Complex Adaptive Systems
(M.Sc. in Bioinformatics, University of Athens)

Readings (2008)

Lecture 1. Introduction

FUNDAMENTAL

G.Weisbuch : The complex adaptive systems approach to biology, Evolution and Cognition, 1999.
PDF, 11 pages, 109K

ADDITIONAL

N.Packard, S.Wolfram : Two-dimensional cellular automata, Journal of Statistical Physics, 38:901-946, March 1985.
PDF, 51 pages, 890K

Lecture 2. History, roots, topics

FUNDAMENTAL

Introduction to the greek edition of Maturana & Varela's "Tree of knowledge", 1992 (by S.Manousselis).
PDF, 28 pages, 3501K
M.A.Bedau et al. : Open problems in artificial life, Artificial Life Journal, 2000.
PDF, 14 pages, 126K
M.A.Bedau : Artificial life, in "Blackwell Guide to the Philosophy of Computing and Information", by L.Floridi (Ed.), 2001.
PDF, 24 pages, 98K
R.A.Brooks : Intelligence without representation, Artificial Intelligence Journal, 1991.
PDF, 12 pages, 712K
P.Maes : Modeling adaptive autonomous agents, Artificial Life Journal, 1994.
PDF, 37 pages, 251K

ADDITIONAL

P.Agre : Routines, MIT Artificial Intelligence Lab. Memo 828, 1985.
PDF, 28 pages, 3512K
P.Agre, D.Chapman : What are plans for?, MIT Artificial Intelligence Lab. Memo 1050a, 1989.
PDF, 30 pages, 2316K
M. Boden : Autonomy and artificiality, AISB Quarterly, 1993/4, also Univ. of Sussex CSRP 307 (Cognitive Science Research Paper).
PDF, 14 pages, 63K
R.A.Brooks : Intelligence without reason, Artificial Intelligence Memo 1293, MIT AI Lab, April 1991.
PDF, 28 pages, 342K
L.Steels : The artificial life roots of artificial intelligence, Artificial Life Journal, 1994.
PDF, 87 pages, 400K
A.M.Turing : Computing machinery and intelligence, Mind 59:433-460, 1950.
PDF, 21 pages, 150K

Lecture 3. Behavior I (Navigation, control, regulation)

FUNDAMENTAL

V. Braitenberg : Vehicles, 1986 (chapters 1-7).
PDF, 31 pages, 4015K
D.Cliff : Biologically-Inspired Computing Approaches to Cognitive Systems: A partial tour of the literature, HP Bristol Report HPL-2003-11.
PDF, 56 pages, 718K
D.Cliff : Neuroethology, Computational, in M.A.Arbib (ed.), Handbook of Brain Theory and Neural Networks, 2nd edition, 2003.
PDF, 22 pages, 168K
A.Guillot, J.-A.Meyer : The animat contribution to cognitive systems research, Journal of Cognitive Systems Research, 2000.
PDF, 8 pages, 60K
D.McFarland: Animals as cost-based robots, International Studies in the Philosophy of Science, 6(2):133-153, 1992.
PDF, 43 pages, 14632K
A.Tyrrell : The use of hierarchies for action selection, Adaptive Behavior Journal, 1993.
PDF, 34 pages, 14163K

ADDITIONAL

R.D.Beer, H.J.Chiel : Neural implementation of motivated behavior: Feeding in an artificial insect, in D. Touretzky (Ed.), Advances in Neural Information Processing Systems 2, Morgan Kaufmann, pp. 44-51, 1989.
PDF, 8 pages, 859K
D.McFarland : Animal behavior, 3rd edition, 1998 (chapters 24,25, animal economics & robotics).
PDF, 43 pages, 14632K
B.Webb, R.Harrison : Integrating sensorimotor systems in a robot model of cricket behaviour, SPIE Proceedings, 2000.
PDF, 12 pages, 309K

Lecture 4. Behavior II (Learning)

FUNDAMENTAL

D.Hebb : The organization of behavior, 1949 (introduction and chapter 4, growth of assembly, included in "Neurocomputing - Foundations of research" by Anderson & Rosenfeld, 1988).
PDF, 14 pages, 4562K
D.McFarland : Animal behavior, 3rd edition, 1998 (chapter 17, conditioning & learning).
PDF, 15 pages, 2932K
R.S.Sutton, A.G.Barto : Reinforcement learning - An introduction, 1998, (chapter 1, introduction).
PDF, 25 pages, 76K
O.Trullier et al. : Biologically-based artificial navigation systems - Review and prospects, Progress in Neurobiology, 1997.
PDF, 94 pages, 967K

