Systems biology and the integration of mechanistic explanation and mathematical explanation

Studies in History and Philosophy of Science Part C :Studies in History and Philosophy of Biological and Biomedical Sciences

Volumn 44, Issue 4, 2013, Pages 477-492

  Brigandt, Ingo ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Integration; Mathematical models; Mechanisms; Mechanistic explanation; Systems biology

Indexed keywords

BIOLOGICAL MODEL; PHILOSOPHY; PROCEDURES; SYSTEMS BIOLOGY;

MODELS, BIOLOGICAL; PHILOSOPHY; SYSTEMS BIOLOGY;

EID: 84904641287     PISSN: 13698486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.shpsc.2013.06.002     Document Type: Article

References (167)

1. Abud, H. E. (2004). Shaping developing tissues by apoptosis. Cell Death & Differentiation, 11, 797-799.
2. Albert, R., & Othmer, H. G. (2003). The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. Journal of Theoretical Biology, 223, 1-18.
3. Alon, U. (2007). An introduction to systems biology: Design principles of biological circuits. Boca Raton: Chapman & Hall/CRC Press.
4. Baetu, T. (in press). From mechanisms to mathematical models and back to mechanisms: Quantitative mechanistic explanations. In C. Malaterre & P.-A. Braillard (Eds.), Explanation in biology: An enquiry into the diversity of explanatory patterns in the life sciences. Berlin: Springer. in press.
5. Bagci, E. Z., Vodovotz, Y., Billiar, T. R., Ermentrout, G. B., & Bahar, I. (2006). Bistability in apoptosis: Roles of Bax, Bcl-2, and mitochondrial permeability transition pores. Biophysical Journal, 90, 1546-1559.
6. Baggs, J. E., Price, T. S., DiTacchio, L., Panda, S., FitzGerald, G. A., & Hogenesch, J. B. (2009). Network features of the mammalian circadian clock. PLoS Biology, 7, e1000052.
7. Baker, R. E., & Schnell, S. (2009). How can mathematics help us explore vertebrate segmentation? HFSP Journal, 3, 1-5.
8. Baker, R. E., Schnell, S., & Maini, P. K. (2008). Mathematical models for somite formation. In S. Schnell, P. K. Maini, S. A. Newman, & T. J. Newman (Eds.), Multiscale modeling of developmental systems (pp. 183-203). New York: Academic Press.
9. Barabási, A.-L., & Oltvai, Z. N. (2004). Network biology: Understanding the cell's functional organization. Nature Reviews Genetics, 5, 101-113.
10. Barabási, A.-L., Gulbahce, N., & Loscalzo, J. (2011). Network medicine: A networkbased approach to human disease. Nature Reviews Genetics, 12, 56-68.
11. Barberis, M., Klipp, E., Vanoni, M., & Alberghina, L. (2007). Cell size at S phase initiation: An emergent property of the G1/S network. PLoS Computational Biology, 3, e64.
12. Bechtel, W. (2006). Discovering cell mechanisms: The creation of modern cell biology. Cambridge: Cambridge University Press.
13. Bechtel, W. (2010). The downs and ups of mechanistic research: Circadian rhythm research as an exemplar. Erkenntnis, 73, 313-328.
14. Bechtel, W. (2011). Mechanism and biological explanation. Philosophy of Science, 78, 533-557.
15. Bechtel, W. (2012). Understanding endogenously active mechanisms: A scientific and philosophical challenge. European Journal for Philosophy of Science, 2, 233-248.
16. Bechtel, W. (2013). From molecules to behavior and the clinic: Integration in chronobiology. Studies in History and Philosophy of Biological and Biomedical, Sciences, 44, 493-502.
17. Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36, 421-441.
18. Bechtel, W., & Abrahamsen, A. (2010). Dynamic mechanistic explanation: Computational modeling of circadian rhythms as an exemplar for cognitive science. Studies in History and Philosophy of Science, 41, 321-333.
19. 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.
20. Bechtel, W., & Richardson, R. C. (1993). Discovering complexity: Decomposition and localization as strategies in scientific research. Princeton: Princeton University Press.
