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en Book Futuyma, Douglas J. Science / Biology / Evolution 5 +"Adaptive phenotype plasticity in response to ecological conditions", see p39 [f:Genotype G x Environment E ->Phenotype P, f(G,E)->P] +"The intensity of competition between two species can be modified by the presence of a third competitor" (p34) 2005-05-01 de Book Riedl, Rupert Science / Epistemology 5 2005-02-01 de Book Russell, Bertrand philosophy 4 English title: A History of Western Philosophy 2004-10-01 de Book Rifkin, Jeremy Sociology / Future economy 4 English title: The end of work 2004-10-01 en Book Keller, Laurent, editor Science / Biology / Evolution 4 2005-05-01 de Book Riedl, Rupert Sociology / Future economy 5 Evolutionary theory (/epistemology) applied to our societies and states. 2005-05-01 de Book Rojas, Roul Science / Computer Science / Neural Nets 3 Very systematic, basic introduction to standard methods. 2002-01 @book{RojasNN, author = {Rojas, Raul}, publisher = {Springer}, series = {Springer--Lehrbuch}, title = {Theorie der neuronalen Netze: Eine systematische Einführung}, year = {1993} } en Book Haykin, Simon Science / Computer Science / Neural Nets 4 Very formal mathematical but good introduction to standard methods. 2002-01 de Book Eckhardt, Bruno Science / Dynamical Systems 2 Much too compact! 2005-02-01 de Book Riedl, Rupert and Wuketits, Franz M. editors Science / Epistemology 3 Evolutionary epistomlogy from a very philosophic point of view... 2005-04-01 en Book Bäck, T. and Fogel, D. B. and Michalewicz, T. Science / Biology / Evolution 3 Good introduction to the basics, little boring at times. 2004-01 de Book Lorenz, Konrad Science / Biology 4 2003-01 de Book Hesse, Hermann Literature / Fiction 4 2004-01 en Book Tomasello, M. and Call, J. Science / Biology 3 What can we learn from ape behaviour experiments about consciousness? Are apes a model for humans - are they conscious at our level at all? Not finally answered here but a good overview. 2004-10-01 en Book Krebs, J.R. and Davies, N.B. Science / Biology 5 Excellent overview; good maths, good evidence. 2005-03-01 en Book Trappe, W. and Washington, L.C. Science / Computer Science 3 2003-09-01 en Book Kumar, S. and Bentley, P.J. editors Science / Dynamical Systems 3 2003-12-01 en Book Langton, C.G. editor Science / Dynamical Systems 4 All the pioneers from the 1988 workshop. 2003-01 en Book Langton, C.G. et. al. editors Science / Dynamical Systems 4 2003-01 de Book Schlee, Walter Science / Mathematics 2005-02-01 en Book Langdon, W.B. and Poli, R. science / computer science / evolutionary algorithms 3 2003-01 de Book Beltrami, E. Science / Dynamical Systems 4 Mathematical models in biology and sociology. 2003-01 de Book Gerhardt, M. and Schuster, H. Science / Dynamical Systems 3 Cellular automata 2003-01 de Book Deutsch, A. editor Science / Dynamical Systems 3 Patterns and self organization 2003-01 de Book Waldrop, M.M. Science / Dynamical Systems 3 The historical development of systems science 2003-01 de Book Schindewolf, D. Science / Biology 4 Maybe the topic is more sociology/psychology; the development of perception and behaviour of humans from a very general viewpoint. 2004-08-01 en Book Mayr, Ernst Science / Biology / Evolution 4 Excellent historical overview and introduction. Of course only basics. 2005-01-01 en article Stanley, Kenneth O. et. al. Science / Artificial Evolution / Artificial Embryogeny 5 Good *historical* overview (list most older works), term Artificial Embryogeny introduced, show functional similarities between L-systems/grammar and cell chemistry approaches, propose benchmarks taxonomy: 5 major dimensions of development (names very cell chemistry biased): -cell fate (differentiation mechanism) -targeting (where to interact; fixed / relative) -heterochrony (timing and order of events, e.g. centrol toe of horses developed so fast that other 4 toes became irrelevant) -canalization (slight gene changes do seldomly cause related or connected components to fail in nature) [proposed mechanisms: stochastic events during development to increase stability; flexible resource allocation among developing parts and overproduction of cells (should have apoptosis then), see p.114] -complexification (new genes, e.g. by duplication) [variable length genotypes -> speciation; sexual matching -> historical marking (global gene numbering)] [gene duplicate results must be carefully integrated (not too much disturbance)] 2005-06-13-01 @article{860915, author = {Kenneth O. Stanley and Risto Miikkulainen}, title = {A Taxonomy for artificial embryogeny}, journal = {Artif. Life}, volume = {9}, number = {2}, year = {2003}, issn = {1064-5462}, pages = {93--130}, doi = {http://dx.doi.org/10.1162/106454603322221487}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, } en article Calabretta, Raffaele et. al. Science / Artificial Evolution 3 important clue: There is less computational power, i.e., number of neurons and connections, in the non-modular than in the modular architectures (see p.5) Results support model by Hughes1994: Functional specialization facilitated when genes serving multiple functions are duplicated - after duplication genes are released from conflicting demands and each copy can specialize on one function of the ancestral gene (only one specialization factor, though) copies must not interfere too much initially for that to work, no? 2005-06-16-01 @article{DBLP:journals/alife/CalabrettaNPW00, author = {Raffaele Calabretta and Stefano Nolfi and Domenico Parisi and G{ü}nter P. Wagner}, title = {Duplication of Modules Facilitates the Evolution of Functional Specialization.}, journal = {Artificial Life}, volume = {6}, number = {1}, year = {2000}, pages = {69-84}, bibsource = {DBLP, http://dblp.uni-trier.de}, ee = {http://cogprints.org/1296/00/calabretta.duplication.pdf} } en inproceedings Dawkins, Richard Science / Artificial Evolution / Artificial Embryogeny 4 poor implementation (but consider the time...); good theoretical ideas: +there must be embryology of some kind (however simple) +one-to-one genotype-phenotype mapping bad, as no [little] architectorial bias (/restrictions) toward *good* phenotypes and thus waiting till "kingdom-come" +recursivity: is a must and similar to natural processes (first segmented animal was probably not very successful but had high evolutionary potential as can be seen from its descendants) +"tendency to speciate" (~evolutionary potential) might be a higher level evo property, as species speciate not individuals 2005-06-16-01 @inproceedings{DBLP:conf/alife/Dawkins87, author = {Richard Dawkins}, title = {The Evolution of Evolvability.}, booktitle = {ALIFE}, year = {1987}, pages = {201-220}, crossref = {DBLP:conf/alife/1987}, bibsource = {DBLP, http://dblp.uni-trier.de} } de Book Hesse, Hermann literature / bildungsroman 4 Life is to short to take it seriously. Only minor differences to the Siddhartha philosophy. 2005-06-01 de Book Hesse, Hermann literature / bildungsroman 4 Pleading for more imperturbability. Thoughts, feelings and insights can not always be worded and communicated without loss (but maybe it works indirectly, by describing "the path"). 2005-06-01 en article Wagner, Gunter P. et. al. Science / Artificial Evolution / Artificial Embryogeny 5 +representation problem: "evolvability critically depends on the way genetic variation maps onto phenotypic variation" +Evidence that phenotypic variation is under genetic control: canalization; mutant phenotypes often show more variation than the wild phenotype (see p.7) "the variability of the traits itself can evolve" +cites Halder1995: Drosophila eyeless - out-of-place eye production can be triggered by a single signal +"genotype-phenotype map underlying theme of: genetic canalization, developmental constraints, biological versatility, developmental dissociability, morphological integration" and more +genotype-phenotype map evolves, main selective forces: epistatic mutations, creation of new genes +"Variability needs to be distinguished from variation" (variability: potential to vary [*dispositional* concept, not actual state but expected development of a phenotypic trait in response to genetic and environmental influences] - variation: actually realized differences between individuals) +cites Levinton1988: generation of variability needs to be studied +Evolution of complex adaptations requires a match between the functional relationships of the phenotypic characters and their genetic representation - cites Riedl1975: "If the epigenetic regulation of gene expression 'imitates' the functional organization of the traits then the improvement by mutation and selection is facilitated" (helps when sexual recombination, p.11) +cites Wright1968 "Pleiotropy cannot be wholly universal" - how limit: modularity, interaction mainly short range, less frequent between members of different complexes +evolution of modularity: origin of differentiated animals dominated by parcellation / detachment (opposed to integration of distinct parts) but where shall we put delimitations??? 2005-06-18-01 @article{wagner-altenberg-evolution-of-evolvability, abstract = {: The problem of complex adaptations is studied in two largely disconnected research traditions: evolutionary biology and evolutionary computer science. This paper summarizes the results from both areas and compares their implications. In evolutionary computer science it was found that the Darwinian process of mutation, recombination and selection is not universally effective in improving complex systems like computer programs or chip designs. For adaptation to occur, these systems must possess ...}, author = {Wagner, Gunter P. and Altenberg, Lee }, citeulike-article-id = {126862}, journal = {Evolution}, keywords = {change evolvability in representation}, priority = {2}, title = {Complex Adaptations and the Evolution of Evolvability}, url = {http://citeseer.ist.psu.edu/148444.html}, year = {1996} } en Book Howard, D.J. and Berlocher, S. H. ed. Science / Biology / Evolution 2005-06-01 @book{howard98, author = {Howard, Daniel J. and Berlocher, Stewart H. }, month = {October}, publisher = {{Oxford University Press}}, title = {Endless Forms: Species and Speciation}, year = {1998} } de Book Tipler, Paul A. Science / Physics 2005-06-01 de Book Kierkegaard, Sören Literature / Fiction 4 Much easier to read than his pure philosophical works. 2003-01-01 de Book Heisenberg, Werner Literature / Biography 2004-01-01 de Book Russell, B. science / popular science 4 2001-01-01 de Book Rousseau, J. J. Sociology / Politics 3 considering the time it was written: good ideas 2003-01-01 de Book Huch, Ricarda Sociology / Politics 3 2003-01-01 de Book Orwell, G. Literature / Fiction / Utopia 5 1999-01-01 en Book Huxley, Aldous Literature / Fiction / Utopia 4 2000-01-01 de Book Montherlant, Henry de Literature / Fiction 4 2004-01-01 de Book Orwell, G. Literature / Biography 5 2003-01-01 en Book Bäck, T and Fogel, D B and Michalewicz, Z ed. Science / Artificial Evolution 2004-01-01 en Book Paulson, L. C. Science / Computer Science 4 Excellent introduction to functional programming if you already know some basics. 2003-01-01 de Book Stuhlmann-Laeisz, Rainer Philosophy / Logic 3 2002-01-01 de Book Dörner, Dietrich Science / Artificial Intelligence 2 2003-01-01 en Book Reichgelt, Han Science / Artificial Intelligence 3 2003-01-01 en Book Locke, J Sociology / Politics 4 2003-01-01 de Book Chomsky, Noam Science / Linguistics 4 more epistemology than linguistics 2000-01-01 de Book Chomsky, Noam Science / Linguistics 3 2001-01-01 de Book Chomsky, Noam Science / Linguistics 3 2001-01-01 de Book Habermas, Jürgen Philosophy 3 2001-01-01 de Book Chomsky, Noam Science / Linguistics 3 2001-01-01 de Book Piaget, Jean Science / Epistemology 4 2002-01-01 en Book Weiss, G. ed. Science / Artificial Intelligence 4 good overview 2004-01-01 de Book Nüsslein-Volhard, Christiane science / biology / morphogenesis 3 to little depth, popular science 2004-01-01 de Book Diekmann, A. and Moser, R. ed. Science / Biology / Evolution 3 2003-01-01 en Book Trappenberg, T. P. Science / Computer Science / Neural Nets 3 probably later editions will be better readable 2003-01-01 de Book Erben, Heinrich K. Science / Biology / Evolution 5 Rules of evolution from the Paleontologists point of view. 2004-01-01 en Book Baba, N. and Jain, L. ed. Science / Artificial Intelligence 3 2003-01-01 en article Beer, Randall D. Science / Artificial Life 3 Nice tribute to Maturanas and Varelas idea of defining a system as alive when it keeps up its structure and has some boundary which seperates it from the environment. Applying these principles to a very simplicistic artificial system (which is destroyed by virtually any perturbation from the environment and has a 100 percent permeable boundary) is not too helpful. The problems of the concept remain. 2005-06-20 @article{1029273, author = {Randall D. Beer}, title = {Autopoiesis and cognition in the game of life}, journal = {Artif. Life}, volume = {10}, number = {3}, year = {2004}, issn = {1064-5462}, pages = {309--326}, doi = {http://dx.doi.org/10.1162/1064546041255539}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, } de Book Leonhard, Wolfgang Literature / Biography 4 One gets a feeling for the hope many had put into communism and the disappointment when those ideals do not fit human nature and Stalinism causes trouble. 2005-05-01 en Book Burgess, Anthony Literature / Fiction 4 2000-01-01 en Book Orwell, George Literature / Fiction 5 2001-01-01 en book Dawkins, R. Science / Biology / Evolution 5 excellent writing style 2005-06-23 @book{Dawkins83, author = {Dawkins, R.}, title = {The extended phenotype: {T}he gene as a unit of selection}, publisher = {Oxford University Press}, address = {Oxford}, year = 1983, annote = {Extension of the ideas presented in ``The Selfish Gene''.}} de Book Riedl, Rupert Science / Biology / Evolution 2005-06-24 en article Stanley, Kenneth O. et. al. 4 uses direct coding, since, cite: "Although CE [Gruau s (1993) Cellular Encoding (CE)] demonstrates that it is possible to evolve developmental systems, we chose direct encoding for NEAT because, as Braun andWeisbrod (1993) argue, indirect encoding requires more detailed knowledge of genetic and neural mechanisms. In other words, because indirect encodings do not map directly to their phenotypes, they can bias the search in unpredictable ways. To make good use of indirect encodings, we need to first understand them well enough to make sure that they do not focus the search on some suboptimal class of topologies. Further, experimental results suggest that CE is not necessarily more efficient than direct encoding methods (Section 4.3.3)." describes "historical marking" to allow for save crossover (but needs global counter) - ligning up genes with equal number; genes which are only present in one parent are either ignored (less fit) or completely used (more fit parent) "explicit fitness sharing" of similar genotypes to facilitate speciation (each on a different "peak") mutation always adds (though genes might become disabled); either synapse or neuron (split connection) pole-balancing as benchmark, despite of huge similarities to ENS^3 no reference to Pasemann results (but source code available!) 2005-06-28 @article{638554, author = {Kenneth O. Stanley and Risto Miikkulainen}, title = {Evolving neural networks through augmenting topologies}, journal = {Evol. Comput.}, volume = {10}, number = {2}, year = {2002}, issn = {1063-6560}, pages = {99--127}, doi = {http://dx.doi.org/10.1162/106365602320169811}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, } de Book Bischof, H.-J. Science / Biology 4 classical neuro ethology 2005-03-01 en Book Dawkins, Richard Science / Biology / Evolution 2005-06-01 de Book Cockburn, Andrew Science / Biology / Evolution 2005-06-01 de Book Strogatz, Steven Science / Dynamical Systems 2005-06-01 de Book Rauchfuss, Horst Science / Biology / Evolution 3 Switching between pure speculation and low level chemical formulas I missed explanations of the functionality of the interacting chemical complexes. "Oftmals erweist sich eine kurze, wissenschaftshistorische Rückschau als sinnvoll, um komplexe Sachverhalte einsichtiger zu gestalten" 2005-05-01 en inproceedings Nehaniv, Chrystopher L. Science / Artificial Life 5 2005-08-15 @inproceedings{NehanivAsynchronicity, author = {Chrystopher L. Nehaniv}, title = {Self-Replication, Evolvability and Asynchronicity in Stochastic Worlds.