On the nature of the lexicon: the status of rich lexical meanings

The main goal of this paper is to show that there are many phenomena that pertain to the construction of truth-conditional compounds that follow characteristic patterns, and whose explanation requires appealing to knowledge structures organized in specific ways. We review a number of phenomena, ranging from non-homogenous modification and privative modification to polysemy and co-predication that indicate that knowledge structures do play a role in obtaining truth-conditions. After that, we show that several extant accounts that invoke rich lexical meanings to explain such phenomena face problems related to inflexibility and lack of predictive power. We review different ways in which one might react to such problems as regards lexical meanings: go richer, go moderately richer, go thinner, and go moderately thinner. On the face of it, it looks like moderate positions are unstable, given the apparent lack of a clear cutoff point between the semantic and the conceptual, but also that a very thin view and a very rich view may turn out to be indistinguishable in the long run. As far as we can see, the most pressing open questions concern this last issue: can there be a principled semantic/world knowledge distinction? Where could it be drawn: at some upper level (e.g. enriched qualia structures) or at some basic level (e.g. constraints)? How do parsimony considerations affect these two different approaches? A thin meanings approach postulates intermediate representations whose role is not clear in the interpretive process, while a rich meanings approach to lexical meaning seems to duplicate representations: the same representations that are stored in the lexicon would form part of conceptual representations. Both types of parsimony problems would be solved by assuming a direct relation between word forms and (parts of) conceptual or world knowledge, leading to a view that has been attributed to Chomsky (e.g. by Katz 1980) in which there is just syntax and encyclopedic knowledge

Shapes in the Shadow: Evolutionary Dynamics of Morphogenesis

This article investigates the evolutionary dynamics of morphogenesis. In this study, morphogenesis arises as a side-effect of maximization of number of cell types. Thus, it investigates the evolutionary dynamics of side-effects. Morphogenesis is governed by the interplay between differential cell adhesion, gene-regulation, and intercellular signaling. Thus, it investigates the potential to generate complex behavior by entanglement of relatively "boring" processes, and the (automatic) coordination between these processes. The evolutionary dynamics shows all the hallmarks of evolutionary dynamics governed by nonlinear genotype phenotype mapping: for example, punctuated equilibria and diffusion on neutral paths. More striking is the result that interesting, complex morphogenesis occurs mainly in the "shadow" of neutral paths which preserve cell differentiation, that is, the interesting morphologies arise as mutants of the fittest individuals. Characteristics of the evolution of such side-effects in the shadow appear to be the following: (1) The speci?c complex morphologies are unique (or at least very rare) among the set of de novo initiated evolutionary histories. (2) Similar morphologies are reinvented at large temporal distances during one evolutionary history and also when evolution is restarted after the main cell differentiation pattern has been established. (3) A mosaic-like evolution at the morphological level, where different morphological features occur in many combinations, while at the genotypic level recombination is not implemented and genotypes diverge linearly and at a constant rate

Attractors and Spatial Patterns in Hypercycles with Negative Interactions

This study reports on the effect of adding negative interaction terms to the hypercycle equation. It is shown that there is a simple parameter condition at which the behaviour of the hypercycle switches from dominant catalysis to dominant suppression. In the suppression!dominated hypercycles the main attractor turns out to be different for cycles consisting of an even or odd number of species. In "odd" cycles there is typically a limit cycle attractor, whereas in "even" cycles there are two alternative stable attractors each containing half of the species. In a spatial domain, odd cycles create spiral waves. Even cycles create a "voting pattern", i.e. initial fluctuations are quickly frozen into patches of the alternative attractors and subsequently, very slowly, small patches will disappear and only one of the two attractors remains. In large cycles (both even and odd) there are additional limit cycle attractors[ In a spatial domain these limit cycles fail to form stable spiral waves, but they can form stable rotating waves around an obstacle. However, these waves are outcompeted by the dominant spatial pattern of the system[ In competition between even and odd cycles, the patches of even cycles are generally stronger than the spiral waves of odd cycles. If the growth parameters of the species vary a little, a patch will no longer contain only half of the species but will instead attract "predator" species from the other patch type. In such a system one of the patch types will slowly disappear and the final dynamics resembles that of a predator-prey system with multiple trophic levels. The conclusion is that adding negative interactions to a hypercycle tends to cause the cycle to break and thereafter the system attains an ecosystem type of dynamics

