Abstract
Systems biology represents an effort to develop new modelling approaches in molecular and cell biology, drawing inspiration from disciplines like physics, computer sciences and engineering. In particular, many scientists have called for a transfer of methods, models and concepts from engineering in order to analyze and explain biological systems in all their complexity. In this paper, I examine how such transfer can contribute to systems biology explanatory project. Model building in the context of post-genomic biology raises a number of difficult challenges, mainly due to the complexity of the processes studied and their intricate dynamical features. Engineering methods can be used to efficiently analyze quantitative data about systems behaviour and use them to build mathematical dynamical models, in a way that goes beyond classical mechanistic approaches. More generally, engineering has suggested adopting a modular framework, as a general approach of decomposition and explanation based on analogies between biological and engineered systems, which promises to identify intelligible principles in the complex organization of molecular networks. I discuss the nature of this explanatory framework and on what assumptions it rests.
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Notes
- 1.
- 2.
Note that I do not offer an explication of the notion of explanation. This might sound problematic in a volume about explanation, however instead of developing a general account of explanation in biology, I think that it is more interesting to analyze the various models that are considered as explanatory and how they relate to each other. Hence the analysis offered in this chapter should bring useful elements for an understanding of how engineering contributes to modify and enrich explanatory models in biology, even without a general account of what it means to explain.
- 3.
For a discussion of the challenges and methods of reverse engineering, see for example Kell and Knowles 2006, Chapter 11.
- 4.
Some of the modelling methods used in engineering are also used in other domains and are indeed very general, especially the whole framework of dynamic systems theory. But the point is that many of these methods, tough they are not purely belonging to engineering, have been developed and put to use by engineers in the study and design of complex systems.
- 5.
What I mean by these expressions will become clear in the following discussion.
- 6.
A word of caution: even if one restricts oneself to SB, the concept of module can be differently understood. The following analysis does not pretend to capture all of these uses and dimensions. Everyone in the field certainly does not hold some of the views and other modular approaches will not be discussed here.
- 7.
One might object that motifs are different from modules, but the explanatory goal is the same: model a small sub-system and capture its essential dynamical properties.
- 8.
One might object that these are biological functions. However, the focus is for example on how a signal is transformed, regardless of the nature of the signal or its biological function. Of course, the goal is always to explain biological function, but I maintain that often in this kind of approach biological function becomes less important.
- 9.
When talking about robustness, it is important to keep in mind that it is meaningless if not defined in terms of specific properties of the systems that are robust to specific changes (internal or external). A feature of a given mechanism can be robust to one perturbation and very sensitive to a different one. Hence we must say that functional property P is robust to perturbation X.
- 10.
For one of the first philosophical discussions of the need for different types of decomposition in biology, see (Wimsatt 1974).
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Acknowledgments
The ideas discussed in this paper have been presented at different occasions, mainly at the 2013 ISHPSSB meeting in Montpellier and at the IHPST Paris-CAPE Kyoto philosophy of biology workshop. I would like to thank the audiences for useful discussions. An earlier version of this paper also benefited from comments from Christophe Malaterre, as well from two anonymous reviewers.
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Braillard, PA. (2015). Prospect and Limits of Explaining Biological Systems in Engineering Terms. In: Explanation in Biology. History, Philosophy and Theory of the Life Sciences, vol 11. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9822-8_14
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