Investigating biocomplexity through the agent-based paradigm.

Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines--or agents--to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex

Aerospace medicine and biology: A continuing bibliography with indexes, supplement 197, September 1979

This bibliography lists 193 reports, articles, and other documents introduced into the NASA scientific and technical information system in August 1979

Norm-Establishing and Norm-Following in Autonomous Agency

Living agency is subject to a normative dimension (good-bad, adaptive-maladaptive) that is absent from other types of interaction. We review current and historical attempts to naturalize normativity from an organism-centered perspective, identifying two central problems and their solution: (1) How to define the topology of the viability space so as to include a sense of gradation that permits reversible failure, and (2) how to relate both the processes that establish norms and those that result in norm-following behavior. We present a minimal metabolic system that is coupled to a gradient-climbing chemotactic mechanism. Studying the relationship between metabolic dynamics and environmental resource conditions, we identify an emergent viable region and a precarious region where the system tends to die unless environmental conditions change. We introduce the concept of normative field as the change of environmental conditions required to bring the system back to its viable region. Norm-following, or normative action, is defined as the course of behavior whose effect is positively correlated with the normative field. We close with a discussion of the limitations and extensions of our model and some final reflections on the nature of norms and teleology in agency

Chytridiomycosis of marine diatoms : the role of stress physiology and resistance in parasite-host recognition and accumulation of defense molecules

Little is known about the role of chemotaxis in the location and attachment of chytrid zoospores to potential diatom hosts. Hypothesizing that environmental stress parameters affect parasite-host recognition, four chytrid-diatom tandem cultures (Chytridium sp./Navicula sp., Rhizophydium type I/Nitzschia sp., Rhizophydium type IIa/Rhizosolenia sp., Rhizophydium type IIb/Chaetoceros sp.) were used to test the chemotaxis of chytrid zoospores and the presence of potential defense molecules in a non-contact-co-culturing approach. As potential triggers in the chemotaxis experiments, standards of eight carbohydrates, six amino acids, five fatty acids, and three compounds known as compatible solutes were used in individual and mixed solutions, respectively. In all tested cases, the whole-cell extracts of the light-stressed (continuous light exposure combined with 6 h UV radiation) hosts attracted the highest numbers of zoospores (86%), followed by the combined carbohydrate standard solution (76%), while all other compounds acted as weak triggers only. The results of the phytochemical screening, using biomass and supernatant extracts of susceptible and resistant host-diatom cultures, indicated in most of the tested extracts the presence of polyunsaturated fatty acids, phenols, and aldehydes, whereas the bioactivity screenings showed that the zoospores of the chytrid parasites were only significantly affected by the ethanolic supernatant extract of the resistant hosts

Trivial movements and redistribution of polyphagous insect herbivores in heterogeneous vegetation

The aim of this thesis was to study the interplay between movement patterns of polyphagous insect herbivores and vegetation heterogeneity within agricultural fields. I examined if and how 1) host plant species, 2) host plant quality, 3) vegetation architecture, and 4) trap crop physical design influence movement patterns of individuals and spatial distribution of populations. Foragers may aggregate in profitable areas by tactic movement, or by area-restricted search, i.e. by moving randomly but slowing down movement and increasing rate of turning after encountering a profitable patch. Movement patterns of polyphagous herbivores have a high potential for influencing their distribution among hosts differing in quality. However, information on the role random vs. non-random components in their movement behavior is scarce. The results of this thesis show that both host plant species and within species differences in host plant quality affect movement behavior of a polyphagous herbivore, the European tarnished plant bug nymphs. The host plant induced movement patterns also explained the distribution of nymphs in heterogeneous vegetation. Because redistribution was very fast, it appears that no tactic behavior is needed for the nymphs to locate preferred hosts in heterogeneous vegetation composed of small patches. Instead the nymphs may successfully locate superior hosts merely by random movement coupled with sensitivity to local host quality. The physical structure of environment influences redistribution of populations at several spatial scales. At small scale the architecture of vegetation may influence redistribution of insects that move on the plant surface. At large scale e.g. trap crop physical design may affect redistribution of pests. In this thesis I derive a model for predicting the impact of vegetation architecture on the rate of displacement by insects moving on the plant surface. I also present and explore models of the interplay between pest movement and trap crop physical design. The trap crop models suggest that considerable reduction in pest density may be achieved using small trap crop cover with trap crops that the pest distinctly prefers over the crop. It supports also the idea that trap crop placement may have a dramatic impact on the efficiency of the trap crops

Rapid behavioral transitions produce chaotic mixing by a planktonic microswimmer

Despite their vast morphological diversity, many invertebrates have similar larval forms characterized by ciliary bands, innervated arrays of beating cilia that facilitate swimming and feeding. Hydrodynamics suggests that these bands should tightly constrain the behavioral strategies available to the larvae; however, their apparent ubiquity suggests that these bands also confer substantial adaptive advantages. Here, we use hydrodynamic techniques to investigate "blinking," an unusual behavioral phenomenon observed in many invertebrate larvae in which ciliary bands across the body rapidly change beating direction and produce transient rearrangement of the local flow field. Using a general theoretical model combined with quantitative experiments on starfish larvae, we find that the natural rhythm of larval blinking is hydrodynamically optimal for inducing strong mixing of the local fluid environment due to transient streamline crossing, thereby maximizing the larvae's overall feeding rate. Our results are consistent with previous hypotheses that filter feeding organisms may use chaotic mixing dynamics to overcome circulation constraints in viscous environments, and it suggests physical underpinnings for complex neurally-driven behaviors in early-divergent animals.Comment: 20 pages, 4 figure

Space Station Centrifuge: A Requirement for Life Science Research

A centrifuge with the largest diameter that can be accommodated on Space Station Freedom is required to conduct life science research in the microgravity environment of space. (This was one of the findings of a group of life scientists convened at the University of California, Davis, by Ames Research Center.) The centrifuge will be used as a research tool to understand how gravity affects biological processes; to provide an on-orbit one-g control; and to assess the efficacy of using artificial gravity to counteract the deleterious biological effect of space flight. The rationale for the recommendation and examples of using ground-based centrifugation for animal and plant acceleration studies are presented. Included are four appendixes and an extensive bibliography of hypergravity studies

Artificial consciousness and the consciousness-attention dissociation

Artificial Intelligence is at a turning point, with a substantial increase in projects aiming to implement sophisticated forms of human intelligence in machines. This research attempts to model specific forms of intelligence through brute-force search heuristics and also reproduce features of human perception and cognition, including emotions. Such goals have implications for artificial consciousness, with some arguing that it will be achievable once we overcome short-term engineering challenges. We believe, however, that phenomenal consciousness cannot be implemented in machines. This becomes clear when considering emotions and examining the dissociation between consciousness and attention in humans. While we may be able to program ethical behavior based on rules and machine learning, we will never be able to reproduce emotions or empathy by programming such control systems—these will be merely simulations. Arguments in favor of this claim include considerations about evolution, the neuropsychological aspects of emotions, and the dissociation between attention and consciousness found in humans. Ultimately, we are far from achieving artificial consciousness