So what do we really mean when we say that systems biology is holistic?

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Gatherer, Derek ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; CLASSIFICATION; NOMENCLATURE; PHILOSOPHY; REVIEW; SYSTEMS BIOLOGY;

MODELS, BIOLOGICAL; PHILOSOPHY; SYSTEMS BIOLOGY; TERMINOLOGY AS TOPIC;

EID: 77949479491     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-22     Document Type: Article

References (105)

1. Aggarwal K, Lee KH. Functional genomics and proteomics as a foundation for systems biology. Briefings in functional genomics & proteomics 2003, 2:175-184.
2. Cornish-Bowden A, Cardenas ML, Letelier JC, Soto-Andrade J, Abarzua FG. Understanding the parts in terms of the whole. Biol Cell 2004, 96:713-717. 10.1016/j.biolcel.2004.06.006, 15567526.
3. Mesarovic MD, Sreenath SN, Keene JD. Search for organising principles: understanding in systems biology. Syst Biol (Stevenage) 2004, 1:19-27. 10.1049/sb:20045010, 17052112.
4. Van Regenmortel MHV. Reductionism and complexity inmolecular biology. EMBO Reports 2004, 5:1016-1020. 10.1038/sj.embor.7400284, 1299179, 15520799.
5. Aderem A. Systems biology: its practice and challenges. Cell 2005, 121:511-513. 10.1016/j.cell.2005.04.020, 15907465.
6. Bork P, Serrano L. Towards cellular systems in 4D. Cell 2005, 121:507-509. 10.1016/j.cell.2005.05.001, 15907464.
7. Cornish-Bowden A, Cardenas ML. Systems biology may work when we learn to understand the parts in terms of the whole. Biochem Soc Trans 2005, 33:516-519. 10.1042/BST0330516, 15916554.
8. Friboulet A, Thomas D. Systems Biology-an interdisciplinary approach. Biosensors & bioelectronics 2005, 20:2404-2407.
9. Latterich M. Molecular systems biology at the crossroads: to know less about more, or to know more about less?. Proteome Sci 2005, 3:8. 10.1186/1477-5956-3-8, 1283152, 16248894.
10. O'Malley MA, Dupre J. Fundamental issues in systems biology. Bioessays 2005, 27:1270-1276. 10.1002/bies.20323, 16299766.
11. Sorger PK. A reductionist's systems biology. Current Opinion in Cell Biology 2005, 17:9-11. 10.1016/j.ceb.2004.12.012, 15661513.
12. Strange K. The end of "naive reductionism": rise of systems biology or renaissance of physiology?. Am J Physiol Cell Physiol 2005, 288:C968-974. 10.1152/ajpcell.00598.2004, 15840560.
13. Strippoli P, Canaider S, Noferini F, D'Addabbo P, Vitale L, Facchin F, Lenzi L, Casadei R, Carinci P, Zannotti M, et al. Uncertainty principle of genetic information in a living cell. Theor Biol Med Model 2005, 2:40. 10.1186/1742-4682-2-40, 1262781, 16197549.
14. Sweetlove LJ, Fernie AR. Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. The New phytologist 2005, 168:9-24. 10.1111/j.1469-8137.2005.01513.x, 16159317.
15. Verpoorte R, Choi YH, Kim HK. Ethnopharmacology and systems biology: a perfect holistic match. J Ethnopharmacol 2005, 100:53-56. 10.1016/j.jep.2005.05.033, 16026949.
16. Wang M, Lamers RJ, Korthout HA, van Nesselrooij JH, Witkamp RF, Heijden R, Voshol PJ, Havekes LM, Verpoorte R, Greef J. Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology. Phytother Res 2005, 19:173-182. 10.1002/ptr.1624, 15934013.
17. Ahn AC, Tewari M, Poon C-S, Phillips RS. The limits of reductionism in medicine: could systems biology offer an alternative?. PLoS Medicine 2006, 3:e208. 10.1371/journal.pmed.0030208, 1459480,1459480, 16681415.
18. Cornish-Bowden A. Putting the systems back into systems biology. Perspect Biol Med 2006, 49:475-489. 10.1353/pbm.2006.0053, 17146133.
19. Jordan BA, Ziff EB. Getting to synaptic complexes through systems biology. Genome Biol 2006, 7:214. 10.1186/gb-2006-7-4-214, 1558000, 16677427.
