seeing structure and function as either independent and separable characteristics, or deeply interdependent ones. The development of a more flexible conception of mechanism than, for example, that articulated by Machamer, Darden & Craver (2000)* might be helpful in — and might reciprocally be assisted by — thinking through structure/function relationships in synthetic biology.
Finally, JANE CALVERT (University of Edinburgh) considered some of the cultural similarities and differences between biologists and engineers in synthetic biology. In particular, she highlighted the different intentions of biology and engineering (relating to understanding and design/construction). She asked whether biological systems are inherently modular, or whether scientists try to impose modularity on living organisms. Jane not only considered the attempts by synthetic biologists to turn biology into an engineering discipline, but also discussed ways in which biology might in turn help to refine and develop engineering principles.
* Machamer, P., Darden, L. & Craver, C.F. (2000) Thinking about mechanisms. Philosophy of Science 67(1), 1–25.
SESSION OVERVIEW
The engineering of biology has received new attention with the rise of synthetic biology. This session aims to explore the role of engineering in this field, examining issues such as: what exactly is meant by the desire to turn biology into an engineering discipline? How does the engineer’s approach to discovery and complexity differ from the biologist’s? To what extent is synthetic biology continuous with earlier and extant bio-engineering fields, such as genetic, protein and metabolic engineering?
Title: The Philosophical Basis of Synthetic Biology
Speaker: Dan Nicholson
Institution: Egenis, University of Exeter
What is new and what is not new in the emerging field of synthetic biology? How does synthetic biology relate to other biological sub-disciplines like genetic engineering, systems biology, and origins of life research? What are the programmatic objectives of synthetic biology, and how do they relate to the way synthetic biologists understand life? Are synthetic biology and evolutionary biology complementary disciplines? Is synthetic biology truly synthetic? How does biology relate to engineering, and how genuinely biological is synthetic biology? Will synthetic biology fulfil its aims, and if so, how will we know it?
A whole range of interesting questions arise when considering the philosophical basis of synthetic biology. This paper engages with these questions and suggests possible ways in which they may be fruitfully addressed. In the course of the examination of these questions, this paper also strives to flesh out the basic epistemic and ontological presuppositions informing synthetic biology research in order to situate the field in its appropriate historical and philosophical contexts. In this way, this paper attempts to offer potential resources for making sense of the nature of synthetic biology, where it is coming from, and where it is going.
Title: Cells, Mechanisms and Biological Engineering
Speaker: Alex Powell
Institution: Egenis, University of Exeter
Synthetic biology in its various current incarnations is in many respects continuous with previous bioengineering efforts such as genetic engineering from the mid-1970s and protein engineering from the late 1980s. The greater scale of its ambitions, however, brings into sharp focus fundamental questions concerning the nature of biological systems such as cells. How are we to make sense of the processes they involve?
The accomplishments of molecular cell biology, for example its illumination of the principles underlying the cell cycle, are unquestionably impressive. To view the cell as a collection of semi-autonomous molecular mechanisms – if we take that to be the standard contemporary stance – does not obviously represent a wholly impotent strategy, then. Some argue, however, that addressing satisfactorily the fundamental properties of metabolism, genome replication and cell division requires that we take into account in an explicit way the integrated and circular nature of cellular causality. I shall reflect on the conditions for success of the molecular cell biological outlook, and on whether the sense of mechanism it involves can be reconciled with the requirements of other, more holistic, theoretical orientations. I shall also consider how a biologically meaningful view of mechanisms relates to the largely solid-state products of macroscopic material engineering and to the syntax-driven abstractions of software engineering.
Title: Biology as Engineering or Engineering as Biology?
Speaker: Jane Calvert
Institution: Innogen, University of Edinburgh
One of the often-expressed aims of the emerging field of synthetic biology is to ‘make biology into an engineering discipline’. This paper explores what is meant by this objective. It looks at how the engineering approach has exhibited itself in the ‘BioBricks’ school of synthetic biology, which attempts to apply the principles of standardisation, decoupling and abstraction to biology. The aim is to develop interchangeable, modular components, and ultimately to construct biological systems which are manipulable and instrumentalizable, in a way which mimics the (apparently) obvious success of engineering.
There is disagreement about the extent to which such a ‘nuts and bolts’ view will successfully transfer to the study of complex biological systems. A key objective of the engineering approach is to reduce biological complexity, but some commentators think that in their attempts to do this, synthetic biologists will end up eliminating the emergent properties that make living systems what they are.
Focusing on the tensions between biology and engineering in this way, may, however, miss some interesting subtleties. Although much synthetic biology appears to be driven by the assumption that engineering is more successful than biology, some synthetic biologists point out that there are ways in which biological systems are actually better than engineered systems (in terms of their robustness, for example). In these ways, the study of biology can perhaps contribute to the development of engineering knowledge.