21. Behe, M. J. (1996). Darwin's black box: The biochemical challenge to evolution. New York: Free Press.
22. Bhalla, U. S., & Iyengar, R. (1999). Emergent properties of networks of biological signaling pathways. Science, 283, 381-387.
23. Bogen, J. (2005). Regularities and causality; generalizations and causal explanations. Studies in History and Philosophy of Biological and Biomedical Sciences, 36, 397-420.
24. Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J.-H. S., & Westerhoff, H. V. (2007a). 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. 3-19). Amsterdam: Elsevier.
25. Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J.-H. S., & Westerhoff, H. V. (Eds.). (2007b). Systems biology: Philosophical foundations. Amsterdam: Elsevier.
26. Boogerd, F. C., Bruggeman, F., Richardson, R., Stephan, A., & Westerhoff, H. (2005). Emergence and its place in nature: A case study of biochemical networks. Synthese, 145, 131-164.
27. Braendle, C., & Félix, M.-A. (2008). Plasticity and errors of a robust developmental system in different environments. Developmental Cell, 15, 714-724.
28. Brigandt, I. (2010). Beyond reduction and pluralism: Toward an epistemology of explanatory integration in biology. Erkenntnis, 73, 295-311.
29. Brigandt, I. (2013a). Explanation in biology: Reduction, pluralism, and explanatory aims. Science & Education, 22, 69-91.
30. Brigandt, I. (2013b). Intelligent design and the nature of science: Philosophical and pedagogical points. In K. Kampourakis (Ed.), The philosophy of biology: A companion for educators (pp. 205-238). Berlin: Springer.
31. Brigandt, I. (in press). Evolutionary developmental biology and the limits of philosophical accounts of mechanistic explanation. In P.-A. Braillard & C. Malaterre (Eds.), Explanation in biology: An enquiry into the diversity of explanatory patterns in the life sciences. Berlin: Springer. in press.
32. Brigandt, I., & Love, A. C. (2010). Evolutionary novelty and the evo-devo synthesis: Field notes. Evolutionary Biology, 37, 93-99.
33. Brigandt, I., & Love, A. C. (2012a). Conceptualizing evolutionary novelty: Moving beyond definitional debates. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 318, 417-427.
34. Brigandt, I., & Love, A. C. (2012b). Reductionism in biology. In E. N. Zalta (Ed.), The Stanford encyclopedia of philosophy. .
35. 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.
36. Cedersund, G., & Roll, J. (2009). Systems biology: Model based evaluation and comparison of potential explanations for given biological data. FEBS Journal, 276, 903-922.
37. Craver, C. F. (2005). Beyond reduction: Mechanisms, multifield integration and the unity of neuroscience. Studies in the History and Philosophy of Biological and Biomedical Sciences, 36, 373-395.
38. Craver, C. F. (2006). When mechanistic models explain. Synthese, 153, 355-376.
39. Craver, C. F. (2007). Explaining the brain: Mechanisms and the mosaic unity of neuroscience. Oxford: Oxford University Press.
40. Craver, C. F. (2008). Physical law and mechanistic explanation in the Hodgkin and Huxley model of the action potential. Philosophy of Science, 75, 1022-1033.
41. Craver, C. F. (in press). The ontic account of scientific explanation. In A. Hütteman & M. Kaiser (Eds.), Explanation in the special sciences: The case of biology and history. Berlin: Springer. in press.
42. Craver, C. F., & Darden, L. (Eds.). (2005). Mechanisms in biology. Special issue of Studies in History and Philosophy of Biological and Biomedical Sciences. (Vol. 36, Issue 2).
43. Crawford, J. W., Harris, J. A., Ritz, K., & Young, I. M. (2005). Towards an evolutionary ecology of life in soil. Trends in Ecology and Evolution, 20, 81-87.
44. Cui, J., Chen, C., Lu, H., Sun, T., & Shen, P. (2008). Two independent positive feedbacks and bistability in the Bcl-2 apoptotic switch. PLoS ONE, 3, e1469.
45. Darden, L. (2005). Relations among fields: Mendelian, cytological and molecular mechanisms. Studies in History and Philosophy of Biological and Biomedical Sciences, 36, 349-371.
