Readings
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 (Locomotion, control, regulation)
FUNDAMENTAL
- V. Braitenberg : Vehicles, 1986 (chapters 1-7).
PDF, 22 pages, 309K
- 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, 21 pages, 1121K
- 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, 28 pages, 1699K
- 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. Molecular models
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, 902K
- 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, 26 pages, 2267K
- 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, 25 pages, 2514K
- 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 (Forms, types, laws)
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 II (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, 26 pages, 774K
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 (Population 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, 34 pages, 3368K
- Memetics website
http://www.ing.unlp.edu.ar/cetad/mos/memetic_home.html
Lecture 11. Evolution 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 and 17-52, 1964.
Part I, PDF, 16 pages, 1036K
Part II, PDF, 36 pages, 2688K
- R.Trivers : The evolution of reciprocal altruism, Quarterly Review of Biology, 46(4):35-57, 1971.
PDF, 53 pages, 198K
- 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
Page last updated 1 April 2009.
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