Stem cells and systems models: clashing views of explanation

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• 作者：Melinda Bonnie Fagan
• 关键词：Explanation ; Mechanisms ; Covering law ; Stem cells ; Systems biology ; Interdisciplinarity
• 刊名：Synthese
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：193
• 期：3
• 页码：873-907
• 全文大小：1,240 KB
• 参考文献：Bechtel, W. (2011). Mechanism and biological explanation. Philosophy of Science, 78, 533–557.CrossRef
  Bechtel, W., & Abrahamson, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36, 421–441.CrossRef
  Boogerd, F., Bruggeman, F., Hofmeyr, J.-H., & Westerhoff, H. (Eds.). (2007). Systems biology: Philosophical foundations. Amsterdam: Elsevier.
  Braillard, P.-A., & Malaterre, C. (Eds.). (forthcoming). Explanation in biology: An enquiry into the diversity of explanatory patterns in the life sciences. 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.CrossRef
  Calvert, J., & Fujimura, J. H. (2011). Calculating life? Duelling discourses in interdisciplinary systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 42, 155–163.CrossRef
  Craver, C. (2007). Explaining the brain: Mechanisms and the mosaic unity of neuroscience. Oxford: Oxford University Press.CrossRef
  Darden, L. (2006). Reasoning in biological discoveries: Essays on mechanisms, interfield relations, and anomaly resolution. Cambridge: Cambridge University Press.CrossRef
  Fagan, M. (2012a). Waddington redux: Models and explanation in stem cell and systems biology. Biology and Philosophy, 27, 179–213.CrossRef
  Fagan, M. (2012b). The joint account of mechanistic explanation. Philosophy of Science, 79, 448–472.CrossRef
  Fagan, M. (2013a). Philosophy of stem cell biology. London: Palgrave Macmillan.CrossRef
  Fagan, M. (2013b). Philosophy of stem cell biology: An introduction. Philosophy Compass, 8, 1147–1158.CrossRef
  Furusawa, C., & Kaneko, K. (1998). Emergence of rules in cell society: Differentiation, hierarchy, and stability. Bulletin of Mathematical Biology, 60, 659–687.CrossRef
  Furusawa, C., & Kaneko, K. (2001). Theory of robustness of irreversible differentiation in a stem cell system: Chaos hypothesis. Journal of Theoretical Biology, 209, 395–416.CrossRef
  Furusawa, C., & Kaneko, K. (2009). Chaotic expression dynamics implies pluripotency: When theory and experiment meet. Biology Direct, 4, 17. doi:10.​1186/​1745-6150-4-17 .CrossRef
  Furusawa, C., & Kaneko, K. (2012). A dynamical-systems view of stem cell biology. Science, 338, 215–217.CrossRef
  Glennan, S. (1996). Mechanisms and the nature of causation. Erkenntnis, 44, 49–71.CrossRef
  Glennan, S. (2002). Rethinking mechanistic explanation. Philosophy of Science, 69, S342–S353.CrossRef
  Green, S. (Ed.). (in press). Systems biology: 5 Questions. Copenhagen: Automatic Press/VIP.
  Green, S., Bechtel, W., & Levy, A. (2015). Design sans adaptation. European Journal for Philosophy of Science, 5, 15–29.CrossRef
  Green, S., Fagan, M., & Jaeger, J. (2015). Explanatory integration challenges in evolutionary systems biology. Biological Theory, 9, 18–35.CrossRef
  Gunawardena, J. (2010). Models in systems biology: The parameter problem and the meanings of robustness. In H. M. Lodhi & S. H. Muggleton (Eds.), Elements of computational systems biology (pp. 21–47). Hoboken: Wiley & Sons.
  Hackett, J. A., & Surani, M. A. (2014). Regulatory principles of pluripotency: From the ground state up. Cell Stem Cell, 15, 416–430.CrossRef
  Hempel, C. G., & Oppenheim, P. (1948). Studies in the logic of explanation. Philosophy of Science, 15, 135–175.CrossRef
  Huang, S. (2009a). Reprogramming cell fates: Reconciling rarity with robustness. Bioessays, 31, 546–560.CrossRef
  Huang, S. (2009b). Non-genetic heterogeneity of cells in development: More than just noise. Development, 136, 3853–3862.CrossRef
