SPRING O5 ARCHIVE Readings

Week 1: Jan 18, 20 -- introduction and overview

1. Crist E (2002) The inner life of earthworms: Darwin's argument and its implications. In Bekoff M, Allen C and Burghardt G (eds) The Cognitive Animal. MIT Press. pp. 3-8 (6 pp).
   assessing animal intelligence/cognition; observing behavior in the animal's natural environment; interpretation of behavior.
2. Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. MIT Press. pp. 1-14 (14 pp)
   Introduction; Vehicle 1: Getting Around; Vehicle 2: Fear and Agression; Vehicle 3: Love;
3. Belew RK (1991) Artificial life: A constructive lower bound for artificial intelligence. IEEE Expert, 6(1):8-15 (8 pp)
   artificial life research, Alife as a lower bound on AI, centrality of evolution, modeling the environment, computational ethology.
4. Dennett DC (1998) Out of the Armchair and into the Field. In: Brainchildren: Essays on Designing Minds by DC Dennett. MIT Press. pp. 289-306 (18 pp).
   cognitive ethology, vocal communication in vervet monkeys, field studies in Keyna, observing behavior in the animal's natural environment, interpretation of behavior.

Week 2: Jan 25, 27 -- evolutionary perspectives on behavior, emergence of life, life at small scale

1. Alcock J (2001) Animal Behavior, Chapter 1, Evolutionary Approach to Animal Behavior, pp 1-21 (21 pp).
   proximate and ultimate causes of behavior, Darwinian theory
2. Maynard Smith J, Szathmary E (1995) The Major Transitions in Evolution, Chapter 1, Introduction, pp 2-14 (13 pp).
   fallacy of progress in evolution, measurement of complexity, major transitions, duplication, symbiosis, epigenesis
3. Maynard Smith J, Szathmary E (1995) The Major Transitions in Evolution, Chapter 2, What is Life? pp 17-23 (7 pp).
   definition of life, the Oklo reactor, the chemoton
4. Dusenbery DB (1996) Life at Small Scale. Scientific American Library. Chapter 1, Invisible Organisms, pp 2-17 (16 pp).
   intro to microbes, basic problems faced by microbes, diffusion processes, evolutionary history, food chains, hunting and farming life styles in the micro world
5. Conway's Game of Life (website)
6. (Another) Conway's Game of Life (website, with Java applet)
7. Wonders of Math - The Game of Life (website)

Week 3: Feb 01, 03 -- behavior without a nervous system, bacterial chemotaxis

1. Dusenbery DB (1996) Life at Small Scale. Chapter 2, Locomotion Without Legs. 20-45 (26 pp).
   viscosity, Stoke's law, Reynolds number, propellers, oars, body undulations, creeping and gliding, scaling of speed with body length
2. Jurica MS, Stoddard BL (1998) Mind your Bs and Rs: Bacterial Chemotaxis, signal transduction, and protein recognition" Structure 6:809-813 (5 pp)
   bacterial chemotaxis, signaling pathway, coupling of sensor to effector elements
3. Taylor BL, Zhulin IB, Johnson MS (1999). Aerotaxis and other energy-sensing behavior in bacteria. Annu Rev Microbiol 53:103-28 (26 pp)
   energy taxis in motile bacteria, energy sensing as a survival strategy, how cells sense energy.

1. Spiro P A, Parkinson JS, and Othmer HG (1997) A model of excitation and adaptation in bacterial chemotaxis. Proc. Natl. Acad. Sci. USA 94:7263-7268 (6 pp)
   A detailed biochemical model of the signaling pathway.
2. Strong SP, Freedman B, Bialek W & Koberle R (1998) Adaptation and optimal chemotactic strategy for E. Coli. Phys Rev E 57:4604-4617 (14 pp)
   A detailed mathematical analysis of chemotaxis behavior. Unfortunately, this sort of analytic approach becomes intractable for even modestly complex behaviors and environments.

Week 4: Feb 08, 10 -- energy/mass acquisition, kinesis, taxis, electrical versus chemical signaling

1. Dusenbery DB (1996) Life at Small Scale. Chapter 4, Navigating Through a Chemical Sea, pp. 64-89, (26 pp)
   sensing environmental change, choosing a response, sensory adaptation, a cyanobacterium's strategy for finding light, simultaneous sampling, sequential sampling, avoiding obstacles
2. Zupanc GKH (2004) Behavioral Neurobiology: An Integrative Approach. Oxford Press. 80-88 (9 pp)
   classification of orienting movements; orienting behavior without a nervous system; cellular mechanisms of taxis behavior in paramecians.
3. Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. pp. 15-25 (11 pp)
   Vehicle 4: Values and Special Tastes; nonlinearity, instincts; Vehicle 5: Logic. "Law of uphill analysis and downhill invention", threshold devices, memory.