20. Palsson BO. Systems Biology. Properties of Reconstructed Networks 2006, Cambrdige: Cambrdige University Press.
21. Trewavas A. A brief history of systems biology. "Every object that biology studies is a system of systems." Francois Jacob (1974). The Plant cell 2006, 18:2420-2430. 10.1105/tpc.106.042267, 1626627, 17088606.
22. Alfieri R, Merelli I, Mosca E, Milanesi L. A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Syst Biol 2007, 1:35. 10.1186/1752-0509-1-35, 1995223, 17678529.
23. Conti F, Valerio MC, Zbilut JP, Giuliani A. Will systems biology offer new holistic paradigms to life sciences?. Systems and synthetic biology 2007, 1:161-165. 10.1007/s11693-008-9016-1, 2553325, 19003440.
24. Robertson SH, Smith CK, Langhans AL, McLinden SE, Oberhardt MA, Jakab KR, Dzamba B, DeSimone DW, Papin JA, Peirce SM. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. BMC Syst Biol 2007, 1:46. 10.1186/1752-0509-1-46, 2190763, 17953751.
25. Rose MR, Oakley TH. The new biology: beyond the Modern Synthesis. Biology direct 2007, 2:30. 10.1186/1745-6150-2-30, 2222615, 18036242.
26. Bennett M, Monk N. The flowering of systems approaches in plant and crop biology. The New phytologist 2008, 179:567-568. 10.1111/j.1469-8137.2008.02565.x, 18715319.
27. Calvert J. The commodification of emergence: systems biology, synthetic biology and intellectual property. BioSocieties 2008, 3:383-398.
28. Cascante M, Marin S. Metabolomics and fluxomics approaches. Essays in biochemistry 2008, 45:67-81. 10.1042/BSE0450067, 18793124.
29. Long TA, Brady SM, Benfey PN. Systems approaches to identifying gene regulatory networks in plants. Annu Rev Cell Dev Biol 2008, 24:81-103. 10.1146/annurev.cellbio.24.110707.175408, 2739012, 18616425.
30. Hood L, Rowen L, Galas DJ, Aitchison JD. Systems biology at the Institute for Systems Biology. Brief Funct Genomic Proteomic 2008, 7:239-248. 10.1093/bfgp/eln027, 18579616.
31. Marcum JA. Does systems biology represent a Kuhnian paradigm shift?. The New phytologist 2008, 179:587-589. 10.1111/j.1469-8137.2008.02486.x, 18482229.
32. Morange M. The death of molecular biology?. History and philosophy of the life sciences 2008, 30:31-42.
33. Noble D. Claude Bernard, the first systems biologist, and the future of physiology. Exp Physiol 2008, 93:16-26. 10.1113/expphysiol.2007.038695, 17951329.
34. Syriopoulos C, Panayotarou A, Lai K, Klapa MI. Transcriptomic analysis of Saccharomyces cerevisiae physiology in the context of galactose assimilation perturbations. Molecular bioSystems 2008, 4:937-949. 10.1039/b718732g, 18704232.
35. Bylesjo M, Nilsson R, Srivastava V, Gronlund A, Johansson AI, Jansson S, Karlsson J, Moritz T, Wingsle G, Trygg J. Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen. Journal of proteome research 2009, 8:199-210. 10.1021/pr800298s, 19053836.
36. Butterfield H. The Origins of Modern Science 1300-1800 new edition edn 1957, London: G.Bell and Sons.
37. Canguilhem G. A Vital Rationalist. Selected Writings from Georges Canguilhem 1994, New York: Zone Books.
38. Grene M. Animal mechanism and the Cartesian vision of nature. Physics, Philosophy and the Scientific Community Essays in the philosophy and history of the natural sciences and mathematics In honor of Robert S Cohen 1995, 189-204. Dordrecht: Kluwer Academic Publishers, Gavroglu K, Stachel J, Wartofsky MW.
39. Bergson H. Creative Evolution 1910 (L'Evolution créatrice 1907) 1983, University Press of America.
40. Driesch H. The History and Theory of Vitalism. 1914, London: Macmillan.
41. Nagel E. The structure of science: problems in the logic of scientific explanation. 1961, London: Routledge & K. Paul.
42. Loeb J. The Mechanistic Conception of Life. 1912, Chicago: University of Chicago Press.
43. Collective Evolution in the Light of Modern Knowledge. 1925, London: Blackie and Son, Collective.
44. Lloyd Morgan C. Emergent Evolution. 1923, London: Williams and Norgate.
45. Koestler A. The Case of the Midwife Toad. 1971, London: Hutchinson.
46. Smuts JC. Holism and Evolution. 1926, London: Macmillan and Co..
47. Gruber JW. A Conscience in Conflict. The Life of St. George Jackson Mivart. 1960, New York: Temple University Publications by Columbia University Press.