}, booktitle = {Proc. 3rd Intl. Symp. on Stochastic Algorithms, Foundations and Applicaitons (SAGA 2005)}, year = {2005} } en book West-Eberhard, M. J. science / biology / evo-devo 2005-08-19 @book{westeberhard, author = {West-Eberhard, Mary J. }, howpublished = {Paperback}, isbn = {0195122356}, keywords = {biology evolution}, month = {February}, publisher = {{Oxford University Press}}, title = {Developmental Plasticity and Evolution}, year = {2003} } en article Rocha, Luis M. et. al. Science / Artificial Life 4 try to bring together connectionist and symbolist approaches to cognition from the description of connectionist systems: -"Indeed, the emergent behavior of agents that are dynamically coherent with their environments (embodied agents) is as much a result of the production rules of the agent as of the laws of the environment [Beer ,1995] [Clark ,1996] [Rocha and Joslyn ,1998]." -Do current *intelligent* dynamical systems scale? "What needs to be stressed here is that evolutionary systems require both dynamic and [genetic] memory components for selection." 2005-08-22 @article{GeneticCode2EvolutionCellularAutomata, author = {Luis M. Rocha and Wim Hordijk}, title = {Material Representations: From the Genetic Code to the Evolution of Cellular Automata}, journal = {Artificial Life}, volume = {11}, number = {1-2}, year = {2005}, pages = {189--214}, url = {http://informatics.indiana.edu/rocha/caalife04.html} } de Book Gould, S. J. science / popular science English title: The Panda's Thumb: More Reflections in Natural History (1980) 2005-08-23 de Book Renn, Jrgen (Hrsg.) literature / biography Book accompanying the Max-Planck societie's 2005 exhibition. 2005-08-27 de Book Lesch, Harald et. al. Science / Popular Science 3 Physics and chemistry look at the origin of life in general and on earth in special. Interesting chapter on the functional role some molecules play for life. Leben: Ein sich selbst organisierendes Nichtgleichgewichtssystem, das zu identischer Reproduktion einschliesslich seines genetischen Codes befähigt ist. 2005-08-28 @book{leschPhysicOfLife, author = {Harald Lesch and Jörn Müller}, publisher = {Goldmann}, title = {Big Bang, zweiter Akt}, year = {2005} } de book Zeilinger, Anton Science / Popular Science 3 Good introduction to quantum physics; explanation by lots of experiments. Conects information and matter. Where does objective chance come into play? Particle and wave properties of light (observation of small molecules changes their behaviour). 2005-08-28 @book{zeilingerEinsteinsSchleier, author = {Anton Zeilinger}, publisher = {Goldmann}, title = {Einsteins Schleier}, year = {2003} } en book Sipper, Moshe Science / Popular Science 2 Artificial Life, but very much popular science; at most a first, very basic, overview. page 185: Nature has come up not only with ingenious solutions to specific problems - for example, structural designs such as eyes or wings - but indeed has found (and founded) entirely new processes to aid in the emergence of complex organisms. Two of the most important ones are ontogeny (the development of a multicellular organism from a single mother cell) and learning. 2005-09-01 @book{sipperMachineNature, author = {Moshe Sipper}, publisher = {McGraw-Hill}, title = {Machine Nature: The Coming Age of Bio-Inspired Computing}, year = {2002} } de book Einstein, Albert et. al. Science / Popular Science 3 2005-09-06 @book{einsteinEvoPhysics, author = {Albert Einstein and Leopold Infeld}, publisher = {Rowohlt}, title = {Die Evolution der Physik}, year = {1956} } de book Basieux, Pierre Science / Mathematics 2005-08-15 de book Schrödinger, Erwin Science / Physics 4 2005-09-07 @book{SchroedingerWhatIsLife, author = {Erwin Schrödinger}, publisher = {Piper}, title = {Was ist Leben}, year = {2004} } de Book Nietzsche, F. Philosophy 3 2001-01-01 de Book Wittgenstein, L. Philosophy 4 2001-01-01 de Book Varela, F. J. Philosophy 4 2001-01-01 de Book Johan Huizinga Philosophy 3 2001-01-01 de Book Frisch, M. Literature 3 2002-01-01 de Book Mann, T. Literature 4 2005-10-02 en book Davidson, Eric H. science / biology / evo-devo 4 hierarchisch: generelle Dinge wie anterior/posterior Ausrichtung zuerst, dann mehr und mehr Details "heart of pattern formation: regional specification" 2005-10-02 @book{davidsonGeneRegulatorySystems, author = {Eric H. Davidson}, publisher = {Academic Press}, title = {Genomic Regulatory Systems: Development and Evolution}, year = {2001} } de book Sigmund, K. Science / Artificial Life 5 A very broad and not too scientific overview, but excellent introductory reading. Gives an overview of ALife, Game Theory and more 2003-01-01 @book { author = {Sigmund, Karl}, edition = {1. Aufl.}, publisher = {Hoffmann und Campe}, title = {Spielpl{"a}ne}, year = {1995}, ISBN = {3-455-08579-2}, keywords = {Evolution,Abstammung ,Spieltheorie,Game theory}, language = {dt.} } en inproceedings Kumar, Sanjeev science / artificial life / genetic regulatory networks 4 2005-10-06 @inproceedings{kumar05developmental, author = {Sanjeev Kumar}, title = {A Developmental Genetics-Inspired Approach to Robot Control}, booktitle = {Proceedings of the Second Workshop On Self-Organization in Representations For Evolutionary Algorithms: Building complexity from simplicity, GECCO-2005}, publisher = {ACM Press}, year = {2005}, ee = {PDF,http://cs.gmu.edu/~eclab/papers/kumar05developmental.pdf} } en inproceedings Quick, Tom et. al. science / artificial life / genetic regulatory networks 4 very simplicistic, but first approach to use GRNs for Robot Control 2005-10-05 @inproceedings{DBLP:conf/ecal/QuickNDR03, author = {Tom Quick and Chrystopher L. Nehaniv and Kerstin Dautenhahn and Graham Roberts}, title = {Evolving Embodied Genetic Regulatory Network-Driven Control Systems.}, booktitle = {ECAL}, year = {2003}, pages = {266-277}, ee = {http://www.cs.ucl.ac.uk/staff/t.quick/papers/QuickT_2003_ECAL_GRNControl.pdf}, crossref = {DBLP:conf/ecal/2003} } en inproceedings Jong, Hidde de et. al. science / artificial life / genetic regulatory networks 3 2005-10-08 @inproceedings{DBLP:conf/hybrid/JongGHPSG03, author = {Hidde de Jong and Jean-Luc Gouz{'e} and C{'e}line Hernandez and Michel Page and Tewfik Sari and Johannes Geiselmann}, title = {Hybrid Modeling and Simulation of Genetic Regulatory Networks: A Qualitative Approach.}, booktitle = {HSCC}, year = {2003}, pages = {267-282}, ee = {http://link.springer.de/link/service/series/0558/bibs/2623/26230267.htm}, crossref = {DBLP:conf/hybrid/2003}, bibsource = {DBLP, http://dblp.uni-trier.de} } en article Jong, Hidde de 5 2005-10-08 @article{citeulike:402225, author = {Hidde de Jong}, doi = {http://dx.doi.org/10.1089/10665270252833208}, issn = {1066-5277}, journal = {J Comput Biol}, number = {1}, pages = {67--103}, title = {Modeling and simulation of genetic regulatory systems: a literature review.}, url = {http://dx.doi.org/10.1089/10665270252833208}, volume = {9}, year = {2002} } en inproceedings Schilstra, Maria J. et. al. Science / Biology / GRN 4 2005-10-12 @inproceedings{ author = {Maria J. Schilstra and Hamid Bolouri}, title = {The Logic of Gene Regulation}, year = {2002}, ee = {http://strc.herts.ac.uk/bio/maria/NetBuilder/Theory/GeneRegulationLogic.htm} publisher = {Abstract for the 3rd International Conference on Systems Biology, December 11-15, 2002, Karolinska Institutet, Stockholm, Sweden} } en report Schilstra, Maria J. et. al. Science / Biology / GRN 4 2005-10-13 @report{ author = {Maria J. Schilstra and Hamid Bolouri}, title = {Modelling the Regulation of Gene Expression in Genetic Regulatory Networks}, year = {2002}, ee = {http://strc.herts.ac.uk/bio/maria/NetBuilder/Theory/NetBuilderModelling.htm} publisher = {Technical Report} } en inproceedings Taylor, Tim science / artificial life / genetic regulatory networks 4 2005-10-13 @inproceedings{edinburghUnderwaterTaylorGRN, author = {Tim Taylor}, title = {A Genetic Regulatory Network-Inspired Real-Time Controller for a Group of Underwater Robots.}, booktitle = {Intelligent Autonomous Systems 8 (Proceedings of IAS8)}, editors = {F. Groen, N. Amato, A. Bonarini, E. Yoshida and B. Kröse}, year = {2004}, pages = {403-412}, ee = {http://www.inf.ed.ac.uk/publications/report/0184.html} } en Book Dostoevsky, F. Literature 4 2005-10-11 en inproceedings Bongard, Josh C. science / artificial life / genetic regulatory networks 3 2005-10-13 @inproceedings{Bongard:2002:EMGRN, author = {Josh C. Bongard}, title = {Evolving Modular Genetic Regulatory Networks}, booktitle = {Proceedings of the 2002 Congress on Evolutionary Computation CEC2002}, editor = {David B. Fogel and Mohamed A. El-Sharkawi and Xin Yao and Garry Greenwood and Hitoshi Iba and Paul Marrow and Mark Shackleton}, pages = {1872--1877}, year = {2002}, publisher = {IEEE Press}, publisher_address = {445 Hoes Lane, P.O. Box 1331, Piscataway, NJ 08855-1331, USA}, organisation = {IEEE Neural Network Council (NNC), Institution of Electrical Engineers (IEE), Evolutionary Programming Society (EPS)}, ISBN = {0-7803-7278-6}, notes = {CEC 2002 - A joint meeting of the IEEE, the Evolutionary Programming Society, and the IEE. Held in connection with the World Congress on Computational Intelligence (WCCI 2002)}, ee = {http://www.mae.cornell.edu/bongard/papers/BongardWCCI2002.pdf} } en inproceedings Bentley, Peter science / artificial life / genetic regulatory networks 3 for citing: "However, the recent work of Quick (2003) is highly relevant, describing the evolution of a simple GRN for control of a Khepera robot. Quick emphasises the need for GRNs to be embodied (linked or coupled) to their environments, with changes in environment causing changes in the GRN (Quick 2003). He successfully evolved light-finding behaviour, although there seem to be evolvability issues with his simple representation of genes and proteins." 2005-10-13 @inproceedings{bentleyFractalGRNs, booktitle = {Proceedings of Gecco 2004}, year = {2004}, title = {Adaptive Fractal Gene Regulatory Networks for Robot Control}, author = {Peter Bentley}, ee = {http://www.cs.bham.ac.uk/~wbl/biblio/gecco2004/WWOR001.pdf} } en inproceedings Banzhaf, Wolfgang Science / Artificial Life / Genetic Regulatory Networks 4 2005-10-18 @inproceedings{DBLP:conf/dagstuhl/Banzhaf03, author = {Wolfgang Banzhaf}, title = {On Evolutionary Design, Embodiment, and Artificial Regulatory Networks.}, booktitle = {Embodied Artificial Intelligence}, year = {2003}, pages = {284-292}, ee = {http://www.cs.mun.ca/~banzhaf/papers/embodied.pdf}, crossref = {DBLP:conf/adhoc-now/2003}, bibsource = {DBLP, http://dblp.uni-trier.de} } en Book Cervantes, M. de Literature 2005-10-22 en inproceedings Banzhaf, Wolfgang Science / Artificial Life / Genetic Regulatory Networks 4 2005-10-24 @inproceedings{DBLP:conf/ecal/Banzhaf03, author = {Wolfgang Banzhaf}, title = {On the Dynamics of an Artificial Regulatory Network.}, booktitle = {ECAL}, year = {2003}, pages = {217-227}, ee = {http://www.cs.mun.ca/~banzhaf/papers/ecal2003_final.pdf}, crossref = {DBLP:conf/ecal/2003}, bibsource = {DBLP, http://dblp.uni-trier.de} } en inproceedings Reil, Torsten Science / Artificial Life / Genetic Regulatory Networks 3 2005-10-26 @inproceedings{DBLP:conf/ecal/Reil99, author = {Torsten Reil}, title = {Dynamics of Gene Expression in an Artificial Genome - Implications for Biological and Artificial Ontogeny.}, booktitle = {ECAL}, year = {1999}, pages = {457-466}, crossref = {DBLP:conf/ecal/1999}, bibsource = {DBLP, http://dblp.uni-trier.de} } en book Kauffman, Stuart A. Science / Dynamical Systems 4 2005-10-30 @book{kauffman93, author = {Stuart A. Kauffman}, year = {1993}, title = {The origins of Order: Self-Organization and Selection in Evolution}, publisher = {Oxford University Press}, location = {New York} } en Article Vohradsky, Jiri Science / Biology / GRN 3 2005-10-31 @Article{NNGRNModel, author = {Jiri Vohradsky}, title = {Neural network model of gene expression}, journal = {The FASEB Journal}, year = {2001}, volume = {15}, pages = {846--854}, ee = {http://www.fasebj.org/cgi/reprint/15/3/846} } en Article Sales, J. A. de et. al. Science / Artificial Life / Genetic Regulatory Networks 3 2005-11-08 @Article{SalesCAGeneNetworks, author = {J. A. de Sales and M. L. Martins and D. A. Stariolo}, title = {Cellular automata model for gene networks}, journal = {Phyical Review E}, year = {1997}, volume = {55}, pages = {3262--3270}, ee = {http://prola.aps.org/pdf/PRE/v55/i3/p3262_1} } en Book Nehaniv, Chrystopher L., ed. Science / Artificial Life / Biological basis 4 2005-11-11 @Book{nehanivEd, editor = {Chrystopher L. Nehaniv}, title = {Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity and Digital Evolution}, publisher = {American Mathematical Society}, year = {1999}, volume = {26}, series = {Lectures in Life Sciences Series}, address = {Providence, Rhode Island, U. S. A.} } en Book Stewart, Ian science / popular science 3 recommended by Rene te Boekhorst, but very basic... 2005-11-12 @Book{Stewart1989DGP, author = {Ian Stewart}, title = {Does God Play Dice? The Mathematics of Chaos}, publisher = {Basil Blackwell}, address = {Oxford}, year = {1989} } en Article Baguna, Jaume et. al. Science / Biology / Evo-Devo 4 Might be useful for citing: "The premium is to understand the big misteries of Biology, such as how cells divide and animals develop to how evolution took place. As regards Evo-Devo, uncovering the structure, functioning and properties of genetic regulatory networks (GRNs) is one of the greatest challenges of the postgenomic era." "Repatterning and redeployment of pre-existing developmental potential within a novel ecological milieu may have been largely responsible for the radiation (Erwin, 2000; Conway-Morris, 2003), but invention of new genes, extensive or non-extensive gene duplication and the expansion of particular gene families, such as Hox genes, have yet to be fully explored (Ferrier and MinguillÃÆ’³n, 2003)." 2005-11-14 @Article{, author = {Jaume Baguna and Jordi Garcia-Fernandez}, title = {Evo-Devo: the long and winding road.}, journal = {Int. J. Dev. Biol.}, year = {2003}, volume = {47}, number = {7--8}, pages = {705--713}, ee={http://www.ijdb.ehu.es/web/contents.php?vol=47&issue=7-8&doi=14756346} } en Article Revilla-i-Domingo, Roger et. al. Science / Biology / GRN 2005-11-14 @Article{, author = {Roger Revilla-i-Domingo and Eric H Davidson}, title = {Developmental gene network analysis.}, journal = {Int. J. Dev. Biol.}, year = {2003}, volume = {47}, number = {7--8}, pages = {695--703}, ee={http://www.ijdb.ehu.es/web/contents.php?vol=47&issue=7-8&doi=14756345} } en Article Solé, Ricard V et. al. Science / Artificial Life / Genetic Regulatory Networks 2005-11-14 @Article{, author = {Ricard V Solé and Pau Fernández and Stuart A Kauffman}, title = {Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion.}, journal = {Int. J. Dev. Biol.}, year = {2003}, volume = {47}, number = {7--8}, pages = {685--693}, ee={http://www.ijdb.ehu.es/web/contents.php?vol=47&issue=7-8&doi=14756344} } en article Bornholdt, Stefan et. al. Science / Artificial Life / Genetic Regulatory Networks 3 searching for evolutionary origin of differentiation this was not what I wanted but might lateron be interesting. Strongly relates to Kauffman RBN 2005-11-15 @article{ga98bBornholdt, author = {Stefan Bornholdt and K. Sneppen}, title = {Neutral mutations and punctuated equilibrium in evolving genetic networks}, journal = {Physical Review Letters}, year = {1998}, volume = {81}, pages = {236--23}, notes = {1998}, ee= {http://arxiv.org/pdf/physics/9708026} } en Article Gurdon, J. B. Science / Biology / Morphogenesis 3 Abstract: In animal development, the first tissues to be formed include such major components as muscle, nerve cord, notochord and the eye. In the vertebrates, all of these tissues are formed by embryonic induction, a process by which some of the cells within a mass of tissue are caused to change their direction of differentiation as a result of close proximity to cells of another kind. The induced cells typically form a solid coherent mass with a distinct border between them and the remaining uninduced cells. This clean separation between induced and uninduced cells is much sharper than can readily be explained as a result of the induction process. We describe here the culture of amphibian cell and tissue recombinations in solid gels containing cytochalasin in which cell division and cell movement is inhibited during response to induction. This has revealed an effect in which the ability of a cell to respond to induction by differentiating as muscle is enhanced by, or even dependent on, other neighbouring cells differentiating in the same way at the same time. This seems to be a newly described process in animal development, termed the community effect. It helps to explain the formation of blocks of tissue from sheets of cells, and could be of widespread occurrence and significance in morphogenesis resulting from embryonic induction. 