# Animal Behavior/Sensory Biology
## Sensory Biology

Behavior requires that an animal obtains information about its environment. Thus, to understand behavior we need to understand how organisms perceive their environment (i.e., sensory systems biology, sensory biology). By understanding how your senses gather information, we gain a better and more thorough understanding of their behavior. Common research questions in sensory biology focus on:
* What is the stimulus (modality of information)? Is it mechanical, chemical, etc?
* How does the sensory system encode the stimulus? Sensory filtering, transformation, transduction, amplification
* Where is this information processed? Neural anatomy, network connections, etc.
A stimulus is any form of energy pattern that can be detected and registered by the senses. Its Dynamic range is the ratio between the highest and lowest values of a stimulus intensity, such as for sound or light. A signal is the physical coding of information (e.g., a message) capable of transmission through the environment. Sensory processing includes all central acts of information processing, which link the initial stages of sensory reception with the creation of a subjective sensory precept. Sensation is the neuronal activity resulting from the transduction of stimulus energy into electrical activity (also Sensory processing). A sensory cue is a statistic or signal from sensory input that measures the state of some property of the world that the perceiver is interested in.
Sensory systems allow us to form internal representations of our surrounding world, by transducing stimulus energy into trains of neural signals which are conveyed along specific neural pathways. Consider the following example using Jelly Beans. Hawaiian punch and Cherry flavored beans have the same color. Visual information about jelly beans is incomplete. By blocking your nose while eating a jelly bean, you prevent the smell from providing information. Taste does not allow you to determine which bean is punch and which is cherry. With olfactory information added, this decision becomes easy. If you allow air to flow through your nose while you taste the jelly beans, the cinnamon bean activates your trigeminal system providing critical information independent of taste and smell.
* Reception the ability of a cell to respond when matter or a specific form of energy acts upon a Sensory Receptor: A cell endowed with the ability to absorb a specific kind of stimulus energy. Stimulus filtering (also stimulus tuning): A receptor responds only to a narrow cocktail of (physical) characteristics.
* Sensory Transduction chain of physiological reactions which convert sensory input into electrical impulses. This process translates the amount of stimulus energy into changes in membrane permeability (e.g., opening sodium channels towards the production of an action potential). Initial receptor responses are often graded and proportional to the strength of the input signal (e.g. membrane permeability of stretch receptors to ions is proportional to the force applied to the receptor).
* Amplification when weak sensory inputs are intensified
* Transmission as input signals are conveyed to the nervous system. The intensity of the graded response determines the frequency of generated action potentials. The rapid depolarisation and hyperpolarisation of an all-or-nothing action potential spike are fairly uniform in amplitude and duration (< 2 msec). Frequency code: Information transfer based on the rate of action potentials of up to 500AP/s for intense stimuli. Sensory receptors may be neurons who themselves project axons to the CNS or non-neuronal receptors which activate neurons via synaptic (i.e., neurotransmitter) signals
* Integration: Processing of information begins as soon as stimuli are received (e.g. Sensory adaptation). Summation of multiple graded responses influences the frequency of action potentials.
The signal's Signal-to-noise ratio refers to the power of a particular signal relative to the level of background noise.

## Sensory Stimuli

There are three main forms of Stimulus Energy that can alter cellular processes and thereby activate sensory systems. A stimulus may be on for some time as a steady-state stimulus or may come on and go off again shortly afterward as a transient stimulus.

### Mechanical

(particle movement - near field, pressure waves - far field, compressional vs. transverse waves): Hearing, Vestibular, Touch (via hair cells in the cochlea, statocyst, or semicircular canals) via hair cells in acoustic, equilibrium, and lateral-line systems are responsible for the transduction process from cilia that respond to shearing forces and end with processes that depolarize the cell membrane of afferent neurons. Stimulus specificity is provided through Accessory Structures (e.g. tectal membrane, statolith, and cupula). Touch: routing response in babies, lordosis, grooming. Sound and Vibration: mechanoreception, proprioceptors, sound window, transmission in water vs. air, boundaries (surface waves), complex content (frequency modulation, amplitude modulation), Example: bird and whale songs, human speech, echolocation in bats and whales, long-distance communication in elephants and whales. Movement of particles: Example: spiders

### Electromagnetic

(waves): Light, Heat, Electrical, Magnetic (e.g., Phototransduction, heat sensors). Radiant Heat: thermoreceptor, Example: Detection of prey in rattlesnakes; Electric Fields: electroreception, Examples: Detection of prey in sharks, communication in electric fish; Light: perception of absolute light levels, color balance, polarization, Examples: fireflies