ADDITIONAL

C.Balkenius : Spatial learning with perceptually grounded representations, Robotics and Autonomous systems, 25(1998):165-175.
PDF, 11 pages, 751K
G.Beauchamp : Learning rules for social foragers: Implications for the producer-scrounger game and ideal-free distribution theory, Journal of Theoretical Biology, 207(2000):21-35.
PDF, 15 pages, 208K
T.Hartley, N.Burgess, C.Lever, F.Cacucci, J.O'Keefe : Modeling place fields in terms of the cortical inputs to the hippocampus, Hippocampus 10:369-379, 2000.
PDF, 11 pages, 434K
M.J.Mataric : Integration of representation into goal-driven behavior-based robots, IEEE Transactions on Robotics and Automation, 8(3):304-312, 1992.
PDF, 9 pages, 1747K
E.C.Tolman : Cognitive maps in rats and men, The Psychological Review, 55(4):189-208, 1948.
PDF, 14 pages, 237K

Lecture 5. Populations

FUNDAMENTAL

R.Durrett, S. Levin : The importance of being discrete (and spatial), Theoretical Population Biology, 46:363-394, 1994.
PDF, 32 pages, 1162K
S.Railsback : Complex from complex adaptive systems as a framework for individual-based modeling, Ecological Modeling, 139:47-62, 2001.
PDF, 16 pages, 124K
C.Reynolds : Flocks, herds and schools : A distributed behavioral model, SIGGRAPH-87, 21(4).
PDF, 13 pages, 120K
J.Schull : Are species intelligent?, Behavioral and Brain Sciences, 13:63-108, 1990.
PDF, 28 pages, 3526K
W.G.Wilson : Lotka's game in predator-prey theory : Linking populations to individuals, Theoretical Population Biology, 50:368-393, 1996.
PDF, 26 pages, 2040K

ADDITIONAL

R.Schoonderwoerd, O.Holland, J.Bruten, L.Rothkrantz : Ant-based load balancing in telecommunication networks, Adaptive Behavior Journal, 5(2):169-207, 1997.
PDF, 26 pages, 152K

Lecture 6. Molecules

FUNDAMENTAL

R.J. Bagley, J.D. Farmer and W.Fontana : Evolution of a Metabolism, in: Artificial Life II, C.G.Langton et al. (eds.), pp. 141-158, Addison-Wesley, 1991.
PDF, 10 pages, 6880K
H. de Jong : Modeling and simulation of genetic regulatory systems: A literature review, INRIA Research Report 4032, September 2000.
PDF, 46 pages, 493K
W.Fontana : Algorithmic Chemistry, in: Artificial Life II, C.G.Langton et al. (eds.), pp. 159-209, Addison-Wesley, 1991.
PDF, 51 pages, 3329K
R.V.Sole, R.Pastor-Satorras : Complex networks in genomics and proteomics, In: Handbook of Graphs and Networks, S. Bornholdt & H. G. Schuster (eds.), John Wiley-VCH, 2002.
PDF, 25 pages, 694K
O.Wolkenhauer, H.Kitano, K-H.Cho : An introduction to systems biology, IEEE Control Systems Magazine, Vol.23, No.4, 38-48, August 2003.
PDF, 14 pages, 238K

ADDITIONAL

R. J.Bagley, J.D.Farmer : Spontaneous emergence of a metabolism, in: Artificial Life II, C.G.Langton et al. (eds.), pp. 93-140, Addison-Wesley, 1991.
PDF, 26 pages, 5036K>

H.Baltscheffsky, C.Blomberg, H.Liljenstroem, B.I.B.Lindahl, P.Arhem : On the origin and evolution of life - An introduction, Journal of Theoretical Biology, 187(1997):453-459.
PDF, 7 pages, 153K

W.Fontana, L.W.Buss: What would be conserved if "the tape were played twice"?, Proceedings of the National Academy of Sciences (USA), Vol.91, 757-761, January 1994.
PDF, 5 pages, 1150K

L.Raeymaekers : Dynamics of boolean networks controlled by biologically meaningful functions, Journal of Theoretical Biology, 218:331-341, 2002.
PDF, 11 pages, 160K

I.Shmulevich, E.Dougherty, S.Kim, W.Zhang : Probabilistic boolean networks - A rule-based uncertainty model for gene regulatiry networks, Bioinformatics 18(2):261-274, 2002.
PDF, 14 pages, 198K

L.Varetto : Studying artificial life with a molecular automaton, Journal of Theoretical Biology, 193(1998):257-285.
PDF, 29 pages, 508K

Journal of Theoretical Biology, Special issue on Metabolic Control Vol. 182, Issue 3, 7 October 1996.
Available online from Science Direct

Lecture 7. Development I (Structures, forms, rules)