46. Darden, L., & Maull, N. (1977). Interfield theories. Philosophy of Science, 44, 43-64.
47. Davidson, E. H. (2006). The regulatory genome: Gene regulatory networks in development and evolution. London: Academic Press.
48. Davidson, E. H., & Erwin, D. H. (2006). Gene regulatory networks and the evolution of animal body plans. Science, 311, 796-800.
49. Dean, E. J., Davis, J. C., Davis, R. W., & Petrov, D. A. (2008). Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genetics, 4, e1000113.
50. Dequéant, M.-L., Glynn, E., Gaudenz, K., Wahl, M., Chen, J., Mushegian, A., et al. (2006). A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science, 314, 1595-1598.
51. Dequéant, M.-L., & Pourquié, O. (2008). Segmental patterning of the vertebrate embryonic axis. Nature Reviews Genetics, 9, 370-382.
52. Economou, A. D., Ohazama, A., Porntaveetus, T., Sharpe, P. T., Kondo, S., Basson, M. A., et al. (2012). Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate. Nature Genetics, 44, 348-351.
53. Edwards, J. S., & Palsson, B. O. (1999). Systems properties of the Haemophilus influenzae Rd metabolic genotype. Journal of Biological Chemistry, 274, 17410-17416.
54. Edwards, J. S., & Palsson, B. O. (2000a). The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proceedings of the National Academy of Sciences USA, 97, 5528-5533.
55. Edwards, J. S., & Palsson, B. O. (2000b). Robustness analysis of the Escherichia coli metabolic network. Biotechnology Progress, 16, 927-939.
56. Eissing, T., Allgöwer, F., & Bullinger, E. (2005). Robustness properties of apoptosis models with respect to parameter variations and intrinsic noise. Systems Biology, IEE Proceedings, 152, 221-228.
57. Eissing, T., Conzelmann, H., Gilles, E. D., Allgöwer, F., Bullinger, E., & Scheurich, P. (2004). Bistability analyses of a caspase activation model for receptor-induced apoptosis. Journal of Biological Chemistry, 279, 36892-36897.
58. Elmore, S. (2007). Apoptosis: A review of programmed cell death. Toxicologic Pathology, 35, 495-516.
59. Fagan, M. B. (2012). Waddington redux: Models and explanation in stem cell and systems biology. Biology and Philosophy, 27, 179-213.
60. Faratian, D., Clyde, R. G., Crawford, J. W., & Harrison, D. J. (2009). Systems pathology-Taking molecular pathology into a new dimension. Nature Review Clininical Oncolology, 6, 455-464.
61. Fell, D. A. (2007). How can we understand metabolism? In F. C. Boogerd, F. J. Bruggeman, J.-H. S. Hofmeyr, & H. V. Westerhoff(Eds.), Systems biology: Philosophical foundations (pp. 87-101). Amsterdam: Elsevier.
62. Ferrell, J. E., Tsai, T. Y.-C., & Yang, Q. (2011). Modeling the cell cycle: Why do certain circuits oscillate? Cell, 144, 874-885.
63. Fisher, J., Piterman, N., Hajnal, A., & Henzinger, T. A. (2007). Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Computational Biology, 3, e92.
64. Fraser, I. D. C., & Germain, R. N. (2009). Navigating the network: Signaling cross-talk in hematopoietic cells. Nature Immunology, 10, 327-331.
65. Fu, P., & Panke, S. (Eds.). (2009). Systems biology and synthetic biology. Hoboken: Wiley.
66. Fussenegger, M., Bailey, J. E., & Varner, J. (2000). A mathematical model of caspase function in apoptosis. Nature Biotechnology, 18, 768-774.
67. Gerson, E. M. (2013). Integration of specialties: An institutional and organizational view. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 514-524.
68. Glennan, S., Darden, L., & Woodward, J. (2002). 'Mechanism: Explanation, discovery, and experimentation' (PSA 2000 symposium). Philosophy of Science, 69, S342-S377.
69. Goldbeter, A., & Pourquié, O. (2008). Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. Journal of Theoretical Biology, 252, 574-585.