### Chemical

(particle movement): Olfaction/Pheromones/Taste (via chemical receptors trigeminal, taste, smell Odor: chemoreception, pheromones species-specific odor cues (priming, releasing), Example: silk moths

#### Pheromones

One of the many ways in which organisms can communicate with each other is through the use of pheromones. An organism generates and emits these hormonal chemicals in order to relay a message to another member of the same species. Ants and bees demonstrate two prominent examples of pheromone usage, which acknowledges their incredible capability to organize the behaviors of the whole colony. Ants produce numerous different pheromones, each with its own distinct purpose. Ants secrete pheromones to attract mates, to signal danger to the colony, or to give directions to a location. Other pheromones act as deterrents keeping out unwanted ants from foreign colonies or preying insectivores. Still, other pheromones communicate ants to congregate. This explains how assiduous ants exercise remarkable cooperation in building a colony. Pheromones maintain the cohesiveness and organization of the complex ant communities. Certain types, such as alarm pheromones, produce a “releaser effect”, which induces a quick response and may be used to tell other ants to evacuate a dangerous area such as an approaching lawnmower. For example, when a spider approaches an ant will release alarm pheromones that alert all the other ants. Ants may also discharge alarm pheromones as a result from being diverted from their work, e.g. heavy human steps. Releaser pheromones are also used to mark territory. As the chemical deposited dries, it signals to other species members of the territory’s occupant.
Other pheromones create a “primer effect” that entices other ants for actions. Such pheromones are useful in mating rituals and only affect ants of the opposite sex. Primer pheromones can send signals to the endocrine system, to make appropriate changes, for instance, ovulation required for successful mating.
Biologist E.O. Wilson discovered in the 1960’s that the organic chemical for each pheromone varies tremendously depending on what signal it entails. Ants taste and smell a substance that evaporates off the chemical laid down by another ant. Wilson observed in slow motion films that ants do this by moving their antennae from side to side. For example, alarm pheromones are discharged into the air and expand in a circle of smell. Ants can determine the concentration of the pheromone, and thus determine the proximity of the source of danger. Bees are also well known for communicating through the use of pheromones. Like ants, bees have a variety of purposes associated with the pheromones, such as marking and behavior. Honeybees release chemical signals for marking food sources, marking their hive, in scenting potential hive sites, and in assembling swarms for flight. Although each hive has a particular scent, different colonies can be easily integrated during times when the honey flow is heavy since the colony’s odor is inundated with the scent of nectar. Virgin queen bees emit a behavioral pheromone released with their feces. When the new queen feels threatened by the workers she uses this pheromone as a repellent.
Another widely identified chemical signal in bees is the Queen Mandibular Pheromone (QMP). This pheromone ensures that the queen is the only reproductive female in the hive by compromising the reproductive systems of worker bees. It also provides an attractant signal to the drones.

### Stimulus Properties

Table summarizes the types of information encoded by different stimulus energies. Some types of stimuli are better suited for some types of information. It is important to consider limits to information, communication, or stimulus use. In this table a + indicate how well that stimulus functions for that information.
| Signal, Sensory Chanel | Summary |
| odor molecules - smell, taste, olfactory and gustatory chemoreceptors | works in both dark and light scenarios, long and short distance, travels around or through obstacles, persists, efficient production, slow, little directionality, cannot be turned off quickly, presence/absence (low complexity), low resolution |
| compressional waves - hearing, mechanoreceptors | dark/light, complex content, fast at short distances, slow at long distances, resolution (frequency dependent), may travel far and around obstacles (low frequency), attenuates quickly (high frequency), directionality |
| substrate vibration - mechanoreceptors, proprioreceptors | dark/light, complex content (frequency modulation, amplitude modulation), fast at short distances, slow at long distances, resolution (frequency dependent), travels far/around obstacles, directionality |
| movement of particles - wind, mechanoreceptors | dark/light, short-range only, directionality |
| touch, proprioreceptors | dark/light, contact necessary, complex content (perception of size, shape, texture, movement across skin) |
| electric fields - active and passive electroreception, electroreceptors | dark/light, short range, spatial resolution, travels around and through most objects |
| light energy - vision, photoreceptors | light necessary, direct line of sight, immediate and precise localisation, fine resolution, complex content, visual displays, |
| thermal energy - detection of radiant heat, infrared vision thermoreceptors | dark/light, short range, does not travel around and through objects, spatial resolution |

## Sensory Modalities
### Electroreception

Electroreception refers to the biological ability to sense electrical impulses. As water is a better conductor than air, electroreception is more common in aquatic creatures. Individuals utilize this sense to locate living organisms as sources of electrical energy.

