Evolvable Virtual Machines

The Evolvable Virtual Machine abstract architecture (EVMA) is a computational architecture for dynamic hierarchically organised virtual machines. The concrete EVM instantiation (EVMI) builds on traditional stack-based models of computation and extends them by notions of hierarchy and reflection on the virtual machine level. The EVM Universe is composed of a number of autonomous and asynchronously communicating EVM machines. The main contribution of this work lies in the new model of computation and in the architecture itself: a novel, compact, flexible and expressive representation of distributed concurrent computation. The EVMA provides a way of expressing and modelling auto-catalytic networks composed of a hierarchical hypercycle of autopoietic subsystems characterised by self-adaptable structural tendencies and self-organised criticality. EVMA provides capabilities for: a) self-learning of dynamical patterns through continuous observation of computable environments, b) self-compacting and generalisation of existing program structures, c) emergence of efficient and robust communication code through appropriate machine assembly on both ends of communication channel. EVMA is in one sense a multi-dimensional generalisation of stack machine with the purpose of modelling concurrent asynchronous processing. EVMA approach can be also seen as a meta-evolutionary theory of evolution. The EVMA is designed to model systems that mimic living autonomous and adaptable computational processes. The EVMI prototype has been designed and developed to conduct experimental studies on complex evolving systems. The generality of our approach not only provides the means to experiment with complex hierarchical, computational and evolutionary systems, but it provides a useful model to evaluate, share and discuss the complex hierarchical systems in general. The EVMA provides a novel methodology and language to pursue research, to understand and to talk about evolution of complexity in living systems. In this thesis, we present the simple single-cell EVMI framework, discuss the multi-cell EVM Universe architecture, present experimental results, and propose further extensions, experimental studies, and possible hardware implementations of the EVMI.

[1]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[2]  J. Ziegler,et al.  Artificial Chemistries-A Review , 2001 .

[3]  John R. Koza,et al.  Gene Duplication to Enable Genetic Programming to Concurrently Evolve Both the Architecture and Work-Performing Steps of a Computer Program , 1995, IJCAI.

[4]  G. Nagarjuna,et al.  The Role of Inversion in the Genesis, Development and the Structure of Scientific Knowledge , 1994 .

[5]  P. Ricoeur,et al.  Hermeneutics and the Human Sciences: Essays on Language, Action and Interpretation , 2016 .

[6]  J. F. Thomson,et al.  Tasks and Super-Tasks , 1954 .

[7]  Clive Fitts Man and His Science , 1969 .

[8]  G. Chaitin Meta Math!: The Quest for Omega , 2004, math/0404335.

[9]  Eörs Szathmáry,et al.  The Major Transitions in Evolution , 1997 .

[10]  Jens H. Krüger,et al.  GPGPU: general purpose computation on graphics hardware , 2004, SIGGRAPH '04.

[11]  Russell K. Standish Prospects for Open-Ended Evolution in Artificial Life , 2001 .

[12]  Riccardo Poli,et al.  Why “Building Blocks” Don’t Work on Parity Problems , 1998 .

[13]  Barry McMullin Computational Autopoiesis: The Original Algorithm , 1997 .

[14]  Corso Elvezia A General Method for Incremental Self-improvement and Multi-agent Learning in Unrestricted Environments , 1996 .

[15]  Riccardo Poli,et al.  Foundations of Genetic Programming , 1999, Springer Berlin Heidelberg.

[16]  Rocco De Nicola,et al.  CCS without tau's , 1987, TAPSOFT, Vol.1.

[17]  A. Gray,et al.  I. THE ORIGIN OF SPECIES BY MEANS OF NATURAL SELECTION , 1963 .

[18]  Charles Ofria,et al.  Avida , 2004, Artificial Life.

[19]  Christian Piguet,et al.  Embryological development on silicon , 1994 .

[20]  Thomas S. Ray,et al.  An Evolutionary Approach to Synthetic Biology: Zen and the Art of Creating Life , 1993, Artificial Life.

[21]  Vannevar Bush,et al.  As we may think , 1945, INTR.