48. Elsasser WM. Reflections on a Theory of Organisms. Holism in Biology. 1998, Baltimore: The Johns Hopkins University Press.
49. Lewontin RC, Rose S, Kamin LJ. Not in Our Genes. 1984, New York: Pantheon Books.
50. Monod J. Chance and Necessity: an Essay on the Natural Philosophy of Modern Biology. 1971, New York: Knopf.
51. Nagel T. Reductionism and antireductionism. The Limits of Reductionism in Biology Novartis Foundation Symposium 213 1998, 3-14. Chichester.: John Wiley and Sons, Bock GR, Goode JA.
52. Carnap R. The Unity of Science. 1995, Bristol: Thoemmes Press.
53. Medawar P. Pluto's Republic. 1982, Oxford: Oxford University Press.
54. Medawar PB. Advice to a Young Scientist. 1979, NewYork: Harper & Row.
55. Brandon R, Rosenberg A. Philosophy of biology. Philosophy of Science Today 2003, 147-180. Oxford: Clarendon Press, Clark P, Hawley K.
56. Crick F. Of Molecules and Men. 1966, Seattle: University of Washington Press.
57. Dawkins R. The God Delusion. 2007, London: Black Swan.
58. Ackermann R. Mechanism, methodology, and biological theory. Synthese 1969, 20:219-229.
59. Roll-Hansen N. On the reduction of biology to physical science. Synthese 1969, 20:277-289.
60. Nagel E. The meaning of reductionism in the natural sciences. Philosophy of Science 1960, 288-312. Cleveland: Meridian, Danto A, Morgenbesser S.
61. Polanyi M. Life's irreducible structure: Live mechanisms and information in DNA are boundary conditions with a sequence of boundaries above them. Science 1968, 160:1308-1312. 10.1126/science.160.3834.1308, 5651890.
62. Strohman RC. Genetic determinism as a failing paradigm in biology and medicine: implications for health and wellness. Journal of Social Work Education 2003, 39.
63. Drack M, Apfalter W. Is Paul Weiss' and Ludwig von Bertalannfy's System Thinking still valid today?. 50th Annual Meeting of the International Society for the Systems Sciences 2006,
64. Waddington CH. The basic ideas of biology. Towards a Theoretical Biology 1 Prolegomena 1968, 1:167-173. Edinburgh: Edinburgh University Press, Waddington C.
65. Waddington CH. The Evolution of an Evolutionist. 1975, Edinburgh: Edinburgh University Press.
66. MacKay DM. Man as mechanism. The Open Mind and Other Essays 1965, 45-53. Leicester: Inter-Varsity Press, Tinker DMMM.
67. Laszlo E. Introduction to Systems Philosophy. Toward a New Paradigm of Contemporary Thought 1972, New York: Gordon and Breach.
68. Gatherer D. Finite universe of discourse. The systems biology of Walter Elsasser (1904-1991). The Open Biology Journal 2008, 1:9-20.
69. Gatherer D. Less is more: the battle of Moore's Law against Bremermann's Limit on the field of systems biology. BMC Systems Biology 2007, 1(1 supp):53. 10.1186/1752-0509-1-S1-P53, 2233643, 18028551.
70. Kurzweil R. The Singularity is Near. When Humans Transcend Biology 2005, London: Viking/Penguin.
71. Moore G. Cramming more components onto integrated circuits. Electronics Magazine 1965,
72. Lloyd S. Ultimate physical limits to computation. Nature 2000, 406:1047-1054. 10.1038/35023282, 10984064.
73. Bremermann H. Minimum energy requirements of information transfer and computing. Int J Theor Phys 1982, 21:203-217.
74. Jedrzejas MJ, Huang WJM. Bacillus species proteins involved in spore formation and degradation: From identification in the genome, to sequence analysis, and determination of function and structure. Critical Reviews in Biochemistry and Molecular Biology 2003, 38:173-198. 10.1080/713609234, 12870714.
75. Laszlo E. The Systems View of the World. The Natural Philosophy of the New Developments in the Sciences 1972, Oxford: Basil Blackwood.
76. Elsasser WM. The role of individuality in biological theory. Towards a Theoretical Biology 3 Drafts 1970, 3:137-166. Edinburgh: Edinburgh University Press, Waddington C.
