Is synthetic biology mechanical biology?

Abstract

A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

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Notes

  1. 1.

    For an excellent overview of the heterogeneity and unifying features of synthetic biology research approaches see O’Malley et al. (2008). In this paper I focus on the guiding aims and ideas of what O’Malley et al. refer to as “genome-driven cell-engineering” and “DNA-based device construction”.

  2. 2.

    The quote is from an interview with Drew Endy in the online magazine Edge. http://edge.org/3rd_culture/endy08/endy08_index.html (accessed January 15, 2015).

  3. 3.

    The registry can be found at http://parts.igem.org/Main_Page.

  4. 4.

    This is a feature that enables reliable modelling and simulation, something which is also highly desirable for efficient design of biotechnological systems (Heinemann and Panke 2006, p. 2796).

  5. 5.

    The quote is from an online interview with Drew Endy. For reference see note 2.

  6. 6.

    Nicholson references the papers by Andrianantoandro et al. (2006) and Endy (2005) in support of his claim that synthetic biology is driven by a mechanical understanding of life and assumes the ontological identity of organisms and machines. In Sect. 5 I show that this conclusion is not warranted.

  7. 7.

    The references to Descartes are to Oeuvres De Descartes, 11 vols. edited by Charles Adam and Paul Tannery,  Librairie Philosophique J. Vrin, Paris 1983 (AT) and to The Philosophical Writings Of Descartes, 3 vols., translated by John Cottingham, Robert Stoothoff, and Dugald Murdoch,  Cambridge: Cambridge University Press 1988 (CSM).

  8. 8.

    The criticisms presented by Nicholson summarizes arguments and objections found in important work in the organicist tradition (see Nicholson 2012 for references).

  9. 9.

    This idea goes back to Kant and his characterization of organisms as “natural purposes” (Kant 1790/2000, Sect. 64).

  10. 10.

    An informative presentation of some of the challenges confronting synthetic biologists is given in Kwok (2010).

  11. 11.

    See Lewens (2013) for the notion of a design continuum.

  12. 12.

    Let me note that when I equate degree of machine-likeness with degree of rational design I do not want to rule out a priori the possibility that highly predictable and modular (machine-like) systems can result from “irrational” or “blind” evolution. My point is simply that synthetic biologists who aim to rationally engineer organisms do so partly because they aim to construct living systems that are more machine-like than naturally evolved life. Hence, there seems to be an assumption that rational design and machine-likeness as a matter of fact are correlative. I would like to thank an anonymous reviewer for raising this point.

  13. 13.

    Ablondi (1998).

  14. 14.

    And in the letter to Pollot we were told that the living automata composed by nature turned out to be “incomparably more accomplished” than the automata constructed by the man who had never encountered natural living animals. This thought is echoed in Leibniz’ remark that “each organized body of a living being is a kind of divine machine or natural automaton, which infinitely surpasses all artificial automata” (Leibniz 1989, p. 221).

References

  1. Ablondi, F. (1998). Automata, living and non-living: Descartes’ mechanical biology and his criteria for life. Biology and Philosophy, 13, 179–186.

    Article  Google Scholar 

  2. Andrianantoandro, E., Basu, S., Karig, D. K., & Weiss, R. (2006). Synthetic biology: New engineering rules for an emerging discipline. Molecular Systems Biology, 2, 1–14.

    Article  Google Scholar 

  3. Arkin, A. (2008). Setting the standard in synthetic biology. Nature Biotechnology, 26, 771–774.

    Article  Google Scholar 

  4. Ball, P. (2004). Synthetic biology: Starting from scratch. Nature, 431, 624–626.

    Article  Google Scholar 

  5. Benner, S. A., & Sismour, A. M. (2005). Synthetic biology. Nature Reviews Genetics, 6, 533–543.

    Article  Google Scholar 

  6. Boudry, M., & Pigliucci, M. (2013). The mismeasure of machine: Synthetic biology and the trouble with engineering metaphors. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 669–678.

    Article  Google Scholar 

  7. Brent, R. (2004). A partnership between biology and engineering. Nature Biotechnology, 22, 1211–1214.

    Article  Google Scholar 

  8. Cameron, D. E., Bashor, C. J., & Collins, J. J. (2014). A brief history of synthetic biology. Nature Reviews Microbiology, 12, 381–390.

