A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity and cost

Molecular codes translate information written in one type of molecule into another molecular language. We introduce a simple model that treats molecular codes as noisy information channels. An optimal code is a channel that conveys information accurately and efficiently while keeping down the impact of errors. The equipoise of the three conflicting needs, for minimal error load, minimal cost of resources and maximal diversity of vocabulary, defines the fitness of the code. The model suggests a mechanism for the emergence of a code when evolution varies the parameters that control this equipoise and the mapping between the two molecular languages becomes non-random. This mechanism is demonstrated by a simple toy model that is formally equivalent to a mean-field Ising magnet.     

Active foragers vs. sit-and-wait predators: a simple model

I propose a simple model for the decision of when to leave a foraging site in a variable environment for a predator that does not deplete its local resources. Active foraging is favored when the cost of moving is small or the difference between good and poor sites is large. The model corresponds to the behavior of two guilds of web-spinning spiders.     

Oscillatory coexistence in a food chain model with competing predators

A food chain model with two predators feeding on a single prey in a chemostat is studied. Using a multiparameter bifurcation analysis, we find parameters values for which there is stable oscillatory coexistence of the predators. It is also shown how these coexistent states provide a transition between two possible states of competitive exclusion. It is shown that the competitive exclusion principle need not hold if one or more of the predators has oscillatory behavior in the absence of other predators.This work was partially supported by National Science Foundation Grant MCS 83-01881     

Alternative food, switching predators, and the persistence of predator-prey systems

Sigmoid functional responses may arise from a variety of mechanisms, one of which is switching to alternative food sources. It has long been known that sigmoid (Holling's Type III) functional responses may stabilize an otherwise unstable equilibrium of prey and predators in Lotka-Volterra models. This poses the question of under what conditions such switching-mediated stability is likely to occur. A more complete understanding of the effect of predator switching would therefore require the analysis of one-predator/two-prey models, but these are difficult to analyze. We studied a model based on the simplifying assumption that the alternative food source has a fixed density. A well-known result from optimal foraging theory is that when prey density drops below a threshold density, optimally foraging predators will switch to alternative food, either by including the alternative food in their diet (in a fine-grained environment) or by moving to the alternative food source (in a coarse-grained environment). Analyzing the population dynamical consequences of such stepwise switches, we found that equilibria will not be stable at all. For suboptimal predators, a more gradual change will occur, resulting in stable equilibria for a limited range of alternative food types. This range is notably narrow in a fine-grained environment. Yet, even if switching to alternative food does not stabilize the equilibrium, it may prevent unbounded oscillations and thus promote persistence. These dynamics can well be understood from the occurrence of an abrupt (or at least steep) change in the prey isocline. Whereas local stability is favored only by specific types of alternative food, persistence of prey and predators is promoted by a much wider range of food types.     

A simple model of information use in the exploitation of patchily distributed food

In this paper we consider a simple model of an environment in which prey are distributed in patches. It is assumed that each patch contains at most one item, but items may vary in the ease with which they can be found. The time spent in unsuccessful search on a patch gives information of whether a patch contains an item, and if it does, how difficult that item is to find. We show how this information can be used to find the policy which maximizes the mean rate of reward for the environment. The analysis is illustrated by two examples.     

Habitat and food specificity in aphidophagous predators

Current knowledge of the processes underlying prey location and choice by aphidophagous predators is reviewed by considering the succession of behavioural mechanisms required for the predator to obtain prey. The predator may locate areas where prey are likely to be found by responding to physical aspects of the habitat, or to semiochemicals produced by the host plant. The predator may then respond to visual or olfactory cues to locate the aphid prey. The predator's readiness to attack and consume aphids is influenced by any behavioural or chemical defence strategies, and by the palatability or nutrient value of the aphids. Toxic allelochemicals ingested by aphids from their host plant may have a detrimental effect on predators.     

A simple model for the arterial system

We present a simple model for the arterial part of the cardiovascular system, based on Poiseuille flow constrained by the power dissipated into the cells lining the vessels. This, together with the assumption of a volume-filling network, leads to correct predictions for the evolution of vessel radii, vessel lengths and blood pressure in the human arterial system. The model can also be used to find exponents for allometric scaling, and gives good agreement with data on mammals.     

A binocular model for the simple cell

We authors propose a mathematical model for simple cell binocular response. It comprises two Gabor-type receptive fields (RF) having the same RF center, preferred spatial frequency, and preferred orientation. The model integrates the equally weighted signals from both eyes and performs a threshold operation. Poggio and Fischer (1977) classified binocular disparity cells in the striate cortex into four groups: tuned excitatory (TE), tuned inhibitory (TI), near, and far cells. They also found that most of the TE cells are ocularly balanced and that the other three types are usually unbalanced. This model can imitate these four types of disparity sensitivities and their ocular dominance tendency. We perform model fittings to Poggio's data using the “simulated annealing” method and discuss parameter dependence of the model's response. The model can also respond with exceptional disparity sensitivity: i.e., flat type, alternating type, and intermediate type.     

A simple morphological predictor of bite force in rodents

Bite force was quantified for 13 species of North American rodents using a piezo-resistive sensor. Most of the species measured (11) formed a tight relationship between body mass and bite force (log 10(bite force)=0.43(log 10(body mass))+0.416; R ²>0.98). This high correlation exists despite the ecological (omnivores, grazers and more carnivorous) and taxonomic (Cricetidae, Heteromyidae, Sciuridae and Zapodidae) diversity of species. Two additional species, Geomys bursarius (Geomyidae) and a Sciurus niger (Sciuridae), bit much harder for their size. We found a simple index of strength based on two measurements of the incisor at the level of the alveolus ( Z_i =((anterior-posterior length)²× (medial-lateral width))/6) that is highly predictive of bite force in these rodents (R²>0.96). Z_i may be useful for prediction of bite force (log10 (Bite Force)=0.566log10 ( Z_i )+1.432) when direct measurements are not available.     

