Complex system biology
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Complex systems biology (CSB) is a branch or subfield of mathematical and theoretical biology concerned with complexity of both structure and function in biological organisms, as well as the emergence and evolution of organisms and species, with emphasis being placed on the complex interactions of, and within, bionetworks[1], and on the fundamental relations and relational patterns that are essential to life[2][3][4][5][6]. CSB is thus a field of theoretical sciences aimed at discovering and modeling the relational patterns essential to life that has only a partial overlap with complex systems theory, and also with the systems approach to biology called systems biology; this is because the latter is restricted primarily to simplified models of biological organization and organisms, as well as to only a general consideration of philosophical or semantic questions related to complexity in biology[7]. Moreover, a wide range of abstract theoretical complex systems are studied as a field of applied mathematics, with or without relevance to biology, chemistry or physics.
Contents |
Topics in complex systems biology
The following is only a partial list of topics covered in complex systems biology:
- Evolution theories and population genetics
- Population genetics models
- Molecular evolution theories
- Quantum biocomputation
- Quantum genetics[8]
- Relational biology[9][10][11][12]
- Self-reproduction[13] (also called self-replication in a more general context)
- Computational gene models
- Evolutionary developmental biology
- Autopoiesis
- Protein folding
- Telomerase conformations and functions in vivo
- Epigenetics
- Interactomics[14][15]
- Cell signaling
- Signal transduction networks
- Complex neural nets
- Genetic networks
- Morphogenesis
- Digital morphogenesis
- Complex adaptive systems
- Topological models of morphogenesis
- Population dynamics of fisheries
- Epidemiology
Related journals
- Acta Biotheoretica
- Bioinformatics
- Biological Theory
- BioSystems
- Bulletin of Mathematical Biology
- Ecological Modelling
- Journal of Mathematical Biology
- Journal of Theoretical Biology
- Mathematical Biosciences
- Medical Hypotheses
- Theoretical and Applied Genetics
- Theoretical Biology and Medical Modelling
- Theoretical Population Biology
- Theory in Biosciences (formerly: Biologisches Zentralblatt)
CBS societies and institutes
- Society for Mathematical Biology
- ESMTB: European Society for Mathematical and Theoretical Biology
- Division of Mathematical Biology at NIMR
- The Israeli Society for Theoretical and Mathematical Biology
- Société Francophone de Biologie Théorique
- International Society for Biosemiotic Studies
See also
Biographies
References cited
- J.D. Murray, Mathematical Biology. Springer-Verlag, 3rd ed. in 2 vols.: Mathematical Biology: I. An Introduction, 2002 ISBN 0-387-95223-3; Mathematical Biology: II. Spatial Models and Biomedical Applications, 2003 ISBN 0-387-95228-4.
- Thompson, D'Arcy W., 1992. On Growth and Form. Dover reprint of 1942, 2nd ed. (1st ed., 1917). ISBN 0-486-67135-6
- Nicolas Rashevsky. (1938)., Mathematical Biophysics. Chicago: University of Chicago Press.
- Robert Rosen.1970. Dynamical system theory in biology. New York, Wiley-Interscience. ISBN 0-471-73550-7
- Israel, G., 2005, "Book on mathematical biology" in Grattan-Guinness, I., ed., Landmark Writings in Western Mathematics. Elsevier: 936-44.
- Israel G (1988). "On the contribution of Volterra and Lotka to the development of modern biomathematics". History and Philosophy of the Life Sciences 10 (1): 37–49. PMID 3045853.
- Scudo FM (March 1971). "Vito Volterra and theoretical ecology". Theoretical Population Biology 2 (1): 1–23. doi:10.1016/0040-5809(71)90002-5. PMID 4950157.
- S.H. Strogatz, Nonlinear dynamics and Chaos: Applications to Physics, Biology, Chemistry, and Engineering. Perseus, 2001, ISBN 0-7382-0453-6
- N.G. van Kampen, Stochastic Processes in Physics and Chemistry, North Holland., 3rd ed. 2001, ISBN 0-444-89349-0
- I. C. Baianu., Computer Models and Automata Theory in Biology and Medicine., Monograph, Ch.11 in M. Witten (Editor), Mathematical Models in Medicine, vol. 7., Vol. 7: 1513-1577 (1987),Pergamon Press:New York, (updated by Hsiao Chen Lin in 2004 ISBN 0-08-036377-6
- P.G. Drazin, Nonlinear systems. C.U.P., 1992. ISBN 0-521-40668-4
- L. Edelstein-Keshet, Mathematical Models in Biology. SIAM, 2004. ISBN 0-07-554950-6
- G. Forgacs and S. A. Newman, Biological Physics of the Developing Embryo. C.U.P., 2005. ISBN 0-521-78337-2
- E. Renshaw, Modelling biological populations in space and time. C.U.P., 1991. ISBN 0-521-44855-7
- Rosen, Robert.1991, Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life, Columbia University Press, published posthumously:
- Rosen, Robert. 2000, Essays on Life Itself, Columbia University Press.
- Rosen, Robert. 2003, "Anticipatory Systems; Philosophical, Mathematical, and Methodolical Foundations", Rosen Enterprises publs.
- S.I. Rubinow, Introduction to mathematical biology. John Wiley, 1975. ISBN 0-471-74446-8
- L.A. Segel, Modeling dynamic phenomena in molecular and cellular biology. C.U.P., 1984. ISBN 0-521-27477-X.
- D.W. Jordan and P. Smith, Nonlinear ordinary differential equations, 2nd ed. O.U.P., 1987. ISBN 0-19-856562-3
- L. Preziosi, Cancer Modelling and Simulation. Chapman Hall/CRC Press, 2003. ISBN 1-58488-361-8.
