Teaser
The intention with this volume is to provide a format for scholars to express their personal viewpoints and tell their story in response to the same set of questions (see Preface). Unlike many edited volumes, this book is therefore not divided into thematic sections. The aim of this introduction is to summarize core common themes among the contributor’s chapters so as to guide readers interested in specific topics. Given the richness of the contributions that touch upon many diverse topics in response to the posed questions, I have not summarized each contribution separately. Rather, I focus on core questions and highlight where more information on common themes and novel insights can be found. I also hope that the introduction will provide some background for scientists, philosophers, as well as other readers interested in discussing the philosophical implications of systems biology.
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Notes
- 1.
http://evolutionarysystemsbiology.org, accessed 28-07-2016.
- 2.
As pointed out by Boogerd (personal communication), a high-quality model will indeed reproduce experimental findings but can also be used to do so-called computer-experiments, i.e. experiments that are not yet done or that just cannot be done in reality. For instance, they may be used to test design explanations (Wouters 2007) or to model evolutionary trajectories (Jaeger, Chap. 13). The evidence status of this kind of model results is an interesting epistemological question on its own, and disagreement on this question among scientists can also be a source of insight to different epistemic cultures (Carusi, Chap. 5).
- 3.
Interactional expertise does not require expertise to make specific contributions to the other field.
References
Aderem, A. S. (2005). Systems biology: Its practice and challenges. Cell, 121, 511–513.
Alberghina, L., & Westerhoff, H. V. (2005). Systems biology: Definitions and perspectives. New York: Springer.
Allen, J. F. (2001). Bioinformatics and discovery: Induction beckons again. BioEssays, 23, 104–107.
Alon, U. (2007). An introduction to systems biology; design principles of biological circuits. Boca Raton: Chapman and Hall.
Alves, R., & Sorribas, A. (2011). Special issue on biological design principles. Mathematical Biosciences, 231, 1–2.
Andersen, H. (2013). Interdisciplinarity. In W. Dubitzky, O. Wolkenhauer, H. Yokota, & K. H. Cho (Eds.), Encyclopedia of systems biology (pp. 1032–1033). Amsterdam: Springer.
Andersen, H. (2016). Collaboration, interdisciplinarity, and the epistemology of contemporary science. Studies in History and Philosophy of Science Part A, 56, 1–10.
Anderson, C. (2008). The end of theory. Wired Magazine, 16.07.
Ankeny, R. A., & Leonelli, S. (2015). Valuing data in postgenomic biology: How data donation and curation practices challenge the scientific publication system. In H. Stevens & S. R. Richardson (Eds.), PostGenomics. Perspectives on biology after the genome (pp. 126–149). Durham: Duke University Press.
Bechtel, W. (2011). Mechanism and biological explanation. Philosophy of Science, 78, 533–557.
Bechtel, W. (2015). Generalizing mechanistic explanations using graph-theoretic representations. In P.-A. Braillard & C. Malaterre (Eds.), Explanation in biology. An enquiry into the diversity of explanatory patterns in the life sciences (pp. 199–225). Dordrecht: Springer.
Bechtel, W., & Abrahamsen, A. (2011). Complex biological mechanisms: Cyclic, oscillatory, and autonomous. In C. Hooker (Ed.), Philosophy of complex systems (pp. 257–285). Amsterdam: Elsevier.
Bechtel, W., & Abrahamsen, A. (2012). Thinking dynamically about biological mechanisms: Networks of coupled oscillators. Foundations of Science, 18, 707–723.
Bechtel, W., & Richardson, R. C. (1993/2010). Discovering complexity: Decomposition and localization as strategies in scientific research. Princeton: Princeton University Press.
Bentele, M., & Eils, R. (2005). Systems biology of apoptosis. In H. V. Westerhoff & L. Alberghina (Eds.), Systems biology. Definitions and perspectives (pp. 349–371). Amsterdam: Springer.
Bertolaso, M. (2011). Hierarchies and causal relationships in interpretative models of the neoplastic process. History and Philosophy of the Life Sciences, 33, 515–536.
Boogerd, F. C., Bruggeman, F., Richardson, R., Achim, S., & Westerhoff, H. V. (2005). Emergence and its place in nature: A case study of biochemical networks. Synthese, 145, 131–164.
Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J.-H. S., & Westerhoff, H. V. (Eds.). (2007). Systems biology: Philosophical foundations. Amsterdam: Elsevier.
Boogerd, F. C., Bruggeman, F. J., & Richardson, R. C. (2013). Mechanistic explanations and models in molecular systems biology. Foundations of Science, 18, 725–744.
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, 660–668.
Braillard, P. (2010). Systems biology and the mechanistic framework. History and Philosophy of the Life Sciences, 32, 43–62.