[22]  G. Odell,et al.  Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network. , 2002, The Journal of experimental zoology.

[23]  Cristian S. Calude,et al.  Discrete Mathematics and Theoretical Computer Science , 2003, Lecture Notes in Computer Science.

[24]  E. Schrödinger,et al.  What is life? : the physical aspect of the living cell , 1946 .

[25]  Ann,et al.  Truth and method , 1994, Journal of Religion and Health.

[26]  J. L. King,et al.  Non-Darwinian evolution. , 1969, Science.

[27]  David M. Raup,et al.  How Nature Works: The Science of Self-Organized Criticality , 1997 .

[28]  Dina Q. Goldin,et al.  Interaction, Computability, and Church's Thesis Interaction, Computability, and Church's Thesis Contents 1. Interaction Machines 1.1. Sequential Interaction Machines (sims) 1.2. Interactive Behavior and Expressiveness 1.3. Multi-stream Interaction Machines (mims) 2. Extensions of Expressiveness 2.1. , 1999 .

[29]  Peter Nordin,et al.  A compiling genetic programming system that directly manipulates the machine-code , 1994 .

[30]  Bentley Glass,et al.  Forerunners of Darwin, 1745-1859 , 1959 .

[31]  Robin Milner,et al.  A Calculus of Mobile Processes, II , 1992, Inf. Comput..

[32]  Wolfgang Banzhaf,et al.  Linear-Tree GP and Its Comparison with Other GP Structures , 2001, EuroGP.

[33]  Moshe Sipper,et al.  Fifty Years of Research on Self-Replication: An Overview , 1998, Artificial Life.

[34]  M. Delorme,et al.  An Introduction to Cellular Automata , 1999 .

[35]  Karl Svozil,et al.  Computational universes , 2003, physics/0305048.

[36]  L. Margulis Symbiosis in cell evolution: Life and its environment on the early earth , 1981 .

[37]  J. Neumann The General and Logical Theory of Au-tomata , 1963 .

[38]  J. Vogel,et al.  RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. , 2003, Nucleic acids research.

[39]  B. Jack Copeland,et al.  The Broad Conception of Computation , 1997 .

[40]  Betsey Dexter Dyer,et al.  The origin of eukaryotic cells , 1985 .

[41]  James S. Albus,et al.  New Approach to Manipulator Control: The Cerebellar Model Articulation Controller (CMAC)1 , 1975 .

[42]  M. Heidegger,et al.  Introduction to Metaphysics , 2017 .

[43]  R. Badii,et al.  Complexity: Hierarchical Structures and Scaling in Physics , 1997 .

[44]  R. Punnett,et al.  The Genetical Theory of Natural Selection , 1930, Nature.

[45]  Carlo C. Maley,et al.  Four steps toward open-ended evolution , 1999 .

[46]  H. Maturana,et al.  Autopoiesis and Cognition : The Realization of the Living (Boston Studies in the Philosophy of Scie , 1980 .

[47]  George C. Williams,et al.  Adaptation and Natural Selection , 2018 .

[48]  Moshe Sipper Notes on the origin of evolutionary computation , 1999, Complex..

[49]  Lee Spector,et al.  Genetic Programming and Autoconstructive Evolution with the Push Programming Language , 2002, Genetic Programming and Evolvable Machines.

[50]  H. Gadamer,et al.  Heidegger's Ways , 1993 .

[51]  Jeffrey D. Ullman,et al.  Introduction to Automata Theory, Languages and Computation , 1979 .

[52]  Stephen Jay Gould,et al.  An Urchin in the Storm , 1987 .

[53]  Harold C. Morris Typogenetics: A Logic for Artificial Life , 1987, ALIFE.

[54]  Antonio Lima-de-Faria,et al.  Evolution without selection : form and function by autoevolution , 1988 .

[55]  Emin Erkan Korkmaz,et al.  Controlled Genetic Programming Search for Solving Deceptive Problems , 2002, GECCO Late Breaking Papers.

[56]  Alfred Russel Wallace,et al.  Contributions to the Theory of Natural Selection: On the Tendency of Varieties to depart indefinitely from the Original Type , 2016 .