70. Green, S. (2013). When one model is not enough: Combining epistemic tools in systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 170-180.
71. Greenbury, S. F., Johnston, I. G., Smith, M. A., Doye, J. P. K., & Louis, A. A. (2010). The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks. Journal of Theoretical Biology, 267, 48-61.
72. Griesemer, J. (2013). Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology. Studies in History and Philosophy of Biological and Biomedical Sciences., 44, 525-536.
73. Helms, V. (2008). Principles of computational cell biology. Weinheim: Wiley-VHC.
74. Hempel, C. G. (1965). Aspects of scientific explanation and other essays in the philosophy of science. New York: Free Press.
75. Hempel, C. G., & Oppenheim, P. (1948). Studies in the logic of explanation. Philosophy of Science, 15, 135-175.
76. Hentschel, H. G. E., Glimm, T., Glazier, J. A., & Newman, S. A. (2004). Dynamical mechanisms for skeletal pattern formation in the vertebrate limb. Proceedings of the Royal Society of London B: Biological Sciences, 271, 1713-1722.
77. Herrgen, L., Ares, S., Morelli, L. G., Schröter, C., Jülicher, F., & Oates, A. C. (2010). Intercellular coupling regulates the period of the segmentation clock. Current Biology, 20, 1244-1253.
78. Ho, K. L., & Harrington, H. A. (2010). Bistability in apoptosis by receptor clustering. PLoS Computational Biology, 6, e1000956.
79. Hooker, C. (Ed.). (2011). Philosophy of complex systems. Amsterdam: Elsevier.
80. Ihekwaba, A. E. C., Broomhead, D. S., Grimley, R., Benson, N., White, M. R. H., & Kell, D. B. (2005). Synergistic control of oscillations in the nf-jb signalling pathway. IEE Proceedings Systems Biology, 152, 153-160.
81. Ihmels, J., Collins, S. R., Schuldiner, M., Krogan, N. J., & Weissman, J. S. (2007). Backup without redundancy: Genetic interactions reveal the cost of duplicate gene loss. Molecular Systems Biology, 3, 86.
82. Ingolia, N. T. (2004). Topology and robustness in the Drosophila segment polarity network. PLoS Biology, 2, e123.
83. Jansson, J. K., Neufeld, J. D., Moran, M. A., & Gilbert, J. A. (2012). Omics for understanding microbial functional dynamics. Environmental Microbiology, 14, 1-3.
84. Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., & Barabási, A. L. (2000). The large-scale organization of metabolic networks. Nature, 407, 651-654.
85. Jørgensen, C., & Linding, R. (2010). Simplistic pathways or complex networks? Current Opinion in Genetics & Development, 20, 15-22.
86. Kafri, R., Bar-Even, A., & Pilpel, Y. (2005). Transcription control reprogramming in genetic backup circuits. Nature Genetics, 37, 295-299.
87. Kaplan, D. M., & Craver, C. F. (2011). The explanatory force of dynamical and mathematical models in neuroscience: A mechanistic perspective. Philosophy of Science, 78, 601-627.
88. Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., et al. (2012). A whole-cell computational model predicts phenotype from genotype. Cell, 150, 389-401.
89. Kirschner, M. W., & Gerhart, J. C. (2005). The plausibility of life: Resolving Darwin's dilemma. New Haven: Yale University Press.
90. Kitano, H. (Ed.). (2001). Foundations of systems biology. Cambridge, MA: MIT Press.
91. Kitano, H. (2004a). Biological robustness. Nature Reviews Genetics, 5, 826-837.
92. Kitano, H. (2004b). Cancer as a robust system: Implications for anticancer therapy. Nature Reviews Cancer, 4, 227-235.
93. Kitano, H. (2006). Computational cellular dynamics: A network-physics integral. Nature Reviews Molecular Cell Biology, 7, 163.
94. Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Lehrach, H., & Herwig, R. (2010). Systems biology: A textbook. Weinheim: Wiley-VCH.
