When one model is not enough: Combining epistemic tools in systems biology

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

Volumn 44, Issue 2, 2013, Pages 170-180

  Green, Sara ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Engineering analogies; Historical epistemology; Modeling; Network motifs; Reverse engineering; Rheinberger

Indexed keywords

BIOENGINEERING; BIOLOGICAL MODEL; KNOWLEDGE; PROCEDURES; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

BIOENGINEERING; KNOWLEDGE; MODELS, BIOLOGICAL; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

EID: 84877662938     PISSN: 13698486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.shpsc.2013.03.012     Document Type: Article

References (43)

1. Alon U. Biological networks: The tinkerer as an engineer. Science 2003, 301(5641):1866-1867.
2. Alon U. An introduction to systems biology. Design principles of biological circuits 2006, Chapman and Hall/CRC Mathematical & Computational Biology.
3. Alon U. Network motifs: Theory and experimental approaches. Nature Reviews Genetics 2007, 8:450-481.
4. Alon U. Simplicity in biology. La Nature 2007, 446(7135):497.
5. Ankeny R.A., Leonelli S. What's so special about model organisms?. Studies in History and Philosophy of Science Part A 2011, 42(2):313-323.
6. Borenstein E., Kupiec M., Feldman M.W., Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proceedings of the National Academy of Science 2008, 105(38):14482-14487.
7. Cordero O.X., Hogeweg P. Feed-forward loop circuits as a side effect of genome evolution. Molecular Biology and Evolution 2006, 23(10):1931-1936.
8. Dekel E., Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436(7050):588.
9. Dekel E., Mangan S., Alon U. Environmental selection of the feed-forward loop circuit in gene-regulation networks. Physical Biology 2005, 2(2):81.
10. Doyle F.J., Stelling J.F.J. Systems interface biology. Journal of the Royal Society 2006, 3(10):603-616.
11. Kalisky T., Dekel E., Alon U. Cost-benefit theory and optimal design of gene regulation functions. Physical Biology 2007, 4(4):229-245.
12. Kashtan N., Alon U. Spontaneous evolution of modularity and network motifs. Proceedings of the National Academy of Sciences 2006, 102(39):13773-13778.
13. Knabe J.F., Nehaniv C.L., Schilstra M.J. Do motifs reflect evolved function? No convergent evolution of genetic regularoty network subgraph toplogies. Biosystems 2008, 94:68-74.
14. Knuuttila T. Modeling and representing: An artefactual approach to model-based representation. Studies in History and Philosophy of Science 2011, 42:262-271.
15. Knuuttila, T. & Loettgers, A. (2010). Modeling and experimenting: The combinatorial strategy in synthetic biology. In Philosophy of scientific experimentation: A challenge to philosophy of science (Pittsburgh; October 15-17, 2010). Available from (Accessed May 21, 2012). http://philsci-archive.pitt.edu/8329/.
16. Knuuttila T., Loettgers A. Causal isolation robustness analysis: The combinatorial strategy of circadian clock research. Biology and Philosophy 2011, 26(5):773-791.
17. Knuuttila, T., & Loettgers, A. (in press). Varieties of noise: Analogical reasoning in synthetic biology. Studies in History and Philosophy of Science.
18. Knuuttila T., Loettgers A. Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering. Studies in History and Philosophy of Biological and Biomedical Sciences 2013, 44:158-169.
19. Kuo D.P., Banzhaf W., Leier A. Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence. Biosystems 2006, 85(3):177-200.
20. Leonelli S. What is in a model? Combining theoretical and material models to develop intelligible theories. Modeling biology. Structure behaviors evolution 2007, 15-35. The MIT Press, Cambridge, MA. M.D. Laubichler, G.B. Müller (Eds.).
21. Levins R. The strategy of model building in population biology. American Scientist 1966, 54:421-431.
22. Levins R. Strategies of abstraction. Biolology and Philosophy 2006, 21:741-755.
23. Levy, A. & Bechtel, W. (in press). Abstraction and the organization of mechanisms. Philosophy of Science.
24. Lynch M. The evolution of genetic networks by non-adaptive processes. Nature Reviews Genetics 2007, 8:803-813.
25. Mangan S., Alon U. Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Science 2003, 100(21):11980.
26. Mazurie A., Bottani S., Vergassola M. An evolutionary and functional assessment of regulatory network motifs. Genome Biology 2005, 6(35):1-35.
27. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U. Network motifs: Simple building blocks of complex networks. Science 2002, 298(5594):824-827.
28. Morgan M.S., Morrison M. Models as mediators: Perspectives on natural and social science 1999, Cambridge University Press, Cambridge.
29. Nersessian N. Model-based reasoning in conceptual change. Model-based reasoning in scientific discovery 2002, 5-22. Kluwer Academic/Plenum Publishers, New York. L. Magnani, N. Nersessian, P. Thagard (Eds.).
30. Nersessian N. Maxwell and 'the Method of Physical Analogy': Model-based reasoning, generic abstraction, and conceptual change. Essays in the history and philosophy of science and mathematics 2002, 129-166. Open Court, Lasalle, Il. D. Malament (Ed.).
31. O'Malley M. Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case. History and Philosophy of the Life Sciences 2007, 29(3):337-360.
32. O'Malley M., Soyer O. The roles of integration in molecular systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences 2011, 43(1):55-68.
33. Rheinberger H. Towards a history of epistemic things. Synthesizing proteins in the test tube 1997, Stanford University Press, Stanford.
34. Rheinberger H. Recent science and its exploration: The case of molecular biology. Studies in History and Philosophy of Biological and Biomedical Sciences 2009, 40(1):6-12.
35. Rheinberger H. Experimental model systems: An epistemological apercu from the perspective of molecular biology. Modeling biology. Structure, behavior, evolution 2007, 37-46. The MIT Press, Cambridge, MA. M.D. Laubichler, G.B. Müller (Eds.).
36. Rheinberger H. An epistemology of the concrete. Twentieth-century histories of life 2010, Duke University Press, Durham.
37. Shen-Orr S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics 2002, 31(1):64.
38. Solé R.V., Valverde S. Are network motifs the spandrels of cellular complexity?. TRENDS in Ecology and Evolution 2006, 21(8):419-422.
39. Steinle F. Entering new fields: Exploratory uses of experimentation. Philosophy of Science 1997, 64:65-74.
40. Weisberg M.M. Robustness analysis. Philosophy of Science 2006, 73(5):730-742.
41. Wimsatt W.C. Re-engineering philosophy for limited beings: Piecewise approximations to reality 2007, Harvard University Press, Cambridge, MA.
42. Wimsatt W. Robustness, reliability, and overdetermination. Scientific inquiry and the social sciences 1981, 124-163. Jossey Bass, San Francisco. M. Brewer, A. Hoffman (Eds.).
43. Winther R.G. Parts and theories in compositional biology. Biology & Philosophy 2006, 21(4):471-499.