Revisiting generality in biology: systems biology and the quest for design principles

Biology and Philosophy

Volumn 30, Issue 5, 2015, Pages 629-652

  Green, Sara ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Biological laws; Constraints; Design principles; Generic abstraction; Systems biology; Unification

Indexed keywords

BIOLOGY; COMPLEXITY; DESIGN; HEURISTICS; THEORETICAL STUDY;

EID: 84940602448     PISSN: 01693867     EISSN: 15728404     Source Type: Journal    
DOI: 10.1007/s10539-015-9496-9     Document Type: Article

References (81)

1. Alon U (2007) An introduction to systems biology: design principles of biological circuits. Chapman and Hall, Boca Raton
2. Alon U, Surette MG, Barkai N, Leibler S (1999) Robustness in bacterial chemotaxis. Nature 397:168–171
3. Amundson R (1994) Two concepts of constraint: adaptationism and the challenge from developmental biology. Philos Sci 61:556–578
4. Ang J, Bagh S, Ingalls BP, McMillen DR (2010) Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network. J Theor Biol 266:723–738
5. Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387:913–917
6. Batterman RW (2002) The devil in the details: asymptotic reasoning in explanation, reduction, and emergence. Oxford University Press, Oxford
7. Beatty J (1995) The evolutionary contingency thesis. In: Wolters G, Lennox J, McLaughlin P (eds) Concepts, theories and rationality in the biological sciences. University of Pittsburgh Press, Pittsburgh, pp 45–81
8. Bertalanffy Lv (1967) Robots, men and minds. George Braziller, New York
9. Braillard P (2010) Systems biology and the mechanistic framework. Hist Philos Life Sci 32:43–62
10. Briat C, Gupta A, Khammash M (2014) Integral feedback generically achieves perfect adaptation in stochastic biochemical networks. http://arxiv.org/pdf/1410.6064v3.pdf
11. Brigandt I (2015) From developmental constraint to evolvability: how concepts figure in explanation and disciplinary identity. In: Love A (ed) Conceptual change in biology. Springer, Amsterdam, pp 305–325
12. Burian R, Richardson RC, Van der Steen W (1996) Against generality: meaning in genetics and philosophy. Stud Hist Philos Sci 27:1–29
13. Collins JP, Gilbert S, Laubichler MD, Müller G (2007) Modeling in EvoDevo: how to integrate development, evolution, and ecology. In: Laubichler MD, Müller G (eds) Modelling biology: structures, behaviors, evolution. MIT Press, Cambridge, pp 355–378
14. Cordero OX, Hogeweg P (2006) Feed-forward loop circuits as a side effect of genome evolution. Mol Biol Evol 23:1931–1936
15. Csete ME, Doyle JC (2002) Reverse engineering of biological complexity. Science 295:1664–1669
16. Darwin C (1859) On the origin of species by means of natural selection. John Murray, London
17. Dawkins R (1978) The selfish gene. Oxford University Press, Oxford
18. Dennett DC (1995) Darwin’s dangerous idea: evolution and the meanings of life. Penguin, London
19. Depew DJ, Weber BH (1995) Darwinism evolving: Systems dynamics and the genealogy of natural selection. MIT Press, Cambridge
20. Dupré J (2007) Is biology reducible to the laws of physics? Am Sci 95:274–276
21. Friedman M (1974) Explanation and scientific understanding. J Philos 71:5–19
22. Goodwin B (1994) How the Leopard changed its spots. The evolution of complexity. Phoenix, London
23. Goodwin B (2009) Beyond the Darwinian paradigm: understanding biological forms. In: Ruse M, Travis J (eds) Evolution: the first four billion years. Harvard University Press, Cambridge, pp 299–312
24. Gould SJ (1977/1996) Size and shape. In: McGarr P, Rose S (eds) The richness of life. The essential Stephen Jay Gould. Vintage Books, London, pp 317–323
25. Gould SJ (1982) Darwinism and the expansion of evolutionary theory. Science 216:380–387
26. Gould SJ (1983/2006) How the zebra gets its stripes. In: McGarr P, Rose S (eds) The richness of life. The essential Stephen Jay Gould. Vintage Books, London, pp 325–332
27. Green S (2014) A philosophical evaluation of adaptationism as a heuristic strategy. Acta Biotheor 64:479–498
28. Green S, Wolkenhauer O (2013) Tracing organizing principles: learning from the history of systems biology. Hist Philos Life Sci 35:555–578
29. Green S, Fagan M, Jaeger J (2015a) Explanatory integration challenges in evolutionary systems biology. Biol Theory 10:18–35
30. Green S, Levy A, Bechtel W (2015b) Design sans adaptation. Eur J Philos Sci 5:15–29
31. Griesemer J (2012) Formalization and the meaning of “Theory” in the inexact biological sciences. Biol Theory 7:298–310
32. Hamilton A (2007) Laws of biology, laws of nature: problems and (dis) solutions. Philos Compass 2:592–610
33. Haufe C (2015) Gould’s laws. Philos Sci 82:1–20
34. Hofmeyr J (2007) The biochemical factory that autonomously fabricates itself: a systems biological view of the living cell. In: Boogerd FC, Bruggeman F, Hofmeyr J-H, Westerhoff HV (eds) Systems biology: philosophical foundations. Elsevier, Amsterdam, pp 217–242
35. Hogeweg P (2012) Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. In: Soyer O (ed) Evolutionary systems biology. Springer, London, pp 195–223
36. Huang S (2004) Back to the biology in systems biology: What can we learn from biomolecular networks? Brief Funct Genomic Proteomic 2:279–297
37. Huneman P (2010) Topological explanations and robustness in biological sciences. Synthese 117:213–245