Braillard, P. A. (2015). Prospect and limits of explaining biological systems in engineering terms. In P.-A. Braillard & C. Malaterre (Eds.), Explanation in biology. An enquiry into the diversity of explanatory patterns in the life sciences (pp. 319–344). Dordrecht: Springer.
Brigandt, I. (2013). Systems biology and the integration of mechanistic explanation and mathematical explanation. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 477–492.
Brigandt, I., Green, S., & O’Malley, M. (forthcoming). Systems biology and mechanistic explanation. In S. Glennan & P. Illiary (Eds.), Routledge handbook of the philosophy of mechanisms. New York: Routledge.
Calcott, B., Levy, A., Siegal, M. L., Soyer, O. S., & Wagner, A. (2015). Engineering and biology: Counsel for a continued relationship. Biological Theory, 10, 50–59.
Carusi, A., Burrage, K., & Rodríguez, B. (2012). Bridging experiments, models and simulations: An integrative approach to validation in computational cardiac electrophysiology. American Journal of Physiology – Heart and Circulatory Physiology, 303, H144–H155.
Collins, H. M., & Evans, R. (2002). The third wave of science studies: Studies of expertise and experience. Social Studies of Science, 32, 235–296.
De Grandis, G., & Halgunset, V. (2016). Conceptual and terminological confusion around personalised medicine: A coping strategy. BMC Medical Ethics, 17, 43.
Drack, M., & Wolkenhauer, O. (2011). System approaches of Weiss and Bertalanffy and their relevance for systems biology today. Seminars in Cancer Biology, 21, 150–155.
Fagan, M. B. (2012). Waddington redux: Models and explanation in stem cell and systems biology. Biology and Philosophy, 27, 179–213.
Fagan, M. B. (2016). Stem cells and systems models: Clashing views of explanation. Synthese, 193, 873–907.
Goodwin, B. (1994). How the leopard changed its sports. The evolution of complexity. London: Phoenix.
Green, S. (2013). When one model is not enough: Combining epistemic tools in systems biology. Studies in History and Philosophy of Biology and Biomedical Sciences, 44, 170–180.
Green, S. (2014). A philosophical evaluation of adaptationism as a heuristic strategy. Acta Biotheoretica, 62, 479–498.
Green, S. (2015a). Can biological complexity be reverse engineered? Studies in History and Philosophy of Biology and Biomedical Sciences, 53, 73–83.
Green, S. (2015b). Revisiting generality in the life sciences: Systems biology and the quest for design principles. Biology and Philosophy, 30, 629–652.
Green, S., & Vogt, H. (2016). Personalizing medicine: Disease prevention in silico and in socio. In M. Bertolaso & M. MacLeod (Eds.), In silico medicine: The human factor, Humana.Mente, 30, 105–145.
Green, S., & Wolkenhauer, O. (2013). Tracing organizing principles – Learning from the history of systems biology. History and Philosophy of the Life Sciences, 35, 553–576.
Green, S., Fagan, M., & Jaeger, J. (2015a). Explanatory integration challenges in evolutionary systems biology. Biological Theory, 10, 18–35.
Green, S., Levy, A., & Bechtel, W. (2015b). Design sans adaptation. European Journal of Philosophy of Science, 5, 15–29.
Gross, F. (2013). The Sum of the Parts: Heuristic Strategies in Systems Biology. PhD thesis in Foundations of the Life Sciences and Their Ethical Consequences (FOLSATEC), European School for Molecular Medicine (SEMM) and the University of Milan, Italy.
Gross, F. (2015). The relevance of irrelevance: Explanation in systems biology. In P.-A. Braillard & C. Malaterre (Eds.), Explanation in biology. An enquiry into the diversity of explanatory patterns in the life sciences (pp. 175–198). Dordrecht: Springer.
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. 215–242). Amsterdam: Elsevier.
Hood, L., & Flores, M. (2012). A personal view on systems medicine and the emergence of proactive P4 medicine: Predictive, preventive, personalized and participatory. New Biotechnology, 29, 613–624.
Huneman, P. (2010). Topological explanations and robustness in biological sciences. Synthese, 177, 213–245.
Isalan, M., Lemerle, C., Michalodimitrakis, K., Horn, C., Beltrao, P., Raineri, E., Garriga- Canut, M., & Serrano, L. (2008). Evolvability and hierarchy in rewired bacterial gene networks. Nature, 452, 840–846.
Issad, T., & Malaterre, C. (2015). Are dynamic mechanistic explanations still mechanistic? In P.-A. Braillard & C. Malaterre (Eds.), Explanation in biology. An enquiry into the diversity of explanatory patterns in the life sciences (pp. 265–292). Dordrecht: Springer.
Jaeger, J., & Crombach, A. (2012). Life’s attractors: Understanding developmental systems through reverse engineering and in silico evolution. In O. Soyer (Ed.), Evolutionary systems biology (pp. 93–120). Berlin: Springer.
