Survey
Selection, tinkering, and emergence in complex networks
Ricard V. Solé,
Ramon Ferrer-Cancho,
Jose M. Montoya,
Sergi Valverde,
Ricard V. Solé
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Sante Fe Institute, Santa Fe, NM 87501
Search for more papers by this authorRamon Ferrer-Cancho
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Search for more papers by this authorJose M. Montoya
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Department of Ecology, University of Alcalá, Madrid, Spain
Search for more papers by this authorSergi Valverde
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Search for more papers by this author
Ricard V. Solé,
Ramon Ferrer-Cancho,
Jose M. Montoya,
Sergi Valverde,
Ricard V. Solé
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Sante Fe Institute, Santa Fe, NM 87501
Search for more papers by this authorRamon Ferrer-Cancho
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Search for more papers by this authorJose M. Montoya
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Department of Ecology, University of Alcalá, Madrid, Spain
Search for more papers by this authorSergi Valverde
ICREA-Complex Systems Lab, GRIB-UPF, Barcelona, Spain
Search for more papers by this author
REFERENCES
- 1 Standage, T. The Victorian Internet; Walker and Co.: New York, 1998.
- 2 Inose, H. Communication networks. Sci Am 1972, 3, 117–128.
- 3 Kauffman, S.A. Origins of Order; Oxford: New York, 1993.
- 4 Monod, J. Le hasard et la nécessité, Editions du Seuil: Paris, 1970.
- 5 Jacob, F. Evolution as tinkering. Science 1977, 196, 1161–1166.
- 6 Gould, S.J. Wonderful Life; Penguin: London, 1989.
- 7 Conway, M.S. The Crucible of Creation. Oxford University Press: New York, 1998.
- 8 Gould, S.J. The Structure of Evolutionary Theory; Belknap Press: Cambridge, MA, 2002.
10.2307/j.ctvjsf433 Google Scholar
- 9 Brown, J.H.; West, G.B. Scaling in Biology. Oxford University Press: New York, 2000.
10.1093/oso/9780195131413.001.0001 Google Scholar
- 10 Alberch, P. Developmental constraints in evolutionary processes. In: Evolution and Development, J.T. Bonner, ed. (Berlin, Springer-Verlag) 1982, p 313–332.
10.1007/978-3-642-45532-2_15 Google Scholar
- 11 Goodwin, B.C. How the Leopard Changed Its Spots: the Evolution of Complexity. Charles Scribner's Sons: New York, 1994.
- 12 Bollobás, B. Random Graphs. Academic Press: London, 1985.
- 13 Newman, M.E.J. Random Graphs as Models of Networks. Santa Fe Institute Working Paper 02-02-005, 2002.
- 14 May, R.M. Stability and Complexity in Model Ecosystems; Princeton University Press: Princeton, 1976.
- 15 Cohen, J.E. Food webs and niche space. Monographs in Population Biology 11, Princeton University Press, 1978.
- 16 Kauffman, S.A. Metabolic stability and epigenesis in randomly connected nets. J Theor Biol 1962, 22, 437–467.
- 17 Hertz, J.; Krogh, A.; Palmer, R.G. Introduction to the Theory of Neural Computation. Addison-Wesley: Reading, 1991.
10.1063/1.2810360 Google Scholar
- 18 Sompolinsky, H.; Crisanti, A.; Sommers, H.J. Chaos in random neural networks. Phys Rev Lett 1988, 61, 259–262.
- 19 Watts, D.J.; Strogatz, S.H. Collective Dynamics in ‘small-world’ networks. Nature (Lond.) 1998, 393, 440–442.
- 20 Newman, M.E.J. Models of the small world. J Stat Phys 2000, 101, 819–841.
- 21 Dorogovtsev, S.N.; Mendes, J.F.F. Evolution of Random Networks. Adv Phys 2002, 51, 1079–1187.
- 22 Amaral, L.A.N.; Scala, A.; Barthélemy, M.; Stanley, H.E. Classes of behavior of small-world networks. Proc Nat Acad Sc USA 2000, 97, 11149–11152.