2005-11-17 @Article{, author = {J. B. Gurdon}, title = {A community effect in animal development}, journal = {Nature}, year = {1988}, number = {336}, pages = {772--774}, month = {December} } en Article Pastor-Satorras, Romualdo et. al. Science / Biology / GRN 3 2005-11-17 @Article{, author = {Romualdo Pastor-Satorras and Eric Smith and Ricard V. Solé}, title = {Evolving Protein Interaction Networks through Gene Duplication}, journal = {Journal of Theoretical Biology}, year = {2003}, number = {222}, pages = {199--210}, ee={http://complex.upf.es/~ricard/JTBproteome.pdf} } en inproceedings Calabretta, Raffaele et. al. Science / Artificial Life / Modularity 4 "Li (1983) claims that 'gene duplication is probably the most important mechanism for generating new genes and new biochemical processes that have facilitated the evolution of complex organisms from primitives ones'. Tautz (1992) argues that 'redundancy of gene actions may [...] be a necessary requirement for the development and evolution of complex life forms' and in fact 'redundancy seems to be widespread in genomes of higher organisms' (Nowak 1997). In the neutral theory of molecular evolution (Kimura 1983), the duplication relaxes the selective constraints on one of the two copies allowing the accumulation of mutations leading to the emergence of a new function (Coissac, Maillier, and Netter 1997; see also Ohta 1989)." 2005-11-17 @inproceedings{286170, author = {Raffaele Calabretta and Stefano Nolfi and Domenico Parisi and Günter P. Wagner}, title = {A case study of the evolution of modularity: towards a bridge between evolutionary biology, artificial life, neuro- and cognitive science}, booktitle = {ALIFE: Proceedings of the sixth international conference on Artificial life}, year = {1998}, isbn = {0-262-51099-5}, pages = {275--284}, location = {Madison, Wisconsin, United States}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, ee={http://gral.istc.cnr.it/rcalabretta/calabretta.modul3.pdf} } en article Altenberg, Lee Science / Biology / Evolvability 4 2005-11-18 @article{185991, author = {Lee Altenberg}, title = {The evolution of evolvability in genetic programming}, book = {Advances in genetic programming}, year = {1994}, isbn = {0-262-11188-8}, pages = {47--74}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, ee={http://dynamics.org/Altenberg/FILES/LeeEEGP.pdf} } en Book Ptashne, Mark Science / Biology / GRN 3 2005-11-20 @Book{, author = {Mark Ptashne}, title = {A Genetic Switch}, publisher = {Cell Press and Blackwell Science}, year = {1992}, edition = {2nd ed.} } en article Geard, Nicholas et. al. Science / Artificial Life / Genetic Regulatory Networks 3 2005-11-21 @article{citeulike251246, author = {Nicholas Geard and Janet Wiles}, issn = {1064-5462}, journal = {Artificial Life}, number = {3}, pages = {249--268}, publisher = {MIT Press}, title = {A Gene Network Model for Developing Cell Lineages}, ee = {http://citeseer.ist.psu.edu/704372.html}, volume = {11}, year = {2005} } en Article Suzuki, Hideaki Science / Artificial Life / Evolvability 3 2005-11-24 @Article{, author = {Hideaki Suzuki}, title = {An example of design optimization for high evolvability: string rewriting grammar}, journal = {BioSystems}, year = {2003}, number = {69}, pages = {211--221}, ee={http://www.nis.atr.jp/~hsuzuki/papers/2001_BioSystems.pdf} } en article Lohn, J. D. et. al. Science / Artificial Life / Self Replication 3 2005-11-24 @article{ lohn97automatic, author = {J. D. Lohn and J. A. Reggia}, title = {Automatic Discovery of Self-Replicating Structures in Cellular Automata}, journal = {{IEEE} {T}rans. on {E}volutionary {C}omputation}, volume = {1}, number = {3}, pages = {165--178}, year = {1997}, citeseer = {citeseer.ist.psu.edu/lohn97automatic.html} ee = {http://cba.mit.edu/events/03.11.ASE/docs/Lohn.pdf} } en article Reggia, James A. et. al. Science / Artificial Life / Self Replication 3 2005-11-24 @article{DBLP:journals/alife/ReggiaLC98, author = {James A. Reggia and Jason D. Lohn and Hui-Hsien Chou}, title = {Self-Replicating Structures: Evolution, Emergence and Computation.}, journal = {Artificial Life}, volume = {4}, number = {3}, year = {1998}, pages = {283-302}, ee = {http://ic.arc.nasa.gov/people/jlohn/Papers/alife1998.pdf} } en Article Kollmann, Markus et. al. Science / Biology / GRN 3 2005-11-24 @Article{, author = {Markus Kollmann and Linda Lovdok and Kilian Bartholome and Jens Timmer and Victor Sourjik}, title = {Design principles of a bacterial signalling network}, journal = {Nature}, year = {2005}, volume = {438}, OPTpages = {504--507} } en article Dittrich, Peter et. al. Science / Artificial Life / Artificial Chemistry 4 "What has been left open, however, by the theory of evolution are questions relating to the origin of evolutionary units: How come the prerequisites into being, i.e. the entities that are varied and selected? How did qualitatively new evolutionary mechanisms emerge, such as sexual recombination, regulation of mutation rates, or the genetic code? Abstract models that should be able to explain the origin of evolutionary systems would allow to investigate the theoretical conditions for the origin and evolution of life. This is one of the fundamental goals of the AL subfield of artificial chemistry (AC) re- search. By abstracting from natural molecular processes, AC tries to investigate the dynamics of these complex systems. AC deals with combinatorial elements which change or maintain themselves and especially with systems that are able to construct new compo- nents. AC thus deals with forms of organization, self-maintenance, self-construction and with the conditions for those structures to arise." 2005-12-06 @article{DBLP:journals/alife/DittrichZB01, author = {Peter Dittrich and Jens Ziegler and Wolfgang Banzhaf}, title = {Artificial Chemistries - A Review}, journal = {Artificial Life}, volume = {7}, number = {3}, year = {2001}, pages = {225-275}, bibsource = {DBLP, http://dblp.uni-trier.de}, ee={http://www.comp.nus.edu.sg/~cs6211/papers/artchemreview.pdf} } en inproceedings Ono, Naoaki et. al. Science / Artificial Life / Artificial Chemistry 3 2005-12-06 @inproceedings{DBLP:conf/ecal/OnoI99, author = {Naoaki Ono and Takashi Ikegami}, title = {Model of Self-Replicating Cell Capable of Self-Maintenance.}, booktitle = {ECAL}, year = {1999}, pages = {399-406}, crossref = {DBLP:conf/ecal/1999}, bibsource = {DBLP, http://dblp.uni-trier.de}, ee={http://sacral.c.u-tokyo.ac.jp/~nono/book2/publications/ECAL99.pdf}, url={http://sacral.c.u-tokyo.ac.jp/~nono/book2/links.html} } en Book Arthur, Wallace Science / Biology / Evo-Devo 4 2005-12-09 @Book{, author = {Wallace Arthur}, title = {The Origin of Animal Body Plans}, publisher = {Cambridge University Press}, year = {2000}, edition = {Paperback edition} } en Article Hughes, Austin L. et. al. Science / Biology / GRN 3 2005-12-13 @Article{, author = {Austin L. Hughes and Robert Friedman}, title = {Gene Duplication and the Properties of Biological Networks}, journal = {Journal of Molecular Evolution}, year = {2005}, volume = {61}, number = {6}, pages = {758--764}, month = {Dec} } en inproceedings Kumar, R. et. al. Science / Computer Science / Graphs 3 2005-12-14 @inproceedings{796570, author = {R. Kumar and P. Raghavan and S. Rajagopalan and D. Sivakumar and A. Tomkins and E. Upfal}, title = {Stochastic models for the Web graph}, booktitle = {FOCS '00: Proceedings of the 41st Annual Symposium on Foundations of Computer Science}, year = {2000}, isbn = {0-7695-0850-2}, pages = {57}, publisher = {IEEE Computer Society}, address = {Washington, DC, USA}, ee = {http://www.cs.brown.edu/research/webagent/focs-2000.pdf} } en book Gregory, Ryan T. Science / Biology / Genetics 4 2005-12-16 @book{, abstract = {{<b>The Evolution of the Genome</b> provides a much needed overview of genomic study through clear, detailed, expert-authored discussions of the key areas in genome biology. This includes the evolution of genome size, genomic parasites, gene and ancient genome duplications, polypoidy, comparative genomics, and the implications of these genome-level phenomena for evolutionary theory. In addition to reviewing the current state of knowledge of these fields in an accessible way, the various chapters also provide historical and conceptual background information, highlight the ways in which the critical questions are actually being studied, indicate some important areas for future research, and build bridges across traditional professional and taxonomic boundaries.<br><br><b>The Evolution of the Genome</b> will serve as a critical resource for graduate students, postdoctoral fellows, and established scientists alike who are interested in the issue of genome evolution in the broadest sense.<br><br>· Provides detailed, clearly written chapters authored by leading researchers in their respective fields<br>· Presents a much-needed overview of the historical and theoretical context of the various areas of genomic study<br>· Creates important links between topics in order to promote integration across subdisciplines, including descriptions of how each subject is actually studied<br>· Provides information specifically designed to be accessible to established researchers, postdoctoral fellows, and graduate students alike}}, author = {Ryan T. Gregory}, isbn = {0123014638}, keywords = {book genome genome_evolution genome_size}, month = {December}, priority = {2}, publisher = {{Academic Press}}, title = {The Evolution of the Genome}, year = {2004} } de book Jewgenij Samjatin literature / fiction / utopia 4 original from 1920 (my in russian)! 2005-12-31 en book Kirschner, M. W. et. al. Science / Biology / Evolvability 2006-01-18 @book{citeulike:369764, author = {M. W. Kirschner and J. C. Gerhart}, citeulike-article-id = {369764}, howpublished = {Hardcover}, isbn = {0300108656}, keywords = {evolution}, month = {October}, priority = {2}, publisher = {{Yale University Press}}, title = {The Plausibility of Life: Resolving Darwin's Dilemma}, year = {2005} } en book Carroll, Sean B. Science / Biology / Evo-Devo 4 2006-01-19 @book{citeulike:238626, author = {Sean B. Carroll}, howpublished = {Hardcover}, isbn = {0393060160}, month = {April}, publisher = {{W. W. Norton and Company}}, title = {Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom}, year = {2005} } en Article Kumar, S. Science / Artificial Life / Genetic Regulatory Networks 3 Gecco 2004 workshop on: Self-organization in Representations for Evolutionary Algorithms EE= {http://ivan.research.ucf.edu/SOE/SOE001.pdf} 2006-01-24 en inproceedings Kumar, Sanjeev et. al. Science / Artificial Life / Genetic Regulatory Networks 3 2006-01-24 @inproceedings{DBLP:conf/ices/KumarB03, author = {Sanjeev Kumar and Peter J. Bentley}, title = {Biologically Inspired Evolutionary Development.}, booktitle = {ICES}, year = {2003}, pages = {57-68}, ee = {http://www.cs.ucl.ac.uk/staff/P.Bentley/KUBEC3.pdf}, bibsource = {DBLP, http://dblp.uni-trier.de} } en article Sole, R. V. et. al. Science / Artificial Life / Evo-Devo 3 simple initial signal (one gene activated) 2006-01-26 @article{citeulike:449993, address = {ICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB), Barcelona, Spain. ricard.sole@upf.edu}, author = {R. V. Sole and P. Fernandez and S. A. Kauffman}, issn = {0214-6282}, journal = {Int J Dev Biol}, keywords = {gene networks paleontology}, number = {7-8}, pages = {685--693}, priority = {0}, title = {Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion.}, ee = {http://www.santafe.edu/research/publications/workingpapers/03-07-043.pdf} volume = {47}, year = {2003} } en article Kashtan, N., et. al. Science / Artificial Life / Evolvability 3 2006-01-27 @article{NadavKashtan09272005, author = {Kashtan, Nadav and Alon, Uri}, title = {{From the Cover: Spontaneous evolution of modularity and network motifs}}, journal = {PNAS}, volume = {102}, number = {39}, pages = {13773-13778}, doi = {10.1073/pnas.0503610102}, year = {2005}, abstract = {Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such "modularly varying goals" lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems. }, URL = {http://www.pnas.org/cgi/content/abstract/102/39/13773}, ee = {http://www.pnas.org/cgi/reprint/102/39/13773.pdf} } en Book Knoll, Andrew H. Science / Biology / Paleontology 2006-01-30 en book Judson, Horace Freeland Science / Biology / GRN 2006-01-30 @book{judson96theeighth, author={Horace Freeland Judson}, title={The eighth day of creation: makers of the revolution in biology}, year={1996}, address={Plainview, N.Y.}, keywords={distk}, publisher={CSHL Press} } en article Sordino, P. et. al. Science / Biology / Morphogenesis 3 2006-01-31 @article{sordino95hox, AUTHOR = {P. Sordino and F. Van Der Hoeven and D. Duboule}, TITLE = {Hox Gene Expression in Teleost Fins and the Origin of Vertebrate Digits}, JOURNAL = {Nature}, YEAR = {1995}, volume = {375}, number = {6533}, pages = {678-681}, month = jun } en article Albert, Reka et. al. Science / Artificial Life / Complex Systems 2006-02-06 @article {Albert-2002-SMC, author= {Reka Albert and Albert-Laszlo Barabasi}, journal= {Reviews of Modern Physics}, number= {1}, pages= {48--97}, title= {Statistical Mechanics of Complex Networks}, volume= {72}, year= {2002}, url= {http://prola.aps.org/abstract/RMP/v74/i1/p47_1} } en misc Frank, S. Science / Artificial Life / Genetic Regulatory Networks 2006-02-06 @misc{ frank99population, author = {S. Frank}, title = {Population and quantitative genetics of regulatory networks}, text = {S. A. Frank. Population and quantitative genetics of regulatory networks. Journal of Theoretical Biology, 197:281--294, 1999. [Link].}, year = {1999}, url = {citeseer.csail.mit.edu/frank99population.html} } en misc Sole, Ricard V. et. al. Science / Artificial Life / Complex Systems cite: "Modularity can arise in two ways: by parcellation or by integration. Parcellation consists of the differential elimination of cross-interactions involving different parts of the system. Instead, if the network is originally formed by many independent, disconnected parts, it is conceivable that modularity arises by differential integration of those independent characters serving a common functional role." 2006-02-06 @misc{ sole-selection, author = {Ricard V. Sole and Ramon Ferrer-Cancho and Jose M. Montoya and Sergi Valverde}, title = {Selection, Tinkering, and Emergence in Complex Networks - Crossing the Land of Tinkering}, url = {citeseer.ist.psu.edu/sole03selection.html} } en misc Wuensche, A. Science / Artificial Life / Genetic Regulatory Networks 2006-02-06 @inproceedings{ wuensche98genomic, booktitle={Procceedings of Pacic Symposium on Biocomputing'98}, author = {A. Wuensche}, title = {Genomic regulation modeled as a network with basins of attraction}, publisher = {World Scientific}, year = {1998}, url = {http://www.cogs.susx.ac.uk/users/andywu/h_att4a/index.html} } en Article Strogatz, Steven H. Science / Artificial Life / Complex Systems 2006-02-06 @Article{Strogatz:2001, Author={Steven H. Strogatz}, Title={Exploring complex networks}, Journal={Nature}, Year={2001}, Volume={410}, Pages={268-276}, ee={http://www.nature.com/nature/journal/v410/n6825/pdf/410268a0.pdf} } en article Milo, R. et. al. Science / Artificial Life / Complex Systems 2006-02-06 @article{citeulike:101, address = {Departments of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100.}, author = {Milo, R. and Shen-Orr, S. and Itzkovitz, S. and Kashtan, N. and Chklovskii, D. and Alon, U.}, citeulike-article-id = {101}, comment = {Studies the frequency of small units of links (rings, stars, etc.) in different network types.