Jaeger, J., & Monk, N. (2014). Bioattractors: Dynamical systems theory and the evolution of regulatory processes. Journal of Physiology, 592, 2267–2281.
Jones, N. (2014). Bowtie structures, pathway diagrams, and topological explanation. Erkenntnis, 79, 1135–1155.
Jones, N., & Wolkenhauer, O. (2012). Diagrams as locality aids for explanation and model construction in cell biology. Biology and Philosophy, 27, 705–721.
Kastenhofer, K. (2007). Converging epistemic cultures? A discussion drawing on empirical findings. Innovation: The European Journal of Social Science Research, 20, 359–373.
Kastenhofer, K. (2013a). Synthetic biology as understanding, control, construction and creation? Techno-epistemic and socio-political implications of different stances in talking and doing technoscience. Futures, 48, 13–22.
Kastenhofer, K. (2013b). Two sides of the same coin? The (techno)epistemic cultures of systems and synthetic biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 130–140.
Kell, D. B., & Oliver, S. G. (2003). Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis‐driven science in the post‐genomic era. BioEssays, 26, 99–105.
Kitano, H. (Ed.). (2001). Foundations of systems biology. Cambridge, MA: MIT Press.
Kitano, H. (2002a). Computational systems biology. Nature, 420, 206–210.
Kitano, H. (2002b). Systems biology: A brief overview. Science, 295, 1662–1664.
Kohl, P., & Noble, D. (2009). Systems biology and the virtual physiological human. Molecular Systems Biology, 5, 292.
Kolodkin, A. N., & Westerhoff, H. V. (2011). Parsimony for systems biology: Shaving Occam’s razor away. European Communications in Mathematical and Theoretical Biology, 14, 149–152.
Kolodkin, A., Boogerd, F. C., Plant, N., Bruggeman, F. J., Goncharuk, V., Lunshof, J., … Westerhoff, H. V. (2011). Emergence of the silicon human and network targeting drugs. European Journal of Pharmaceutical Sciences, 46, 190–197.
Kolodkin, A., Simeonidis, E., Balling, R., & Westerhoff, H. (2012). Understanding complexity in neurodegenerative diseases: In silico reconstruction of emergence. Frontiers in Physiology, 3, 291.
Krohs, U. (2012). Convenience experimentation. Studies in History and Philosophy of Biological and Biomedical Sciences, 43, 52–57.
Krohs, U., & Callebaut, W. (2007). Data without models merging with models without data. In F. Boogerd, F. Bruggeman, J. Hofmeyr, & H. Westerhoff (Eds.), Systems biology. Philosophical foundations (pp. 181–212). Amsterdam: Elsevier.
Lazebnik, Y. (2010). What are the hallmarks of cancer? Nature Comment, 10, 232–233.
Leonelli, S. (2012). Introduction: Making sense of data-driven research in the biological and biomedical sciences. Studies in History and Philosophy of Biological and Biomedical Sciences, 43, 1–3.
Leonelli, S. (2014). What difference does quantity make? On the epistemology of big data in biology. Big Data & Society, 1, 2053951714534395.
Levy, A., & Bechtel, W. (2013). Abstraction and the organization of mechanisms. Philosophy of Science, 80, 241–261.
Loscalzo, J., & Barabasi, A. L. (2011). Systems biology and the future of medicine. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 3, 619–627.
Machamer, P., Darden, L., & Craver, C. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25.
MacLeod, M., & Nersessian, N. J. (2015). Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 49, 1–11.
Mekios, C. (2015). Explanation in systems biology: Is it all about mechanisms? In P.-A. Braillard & C. Malaterre (Eds.), Explanation in Biology: An enquiry into the diversity of explanatory patterns in the life sciences (pp. 47–72). Dordrecht: Springer.
Mesarović, M. D. (1968). Systems theory and biology – View of a theoretician. In M. D. Mesarovic (Ed.), Systems theory and biology. Proceedings of the III systems symposium at case institute of technology (pp. 59–87). New York: Springer.
Mesarović, M., & Sreenath, S. N. (2006). Beyond the flat earth perspective in systems biology. Biological Theory, 1, 33.
Nicholson, D. J. (2013). Organisms ≠ machines. Studies in History and Philosophy of Biological and Biomedical Sciences, 44(4), 669–678.
Noble, D. (2012). A theory of biological relativity: No privileged level of causation. Interface Focus, 2, 55–64.
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.
O’Malley, M. A. (2013). Philosophy and the microbe: A balancing act. Biology & Philosophy, 28, 153–159.
O’Malley, M. A., & Dupré, J. (2005). Fundamental issues in systems biology. BioEssays, 27, 1270–1276.
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.