95. Krohs, U., & Callebaut, W. (2007). Data without models merging with models without data. In F. C. Boogerd, F. J. Bruggeman, J.-H. S. Hofmeyr, & H. V. Westerhoff(Eds.), Systems biology: Philosophical foundations (pp. 181-213). Amsterdam: Elsevier.
96. Lavrik, I. N. (Ed.). (2013). Systems biology of apoptosis. Berlin: Springer.
97. Layek, R. K., Datta, A., & Dougherty, E. R. (2011). From biological pathways to regulatory networks. Molecular BioSystems, 7, 843-851.
98. Legewie, S., Blüthgen, N., & Herzel, H. (2006). Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Computational Biology, 2, e120.
99. Leonelli, S. (2013). Integrating data to acquire new knowledge: Three modes of integration in plant science. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 503-514.
100. Levy, A. (in press). What was Hodgkin and Huxley's achievement? British Journal for the Philosophy of Science. http://dx.doi.org/10.1093/bjps/axs043. in press.
101. Levy, A., & Bechtel, W. (2013). Abstraction and the organization of mechanisms. Philosophy of Science, 80, 241-261.
102. Li, R., & Bowerman, B. (2010a). Symmetry breaking in biology. Cold Spring Harbor Perspectives in Biology, 2, a003475.
103. Li, R., & Bowerman, B. (Eds.). (2010b). Symmetry breaking in biology. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
104. Li, X., Cassidy, J. J., Reinke, C. A., Fischboeck, S., & Carthew, R. W. (2009). A microRNA imparts robustness against environmental fluctuation during development. Cell, 137, 273-282.
105. Linksvayer, T. A., Fewell, J. H., Gadau, J., & Laubichler, M. D. (2012). Developmental evolution in social insects: Regulatory networks from genes to societies. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 318, 159-169.
106. Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67, 1-25.
107. Manu, Surkova, S., Spirov, A. V., Gursky, V. V., Janssens, H., Kim, A.-R., et al. (2009a). Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Computational Biology, 5, e1000303.
108. Manu, Surkova, S., Spirov, A. V., Gursky, V. V., Janssens, H., Kim, A.-R., et al. (2009b). Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biology, 7, e1000049.
109. Masamizu, Y., Ohtsuka, T., Takashima, Y., Nagahara, H., Takenaka, Y., Yoshikawa, K., et al. (2006). Real-time imaging of the somite segmentation clock: Revelation of unstable oscillators in the individual presomitic mesoderm cells. Proceedings of the National Academy of Sciences USA, 103, 1313-1318.
110. Maull, N. (1977). Unifying science without reduction. Studies in History and Philosophy of Science, 8, 143-171.
111. Mazzitello, K. I., Arizmendi, C. M., & Hentschel, H. G. E. (2008). Converting genetic network oscillations into somite spatial patterns. Physical Review E, 78, 021906.
112. Meinhardt, H. (2009). The algorithmic beauty of sea shells (4th ed.). Berlin: Springer.
113. Milloz, J., Duveau, F., Nuez, I., & Félix, M.-A. (2008). Intraspecific evolution of the intercellular signaling network underlying a robust developmental system. Genes & Development, 22, 3064-3075.
114. Mitchell, S. D. (2009). Unsimple truths: Science, complexity, and policy. Chicago: University of Chicago Press.
115. Mitchell, S. D. (2012). Emergence: Logical, functional and dynamical. Synthese, 185, 171-186.
116. Mogilner, A., Allard, J., & Wollman, R. (2012). Cell polarity: Quantitative modeling as a tool in cell biology. Science, 336, 175-179.
117. Morelli, L. G., Ares, S., Herrgen, L., Schröter, C., Jülicher, F., & Oates, A. C. (2009). Delayed coupling theory of vertebrate segmentation. HFSP Journal, 3, 55-66.
118. Morelli, L. G., Uriu, K., Ares, S., & Oates, A. C. (2012). Computational approaches to developmental patterning. Science, 336, 187-191.
119. Moreno, A. (2007). A systemic approach to the origin of biological organization. In F. C. Boogerd, F. J. Bruggeman, J.-H. S. Hofmeyr, & H. V. Westerhoff(Eds.), Systems biology: Philosophical foundations (pp. 243-268). Amsterdam: Elsevier.