}, doi = {10.1126/science.298.5594.824}, issn = {1095-9203}, journal = {Science}, keywords = {web-graph}, month = {October}, number = {5594}, pages = {824--827}, priority = {0}, title = {Network motifs: simple building blocks of complex networks.}, url = {http://www.sciencemag.org/cgi/content/abstract/298/5594/824}, volume = {298}, year = {2002} } en book Buss, L. W. Science / Biology / Evo-Devo cites Rensch: "by far most phylogenetic changes in form arise by heterochrony" 2006-02-16 @book{buss, author={L. W. Buss}, title={The Evolution of Individuality}, year={1987}, address={New York}, publisher={Columbia University Press} } en article Francino, Pilar P. Science / Biology / Evo-Devo 3 2006-02-22 @article{francino-adaptive-radiation-model-2005, author = {Pilar P. Francino}, citeulike-article-id = {212295}, doi = {10.1038/ng1579}, issn = {1061-4036}, journal = {Nature Genetics}, keywords = {no-tag}, month = {May}, number = {6}, pages = {573--578}, priority = {4}, publisher = {Nature Publishing Group}, title = {An adaptive radiation model for the origin of new gene functions}, ee = {http://repositories.cdlib.org/cgi/viewcontent.cgi?article=3776&context=lbnl}, volume = {37}, year = {2005} } en Article Hooper, S. et. al. Science / Biology / Evo-Devo (3) Duplications are more likely to be retained or occur in genes that are poorly optimized. Thus, amplification is more likely to succeed in category A since there is a lower risk of counter-selection and a greater chance of discovering a weak but novel function. 2006-02-23 @Article{12914657, AUTHOR = {Hooper, Sean and Berg, Otto}, TITLE = {Duplication is more common among laterally transferred genes than among indigenous genes}, JOURNAL = {Genome Biology}, VOLUME = {4}, YEAR = {2003}, NUMBER = {8}, PAGES = {R48}, URL = {http://genomebiology.com/2003/4/8/R48}, DOI = {http://dx.doi.org/10.1186/gb-2003-4-8-r48}, ISSN = {1465-6906}, } en article Wolpert, D. H. et. al. Science / Artificial Life / Evolutionary Algorithms 4 "However, all this previous work has been cast in a manner that does not cover repeated game scenarios where the "objective function" for one player or agent can vary based on the response of another player. In particular, the NFL theorems do not cover such scenarios. These game-like scenarios are usually called "coevolutionary" since they involve the behaviors of more than a single agent or player." "The NFL theorems concern averages over all f of quantities depending on C. For those theorems to hold in a GO scenario - for f-averages of C to be independent of the search algorithm—it is crucial that for fixed d_m, C does not depend on f." 2006-02-24 @article{CoevolutionaryFreeLunches, author = {D. H. Wolpert and W. G. Macready}, doi = {10.1109/TEVC.2005.856205}, journal = {IEEE Transactions on Evolutionary Computation}, month = {December}, number = {6}, pages = {721--735}, title = {Coevolutionary free lunches}, volume = {9}, year = {2005} } en book Camazine, Scott et. al. Science / Biology / Self-Organization 2 2006-02-27 @book{601161, author = {Scott Camazine and Nigel R. Franks and James Sneyd and Eric Bonabeau and Jean-Louis Deneubourg and Guy Theraula}, title = {Self-Organization in Biological Systems}, year = {2001}, isbn = {0691012113}, publisher = {Princeton University Press}, address = {Princeton, NJ, USA}, } en article Ohta, T. Science / Biology / Genetics 3 2006-02-27 @article{citeulike:3557, address = {National Institute of Genetics, Mishima, Japan.}, author = {T. Ohta}, citeulike-article-id = {3557}, issn = {0016-6731}, journal = {Genetics}, month = {November}, number = {3}, pages = {841--847}, title = {Evolution by gene duplication and compensatory advantageous mutations.}, ee = {http://www.genetics.org/cgi/reprint/120/3/841.pdf} volume = {120}, year = {1988} } en article Walsh, J. B. Science / Biology / Genetics 2006-02-27 @article{Walsh01011995, author = {J. B. Walsh}, title = {{How Often Do Duplicated Genes Evolve New Functions?}}, journal = {Genetics}, volume = {139}, number = {1}, pages = {421-428}, year = {1995}, ee = {http://www.genetics.org/cgi/reprint/139/1/421.pdf} } en article Lynch, Michael et. al. Science / Biology / Genetics 2006-02-27 @article{citeulike:307330, author = {Michael Lynch and John S. Conery}, citeulike-article-id = {307330}, doi = {10.1126/science.290.5494.1151}, journal = {Science}, keywords = {evolution gene-duplication}, month = {November}, number = {5494}, pages = {1151--1155}, priority = {0}, title = {The Evolutionary Fate and Consequences of Duplicate Genes}, ee = {http://bioportal.weizmann.ac.il/course/evogen/GeneDup/Lynch_Conery.pdf}, volume = {290}, year = {2000} } en article Lieberman, Erez et. al. Science / Artificial Life / Evolutionary Algorithms 2006-03-01 @article{Lieberman05a, author = {Erez Lieberman and Christoph Hauert and Martin A. Nowak}, journal = {Nature}, keywords = {bibtex-import}, number = {7023}, pages = {312--316}, title = {Evolutionary dynamics on graphs}, ee = {http://dx.doi.org/10.1038/nature03204}, volume = {433}, year = {2005} } en misc Lerena, P. et. al. Science / Artificial Life / Agent Systems 2 Idea of mobile Cellular Automata for an Agent based system (>Multicellularity<) 2006-03-06 @misc{lerena96biomachines, author = {P. Lerena and M. Courant}, title = {Bio-machines}, text = {P. Lerena and M. Courant. Bio--machines. In Proceedings of Artificial Life, volume V, Nara, Japan, 1996.}, year = {1996}, ee = {http://citeseer.csail.mit.edu/cache/papers/cs/2526/ftp:zSzzSzftp-iiuf.unifr.chzSzpubzSzi3smzSzpublicationszSz96zSz65-PL-MC-ALV.pdf/bio-machines.pdf}, url = "citeseer.ist.psu.edu/51823.html" } de Book Zuse, Konrad Science / Artificial Life / Complex Systems 4 Note that the link provided gives you the English translation: Calculating Space, MIT Technical Translation AZT-70-164-GEMIT, MIT (Proj. MAC), Cambridge, Mass. 02139, Feb. 1970. 2006-03-06 @Book{Zuse, publisher = {Vieweg & Sohn}, title = {Rechnender Raum}, series = {Schriften zur Datenverarbeitung}, author = {Konrad Zuse}, year = {1967}, ee = {ftp://ftp.idsia.ch/pub/juergen/zuserechnenderraum.pdf}, address = {Braunschweig}} en misc Schuster, P. et. al. Science / Biology / Molecular 4 properties of the RNA map were derived: "For sequence spaces of chain lengths n > 10 there are orders of magnitude more sequences than structures and hence, the map is many-to-one (as predicted analytically above)." "Few common and many rare structures." "In other words, for each arbitrarily chosen pair of structures there will be at least on sequence that can form both." Very general but nice conclusion: "We have discussed here only four classes of the networks which play a central role in molecular biology. Networks of gene regulation, both at level of the single cell and the signaling networks of multicellular organisms are just as important. In higher organisms neural networks form an additional layer of complexity (see Olaf Sporn's contribution in this issue). While we begin to understand structure and function of networks within each class, for which ample data are available at least in some cases, little is known on the interaction of the various levels. The mechanisms governing crosstalk between hierarchical levels are, nevertheless, equally important if not more relevant for proper functioning of organisms. They are in the center of topdown control and regulation, without which every form of organization is doomed to break down. What makes this type of control tricky in but not only in biology is the partial autonomy of agents at the lower level. More and more detailed knowledge on communication between cells will help us to explore successfully the subtle interplay between local independence and global control." 2006-03-06 @misc{ schuster02networks, author = {P. Schuster and P. Stadler}, title = {Networks in molecular evolution}, journal ={Complexity}, volume={8}, pages={34--42}, year = {2002}, url = {http://citeseer.ist.psu.edu/schuster02networks.html}, ee={http://citeseer.ist.psu.edu/rd/0%2C598572%2C1%2C0.25%2CDownload/http://citeseer.ist.psu.edu/cache/papers/cs/29378/http:zSzzSzwww.tbi.univie.ac.atzSzpaperszSzAbstractszSz02-pks-003.pdf/schuster02networks.pdf} } en book Crutchfield, J. P. et. al. Science / Biology / Evo-Devo 2006-03-08 @book{EvolutionaryDynamics, author={J. P. Crutchfield and P. Schuster}, title={Evolutionary Dynamics: Exploring the Interplay of Selection, Accident, Neutrality and Function.}, year={2003}, publisher={Oxford University Press} } en misc Sole, R. V. et. al. Science / Dynamical Systems 2006-03-08 @misc{InformationTheoryComplexNetworks, author = {R. V. Sole and S. Valverde}, title = {Information Theory of Complex Networks: On Evolution and Architectural Constraints}, ee = {http://www.santafe.edu/research/publications/workingpapers/03-11-061.pdf}} en inbook Crutchfield, James P. Science / Dynamical Systems In summary, three notions will be distinguished: 1. The intuitive definition of emergence: “something new appears”; 2. Pattern formation: an observer identifies “organization” in a dynamical system; and 3. Intrinsic emergence: the system itself capitalizes on patterns that appear. 2006-03-09 @inbook{336681, author = {James P. Crutchfield}, title = {Is anything ever new?: considering emergence}, book = {Complexity: metaphors, models, and reality}, year = {1999}, isbn = {0-7382-0232-0}, pages = {515--537}, publisher = {Perseus Books}, address = {Cambridge, MA, USA}, url={ftp://ftp.santafe.edu/pub/CompMech/papers/EverNew.pdf} } de book Mann, H. Literature 5 Wow, from 1905, but still so good! 2006-03-13 de book Gernhardt, R. Literature 2006-03-13 en article Verma, Malkhey et. al. Science / Biology / GRN 2006-03-15 @article{AutoRegulation2005, author = {Malkhey Verma and Subodh Rawool and Paike Jayadeva Bhat and K.V. Venkatesh}, journal = {Biosystems}, number = {1}, pages = {39--48}, title = {Biological significance of autoregulation through steady state analysis of genetic networks}, ee = {http://www.sciencedirect.com:80/science?_ob=GatewayURL&_origin=MDL&_urlversion=3&_method=citationSearch&_refkey=Verma%232006%2339%2348%23M&_volkey=0303-2647%2384%2339%231&_src=F&_version=1&md5=022e6301eef76c129c00dd1fbab95afd&LITLINKDATA:SITEID=1&LITTYPEID=1&LITITEMID=497&INDICATOR=1}, volume = {84}, year = {2006} } en InCollection Altenberg, Lee Science / Biology / Evo-Devo 2006-03-22 @InCollection{Altenberg:1995GGEGPM, author = {Lee Altenberg}, year = {1995}, title = {Genome growth and the evolution of the genotype-phenotype map}, booktitle = {Evolution as a Computational Process}, editor = {Wolfgang Banzhaf and Frank H. Eeckman}, publisher = {Springer-Verlag}, address = {Berlin, Germany}, pages = {205--259}, keywords = {genetic algorithms, genetic programming}, URL = {http://dynamics.org/~altenber/PAPERS/GGEGPM/}, ee = {http://dynamics.org/Altenberg/FILES/LeeGGEGPM.pdf} } de article Skusa, Andre et. al. Science / Artificial Life / Artificial Chemistry 4 2006-04-12 @article{DBLP:journals/ki/SkusaBBDZ00, author = {Andre Skusa and Wolfgang Banzhaf and Jens Busch and Peter Dittrich and Jens Ziegler}, title = {Kuenstliche Chemie}, journal = {KI}, volume = {14}, number = {1}, year = {2000}, pages = {12-19}, bibsource = {DBLP, http://dblp.uni-trier.de} } de book Mann, H. Literature 4 2006-04-08 de Book Mann, H. Literature 4 2006-04-08 en article Kim, Jan T. Science / Artificial Life / Evo-Devo 2006-04-13 @article{DBLP:journals/ki/Kim00, author = {Jan T. Kim}, title = {LindEvol: Artificial Models for Natural Plant Evolution}, journal = {KI}, volume = {14}, number = {1}, year = {2000}, pages = {26-32}, bibsource = {DBLP, http://dblp.uni-trier.de} } en Book Mueller, Gerd B. et. al., ed. Science / Biology / Morphogenesis 3 2006-04-19 @Book{OrganismalFormBook, editor = {Gerd B. Mueller and Stuart A. Newman}, title = {Origination of Organismal Form}, publisher = {MIT Press}, year = {2003} } en book Flake, Gary William Science / Artificial Life / Complex Systems 3 2006-04-19 @book{286918, author = {Gary William Flake}, title = {The computational beauty of nature}, year = {1998}, isbn = {0-262-06200-3}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, } de Book Unsoeld, Albrecht Science / Dynamical Systems 2006-04-22 @Book{evoStruktUnsoeld, author = {Albrecht Unsoeld}, title = {Evolution kosmischer, biologischer und geistiger Strukturen}, publisher = {Wissenschaftliche Verlagsgesellschaft mbH Stuttgart}, year = {1983}, series = {Buecher der Zeitschrift Naturwissenschaftliche Rundschau}, address = {Stuttgart}, edition = {2. Auflage} } en Article Nehaniv, Chrystopher L. et. al. Science / Artificial Life / Complex Systems 2006-05-03 @Article{hierarchicalComplexityAlgebraic, author = {Chrystopher L. Nehaniv and John L. Rhodes}, title = {The evolution and understanding of hierarchical complexity in biology from an algebraic perspective}, journal = {Artificial Life}, year = {2000}, volume = {6}, number = {1}, pages = {45--67} } en book Maynard-Smith, J. et. al. Science / Biology / Evolvability 2006-05-03 @book{maynard-smith1997majorTransitions, author={J. Maynard-Smith and E. Szathmary}, title={The Major Transitions in Evolution}, year={1997}, url={http://www.isrl.uiuc.edu/~amag/langev/paper/maynardsmith1997majorTransitions.html}, publisher={New York: Oxford University Press} } en book Winfree, Arthur T. Science / Biology 2006-03-04 @book{BioClocks, author={Arthur T. Winfree}, title={The Timing of Biological Clocks}, publisher={Scientific American Books, Inc.}, year=1986 } en book Neumann, John von Science / Artificial Life / Artificial Chemistry 5 2006-05-05 @book{NeumannAutomata, author = {John von Neumann}, year = {1966}, title = {Theory of Self-Reproducing Automata}, publisher = {University of Illinois Press}, address = {Urbana, Illinois}, ee = {http://www.walenz.org/vonNeumann/} } en article Ziemke, T. et. al. Science / Dynamical Systems 2006-05-25 @article{TomZiemke07012002, author = {Ziemke, Tom and Thieme, Mikael}, title = {{Neuromodulation of Reactive Sensorimotor Mappings as a Short-Term Memory Mechanism in Delayed Response Tasks}}, journal = {Adaptive Behavior}, volume = {10}, number = {3-4}, pages = {185-199}, year = {2002}, URL = {http://adb.sagepub.com/cgi/content/abstract/10/3-4/185}, ee = {http://adb.sagepub.com/cgi/reprint/10/3-4/185.pdf} } en article Kim, DaeEun Science / Dynamical Systems 2006-05-25 @article{KimTmaze04, author = {DaeEun Kim}, title = {{Evolving internal memory for T-maze tasks in noisy environments}}, journal = {Connection Science}, volume = {16}, number = {3}, pages = {183-210}, year = {2004}, ee = {http://dx.doi.org/10.1080/09540090412331314812} } en InProceedings Saggie, Keren et. al. Science / Dynamical Systems 2006-05-25 @InProceedings{ecal2003, author = {Keren Saggie and Alon Keinan and Eytan Ruppin}, title = {Solving a Delayed Response Task with Spiking and McCulloch-Pitts Agents}, booktitle = {Advances in Artificial Life - Proceedings of the 7th European Conference on Artificial Life (ECAL)}, pages = {199--208}, year = {2003}, editor = {W. Banzhaf and T. Christaller and P. Dittrich and J. T. Kim and J. Ziegler}, volume = {2801}, series = {Lecture Notes in Artificial Intelligence}, publisher = {Springer Verlag Berlin, Heidelberg} } de book Tucholsky, K. Literature 4 online at http://www.textlog.de/kurt-tucholsky.html 2006-05-29 de book Puig, M. Literature 2006-05-23 en article Suzuki, Hideaki et. al. Science / Artificial Life / Biological basis 2006-06-13 @article{860917, author = {Hideaki Suzuki and Naoaki Ono and Kikuo Yuta}, title = {Several necessary conditions for the evolution of complex forms of life in an artificial environment}, journal = {Artif. Life}, volume = {9}, number = {2}, year = {2003}, issn = {1064-5462}, pages = {153--174}, url = {http://dx.doi.org/10.1162/106454603322221504}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, } en Article Waechtershaeuser, G. Science / Biology / Self-Organization 2006-06-14 @Article{deepseeorigin, author = {G. Waechtershaeuser}, title = {Before enzymes and templates: theory of surface metabolism.