  Huang, S. (2011a). Understanding gene circuits at cell-fate branch points for rational cell reprogramming. Trends in Genetics, 27, 55–62.CrossRef
  Huang, S. (2011b). Systems biology of stem cells: Three useful perspectives to help overcome the paradigm of linear pathways. Philosophical Transactions of the Royal Society, Series B, 366, 2247–2259.CrossRef
  Huang, S., Ernberg, I., & Kauffman, S. (2009). Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective. Seminars in Developmental Biology, 20, 869–876.CrossRef
  Huang, S., Guo, Y. P., May, G., & Enver, T. (2007). Bifurcation dynamics of cell fate decision in bipotent progenitor cells. Developmental Biology, 305, 695–713.CrossRef
  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. 93–119). London: Springer.CrossRef
  Jaeger, J., Irons, D., & Monk, N. (2012). The inheritance of process: A dynamical systems approach. Journal of Experimental Zoology Series B (Molecular and Developmental Evolution), 318B, 591–612.CrossRef
  Jaeger, J., & Sharpe, J. (2014). On the concept of mechanism in development. In A. Minelli & T. Pradeu (Eds.), Towards a theory of development (pp. 56–78). Oxford: Oxford University Press.CrossRef
  Kaneko, K. (2011). Characterization of stem cells and cancer cells on the basis of gene expression profile stability, plasticity, and robustness. BioEssays, 33, 403–413.CrossRef
  Kaneko, K., Sato, K., Michiue, T., Okabayashi, K., Ohnuma, K., Danno, H., et al. (2008). Developmental potential for morphogenesis in vivo and in vitro. Journal of Experimental Zoology (Molecular and Developmental Evolution), 310B, 492–503.CrossRef
  Kaneko, K., & Yomo, T. (1999). Isologous diversification for robust development of cell society. Journal of Theoretical Biology, 99, 243–256.CrossRef
  Kaplan, D., & Craver, C. (2011). The explanatory force of dynamical and mathematical models in neuroscience: A mechanistic perspective. Philosophy of Science, 78, 601–627.CrossRef
  Kauffman, S. (1969). Metabolic stability and epigenetics in randomly constructed genetic nets. Journal of Theoretical Biology, 22, 437–467.CrossRef
  Kauffman, S. (1971). Differentiation of malignant to benign cells. Journal of Theoretical Biology, 31, 429–451.CrossRef
  Kauffman, S. (1973). Control circuits for determination and transdetermination. Science, 181, 310–318.CrossRef
  Kauffman, S. (1993). The origins of order: Self-organization and selection in evolution. New York: Oxford University Press.
  Kitano, H. (2002). Looking beyond the details: A rise in system-oriented approaches in genetics and molecular biology. Current Genetics, 41, 1–10.CrossRef
  Kitcher, P. (1981). Explanatory unification. Philosophy of Science, 48, 507–531.CrossRef
  Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Lehrach, H., & Herwig, R. (2009). Systems biology: A textbook. Weinheim: Wiley-VCH.
  Knuuttila, T., & Loettgers, A. (2013). Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 158–169.CrossRef
  Laplane, L. (forthcoming). Cellule souche cancéreuses: Ontologies et therapies. Ph.D. dissertation, Université Paris Ouest Nanterre La Défense and Sorbonne Université. To be published (in translation) by Harvard University Press.
  Levy, A., & Bechtel, W. (2013). Abstraction and the organization of mechanisms. Philosophy of Science, 80, 241–261.CrossRef
  Machamer, P., Darden, L., & Craver, C. (2000). Thinking about mechanisms. Philosophy of Science, 67, 1–25.CrossRef
  MacLeod, M., & Nersessian, N. J. (2013a). Coupling simulation and experiment: The bimodal strategy in integrative systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 572–584.CrossRef
  MacLeod, M., & Nersessian, N. J. (2013b). Building simulations from the ground up: Modeling and theory in systems biology. Philosophy of Science, 80, 533–556.CrossRef
  MacLeod, M., & Nersessian, N. J. (2014). Strategies for coordinating experimentation and modeling in integrative systems biology. Journal of Experimental Zoology (Molecular and Developmental Evolution), 322B, 230–239.CrossRef
