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Systems Biology in the Broad Sense

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Philosophy of Systems Biology

Part of the book series: History, Philosophy and Theory of the Life Sciences ((HPTL,volume 20))

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“Although, as said, I am skeptical about the merits of backward-looking evolutionary theories for systems biology, I would like to adjust and fine-tune my position in this respect, because what is needed in my opinion is not so much the common backward-looking evolutionary theories but instead a forward-looking evolutionary approach, in the way explicated by the philosopher Paul Griffiths (Griffiths PE. Acta Biotheor 57:11–32, 2009). Moreover, I think that such a theoretical predictive approach of evolutionary theory can be adequately complemented and extended by the perspectives of the new discipline of experimental microbial evolution. Both forward-looking evolutionary theories and experimental microbial evolution fit well into systems biology sensu lato.”

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References

  • Bedau, M. A. (2011). Introduction to philosophical problems about life. Synthese, 185, 1–3.

    Article  Google Scholar 

  • Bolhuis, J. J., Brown, G. R., Richardson, R. C., & Laland, K. N. (2011). Darwin in mind: New opportunities for evolutionary psychology. PLoS Biology, 9, e1001109.

    Article  Google Scholar 

  • Boogerd, F. C., Bruggeman, F., Jonker, C., de Jong, H. L., Tamminga, A., Treur, J., Westerhoff, H., & Wijngaards, W. (2002). Inter-level relations in computer science, biology, and psychology. Philosophical Psychology, 15, 463–471.

    Google Scholar 

  • Boogerd, F. C., Bruggeman, F., Richardson, R., Stephan, A., & Westerhoff, H. V. (2005). Emergence and its place in nature: A case study of biochemical networks. Synthese, 145, 131–164.

    Google Scholar 

  • Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J-H. S., Westerhoff H. V. (Eds.). (2007). Systems biology: Philosophical foundations. Amsterdam: Elsevier.

    Google Scholar 

  • Boogerd, F. C., Bruggeman, F. J., & Richardson, R. C. (2013). Mechanistic explanations and models in molecular systems biology. Foundations of Science, 18, 725–744.

    Google Scholar 

  • Bruggeman, F. (2005). Of molecules and cells. Emergent mechanisms. Amsterdam: VU University Amsterdam.

    Google Scholar 

  • Bruggeman, F. J. (2007). Systems biology: At last an integrative wet and dry biology! Biological Theory, 2, 183–188.

    Article  Google Scholar 

  • Bruggeman, F. J., & Westerhoff, H. V. (2007). The nature of systems biology. Trends in Microbiology, 15, 45–50.

    Article  Google Scholar 

  • Bruggeman, F. J., Westerhoff, H. V., & Boogerd, F. C. (2002). BioComplexity: A pluralist research strategy is necessary for a mechanistic explanation of the “live” state. Philosophical Psychology, 15, 411–440.

    Article  Google Scholar 

  • Buitelaar, J. K. (2012). Understanding comorbidity: From epidemiological designs and model-fitting approaches to systems biology as a new tool. European Child & Adolescent Psychiatry, 21, 1–3.

    Article  Google Scholar 

  • Cain, C. J., Conte, D. A., García-Ojeda, M. E., Daglio, L. G., Johnson, L., Lau, E. H., et al. (2008). What systems biology is (not, yet). Science, 320, 1013–1014.

    Article  Google Scholar 

  • Callebaut, W. (2005). Again, what the philosophy of biology is not. Acta Biotheoretica, 53, 93–122.

    Article  Google Scholar 

  • Callebaut, W. (2012). Scientific perspectivism: A philosopher of science’s response to the challenge of big data biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 43, 69–80.

    Article  Google Scholar 

  • Church, G. M. (2005). The personal genome project. Molecular Systems Biology, 1, 2005.

    Google Scholar 

  • Deisboeck, T. S. (2009). Personalizing medicine: A systems biology perspective. Molecular Systems Biology, 5, 249.

    Article  Google Scholar 

  • Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. The American Biology Teacher, 35, 125–129.

    Google Scholar 

  • Geenen, S., Taylor, P. N., Snoep, J. L., Wilson, I. D., Kenna, J. G., & Westerhoff, H. V. (2012). Systems biology tools for toxicology. Archives of Toxicology, 86, 1251–1271.

    Article  Google Scholar 

  • Geenen, S., du Preez, F. B., Snoep, J. L., Foster, A. J., Sarda, S., Kenna, J. G., et al. (2013). Glutathione metabolism modeling: A mechanism for liver drug-robustness and a new biomarker strategy. Biochimica et Biophysica Acta, 1830, 4943–4959.

    Article  Google Scholar 

  • Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329, 52–56.