[57]  Lamberto Cesari,et al.  Optimization-Theory And Applications , 1983 .

[58]  P. Raven,et al.  ORIGIN OF EUKARYOTIC CELLS , 1971 .

[59]  Albert-László Barabási,et al.  Statistical mechanics of complex networks , 2001, ArXiv.

[60]  Dina Q. Goldin Persistent Turing Machines as a Model of Interactive Computation , 2000, FoIKS.

[61]  Gregory J. Chaitin,et al.  The Unknowable , 1999, Nabokov and Indeterminacy.

[62]  Jacques Herbrand Sur la non-contradiction de l'Arithmétique. , 1932 .

[63]  Magdolna Hargittai,et al.  GERARD 'T HOOFT , 2004 .

[64]  R. Fisher XV.—The Correlation between Relatives on the Supposition of Mendelian Inheritance. , 1919, Transactions of the Royal Society of Edinburgh.

[65]  Mariusz Nowostawski,et al.  Hierarchical Code Generators , 2002 .

[66]  Nichael Lynn Cramer,et al.  A Representation for the Adaptive Generation of Simple Sequential Programs , 1985, ICGA.

[67]  Steve Grand,et al.  Creation: Life and How to Make It , 2001 .

[68]  David J. Montana,et al.  Strongly Typed Genetic Programming , 1995, Evolutionary Computation.

[69]  Edsger W. Dijkstra,et al.  Letters to the editor: go to statement considered harmful , 1968, CACM.

[70]  W. E. Ritter AS TO THE CAUSES OF EVOLUTION. , 1923, Science.

[71]  CERN,et al.  Universal Limits on Computation , 2004 .

[72]  Herbert A. Simon,et al.  The Sciences of the Artificial , 1970 .

[73]  Frederick P. Brooks,et al.  No Silver Bullet: Essence and Accidents of Software Engineering , 1987 .

[74]  M. Holcombe,et al.  Information Processing in Cells and Tissues , 1998, Springer US.

[75]  Kurt Gödel,et al.  On undecidable propositions of formal mathematical systems , 1934 .

[76]  Charles H. Moore,et al.  Forth - a language for interactive computing , 1970 .

[77]  Austin L Hughes Evolution without selection: Form and function by autoevolution , 1990 .

[78]  Gérard Berry,et al.  The chemical abstract machine , 1989, POPL '90.

[79]  F. Crick,et al.  Selfish DNA: the ultimate parasite , 1980, Nature.

[80]  Jonas Schreiber,et al.  The Analysis of Mind , 1935, Nature.

[81]  E. Schrödinger What is life? : the physical aspect of the living cell , 1944 .

[82]  J. Mattick,et al.  The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. , 2001, Molecular biology and evolution.

[83]  Riccardo Poli,et al.  Boolean Functions Fitness Spaces , 1999, EuroGP.

[84]  Scott Aaronson,et al.  NP-complete Problems and Physical Reality , 2005, Electron. Colloquium Comput. Complex..

[85]  C. Langton Self-reproduction in cellular automata , 1984 .

[86]  Béla Bollobás,et al.  Random Graphs , 1985 .

[87]  Anil K. Seth,et al.  The evolution of complexity and the value of variability , 1998 .

[88]  Sivarama P. Dandamudi Introduction to Assembly Language Programming , 1998, Undergraduate Texts in Computer Science.

[89]  Leonard Huxley,et al.  Life and letters of Thomas Henry Huxley , 1900 .

[90]  Sebastian Thrun,et al.  Learning to Learn , 1998, Springer US.

[91]  Sebastian Thrun,et al.  Is Learning The n-th Thing Any Easier Than Learning The First? , 1995, NIPS.

[92]  E. Fischer Conditioned Reflexes , 1942, American journal of physical medicine.

[93]  Marston Bates The Nature Of Natural History , 1950 .

[94]  Larry Stewart,et al.  Erasmus Darwin: a life of unequalled achievement , 2001, Medical History.

[95]  F. W. H.,et al.  Mutual Aid, a Factor of Evolution , 1903, Nature.