120. Murray, J. D. (2003). Mathematical biology II: Spatial models and biomedical applications. Berlin: Springer.
121. Nakamasu, A., Takahashi, G., Kanbe, A., & Kondo, S. (2009). Interactions between zebrafish pigment cells responsible for the generation of Turing patterns. Proceedings of the National Academy of Sciences USA, 106, 8429-8434.
122. Newman, S. A., & Bhat, R. (2007). Activator-inhibitor dynamics of vertebrate limb pattern formation. Birth Defects Research Part C: Embryo Today: Reviews, 81, 305-319.
123. Newman, S. A., Christley, S., Glimm, T., Hentschel, H. G. E., Kazmierczak, B., Zhang, Y.-T., et al. (2008). Multiscale models for vertebrate limb development. In S. Schnell, P. K. Maini, S. A. Newman, & T. J. Newman (Eds.), Multiscale modeling of developmental systems (pp. 311-340). New York: Academic Press.
124. Newman, S. A., & Müller, G. B. (2005). Origination and innovation in the vertebrate limb skeleton: An epigenetic perspective. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 304B, 593-609.
125. Noble, D. (2002). Modeling the heart-From genes to cells to the whole organ. Science, 295, 1678-1682.
126. Noble, D. (2006). The music of life: Biology beyond the genome. Oxford: Oxford University Press.
127. O'Malley, M. A., & Dupré, J. (2005). Fundamental issues in systems biology. BioEssays, 27, 1270-1276.
128. 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.
129. O'Malley, M. A. (2013). When integration fails: Prokaryote phylogeny and the tree of life. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 551-562.
130. Oates, A. C., Morelli, L. G., & Ares, S. (2012). Patterning embryos with oscillations: Structure, function and dynamics of the vertebrate segmentation clock. Development, 139, 625-639.
131. Patel, M., & Nagl, S. (Eds.). (2010). The role of model integration in complex systems modelling: An example from cancer biology. Berlin: Springer.
132. Plikus, M. V., Baker, R. E., Chen, C.-C., Fare, C., de la Cruz, D., Andl, T., et al. (2011). Self-organizing and stochastic behaviors during the regeneration of hair stem cells. Science, 332, 586-589.
133. Plutynski, A. (2013). Cancer and the goals of integration. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 466-476.
134. Putnam, H. (1975). Philosophy and our mental life. In H. Putnam (Ed.), Philosophical papers. Mind, language and reality (Vol. 2, pp. 291-303). Cambridge: Cambridge University Press.
135. Riedel-Kruse, I. H., Müller, C., & Oates, A. C. (2007). Synchrony dynamics during initiation, failure, and rescue of the segmentation clock. Science, 317, 1911-1915.
136. Robins, S. K., & Craver, C. F. (2009). Biological clocks: Explaining with models of mechanisms. In J. Bickle (Ed.), Oxford handbook of philosophy and neuroscience (pp. 41-67). Oxford: Oxford University Press.
137. Salazar-Ciudad, I., & Jernvall, J. (2002). A gene network model accounting for development and evolution of mammalian teeth. Proceedings of the National Academy of Sciences USA, 99, 8116-8120.
138. Salazar-Ciudad, I., & Jernvall, J. (2010). A computational model of teeth and the developmental origins of morphological variation. Nature, 464, 583-586.
139. Santillán, M., & Mackey, M. C. (2008). A proposed mechanism for the interaction of the segmentation clock and the determination front in somitogenesis. PLoS ONE, 3, e1561.
140. Schnell, S., Maini, P. K., Newman, S. A., & Newman, T. J. (Eds.). (2008). Multiscale modeling of developmental systems. New York: Academic Press.
141. Shiraishi, T., Matsuyama, S., & Kitano, H. (2010). Large-scale analysis of network bistability for human cancers. PLoS Computational Biology, 6, e1000851.
142. Siegal, M., Promislow, D., & Bergman, A. (2007). Functional and evolutionary inference in gene networks: Does topology matter? Genetica, 129, 83-103.