Fish predators, food availability and diel vertical migration in Daphnia

Diel vertical migration of zooplankton is a highly variableand complex behaviour which apparently cannot be explained byany single factor. We determined the relative importance offish predation, food availability and water depth in shapingthe migratory behaviour of Daphnia. A modified 2x2x2 factorialexperiment provided two levels of fish density (present/absent),food availability (ambient/high) and depth (4–10 m); shallowtreatments with fish were excluded. Triplicate 1.2 m diameterenclosures for each of the six treatments were held in an 18unit array in Peter Lake, Gogebic Co., MI, USA. Repeated measuresANOVA identified significant trends in daphnid density, migrationand fitness (determined by lipid-ovary-egg index, LOE) as wellas in chlorophyll a content of the water column for part ofa 4-week experiment in July 1988. In deep enclosures with fish,Daphnia performed significantly more intense migrations thanin fishless enclosures, save those in fishless ambient-foodenclosures. Daphnia in deep fishless enclosures without abundantfood at depth performed significantly reduced migrations. DaphnidLOE index was significantly influenced only by food content.Our results were consistent with the predator-avoidance hypothesisas well as with observations of greatest migrations where largevertical differences in food abundance exist. They support ahierarchical view of vertical migration, with presence of fishthe primary factor, and food availability the secondary factor.     

The interplay of ontogeny and scaling in the interactions of fish larvae and their predators

In this review and synthesis, new data from field and laboratory experiments on red drum, Sciaenops ocellatus , larvae as prey to larger fishes are presented to illustrate two approaches to the study of developmental effects on predation. Various sizes and species of predatory fishes imposed very different levels of mortality on experimental populations of red drum larvae. Differences in predator size explained little of the overall variation in mortality rates. In the laboratory, responsiveness of red drum to a single size and species of predatory fish was relatively low through much of the developmental period but increased steadily. Response effectiveness improved and the predator's capture success decreased once the prey exceeded 20 mm in length. General ontogenetic trends in the behavioural interaction of various larvae and their piscine predators are described by combining 22 data sets on a scale of roughly comparable ontogenetic state. This scale, together with absolute and relative measures of predator and prey size, are used to assess the roles of ontogeny and scaling in the predation interaction. Ontogeny is shown to be a significant contributor to changes in responsiveness, response effectiveness, and capture success. The influence of scaling always took the form of an interaction with ontogeny and not a main effect.     

A protocol for a lung neovascularization model in rodents

By providing insight into the cellular events of vascular injury and repair, experimental model systems seek to promote timely therapeutic strategies for human disease. The goal of many current studies of neovascularization is to identify cells critical to the process and their role in vascular channel assembly. We propose here a protocol to analyze, in an in vivo rodent model, vessel and capillary remodeling (reorganization and growth) in the injured lung. Sequential analyses of stages in the assembly of vascular structures, and of relevant cell types, provide further opportunities to study the molecular and cellular determinants of lung neovascularization.     

A model for the interplay of receptor recycling and receptor-mediated contact in T cells

Orientation of organelles inside T cells (TC) toward antigen-presenting cells (APC) ensures that the immune response is properly directed, but the orientation mechanisms remain largely unknown. Structural dynamics of TC are coupled to dynamics of T-cell receptor (TCR), which recognizes antigen on the APC surface. Engagement of the TCR triggers its internalization followed by delayed polarized recycling to the plasma membrane through the submembrane recycling compartment (RC), which organelle shares intracellular location with the TC effector apparatus. TCR engagement also triggers TC-APC interface expansion enabling further receptor engagement. To analyze the interplay of the cell-cell contact and receptor dynamics, we constructed a new numerical model. The new model displays the experimentally observed selective stabilization of the contact initiated next to the RC, and only transient formation of contact diametrically opposed to the RC. In the general case wherein the TC-APC contact is initiated in an arbitrary orientation to the RC, the modeling predicts that the contact dynamics and receptor recycling can interact, resulting effectively in migration of the contact to the TC surface domain adjacent to the submembrane RC. Using three-dimensional live-cell confocal microscopy, we obtain data consistent with this unexpected behavior. We conclude that a TC can stabilize its contact with an APC by aligning it with the polarized intracellular traffic of TCR. The results also suggest that the orientation of TC organelles, such as the RC and the effector apparatus, toward the APC can be achieved without any intracellular translocation of the organelles.     

Intraguild predation,invertebrate predators,and trophic cascades in lake food webs

The top-down and bottom-up properties of model food webs that include intraguild predation and self-limiting factors such as cannibalism are investigated. Intraguild predation can dampen or even reverse the top-down effects predicted by food chain theory. The degree of self-limitation among the intraguild prey is a key factor in determining the direction and strength of the top-down response. Intraguild predation and self-limiting factors can also substantially alter the bottom-up effects of enrichment. These results can help explain the disparate results of trophic cascade experiments in lakes, where cascades are usually seen when large Daphnia are the primary herbivores, but not when smaller-bodied herbivores are dominant. Top-down manipulations should cascade at least modestly to phytoplankton in those lakes whose food web can be reasonably approximated by a chain (typically, those where Daphnia is the dominant herbivore), as predicted by food chain theory. On the other hand, smaller-bodied zooplankton are often preyed upon heavily by invertebrate predators as well as by planktivorous fish, thereby introducing elements of intraguild predation into these food webs. In this case, conventional food chain theory is likely to give incorrect predictions. Very large cascade effects may be due primarily to regime shifts between intraguild predation-dominated food webs and those that more resemble food chains, rather than due to the simple food chain cascade usually considered.