    Article  Google Scholar 

  • Green, S., & Wolkenhauer, O. (2012). Integration in action. EMBO Reports, 13, 769–771.

    Article  Google Scholar 

  • Griffiths, P. E. (2009). In what sense does ‘nothing make sense except in the light of evolution’? Acta Biotheoretica, 57, 11–32.

    Article  Google Scholar 

  • Haanstra, J. R., Kerkhoven, E. J., van Tuijl, A., Blits, M., Wurst, M., van Nuland, R., et al. (2011). A domino effect in drug action: From metabolic assault towards parasite differentiation. Molecular Microbiology, 79, 94–108.

    Article  Google Scholar 

  • Hofmeyr, J. (2007). The biochemical factory that autonomously fabricates itself: A systems biological view of the living cell. In F. C. Boogerd, F. J. Bruggeman, J.-H. Hofmeyr, & H. V. Westerhoff (Eds.), Systems biology. Philosophical foundations (pp. 217–242). Amsterdam: Elsevier.

    Google Scholar 

  • Hofmeyr, J.-H. S. (2008). The harmony of the cell: The regulatory design of cellular processes. Essays in Biochemistry, 45, 57–66.

    Article  Google Scholar 

  • Jagers op Akkerhuis, G. (2010). The operator hierarchy. Nijmegen: Radboud Universiteit Nijmegen, the Netherlands.

    Google Scholar 

  • Jensen, P. R., Michelsen, O., & Westerhoff, H. V. (1993a). Control analysis of the dependence of Escherichia coli physiology on the H+-ATPase. Proceedings of the National Academy of Sciences USA, 90, 8068–8072.

    Google Scholar 

  • Jensen, P. R., Westerhoff, H. V., & Michelsen, O. (1993b). Excess capacity of H+-ATPase and inverse respiratory control in Escherichia coli. The EMBO Journal, 12, 1277–1282.

    Google Scholar 

  • Kell, D. B., & Goodacre, R. (2014). Metabolomics and systems pharmacology: Why and how to model the human metabolic network for drug discovery. Drug Discovery Today, 19, 171–182.

    Article  Google Scholar 

  • Kendler, K. S. (2014). The structure of psychiatric science. The American Journal of Psychiatry, 171, 931–938.

    Article  Google Scholar 

  • Kolodkin, A. N., Boogerd, F. C., Bruggeman, F. J., & Westerhoff, H. V. (2011). Modeling approaches in systems biology, including silicon cell models. In M. te Pas, H. Woelders, & A. Bannink (Eds.), Systems biology and livestock science (pp. 31–51). Chichester: Wiley-Blackwell.

    Chapter  Google Scholar 

  • Kolodkin, A., Boogerd, F. C., Plant, N., Bruggeman, F. J., Goncharuk, V., Lunshof, J., et al. (2012). Emergence of the silicon human and network targeting drugs. European Journal of Pharmaceutical Sciences, 46, 190–197.

    Article  Google Scholar 

  • Loewe, L. (2009). A framework for evolutionary systems biology. BMC Systems Biology, 3, 27.

    Article  Google Scholar 

  • Lunshof, J. E., & Ball, M. P. (2013). Our genomes today: Time to be clear. Genome Medicine, 5, 52.

    Article  Google Scholar 

  • Lunshof, J. E., & Chadwick, R. (2011). Editorial: Genetic and genomic research-changing patterns of accountability. Accountability in Research, 18, 121–131.

    Article  Google Scholar 

  • Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67, 1–25.

    Article  Google Scholar 

  • Mahner, M., & Bunge, M. (1997). Foundations of biophilosophy. Berlin: Springer Science & Business Media.

    Book  Google Scholar 

  • Mahner, M., & Bunge, M. (2001). Function and functionalism: A synthetic perspective. Philosophy of Science, 68, 75–94.

    Article  Google Scholar 

  • Mayr, E. (1961). Cause and effect in biology. Science, 134, 1501–1506.

    Article  Google Scholar 

  • McAllister, J. W. (1997). Philosophy of science in The Netherlands. International Studies in the Philosophy of Science, 11, 191–204.

    Article  Google Scholar 

  • McIntosh, A. M. (2013). Toward a systems biology of mood disorder. Biological Psychiatry, 73, 107–108.

    Article  Google Scholar 

  • Mo, M. L., Jamshidi, N., & Palsson, B. Ø. (2007). A genome-scale, constraint-based approach to systems biology of human metabolism. Molecular BioSystems, 3, 598–603.

    Article  Google Scholar 

  • Müller, G. B. (2007). Evo-devo: Extending the evolutionary synthesis. Nature Reviews Genetics, 8, 943–949.