### Umwelt

There are many species-specific differences in sensory reception. Human perception utilizes 5 primary sensory modalities: sight, hearing, touch, taste, and smell. Receptors are classified based on the source of the stimulus. Interoreceptors convey information from within the organism; Proprioreceptors report on the spatial position of body parts relative to one another; Exteroreceptors obtain information about the outside. Subcategories of the latter include Somatoreceptors that capture events on the body's surface and Teloreceptors which monitor stimuli at a distance from the body. Sensory selectivity: refers to the subset of stimuli, which an animal detects and responds to; the Umwelt: Sensory World. Subjective set of stimuli to which an animal is responsive in a given motivational state. Each species has evolved responses only to those stimuli that prove relevant. It is this simpler world that actually falls within the animal's perception at any particular moment. (Jakob von Uexküll). <Psychophysics>: uses behavioral assays to establish sensory abilities of organisms.

## Sensory Receptors

Sensory receptors are able to respond to a particular stimulus energy (i.e., sensory modality) and transduce it into neural impulses. Neuronal tuning describes a neuron's property to selectively represent a particular kind of sensory information. For example, an auditory system neuron which responds best to the sound of a particular frequency is said to be tuned to that frequency. In the visual system, neurons are tuned to particular objects, for example, edges of a particular orientation. The receptor's dynamic range refers to the stimulus intensities which a given sensory receptor is able to represent in a quantitative fashion. At its operating point the stimulus elicits a 50% response. Tonic receptors respond with a constant rate of firing as long as the stimulus is applied (e.g., pain). In contrast, phasic receptors produce a burst of activity during the onset of the stimulus but quickly reduce their firing rate if the stimulus is maintained (e.g., odor, touch, & temperature). With sensory adaptation, the organism ceases to pay attention to constant stimuli. The adequate stimulus for a particular receptor is the one that requires the least amount of energy to activate the receptor.

### Mechanoreceptors

   * Hair Cells: Hair cells are sensory receptors that transduce physical forces into changes in electrical activity. Their name derives from a bundle of cilia on the apical surface of the cell. Embedded bundles of cross-linked actin filaments are anchored to the top of the cell membrane, where they control ion currents across a set of channels. Shearing of the tuft of cilia towards one side or the other changes the conductance of ions across a set of stretch-activated ion channels (i.e., tip links).
   * Stretch receptors (MRO): The muscle receptor organ spans the joint between two adjacent abdominal segments in crayfish. These are sensory organs that provide information about posture and movement of the individual. Each MRO has a thin muscle fiber that runs in parallel to a muscle bundle used by the animal to maintain the position of its abdomen. When the muscles contract or are stretched they cause the MRO to change its firing pattern, providing information to the nervous system regarding the relative position of the abdominal segments. There are two kinds of MROs. Tonic MROs respond to chronic stretch with continuous firing and habituate slowly. Phasic MROs respond to rapid changes in posture but habituate quickly when the posture is maintained for more than a few moments.

### Electro-Magnetic Receptors

   * Light-sensitive neurons: rods (B/W) and cones (color) in the mammalian retina contain dense stacks of membrane with large numbers of light-sensitive pigments. The latter consist of a protein (opsin) and a bound chromophore (retinal). Retinal is able to capture photons, induce a conformational change in opsin, and thereby activate a G protein-coupled second messenger cascade.
   * Electroreceptors: Electric fish, Sharks, Platypus: Some animal possess specialized sensory cells that enable them to detect changes in the electromagnetic field around them. These organs can be used by predators to locate prey by the electrical activity of their nervous systems and muscles, or in some cases as a means of communication (when coupled with the ability to produce pulses of electricity as seen in some electric fish).
   * Thermoreceptors: Snakes: Some snakes hunt their prey using body heat. Heat travels through the atmosphere as infrared (long wavelength) electromagnetic radiation, and is detected by cells sensitive to changes in temperature.

### Accessory Structures
## Sensory Processing

The receptive field of a sensory neuron is the specific region of a sensory surface (e.g., area on the retina) that, when stimulated, causes a change in activity of a neuron. The spatial organization of receptors within a sensory surface is generally maintained throughout processing in the form of somatotopic maps. For example, sensory information maintains its structure (i.e. sensory information on the hand remains next to sensory information on the arm) throughout the spinal cord and brain.