FUNDAMENTAL

P.Agarwal : Cellular segregation and engulfment simulations using the Cell Programming Language, Journal of Theoretical Biology, 176(1995):79-89.
PDF, 11 pages, 1290K
R.Dawkins : The blind watchmaker, Longman Press, 1986 (chapter 3 : Accumulating small changes, greek translation)
Chapter 3, PDF, 45 pages, 17108K
P.Prusinkiewicz, M.Hammel, J.Hana, R.Mech: Visual models of plant development, In: Handbook of Formal Languages, by G.Rozenberg and A.Salomaa (Eds.), Springer Verlag, 1996.
PS, 49 pages, 7645K

ADDITIONAL

A.Cangelosi, D.Parisi, S.Nolfi : Cell division and migration in a 'genotype' for neural networks, Network, 5:497-515, 1994.
PDF, 25 pages, 126K
A.M.Turing : The chemical basis of morphogenesis, Philosophical Transactions of the Royal Society of London, Series B (Biological Sciences), Volume 237, Issue 641, pages 37-72, August 1952.
PDF, 37 pages, 5356K

Lecture 8. Development ΙI (Equilibria, pathologies)

FUNDAMENTAL

C.Furusawa, K.Kaneko : Emergence of rules in cell society : Differentiation, Hierarchy and Stability, Bulletin of Mathematical Biology, 60:659-687, 1998.
PDF, 29 pages, 1245K
A.Perelson, G.Weisbuch : Immunology for physicists, Review of Modern Physics, 69(4):1219-1267, 1997.
PDF, 49 pages, 1828K
B.K.Hall : Evolutionary Developmental Biology, 2nd Edition, Kluwer, 1999. Chapters 23 (Time and place in development) & 24 (Time and place in evolution: Heterochrony and heterotopy).
PDF, 26 pages, 5485K

ADDITIONAL

R.J.De Boer, A.A.Freitas, A.S.Perelson : Resource competition determines selection of B cell repertoires, Journal of Theoretical Biology, 212(2001):333-343.
PDF, 11 pages, 313K

Lecture 9. Evolution I (Techniques)

FUNDAMENTAL

R.D.Beer, R.D.Quinn, H.J.Chiel, R.E.Ritzmann : Biologically inspired approaches to robotics, Communications of the ACM, 40(3):30-38, March 1997.
PDF, 9 pages, 1157K
J.Koza : Genetic evolution and co-evolution of computer programs, Proceedings Artificial Life II, 1990.
PDF, 33 pages, 190K
Z.Michalewicz, R.Hinterding, M.Michalewicz : Evolutionary algorithms, Chapter 2 in Fuzzy Evolutionary Computation, W.Pedrycz (editor), Kluwer Academic, 1997.
PDF, 29 pages, 324K
M.Mitchell : An introduction to genetic algorithms, MIT Press, 1996 (chapter 1 : general overview).
PDF, 34 pages, 8912K

ADDITIONAL

M.Dorigo, G.DiCaro, L.M.Gambardella : Ant algorithms for discrete optimization, Journal of Artificial Life, 1999.
PDF, 36 pages, 339K
P.Husbands, I.Harvey, D.Cliff, G.Miller : Artificial evolution - A new path for artificial intelligence?, Brain and Cognition, 34(1997):130-159.
PDF, 30 pages, 909K
D.Jefferson, R.Collins, C.Copper, M.Dyer, M.Flowers, R.Korf, C.Taylor, A.Wang, Evolution as a Theme in Artificial Life : The Genesys/Tracker System, in Langton et al. (Ed.), Artificial Life II, 1991.
PDF, 15 pages, 216K>
S.Nolfi : Learning and evolution in neural networks, in M. A.Arbib (Ed.), Handbook of brain theory and neural networks, Second Edition. Cambridge, MA: MIT Press, pp.415-418..
PDF, 8 pages, 30K
S.Nolfi, D.Parisi : Evolution of artificial neural networks, in M. A.Arbib (Ed.), Handbook of brain theory and neural networks, Second Edition. Cambridge, MA: MIT Press, pp.418-421.
PDF, 8 pages, 41K

Lecture 10. Evolution II (Populational phenomena)

FUNDAMENTAL

R.Dawkins : The selfish gene, Oxford University Press, 1976 (chapter 1 : What is man ?, chapter 11 : Memes, the new replicators, greek translation)
Chapter 1, PDF, 11 pages, 2400K
Chapter 11, PDF, 12 pages, 3280K
P.Turney : Myths and legends of the Baldwin effect, Proceedings of the Workshop on "Evolutionary Computation and Machine Learning", 13th International Conference on Machine Learning, Bari, Italy, 1996.
PDF, 8 pages, 33K
T.S.Ray : An evolutionary approach to synthetic biology - Zen and the art of creating life, Artificial Life Journal, 1994.
PDF, 39 pages, 271K
S.A.L.M.Kooijman, P.Auger, J.C.Poggiale, B.W.Kooi : Quantitative steps in symbiogenesis and the evolution of homeostasis, Biol.Rev. 2003.
PDF, 29 pages, 404K
U. Dieckmann, M. Doebeli : On the origin of species by sympatric speciation, Nature, 400(6742):311-2, Jul 22 1999.
PDF, 19 pages, 486K