77. Elsasser WM. Acausal phenomena in physics and biology: a case for reconstruction. Am Sci 1969, 57:502-516.
78. Collier J. Supervenience and reduction in biological hierarchies. Philosophy and Biology Canadian Journal of Philosophy Supplementary 1988, 14:209-234. Calgary: The University of Calgary Press, Matthen M, Linsky B.
79. Elsasser WM. The Physical Foundations of Biology. An Analytical Study 1958, London: Pergamon Press.
80. Rubin H. Cell aging in vivo and in vitro. Mechanisms of Ageing and Development 1997, 98:1-35. 10.1016/S0047-6374(97)00067-5, 9255755.
81. Porsch H. Michael Polanyi: A Critical Exposition 1986, Albany: State University of New York Press.
82. Kuhn TS. The Structure of Scientific Revolutions. 1962, Chicago: Chicago University Press.
83. Bothwell JH. The long past of systems biology. The New phytologist 2006, 170:6-10. 10.1111/j.1469-8137.2006.01676.x, 16539598.
84. Schaffner KF. The Watson-Crick model and reductionism. Topics in the Philosophy of Biology 1976, 101-127. Dordrecht.: D. Reidel, Grene M, Mendelsohn E.
85. Hull DL. Philosophy of Biological Science. 1974, Englewood Cliffs, NJ: Prentice-Hall.
86. Kitcher P. 1953 and all that: a tale of two sciences. The Philosophical review 1984, 93:335-373. 10.2307/2184541, 11617920.
87. Dawkins R. Universal Darwinism. Evolution from Molecules to Men 1983, Cambridge: Cambridge University Press, Bendall D.
88. Davies P. The Cosmic Blueprint. 1987, London: Heinemann.
89. Henderson R. Macromolecular structure and self-assembly. The Limits of Reductionism in Biology Novartis Foundation Symposium 213 1998, 36-55. Chichester.: John Wiley and Sons, Bock GR, Goode JA.
90. Holmes KC. Muscle constraction. The Limits of Reductionism in Biology Novartis Foundation Symposium 213 1998, 76-105. Chichester.: John Wiley and Sons, Bock GR, Goode JA.
91. Ashmore J. Hearing. The Limits of Reductionism in Biology Novartis Foundation Symposium 213 1998, 133-141. Chichester.: John Wiley and Sons, Bock GR, Goode JA.
92. Quinn WG. Reductionism in learning and memory. The Limits of Reductionism in Biology Novartis Foundation Symposium 213 1998, 117-132. Chichester.: John Wiley and Sons, Bock GR, Goode JA.
93. Dennett DC. Darwin's Dangerous Idea: Evolution and the Meanings of Life. 1995, Simon & Schuster.
94. Edmonds B. Pragmatic holism (or pragmatic reductionism). Foundations of Science 1999, 4:57-82.
95. Longtin R. An integrated approach: systems biology seeks order in complexity. J Natl Cancer Inst 2005, 97:476-478.
96. Ye X, Chu J, Zhuang Y, Zhang S. Multi-scale methodology: a key to deciphering systems biology. Front Biosci 2005, 10:961-965. 10.2741/1590, 15569634.
97. Rosenberg A. Reductionism (and antireductionism) in biology. The Cambridge Companion to the Philosophy of Biology 2007, 120-138. Cambridge: Cambridge University Press, Hull DL, Ruse M.
98. Smart JJC. Philosophy and Scientific Realism. 1963, London: Routledge & Kegan Paul.
99. Gribbin J. In Search of Schrodinger's Cat. Quantum Physics and Reality. 1984, Toronto: Bantam Books.
100. Hon G. The Limits of Experimental Method. Experimenting on an entangled system: The case of biophysics. Science at Century's End Philosophical Questions on the Progress and Limits of Science 2000, Pittsburgh: University of Pittsburgh Press, Carrier M, Massey GJ, Ruetsche L.
101. Kim J. Making sense of emergence. Philosophical Studies 1999, 95:3-36.
102. Rosen R. Anticipatory Systems. Philosophical, Mathematical and Methodological Foundations 1979, Rosen Enterprises.
103. Rosen R. Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. 1991, New York: Columbia University Press.
104. Elsasser WM. Quanta and the concept of organismic law. J Theor Biol 1961, 1:27-58. 10.1016/0022-5193(61)90025-X, 13726551.
105. Lakatos I, Musgrave A, . (eds) Criticism and the Growth of Knowledge. 1970, London: Cambridge University Press, (eds).