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Systems Biology and Evolutionary Biology

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Handbook of Evolutionary Thinking in the Sciences

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Abstract

In this chapter, I examine the recent development of systems biology in the light of its relations with evolutionary biology. Although a large part of systems biology is not basically interested in evolutionary issues, I show that it cannot ignore these. I focus particularly on the search of design principles, which are general principles of regulation and organization thought to be similar in engineering and biological systems. These design principles are seen as the result of convergent evolution at the molecular level, but those scientists trying to uncover such principles follow mainly approaches inspired by engineering and have rarely integrated genuine evolutionary methods. Several arguments for and against the study of biological systems based on analogies with artificial systems are discussed, but in the end I show that systems biology cannot move forward on these issues without stronger and deeper integration with evolutionary approaches.

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Notes

  1. 1.

    Ernst Mayr famously defended the autonomy of evolutionary biology, but one can find similar examples in physiology or other traditional fields.

  2. 2.

    This is now changing, with the emergence of variety of evolutionary systems biology research. See for example (Koonin and Wolf 2006; Knight and Pinney 2009; Rodrigues and Wagner 2009; Papp et al. 2011; Soyer 2012). For a general historical and philosophical analysis of the field, see (O’Malley 2012).

  3. 3.

    For introductory textbooks, see for example (Alberghina and Westerhoff 2007; Alon 2007; Bringmann et al. 2006; Palsson 2006). For an early review, see (Kitano 2002). A collection of philosophical discussions on systems biology can be found in Boogerd et al. (2007b).

  4. 4.

    Alex Rosenberg (1994) has argued that natural selection selects for functions and is blind to structures when they are functionally equivalent. This argument is based on the concept of multiple realizability, which states that a function can be produced by many different structures.

  5. 5.

    This idea is close to Dennett’s “forced moves” or “good tricks” in the design space (Dennett 1995).

  6. 6.

    Ideas coming from engineering are of course not new in molecular biology, but only recently has a general and rigorous analysis started to be conducted.

  7. 7.

    See Beatty 1995.

  8. 8.

    The most complete discussion on the issue of robustness, which is central in systems biology, is Wagner (2005).

  9. 9.

    But the idea that motifs can be analysed relatively independently from the larger context is problematic (Mazurie et al. 2005; Valverde and Sole 2005).

  10. 10.

    One can find many studies illustrating how computational and experimental approaches are complementary. See for example (Gardner et al. 2000; Elowitz and Leibler 2000, or more recently Stricker et al. 2008).

  11. 11.

    But see (Wouters 2007).

  12. 12.

    Such events are probably frequent in evolution (Zhang 2003).

  13. 13.

    For another criticism of Alon’s hypothesis, see (Konagurthu and Lesk 2008; Knabe et al. 2008; Sole and Valverde 2008).

  14. 14.

    See also Sole and Valverde (2006)

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Authors and Affiliations

  1. Independent Scholar, Peyregrand, 12350, Drulhe, France

    Pierre-Alain Braillard

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  1. Pierre-Alain Braillard
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Correspondence to Pierre-Alain Braillard .

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Editors and Affiliations

  1. Génétique Animale et Biologie Intégrative, INRA, UMR 1313, Jouy-en-Josas, France

    Thomas Heams

  2. Institut d’Histoire et de Philosophie des Sciences et des Techniques, CNRS/Université Paris I Sorbonne/ENS, Paris, France

    Philippe Huneman

  3. Museum National d'Histoire Naturelle (MNHN), Paris, France

    Guillaume Lecointre

  4. Éditions Matériologiques, Paris, France

    Marc Silberstein

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Braillard, PA. (2015). Systems Biology and Evolutionary Biology. In: Heams, T., Huneman, P., Lecointre, G., Silberstein, M. (eds) Handbook of Evolutionary Thinking in the Sciences. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9014-7_16

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