    Article  Google Scholar 

  • O’Malley, M. A. (2009). What did Darwin say about microbes, and how did microbiology respond? Trends in Microbiology, 17, 341–347.

    Article  Google Scholar 

  • O’Malley, M. A. (2012). Evolutionary systems biology: Historical and philosophical perspectives on an emerging synthesis. Advances in Experimental Medicine and Biology, 751, 1–28.

    Article  Google Scholar 

  • O’Malley, M. A. (2013). Philosophy and the microbe: A balancing act. Biology & Philosophy, 28(2), 153–159.

    Article  Google Scholar 

  • O’Malley, M. A., & Dupré, J. (2007). Towards a philosophy of microbiology. Studies in History and Philosophy of Biological and Biomedical Sciences, 38, 775–779.

    Article  Google Scholar 

  • O’Malley, M. A., & Soyer, O. S. (2012). The roles of integration in molecular systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 43, 58–68.

    Article  Google Scholar 

  • Soyer, O. S., & O’Malley, M. A. (2013). Evolutionary systems biology: What it is and why it matters. BioEssays, 35, 696–705.

    Article  Google Scholar 

  • Teusink, B., Westerhoff, H. V., & Bruggeman, F. J. (2010). Comparative systems biology: From bacteria to man. Wiley Interdisciplinary Reviews. Systems Biology and Medicine, 2, 518–532.

    Article  Google Scholar 

  • Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., et al. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31, 419–425.

    Article  Google Scholar 

  • Tretter, F., Winterer, G., Gebicke-Haerter, P. J., & Mendoza, E. R. (2010). Systems biology in psychiatric research. Weinheim: Wiley.

    Book  Google Scholar 

  • van der Stel, J. C. (2009). Psychopathologie. Boom, The Netherlands: Psychiatrie & Filosofie.

    Google Scholar 

  • Westerhoff, H. V., & Palsson, B. Ø. (2004). The evolution of molecular biology into systems biology. Nature Biotechnology, 22, 1249–1252.

    Article  Google Scholar 

  • Westerhoff, H. V., Brooks, A. N., Simeonidis, E., García-Contreras, R., He, F., Boogerd, F. C., et al. (2014). Macromolecular networks and intelligence in microorganisms. Frontiers in Microbiology, 5, 379.

    Article  Google Scholar 

  • Wouters, A. G. (1999). Explanation without a cause. Utrecht: Zeno Institute of Philosophy. Electronically available at http://morepork.home.xs4all.nl/diss/index.html)

  • Wouters, A. G. (2003). Four notions of biological function. Studies in History and Philosophy of Biological and Biomedical Sciences, 34, 633–668.

    Article  Google Scholar 

  • Wouters, A. (2005). The function debate in philosophy. Acta Biotheoretica, 53, 123–151.

    Article  Google Scholar 

  • Wouters, A. G. (2007). Design explanation: Determining the constraints on what can be alive. Erkenntnis, 67, 65–80.

    Article  Google Scholar 

  • Wouters, A. G. (2013). Biology’s functional perspective: Roles, advantages and organization. In K. Kampourakis (Ed.), History, philosophy and theory of the life sciences (Vol. 1, pp. 455–486). Dordrecht: Springer.

    Google Scholar 

Suggested Readings by Fred Boogerd

  • Boogerd, F. C., Bruggeman, F., Richardson, R., Stephan, A., & Westerhoff, H. V. (2005). Emergence and its place in nature: A case study of biochemical networks. Synthese, 145, 131–164.

    Google Scholar 

  • Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J-H. S., & Westerhoff, H. V. (2007). Towards philosophical foundations of Systems Biology: Introduction. In F. C. Boogerd, F. J. Bruggeman, J-H. S. Hofmeyr, & H. V. Westerhoff (Eds.), Systems biology – Philosophical foundations (pp. 3–20). Amsterdam: Elsevier.

    Google Scholar 

  • Boogerd, F. C., Bruggeman, F. J., & Richardson, R. C. (2013). Mechanistic explanations and models in molecular systems biology. Foundations of Science, 18, 725–744.

    Google Scholar 

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Authors and Affiliations

  1. Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, O|2 Building, de Boelelaan 1108, NL-1081 HZ, Amsterdam, The Netherlands

    Fred C. Boogerd

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  1. Fred C. Boogerd
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Correspondence to Fred C. Boogerd .

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  1. Department of Science Education, University of Copenhagen, Copenhagen, Denmark

    Sara Green

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Boogerd, F.C. (2017). Systems Biology in the Broad Sense. In: Green, S. (eds) Philosophy of Systems Biology. History, Philosophy and Theory of the Life Sciences, vol 20. Springer, Cham. https://doi.org/10.1007/978-3-319-47000-9_4

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