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Systems Biology and Education

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The Philosophy of Biology

Part of the book series: History, Philosophy and Theory of the Life Sciences ((HPTL,volume 1))

Abstract

According to most commentators, systems biology is transforming the biological sciences in many ways, although it is debatable exactly at what levels and to what extent. The formalization and use of computational models, the development of high-throughput experimental techniques, the new links with other scientific domains (like physics, engineering, mathematics, or computer sciences) and the transfers of explanatory models that have resulted, and other changes have had a profound impact on how biological research is conducted and, consequently, how biology must be taught. In this chapter, I will particularly focus on what challenges and opportunities the massive use of formal models has brought to biology. Not only must biologists learn how to use new tools in order to represent and analyze their objects of study, but they also have to realize that new questions must be asked in order to reveal aspects of biological systems that remained hidden in the framework of traditional molecular biology and genetics. Systems biology is integrative and interdisciplinary but transfers of methods, models and concepts are not straightforward and they raise many difficult questions. Another problem is that the transformation of biology into a “complex science” leads to a partial loss of intuitive understanding, which can be troubling for biologists, who are used to think with the help of words and diagrams. How can biologists regain some intelligibility? I will also discuss how systems biology has already started to challenge some of the standard views about the status of biology as a science, the nature of biological explanations, the relation between different domains of biology, or the nature of living systems and their evolution. I will argue that these philosophical analyses of systems biology’s foundations must be seriously integrated in contemporary reflections on biology education.

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Notes

  1. 1.

    Genomics can be defined as projects aiming at the establishment of complete maps (genetic and DNA sequences) of organisms’ genomes (Brent 2000).

  2. 2.

    For introductory textbooks, see for example Alberghina and Westerhoff (2007), Alon (2007), Bringmann et al. (2006), Palsson (2006), and for an early general review see Kitano (2002a, b).

  3. 3.

    For some philosophical analyses on systems biology, see for example (O’Malley and Dupré 2005, Boogerd et al. 2007, Braillard 2010, O’Malley and Soyer 2012).

  4. 4.

    The old preformationism being the view holding that organisms develop from miniature versions of themselves, which was widely held during the eighteenth and nineteenth century.

  5. 5.

    Biologists’ views should however not be caricatured. When they use the expression “gene for”, what they mean is that different alternative alleles of a gene correspond to differences in forms of a phenotypic trait. But of course this relation depends on other genes and the environment. However, even though all biologists acknowledge this, it remains true that there has been a tendency to view the causal origin of many traits in one or few genes and to consider the rest of the system and the environment as only background conditions, necessary but not explanatory important.

  6. 6.

    In this process, exons of pre-mRNA are put together in multiple combinations. With this process, a single gene can produce different mRNAs and hence different proteins.

  7. 7.

    Few models really try to represent processes at the whole-cell level, but this is where some modeling strategies are aiming at.

  8. 8.

    Of course, both dimensions are closely linked since the goal is to understand the dynamics of the whole system.

  9. 9.

    See also van Leeuwen et al. (2007) and Hornberg et al. (2006).

  10. 10.

    See for example the dream of many that in a near future it will become possible to select one’s child intellectual or artistic abilities through preimplantation genetic diagnosis or even genetic engineering.

  11. 11.

    A word of caution should be added. Although describing systems biology as antireductionist or organicist certainly captures important aspects of its explanatory strategies, one should avoid any oversimplification. It cannot be denied that systems biology also continues in an important sense molecular biology’s fundamental enterprise, which is to uncover molecular mechanisms underlying biological phenomena.

  12. 12.

    See also Bialek and Botstein (2004), Gross et al. (2004), and Hodgson et al. (2005).

  13. 13.

    For a review on complex network models see for example de Silva and Stumpf (2005).

  14. 14.

    The functional constraints are linked to the selective pressures acting on these systems. Because each type of network plays specific roles in the functioning of the systems (transfer of energy, “treatment” of external signals, regulation of developmental events, etc.) its functional requirements (for example robustness) and its ability to evolve (be “rewired”) are different.

  15. 15.

    Logic gates process signals, which represent true (1) or false (0). The AND logical gate associates an output 1 if the first and the second input are 1. In the case of OR gate, the output is 1 if either or both inputs are 1.

  16. 16.

    Famous cases of convergent evolution are the eye and the wing.

  17. 17.

    Richard Lewin asked “why is development so illogical?” (Lewin 1984) and other scientists started to describe molecular mechanisms as baroque.

  18. 18.

    See for example Conrad Waddington’s constant efforts in this direction (1968 1969, 1970, 1972), and more recently Stuart Kauffman (1993) or Brian Goodwin (Goodwin and Saunders 1989).

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Acknowledgments

I would like to thank Kostas Kampourakis and an anonymous referee for very useful comments on a previous draft of this chapter.

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  1. UFR de Biologie, Cité scientifique-Bâtiment SN3, Université Lille 1, France

    Pierre-Alain Braillard

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  1. Educational Research & Development, Geitonas School, Vari Attikis, Athens, 1234, Attiki, Greece

    Kostas Kampourakis

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Braillard, PA. (2013). Systems Biology and Education. In: Kampourakis, K. (eds) The Philosophy of Biology. History, Philosophy and Theory of the Life Sciences, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6537-5_24

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