Why and How Does the 'Complexity' of Self-replicating Agents Increase?
Artificial Life: The Solid-State Apporoach to Self-Replication.
Chemoton Theory: The Fluid Automata Approach to Self-Replication.
Chemical Evolution
The Evolution of Non-Enzymatic Template Replication.
A Case Study of Prion Self-Replication.
Bibliography
Azevedo, R.B.R. et al. The Simplicity of Metazoan Cell Lineages. (2005), 433, 152-156 Download pdf.
Bada, J.L. How Life bagan on Earth: a status report. (2004) Earth and Planatery Science Letters 226, 1-15. Download pdf.
Bada, J.L. and Lazcano, A. Prebiotic Soup - Revisiting the Miller Experiment. (2003) Science 300, 745-746 Download pdf.
Bennet, C.H. The Thermodynamics of Computation - a Review. (1981) International Journal of Theoretical Physics, 21(12), 905-940. Download pdf.
Bernstein, H. Byerly, H.C. Hopf, F.A. Michod R.A. Vemulapalli, K. The Darwinian Dynamic (1983) The Quarterly Review of Biology 58 (2), 185-207 Download pdf.
Boyd, R. and Richerson, P.J. Group Selection amoung Alternative Evolutionarily Stable Strategies. (1990). J. Theor. Biol. 145(3), 331-342. iPhoto.
Bozic, B. Svetina, S. A relationship between membrane properties forms the basis of a selectivity mechanism for vesicle self-reproduction. (2004) Eur Biophys. J. 33, 565-571 Download pdf.
Braun, D. Libchaber, A. Thermal Force Approach to Molecular Evolution. (2004) Phys. Biol. 1, 1-8. Download pdf.
Bray, D. Molecular Prodigality. (2003) Science, 299, 1189-1190. Download pdf.
Breslow, R. On the Mechanism of the Formose Reaction. (1959) Tetrahedron Letters 21, 22-26. Pergamon Press Ltd. Download pdf
Burke, D.H. Ribozyme-catalyzed Genetics, (2004). Chapter 5 in The Genetic Code and the Origin of Life, ed. L. Ribas de Pouplana, pp 49-75. Download pdf.
Chen, I.A. Roberts. R.W. Szostak, J.W. The Emergence of Competition Between Model Protocells. (2004) Science 305, 1474-1476 Download pdf.
Dayhoff, M.O. Lippincott, R.V. Eck. Thermodynamic Equilibria in Prebiological Atmospheres. (1964) Science, 146(3650), 1461-1464. Download pdf
Deamer, D.W. The First Living Systems: a Bioenergetic Perspective. (1997) Microbiology and Molecular Biology Reviews. 61(2), 239-261. Download pdf.
Deamer, D. Dworkin, J.P. Sandford S.A. Bernstein, M.P. Allanmandola L.J. Review: The First Cell Membranes. (2002) Astrobiology 2(4), 371-381 Download pdf.
Debat, V. and David, P. Mapping pheontypes: canalization, plasticity and developmental stability. (2001) Trends in Ecology and Evolution, 16(10), 555-561 Download pdf.
Decker, P. Schweer, H. Pohlmann, R. Bioids X. Identification of formose sugers, presumable prebiotic metabolites, using capillary gas chromatography/gas chromatography-mass spectrometry of n-butoxime tri-flouroacetates on ov-255. (1982) Journal of Chromatography 244, 281-291. Download pdf.
Eschenmoser (Review by Nina Hall). The Quest for the chemical roots of life. (2004). Chemical Communications, 11, 1247-1252. iPhoto.
Etxeberria, A. Autopoiesis and Natural Drift: Genetic Information, Reproduction, and evolution revisited. Download pdf.
Farmer, J.D. Kauffman S.A. Packard, N.H. Autocatalytic Replication of Polymers. (1996) Physica 22D, 50-67. Download pdf.
Fell, D.A. and Wagner, A. Structural Properties of Metabolic Networks: Implications for evolution and modelling of metabolism. Download pdf.
Fontana, W. and Buss, L.W. The Arrival of the Fittest: Toward a Theory of Biological Organization. (1994), Bull. Math. Biol., 56, 1-64 Download pdf.
Forst, C.V. Schulten, K. Evolution of Metabolisms: A new method for the Comparison of Metabolic pathways. (1999) J. Comput. Biol. 6(3-4), 343-360. Download pdf.