### Feature Extraction

Logical gates can be created by driving an action potential in the postsynaptic cell only if e.g., multiple input sources are active concurrently (i.e., spatial summation)
* Coincidence detection: Activity in any presynaptic neuron alone is usually not sufficient to produce and action potential in the postsynaptic neuron. Summation of synaptic inputs can occur, however, when a neuron receives multiple excitatory inputs in short order. Spatial summation allows a cell to fire if two inputs are active at the very same time. The window of opportunity during which concurrent events must occur depends on the time constant of the neuronal membrane. For coincidence detectors the time constant must be short; if the cell works as a temporal integrator, it must be long.
When localizing a stimulus source, systems for the discrimination of left vs. right are often based on two sub-systems. These are often mirror-images of each other and located to the left and the right of the midline (i.e., Omega neurons in crickets). They are tightly coupled through lateral inhibition, where activation of one side automatically shuts off its contralateral (i.e., opposite side) opponent. Such a design is uniquely able to allow resolution of extremely small time differences in when a sound signal arrives at the ear facing the source than in the one facing away.
* Contrast enhancement: Lateral Inhibition: Multiple units with similar characteristics are wired to inhibit each other's activity. The unit that fires first/strongest will prevent all others from firing. (e.g., Discrimination of left vs. right in auditory signals using a pair of Omega neurons in crickets).
* Measure time-delay between two inputs: Delay Lines: Action potentials (AP) travel along axons at a defined speed. They thus take longer to arrive at the target the further the AP needs to travel. Multiple neurons with similar characteristics are laid out in a longitudinal array. They receive input from two sources one fed in from one side of the array, the other from the other side. Acting as coincidence detectors they respond best when the signals on both inputs match. Each member of the array is most sensitive to a particular time difference. (e.g., Spatial localization of auditory signals in the laminar nucleus of Owls).

## Sensory Perception

Sensory perception is the interpretation of sensory signals within the CNS where it produces an internal representation of electrical activity from sensory organs. Specificity of sensory impulses derives from transmission via labeled lines, perception for a particular modality depends on which part of the brain receives the signals.
Most human senses have very high dynamic range. A human is capable of hearing (and usefully discerning) anything from a quiet murmur in a soundproofed room to the sound of the loudest heavy metal concert. Such a difference can exceed 100 dB which represents a factor of 100,000 in amplitude and a factor 10,000,000,000 in power. We can see objects in starlight or in bright sunlight, even though on a moonless night objects receive 1/1,000,000,000 of the illumination they would on a bright sunny day: that is a dynamic range of 90 dB. A human cannot perform these feats of perception at both extremes of the scale at the same time as the eyes take time to adjust the dynamic range to different light levels.

## Example: Vision

Vision depends on the transduction and decoding of electromagnetic stimulus energies. Photons allow ...

### Eye

Vertebrate Eye The resolution of the retina varies between different regions. A sensitive, b/w, high-resolution central region (i.e., fovea) is surrounded by a peripheral field with poor resolution and color reception. No photoreceptors are present at the location (i.e., blind spot)) where ganglion cell axons leave the eyeball to project to the brain via the optic nerve. Mollusc Eye Arthropod Eye

### Visual Processing

Systems for the processing of visual information extract features from the visual field at multiple hierarchical levels. The photoreceptor cells in the retina detect points of light (image). The retinal ganglion cells respond to point contrast (form and color). Thelateral geniculate nucleus (LGN) provides a first rapid analysis of high-contrast, black and white features. The primary visual cortex (V1) provides a slower but more in-depth analysis with an emphasis on linear contrast, color, depth, object vs. background motion.
Retinal receptor cells (i.e., cones for color and rods for black and white) feed into bipolar on or off cells in the retina. Retinal ganglion neurons and LGN Neurons have center-surround characteristics and thus respond to spots of light of a particular size and in specific places of the visual field. Their receptive fields are circular and monocular. Many axons cross to the opposite side as they project towards the lateral geniculate nucleus and the primary visual cortex. At these stages, binocular information is brought together as information from the corresponding visual fields from the two eyes projects to neighboring places.
The visual cortex is arranged in multiple horizontal layers with outer layers focused on the processing of simpler features. Most neurons respond best to oriented bar stimulus, sensitive to motion, monocular or binocular. As the information proceeds further into the structure, features at increasing levels of abstraction are analyzed. Vertical columns across these layers primarily respond to input from one specific eye and respond to a particular feature orientation. Simple cells respond best to bars of given orientation at given location within the receptive field. These oriented edge detection neurons feed their output into motion-sensitive neurons. Complex cells are less sensitive to stimulus position within the receptive field and more sensitive to stimulus motion. Hypercomplex cells respond like complex cells, but feature in addition an inhibitory region at one end. Some neurons at the highest-level receptive fields are quite specific i.e. a neuron that only responds to faces, faces with particular expressions, or belonging to one particular individual (i.e., grandmother neuron). Flicker fusion frequency, the lateral geniculate body, and dyslexia
The visual parts of the brain strive for hypotheses about the contents of the outside world working in essence with an image of rather poor quality and thereby is able to produce our rich everyday visual experience