143. Smart, A. G., Amaral, L. A. N., & Ottino, J. M. (2008). Cascading failure and robustness in metabolic networks. Proceedings of the National Academy of Sciences USA, 105, 13223-13228.
144. Soriano, J., Rüdiger, S., Pullarkat, P., & Ott, A. (2009). Mechanogenetic coupling of Hydra symmetry breaking and driven Turing instability model. Biophysical Journal, 96, 1649-1660.
145. Strevens, M. (2008). Depth: An account of scientific explanation. Harvard: Harvard University Press.
146. Turing, A. M. (1952). The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 237, 37-72.
147. Umulis, D., O'Connor, M. B., & Othmer, H. G. (2008). Robustness of embryonic spatial patterning in Drosophila melanogaster. In S. Schnell, P. K. Maini, S. A. Newman, & T. J. Newman (Eds.), Multiscale modeling of developmental systems (pp. 65-111). New York: Academic Press.
148. Uriu, K., Morishita, Y., & Iwasa, Y. (2010). Random cell movement promotes synchronization of the segmentation clock. Proceedings of the National Academy of Sciences USA, 107, 4979-4984.
149. van der Gucht, J., & Sykes, C. (2009). Physical model of cellular symmetry breaking. Cold Spring Harbor Perspectives in Biology, 1, a001909.
150. von Dassow, G., Meir, E., Munro, E. M., & Odell, G. M. (2000). The segment polarity network is a robust developmental module. Nature, 406, 188-192.
151. von Dassow, G., & Odell, G. M. (2002). Design and constraints of the Drosophila segment polarity module: Robust spatial patterning emerges from intertwined cell state switches. Journal of Experimental Zoology (Molecular and Developmental Evolution), 294, 179-215.
152. Wagner, A. (2005a). Distributed robustness versus redundancy as causes of mutational robustness. BioEssays, 27, 176-188.
153. Wagner, A. (2005b). Robustness and evolvability in living systems. Princeton: Princeton University Press.
154. Wang, E. (Ed.). (2010). Cancer systems biology. Boca Raton: CRC Press.
155. Wang, Y., Zhang, X.-S., & Xia, Y. (2009). Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Research, 37, 5943-5958.
156. Weiss, J. N., Qu, Z., & Garfinkel, A. (2003). Understanding biological complexity: Lessons from the past. FASEB Journal, 17, 1-6.
157. Westerhoff, H. V., & Kell, D. B. (2007). The methodologies of systems biology. In F. C. Boogerd, F. J. Bruggeman, J.-H. S. Hofmeyr, & H. V. Westerhoff(Eds.), Systems biology: Philosophical foundations (pp. 23-70). Amsterdam: Elsevier.
158. Wilhelm, T. (2009). The smallest chemical reaction system with bistability. BMC Systems Biology, 3, 90.
159. Wimsatt, W. C. (2007). Re-engineering philosophy for limited beings: Piecewise approximations to reality. Cambridge, MA: Harvard University Press.
160. Wing, S. S., Lecker, S. H., & Jagoe, R. T. (2011). Proteolysis in illness-associated skeletal muscle atrophy: From pathways to networks. Critical Reviews in Clinical Laboratory Science, 48, 49-70.
161. Winther, R. G. (2006). Parts and theories in compositional biology. Biology and Philosophy, 21, 471-499.
162. Winther, R. G. (2011). Part-whole science. Synthese, 178, 397-427.
163. Wolkenhauer, O., & Muir, A. (2011). The complexity of cell-biological systems. In C. Hooker (Ed.), Philosophy of complex systems (pp. 355-385). Amsterdam: Elsevier.
164. Woodward, J. (2002). What is a mechanism? A counterfactual account. Philosophy of Science, 69, S366-S377.
165. Woodward, J. (2003). Making things happen: A theory of causal explanation. Oxford: Oxford University Press.
166. Yang, Q., & Ferrell, J. E. (2013). The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch. Nature Cell Biology, 15, 519-525.
167. Zhu, J., Zhang, Y.-T., Alber, M. S., & Newman, S. A. (2010). Bare bones pattern formation: A core regulatory network in varying geometries reproduces major features of vertebrate limb development and evolution. PLoS ONE, 5, e10892.