- 23 Albert, R.; Jeong, H.; Barabási, A.-L. Error and attack tolerance of complex networks. Nature 2000, 406, 542.
- 24 Albert, R.; Jeong, H.; Barabási, A.-L. Correction: Error and attack tolerance of complex networks. Nature 2000, 409, 378–382.
- 25 Albert, R.; Barabási, A.-L. Statistical mechanics of complex networks. Rev Mod Phys 2001, 74, 47–97.
- 26 Jeong, H.; Mason, S.; Barabási, A.L.; Oltvai, Z.N. Lethality and centrality in protein networks. Nature 2001, 411, 41.
- 27 Jeong, H.; Tombor, B.; Albert, R.; Oltvai, Z.N.; Barabasi, A.-L. The large-scale organization of metabolic networks. Nature 2000, 407, 651–654.
- 28 Solé, R.V.; Montoya, J.M. Complexity and fragility in ecological networks. Proc Roy Soc Lond Ser B 2001, 268, 2039–2045.
- 29 Dunne, J.A.; Williams, R.J.; Martinez, N.D. Food-web structure and network theory: The role of connectance and size. Proc Natl Acad Sci USA 2002, 99, 12917–12922.
- 30 Jordano, P.; Bascompte, J.; Olesen, J.N. Invariant properties in coevolutionary networks of plant-animal interactions. Ecology Lett 2002 (in press).
- 31 Ferrer-Cancho, R.; Janssen, C.; Solé, R.V. The topology of technology graphs: small world pattern in electronic circuits. Phys Rev E 2001, 64, 32767.
- 32 Caldarelli, G.; Marchetti, R.; Pietronero, L. The Fractal Properties of Internet. Europhys Lett 2000, 52, 386–390.
- 33 Newman, M.E.J. The structure of scientific collaboration networks. Proc Natl Acad Sci USA 2001, 98, 404–409.
- 34 Ferrer-Cancho, R.; Solé, R.V. The small world of human language. Procs Roy Soc London B 2001a, 268, 2261–2266.
- 35 Wagner, A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. J Molec Evol 2001, 18, 1283–1292.
- 36 Edelman, G.M.; Gally, J.A. Degeneracy and complexity in biology systems. Proc Natl Acad Sci USA 2001, 98, 13763–13768.
- 37 Tononi, G.; Sporns, O.; Edelman, G.M. Measures of degeneracy and redundancy in biological networks. Proc Natl Acad Sci USA 1999, 96, 3257–3262.
- 38 Hartwell, L.H.; Hopfield, J.J.; Leibler, S.; Murray, A.W. From molecular to modular cell biology. Nature 1999, 42 supp, c47–252.
- 39 von Dassow, G.; Meir, E.; Munro, E.M.; Odell, G.M. Nature 2000, 406, 188–194.
- 40 Solé, R.V.; Salazar, I.; Newman, S.A. Gene network dynamics and the evolution of development. Trends Ecol Evol 2000, 15, 479–480.
- 41 Solé, R.V.; Salazar, I.; Garcia-Fernandez, J. Common Pattern Formation, Modularity and Phase Transitions in a Gene Network Model of Morphogenesis. Physica A 2002a, 305, 640–647.
- 42 Wagner, G. Adaptation and the modular design of organisms. In: Advances in Artificial Life, F. Moran, J.J. Merelo and P. Chacou, Eds. Springer-Verlag: Berlin, 1995.
10.1007/3-540-59496-5_308 Google Scholar
- 43 Lodish, H.; Berk, A.; Zipursky, S.L.; Matsudaira, P. Molecular Cell Biology ( 4th edition). W. H. Freeman: New York, 2000.
- 44 Bray, D. Protein molecules as computational elements in living cells. Nature 1995, 376, 307–312.
- 45 Wagner, A. Mutational robustness in genetic networks of yeast. Nature Genetics 2000, 24, 355–361.
- 46 Maslov, S.; Sneppen, K. Specificity and stability in topology of protein networks. Science 2002, 296, 910–913.
