Lecture 1

1. Timeline: universe formation (~15 BYA), solar system and earth formation (~4.5 BYA), life first appeared (~ 4 BYA), first fossil evidence of life (cyanobacteria, ~3.5 BYA), prokaryotes were dominant life form (4.0-2.0 BYA), eukaryotes emerge (~2 BYA), multicellular organisms (~1 BYA), first animals, sponges (~0.6 BYA), first animals with nervous systems, worms, cnidaria (~0.60-0.55 BYA), Cambrian explosion (~0.55-0.50 BYA), first vertebrates (~0.50 BYA).
2. Protocells, memory-based self-replication, variation and selection
3. Earthworm 'intelligence', Darwin's observations
4. Hawking's thoughts on 'Life in the Universe'

Lecture 3

1. General structure of early tree of life (bacteria, archaea, eukaryotes) arising from tangled web of relationships at the root level
2. General problems that all organisms must solve: nutrients and energy acquisition, growth, reproduction, protection (self-, offspring-)
3. Energy budgets: maintenance, growth, 'behavior' (e.g. taxis), reproduction, waste
4. Distinguish between 'hunting' and 'farming' lifestyle of microbes. (farmers stay in one area, hunters move to where conditions are better)
5. Chemotaxis: identify functional components of signaling pathway (sensor, transmitter, messenger, receiver, output)
6. Run/tumble strategy (biased random walk). how is tumble probability modified (tumble probability decreases when chemical concentration gradient is increasing)
7. Understand kinesis and taxis behaviors: kinesis (non-directed movement, rate depends on stimulus intensity), taxis (directed movement toward or away from a stimulus)
8. types of kinesis: orthokinesis (velocity is altered based on stimulus intensity), klinokinesis (frequency or magnitude of turning behavior is altered based on stimulus intensity)
9. differential or adaptive klinokinesis: turning behavior is altered based on CHANGES IN stimulus intensity (as opposed to the absolute magnitude of the stimulus)
10. Understand the role of sensory adaptation in bacterial chemotaxis (temporal derivative of stimulus, necessary for adaptive klinotaxis)

Lecture 4

1. Prokaryotic-Eukaryotic transition
2. Obstacle avoidance behavior in paramecia. How does a paramecium distinguish anterior versus posterior contact? (anterior: Ca influx, depolarization; posterior: K+ efflux, hyperpolarization)
3. Similarities and differences between chemical and electrical modes of intracellular signaling: both can couple sensory stimulus to motor response; both can signal increases and decreases about a baseline level; electrical is faster and hence better for larger cells (paramecium vs. E. coli)
4. Electrical signaling in single-celled organisms as an evolutionary precursor to electrical signaling (action potentials) in neurons

Lecture 5

1. Volvox - a simple multicellular organism (colonial algae, plant not animal); individual cells are flagellated, spherical colony can perform phototaxis behavior based on changes in beat frequency on different sides of the colony; all cells the same, no division of labor
2. Braitenberg vehicles: given a simple vehicle wiring diagram from chapters 2-3, describe its behavior. Given a simple behavior (e.g. approach a light source and slow down), generate the corresponding wiring diagram.
3. What distinctions does Dusenbery make between 'causal' agents and 'informational' agents? ( causal: direct effect on organism, influences can't be 'ignored'. informational: indirect effect on organism; important because of their association with some causal agent; influences can be ignored;
4. What three information pathways did Dusenbery describe that converge to influence an organism's behavior? (genome, memory, sensory systems)
5. Over what time scales do each of these three information processing pathways acquire and store information? (genome: evolutionary time scales; memory: organism's own lifetime; sensory: current state of the environment)
6. What functional role does thermotaxis play in the life of root-node nematodes? (Juvenile worms use temperature gradients in the soil for moving to an optimal depth for encountering root tips, from which they extract nutrients. Dusenbery would classify the temperature gradients as 'informational' and the nutrients as 'causal'.)

Lecture 6

1. Understand Cariani's distinction between syntactic (computational), semantic (meaning) and pragmatic (usefulness, fitness) axes in the analysis of information processing agents
2. Understand proposed relationships between sensory modalities based on solvent vs. solute sensing. Which modalities group together? (solute: smell, taste, vision; solvent: osmolarity, mechanosense, touch, pain, hearing).
3. Chemical sensing (solute sensing) in single-celled organisms as an evolutionary precursor to neurotransmitter sensing (chemical synapses) in neurons
4. Porifera (sponges) - anatomy: more complex than volvox, multiple cell types including flagellated cells that pump water and extract food, primitive cellular division of labor, no nervous system
5. Cnidaria (jellyfish, sea anemones) - first organisms to evolve nervous systems, jellyfish lifecycle (sessile/free-swimming stages), nerve nets
6. C. elegans (nematode, roundworm) - number of cells, neurons and synapses: 959 cells, 302 neurons, ~5000 synapses

Lecture 7

1. amphid sense organs - know general structure and sensory modalities. Chemosensors with sensory endings in pore exposed to the environment (taste); chemosensors next to the pore (wing cells) not directly exposed to the environment (volatile chemicals, 'smell'); temperature sensor ('finger cell').
2. C. elegans neuron morphology and location. Most sensory and interneruon cell bodies are in the nerve ring; most motor neuron cell bodies lie along the ventral nerve cord; many sensory neurons have neurites that project to the tip of the nose; primary (sensory) interneurons have neurites that tend to be confined to the nerve ring; secondary (pre-motor) interneurons have neurites that project down the ventral nerve cord; motor neurons have neurites that project onto body wall muscles.
3. In a schematic diagram of the C. elegans chemotaxis or thermotaxis network, be able to identify which neurons are a) sensory neurons, b) primary (sensory) interneurons, c) secondary (pre-motor) interneurons, and d) motor neurons.
4. Understand the neuron and synapse models used in the Ferree and Lockery chemotaxis paper.
5. Understand why computing a temporal derivative is important for chemotaxis behavior in C. elegans.

Lecture 8

1. Nervous system complexity evolved rapidly during the Cambrain period. The Cambrian Period began approximately 550 million years ago and lasted approximately 50 million years. This is the time when most of the major groups of animals first appear in the fossil record
2. Be able to list several factors that contributed to the explosion of body plans, sensing capabilities and nervous system architecture during this period. Answers: i) climate instability resulted in repeated creation and destruction of new niches and diversification of phyla; ii) predator-prey arms race created a positive feedback effect which favored rapid evolution of better sensing, movement and neural control strategies, iii) axons and action potentials allowed neural communication of longer distances, allowing the evolution of large, complex organisms.
3. Amphioxus (brachiostoma) - eel-like chordate, dorsal nerve cord, clustered sense organs in head region, frontal eye spots, lacks telencephalon
4. Early vertebrates - 'new and improved' design: gills, jaws, enhanced sensory systems (visual, olfactory), brain maps, cerebellum, myelinated axons.