}, journal = {Microbiological Reviews}, year = {1988}, volume = {52}, number = {4}, pages = {452--484}, url = {http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=3070320} } en Article Schneider, E.D. et. al. Science / Biology / Self-Organization 2006-05-14 @Article{SchneiderThermodynamics, author = {E.D. Schneider and J.J. Kay}, title = {Life as a Manifestation of the Second Law of Thermodynamics}, journal = {Mathematical and Computer Modelling}, year = {1994}, volume = {19}, number = {6--8}, pages = {25--48}, url = {http://citeseer.ist.psu.edu/cache/papers/cs/16402/http:zSzzSzwww.fes.uwaterloo.cazSzuzSzjjkayzSzpubszSzLife_aszSzlifeas.pdf/schneider94life.pdf} } en PhdThesis Kay, J. J. Science / Dynamical Systems -According to Prigogine, in a steady state situation the system is stable (i.e. damps out rate changes in irreversible processes) with respect to environmental perturbations (changes in flow rates). It minimizes its dissipation (due to irreversible processes). This is the MINIMUM DISSIPATION RULE. However, Prigogine shows that as the input flow rates increase, a critical threshold is approached. Beyond this threshold a catastrophe occurs. The system will rapidly dissipate energy and material and enter a new more ordered steady state. Just which new state is entered is determined by which flow rate exceeds its critical threshold first. -First, the second law of thermodynamics is the only physical law with a time sense and hence must be intimately linked to any discussion of the temporal phenomena, organization. Second, environmental fluctuations are required for the emergence of organization; and third, as systems evolve there is an increase in entropy production per component. -"The second law of thermodynamics prescribes that all irreversible chemical processes increase the overall randomness of matter-energy in the universe. Whereas this is a disordering directive, it is not necessarily disorganizing. I have tried to show that the evolution of molecular organization is, in fact, a natural consequence of the operation of this law. Molecular organization is achieved through chemical bonding. Chemical bonding, in turn, provides a means through which the randomization of matter and energy can occur." (Wicken, 1978, p.202). If one accepts that, in a pre-biotic soup such as found on Earth before life began, the generation of complex molecular forms is mandated by the second law, then Wicken argues that one would expect the eventual emergence of "quasi-stable, self perpetuating patterns of information flow, of catalytic cycles ..."(Wicken, 1980, p.16) that would guarantee the degradation of the flow of high quality energy. If these patterns and cycles could evolve and stabilize sufficiently to form systems which are self-maintaining, reproduce and continue to operate (i.e. degrade energy) in the face of environmental fluctuations, then one would have a permanent organization for satisfying the second law's requirement that the high quality energy flux to the system be continually degraded. One would also have life. -Consider a chemical soup bombarded with solar energy. Wicken's work suggests that the second law [10] of thermodynamics dictates the emergence of chemical factories in this soup. The factories would degrade (i.e. increase the entropy of) the solar energy impinging on the earth. Degradation would be accomplished largely by utilizing the available molecules and energy to form new more complex molecules. The process of formation of new molecules could degrade the available potential energy by transforming it into bond, translational, and vibrational energy, and into heat. Many different types of processes and molecular forms should emerge as the larger their number the more thoroughly degraded the incoming solar energy becomes. As time goes on, these systems (the chemical factories) should become STABLE. That is they would evolve mechanisms to stabilize their internal chemical processes and to maintain the functioning of the system in the face of environmental changes. The degradation of the incoming solar energy, as required by the second law, would then be assured. This expectation would be justified by the second law alone, but is reinforced by Prigogine's findings regarding the emergence of stable dissipative structures. Suppose, for now, that the physical environment is homogeneous. As stated, the emergence of primary producers who would use the incoming solar energy to produce complex molecules and stored energy is expected. These primary producers would be expected to degrade into lower quality forms as much of the incoming energy as possible. They would only produce as much stored potential energy (via for example photosynthesis) as is required to fuel the processes necessary for the internal stability of the system. The stored potential energy of the primary producers could be further degraded if it is used by other chemical factories to fuel more production of complex molecules. Chains of such systems, each system feeding on the stored potential energy of another system, would emerge in accordance with Prigogine's order through fluctuations scenario. The characteristics of these chains is that they would degrade as much of the incoming energy as possible per unit production of complex molecules. Such chains will be referred to as ENERGY DEGRADING CHAINS. If only energy degrading chains existed, they would quickly run out of material to be used as inputs. Thus we should expect the emergence of consumers who would use the complex molecules and stored energy of the energy degrading chains, as inputs to processes which simplify the complex molecules. The existence of such MATTER SIMPLIFYING chemical factories would guarantee the supply of simple molecules to be used by the primary producers. These consumers would be expected to simplify the molecules as much as possible per unit of energy flow. -The number of different solutions possible in any given supersystem is large and the details of specific solutions unpredictable. This leads to the expectation that there would be many different forms of life. 2006-06-22 @PhdThesis{KeySelfOrg, author = {J. J. Kay}, title = {Self-Organization In Living Systems}, school = {Department of Systems Design Engineering, University of Waterloo}, year = {1984}, address = {Waterloo, Ontario, Canada}, url = {http://www.nesh.ca/jameskay/www.fes.uwaterloo.ca/u/jjkay/pubs/thesis/toc.html} } de book Schnitzler, A. Literature 4 you feel the influence of Freud's work the book is not outdated despite of the birth control pill, maybe only the end needs a re-interpretation 2006-07-30 en book Schneider, Eric D. et. al. Science / Physics / Thermodynamics 2006-07-30 @book{citeulike:700987, author = {Eric D. Schneider and Dorion Sagan}, citeulike-article-id = {700987}, howpublished = {Hardcover}, isbn = {0226739368}, keywords = {book ecosystemthermodynamics keypaper originsoflife}, month = {June}, priority = {3}, publisher = {{University Of Chicago Press}}, title = {Into the Cool : Energy Flow, Thermodynamics, and Life}, year = {2005} } en article Jain, S. et. al. Science / Dynamical Systems 4 2006-07-31 @article{citeulike:566295, author = {Sanjay Jain and Sandeep Krishna}, citeulike-article-id = {566295}, eprint = {nlin.AO/0210070}, keywords = {artificialchemistry emergence graphteory networks topology}, month = {Oct}, priority = {3}, title = {Graph Theory and the Evolution of Autocatalytic Networks}, url = {http://arxiv.org/abs/nlin.AO/0210070}, year = {2002} } en article Hinton, G. E., et. al. Science / Computer Science 2006-08-01 @article{Hinton07282006, author = {Hinton, G. E. and Salakhutdinov, R. R.}, title = {{Reducing the Dimensionality of Data with Neural Networks}}, journal = {Science}, volume = {313}, number = {5786}, pages = {504-507}, doi = {10.1126/science.1127647}, year = {2006}, abstract = {High-dimensional data can be converted to low-dimensional codes by training a multilayer neural network with a small central layer to reconstruct high-dimensional input vectors. Gradient descent can be used for fine-tuning the weights in such "autoencoder" networks, but this works well only if the initial weights are close to a good solution. We describe an effective way of initializing the weights that allows deep autoencoder networks to learn low-dimensional codes that work much better than principal components analysis as a tool to reduce the dimensionality of data. }, URL = {http://www.sciencemag.org/cgi/content/abstract/313/5786/504}, ee = {http://www.sciencemag.org/cgi/reprint/313/5786/504.pdf} } en book Jeffrey S. Wicken Science / Physics / Thermodynamics 2006-08-22 en article Wray, G. A. et. al. Science / Biology / Evo-Devo 2006-08-23 @article{GAWray09012003, author = {Wray, Gregory A. and Hahn, Matthew W. and Abouheif, Ehab and Balhoff, James P. and Pizer, Margaret and Rockman, Matthew V. and Romano, Laura A.}, title = {{The Evolution of Transcriptional Regulation in Eukaryotes}}, journal = {Mol Biol Evol}, volume = {20}, number = {9}, pages = {1377-1419}, doi = {10.1093/molbev/msg140}, year = {2003}, URL = {http://mbe.oxfordjournals.org/cgi/content/abstract/20/9/1377}, ee = {http://mbe.oxfordjournals.org/cgi/reprint/20/9/1377.pdf} } en article Shen-Orr, Shai S. et. al. Science / Biology / GRN 2006-08-25 @article{citeulike307461, author = {Shen-Orr, Shai S. and Milo, Ron and Mangan, Shmoolik and Alon, Uri }, citeulike-article-id = {307461}, doi = {10.1038/ng881}, journal = {Nat Genet}, keywords = {ecoli networks regulation}, month = {May}, number = {1}, pages = {64--68}, priority = {2}, title = {Network motifs in the transcriptional regulation network of Escherichia coli}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11967538}, volume = {31}, year = {2002} } en Book Bornholdt, Stefan et. al., ed. Science / Computer Science / Graphs 2006-08-31 @Book{bshoganftgtti2003, editor = {Stefan Bornholdt and Heinz Georg Schuster}, title = {Handbook of Graphs and Networks - From the Genome to the Internet}, year = {2003}, publisher = {Wiley-VCH}, } en article Mayo, A. E. et. al. Science / Biology / GRN 2006-09-01 @article{citeulike:582434, address = {Departments of Molecular Cell Biology and Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel.}, author = {Mayo, A. E. and Setty, Y. and Shavit, S. and Zaslaver, A. and Alon, U. }, citeulike-article-id = {582434}, doi = {10.1371/journal.pbio.0040045}, issn = {1545-7885}, journal = {PLoS Biol}, keywords = {evolution genecircuits}, month = {April}, number = {4}, priority = {2}, title = {Plasticity of the cis-Regulatory Input Function of a Gene.}, url = {http://dx.doi.org/10.1371/journal.pbio.0040045}, volume = {4}, year = {2006} } en article Kashtan, Nadav et. al. Science / Artificial Life / Evo-Devo -Good quantitative measure of modularity -interesting but quite unrealistic model 2006-09-01 @article{citeulike:333353, address = {Departments of Molecular Cell Biology and Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel.}, author = {Kashtan, Nadav and Alon, Uri }, citeulike-article-id = {333353}, doi = {10.1073/pnas.0503610102}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {evolution modularity network simulation}, month = {September}, priority = {4}, title = {Spontaneous evolution of modularity and network motifs.}, url = {http://www.pnas.org/cgi/content/abstract/102/39/13773}, year = {2005} } en book Brecht, B. Literature 2006-09-06 de book Popper, Karl R. Literature 2006-09-11 en inproceedings McKay, Brendan D. Science / Computer Science / Graphs 2006-09-12 @inproceedings{McKay78, author = {Brendan D. McKay}, title = {Computing automorphisms and canonical labellings of graphs}, booktitle = {Combinatorial Mathematics}, year = 1978, series = {Lecture Notes in Math.}, publisher = {Springer-Verlag}, volume = 686, editor = {D. A. Holton and Jennifer Seberry}, organisation = {Canberra (1977)} } en article Guimera, Roger et. al. Science / Computer Science / Graphs Care has to be taken with equation one; the 2L in it can be very misleading. When implementing the measure I first ended up with very strange results and only looking through the references (esp. Newman, Fast algorithm for detecting community structure in networks) helped. It becomes clearer when you think about the statement "A good partition of a network into modules must comprise many within-module links and as few as possible between-module links. Equation (1) addresses this diffiulty by imposing that M=0 if nodes are placed at random into modules or if all nodes are in the same cluster.". The latter is not true if you naively implement this as putting the whole network into one module leads to: l_s = d_s implying [l_s / L - (d_s / 2L)^2]= [1 - 1/4 * 1]= 0.75 !!!!!!!!!!!!!! 2006-09-20 @article{guimera-2005-433, author = {Roger Guimera and Luis A. Nunes Amaral}, title = {Functional cartography of complex metabolic networks}, journal = {Nature}, volume = {433}, pages = {895}, ee = {http://arxiv.org/pdf/q-bio.MN/0502035}, url= {http://www.nature.com/nature/journal/v433/n7028/full/nature03288.html} year = {2005} } de book Strindberg, August Literature http://gutenberg.spiegel.de/strindbe/heiraten/toc.htm http://www.gutenberg.org/browse/authors/s#a1609 2006-10-02 en inproceedings Watson, Richard A. Science / Artificial Life / Complex Systems 2006-10-10 @inproceedings{watson02, author = {Richard A. Watson}, booktitle = {Workshop Proceedings}, citeulike-article-id = {125970}, editor = {Bilotta, Eleanora and Al}, {em e. }, keywords = {hiff-schema-gecco-05}, month = {December}, organization = {8th International Conference on the Simulation and Synthesis of Living Systems}, url = {http://citeseer.ist.psu.edu/watson03modular.html}, title = {Modular Interdependency in Complex Dynamical Systems}, year = {2002} } en inproceedings Polani, Daniel et. al. Science / Artificial Life / Modularity 2006-10-10 @inproceedings{PolaniDU05, author = {Daniel Polani and Peter Dauscher and Thomas Uthmann}, title = {On a Quantitative Measure for Modularity Based on Information Theory.}, booktitle = {ECAL}, year = {2005}, pages = {393--402}, ee = {http://dx.doi.org/10.1007/11553090_40}, bibsource = {DBLP, http://dblp.uni-trier.de} } en article Mulgan, Geoff Sociology http://www.youngfoundation.org.uk/wp-content/social_innovation.pdf http://www.youngfoundation.org.uk/index.php?p=262 2006-10-15 en article Kuo, P.D. et. al. Science / Dynamical Systems See also >Comment on Network Motifs: Simple Building Blocks of Complex Networks< and >Superfamilies of Evolved and Designed Networks< in Science. 2006-10-15 @article{AutoRegulation2005, author = {Kuo, P.D. and Banzhaf, W. and Leier, A.}, journal = {Biosystems}, pages = {177--200}, title = {Network topology and the evolution of dynamics in an artificial regulatory network model created by whole genome duplication and divergence.}, volume = {85}, number = {3}, year = {2006}, ee = {http://chianti.ucsd.edu/~dkuo/ARNModel_revision2.pdf} } de Book Boell, Heinrich Literature 2006-10-21 en book Alon, Uri Science / Dynamical Systems 2006-10-23 @book{alonBook, author = {Uri Alon}, month = {July}, publisher = {{Chapman & Hall/CRC}}, title = {{An Introduction to Systems Biology}}, year = {2006} } de Strindberg, August Literature 2006-10-25 en article Kashtan, N. et. al. Science / Biology / Self-Organization 2006-10-27 @article{itzkovitz-2005-71, author = {N. Kashtan and S. Itzkovitz and R. Milo and U. Alon}, title = {Topological Generalizations of network motifs}, journal = {Physical Review E}, volume = {70}, pages = {031909}, ee = {http://www.weizmann.ac.il/mcb/UriAlon/Papers/TopologicalGeneralizationsOfNetworkMotifs.pdf}, year = {2004} } en article S., Mangan, et. al. Science / Biology / GRN 2006-10-27 @article{citeulike:574734, address = {Department of Molecular Cell Biology and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.}, author = {Mangan, S. and Itzkovitz, S. and Zaslaver, A. and Alon, U.}, citeulike-article-id = {574734}, doi = {10.1016/j.jmb.2005.12.003}, journal = {J Mol Biol}, month = {March}, number = {5}, pages = {1073--1081}, title = {The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli.}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16406067}, volume = {356}, year = {2006} } en article Conant, G. C. et. al. Science / Biology / GRN 2006-10-27 @article{ConvergentMotifEvo, author = {G. C. Conant and A. Wagner}, journal = {Nature Genetics}, number = {3}, pages = {264--266}, publisher = {Nature Publishing Group}, title = {Convergent evolution of gene circuits}, volume = {34}, ee = {http://www.bioc.unizh.ch/wagner/papers/natgen2003.pdf}, year = {2003} } en article Davidson, Eric H. et. al. Science / Biology / GRN 2006-08-30 @article{SchilstraGRN, author = {Davidson, Eric H. and Rast, Jonathan P. and Oliveri, Paola and Ransick, Andrew and Calestani, Cristina and Yuh, Chiou-Hwa and Minokawa, Takuya and Amore, Gabriele and Hinman, Veronica and Arenas-Mena, Cesar and Otim, Ochan and Brown, C. Titus and Livi, Carolina B. and Lee, Pei Yun and Revilla, Roger and Rust, Alistair G. and Pan, Zheng jun and Schilstra, Maria J. and Clarke, Peter J. C. and Arnone, Maria I. and Rowen, Lee and Cameron, R. Andrew and McClay, David R. and Hood, Leroy and Bolouri, Hamid}, title = {{A Genomic Regulatory Network for Development}}, journal = {Science}, volume = {295}, number = {5560}, pages = {1669-1678}, doi = {10.1126/science.1069883}, year = {2002}, URL = {http://www.sciencemag.org/cgi/content/abstract/295/5560/1669}, ee = {http://www.sciencemag.org/cgi/reprint/295/5560/1669.pdf} } en article Buchler, Nicolas E. et. al. Science / Biology / GRN 2006-11-13 @article{citeulike:525416, author = {Buchler, Nicolas E. and Gerland, Ulrich and Hwa, Terence}, citeulike-article-id = {525416}, journal = {PNAS}, keywords = {nsf}, month = {April}, number = {9}, pages = {5136--5141}, priority = {2}, title = {On schemes of combinatorial transcription logic}, url = {http://www.pnas.org/cgi/content/abstract/100/9/5136}, volume = {100}, year = {2003} } en TechReport Morowitz, H. et. al. Science / Biology / Origin of Life Also see http://www.nature.com/news/2006/061113/full/061113-9.html 2006-11-20 @TechReport{, author = {H. Morowitz and E. Smith}, title = {Energy flow and the organization of life}, institution = {Santa Fe Institute Working Paper}, year = {2006}, url = {http://www.santafe.edu/research/publications/workingpapers/06-08-029.pdf} } en book Morowitz, Harold J. Science / Biology / Origin of Life 5 2006-12-08 @book{morowitzBook, author = {Harold J. Morowitz}, publisher = {{Yale University Press}}, title = {{Beginnings of Cellular Life}}, year = {1992} } en book Defoe, Daniel Literature 5 1990 en article Mary-Lee, Dequeant, et. al. Science / Biology / Morphogenesis 2006-12-08 @article{Mary-LeeDequeant12082006, author = {Dequeant, Mary-Lee and Glynn, Earl and Gaudenz, Karin and Wahl, Matthias and Chen, Jie and Mushegian, Arcady and Pourquie, Olivier}, title = {{A Complex Oscillating Network of Signaling Genes Underlies the Mouse Segmentation Clock}}, journal = {Science}, volume = {314}, number = {5805}, pages = {1595-1598}, doi = {10.1126/science.1133141}, year = {2006}, URL = {http://www.sciencemag.org/cgi/content/abstract/314/5805/1595}, ee = {http://www.sciencemag.org/cgi/reprint/314/5805/1595.pdf} } de book Rickens, Christian Sociology 4 Sehr gutes Buch, trotz reisserischem Titel viele empirische Belege. Zitat S.27: "Der Generalverdacht, dass die unteren Gesellschaftsschichten zum eigenverantwortlichen Umgang mit ihrer Freiheit nicht fähig sind, zieht sich durch due gesamte Geschichte des konservativen Denkens. Er hat sich bisher regelmässig als falsch erwiesen." 2006-12-22 de book Popper, Karl R. Philosophy 3 2006-12-26 de book Knippers, Rolf Science / Biology / Genetics 4 2006-12-30 en book Morowitz, Harold J. Science / Physics / Thermodynamics 2007-01-02 @book{citeulike:700991, author = {Harold J. Morowitz}, citeulike-article-id = {700991}, isbn = {0918024137}, keywords = {book ecosystemthermodynamics}, publisher = {Academic Press}, title = {Energy Flow in Biology}, year = {1968} } en article Taylor, Tim Science / Artificial Life / Evolvability 2007-01-10 @article{510352, author = {Tim Taylor}, title = {Creativity in evolution: individuals, interactions, and environments}, book = {Creative evolutionary systems}, year = {2002}, isbn = {1-55860-673-4}, pages = {79--108}, publisher = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco, CA, USA}, } en article Paladugu, S.R. et. al. science / artificial life / genetic regulatory networks 2007-01-18 @article{similar, author = {Paladugu, S.R. and Chickarmane, V. and Deckard, A. and Frumkin, J.P. and McCormack, M. and Sauro, H.M.}, title = {In silico evolution of functional modules in biochemical networks}, journal = {Systems Biology, IEE Proceedings}, volume = {153}, number = {4}, pages = {223--235}, year = {2006}, URL = {http://www.informatics.indiana.edu/schnell/papers/ieepsb153-223.pdf} } en article Salzberg, Chriss Science / Artificial Life / Artificial Chemistry 2007-01-22 @article{reflexiveAC, author = {Chriss Salzberg}, journal = {BioSystems}, month = {January}, number = {1}, pages = {1--12}, title = {A graph-based reflexive artificial chemistry}, url = {http://www.sciencedirect.com/science/article/B6T2K-4JBB319-4/2/843f7eeeabf5cb8739b5b4996d2e715c}, volume = {87}, year = {2007} } en article Benkoe, Gil et. al. 2007-01-22 @article{DBLP:journals/jcisd/BenkoFS03, author = {Gil Benkoe and Christoph Flamm and Peter F. Stadler}, title = {A Graph-Based Toy Model of Chemistry.}, journal = {Journal of Chemical Information and Computer Sciences}, volume = {43}, number = {4}, year = {2003}, pages = {1085-1093}, ee = {http://dx.doi.org/10.1021/ci0200570}, bibsource = {DBLP, http://dblp.uni-trier.de} } en inproceedings Miller, J. F. Science / Artificial Life / Evo-Devo 2007-02-07 @INPROCEEDINGS{miller04evolving, author = {J. F. Miller}, title = {Evolving a Self-Repairing, Self-Regulating, French Flag Organism}, booktitle = {Genetic and Evolutionary Computation - GECCO 2004}, year = {2004}, editor = {K. Deb and R. Poli and W. Banzhaf and H. Beyer and E. K. Burke and P. J. Darwen and D. Dasgupta and D. Floreano and J. A. Foster and M. Harman and O. Holland and P. Luca Lanzi and L. Spector and A. Tettamanzi and D. Thierens and A. M. Tyrrell}, volume = {1}, series = {Lecture Notes in Computer Science}, pages = {129-139}, address = {Berlin, Heidelberg}, publisher = {Springer}, ee = {http://www.elec.york.ac.uk/intsys/users/jfm7/gecco2004.pdf} } en article Federici, Diego et. al. Science / Artificial Life / Evo-Devo 2007-02-07 @article{1182793, author = {Diego Federici and Keith Downing}, title = {Evolution and development of a multicellular organism: scalability, resilience, and neutral complexification}, journal = {Artif. Life}, volume = {12}, number = {3}, year = {2006}, issn = {1064-5462}, pages = {381--409}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, url = {http://www.mitpressjournals.org/doi/abs/10.1162/artl.2006.12.3.381} } en article Troisi, Alessandro et. al. Science / Artificial Life / Artificial Chemistry 2007-02-14 @article{AlessandroTroisi01112005, author = {Alessandro Troisi and Vance Wong and Mark A. Ratner}, title = {{From The Cover: An agent-based approach for modeling molecular self-organization}}, journal = {PNAS}, volume = {102}, number = {2}, pages = {255-260}, doi = {10.1073/pnas.0408308102}, year = {2005}, URL = {http://www.pnas.org/cgi/content/abstract/102/2/255}, eprint = {http://www.pnas.org/cgi/reprint/102/2/255.pdf} } en article Bray, D. Science / Biology / GRN Erratum in: Nature 1995 Nov 23;378(6555):419. 2007-02-21 @article{citeulike:459559, abstract = {Many proteins in living cells appear to have as their primary function the transfer and processing of information, rather than the chemical transformation of metabolic intermediates or the building of cellular structures. Such proteins are functionally linked through allosteric or other mechanisms into biochemical 'circuits' that perform a variety of simple computational tasks including amplification, integration and information storage.}, address = {Department of Zoology, University of Cambridge, UK.}, author = {D. Bray}, citeulike-article-id = {459559}, doi = {10.1038/376307a0}, issn = {0028-0836}, journal = {Nature}, keywords = {cell compsci decision evolution informationtheory intro}, month = {July}, number = {6538}, pages = {307--312}, priority = {4}, title = {Protein molecules as computational elements in living cells.}, url = {http://dx.doi.org/10.1038/376307a0}, volume = {376}, year = {1995} } en article Bolouri, Hamid et. al. Science / Biology / GRN 2007-02-22 @article{citeulike:586426, author = {Hamid Bolouri and Eric H. Davidson}, citeulike-article-id = {586426}, journal = {PNAS}, keywords = {no-tag}, month = {August}, number = {16}, pages = {9371--9376}, priority = {2}, title = {Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics}, url = {http://www.pnas.org/cgi/content/abstract/100/16/9371}, volume = {100}, year = {2003} } en book Smith, John Maynard Science / Biology / Evolution 2007-02-28 @book{smith82, title = {Evolution and the Theory of Games}, address = {Cambridge, UK}, author = {John Maynard Smith}, publisher = {Cambridge University Press}, year = {1982}, keywords = {RMP_CFL game smith evolution theory 1982 maynard } } en book Volkenstein, M.V. Science / Physics / Biophysics 2007-02-28 @book{volkensteinBiophysics, title = {Physics and Biology}, address = {New York}, author = {M.V. Volkenstein}, publisher = {Academic Press}, year = {1982} } en book Hoppe, Walter et.al. Science / Physics / Biophysics 2007-01-01 @book{biophysicsReference, title = {Biophysics}, address = {Berlin}, author = {Walter Hoppe}, publisher = {Springer Verlag}, year = {1983} } en book Wolpert, Lewis et. al. Science / Biology / Morphogenesis 2007-03-01 @book{wolpertDevelopment, title = {Principles of Development}, address = {Oxford}, edition = {3rd}, author = {Lewis Wolpert and Thomas Jessell and Peter Lawrence and Elliot Meyerowitz and Elizabeth Robertson and Jim Smith}, publisher = {Oxford University Press}, year = {2007} } en article Furusawa, Chikara et. al. Science / Artificial Life / Evo-Devo 2007-03-02 @article{DBLP:journals/alife/FurusawaK98, author = {Chikara Furusawa and Kunihiko Kaneko}, title = {Emergence of Multicellular Organisms with Dynamic Differentiation and Spatial Pattern.}, journal = {Artificial Life}, volume = {4}, number = {1}, year = {1998}, pages = {79-93}, bibsource = {DBLP, http://dblp.uni-trier.de}, ee = {http://citeseer.ist.psu.edu/cache/papers/cs/28670/http:zSzzSzchaos.c.u-tokyo.ac.jpzSz%7EfurusawazSz.zSzresearchzSz.zSzalife1.pdf/furusawa98emergence.pdf} } en inproceedings Eggenberger-Hotz, Peter Science / Artificial Life / Morphogenesis 2007-03-04 @inproceedings{Eggenberger:1997:EMOS, title = {Evolving Morphologies of Simulated 3d Organisms Based on Differential Gene Expression}, author = {Peter Eggenberger-Hotz}, editor = {Husbands, P. and Harvey, I. }, booktitle = {Proceedings of the 4th European Conference on Artificial Life (ECAL97)}, year = {1997}, publisher = {MIT Press, Cambridge, MA}, ee={ftp://ftp.ifi.unizh.ch/pub/institute/ailab/techreports/97.20.ps.gz} } en unpublished Harding, S. et. al. Science / Artificial Life / Morphogenesis The original paper seems to be not included in the proceedings, see here: http://www.informatik.uni-trier.de/~ley/db/conf/gecco/gecco2006.html and here: http://portal.acm.org/citation.cfm?id=1143997 2007-03-05 @unpublished{deadstate06, author = {S. Harding and J. F. Miller}, title = {A comparison between developmental and direct encodings. An update of the GECCO 2006 Paper 'The Dead State'}, year = {2006}, note = {The original paper seems to be not included in the proceedings, see here http://portal.acm.org/citation.cfm?id=1143997}, ee = {http://www.cs.mun.ca/~simonh/publications/deadstateupdate.pdf} } en Book Lodish, Harvey F. et. al. Science / Biology / Molecular 2006-03-06 @Book{LodishMolCellBio, author = {Harvey F. Lodish and D. Baltimore and A. Berk and S. L. Zipursky and P. Matsudaira and James E. Darnell}, title = {Molecular Cell Biology}, publisher = {W. H. Freeman}, address = {New York, NY, USA}, edition = {Fifth}, year = {2004} } en book Meinhardt, Hans Science / Artificial Life / Morphogenesis 2007-03-14 @book{meinhardtBook, author={Hans Meinhardt}, title={Models of Biological Pattern Formation}, publisher={Academic Press, London}, year=1982, ee={http://www.eb.tuebingen.mpg.de/departments/former-departments/h-meinhardt/82-book/Bur82.htm} } en article Fontaneto, Diego et. al. Science / Biology / Evolution 2007-03-20 @article{citeulike:1177218, author = {Fontaneto, Diego and Herniou, Elisabeth A. and Boschetti, Chiara and Caprioli, Manuela and Melone, Giulio and Ricci, Claudia and Barraclough, Timothy G. }, citeulike-article-id = {1177218}, doi = {10.1371%2Fjournal.pbio.0050087}, journal = {PLoS Biology}, keywords = {biology evolution speciation}, month = {April}, number = {4}, pages = {e87+}, priority = {2}, title = {Independently Evolving Species in Asexual Bdelloid Rotifers}, url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050087}, volume = {5}, year = {2007} } en inproceedings Zykov, Viktor et. al. Science / Artificial Life / Evolutionary Algorithms 2007-03-20 @inproceedings{1078362, author = {Viktor Zykov and Josh Bongard and Hod Lipson}, title = {Co-evolutionary Variance Can Guide Physical Testing in Evolutionary System Identification}, booktitle = {EH '05: Proceedings of the 2005 NASA/DoD Conference on Evolvable Hardware}, year = {2005}, isbn = {0-7695-2399-4}, pages = {213--220}, doi = {http://dx.doi.org/10.1109/EH.2005.13}, publisher = {IEEE Computer Society}, address = {Washington, DC, USA}, url= {http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1508503}, ee={http://www.mae.cornell.edu/ccsl/papers/EH05_Zykov.pdf} } en article Hillis, W. Daniel Science / Artificial Life / Evolutionary Algorithms 2007-03-21 @article{87560, author = {W. Daniel Hillis}, title = {Co-evolving parasites improve simulated evolution as an optimization procedure}, journal = {Phys. D}, volume = {42}, number = {1-3}, year = {1990}, issn = {0167-2789}, pages = {228--234}, doi = {http://dx.doi.org/10.1016/0167-2789(90)90076-2}, publisher = {Elsevier Science Publishers B. V.}, address = {Amsterdam, The Netherlands, The Netherlands}, url = {http://dx.doi.org/10.1016/0167-2789(90)90076-2} } en book Schlosser, Gerhard et. al., ed. Science / Biology / Evo-Devo 2007-03-24 @book{citeulike:963266, citeulike-article-id = {963266}, editor = {Gerhard Schlosser and Gunter P. Wagner}, howpublished = {Paperback}, isbn = {0226738558}, keywords = {modularity}, month = {July}, priority = {2}, publisher = {University Of Chicago Press}, title = {Modularity in Development and Evolution}, year = {2004} } en article Meyers, Lauren A. et. al. Science / Biology / Evolution 2007-04-26 @article{87560, author = {Lauren A. Meyers and Fredric D. Ancel and Michael Lachmann}, title = {Evolution of Genetic Potential}, journal = {PLoS Computational Biology}, volume = {1}, number = {3}, year = {2005}, url = {http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0010032} } en article Burggren, W. W. et. al. Science / Biology / Complexity 2007-05-09 @article{citeulike:597615, address = {Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA}, author = {W. W. Burggren and M. G. Monticino}, doi = {10.1242/jeb.01762}, issn = {0022-0949}, journal = {J Exp Biol}, month = {September}, number = {Pt 17}, pages = {3221--3232}, title = {Assessing physiological complexity}, url = {http://dx.doi.org/10.1242/jeb.01762}, volume = {208}, year = {2005} } en article Weitz, Joshua S. et. al. Science / Biology / Evolution 2007-05-13 @article{citeulike:1060862, author = {Joshua S. Weitz and Philip N. Benfey and Ned S. Wingreen}, citeulike-article-id = {1060862}, doi = {10.1371%2Fjournal.pbio.0050011}, journal = {PLoS Biology}, keywords = {no-tag}, month = {January}, number = {1}, pages = {e11+}, priority = {2}, title = {Evolution, Interactions, and Biological Networks}, url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050011}, volume = {5}, year = {2007} } en article Wagner, Andreas Science / Biology / Evolution 2007-05-13 @article{citeulike:203500, author = {Andreas Wagner}, citeulike-article-id = {203500}, doi = {10.1093/molbev/msi126}, issn = {0737-4038}, journal = {Molecular Biology and Evolution}, month = {June}, number = {6}, pages = {1365--1374}, priority = {2}, publisher = {Oxford University Press}, title = {Energy Constraints on the Evolution of Gene Expression}, url = {http://mbe.oxfordjournals.org/cgi/content/full/22/6/1365}, volume = {22}, year = {2005} } en article Mazurie, A. et. al. Science / Biology / Evolution "The overabundance of the network motifs does not have any immediate functional or evolutionary counterpart. A likely reason is that motifs within the networks are not isolated, that is, they strongly aggregate and have important edge and/or node sharing with the rest of the network." 