- 47 Kohn, K.W. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell 1999, 10, 2703–2734.
- 48 Vogelstein, B.; Lane, D.; Levine, A.J. Surfing the p53 network. Nature 2000, 408, 307–310.
- 49 Ohono, S. Evolution by gene duplication. Springer: Berlin, 1970.
- 50 Solé, R.V.; Pastor-Satorras, R.; Smith, E.; Kepler, T. A model of large-scale proteome evolution. Adv Complex Syst 2002b, 5, 43–54.
10.1142/S021952590200047X Google Scholar
- 51 Vázquez, A.; Flammini, A.; Maritan, A.; Vespignani, A. Modelling of protein interaction networks. cond-mat/0108043, 2001.
- 52 Pastor-Satorras, R.; Smith, E.; Solé, R.V. Evolving protein interaction networks through gene duplication. J Theor Biol, in press, 2002.
- 53 Wagner, A.; Fell, D.A. The small world inside large metabolic networks. Proc Roy Soc London B 2001, 268, 1803–1810.
- 54 Podani, J.; Oltvai, Z.N.; Jeong, H.; Tombor, B.; Barabási, A.-L.; Szathmáry, E. Comparable system-level organization of Archaca and Eukaryotes. Nature Genetics 2001, 29, 54–55.
- 55 Israel, L. Tumor progression: random mutations or and integrated survival response to cellular stress conserved from unicellular organisms? J Theor Biol 1996, 178, 375–380.
- 56 Jin, A.; Martinek, S.; Joo, W.S.; et al. Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc Natl Acad Sci USA 2000, 97, 7301–7306.
- 57 Brown, J.H. Complex ecological systems. In: Complexity: Metaphors, Models and Reality ( G.A. Cowan, D. Pincs, D. Meltzer, Eds.; Addison-Wesley: Reading, MA, 1994, p 419–443.
- 58 Pimm, S.L. The balance of nature? Chicago University Press: Chicago, 1991.
- 59 Abrams, P.; Menge, B.A.; Mittelbach, G.C.; Spiller, D.; Yodzis, P. The role of indirect effects in food webs. In: Food webs: integration of patterns and dynamics ( G.A. Polis and K.O. Winemiller, Eds.); Chapman & Hall: New York, 1996, pp 371–395.
10.1007/978-1-4615-7007-3_36 Google Scholar
- 60 Williams, R.J.; Martinez, N.D.; Berlow, E.L.; Dunne, J.A.; Barabási, A.-L. Two degrees of separation in complex food webs. Proc Natl Acad Sci USA 2001, 99, 12913–12916.
- 61 Montoya, J.M.; Solé, R.V. Small world patterns in food webs. J Theor Biol 2002, 214, 405–412.
- 62 McCann, K.S. The diversity-stability debate. Nature 2000, 405, 228–233.
- 63 Camacho, J.; Guimerá, R.; Amaral, L.A.N. Robust patterns in food web structure. Phys Rev Lett 2002, 88, 228102.
- 64 Montoya, J.M.; Solé, R.V. Topological properties of food webs: from real data to assembly models. Santa Fe Institute Working Paper 01-11-069, 2001.
- 65 Montoya, J.M.; Solé, R.V.; Pimm, S.L. Unpublished.
- 66 Rutledge, R.; Basore, B.; Mulholland, R. Ecological stability: an information theory viewpoint. J Theo Biol 1976, 57, 355–371.
- 67 Walker, B.H. Biodiversity and ecological redundancy. Conservation Biology 1992, 6, 18–23.
- 68 Naeem, S. Species redundancy and ecosystem reliability. Conservation Biology 1998, 12, 39–45.
- 69 Fonseca, C.R.; Ganade, G. Species functional redundancy, random extinctions and the stability of ecosystems. J An Ecol 2001, 89, 118–125.
- 70 Borvall, C.; Ebenman, B.; Jonson, T. Biodiversity lessens the risk of cascading extinctions. Eco Let 2000, 3, 131–136.