ADDITIONAL

J.M.Baldwin : A new factor in evolution, American Naturalist 30, pages 441-451 and 536-553, June 1896.
PDF, 20 pages, 95K

G.E.Hinton, S.J.Nowlan : How learning can guide evolution, Complex Systems, 1(1987):495-502.
PDF, 5 pages, 104K

L.Margulis : The conscious cell, Annals NY Academy of Sciences, 929:55-70, April 2001.
PDF, 9 pages, 4025K

Wcislo, W.T. : Behavioral environments and evolutionary change, Annual Review of Ecology and Systematics, 20:137-169, 1989.
PDF, 17 pages, 11.4M

Memetics website
http://www.ing.unlp.edu.ar/cetad/mos/memetic_home.html

Lecture 11. Εξέλιξη III (Games and cooperation)

FUNDAMENTAL

R.Axelrod, W.Hamilton : The evolution of cooperation in biological systems, chapter 5 in "The Evolution of Cooperation", by R.Axelrod, Basic Books, 1984.
PDF, 10 pages, 2670K
W.D.Hamilton : The genetical evolution of social behaviour - I & II, Journal of Theoretical Biology, 7:1-16 και 17-52, 1964.
Part I, PDF, 9 pages, 7124K
Part II, PDF, 19 pages, 16644K
R.Trivers : The evolution of reciprocal altruism, Quarterly Review of Biology, 46(4):35-57, 1971.
PDF, 23 pages, 10759K
J.R.Krebs, N.B.Davies : An introduction to behavioural ecology, (chapter 11: On selfishness and altruism), 3rd Edition, Blackwell, 1993.
PDF, 26 pages, 7052K
R.Hoffmann : Twenty years on : The evolution of cooperation revisited, Journal of Artificial Societies and Social Simulation, 3(2), March 2000.
PDF, 13 pages, 159K
E.S.Tzafestas : Spatial games with adaptive tit-for-tats, Proceedings of the 6th "Parallel Problem Solving from Nature" (PPSN-VI), Paris, September 2000.
PDF, 10 pages, 115K
T.N.Sherratt, G.Roberts : The stability of cooperation under variable investment, Journal of Theoretical Biology, 215:47-56, 2002.
PDF, 10 pages, 213K
L.A.Dugatkin : Cooperation in animals : An evolutionary overview, Biology and Philosophy, 17:459-476, 2002.
PDF, 18 pages, 317K
Margulis, L. (1993). Origins of species: acquired genomes and individuality, BioSystems, 31(2-3):121-125.
PDF, 5 pages, 413K

Lecture 12. Dynamics

FUNDAMENTAL

P.E.Griffiths, R.D.Gray : The Developmental Systems Perspective: Organism-environment systems as units of evolution, in K. Preston & M. Pigliucci (Eds.), The Evolutionary Biology of Complex Phenotypes, Oxford University Press, 2004.
PDF, 23 pages, 90K
K.McCann, A.Hastings, S.Harrison, W.Wilson : Population outbreaks in a discrete world, Theoretical Population Biology, 57(2):97-108, March 2000.
PDF, 12 pages, 290K
P.A.Abrams, C.E.Brassil, R.D.Holt : Dynamics and responses to mortality rates of competing predators unergoing predator-prey cycles, Theoretical Population Biology, 64(2):163-176, September 2003.
PDF, 14 pages, 500K
E. Akiyama, K. Kaneko : Dynamical systems game theory and dynamics of games, Physica D, 147:221-258, 2000.
PDF, 38 pages, 959K

Last updated 26 March 2008.
Στείλτε μου mail (brensham@softlab.ece.ntua.gr)

Complex Adaptive Systems (M.Sc. in Bioinformatics, University of Athens)

Readings (2008)

Lecture 1. Introduction

Lecture 2. History, roots, topics

Lecture 3. Behavior I (Navigation, control, regulation)

Lecture 4. Behavior II (Learning)

Lecture 5. Populations

Lecture 6. Molecules

Lecture 7. Development I (Structures, forms, rules)

Lecture 8. Development ΙI (Equilibria, pathologies)

Lecture 9. Evolution I (Techniques)

Lecture 10. Evolution II (Populational phenomena)

Lecture 11. Εξέλιξη III (Games and cooperation)

Lecture 12. Dynamics

Complex Adaptive Systems
(M.Sc. in Bioinformatics, University of Athens)