Ganti, T. Chemoton Theory Vol I and II. (2004) Kluwer.
Ganti, T. The Principles of Life (2004) OUP Eds. Szathmary, E. Greisimer, J.
Gershenfield, N. Signal entropy and the thermodynamics of computation. (1996) IBM Systems Journal, 35 (3&4), 577-586 Download pdf.
Gleiss, P. Stadler P.F. Wagner, A. Fell, D.A. Relavent Cycles in Chemical Reaction Networks. (2001) Adv. Complex Systems 1, 1-000 Download pdf.
Gould, S.J. Lloyd, E.A. individuality and adaptation across levels of selection: How shall we name and generalize the unit of Darwinism? (1999) PNAS, 96(21) , 11904-11909 Download pdf.
Happel, R. and Stadler, P.F. The Evolution of Diversity in Replicator Networks. Santa Fe Working Paper 1997 Download pdf.
Hartman, Hyman. Speculations on the Origin and Evolution of Metabolism. (1975) J. Mol. Evol. 24(4), 359-70. iPhoto.
Horowitz, N.H. On the Evolution of Biochemical Synthesis. (1945) PNAS, 31(6), 153-157. iPhoto.
Huening, H.F. Using self-organising catalytic networks in adaptive systems. DPhil Thesis. UCL (2001) Download ps.
Hutton, T. Simulating Evolution's First Steps. (2003) European Conference of Artificial life (ECAL 2003). Download pdf.
Jablonka, E. and Lamb, M.J. (1995) Epigenetic Inheritance and Evolution - the Lamarckian Dimension, Oxford University Press. iPhoto
Jablonka, E. and Lamb, M.J. Epigenetic Inheritance in Evolution. (1998). Journal of Evolutionary Biology 11 : 159-183. iPhoto
Jablonka, E. and Lamb, M.J. Epigenetic Inheritance and Evolution: the Lamarckian Dimension. ( 1995), Oxford University Press.
Jain, S. and Krishna, S. A Model for the emergence of cooperation, interdependence, and structure in evolving networks. (2001) PNAS 98(2), 543-547. Download pdf.
Joyce, G.F. Booting up Life. (2002) Nature, 410, 278-279 Download pdf.
Kalapos, M.P. A possible evolutionary role of formaldehyde (1999) Experimental and Molecular Medicine 31(1) , 1-6 Download pdf.
Kaneko, K. On Recursive Production and Evolvability of Cells: Catalytic Reaction Network Approach. Download pdf.
Kaneko, K. Recursiveness, Switching, and Fluctuations in a Replicating Catalytic Network. (2003) Physical Review E. 68, 031909 Download pdf. For other Kaneko papers see.
King, G.A.M. Symbiosis and the Origin of Life (1977) Orig. Life 8(1) 39-53. Download TIFF.
King, G.A.M Growth of a Hypercycle and Comparison with Conventional Autocatalysis. (1981). BioSystems, 13, 225-234. Download TIFF. Commentry by Eigen.
King, G.A.M. Recycling, Reproduction, and Life's Origins. (1982) BioSystems, 15, 89-97 Download TIFF.
King, G.A.M. Autocatalysis Download TIFF
Kleidon, A. Beyond Gaia: Thermodynamics of Life and Earth System Functioning. (2004) Climatic Change (in press) Download pdf.
Kleidon, A. and Lorenz, R. Entropy Production by Earth System Processes. in Non-Equilibrium Thermodyanmics and the Production of Entropy: Life, Earth, and Beyond. Springer Verlag (forthcoming 2004). Download pdf.
Krishna, S. Formation and Destruction of Autocatalytic Sets in an Evolving Network Model. PhD Thesis. (2004). Center for Theoretical Studies, Indian Institute of Science, Bangalore, 560012, India. Download pdf.
Lachmann, M. and Jablonka, E. The Inheritance of Phenotypes: an Adaptation to Fluctuating Environments. (1996) J. Theor. Biol 181, 1-9. Download pdf.
Lathe, R. Fast Tidal Cycling and the Origin of Life. (2003) Icarus (in press). Download pdf (uncorrected proof).
Lee, D.H. Severin, K. Yokobayashi, Y and Reza Ghadiri, M. Emergence of symbiosis in peptide self-replication through a hypercyclic network. (1997) Nature, 390 591-594 iPhoto.