Papp, B., Notebaart, R. A., & Pall, C. (2011). Systems-biology approaches for predicting genomic evolution. Nature Review Genetics, 12, 591–602.
Peter, I. S., & Davidson, E. H. (2015). Genomic control process in development and evolution. London: Academic Press/Elsevier.
Peter, I. S., Faure, E., & Davidson, E. H. (2012). Feature article: Predictive computation of genomic logic processing functions in embryonic development. Proceedings of the National Academy of Sciences of the United States of America, 109, 16434–16442.
Pigliucci, M. (2007). Do we need an extended evolutionary synthesis? Evolution, 61, 2743–2749.
Popper, K. R. (1959). The logic of scientific discovery. London: Hutchinson.
Richardson, R. C., & Stephan, A. (2007). Mechanism and mechanical explanation in systems biology. In F. Boogerd, F. Bruggeman, J. Hofmeyr, & H. V. Westerhoff (Eds.), Systems Biology, philosophical foundations (pp. 123–144). Amsterdam: Elsevier Publications.
Rowbottom, D. P. (2011). Approximations, idealizations and ‘experiments’ at the physics–biology interface. Studies in History and Philosophy of Biological and Biomedical Sciences, 42, 145–154.
Savageau, M. A. (1976). Biochemical systems analysis. A study of function and design in molecular biology. Reading: Addison-Wesley Pub. Co.
Savageau, M. A. (1985). A theory of alternative designs for biochemical control systems. Biomedica Biochimica Acta, 44, 875–880.
SBML. (2001). Systems biology markup language. http://sbml.org/
Sonnenschein, C., & Soto, A. M. (1999). The society of cells – Cancer and control of cell proliferation. Oxford: Bios Scientific Publishers.
Soyer, O. (Ed.). (2012). Evolutionary systems biology. London: Springer.
Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. J., III, & Doyle, J. (2004). Robustness of cellular functions. Cell, 118, 675–685.
Tyson, J. J., & Novák, B. (2010). Functional motifs in biochemical reaction networks. Annual Review of Physical Chemistry, 61, 219–240.
Vogt, H., Ulvestad, E., Eriksen, T. E., & Getz, L. (2014). Getting personal: Can systems medicine integrate scientific and humanistic conceptions of the patient? Journal of Evaluation in Clinical Practice, 20, 942–952.
Vogt, H., Hofmann, B., & Getz, L. (2016). The new holism: P4 systems medicine and the medicalization of health and life itself. Medicine, Health Care and Philosophy, 19, 1–17.
Voit, E. O. (2003). Design principles and operating principles: The yin and yang of optimal functioning. Mathematical Biosciences, 182, 81–92.
Voit, E. O. (2012). A first course in systems biology. New York: Garland Science.
Voit, E. O. (2014). Mesoscopic modeling as a starting point for computational analyses of cystic fibrosis as a systemic disease. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1844, 258–270.
Voit, E. O. (2016). The inner workings of life. Vignettes in systems biology. Cambridge: Cambridge University Press.
Voit, E. O., & Brigham, K. L. (2008). The role of systems biology in predictive health and personalized medicine. The Open Pathology Journal, 2, 68–70.
Voit, E. O., Newstetter, W. C., & Kemp, M. L. (2012). A feel for systems. Molecular Systems Biology, 8, 609.
Wagner, A. (2012). Metabolic networks and their evolution. In O. Soyer (Ed.), Evolutionary systems biology (pp. 29–52). New York: Springer.
Westerhoff, H. V., & Hofmeyr, J. S. (2005). What is systems biology? From genes to function and back. In H. V. Westerhoff & L. Alberghina (Eds.), Systems biology. Definitions and perspectives (pp. 119–141). Amsterdam: Springer.
Wolkenhauer, O., & Green, S. (2013). The search for organizing principles as a cure against reductionism in systems medicine. FEBS Journal, 280, 5938–5948.
Wolkenhauer, O., & Mesarović, M. (2005). Feedback dynamics and cell function: Why systems biology is called systems biology. Molecular BioSystems, 1, 14–16.
Wolkenhauer, O., Auffray, C., Jaster, R., Steinhoff, G., & Dammann, O. (2013). The road from systems biology to systems medicine. Pediatric Research, 73, 502–507.
Wouters, A. (2007). Design explanation: Determining the constraints on what can be alive. Erkenntnis, 67, 65–80.
Acknowledgements
I would like to thank Melinda Fagan, William Bechtel, Eberhard Voit, Fred Boogerd, Jan-Hendrik Hofmeyr, Marta Bertolaso, Fridolin Gross, Karen Kastenhofer, Nicholaos Jones, Manfred Drack, and Olaf Wolkenhauer for valuable feedback on an earlier version of the introduction.
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Green, S. (2017). Introduction to Philosophy of Systems Biology. 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_1
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