38. Jaeger J, Crombach A (2012) Life’s attractors. Understanding developmental systems through reverse engineering and in silico evolution. In: Soyer O (ed) Evolutionary systems biology, advances in experimental medicine and biology. Springer, London, pp 93–119
39. Jakobsen L (2010) Vespertilionid bats control the width of their biosonar sound beam dynamically during prey pursuit. Proc Natl Acad Sci 107:13930–13935
40. Jones N (2014) Bowtie structures, pathway diagrams, and topological explanation. Erkenntnis 79:1135–1155
41. Kauffman S (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467
42. Kauffman S (1993) Origins or order in evolution: self-organisation and selection. Oxford University Press, New York
43. Kitano H (2007) Towards a theory of biological robustness. Mol Syst Biol 3:137
44. Kitcher P (1989) Explanatory unification and the causal structure of the world. In: Kitcher P, Salmon WC (eds) Scientific explanation. University of Minnesota Press, Minneapolis, pp 410–505
45. Klir GJ (1991) Facets of systems science. Plenum Press, New York
46. Koonin EV (2011) Are there laws of genome evolution? PLoS Comput Biol 7:e1002173
47. Kuhn TS (1962/1996) The structure of scientific revolutions. University of Chicago Press, Chicago
48. Letelier JC, Cárdenas M, Cornish-Bowden A (2011) From L'Homme Machine to metabolic closure: steps towards understanding life. J Theor Biol 286:100–113
49. Ma W, Trusina A, El-Samad H, Lim WA, Tang C (2009) Defining network topologies that can achieve biochemical adaptation. Cell 138:760–773
50. Mayr E (2005) What makes biology unique? Considerations on the autonomy of a scientific discipline. Cambridge University Press, Cambridge
51. Mesarović M, Takahara Y (1970) Theory of hierarchical, multilevel systems. Academic Press, New York
52. Mesarović M, Takahara Y (1975) General Systems Theory: Mathematical Foundations. Academic Press, New York
53. Mesarovic M, Sreenath SN, Keene JD (2004) Search for organizing principles: understanding in systems biology. Syst Biol 1:19–27
54. Müller G, Newman SA (2003) Origination of organismal form: beyond the gene in developmental and evolutionary biology. MIT Press, Massachusetts
55. Nersessian NJ (2008) Representation and reasoning: analogy, imagery, thought experiment. In: Nersessian NJ (ed) Creating Scientific Concepts. MIT Press, Cambridge, pp 131–181
56. Nickles T (1990) Discovery logics. Philosophica 45:7–32
57. O’Malley M, Dupré J (2005) Fundamental issues in systems biology. BioEssays 27:1270–1276
58. Polanyi M (1968) Life’s irreducible structure. Science 160:1308–1312
59. Rashevsky N (1961) Mathematical principles in biology and their applications. Springfield, LA
60. Rosen R (1967) Optimality principles in biology. Butterworths, London
61. Rosen R (1991) Life itself: a comprehensive inquiry into the nature, origin, and fabrication of life. Columbia University Press, New York
62. Savageau M (1989) Are there rules governing patterns of gene regulation? In: Goodwin B, Saunders P (eds) Theoretical biology, epigenetic and evolutionary order from complex systems. Edinburgh University Press, Edinburgh, pp 42–66
63. Shanks N (2001) Modeling biological systems: the Belousov–Zhabotinsky reaction. Found Chem 3:33–53
64. Shinar G, Feinberg M (2010) Structural sources of robustness in biochemical reaction networks. Science 327:1389–1391
65. Shinar G, Feinberg M (2011) Design principles for robust biochemical reaction networks: what works, what cannot work, and what might almost work. Math Biosci 231:39–48
66. Smart J (1963) Philosophy and scientific realism. Routledge & Kegan Paul, London
67. Sontag ED (2003) Adaptation and regulation with signal detection implies internal model. Syst Control Lett 50:119–126
68. Soyer O ed (2012) Evolutionary systems biology. Springer, London
69. Stelling J, Sauer U, Szallasi Z, Doyle FJ III, Doyle J (2004) Robustness of cellular functions. Cell 118:675–685
70. Sterelny K (2007) Dawkins vs. Gould, survival of the fittest. Icon Books Ltd., Cambridge
71. Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15:221–231
72. Velazquez JL (2009) Finding simplicity in complexity: general principles of biological and nonbiological organization. J Biol Phys 35:209–221
73. von Bertalanffy L (1969) General systems theory. Foundations, development, applications. George Braziller, New York
74. Wiener N (1948) Cybernetics: or control and communication in the animal and the machine. MIT Press, Paris
75. Wilkins JF, Godfrey-Smith P (2009) Adaptationism and the adaptive landscape. Biol Philos 24:199–214
76. Winther RG (2009) Schaffner’s model of theory reduction: critique and reconstruction. Philos Sci 76:119–142
77. Wolkenhauer O, Hofmeyr J (2007) An abstract cell model that describes the self-organization of cell function in living systems. J Theor Biol 246:461–476
78. Wolkenhauer O, Shibata DK, Mesarović M (2011) A stem cell niche dominance theorem. Syst Biol 5:1–16
79. Wolkenhauer O, Shibata D, Mesarović M (2012) The role of theorem proving in systems biology. J Theor Biol 7:57–61
80. Wouters A (2007) Design explanation: determining the constraints on what can be alive. Erkenntnis 67:65–80
81. Yi TM, Huang Y, Simon MI, Doyle J (2000) Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 97:4649–4653