[96]  L Varetto Typogenetics: an artificial genetic system. , 1993, Journal of theoretical biology.

[97]  Hermann J. Muller,et al.  The Gene Material as the Initiator and the Organizing Basis of Life , 1966, The American Naturalist.

[98]  Robin Milner,et al.  Communication and concurrency , 1989, PHI Series in computer science.

[99]  Patrick Forber Evolution and the Levels of Selection , 2008 .

[100]  John R. Koza,et al.  Genetic programming - on the programming of computers by means of natural selection , 1993, Complex adaptive systems.

[101]  G. Hooft Quantum gravity as a dissipative deterministic system , 1999, gr-qc/9903084.

[102]  S. Kleene $\lambda$-definability and recursiveness , 1936 .

[103]  R. Lewontin ‘The Selfish Gene’ , 1977, Nature.

[104]  Douglas B. Lenat,et al.  The Role of Heuristics in Learning by Discovery: Three Case Studies , 1983 .

[105]  Daniel Le Métayer,et al.  A parallel machine for multiset transformation and its programming style , 1988, Future Gener. Comput. Syst..

[106]  Arturas Petronis,et al.  Phenotypic differences in genetically identical organisms: the epigenetic perspective. , 2005, Human molecular genetics.

[107]  Stephan Beck,et al.  From genome to epigenome. , 2005, Human molecular genetics.

[108]  Gil Neiger,et al.  Intel virtualization technology , 2005, Computer.

[109]  Thomas S. Ray,et al.  Evolution, complexity, entropy and artificial reality , 1994 .

[110]  Peter Sestoft,et al.  Partial evaluation and automatic program generation , 1993, Prentice Hall international series in computer science.

[111]  Corso Elvezia,et al.  Environment-independent Reinforcement Acceleration , 1995 .

[112]  Alan M. Frieze,et al.  Random graphs , 2006, SODA '06.

[113]  Francis Crick,et al.  The Genetic Code , 1962 .

[114]  Roland Olsson,et al.  Inductive Functional Programming Using Incremental Program Transformation , 1995, Artif. Intell..

[115]  H. Haken Synergetics: an Introduction, Nonequilibrium Phase Transitions and Self-organization in Physics, Chemistry, and Biology , 1977 .

[116]  C. Teuscher,et al.  Alan Turing: Life and Legacy of a Great Thinker , 2004, Springer Berlin Heidelberg.

[117]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[118]  P. Bowler Evolution: The History of an Idea , 1984 .

[119]  M. Eigen,et al.  The Hypercycle: A principle of natural self-organization , 2009 .

[120]  Thomas S. Ray,et al.  Is It Alive or Is It GA? , 1991, ICGA.

[121]  Ofi rNw8x'pyzm,et al.  The Speed Prior: A New Simplicity Measure Yielding Near-Optimal Computable Predictions , 2002 .

[122]  Justinian Rosca,et al.  Hierarchical learning with procedural abstraction mechanisms , 1997 .

[123]  Fritjof Capra,et al.  The Hidden Connections , 2002 .

[124]  Jonathan Baxter,et al.  A Model of Inductive Bias Learning , 2000, J. Artif. Intell. Res..

[125]  Jürgen Dix,et al.  Programming Multi-Agent Systems, Third International Workshop, ProMAS 2005, Utrecht, The Netherlands, July 26, 2005, Revised and Invited Papers , 2006, PROMAS.

[126]  L. Broglie,et al.  Causality and chance in modern physics , 1984 .

[127]  Steen Rasmussen,et al.  Self-reproduction of dynamical hierarchies in chemical systems , 1998 .

[128]  Selmer Bringsjord,et al.  Superminds: People Harness Hypercomputation, and More , 2003 .

[129]  C. Kurland,et al.  On the origin of mitochondria: a genomics perspective. , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[130]  Alan M. Turing,et al.  Systems of Logic Based on Ordinals , 2012, Alan Turing's Systems of Logic.

[131]  Michael D. Vose,et al.  The simple genetic algorithm - foundations and theory , 1999, Complex adaptive systems.

