Systemic Darwinism

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 33, 2008, Pages 11833-11838

  Winther, Rasmus Grønfeldt ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Biological theory; Ecology; Evolution; Genetics; Systems theory

Indexed keywords

ARTICLE; CONCEPTUAL FRAMEWORK; CONVERGENT EVOLUTION; EVOLUTION; GENOMICS; HUMAN; NATURAL SELECTION; PRIORITY JOURNAL; SYSTEMS BIOLOGY; SYSTEMS THEORY;

ANIMALS; EVOLUTION; HUMANS; MODELS, GENETIC; SELECTION (GENETICS);

EID: 50149119652     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0711445105     Document Type: Article

References (93)

1. Darwin CR (1859/2001) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (Harvard Univ Press, Cambridge, MA).
2. Kitano H (2002) Looking beyond the details: A rise in system-oriented approaches in genetics and molecular biology. Curr Genet 41:1-10.
3. O'Malley MA, Dupré J (2005) Fundamental issues in systems biology. BioEssays 27:1270-1276.
4. Kauffman SA (1993) The Origins of Order. Self-Organization and Selection in Evolution (Oxford Univ Press, London, UK).
5. Solé R, Goodwin B (2000) Signs of Life: How Complexity Pervades Biology (Basic Books, New York).
6. Davidson E (2006) The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic, New York).
7. Forgacs G, Newman SA (2005) Biological Physics of the Developing Embryo (Cambridge Univ Press, Cambridge, UK).
8. Hennig W (1950/1966) Phylogenetic Systematics, trans Davis DD, Zangerl R (Univ of Illinois Press, Urbana, IL).
9. Hull D (1988) Science as a Process. An Evolutionary Account of the Social and Conceptual Development of Science (Univ of Chicago Press, Chicago, IL).
10. Rieppel O (1988) Fundamentals of Comparative Biology (Birkhauser AG, Basel, Switzerland).
11. Fisher RA (1930/1958) The Genetical Theory of Natural Selection (Dover Publications, Inc., New York).
12. Wright S (1986) Evolution: Selected Papers, ed Provine W (Univ of Chicago Press, Chicago).
13. Provine WB (2001) The Origins of Theoretical Population Genetics (Univ of Chicago Press, Chicago, IL), 2nd Ed.
14. Feynman R (1965) The Character of Physical Law (MIT Press, Cambridge, MA).
15. Barrow J (2007) New Theories of Everything (Oxford Univ Press, London, UK).
16. Popper K (1963) Conjectures and Refutations: The Growth of Scientific Knowledge (Routledge, London, UK).
17. Cartwright N (1983) How the Laws of Physics Lie (Oxford Univ Press, London, UK).
18. Wimsatt WC (2007) Re-Engineering Philosophy for Limited Beings: Piecewise Approximations to Reality (Harvard Univ Press, Cambridge, MA).
19. Hull D (1975) Central subjects and historical narratives. Hist Theory 14:253-274.
20. Richards R (1992) The structure of narrative explanation in history and biology. History and Evolution, eds Nitecki MH, Nitecki DV (SUNY Press, Albany, NY), pp 19-53.
21. Abell P (2004) Narrative explanation: An alternative to variable-centered explanation? Annu Rev Sociol 30:287-310.
22. Grant T, Kluge AG (2004) Transformation series as an ideographic character concept. Cladistics 20:23-31.
23. Beatty J (2002) The historicity of nature? Everything that is might have been different? The Philosophy of Marjorie Grene. The Library of Living Philosophers, eds Auxier RE, Hahn LE (Open Court, LaSalle, IL), pp 397-411.
24. Margulis L (2000) Symbiotic Planet. A New Look at Evolution (Basic Books, New York).
25. Camazine S, et al. (2003) Self-Organization in Biological Systems (Princeton Univ Press, Princeton, NJ).
26. Wake DB (1996) Evolutionary developmental biology - prospects for an evolutionary synthesis at the developmental level. New Perspectives on the History of Life: Essays on Systematic Biology as Historical Narrative, eds Ghiselin M, Pinna G (California Academy of Sciences, San Francisco, CA), No. 20, pp 97-107.
27. Shubin N (2008) Your Inner Fish: A Journey into the 3.5 Billion Year History of the Human Body (Pantheon, New York).
28. Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205:581-598.
29. Godfrey-Smith P (2001) Three kinds of adaptationism. Adaptationism and Optimality, eds Orzack SH, Sober E (Cambridge Univ Press, Cambridge, UK), pp 335-357.
