- Weekly links:
- Week 1: Jan 18, 20
- Week 2: Jan 25, 27
- Week 3: Feb 01, 03
- Week 4: Feb 08, 10
- Week 5: Feb 15, 17
- Week 6: Feb 22, 24
- Week 7: Mar 01, 03
- Week 8: Mar 08, 10
- Week 9: Mar 15, 17
- Spring break (Mar 21-25)
- Week 10: Mar 29, 31
- Week 11: Apr 05, 07
- Week 12: Apr 12, 14
- Week 13: Apr 19, 21
- Week 14: Apr 26, 28
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SPRING 05 ARCHIVE Lectures
Schedule and content
The material presented in each class session will be
summarized here, with links to the associated reading
material, web resources, and powerpoint files.
You may need to enter the course userid and password to
access the lecture slides and reading material.
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Week1:
introduction and overview
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Tue, Jan 18
Introduction to the course. Overview of course website.
Course policies. Introduction to
MATLAB.
Readings for this week:
Crist, Belew, Braitenberg, Dennett.
Homework 1 due Tue, Jan 25 (midnight).
Images:
CoverArt,
GeoTimeSpiral,
TreeOfLife1,
TreeOfLife2,
TreeOfLife3
| Thu, Jan 20
Topics: Darwin and earthworms, Braitenberg vehicles,
Belew on artificial life, Dennett with the monkeys.
Matlab:
help with homework 1, running a MATLAB script, using the editor,
scalars and arrays,
matrices
Links:
Darwin's earthworm study,
earthworm biology,
earthworm ecology,
vervet monkey vocalizations
Images:
earthworm exiting burrow,
earthworm in burrow,
vervet monkey
Powerpoint:
Lecture 2
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Week 2:
evolutionary perspectives, emergence of life
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Tue, Jan 25
Announcements: New homework discussion board on Illinois Compass.
Homework 2 is available:
diffusion with boundaries, Conway's Game of Life (due Tue Feb 1).
Topics: Brains, behavior, and info processing: which came first?
From the Big Bang to the Emergence of Life.
Major transistions in evolution. LUCA: last universal common
ancestor. Protocells (the chemoton). MATLAB structure. MATLAB graphics.
Readings for this week:
Alcock, Maynard Smith, Dusenbery.
Powerpoint:
Lecture 3
| Thu, Jan 27
Topics: Proximate and ultimate causes of behavior (Alcock).
Life at small scale, diffusion, Brownian motion, hunting and farming
in the micro world (Dusenbery). Conway's Game of Life. MATLAB programming
style guide. MATLAB advice for homework #2.
Links:
Conway's Game of Life,
another Game of Life site,
Game of Life Applet,
Matlab Programming Style Guide (PDF).
Powerpoint:
Lecture 4
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Week 3:
behavior without a nervous system, bacterial chemotaxis
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Tue, Feb 1
Announcements: New homework discussion board on Illinois Compass.
Homework 3 is available:
bacteria-like animats foraging for food without any sensory
capabilities (due Tue Feb 8).
Topics: Locomotion at the micro scale, viscosity, Stoke's Law,
Reynolds number, constraints on locomotion at low Reynolds number,
bacteria flagella, helical screw drive (Dusenbery).
MATLAB: avoiding FOR loops; the FIND command; graphics HANDLES;
last minute help/advice for homework #2.
Readings for this week:
Dusenbery, Jurica et al, Taylor et al.
Powerpoint:
Lecture 5
| Thu, Feb 3
Announcements: Homework #2 wrap-up
Topics:
Bacterial chemotaxis, aerotaxis, phototaxis; signaling pathways;
energy sensing as a survival strategy; genome sizes, minimal
genomes. MATLAB: code development/debugging tips.
Links:
Genome sizes,
Minimal Genome Project,
estimates from Mycoplasma genitalium: 265 to 310 (Dec 1999),
Another Minimal Genome: Microbe Needs Just 271 Genes (Apr 03)
Powerpoint:
Lecture 6
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Week 4:
energy/mass acquisition, kinesis, taxis, electrical versus chemical signaling
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Tue, Feb 8
Announcements:
Homework 3 due today.
Homework 4 will be available later today:
bacteria-like animats with chemical gradient sensing capabilities (due Tue Feb 15).
Exam I next week (Thu Feb 17)...more details next time.
Topics: genome sizes, bacterial chemotaxis II, energy/mass budgets,
temporal derivatives, sensory adaptation, phototaxis, obstacle avoidance,
electrical versus chemical signaling.
MATLAB: structure of the simulation code.
Readings for this week:
Dusenbery, Zupanc, Braitenberg
Powerpoint:
Lecture 7
| Thu, Feb 10
Announcements: Homework #3 wrap-up; Homework #4 is ready.
Exam I next Thursday.
Topics:
Obstacle avoidance in paramecia; electrical versus chemical
signaling; Braitenberg 4: non-linearities; Braitenberg 5: logic.
Exam I study guide.
Powerpoint:
Lecture 8
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Week 5:
sensory information processing
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Tue, Feb 15
Announcements:
Readings for this week:
Dusenbery.
Homework 4 due today.
Homework 5 will be available tomorrow:
Braitenberg vehicles with food, light and temperature sensing
capabilities (due Tue Feb 22). Exam I on Thursday. Study guide and
sample problems are available on the Exam info
page.
Topics:
Information from a biological perspective (Dusenbery);
informational versus causal agents;
three information processing pathways operating on different timescales:
genome (evolutionary times), memory (lifetime), sensory (current state);
example of informational processing: thermotaxis in root-knot nematodes.
Powerpoint:
Lecture 9
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Thu, Feb 17
First 20 minutes of class: new features in homework 5 (differential drive,
multimodal sensing capabilities, ability to add food, ability to specify
initial number of bots of each color).