2007-05-14 @article{citeulike:307514, address = {Laboratoire de Genetique Moleculaire de la Neurotransmission et des Processus Neurodegeneratifs CNRS UMR 7091, CERVI La Pitie, 91-105 boulevard de l'o´pital, 75013 Paris, France. aurelien.mazurie@oenone.net}, author = {A. Mazurie and S. Bottani and M. Vergassola}, doi = {10.1186/gb-2005-6-4-r35}, issn = {1465-6914}, journal = {Genome Biol}, keywords = {no-tag}, number = {4}, priority = {2}, title = {An evolutionary and functional assessment of regulatory network motifs}, ee={http://genomebiology.com/2005/6/4/R35}, volume = {6}, year = {2005} } en article Yael, Artzy-Randrup, et. al. Science / Dynamical Systems Motifs could just be a by-product of network generation without the need for functional selection (for GRNs evolutionary mechanisms like gene duplication etc.). 2007-05-16 @article{YaelArtzy-Randrup08202004, author = {Artzy-Randrup, Yael and Fleishman, Sarel J. and Ben-Tal, Nir and Stone, Lewi}, title = {{Comment on "Network Motifs: Simple Building Blocks of Complex Networks" and "Superfamilies of Evolved and Designed Networks"}}, journal = {Science}, volume = {305}, number = {5687}, pages = {1107c-}, doi = {10.1126/science.1099334}, year = {2004}, ee = {http://www.sciencemag.org/cgi/reprint/305/5687/1107c.pdf} } en article Wuchty, S. et. al. Science / Biology / GRN 2007-05-17 @article{citeulike:347389, address = {Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA.}, author = {S. Wuchty and Z. N. Oltvai and A. L. Barabasi}, citeulike-article-id = {347389}, doi = {10.1038/ng1242}, issn = {1061-4036}, journal = {Nat Genet}, keywords = {no-tag}, month = {October}, number = {2}, pages = {176--179}, priority = {2}, title = {Evolutionary conservation of motif constituents in the yeast protein interaction network.}, url = {http://dx.doi.org/10.1038/ng1242}, volume = {35}, year = {2003} } en Book Roth, Philip Literature / Fiction 4 2007-05-25 en book Gavalda, Anna Literature / Fiction 2007-06-19 en Book Marias, Javier Literature / Fiction 2007-06-20 en Book Voltaire Literature / Fiction 2007-06-25 de Book Dath, Dietmar Literature 2007-06-25 de Book Hoelderlin, Friedrich Literature 2007-06-25 de Book Walser, Martin Literature 2007-06-25 de Book Goldt, Max Literature 2007-06-25 de Book Coetzee, J. M. Literature 2007-06-25 de Book Kirchner, Barbara and Dath, Dietmar Literature 2007-06-25 en article Balcan, D. et. al. Science / Biology / Molecular 2007-06-26 @article{balcan2007the, title = {The Information Coded in the Yeast Response Elements Accounts for Most of the Topological Properties of Its Transcriptional Regulation Network.}, author={D. Balcan and A. Kabakcioglu and M. Mungan and A. Erzan}, journal={PLoS ONE}, volume={2}, number={6}, pages={e501}, year={2007}, ee={http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000501} } en article Gross, Dominique et. al. Science / Artificial Life 2007-06-26 @article{599567, author = {Dominique Gross and Barry McMullin}, title = {Is it the right ansatz?}, journal = {Artif. Life}, volume = {7}, number = {4}, year = {2002}, issn = {1064-5462}, pages = {355--365}, ee = {http://dx.doi.org/10.1162/106454601317296997}, publisher = {MIT Press}, address = {Cambridge, MA, USA} } en article Hinman, Veronica F. et. al. Science / Biology / GRN 2007-07-09 @article{VeronicaFHinman11112003, author = {Hinman, Veronica F. and Nguyen, Albert T. and Cameron, R. Andrew and Davidson, Eric H.}, title = {{Developmental gene regulatory network architecture across 500 million years of echinoderm evolution}}, journal = {PNAS}, volume = {100}, number = {23}, pages = {13356-13361}, doi = {10.1073/pnas.2235868100}, year = {2003}, URL = {http://www.pnas.org/cgi/content/abstract/100/23/13356}, ee = {http://www.pnas.org/cgi/reprint/100/23/13356.pdf} } en article Barabasi, A. L. et. al. Science / Biology / Complexity 2007-07-09 @article{citeulike:268, address = {Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA. alb@nd.edu}, author = {Barabasi, A. L. and Oltvai, Z. N.}, citeulike-article-id = {268}, doi = {10.1038/nrg1272}, issn = {1471-0056}, journal = {Nat Rev Genet}, keywords = {no-tag}, month = {February}, number = {2}, pages = {101--113}, priority = {2}, title = {Network biology: understanding the cell's functional organization.}, url = {http://dx.doi.org/10.1038/nrg1272}, ee = {http://www.nd.edu/~networks/Publication%20Categories/03%20Journal%20Articles/Biology/NetworkBio_Nature%20Rev%20Genetics%205,%20101-113%20(2004).pdf}, volume = {5}, year = {2004} } en Book Winfree, Arthur T. Science / Biology / Molecular 2007-01-09 @Book{Winfree1980, author = {Arthur T. Winfree}, title = {The Geometry of Biological Time}, volume = "8", publisher = "Springer-Verlag", address = "Berlin, Germany", year = "1980", ISBN = "0-387-09373-7 (New York). 3-540-09373-7 (Berlin)", series = "Biomathematics" } en book Goldberg, David E. science / computer science / evolutionary algorithms 2004-07-11 @book{GoldbergGA, author = {Goldberg, David E.}, isbn = {0201157675}, month = {January}, publisher = {{Addison-Wesley Professional}}, title = {Genetic Algorithms in Search, Optimization, and Machine Learning}, year = {1989} } de Book Robbins, Tom Literature / Fiction 4 2007-07-14 en Book Russell, Bertrand Literature 2007-08-17 en Book Russell, Bertrand Literature 2007-08-18 en article Lungarella, Max et. al. Science / Dynamical Systems 2007-08-22 @article{citeulike917253, author = {Max Lungarella and Olaf Sporns}, doi = {10.1371%2Fjournal.pcbi.0020144}, journal = {PLoS Computational Biology}, month = {October}, number = {10}, pages = {e144+}, title = {Mapping Information Flow in Sensorimotor Networks}, url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.0020144}, volume = {2}, year = {2006} } en article Matos, Artur M. de et. al. Science / Artificial Life / Evo-Devo 2007-08-24 @article{citeulike1588176, author = {Artur M. de Matos and Reiji Suzuki and Takaya Arita}, doi = {10.1007/s10015-007-0425-0}, journal = {Artificial Life and Robotics}, month = {July}, number = {2}, pages = {175--182}, title = {Heterochrony and evolvability in neural network development}, volume = {11}, year = {2007}, ee = {www.alife.cs.is.nagoya-u.ac.jp/~reiji/publications/2006_alife_matos.pdf} } en Book Kandel, Eric R. Science / Biology / Molecular 2007-08-27 @book{KandelBook title={In Search of Memory : the emergence of a new science of mind}, author={Eric R. Kandel}, publisher={Norton}, year={2006}, address={New York, N.Y.}, edition={1st ed} } en article Zhou, Tong et. al. Science / Biology / Complexity 2007-09-03 @article{evoDynAndTolerance author = {Tong Zhou and J. M. Carlson and John Doyle}, doi = {10.1016/j.jtbi.2005.03.023}, journal = {Journal of Theoretical Biology}, month = {October}, number = {4}, pages = {438--447}, priority = {2}, title = {Evolutionary dynamics and highly optimized tolerance}, volume = {236}, year = {2005}, ee = {http://www.physics.ucsb.edu/~complex/pubs/JTB_236.pdf} } en article Kauffman, Stuart Science / Biology / Origin of Life 2007-09-03 @article{KauffmanOrigin author = {Stuart Kauffman}, doi = {10.1007/s11084-007-9093-2}, journal = {Origins of Life and Evolution of Biospheres}, month = {October}, number = {4}, pages = {315--322}, priority = {2}, title = {Question 1: Origin of Life and the Living State}, volume = {37}, year = {2007} } en inproceedings Madina, Duraid et. al. Science / Artificial Life / Artificial Chemistry 2007-09-04 @inproceedings{DBLP:conf/ecal/MadinaOI03, author = {Duraid Madina and Naoaki Ono and Takashi Ikegami}, title = {Cellular Evolution in a 3D Lattice Artificial Chemistry}, booktitle = {ECAL}, year = {2003}, pages = {59-68}, ee = {http://sacral.c.u-tokyo.ac.jp/~ikeg/publications/duraidECAL.pdf}, bibsource = {DBLP, http://dblp.uni-trier.de} } en Article Mayer, Bernd et. al. Science / Artificial Life / Artificial Chemistry 2007-09-04 @Article{PhysRevE.55.4489, title = {Simulation and dynamics of entropy-driven, molecular self-assembly processes }, author = {Bernd Mayer and Gottfried Koehler and Steen Rasmussen}, journal = {Phys. Rev. E}, volume = {55}, number = {4}, pages = {4489--4499}, numpages = {10}, year = {1997}, month = {Apr}, doi = {10.1103/PhysRevE.55.4489}, publisher = {American Physical Society} } en book Maynard Smith, John Science / Biology / Evolution 2007-09-06 @book{MSbooklet title={Shaping Life - Genes, Embryos and Evolution}, author={John Maynard-Smith}, publisher={Weidenfeld and Nicolson}, year={1998}, address={London} } en article Hess, Benno et. al. science / biology / self-organization "The random Brownian motion of macromolecules inside cells is extremely strong. Our estimates of a characteristic traffic time show that within a compartment of a micrometer size any two molecules meet each other within a time of about 1 s." 2007-09-13 @article{SelfOrgCells author = {Benno Hess and Alexander Mikhailov}, title = {Self-Organization in Living Cells}, journal = {Science}, volume = {264}, pages = {223--224}, year = {1994} } en ARTICLE Mikhailov, A.S. et. al. science / biology / self-organization "[...] to seconds (and even much more for the machines involved in genetic expression). For such machines, dynamical processes of conformational relaxation which are responsible for their operation may be significantly longer than all diffusion times characterizing intramolecular communication." 2007-09-14 @ARTICLE{mikhailov02, AUTHOR = {A.S. Mikhailov and B. Hess}, TITLE = {Self-Organization in Living Cells: Networks of Protein Machines and Nonequilibrium Soft Matter}, JOURNAL = {Journal of Biological Physics}, YEAR = {2002}, VOLUME = {28}, NUMBER = {4}, PAGES = {655--672}, url = {http://dx.doi.org/10.1023/A:1021247024192} } de book Enzensberger, Hans M. literature 2003-01-01 en book Maugham, William Somerset literature 5 2007-09-18 en book Orwell, George literature 2007-09-19 en article Gardner, T. S. et. al. science / biology / grn 2007-09-21 @article{citeulike:312, address = {Department of Biomedical Engineering, Center for BioDynamics, Boston University, Massachusetts 02215, USA.}, author = {T. S. Gardner and C. R. Cantor and J. J. 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Martin and Andreas Wagner}, doi = {10.1371/journal.pcbi.0030015}, journal = {PLoS Computational Biology}, month = {February}, number = {2}, pages = {e15+}, title = {Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology}, volume = {3}, url = {http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030015}, year = {2007} } en article Rodrigo, Guillermo et. al. science / biology / grn 2007-09-21 @article{citeulike:1460081, author = {Guillermo Rodrigo and Javier Carrera and Alfonso Jaramillo}, doi = {10.2478/s11535-007-0016-z}, journal = {Central European Journal of Biology}, month = {June}, number = {2}, pages = {233--253}, priority = {5}, title = {Evolutionary mechanisms of circadian clocks}, url = {http://dx.doi.org/10.2478/s11535-007-0016-z}, volume = {2}, year = {2007} } en article Cordero, O.X. et. al. science / biology / evolution 2007-10-09 @article{cordero2006fee, title = {Feed Forward Loop Circuits as a Side Effect of Genome Evolution.}, author={O.X. 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Hogeweg}, journal={Mol Biol Evol}, year={2006}, ee={http://mbe.oxfordjournals.org/cgi/content/full/23/10/1931} } en article van Noort, Vera et. al. science / artificial life / genetic regulatory networks 2007-10-09 @article{NoortGenoEvo, author = {Vera van Noort and Berend Snel and Martijn Huynen}, journal = {EMBO Reports}, month = {March}, number = {3}, pages = {280--284}, priority = {2}, title = {The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1299002}, volume = {5}, year = {2004} } en book Kauffman, Stuart science / physics / thermodynamics "An autonomous agent must be an autocatalytic system able to reproduce and able to perform one or more thermodynamic work cycles." 2007-10-13 en book Bukowski, Charles literature 2007-10-23 en book Bellamy, Edward literature / fiction / utopia 2007-10-02 en book Juenger, Ernst literature / fiction / utopia 2007-10-23 en book Flaubert, Gustave literature 2007-10-20 en article Gould, S. J. et. al. science / biology / evolution Argues against adaptationist assumption - the tendency to assume that everything which is present in an organism must be an adaptation (rather than being e.g. a random effect, or not selected against, or due to mathematico-physical constraint, due to a developmental constraint, etc.). 2007-10-29 @article{gould, author = {S. J. Gould and R. C. Lewontin}, issn = {0080-4649}, journal = {Proc R Soc Lond B Biol Sci}, month = {September}, number = {1161}, pages = {581--598}, priority = {2}, title = {The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme.}, ee = {http://www.blackwellpublishing.com/ridley/classictexts/gould.pdf}, volume = {205}, year = {1979} } en article Wolpert, Lewis science / biology / evo-devo 2007-11-10 @article{wolpertPositional, author = {Lewis Wolpert}, year = {1996}, pages = {359--364}, journal= {Trends in Genetics}, title = {One hundred years of positional information} } en article Jaeger, Johannes et. al. science / biology / evo-devo 2007-11-10 @article{JaegerDynamicPositional, address = {Laboratory of Development and Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-3600, USA}, author = {Johannes Jaeger and John Reinitz}, doi = {10.1002/bies.20494}, journal = {BioEssays}, number = {11}, pages = {1102--1111}, title = {On the dynamic nature of positional information}, url = {http://dx.doi.org/10.1002/bies.20494}, volume = {28}, year = {2006} } en article Monk, N. A. science / biology / evo-devo 2007-11-10 @article{monk1997cel, title = {Cell communities and robustness in development.}, author={N. A. Monk}, journal={Bull Math Biol}, volume={59}, number={6}, pages={1183-9}, year={1997} } en article Volkert, Gwenn L. et. al. science / artificial life / evo-devo 2007-11-10 @article{VolkertWeakInteractions, author = {Gwenn L. Volkert and Michael Conrad}, doi = {10.1006/jtbi.1998.0700}, journal = {Journal of Theoretical Biology}, month = {July}, number = {2}, pages = {287--306}, title = {The Role of Weak Interactions in Biological Systems: the Dual Dynamics Model}, url = {http://www.sciencedirect.com/science/article/B6WMD-45J5B55-3C/2/3a4aeea9fe010484638819899129c80a}, volume = {193}, year = {1998} } en article Gilbert, S.F. et. al. science / biology / evo-devo 2007-11-11 @article{gilbert1996res, title = {Resynthesizing evolutionary and developmental biology.}, author={S.F. Gilbert and J.M. Opitz and R.A. 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Rev.