Using collision cones to assess biological deconfliction methods

An Algorithmic Approach to Natural Behavior

Uncovering the mechanisms and implications of natural behavior is a goal that unites many fields of biology. Yet, the diversity, flexibility, and multi-scale nature of these behaviors often make understanding elusive. Here, we review studies of animal pursuit and evasion - two special classes of behavior where theory-driven experiments and new modeling techniques are beginning to uncover the general control principles underlying natural behavior. A key finding of these studies is that intricate sequences of pursuit and evasion behavior can often be constructed through simple, repeatable rules that link sensory input to motor output: we refer to these rules as behavioral algorithms. Identifying and mathematically characterizing these algorithms has led to important insights, including the discovery of guidance rules that attacking predators use to intercept mobile prey, and coordinated neural and biomechanical mechanisms that animals use to avoid impending collisions. Here, we argue that algorithms provide a good starting point for studies of natural behavior more generally. Rather than beginning at the neural or ecological levels of organization, we advocate starting in the middle, where the algorithms that link sensory input to behavioral output can provide a solid foundation from which to explore both the implementation and the ecological outcomes of behavior. We review insights that have been gained through such an algorithmic approach to pursuit and evasion behaviors. From these, we synthesize theoretical principles and lay out key modeling tools needed to apply an algorithmic approach to the study of other complex natural behaviors.

Competition and cooperation among chimney swifts at roost entry

Chimney swifts (Chaetura pelagica) are highly aerial, small, insectivorous birds well known for roosting en masse in chimneys during their autumn migration. These roosting events require hundreds to thousands of birds to enter a small opening (here 0.64 m²) within a short amount of time (15-30 min). Thus, these entry events pose a complex navigational and behavioral challenge as birds identify their entry route, cooperate with other birds present to form an entry flock, and compete with other birds at the time of chimney entry. We used six synchronized cameras to capture and reconstruct the 3D flight trajectories of swifts before and during chimney entry. Navigation into the chimney is consistent with use of a relative retinal expansion velocity cue, which results in an entry/non-entry decision point about 1.5 m above the chimney, or 0.4 s at typical entry speeds. Entries were highly clustered with 91 of 136 entries occurring within 1 s of another entry. We observed both synchronous (entry within 0.2 s) and sequential entry behavior (entry separated by ~0.4 s). Birds entering the chimney flew in close proximity to other birds (median minimum distance 0.51 m; 1.7 wingspans). In cases where two birds appeared to attempt a near-simultaneous entry, the bird either slightly to the rear or with a velocity vector bringing it closer to the current position of the other bird tended to make an avoidance maneuver and abandon its entry attempt. Overall, these results show how groups of animals execute complex landing and collision avoidance maneuvers in a natural setting without central control authority.

Zebrafish, a Novel Model System to Study Uremic Toxins: The Case for the Sulfur Amino Acid Lanthionine

The non-proteinogenic amino acid lanthionine is a byproduct of hydrogen sulfide biosynthesis: the third endogenous vasodilator gas, after nitric oxide and carbon monoxide. While hydrogen sulfide is decreased in uremic patients on hemodialysis, lanthionine is increased and has been proposed as a new uremic toxin, since it is able to impair hydrogen sulfide production in hepatoma cells. To characterize lanthionine as a uremic toxin, we explored its effects during the early development of the zebrafish (Danio rerio), a widely used model to study the organ and tissue alterations induced by xenobiotics. Lanthionine was employed at concentrations reproducing those previously detected in uremia. Light-induced visual motor response was also studied by means of the DanioVision system. Treatment of zebrafish embryos with lanthionine determined acute phenotypical alterations, on heart organogenesis (disproportion in cardiac chambers), increased heart beating, and arrhythmia. Lanthionine also induced locomotor alterations in zebrafish embryos. Some of these effects could be counteracted by glutathione. Lanthionine exerted acute effects on transsulfuration enzymes and the expression of genes involved in inflammation and metabolic regulation, and modified microRNA expression in a way comparable with some alterations detected in uremia. Lanthionine meets the criteria for classification as a uremic toxin. Zebrafish can be successfully used to explore uremic toxin effects.

Three-dimensional trajectories and network analyses of group behaviour within chimney swift flocks during approaches to the roost

Chimney swifts (Chaetura pelagica) are highly manoeuvrable birds notable for roosting overnight in chimneys, in groups of hundreds or thousands of birds, before and during their autumn migration. At dusk, birds gather in large numbers from surrounding areas near a roost site. The whole flock then employs an orderly, but dynamic, circling approach pattern before rapidly entering a small aperture en masse. We recorded the three-dimensional trajectories of ≈1 800 individual birds during a 30 min period encompassing flock formation, circling, and landing, and used these trajectories to test several hypotheses relating to flock or group behaviour. Specifically, we investigated whether the swifts use local interaction rules based on topological distance (e.g. the n nearest neighbours, regardless of their distance) rather than physical distance (e.g. neighbours within x m, regardless of number) to guide interactions, whether the chimney entry zone is more or less cooperative than the surrounding flock, and whether the characteristic subgroup size is constant or varies with flock density. We found that the swift flock is structured around local rules based on physical distance, that subgroup size increases with density, and that there exist regions of the flock that are less cooperative than others, in particular the chimney entry zone.

Using collision cones to assess biological deconfliction methods

Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows and fish (Myotis velifer, Petrochelidon pyrrhonota and Danio aequipinnatus). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study.