- 71 Ulanowicz, R.E. Growth and Development: ecosystems phenomenology. Springer: New York, 1986.
10.1007/978-1-4612-4916-0 Google Scholar
- 72 Ernest, S.K.M.; Brown, J.H. Homeostasis and compensation: the role of resources in ecosystem stability. Ecology 2001, 82, 2118–2132.
- 73 Brown, J.H.; Heske, E.J. Control of a desert-grassland transition by a keystone rodent guild. Science 1990, 250, 1705–1707.
- 74 Maynard-Smith, J.; Szäthmáry, E. The major transitions in evolution. Oxford University Press, 1997.
10.1093/oso/9780198502944.001.0001 Google Scholar
- 75 Deacon, T.W. The symbolic species: the coevolution of language and the brain. W. W. Norton & Co.: New York, 1997.
- 76 Sigman & Cechi. Global organization of the Word-Net lexicon. Proc Natl Acad Sci USA 2002, 99, 1742–1747.
- 77 Steyvers, M.; Tenenbaum, J.B. The large-scale structure of semantic networks: statistical analyses and a model of semantic growth. Submitted to Cognitive Science. http://www-psych.stanford.edu/∼jbt/, 2002.
- 78 Traugot, E.C.; Heine, B. Approaches to grammaticalization. Volume I. John Benjamins Publishing Company: Amsterdam/Philadelphia, 1991.
- 79 Hopper, P.J. On some principles of grammaticization. In Approaches to grammaticalization ( E.C. Traugot & B. Heine, Eds.). Volume I. John Benjamins Publishing Company: Amsterdam/Philadelphia, 1991.
10.1075/tsl.19.1.04hop Google Scholar
- 80 Prün, C. G. K. Zipf's conception of language as an early prototype of synergetic linguistics. Journal of Quantitative Linguistics, 1999, 6, 78–84.
10.1076/jqul.6.1.78.4147 Google Scholar
- 81 Zipf, G.K. Human Behavior and the Principle of Least Effort. An Introduction to Human Ecology. New York: Hafner reprint, 1972. [ 1st edition: Cambridge, MA: Addison-Wesley, 1949].
- 82 Miller and Gildea. How children learn words. Scient Am 1987, 257, 94–99.
- 83 Ferrer-Cancho, R.; Solé, R.V. Optimization in complex networks. cond-mat/0111222, 2001b.
- 84 Caplan, D. Language. Structure, Processing and Disorders. MIT Press, 1994.
- 85 Pastor-Satorras, R.; Vespignani, A. Epidemic spreading in scale-free networks. Phys Rev Lett 2001, 86, 3200–3203.
- 86 Nelson, M.E.; Bower, J.M. Brain maps and parallel computers. Trends Neurosci 1990, 13, 403–408.
- 87 Kauffman, S.A. At Home in the Universe, Oxford University Press: New York, 1995.
- 88 Mathias, N.; Gopal, V. Small Worlds: How and Why. Phys Rev E 2001, 63, 21117.
- 89 Perry, D.E.; Wolf, A.L. Foundations for the Study of Software Architecture. ACM SIGSOFT Software Engineering Notes, 1992, 17, 4.
10.1145/141874.141884 Google Scholar
- 90 Valverde, S.; Ferrer-Cancho, R.; Solé, R.V. Scale-Free Networks from Optimal Design. Europhys Lett in press, 2002.
- 91 Pressman, R.S. Software Engineering: A Practitioner's Approach. McGraw-Hill, 1992.
- 92 Zuse, H. A Framework for Software Measurement, Walter de Gruyter: Berlin, New York, 1998.
10.1515/9783110807301 Google Scholar
- 93 Gamma, E.; Helm, R.; Johnson, R.; Vlissides, J. Design Patterns, Addison-Wesley: Reading, MA, 1994.
- 94 Brown, W.H.; et al. Anti-Patterns: Refactoring Software, Architectures, and Projects in Crisis. John Wiley & Sons: New York, 1998.
- 95 Barabási, L.-A.; Albert, R. Emergence of scaling in random networks. Science 1999, 286, 509–512.
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