}, month = {December}, number = {4}, pages = {544--564}, priority = {2}, title = {Molecules into Cells: Specifying Spatial Architecture}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16339735}, volume = {69}, year = {2005} } en article Weiss, Kenneth M. science / artificial life / evo-devo 2007-11-14 @article{citeulike:72105, author = {Kenneth M. Weiss}, doi = {10.1038/nrg1502}, issn = {1471-0056}, journal = {Nature Reviews Genetics}, month = {January}, number = {1}, pages = {36--45}, publisher = {Nature Publishing Group}, title = {The phenogenetic logic of life}, url = {http://dx.doi.org/10.1038/nrg1502}, volume = {6}, year = {2005} } en book Carroll, Sean B. et. al. Science / Biology / Evo-Devo 2006-02-14 @book{DNAtoDiversity, author = {Sean B. Carroll and Jennifer K. Grenier and Scott D. Weatherbee}, isbn = {0632045116}, publisher = {{Blackwell Science}}, title = {From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design}, year = {2001} } en article Carroll, Sean B. science / biology / evo-devo 2007-11-14 @article{ChanceandNecessity, author = {Sean B. Carroll}, doi = {10.1038/35059227}, journal = {Nature}, number = {6823}, pages = {1102--1109}, title = {Chance and necessity: the evolution of morphological complexity and diversity}, url = {http://dx.doi.org/10.1038/35059227}, volume = {409}, year = {2001} } en ARTICLE Wilke, Claus O. science / biology / evolution 2007-11-15 @ARTICLE{wilke-2005-5, author = {Claus O. Wilke}, title = {Quasispecies theory in the context of population genetics}, journal = {BMC Evolutionary Biology}, volume = {5}, pages = {44}, url = {http://www.citebase.org/abstract?id=oai:pubmedcentral.gov:1208876}, year = {2005} } en article Rasmussen, Steen et. al. science / artificial evolution 2007-11-19 @article{SteenRasmussen02132004, author = {Steen Rasmussen and Liaohai Chen and David Deamer and David C. Krakauer and Norman H. Packard and Peter F. Stadler and Mark A. Bedau}, title = {{EVOLUTION: Transitions from Nonliving to Living Matter}}, journal = {Science}, volume = {303}, number = {5660}, pages = {963-965}, doi = {10.1126/science.1093669}, year = {2004}, ee = {http://www.sciencemag.org/cgi/reprint/303/5660/963.pdf} } en book Gerhart, John C. et. al. science / biology / evo-devo 4 2007-11-20 @book{GerhartMorphogenesis, author = {John C. Gerhart and Marc Kirschner}, howpublished = {Paperback}, isbn = {0865425744}, month = {June}, publisher = {{Blackwell Publishing}}, title = {{Cells, Embryos And Evolution}}, year = {1997} } en article Kirschner, M. et. al. science / biology / evolvability 2007-11-20 @article{citeulike:1112, address = {Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. marc@hms.harvard.edu}, author = {M. Kirschner and J. Gerhart}, doi = {10.1073/pnas.95.15.8420}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, month = {July}, number = {15}, pages = {8420--8427}, title = {Evolvability}, url = {http://dx.doi.org/10.1073/pnas.95.15.8420}, volume = {95}, year = {1998} } en article West-Eberhard, Mary J. science / biology / evolvability 2007-11-20 @article{citeulike:1943807, author = {Mary J. West-Eberhard}, doi = {10.1073/pnas.95.15.8417}, journal = {Proceedings of the National Academy of Sciences}, month = {July}, number = {15}, pages = {8417--8419}, title = {Evolution in the light of developmental and cell biology, and vice versa}, url = {http://view.ncbi.nlm.nih.gov/pubmed/9671691}, volume = {95}, year = {1998} } en article Davidson, Eric H science / biology / morphogenesis 2007-12-02 @article{DavidsonSpatial, author = {Eric H Davidson}, journal = {Development}, month = {September}, number = {1}, pages = {1--26}, priority = {2}, title = {Spatial mechanisms of gene regulation in metazoan embryos}, url = {http://dev.biologists.org/cgi/content/abstract/113/1/1}, volume = {113}, year = {1991} } en article Conrad, Michael science / biology / evolvability 2007-12-03 @article{ConradEvolvability, author = {Michael Conrad}, journal = {Biosystems}, number = {1}, pages = {61--81}, priority = {2}, title = {The geometry of evolution}, url = {http://dx.doi.org/10.1016/0303-2647(90)90030-5}, volume = {24}, year = {1990} } de book Eigen, Manfred science / biology / origin of life 2007-12-04 en article Meinhardt, Hans science / biology / morphogenesis 2007-12-04 @article{citeulike:2057141, author = {Hans Meinhardt}, doi = {10.1016/0022-5193(78)90078-4}, journal = {Journal of Theoretical Biology}, month = {September}, number = {2}, pages = {307--321}, priority = {2}, title = {Space-dependent cell determination under the control of a morphogen gradient}, ee = {http://www.eb.tuebingen.mpg.de/departments/former-departments/h-meinhardt/Old%20Paper%20PDF/78-genes.pdf}, url = {http://www.eb.tuebingen.mpg.de/departments/former-departments/h-meinhardt/genes.html}, volume = {74}, year = {1978} } en article Meinhardt, Hans science / biology / morphogenesis 2007-12-04 @article{meinhardt1983a, title = {A boundary model for pattern formation in vertebrate limbs}, author={Hans Meinhardt}, journal={J Embryol Exp Morphol}, volume={76}, year={1983}, ee = {http://www.eb.tuebingen.mpg.de/departments/former-departments/h-meinhardt/Old%20Paper%20PDF/83-boundery-vertebrate-limb.pdf}, url = {http://www.eb.tuebingen.mpg.de/departments/former-departments/h-meinhardt/cooperat.html} } en book Lee, Harper literature 2007-12-01 de book Hesse, Hermann literature 4 2008-01-06 de book Arendt, Hannah sociology / politics 2008-01-06 en book Bernstein, Peter L. science / popular science 2008-01-08 en Article Glazier, James A. et. al. science / biology / self-organization Show that self-organization due to few basic cell properties alone are enough to explain a number of biological phenomena. Also lovely model! 2008-01-18 @Article{PhysRevE.47.2128, title = {Simulation of the differential adhesion driven rearrangement of biological cells}, author = {James A. Glazier and Francois Graner}, journal = {Phys. Rev. E}, volume = {47}, number = {3}, pages = {2128--2154}, numpages = {26}, year = {1993}, month = {Mar}, doi = {10.1103/PhysRevE.47.2128}, publisher = {American Physical Society} } en article Hogeweg, Paulien science / artificial life / evo-devo 2008-01-18 @article{HogewegEvoDyn, author = {Paulien Hogeweg}, title = {Shapes in the Shadow: Evolutionary Dynamics of Morphogenesis}, journal = {Artificial Life}, volume = {6}, number = {1}, pages = {85-101}, year = {2000}, doi = {10.1162/106454600568339}, ee = {http://www.mitpressjournals.org/doi/pdf/10.1162/106454600568339} } en book Marquez, Gabriel Garcia literature / fiction 2008-02-15 en article Merks, R. M. H. et. al. science / biology / self-organization 2008-02-17 @article{2005cel, title = {Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling.}, author={R. M. H. Merks and S. V. Brodsky and M. S. Goligorsky and S. A. Newman and J. A. Glazier}, journal={Dev Biol}, volume={289}, pages={44--54}, year={2006} } en article Cickovski, Trevor et. al. science / biology / morphogenesis CompuCell3D description article 2008-02-17 @article{1271973, author = {Trevor Cickovski and Kedar Aras and Maciej Swat and Roeland M. H. Merks and Tilmann Glimm and H. George E. Hentschel and Mark S. Alber and James A. Glazier and Stuart A. Newman and Jesus A. Izaguirre}, title = {From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development}, journal = {Computing in Science and Engg.}, volume = {9}, number = {4}, year = {2007}, issn = {1521-9615}, pages = {50--60}, doi = {http://dx.doi.org/10.1109/MCSE.2007.74}, publisher = {IEEE Educational Activities Department}, address = {Piscataway, NJ, USA} } en article Merks, R. M. H. et. al. science / biology / morphogenesis Why can / should we use the potts model 2008-02-17 @article{273, author = {R. M. H. Merks and J. A. Glazier}, journal = {Physica A: Statistical Mechanics and its Applications}, month = {July}, number = {1}, pages = {113--130}, title = {A cell-centered approach to developmental biology}, volume = {352}, year = {2005} } en book Maupassant, Guy de literature 2008-02-19 en article Dan, Debasis et. al. science / physics / biophysics description of advection / diffusion and viscosity potts implementation 2008-02-20 @article{dan:041909, author = {Debasis Dan and Chris Mueller and Kun Chen and James A. Glazier}, title = {Solving the advection-diffusion equations in biological contexts using the cellular Potts model}, publisher = {APS}, year = {2005}, journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)}, volume = {72}, number = {4}, eid = {041909}, numpages = {10}, pages = {041909}, keywords = {cellular transport; biological tissues; biodiffusion; Potts model; finite difference methods}, url = {http://link.aps.org/abstract/PRE/v72/e041909}, doi = {10.1103/PhysRevE.72.041909} } en book Anderson, Alexander R.A. et. al., ed. science / biology / cell models 2008-02-21 @book{SingleCellBasedModels, editor = {Alexander R.A. Anderson and Mark Chaplain and Katarzyna A. Rejniak}, isbn = {9783764381011}, publisher = {Birkhaeuser}, title = {Single-Cell-Based Models in Biology and Medicine}, ee = {http://www.myebookshare.info/biology-chemistry/single-cell-based-models-in-biology-and-medicine.html}, year = {2007} } en article Zajac, Mark et. al. science / biology / cell models 2008-02-26 @article{ZajacPotts, author = {Mark Zajac and Gerald L. Jones and James A. Glazier}, doi = {10.1016/S0022-5193(03)00033-X}, journal = {Journal of Theoretical Biology}, month = {May}, number = {2}, pages = {247--259}, title = {Simulating convergent extension by way of anisotropic differential adhesion}, url = {http://dx.doi.org/10.1016/S0022-5193(03)00033-X}, volume = {222}, year = {2003} } en inproceedings Devert, Alexandre et. al. science / artificial life / morphogenesis 2008-03-05 @inproceedings{1277156, author = {Alexandre Devert and Nicolas Bredeche and Marc Schoenauer}, title = {Robust multi-cellular developmental design}, booktitle = {GECCO '07: Proceedings of the 9th annual conference on Genetic and evolutionary computation}, year = {2007}, isbn = {978-1-59593-697-4}, pages = {982--989}, location = {London, England}, doi = {http://doi.acm.org/10.1145/1276958.1277156}, publisher = {ACM}, address = {New York, NY, USA}, ee={http://eprints.pascal-network.org/archive/00003167/01/article.pdf} } en inproceedings Federici, D. science / artificial life / morphogenesis 2008-03-05 @inproceedings{federiciworlds, author = {D. Federici}, title = {Increasing evolvability for developmental programs}, booktitle = {proceeding of the Workshop on Regeneration and Learning in Developmental Systems, WORLDS 2004}, editor = {J. Miller}, year = {2004}, url = {citeseer.ist.psu.edu/federici04using.html} } en article Turing, A. M. science / biology / self-organization 2008-03-05 @article{Turing1952tcb, author = {A. M. Turing}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, month = {August}, number = {641}, pages = {37--72}, priority = {4}, title = {The Chemical Basis of Morphogenesis}, volume = {237}, year = {1952} } en article Huang, Sui et. al. science / biology / grn 2008-04-21 @article{citeulike:2697377, author = {Sui Huang and Donald E. 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Bonner}, publisher = {{Princeton University Press}}, Address={Princeton}, title = {First signals: The evolution of multicellular development}, year = {2001} } en article Sengupta, A. M. et. al. science / biology / grn 2008-08-28 @article{TranscriptionSpecificity, address = {Bell Laboratories, Lucent Technologies, Murray Hill, NJ 07974, USA.}, author = {A. M. Sengupta and M. Djordjevic and B. I. Shraiman}, journal = {Proc Natl Acad Sci U S A}, month = {February}, number = {4}, pages = {2072--2077}, title = {Specificity and robustness in transcription control networks}, url = {http://dx.doi.org/10.1073/pnas.022388499}, volume = {99}, year = {2002} } en article Black, D. L. science / biology / molecular 2008-09-01 @article{alternativeSplicingReview, author = {D. L. Black}, doi = {10.1146/annurev.biochem.72.121801.161720}, issn = {0066-4154}, journal = {Annu Rev Biochem}, pages = {291--336}, title = {Mechanisms of alternative pre-messenger RNA splicing.}, url = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.72.121801.161720}, volume = {72}, year = {2003} } de book Goethe, J.W. literature I & II 2002-09-19 de book Ibsen, Henrik literature 2003-03-19 en book Forgacs, G. et. al. science / physics / biophysics 2008-09-26 @book{Forgacs2005, author = {G. Forgacs and S. Newman}, publisher = {Cambridge University Press}, title = {Biological physics of the developing embryo}, year = {2005} } en book Maugham, Somerset W. literature 2008-10-23 en article Carroll, Sean B. science / biology / evo-devo 2008-10-24 @article{CarrollEvoDevoCell, author = {Carroll, Sean B.}, doi = {http://dx.doi.org/10.1016/j.cell.2008.06.030}, journal = {Cell}, month = {July}, number = {1}, pages = {25--36}, title = {Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution}, url = {http://dx.doi.org/10.1016/j.cell.2008.06.030}, volume = {134}, year = {2008} } en article Stricker, Jesse et. al. science / biology / molecular 2008-11-06 @article{EcoliOscillator, author = {Jesse Stricker and Scott Cookson and Matthew R. Bennett and William H. Mather and Lev S. Tsimring and Jeff Hasty}, doi = {http://dx.doi.org/10.1038/nature07389}, issn = {1476-4687}, journal = {Nature}, month = {October}, title = {A fast, robust and tunable synthetic gene oscillator.}, url = {http://dx.doi.org/10.1038/nature07389}, year = {2008} } en article Crombach, Anton et. al. science / artificial life / evolvability 2008-11-10 @article{citeulike:2994233, author = {Anton Crombach and Paulien Hogeweg}, doi = {http://dx.doi.org/10.1371/journal.pcbi.1000112}, journal = {PLoS Comput Biol}, month = {July}, number = {7}, publisher = {Public Library of Science}, title = {Evolution of Evolvability in Gene Regulatory Networks}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000112}, volume = {4}, year = {2008} } en inproceedings Hallinan, Jennifer et. al. science / artificial life / genetic regulatory networks 2008-11-10 @inproceedings{citeulike:3194351, author = {Jennifer Hallinan and Janet Wiles}, booktitle = {Second Asia-Pacific Bioinformatics Conference (APBC2004). Volume 29 of CRPIT., Dunedin, New Zealand, ACS (2004) 291}, pages = {291--296}, title = {Evolving genetic regulatory networks using an artificial genome}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.5.7076}, volume = {29}, year = {2004} } en article Tyson, John J. et. al. science / biology / grn 2008-11-10 @article{citeulike:3362959, author = {John J. Tyson and Reka Albert and Albert Goldbeter and Peter Ruoff and Jill Sible}, doi = {http://dx.doi.org/10.1098/rsif.2008.0179.focus}, journal = {Journal of The Royal Society Interface}, number = {0}, pages = {S1--S8}, title = {Biological switches and clocks}, volume = {5}, year = {2008} } en article Bornholdt, Stefan science / biology / grn 2008-11-11 @article{citeulike:360714, author = {Stefan Bornholdt}, doi = {http://dx.doi.org/10.1126/science.1119959}, journal = {Science}, month = {October}, number = {5747}, pages = {449--451}, title = {Systems Biology: Less Is More in Modeling Large Genetic Networks}, url = {http://dx.doi.org/10.1126/science.1119959}, volume = {310}, year = {2005} } en inproceedings Drennan, Barry et. al. science / artificial life / genetic regulatory networks 2008-11-11 @inproceedings{citeulike:1075343, author = {Barry Drennan and Randall D. 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Emergence of patterns and genotype-phenotype relationships}, journal = {Evolution & Development}, volume = {3}, year = {March 2001}, pages = {84-94(11)} } en article Francois, P. et. al. science / artificial life / genetic regulatory networks 2008-11-16 @article{citeulike:203814, address = {Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique-Unit'{e} Mixte de Recherche 8550, Ecole Normale Sup'{e}rieure, 24, Rue Lhomond, 75231 Paris, France.}, author = {P. Francois and V. Hakim}, doi = {http://dx.doi.org/10.1073/pnas.0304532101}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, month = {January}, number = {2}, pages = {580--585}, title = {Design of genetic networks with specified functions by evolution in silico.}, volume = {101}, year = {2004} } en INPROCEEDINGS Miller, Julian F. science / artificial life / evo-devo 2008-11-20 @INPROCEEDINGS{Miller03evolvingdevelopmental, author = {Julian F. Miller}, title = {Evolving developmental programs for adaptation, morphogenesis, and self-repair}, booktitle = {Proceeding of ECAL 2003}, year = {2003}, pages = {256--265}, publisher = {Springer} } en InProceedings Joachimczak, M. et. al. science / artificial life / evo-devo 2008-11-20 @InProceedings{joachimczak3dEvoDevo, Author = {M. Joachimczak and B. Wrobel}, Title = {Evo-devo in silico: a model of a gene network regulating multicellular development in 3D space with artificial physics}, Editor = {S. Bullock and J. Noble and R. Watson and M. A. Bedau}, BookTitle = {Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems}, Publisher = {MIT Press, Cambridge, MA}, Year = {2008}, Pages = {297--304}, EE = {http://www.alifexi.org/papers/ALIFExi_pp297-304.pdf} } en inproceedings Fleischer, Kurt et. al. science / artificial life / evo-devo 2008-11-20 @inproceedings{fleischerDevel, author = {Kurt Fleischer and Alan H. 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Series B: Biological Sciences}, month = {May}, number = {1422}, pages = {883--892}, title = {Competition for neurotrophic factor in the development of nerve connections}, url = {http://dx.doi.org/10.1098/rspb.1999.0719}, volume = {266}, year = {1999} } en Article Ooyen, Arjen van science / artificial life / neurogenesis 2010-05-08 @Article{synapseGrowthComp01, AUTHOR = {Arjen van Ooyen} TITLE = {Competition in the development of nerve connections: a review of models.}, JOURNAL = {Network}, VOLUME = {12}, YEAR = {2001}, NUMBER = {1}, PAGES = {R1-47}, URL = {http://www.biomedsearch.com/nih/Competition-in-development-nerve-connections/11254084.html}, PubMedID = {11254084}, ISSN = {0954-898X}, } de book Lem, Stansilaw literature / fiction 2010-05-01 de book Fromm, Erich philosophy 2010-04-08 de book Coetzee, J. M. literature / biography 2010-05-03