Class begins January 5, 2016 - Week 1
Class ends March 17, 2016 - Week 11
Final: Tues. March 22, 6:00 - 7:50 pm
WEEK _______________________ LECTURE TOPICS _ ___________________________
1 Introduction to systems biology: concepts and terms . Definition of life. Definition of
2 Introduction to systems: structure and behavior ; Systems thinking.
3 Information processing in life: Information theory; DNA as program code; Computer code
as DNA . Evolution as information processing. Goal directed systems; (+) and (-) feedback.
4 Cell function as a goal-directed system. Cell structure and function. DNA, RNA, and protein
strutcure and function.
5 Evolution, Population genetics: Hardy-Weinberg Equilibrium. Dynamics of gene distributions
6 Population growth dynamics: Exponential growth, logistic growth.
7 Complexity theory and life: Stability; deterministc chaos; order; disorder; self-organization;
8 Ecosystem Ecology: Ecosystem dynamics; adaptive change, resilience. Alternative views
(paradigms) of ecosystem function and management. The Yellowstone story.
9 Biomes/biosphere: Earth's biomes, biome function, biome collapse. Biospheric function: Soft
GAIA, global warming, climate change.
10 Reports by students on their bio-systems analysis of a biological/ecological/environmental
11 Earth and Man: The Anthropocene; Tragedy of the Commons; The human brain and
technology; willful blindness; denial; cognitive dissonance.
W EEK LAB EXERCISES _______
1. Introductions,: Seven Intelligences,
2. Systems diagramming
3. Simulations: information processing
in living systems, role of randomness.
4. DNA model; operons; gene expression –
Cellular automaton, rule 30.
5. Simulations: H-W; natural selection;
sickle cell/malaria; genetic drift.
6. Simulations: population dynamics,
exponential and logistic growth.
7. Simulations: Chaos in populations;
cellular automaton - Game of Life.;
self-organizing bark beetle larvae.
8. Simulations: Predator/prey dynamics;
wolves, elk, and elk carrying capacity.
9. Simulation: Managing lodgepole forests
to optimize carbon sequestration.
10. Student reports completed.
11. Lab Exam