Lenaerts, T. Different Levels of Selection in Artificial Evolutionary Systems: Analysis and Simulation of Selection Dynamics. PhD Thesis, Computational Modeling Lab, Vrije Universiteit Brussel. Download pdf.
Lenton, T.M. Schellnhuber, H.J. Szathmary, E. Climbing the Ladder. (2004) Nature 451 913 Download pdf.
Lenski, R.E. Ofria, C. Pennock, R.T. Adami, C. The Evolutionary Origin of Complex Features. (2003) Nature, 423, 139-144. Download pdf.
Levin, BR & Kilmer, WL Interdemic selection and. the evolution of altruism: a computer simulation study. (1974). Evolution 28, 527–545. iPhoto.
Lifson, S. On the Crucial Stages in the Origin of Animate Matter. (1997) J. Mol Evol. 44, 1-8. Download pdf.
Light, S. Kraulis, P. Network analysis of metabolic enzyme evolution in Escherichia Coli. (2004) BMC Bioinformatics, 5, 1-15 Download pdf.
Mameli, M. Nongenetic Selection and Nongenetic Inheritance. (2004) Brit. J. Phil. Sci 55, 35-71. Download pdf.
Margulis, L. Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons, (1992)., W.H. Freeman, ISBN 0716770288. iPhoto.
Margulis, L. and Rene Fester. Symbiosis as a Source of Evolutionary Innovation. (1991) MIT Press. iPhoto.
Maron, M. An ecological approach to the evolution of organism complexity. (2004) MSc Thesis University of Sussex. Download pdf. (unfinished).
Masel, J. Genetic Assimilation can occur in the absence of selection for the assimilating phenotype, suggesting a role for the canalization heuristic. (2004) J. Evol Biol. 17, 1106-1110. Download pdf.
Maynard-Smith, J. Models of a Dual-Inheritance System. (1990). J. Theor. Biol. 143(1), 41-53. iPhoto.
Melendez-Hevia, E. Waddell, T.G. Cascante, M. The Puzzle of the Krebs Cycle: Assembling the Pieces of Chemically feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution. (1996) J. Mol. Evol 43, 293-303. Download pdf.
Meszena, G. and Szathmary, E. Adaptive Dynamics of Parabolic Replicators (2001) Selection 2, 1-2, 147-159. Download pdf.
McGinness, K.E. Joyce, G.F. In Search of an RNA Replicase Ribozyme (2003) Chemistry and Biology 10, 5-14. Download pdf.
Morowitz H.J. Perspectives on Thermodynamics and the Origin of Life. (1977) Adv. Biol. Med Phys. 16, 151-63. iPhoto.
Morowitz, H.J. Kostelnik, J.D. Yang, J, Cody, G.D. The Origin of Intermediary Metabolism. (2000) PNAS 97(14) 7704-7708 Download pdf.
Mossel, E. Steel, M. Random biochemical networks: the probability of self-sustaining autocatalysis. (in press) J. Theor. Biol. Download pdf.
Nisbet, E.G. and Sleep, N.H. The Habitat and Nature of Early Life (2001) Nature 409, 1083-1091 Download pdf.
Nielsen, S.N. Ulanowicz R.E. On the consistency between thermodynamical and network approaches to ecosystems. (2000) Evological Modelling 132 (2000) 23-31. Download pdf.
Orgal, L.E. Self-Organizing Biochemical Cycles. (2000) PNAS 97(23) , 12503-12507. Download pdf.
Pál, C and Hurst, L.D. (2004) Epigenetic inheritance and evolutionary adaptation In: Organelles, genomes and eukaryote phylogeny: an evolutionary synthesis in the age of genomics. (Ed Hirt, R. P. and Horner, D. S.) CRC Press pp 353-370 Download pdf. [Also see Pal's excellent website for further papers.]
Perry, R. and Kolb, V. On the Applicability of Darwinian Principles to Chemical Evolution that led to life. (2004). International Journal of Astrobiology 3(1) , 45-53. Download pdf.
Pross, A. The Driving Force of Life's Emergence: Kinetic and Thermmodynamic Considerations. (2003) J. Theor. Biol, 220, 393-406. Download pdf.
Pross, A. Khondokovsky, V. Extending the concept of kinetic stability: toward a paradigm for life. (2004) Journal of Physical Organic chemistry, 17,312-316. Download pdf.