Week 5: Feb 15, 17 -- sensory information processing

1. Dusenbery DB (1996) Information is where you find it. Biol. Bull. 191:124-128 (5 pp)
   Information from a biological perspective. Informational versus causal agents; 3 information processing pathways operating on different timescales: genome (evolutionary times), memory (lifetime), sensory (current state). Example of informational processing: thermotaxis in root-knot nematodes.

1. Barlow H (2001) The exploitation of regularities in the environment by the brain. Behav Brain Sci 24: 602-607 (6 pp) Information processing as exploitation of statistical regularities in the environment. Learning as internalization of environmental regularities. Historical overview and recent advances.

Week 6: Feb 22, 24 -- information theory, intro to C. elegans

1. Weaver W (1949) Recent contributions to the mathematical theory of communication, In: The Mathematical Theory of Communication, edited by C. E. Shannon and W. Weaver, University of Illinois Press, Urbana. pp. 3-28 (26 pp) Information from a communications theory perspective. Three levels of analysis (transmission accuracy, semantics, effectiveness). Entropy as a measure of information. Channel capacity. Coding. Continuous versus discrete messages.
2. Mori, I. (1999) Genetics of chemotaxis and thermotaxis in the nematode Caenorhabditis elegans. Ann. Rev. Genet. 33, 399-422 (24 pp)
3. Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. MIT Press. pp. 26-28 (3 pp)
   Vehicle 6: Selection, the Impersonal Engineer;

1. Holland ND (2003) Early central nervous system evolution: an era of skin brains? Nat Rev Neurosci. 4:617-27 (11 pp) speculations on the early evolution of central nervous systems

Week 7: Mar 01, 03 -- chemotaxis and its modulation in C. elegans

1. Ferree TC, Lockery SR (1999) Computational rules for chemotaxis in the nematode C. elegans. J Comput Neurosci 6:263-277 (15 pp)
   a neural model of chemotaxis; computing temporal derivatives using network dynamics
2. Hills T, Brockie PJ, Maricq AV (2004) Dopamine and glutamate control area-restricted search behavior in Caenorhabditis elegans. J Neurosci 24:1217-1225 (9 pp)
   how an environmental stimulus 'reprograms' chemotaxis behavior via neuromodulation

1. Dunn NA, Lockery SR, Pierce-Shimomura JT, Conery JS (2004) A neural network model of chemotaxis predicts functions of synaptic connections in the nematode Caenorhabditis elegans. J Comput Neurosci 17:137-147 (11 pp)
   a sequel to the Ferree and Lockery (1999) modeling work
2. Sawin ER, Ranganathan R, Horvitz HR (2000) C. elegans locomotory rate is modulated by the environment through a dopaminergic pathway and by experience through a serotonergic pathway. Neuron 26:619-631 (13 pp)
   describes two 'slowing responses' to food mediated by different modulatory pathways; worms on Prozac
3. Geng W, Cosman P, Berry CC, Feng Z, Schafer WR (2004) Automatic tracking, feature extraction and classification of C. elegans phenotypes. IEEE Trans Biomed Eng 10:1811-1820.
   a methods paper describing the use of computer vision and image analysis techniques for automating worm behavioral analysis

Week 8: Mar 08, 10 -- evolving brains, natural and artificial

1. Allman JM (2000) Evolving brains. Chapter 4, Eyes, Noses and Brains, pp. 63-83 (21 pp)
   Cambrian explosion, predator-prey arms race, early evolution of eyes, chordates, the rise of vertebrates, gene duplications create a keen sense of smell, tectum: an ancient map, origin of the cerebellum, myelin: a crucial vertebrate innovation, cephalopds: the second great pinnacle of brain evolution
2. Beer R, Chiel J, Sterling L (1991) An artificial insect. American Scientist, 79:444-452 (9 pp)
   A computer simulated cockroach with 78 model neurons and 156 synapses.