[132]  John F. Wakerly,et al.  The programming language PASCAL , 1979, Microprocessors and microsystems.

[133]  Terence C. Fogarty,et al.  A Comparative Study of Steady State and Generational Genetic Algorithms , 1996, Evolutionary Computing, AISB Workshop.

[134]  I. E. Wallin Symbionticism and the Origin of Species , 1927, The Indian Medical Gazette.

[135]  Marcus Hutter The Fastest and Shortest Algorithm for all Well-Defined Problems , 2002, Int. J. Found. Comput. Sci..

[136]  Michael Sipser,et al.  Parity, circuits, and the polynomial-time hierarchy , 1981, 22nd Annual Symposium on Foundations of Computer Science (sfcs 1981).

[137]  Robin Milner,et al.  Elements of interaction , 1993 .

[138]  Jr. Philip J. Koopman,et al.  Stack computers: the new wave , 1989 .

[139]  Eva Jablonka,et al.  Evidence, mechanisms and models for the inheritance of acquired characters , 1992 .

[140]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[141]  L. Brillouin,et al.  Science and information theory , 1956 .

[142]  C A Nelson,et al.  Learning to Learn , 2017, Encyclopedia of Machine Learning and Data Mining.

[143]  Roland Olsson,et al.  How to Invent Functions , 1999, EuroGP.

[144]  Alaa A. Kharbouch,et al.  Three models for the description of language , 1956, IRE Trans. Inf. Theory.

[145]  Neil D. Jones,et al.  Computability and complexity - from a programming perspective , 1997, Foundations of computing series.

[146]  Marco Tomassini,et al.  A phylogenetic, ontogenetic, and epigenetic view of bio-inspired hardware systems , 1997, IEEE Trans. Evol. Comput..

[147]  L. Orgel The Origins of Life: Molecules and Natural Selection , 1973 .

[148]  B. Hiley The Undivided Universe , 1993 .

[149]  W. Doolittle,et al.  Selfish genes, the phenotype paradigm and genome evolution , 1980, Nature.

[150]  Murray Gell-Mann,et al.  What Is Complexity , 2002 .

[151]  Stephen Wolfram,et al.  Universality and complexity in cellular automata , 1983 .

[152]  Evandro Agazzi,et al.  What is Complexity , 2002 .

[153]  Peter Nordin,et al.  Genetic programming - An Introduction: On the Automatic Evolution of Computer Programs and Its Applications , 1998 .

[154]  John L. Casti,et al.  Unconventional Models of Computation , 2002, Lecture Notes in Computer Science.

[155]  B. Lang,et al.  The origin and early evolution of mitochondria , 2001, Genome Biology.

[156]  Patricio Jeraldo,et al.  The Genetic Code , 2006 .

[157]  Henk Corporaal Microprocessor architectures - from VLIW to TTA , 1997 .

[158]  J. Mattick Non‐coding RNAs: the architects of eukaryotic complexity , 2001, EMBO reports.

[159]  David H. Wolpert,et al.  No free lunch theorems for optimization , 1997, IEEE Trans. Evol. Comput..

[160]  Emerson W. Pugh,et al.  IBM's 360 and early 370 systems , 1991 .

[161]  Christopher G. Langton,et al.  Studying artificial life with cellular automata , 1986 .

[162]  Juergen Schmidhuber,et al.  A General Method For Incremental Self-Improvement And Multi-Agent Learning In Unrestricted Environme , 1999 .

[163]  B. Charlesworth Levels of Selection in Evolution , 2000, Heredity.

[164]  M. Kimura Evolutionary Rate at the Molecular Level , 1968, Nature.

[165]  Stephen Jay Gould,et al.  The Flamingo's Smile: Reflections in Natural History , 1985 .

[166]  A. Church An Unsolvable Problem of Elementary Number Theory , 1936 .

[167]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[168]  L. Petitto,et al.  Biological Foundations of Language , 1967, Neurology.

[169]  Y. Ho,et al.  Simple Explanation of the No-Free-Lunch Theorem and Its Implications , 2002 .