- Graeme Donald Snooks, "A general theory of complex living systems: Exploring the demand side of dynamics", Complexity, vol. 13, no. 6, July/August 2008.
- Tsekeris, Charalambos. "Advances in Understanding Human Complex Systems", Australian Journal of Basic and Applied Sciences, vol. 3, no. 4, October/December 2009.
- Bonner, J. T. 1988. The Evolution of Complexity by Means of Natural Selection. Princeton: Princeton University Press.
Further reading
- A general list of Theoretical biology/Mathematical biology references, including an updated list of actively contributing authors.
- A list of references for applications of category theory in relational biology.
- An updated list of publications of theoretical biologist Robert Rosen
- Theory of Biological Anthropology (Documents No. 9 and 10 in English)
- Drawing the Line Between Theoretical and Basic Biology (a forum article by Isidro T. Savillo)
- Semantic Systems Biology
- Synthesis and Analysis of a Biological System, by Hiroyuki Kurata, 1999.
Notes
- ^ Sprites, P; Glymour, C; Scheines, R (2000). Causation, Prediction, and Search: Adaptive Computation and Machine Learning (2nd ed.). MIT Press.
- ^ Graeme Donald Snooks, "A general theory of complex living systems: Exploring the demand side of dynamics", Complexity, vol. 13, no. 6, July/August 2008.
- ^ Bonner, J. T. 1988. The Evolution of Complexity by Means of Natural Selection. Princeton: Princeton University Press.
- ^ Rosen, R.: 1958a, "A Relational Theory of Biological Systems". Bulletin of Mathematical Biophysics 20: 245-260
- ^ Baianu, I. C.: 2006, "Robert Rosen's Work and Complex Systems Biology", Axiomathes 16(1-2):25-34
- ^ Rosen, R.: 1958b, "The Representation of Biological Systems from the Standpoint of the Theory of Categories.", Bulletin of Mathematical Biophysics 20: 317-341.
- ^ http://www.semantic-systems-biology.org/ Semantic Systems Biology Portal
- ^ Rosen, R. 1960. "A quantum-theoretic approach to genetic problems.", Bulletin of Mathematical Biophysics, 22: 227-255
- ^ Rosen, R.: 1958a, "A Relational Theory of Biological Systems". Bulletin of Mathematical Biophysics 20: 245-260.
- ^ Baianu, I. C.: 2006, "Robert Rosen's Work and Complex Systems Biology", Axiomathes 16(1-2):25-34
- ^ Rosen, R.: 1958b, "The Representation of Biological Systems from the Standpoint of the Theory of Categories.", Bulletin of Mathematical Biophysics 20: 317--341.
- ^ http://planetmath.org/?op=getobj&from=objects&id=10921
- ^ "PlanetMath". PlanetMath. http://planetmath.org/?method=l2h&from=objects&name=NaturalTransformationsOfOrganismicStructures&op=getobj. Retrieved 2010-03-17.
- ^ Faith, JJ et al. (2007). "Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles". PLoS Biology 5 (1): 54–66. doi:10.1371/journal.pbio.0050008. PMID 17214507.
- ^ Hayete, B; Gardner, TS; Collins, JJ (2007). "Size matters: network inference tackles the genome scale". Molecular Systems Biology 3: 77. doi:10.1038/msb4100118. PMID 17299414.
- ^ "abstract relational biology (ARB)". PlanetPhysics. http://planetphysics.org/encyclopedia/AbstractRelationalBiologyARB.html. Retrieved 2010-03-17.
- ^ "Molecular Evolution and Protobiology | KLI Theory Lab". Theorylab.org. 2009-05-26. http://theorylab.org/node/52354. Retrieved 2010-03-17.
- ^ Faith, JJ et al. (2007). "Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles". PLoS Biology 5 (1): 54–66. doi:10.1371/journal.pbio.0050008. PMID 17214507.
- ^ Hayete, B; Gardner, TS; Collins, JJ (2007). "Size matters: network inference tackles the genome scale". Molecular Systems Biology 3: 77. doi:10.1038/msb4100118. PMID 17299414.
External links
- Center for Complex Systems and Brain Sciences at Florida Atlantic
- Santa Fe Institute
- Bulletin of Mathematical Biology
- European Society for Mathematical and Theoretical Biology
- Journal of Mathematical Biology
- Biomathematics Research Centre at University of Canterbury
- Centre for Mathematical Biology at Oxford University
- Mathematical Biology at the National Institute for Medical Research
- Institute for Medical BioMathematics
- Mathematical Biology Systems of Differential Equations from EqWorld: The World of Mathematical Equations
- Systems Biology Workbench - a set of tools for modelling biochemical networks
- The Collection of Biostatistics Research Archive
- Statistical Applications in Genetics and Molecular Biology
- The International Journal of Biostatistics
- Theoretical Modeling of Cellular Physiology at Ecole Normale Superieure, Paris
- Theoretical and mathematical biology website
- Complexity Discussion Group
- UCLA Biocybernetics Laboratory
- TUCS Computational Biomodelling Laboratory
- Nagoya University Division of Biomodeling
- Technische Universiteit Biomodeling and Informatics
- New England Complex Systems Institute
- Northwestern Institute on Complex Systems (NICO)
- Complexity Digest
- Centro de Ciencias de la Complejidad, UNAM
- Complexity Complex at the University of Warwick
- Southampton Institute for Complex Systems Simulation
- Center for the Study of Complex Systems at the University of Michigan
- ARC Centre for Complex Systems, Australia
- (European) Complex Systems Society
- (Australian) Complex systems research network.
- Complex Systems Modeling based on Luis M. Rocha, 1999.
- CRM Complex systems research group