30. Lewontin RC (1970) The units of selection. Annu Rev Ecol Syst 1:1-18.
31. Darwin CR (1871/1981) Introduction by JT Bonner and RM May. The Descent of Man and Selection in Relation to Sex (Princeton Univ Press, Princeton, NJ). 2 Vols.
32. Dawkins R (2006) The Selfish Gene (Oxford Univ Press, London, UK), 3rd Ed.
33. Coyne JA, Barton NH, Turelli M (1997) Perspective: A critique of Sewall Wright's shifting balance theory of evolution. Evolution 51:643-671.
34. Wade MJ, Goodnight CJ (1998) The theories of Fisher and Wright in the context of metapopulations. When nature does many small experiments. Evolution 52:1537-1553.
35. Sober E, Wilson DS (1988) Unto Others. The Evolution and Psychology of Unselfish Behavior (Harvard Univ Press, Cambridge, MA).
36. Okasha S (2007) Evolution and the Levels of Selection (Oxford Univ Press, London, UK).
37. Wade MJ (1985) Soft selection, hard selection, kin selection, and group selection. Am Nat 125:61-73.
38. Lehmann L, Keller L, West S, Roze D (2007) Group selection and kin selection: Two concepts but one process. Proc Natl Acad Sci USA 1041:6736-6739.
39. Eldredge N, Gould, SJ (1972) Punctuated equilibria: An alternative to phyletic gradualism. Models in Paleobiology, ed Schopf TJM (Freeman, Cooper & Co., San Francisco, CA), pp 82-115.
40. Stanley SM (1975) A theory of evolution above the species level. Proc Natl Acad Sci USA 72:646-650.
41. Eldredge N (1985) Unfinished Synthesis. Biological Hierarchies and Modern Evolutionary Thought (Oxford Univ Press, London, UK).
42. Gould SJ (2002) The Structure of Evolutionary Theory (Harvard Univ Press, Cambridge, MA).
43. Darwin CR (1975) Charles Darwin's Natural Selection. Being the Second Part of His Big Species Book Written from 1856 to 1858, ed Stauffer RC (Cambridge Univ Press, Cambridge, UK).
44. Jackson JBC, Buss LW, Cook RE (1985) Population Biology and Evolution of Clonal Organisms (Yale Univ Press, New Haven, CT).
45. Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution (W. H. Freeman & Co., London).
46. Michod RE (1999) Darwinian Dynamics. Evolutionary Transitions in Fitness and Individuality (Princeton Univ Press, Princeton, NJ).
47. Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Microbiol 14:303-310.
48. Moran NA (2007) Symbiosis as an adaptive process and source of phenotypic complexity. Proc Natl Acad Sci USA 104(Suppl 1):S8627-S8633.
49. Wolf JB, Brodie EB, III, Wade MJ, eds (2000) Epistasis and the Evolutionary Process. (Oxford Univ Press, London, UK).
50. Dewey J (1981) The influence of Darwinism on philosophy (1910). The Philosophy of John Dewey, ed McDermott JJ (University of Chicago Press, Chicago, IL), pp 31-41.
51. Mayr E (1959) Darwin and the evolutionary theory in biology. Evolution and Anthropology: A Centennial Appraisal, ed Meggers J (Anthropological Society of Washington, Washington, DC), pp 1-10.
52. Darwin CR (1868) The Variation of Animals and Plants Under Domestication (Orange Judd & Co., New York), 2 Vols, 1st Ed.
53. Brusca RC, Brusca GJ (2003) Invertebrates (Sinauer, Sunderland, MA), 2nd Ed.
54. Webster G, Goodwin B (1996) Form and Transformation. Generative and Relational Principles in Biology (Cambridge Univ Press, Cambridge, UK).
55. Goodwin B, Kauffman S, Murray JD (1993) Is morphogenesis an intrinsically robust process? J Theor Biol 163:135-144.
56. Gould SJ (1989) A developmental constraint in Cerion, with comments on the definition and interpretation of constraint in evolution. Evolution 43:516-539.
57. Amundson R (2005) The Changing Role of the Embryo in Evolutionary Thought. Structure and Synthesis (Cambridge Univ Press, Cambridge, UK).
58. Rieppel O (2005) Modules, kinds, and homology. J Exp Zoolog B Mol Dev Evol 304:18-27.
59. Winther RG (2001) Varieties of modules: Kinds, levels, origins and behaviors. J Exp Zoolog B Mol Dev Evol 291:116-129.
60. Brigandt I, Griffiths PE (2007) The importance of homology for biology and philosophy. (Editors' introduction to the special issue). Biology and Philosophy 22:633-641.