[170]  Stephen Wolfram,et al.  A New Kind of Science , 2003, Artificial Life.

[171]  ProgramsWilliam W. CohenAT Learnability of Restricted Logic Programs , 1993 .

[172]  Martin K. Purvis,et al.  Self-adaptation and Dynamic Environment Experiments with Evolvable Virtual Machines , 2005, Engineering Self-Organising Systems.

[173]  H. Hartman,et al.  The origin of the eukaryotic cell. , 1984, Speculations in science and technology.

[174]  A. Turing On Computable Numbers, with an Application to the Entscheidungsproblem. , 1937 .

[175]  Hans-Paul Schwefel,et al.  Evolution and optimum seeking , 1995, Sixth-generation computer technology series.

[176]  Edward A. Lee The problem with threads , 2006, Computer.

[177]  Lawrence Carin,et al.  Multi-Task Learning for Classification with Dirichlet Process Priors , 2007, J. Mach. Learn. Res..

[178]  Konrad Zuse,et al.  Rechnender Raum , 1991, Physik und Informatik.

[179]  Peter A. Whigham,et al.  Grammatically-based Genetic Programming , 1995 .

[180]  H. Cravens,et al.  Thomas Hunt Morgan : the man and his science , 1980 .

[181]  Noam Chomsky,et al.  On Certain Formal Properties of Grammars , 1959, Inf. Control..

[182]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[183]  H T Siegelmann,et al.  Dating and Context of Three Middle Stone Age Sites with Bone Points in the Upper Semliki Valley, Zaire , 2007 .

[184]  L. K. CHARLES,et al.  The Nature of Natural History , 1950, The Yale Journal of Biology and Medicine.

[185]  John McCarthy,et al.  Recursive functions of symbolic expressions and their computation by machine, Part I , 1960, Commun. ACM.

[186]  Selim G. Akl,et al.  THE MYTH OF UNIVERSAL COMPUTATION ∗ , 2005 .

[187]  Barbara Webb,et al.  Swarm Intelligence: From Natural to Artificial Systems , 2002, Connect. Sci..

[188]  Robert A. Waterland,et al.  Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation , 2003, Molecular and Cellular Biology.

[189]  Michael A. Bozarth,et al.  Intracranial self-stimulation as a technique to study the reward properties of drugs of abuse , 1980, Pharmacology Biochemistry and Behavior.

[190]  Riccardo Poli,et al.  Parallel genetic algorithm taxonomy , 1999, 1999 Third International Conference on Knowledge-Based Intelligent Information Engineering Systems. Proceedings (Cat. No.99TH8410).

[191]  Riccardo Poli,et al.  Solving High-Order Boolean Parity Problems with Smooth Uniform Crossover, Sub-Machine Code GP and Demes , 2000, Genetic Programming and Evolvable Machines.

[192]  G. Chaitin,et al.  TOWARD A MATHEMATICAL DEFINITION OF “ LIFE ” , 1979 .

[193]  Michael D. Vose Logarithmic convergence of random heuristic search , 1994, Optics & Photonics.

[194]  Hans-Paul Schwefel,et al.  Evolution strategies – A comprehensive introduction , 2002, Natural Computing.

[195]  D. Wolpert,et al.  No Free Lunch Theorems for Search , 1995 .

[196]  J. Huxley Evolution: The Modern Synthesis , 1943 .

[197]  William Bateson,et al.  Mendel's Principles of Heredity a Defence , 2009 .

[198]  B Korzeniewski,et al.  Cybernetic formulation of the definition of life. , 2001, Journal of theoretical biology.

[199]  E. Mayr,et al.  The Evolutionary synthesis : perspectives on the unification of biology , 1980 .

[200]  Maaike Verrips,et al.  Models of Development , 1990 .

[201]  Timothy Perkis,et al.  Stack-based genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[202]  L. Penrose,et al.  THE CORRELATION BETWEEN RELATIVES ON THE SUPPOSITION OF MENDELIAN INHERITANCE , 2022 .

[203]  Diederich Hinrichsen,et al.  Mathematical Systems Theory I , 2006, IEEE Transactions on Automatic Control.