Ruiz-Mirazo, K. Moreno, A. Basic Autonomy as a Fundemental Step in the Synthesis of Life. (2004) Artificial Life 10, 235-259 Download pdf.
Saier Jr, M.H. Vectorial metabolism and the evolution of transport systems (2000) Journal of Bacteriology, 182(18), 5029-5035. Download pdf.
Salazar-Ciudad, I. Garcia-Fernandez, J. Sole, R.V. Gene Networks Cpaable of Pattern Formation: From Induction to Reaction-Diffusion. (2000) J. Theor. Biol, 205, 587-603. Download pdf.
Santos, M. Zintzaras, E. Szathmary, E. Recombination in Primeval Genomes: A Step Forward but Still a Long Leap from Maintaining a Sizable Genome. (2004) J. Mol. Evol 59, 507-519. Download pdf.
Scharloo, W. Canalization: Genetic and Developmental Aspects. (1991) Annual review of Ecology and Systematics, 22, 65-93 Download pdf
Scheuring, I. Szathmary, E. Survival of Replicators with Parabolic Growth Tendency and Exponential Decay. (2001) J. Theor. Biol 212, 99-105. Download pdf.
Scheuring, I. Czaran, T. Szabo, P. Karolyi, G. Toroczkai, Z. Spatial Models of Prebiotic Evolution: Soup before Pizza? (2003) Origins of Life and Evolution of the Biosphere. 33, 319-355 Download pdf.
Schreiber, S. J. Tobiason, G.A. The Evolution of Resource Use, (2002) Journal of Mathematical Biology. Download pdf.
Schuster, P. Taming combinatorial explosion. (2000) PNAS, 9(14), 7678-7680. Download pdf.
Schuster, P. Sigmund, K. Wolff, R. Mass Action Kinetics of Self-Replication in Flow Reactors. (1980) Journal of Mathematical Analysis and Applications. Download tif
Schuster, P. Stadler P.F. Networks in Molecular Evolution. Complexity, 8:34-42 (2002) Download pdf.
Siegal, M.L. Bergman, A. Waddington's canalization revisited: Developmental stability and evolution. (2002) PNAS, 99(16), 10528-10532. Download pdf. Commentry.
Sigmund, K. The Population Dynamics of Conflict and Cooperation (1998) Interim Report Inernational Institute for Applied Systems Analysis. Download pdf.
Smith, E. and Morowitz, H.J. Universality in Intermediary Metabolism. (2004) PNAS 101(36) , 13168-13173. Download pdf.
Sole, R. Fernandez, P. Kauffman, S.A. Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion. (2003) Int. J. Dev. Biol, 47, 685-693. Download pdf.
Spiegelman, S. An approach to the experimental analysis of precellular evolution. (1971) Quarterly Review of Biophysics 4, 2 & 3, 213-253 Download tif. Download part 2. tif
Stadler P.F. and Happel, R. The Probability of Permanence. (1993) Mathematical Biosciences 113, 25-50. Download tif. Part 2.
Stadler B.M.R, Stadler P.F. Molecular Replicator Dynamics. Adv. Complex Systems, (2002) Download pdf.
Stadler, B.M.R. Stadler P.F. Schuster, P. Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reactions (1999) Bulletin of Mathematical Biology 01, 1-27 Download pdf.
[Other papers by the Stadlers. Schuster et al are available at the excellent website of the bioinformatics group of the university of Liepzig. here.]
Staphan-Otto Attolini, C. Stadler, P.F. Evolving Towards the Hypercycle: A Spatial Model of Molecular Evolution. (2004) Download pdf.
Steel, M. The Emergence of self-catalysing structure in abstract origin-of-life models. (1999) Download pdf.
Suzuki, H. Ono, N. Kikuo, Y. Several necessary conditions for the evolution of complex forms of lfie in an artificial environment. (2003) Artificial Life, 9, 153-174. Download.
Szabo, P. Scheuring, I. Czaran, T. Szathmary, E. In Silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity. (2002), Nature, 420, 340-343. Download pdf.
Szathmary, E. Toy Models for Simple Forms of Multicellularity, Soma and Germ. (1994) J. Theor. Biol, 169, 125-132. Download pdf.
Szathmary, E. and Maynard-Smith, J. From replicators to reproducers: the first major transitons leading to life. (1997) J. Theor. Biol. 187, 555-571. Download pdf.