61. Levesque MP, Benfey PN (2004) Systems biology. Curr Biol 14:R179-R180.
62. Kirschner MW (2005) The meaning of systems biology. Cell 121:503-504.
63. Sorger PK (2005) A reductionist's systems biology. Curr Opin Cell Biol 17:9-11.
64. Kriete A, Eils R (2005) Computational Systems Biology (Academic, New York).
65. Boogerd FC, Bruggeman FJ, Hofmeyr JHS, Westerhoff HV, eds (2007) Systems Biology. Philosophical Foundations. (Elsevier BV, Amsterdam).
66. Herrmann H, Wagner GP (2006) Conceptual continuity as a mode of understanding complex systems. Complexity 11:20-24.
67. Danos JF, Fontana W, Harmer R, Krivine J (2008) Rule-based modelling, symmetries, refinements. Formal Modelling Systems Biology (FMSB 2008), number 5054 in Lecture Notes in Bioinformatics (Springer, New York), pp 103-122.
68. Szallasi Z, Stelling J, Periwal V (2006) System Modeling in Cell Biology. From Concepts to Nuts and Bolts (MIT Press, Cambridge, MA).
69. Winther RG (2008) Schaffner's model of theory reduction: Critique and reconstruction. Philos Sci, in press.
70. Regev A, Shapiro E (2002) Cells as computation. Nature 419:343.
71. Mesarovic MD, Sreenath SN, Keene JD (2004) Search for organising principles: Understanding in systems biology. Syst Biol 1:19-27.
72. Rashevsky N (1954) Topology and life. In search of general mathematical principles in biology and sociology. Bull Math Biophys 16:317-348.
73. Rosen R (1964) Abstract biological systems as sequential machines. Bull Math Biophys 26:103-111.
74. Rosen R, ed (1985) Organisms as causal systems which are not mechanisms: An essay into the nature of complexity. Theoretical Biology and Complexity (Academic, San Diego, CA), pp 165-203.
75. Von Bertalanffy L (1968) General System Theory. Foundations, Development, Applications. (George Braziller, Inc., New York).
76. Mesarovic MD, ed (1968) Systems Theory and Biology (Springer, Berlin).
77. Emery FE, ed (1969) Systems Thinking. (Penguin Education, Harmondsworth, London).
78. Wolkenhauer O (2001) Systems biology: The reincarnation of systems theory applied in biology? Brief Bioinform 2:258-270.
79. Eldredge N (2003) The sloshing bucket: how the physical realm controls evolution. Evolutionary Dynamics. Exploring the Interplay of Selection, Accident, Neutrality, and Function. SFI Studies in the Sciences of Complexity Series, eds Crutchfield J, Schuster P (Oxford Univ Press, London, UK), pp 3-32.
80. Eldredge N (1993) History, function, and evolutionary biology. Evolutionary Biology, eds Hecht MK, MacIntyre RJ, Clegg MT (Plenum, New York), Vol 27, pp 33-50.
81. Brooks DR, Wiley EO (1988) Evolution as Entropy. Toward a Unified Theory of Biology.(University of Chicago Press, Chicago, IL), 2nd Ed.
82. Levins R, Lewontin R (1985). The Dialectical Biologist (Harvard Univ Press, Cambridge, MA).
83. Oyama S (2000) The Ontogeny of Information. Developmental Systems and Evolution. (Duke Univ Press, Durham, NC), 2nd Ed.
84. Jablonka E, Lamb MJ (2006) Evolution in Four Dimensions. Genetic, Epigenetic, Behavioral and Symbolic Variation in the History of Life (MIT Press, Cambridge, MA).
85. Casati R, Varzi A (1999) Parts and Places. The Structures of Spatial Representation (MIT Press, Cambridge, MA).
86. Simons, P (2000) Parts. A Study in Ontology (Oxford Univ Press, London, UK).
87. Lewontin, R (1974) The Genetic Basis of Evolutionary Change. (Columbia Univ Press, New York).
88. Levins R (1966) The strategy of model building in population biology. Am Sci 54:421-431.
89. Levins R (2006) Strategies of abstraction. Biology and Philosophy 21:741-755.
90. Winther RG (2006) Fisherian and Wrightian perspectives in evolutionary genetics and model-mediated imposition of theoretical assumptions. J Theor Biol 240:218-232.
91. Brooks DR (2001) Evolution in the information age: Rediscovering the nature of the organism. Semiosis, Evolution, Energy, Development 1:1-26.
92. May R, McLean A (2007) Theoretical Ecology: Principles and Applications (Oxford Univ Press, London, UK).
93. Raup DM, Jablonski D, eds (1986) Patterns and Processes in the History of Life. (Springer, Berlin).