1. Chiel HJ and Beer RD (1997) The brain has a body: adaptive behavior emerges from interaction of nervous system, body and environment. Trends Neurosci 20:553-557. (5 pp)
   

Week 9: Mar 15, 17 -- Bot Tournament (Surivor Braitu) and Exam II

Week 10: Mar 29, 31 -- modeling single neurons and small networks

1. Koch C, Mo C-H, Softky W (2003) Single-Cell Models. In: The Handbook of Brain Theory and Neural Networks. Second edition (Arbib M, ed) MIT Press, pp. 1044-1049 (6 pp)
   Overview of single neuron modeling techniques
2. Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. MIT Press. pp. 29-49 (21 pp)
   Vehicle 7: Concepts. Vehicle 8: Space, Things, Movements; Vehicle 9: Shapes.

Week 11: Apr 5, 7 -- learning from experience

1. Montague PR, Dayan P, Person C, Sejnowski TJ (1995) Bee foraging in uncertain environments using predictive Hebbian learning. Nature 377:725-728 (4 pp)
OPTIONAL:
2. Carew TJ (2000) Behavioral Neurobiology, Chapter 9, Associative Learning in Honeybees. 271-300 (30 pp)

Week 12: Apr 12, 14 -- communication, social interactions

1. Dusenbery DB (1992) Sensory Ecology. Chapter 13, Communication pp. 321-353 (33 pp).
   
2. Jackson DE, Holcombe M, Ratnieks FLW (2004) Trail geometry gives polarity to ant foraging networks. Nature 432:907-909 (3 pp).

Week 13: Apr 19, 21 -- 'thinking', planning, anticipating the future

1. Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. pp. 50-61 (12 pp)
   Vehicle 10: Getting Ideas; Vehicle 11: Rules and Regularities.
2. Braitenberg V (1984) Vehicles: Experiments in Synthetic Psychology. pp. 62-83 (22 pp)
   Vehicle 12: Trains of Thought; Vehicle 13: Foresight; Vehicle 14: Egotism and Optimism.
3. Byers JA (2002) The ungulate mind. In Bekoff M, Allen C and Burghardt G (eds) The Cognitive Animal. MIT Press. pp. 35-39 (5 pp).
   

Week 14: Apr 26 -- student-selected topics (memory, language)

1. Squire LR (2004) Memory systems of the brain: A brief history and current perspective. Neurobiol Learn Mem 82:171-177 (7 pp.)
2. Clayton NS, Bussey TJ, Dickinson A (2003) Can animals recall the past and plan for the future? Nat Rev Neurosci 4:685-691 (7 pp.)
3. Hauser MD, Chomsky N, Fitch WT (2002) The faculty of language: What is it, who has it, and how did it evolve? Science 298:1569-1579 (11 pp.)

Week 15: May 3 -- student-selected topics (biorobotics, brain-machine interfaces)

1. Webb B (2001) Can robots make good models of biological behaviour? Behav Brain Sci 24:1033-1050 (18 pp.; 62 pp total)
   The target article is 18 pages long; the PDF file aslo includes 44 pages of "open peer commentary" and a long list of references. If you print it out, you might just want the first 18 pages.
2. Mussa-Ivaldi FA, Miller LE(2003) Brain-machine interfaces: computational demands and clinical needs meet basic neuroscience. Trends Neurosci 26:329-334 (6 pp.)

Misc./Overflow

1. Timberlake W (2002) Constructing animal cognition. In Bekoff M, Allen C and Burghardt G (eds) The Cognitive Animal. MIT Press. pp. 105-113 (9 pp).
   
2. Salinas E (2004) Context-dependent selection of visuomotor maps BMC Neuroscience 5:47 (22 pp)
3. Wills TJ, Lever C, Cacucci F, Burgess N, O'Keefe J (2005) Attractor dynamics in the hippocampal representation of the local environment. Science 308:873-876.
4. Dusenbery DB (1992) Sensory Ecology. Chapter 14, Classification of Behaviors Related to Spatial Goals. pp. 357-366 (10 pp).
   
5. Dusenbery DB (1992) Sensory Ecology. Chapter 16, Searching: Looking for Relevant Stimuli. pp. 385-411 (27 pp).
   
6. Dusenbery DB (1996) Life at Small Scale. Chapter 9, Anticipating the Future. pp. 177-187. (11 pp)
   free-running circadian rhythms, setting circadian clocks, timing cell division and other circadian rhythms, following the tides
7. Maynard Smith J, Szathmary E (1995) The Major Transitions in Evolution, Chapter 16, The origins of societies. pp. 257-278 (22 pp).