[204]  G. J. Chaitin,et al.  TO A MATHEMATICAL DEFINITION OF “ LIFE ” , 1970 .

[205]  Bill Venners,et al.  Inside the Java Virtual Machine , 1997 .

[206]  H. Gadamer,et al.  Truth and Method , 1960 .

[207]  D. Bohm,et al.  Causality and Chance in Modern Physics , 1963 .

[208]  Anders Sandberg,et al.  Models of Development , 2000 .

[209]  J. Mattick The Functional Genomics of Noncoding RNA , 2005, Science.

[210]  W. Ahn,et al.  Psychological Studies of Explanation—Based Learning , 1993 .

[211]  J. Rennard Introduction to Cellular automata , 2001 .

[212]  Nelson Minar,et al.  The Swarm Simulation System: A Toolkit for Building Multi-Agent Simulations , 1996 .

[213]  S. Palumbi,et al.  High intron sequence conservation across three mammalian orders suggests functional constraints. , 2003, Molecular biology and evolution.

[214]  Peter Wegner,et al.  The Church-Turing Thesis: Breaking the Myth , 2005, CiE.

[215]  Conway Zirkle FORERUNNERS OF DARWIN , 1959 .

[216]  S. Gould,et al.  Exaptation—a Missing Term in the Science of Form , 1982, Paleobiology.

[217]  Lee Spector,et al.  Hierarchy helps it work that way , 2002 .

[218]  Gary William Flake,et al.  The Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems and Adaptation , 1998 .

[219]  Steven Levy,et al.  Artificial Life: A Report from the Frontier Where Computers Meet Biology , 1993 .

[220]  John H. Bickford Introduction to Assembly , 2007 .

[221]  Stephen F. Smith,et al.  A learning system based on genetic adaptive algorithms , 1980 .

[222]  A. Church A Set of Postulates for the Foundation of Logic , 1932 .

[223]  Stephen Jay Gould,et al.  The Panda's Thumb: More Reflections in Natural History , 1990 .

[224]  Ronald Olson,et al.  Self-improvement For The ADATE Automatic Programming System , 2002, GECCO.

[225]  Rich Caruana,et al.  Multitask Learning , 1997, Machine Learning.

[226]  E. Jablonka,et al.  The Changing Concept of Epigenetics , 2002, Annals of the New York Academy of Sciences.

[227]  Thomas S. Ray,et al.  An Approach to the Synthesis of Life , 1991 .

[228]  Alonzo Church,et al.  A note on the Entscheidungsproblem , 1936, Journal of Symbolic Logic.

[229]  Jürgen Schmidhuber,et al.  Optimal Ordered Problem Solver , 2002, Machine Learning.

[230]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[231]  Bill Blunden Virtual Machine Design and Implementation in C/C++ with Cdrom , 2002 .

[232]  Peter Ross,et al.  Tackling the Boolean Even N Parity Problem with Genetic Programming and Limited-Error Fitness , 1997 .

[233]  Casiano Rodríguez León,et al.  Alan Mathison Turing , 2000 .

[234]  J. Mattick,et al.  Small regulatory RNAs in mammals. , 2005, Human molecular genetics.

[235]  S. Kleene A Theory of Positive Integers in Formal Logic. Part II , 1935 .

[236]  Ashley Montagu Darwin, competition & cooperation , 1952 .

[237]  Robin Milner,et al.  A Calculus of Communicating Systems , 1980, Lecture Notes in Computer Science.

[238]  Kwong-Sak Leung,et al.  Evolving recursive functions for the even-parity problem using genetic programming , 1996 .

[239]  Johan Håstad,et al.  Almost optimal lower bounds for small depth circuits , 1986, STOC '86.

[240]  Ming Li,et al.  An Introduction to Kolmogorov Complexity and Its Applications , 2019, Texts in Computer Science.

[241]  Edsger W. Dijkstra,et al.  Go To Statement Considered Harmful , 2022, Software Pioneers.

