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. 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. kinesis, 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. 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; informational: indirect effect on organism; important because of their association with some causal agent) 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 rules), 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);

2.

3. 4. 5.

chemosensors next to the pore (wing cells) not directly exposed to the environment (volatile chemicals, 'smell'); temperature sensor ('finger cell'). 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. 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. Understand the neuron and synapse models used in the Ferree and Lockery chemotaxis paper. Understand why computing a temporal derivative is important for chemotaxis behavior in C. elegans.

Lecture 8
1. Cambrian explosion (550-500 MYA) - rapid evolution of nervous system complexity, most 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 larger, more complex organisms. 3. Early vertebrates - important new design features: gills, jaws, enhanced sensory systems (visual, olfactory), brain maps, cerebellum, myelinated axons. 4. Amphioxus (brachiostoma) - eel-like chordate, dorsal nerve cord, clustered sense organs in head region, frontal eye spots, lacks telencephalon

Lecture 9: Area-restricted search in C. elegans, Beer's artificial insect (motor control)

1. Understand the general principles associated with area-restricted search (ARS) behavior and why it is useful to the animal. 2. Be familiar with the experimental paradigm that was used to measure ARS behavior in C. elegans and be able to predict what would happen to the high-angle turn frequency under different conditions. 3. Know the functional roles of glutamate and dopamine in C. elegans ARS behavior. 4. Given a schematic diagram of a cockroach body, be able to identify stable and unstable patterns of leg placement; know alternating tripod gait. 5. Given a diagram of an individual leg controller circuit, be able to answer questions about the functional role of various neurons and their interactions.

6. Understand the role of reciprocal inhibition in coordinating motor activity between neighboring legs.

Lecture 10: Beer's artificial insect (action selection)

1. Be able to list four behaviors associated with Beer's artifial insect and understand the behavioral choice hierarchy in Beer's model. 2. Given a block diagram of Beer's behavioral choice hierarchy, be able to identify 'condition-action' pairs. 3. Be able to translate between a Beer-style block diagram of behavioral choice and the corresponding NetLogo code. 4. Given an action-selection strategy coded in NetLogo using a combination of 'Test' blocks, be able to identify which 'action' would be selected under different conditions.

Lecture 11: Action selection, vertebrate brain organization, subsumption architecture

1. In the diagram of a 'generalized vertebrate brain' (from the reading by Prescott, p. 10) be able to identify: telencephalon, diencephalon, midbrain, hindbrain, spinal cord, cerebellum, tectum, thalamus, hypothalamus, striatum, amygdala, olfactory bulb 2. Understand the distinction between serial (horizontal) and parallel (vertical) control architectures. 3. Understand the major features of Brook's subsumption architecture. 4. Be able to provide an example of the hierarchical organization of behavior based on the herring-gull diagram by Baerends. 5. For the rat defense system, be able to match different types of sensory stimuli and motor reponses with the corresponding level of brain processing (e.g. spinal cord, hindbrain, midbrain/hypothalamus, thalamus, cortex) 6. Be able to describe functional parallels between the rat defense system and the subsumption architecture. 7. Understand the role of the amygdala in fear conditioning and how that system differs from midbrain processing of species-specific stimuli. 8. Understand the proposed role of the basal ganglia in action selection

Lecture 12: Vertebrate neuroethology; toad predator/prey system

1. Know the 'conditions' associated with various prey handling actions (orient, approach, fixate, snap) in the toad. 2. Know how the orienting response varies with stimulus length for worm, anti-worm and square stimuli. 3. Be able to describe/recognize response properties of a) retinal ganglion cells, b) thalamic-pretectal, and c) tectal neurons to worm, anti-worm and square stimuli. 4. Understand the role of lateral inhibition in center-surround receptive field organization and in enhancing spatial differences in stimulus intensity.

5. Understand the role of thalamic inhibition in shaping the overall behavioral response; be able to describe the behavioral effects of lesioning the pathway from thalamus to tectum. 6. Given a diagram of the proposed neural architecture mediating visuomotor behaviors (Carew, Fig 4.15) be able to answer questions about the functional role of various components.

Lecture 13: Associative learning, honeybee foraging

1. Under what conditions does 'learning and memory' convey a benefit relative to 'genetically hard-wired' processing? 2. Know the meaning of 'Hebbian' learning and be able to give an example of the sorts of associations that might be useful for an animal to learn using this mechanism 3. Understand the division of labor in honeybees and the sorts of things that foragers need to learn and remember. 4. Be familiar with the general anatomical organization of the bee brain 5. Understand experiments on associative color learning, including time course of retention and time window for learning. 6. Know the classical conditiong terminology (US, UR, CS, CR) and its specific application to the proboscis extension reflex. 7. Be able to compare and contrast associative color learning and the proboscis extension reflex (PER).

Lecture 14: Neural basis of PER; associative learning algorithms, delta rule
1. Know the different pathways for the conditioned and unconditioned reflex in PER, and the role of the VUMmx1 neuron. 2. Understand the sigmoid 'decision' function for choosing a flower color and how the steepness of the transition (beta) influences the tradeoff between exploration and exploitation. 3. Understand how the 'delta rule' can be used to generate 'expected rewards' based on 'actual rewards' and understand the role of the learning-rate parameter, epsilon. 4. Be familiar with the concept of risk aversion in honeybees and humans.