    Article  Google Scholar 

  9. Cardinale, S., & Arkin, A. P. (2012). Contextualizing context for synthetic biology—Identifying causes of failure of synthetic biological systems. Biotechnology Journal, 7, 856–866.

    Article  Google Scholar 

  10. Cobb, R., Sun, N., & Zhao, H. (2013). Directed evolution and a powerful synthetic biology tool. Methods, 60, 81–90.

    Article  Google Scholar 

  11. Deplazes, A., Ganguli-Mitra, A., & Biller-Adorno, N. (2009). The ethics of synthetic biology: Outlining the agenda. In M. Schmidt, A. Kelle, A. Ganguli-Mitra, & H. de Vriend (Eds.), Synthetic biology (pp. 65–80). New York: Springer.

    Google Scholar 

  12. Deplazes, A., & Huppenbauer, M. (2009). Synthetic organisms and living machines. Positioning the products of synthetic biology at the borderline between living and non-living matter. Systems and Synthetic Biology, 3, 55–63.

    Article  Google Scholar 

  13. Dougherty, M., & Arnold, F. (2009). Directed evolution: New parts and optimized function. Current Opinion in Biotechnology, 20, 486–491.

    Article  Google Scholar 

  14. Endy, D. (2005). Foundations for engineering biology. Nature, 438, 449–453.

    Article  Google Scholar 

  15. Heinemann, M., & Panke, S. (2006). Synthetic biology—Putting engineering into biology. Bioinformatics, 22, 2790–2799.

    Article  Google Scholar 

  16. Kant, I. (1790/2000). Critique of the power of judgment. Cambridge: Cambridge University Press.

  17. Keasling, J. (2005). The promise of synthetic biology. Bridge National Academy of Engineering, 35, 18–21.

    Google Scholar 

  18. Kwok, R. (2010). Five hard truths for synthetic biology. Nature, 463, 288–290.

    Article  Google Scholar 

  19. Leibniz, G. W. (1989). Philosophical essays. Indianapolis: Hackett Publishing Company.

    Google Scholar 

  20. Levy, A. (2013). Three kinds of mechanism. Biology and Philosophy, 28, 99–114.

    Article  Google Scholar 

  21. Lewens, T. (2013). From bricolage to biobricks. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 669–678.

    Article  Google Scholar 

  22. Nicholson, D. (2012). The concept of mechanism in biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 43, 152–163.

    Article  Google Scholar 

  23. Nicholson, D. (2013). Organisms ≠ machines. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 669–678.

    Article  Google Scholar 

  24. Nicholson, D. (2014). The machine conception of the organism in development and evolution: A critical analysis. Studies in History and Philosophy of Biological and Biomedical Sciences, 48, 162–174.

    Article  Google Scholar 

  25. O’Malley, M. (2011). Exploration, iterativity and kludging in synthetic biology. Comptes Rendus Chimie, 14, 406–412.

    Article  Google Scholar 

  26. O’Malley, M., Powell, A., Davies, J. F., & Calvert, J. (2008). Knowledge-making distinctions in synthetic biology. BioEssays, 30, 57–65.

    Article  Google Scholar 

  27. Porcar, M. (2010). Beyond directed evolution: Darwinian selection and a tool for synthetic biology. Systems and Synthetic Biology, 4, 16.

    Article  Google Scholar 

  28. Purnick, P. E. M., & Weiss, R. (2009). The second wave of synthetic biology: from modules to systems. Nature Reviews Molecular Cell Biology, 10, 410–422.

    Article  Google Scholar 

  29. Ro, D.-K., Paradise, E. M., Ouellet, M., Fisher, K. J., Newman, K. L., Ndungu, J. M., et al. (2006). Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature, 440, 940–943.

    Article  Google Scholar 

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Acknowledgments

The research for this paper has been supported by the Danish Research Council for Culture and Communication grant number 4180-00146.

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Correspondence to Sune Holm.

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Holm, S. Is synthetic biology mechanical biology?. HPLS 37, 413–429 (2015). https://doi.org/10.1007/s40656-015-0081-y

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Keywords

  • Rational Design
  • Living System
  • Synthetic Biology
  • Machine Analogy
  • Ontological Commitment