[242]  A. M. Turing,et al.  The Essential Turing: Seminal Writings in Computing, Logic, Philosophy, Artificial Intelligence, and Artificial Life plus The Secrets of Enigma , 2004 .

[243]  M. Boden Autopoiesis and life , 2000 .

[244]  Peter Wegner,et al.  Computation beyond turing machines , 2003, CACM.

[245]  Juergen Schmidhuber,et al.  On learning how to learn learning strategies , 1994 .

[246]  Stephen Jones,et al.  Organizing relations and emergence , 2002 .

[247]  Michael O'Neill,et al.  Grammatical Evolution: Evolving Programs for an Arbitrary Language , 1998, EuroGP.

[248]  Susann Ragsdale,et al.  The Common Language Infrastructure Annotated Standard , 2003 .

[249]  Tom Lenaerts,et al.  Towards a Definition of Dynamical Hierarchies , 2002 .

[250]  Jessica M. Young,et al.  Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis , 2005, Nature.

[251]  Ilya Prigogine,et al.  From Being To Becoming , 1980 .

[252]  Jaroslaw Anders Stanislaw Ignacy Witkiewicz , 2009 .

[253]  S. Wright,et al.  Evolution in Mendelian Populations. , 1931, Genetics.

[254]  Robin Gandy,et al.  The confluence of ideas in 1936 , 1988 .

[255]  Martin K. Purvis,et al.  An Architecture for Self-Organising Evolvable Virtual Machines , 2004, Engineering Self-Organising Systems.

[256]  Tom M. Mitchell,et al.  Learning by experimentation: acquiring and refining problem-solving heuristics , 1993 .

[257]  Katrina Relief,et al.  WITH INFINITE , 2007 .

[258]  Wolfgang Banzhaf,et al.  Mesoscopic analysis of self-evolution in an artificial chemistry , 1998 .

[259]  David B. Fogel,et al.  Evolutionary Computation: The Fossil Record , 1998 .

[260]  K. Gödel Über formal unentscheidbare Sätze der Principia Mathematica und verwandter Systeme I , 1931 .

[261]  Justinian P. Rosca,et al.  Learning by adapting representations in genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[262]  Kai Hu,et al.  [The meaning of epigenetics]. , 2002, Yi chuan = Hereditas.

[263]  Christoph Endres,et al.  Introduction to Artificial Life , 2000, Künstliche Intell..

[264]  John von Neumann,et al.  Theory Of Self Reproducing Automata , 1967 .

[265]  Nancy A. Lynch,et al.  An introduction to input/output automata , 1989 .

[266]  Wolfgang Banzhaf,et al.  Linear-Graph GP - A New GP Structure , 2002, EuroGP.

[267]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[268]  Master Gardener,et al.  Mathematical games: the fantastic combinations of john conway's new solitaire game "life , 1970 .

[269]  K. Gödel Über formal unentscheidbare Sätze der Principia Mathematica und verwandter Systeme I , 1931 .

[270]  B. Dickinson,et al.  The complexity of analog computation , 1986 .

[271]  A. Gecow,et al.  Self-improvement in a complex cybernetic system and its implications for biology , 1983, Acta biotheoretica.

[272]  A. Church The calculi of lambda-conversion , 1941 .

[273]  Ricardo Vilalta,et al.  Introduction to the Special Issue on Meta-Learning , 2004, Machine Learning.

[274]  R. Fraser The structure of deoxyribose nucleic acid. , 2004, Journal of structural biology.

[275]  Robin Milner,et al.  A Calculus of Mobile Processes, II , 1992, Inf. Comput..

[276]  Alexander Okhotin On Computational Universality in Language Equations , 2004, MCU.

[277]  Wolfgang Banzhaf,et al.  Efficient evolution of machine code for CISC architectures using instruction blocks and homologous crossover , 1999 .

[278]  Astro Teller,et al.  Evolving programmers: the co-evolution of intelligent recombination operators , 1996 .

[279]  Arthur I. Miller Book-Review - Imagery in Scientific thought - Creating 20TH-CENTURY Physics , 1984 .

[280]  Nick Collier,et al.  Repast: An extensible framework for agent simulation , 2001 .