  Melton, D. A., & Cowan, C. (2009). Stemness: Definitions, criteria, and standards. In R. Lanza et al. (Eds.). Essentials of stem biology (2nd ed., pp. xxii–xxix). San Diego, CA: Academic Press.
  Nagajima, A., & Kaneko, K. (2008). Regulative differentiation as bifurcation of interacting cell population. Journal of Theoretical Biology, 253, 779–787.CrossRef
  Newman, M. (2010). Networks: An introduction. Oxford: Oxford University Press.CrossRef
  Nobel Assembly. (October 2012). Karolinska Institute. Press release, 8.
  O’Malley, M., & Soyer, O. (2012). The roles of integration in molecular systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 43, 58–68.CrossRef
  Ramalho-Santos, M., & Willenbring, H. (2007). On the origin of the term ‘stem cell’. Cell Stem Cell, 1, 35–38.CrossRef
  Salmon, W. (1989). Four decades of scientific explanation. Minneapolis: University of Minnesota Press.
  Strevens, M. (2008). Depth. Cambridge: Harvard University Press.
  Strogatz, S. H. (2000). Nonlinear dynamics and chaos: With applications to physics, biology, chemistry and engineering. New York: Perseus Books.
  Takahashi, K., & Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126, 663–676.CrossRef
  Thomson, J., Itskovitz-Eldor, J., Shapiro, S., Waknitz, M., Swiergel, J., Marshall, V., et al. (1998). Embryonic stem cell lines derived from human blastocysts. Science, 282, 1145–1147.CrossRef
  Vierbuchen, T., & Wernig, M. (2011). Direct lineage conversions: Unnatural but useful? Nature Biotechnology, 29, 892–907.CrossRef
  Waddington, C. H. (1957). The strategy of the genes. London: Taylor & Francis.
  Wang, J., Xu, L., Wang, E., & Huang, S. (2010). The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophysical Journal, 99, 29–39.CrossRef
  Woodward, J. (2003). Making things happen: A theory of causal explanation. Oxford: Oxford University Press.
  Zednik, C. (2008). Dynamical models and mechanistic explanations. In B. C. Love, K. McRae, & V. M. Sloutsky (Eds.), Proceedings of the 30th annual conference of the cognitive science society (pp. 1454–1459). Austin, TX: Cognitive Science Society.
  Zednik, C. (2011). The nature of dynamical explanation. Philosophy of Science, 78, 238–263.CrossRef
  Zhou, J. X., & Huang, S. (2010). Understanding gene circuits at cell-fates branch points for rational cell reprogramming. Trends in Genetics, 27, 55–62.CrossRef
  Zipori, D. (2004). The nature of stem cells. Nature Reviews Genetics, 5, 873–878.CrossRef
  
• 作者单位：Melinda Bonnie Fagan (1)
  
  1. Department of Philosophy, University of Utah, 215 South Central Campus Drive, Carolyn Tanner Irish Humanities Building, 4th Floor, Salt Lake City, UT, 84112, USA
  
• 刊物类别：Humanities, Social Sciences and Law
• 刊物主题：Philosophy
  Philosophy
  Logic
  Epistemology
  Metaphysics
  Philosophy of Language
  
• 出版者：Springer Netherlands
• ISSN：1573-0964

文摘

This paper examines a case of failed interdisciplinary collaboration, between experimental stem cell research and theoretical systems biology. Recently, two groups of theoretical biologists have proposed dynamical systems models as a basis for understanding stem cells and their distinctive capacities. Experimental stem cell biologists, whose work focuses on manipulation of concrete cells, tissues and organisms, have largely ignored these proposals. I argue that ‘failure to communicate’ in this case is rooted in divergent views of explanation: the theoretically-inclined modelers are committed to a version of the covering-law view, while experimental stem cell biologists aim at mechanistic explanations. I propose a way to reconcile these two explanatory approaches to cell development, and discuss the significance of this result for interdisciplinary collaboration in systems biology and beyond.