Szathmary, E. Gladkih, I. (1989) Journal of Theoretical Biology, 138, 55-58
Szathmary, E. The Evolution of Replicators. (2000) Proc. Trans. R. Soc. Lond. B. 355, 1669-1676 Download pdf.
Szathmary, E. In search of the simplest cell. (2005) Nature 433, 469-470. Download pdf.
Szostak, J.W. Bartel D.P. Luigi Luisi, P. Synthesizing Life. (2001) Nature 409, 387-390 Download pdf.
Taylor, Tim. Please see his excellent website. A crucial reference for the Artificial Life approach to Self-Replication.
Tuck, A. The Role of Atmospheric Aerosols in the Origin of Life. (2002) Survays in Geophysics, 23, 376-409. Download pdf.
Ulanowicz, R.E. On the Nature of Ecodynamics. (2004) Ecological Complexity 1, 341-354. Download pdf.
Von Kiedrowski, G. Minimal Replicator Theory I: Parabolic Verses Exponential Growth. (1993) Bioorganic Chemistry Frontiers 3, 114-146 Download pdf.
Wachtershauser, G. Groundworks for an Evolutionary Biochemistry: The Iron-Sulpher World. (1992) Prog. Biophys. Molec. Biol 58, 85-201. Download pdf.
Wagner, A. Does Evolutionary Plasticity Evolve? (1996) Evolution, 50(3),1008-1023. Download pdf.
Watson, R.A. and Pollack, J.B. A Computational Model of Symbiotic Composition in Evolutionary Transitions. Download pdf.
Weber, A.The Sugar Model: Catalysis by Amines and Amino Acid Products. (2001) Origins of Life and Evolution of the Biosphere 31, 71-86. Download pdf.
Whittle, J.R.S. How is developmental stability sustained in the face of genetic variation? (1998) Int. J. Dev. Biol. 42,495-499. Download pdf
Wills, P.R. Evolution of the molecular biological interpreter. (2001) Complexity International, 8, -- Download pdf.
Wills, P.R. Kauffman S.A. Stadler B.M.R. Stadler P.F. Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation. Download pdf.
Wilson, D.S. & Sober, E. Reintroducing group selection to the human behavioral sciences. (1994). Behavioral and Brain Sciences 17 (4), 585-654. iPhoto.
Wilson, D.S. & Sober, E. (1994). Reintroducing group selection to the human behavioral sciences. Behavioral and Brain Sciences 17 (4): 585-654. Download html
Yao, S. Ghosh, I. Zutshi, R. Chmielewski, J. Selective Amplification by Auto- and Cross-Catalysis in a replicating peptide system. (1998) Nature 396, 447-450. Download pdf.
Yurke, B. Tuberfield, A.J. Mills, Jr. Simmel. F.C. Neumann, J.L. A DNA-fuelled molecular machine made of DNA. (2000) Nature 406, 607-608. Download pdf.
Zeilinski, W.S. and Orgel, L.E. Oligoaminonucleoside phosphoramidates. Oligomerization of dimers of 3'-amino-3' deoxynucleotides (GC and CG) in aqueous solution. (1987) Nucleic Acids Research 15(4). 1699-1715. Download pdf.
Zintzaras, E. Santos, M. Szathmary, E. "Living" Under the Challenge of Information Decay: The Stochastic Corrector Model vs. Hypercycles. Jour. Theor. Biol. (2002) 217, 167-181. Download pdf.
Resources.
Lectures.
An external lecture on Kauffman's Autocatalytic Sets. Download ppt.
An external lecture on Hypercycles and QuasiSpecies. Download ppt.
An extrnal lecture on the Origin of Life. Download ppt.
A talk given by Joel Peck at Sussex University on Complexity. Download pdf.
Notes and Reports.
DPhil Proposal (The accumulation of adaptations.) Download ps.
End of 1st Year Report. The evolution of hierarchical levels of organization. Download ps.
End of 2nd Year Report. Epigenetic Algorithms. Download doc.
Complexity, Hierarchy, Thesis aims. Download doc.
Cannalization, Genetic Assimilation notes. Download doc.
Some more notes on Waddingtons book "Evolution of an Evolutionist" Download doc.
Models of Early Replicators (Some mathematica models of replicators) Download Mathematica nb.
Some of my early experiments on a mechanism for the evolution of slow (complex) replicators. Download pdf.