Last hour of class:
EXAM I: First in-class exam. Covers material from Jan 18 through Feb 10.
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Week 6:
info theory / intro to C. elegans
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Tue, Feb 22
Announcements:
Readings for this week:
Weaver, Mori, Braitenberg.
Homework #5 due today. Exam I results. HW #4 wrap-up.
Bot Survivor Challenge (Mar 15)...outwit, outplay, outlast.
Topics:
Information from a communications theory perspective.
Three levels of analysis (transmission accuracy, semantics, effectiveness).
Entropy as a measure of information. Channel capacity. Coding.
Modeling: converting between IF...ELSE... and NEURON-BASED representations.
Powerpoint: Lecture 10
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Thu, Feb 24
Announcements: HW #6 overview.
Topics: Intro to C. elegans. General neural organization:
sensory, sensory interneurons, premotor interneurons, motor neurons.
Powerpoint: Lecture 11
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Week 7:
C. elegans chemotaxis and neuromodulation
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Tue, Mar 1
Announcements: Homework #6 due today. Homework #7 due next Tue.
Readings for this week:
Ferree & Lockery, Hills et al.
Topics:Computational rules for chemotaxis in C. elegans
Powerpoint: Lecture 12
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Thu, Mar 3
Announcements:
Topics: neuromodulation of chemotaxis in C. elegans; area-restricted search; dopamine and serotonin. MATLAB: parameter search techniques
Powerpoint: Lecture 13
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Week 8:
evolving complex brains, natural and artificial
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Tue, Mar 8
Announcements: Homework #7 due today. Homework #8 due ***MONDAY (3/14) NOON ***. Bot tournament Tue (3/15) at 11 AM.
Readings for this week:
Allman, Beer et al.
Topics:Cambrian explosion, predator-prey arms race, early evolution of eyes, chordates,
rise of vertebrates, vertebrate innovations
Powerpoint: Lecture 14
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Thu, Mar 10
Announcements: HW #8 has tournament details. Exam II information.
Topics: Synthetic neurobiology; designing brains; biorobotics research
Powerpoint: Lecture 15
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Week 9:
MARCH MADNESS: MCB 419 Bot Survivor Tournament
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Tue, Mar 15
First 30 minutes of class: review session for Exam II
Last hour of class:
Bot Survivor Challenge: DCL Linux Lab
Student-designed bots compete head-to-head to survive five days
and five nights in the toxic undertow of Braitu island.
Who has the brains to survive? Outwit, Outplay, Outlast.
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Thu, Mar 17
First hour of class:
EXAM II: Second in-class exam. Covers material from Feb 15 through Mar 10.
Enjoy your SPRING BREAK!!!
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Week 10:
single neuron models
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Tue, Mar 29
Announcements: Good job on Exam II!!
Homework #9 will be available soon...due next Tue (Apr 5).
Readings for this week:
Koch et al., Braitenberg
Topics: Single neuron models, integrate-and-fire, Hodgkin-Huxley, compartmental models.
Powerpoint: Lecture 16
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Thu, Mar 31
Announcements: HW #9 is ready.
Topics: Braitenberg 7-9: concepts, forming associations, Hebb rule, topographic maps, motion detection, pattern recognition
Powerpoint: Lecture 17
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Week 11:
reinforcement learning, honeybee foraging
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Tue, Apr 5
Announcements: No class on Thu, Apr 21 (Dr. Nelson is out of town).
Homework #9 due today. Homework #10 will be ready tomorrow.
Readings: Carew, Montague et al.
Topics: associative learning in honeybees
Powerpoint: Lecture 18
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Thu, Apr 7
Announcements: Homework #10 is ready.
Topics: models of associative learning,
Montague et al. 95 ('Bee foraging in uncertain environments using
predictive hebbian learning')
Powerpoint: Lecture 19
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Week 12:
social interactions, communication
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Tue, Apr 12
Announcements: Homework #10 due today. Survey on student-selected topics.
Topics: Animal communication. MATLAB: user-interface elements
Powerpoint: Lecture 20
Matlab example of user-interface elements (buttons, dialogs): myplot.m
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Thu, Apr 14
Announcements: Homework #11 is ready.
Topics: ant foraging trails; hints/advice for homework #11
Powerpoint: Lecture 21
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Week 13: thinking, planning and optimism
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Tue, Apr 19
Announcements: No class on Thursday. Homework #11 due today.
HW #12 is ready (last Matlab exercise for the semester).
Topics: HW #12 overview; Braitenberg on thinking, planning and
optimism; HW #11 help session.
Powerpoint: Lecture 22
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Thu, Apr 21
NO CLASS TODAY (Dr. Nelson is out of town)
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Week 14:
student-selected topics (memory systems, language)
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Tue, Apr 26
Announcements: Homework #12 due today.
Readings: Squire 2004, Clayton et al. 2003, Hauser et al. 2002
Topics: memory systems, language, exam III mini-review, HW #12 help session.
Video clips:
animal communication and cognition
Powerpoint: Lecture 23
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Thu, Apr 28
EXAM III: Third in-class exam. Covers material from Mar 29 through Apr 19.
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Week 15:
student-selected topics (biorobotics, brain-machine interfaces); course wrap-up
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Tue, May 3
LAST CLASS OF THE SEMESTER
Announcements: Homework #13 due today. Exam III scores are posted.
Topics: biorobotics, brain-machine interfaces, course wrap-up,
ICES evaluations
Powerpoint: Lecture 24
Have a great summer!
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Thu, May 5
NO CLASS TODAY (Reading Day)
Make-up/improvement exam on Tue, May 10 at 8 AM!
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