On searching generic properties of non generic phenomena: an approach to bioinformatic theory formation

In this paper we first shortly review the current view of the evolution of complexity and novelty in biotic evo- lution. Next we show that the basic processes thereof do happen automatically and are generic properties of systems including the basic mechanisms of Darwini- an evolution plus local as opposed to global interac- tions. Thus we show that the so generated multilevel evolution can be studied within the paradigm 'simple rules lead to complex phenomena'. We derive some re- sults demonstrating the power of such multilevel evolu- tionary processes to integrate information at multiple space and time scales. Nevertheless we also point out shortcomings of such an approach which necessarily uses a priori chosen and preferentially relatively simple interaction schemes. However, straightforward extensions towards more complex interaction schemes generally leads to ad hoc- ness and over-determinedness, rather than fundamen- tally new behavior of the system, and often to less understanding of that behavior. Nevertheless biologi- cal theory formation needs a method to go beyond the generic behavior of simple interaction schemes. We propose to use evolutionary optimization of very trivial fitness functions which are obtainable in many different ways to push back the necessary a priori choic- es and to zoom in to interesting non generic phenom- ena and their general properties. . We thus derive insights in relationships between sets of derived prop- erties at several scales. We discuss how this approach can be used in biological theory formation, focusing on information accumulation and utilization in replicator systems and immune systems

Phototaxis during the slug stage of Dictyostelium discoideum: a model study

During the slug stage, the cellular slime mould Dictyostelium discoideum moves towards light sources. We have modelled this phototactic behaviour using a hybrid cellular automata/partial differential equation model. In our model, individual amoebae are not able to measure the direction from which the light comes, and differences in light intensity do not lead to differentiation in motion velocity among the amoebae. Nevertheless, the whole slug orientates itself towards the light. This behaviour is mediated by a modification of the cyclic AMP (cAMP) waves. As an explanation for phototaxis we propose the following mechanism, which is basically characterized by four processes: (i) light is focused on the distal side of the slug as a result of the so-called `lens-e¡ect'; (ii) differences in luminous intensity cause differences in NH3 concentration; (iii) NH3 alters the excitability of the cell, and thereby the shape of the cAMP wave; and (iv) chemotaxis towards cAMP causes the slug to turn.We show that this mechanism can account for a number of other behaviours that have been observed in experiments, such as bidirec- tional phototaxis and the cancellation of bidirectionality by a decrease in the light intensity or the addition of charcoal to the medium

Modelling Morphogenesis: From Single Cells to Crawling Slugs

We present a three-dimensional hybrid cellular automata (CA)/partial differential equation (PDE) model that allows for the study of morphogenesis in simple cellular systems. We apply the model to the cellular slime mold Dictyostelium discoideum "from single cells to crawling slug". Using simple local interactions we can achieve the basic morphogenesis with only three processes: production of and chemotaxis to cAMP and cellular adhesion. The interplay of these processes causes the amoebae to spatially self-organize leading to the complex behaviour of stream and mound formation, cell sorting and slug migration all without any change of parameters during the complete morphogenetic process

Sequential Predation: A Multi-model Study

In many ecosystems food resources are available sequentially. The paper analyses a situation with two competing prey species both of which are consumed by a common predator species. Within a season the two prey species are available sequentially, although there may be an overlap. Three modelling methodologies are applied to this system] discrete dynamical systems (difference equations), individual-oriented event-driven simulations and cellular automata. The presence of the predator is shown to have a strong impact on the outcome of the prey species competition. The system of coexisting prey species changes to a system of founder-controlled competition. It appears that sequential predation can even have counterintuitive evolutionary consequences for the prey species. The species which appears later in the season will be more successful in its competition with the early species if it favours the predator; for example, by a high leaf palatability. Spatial structuring and topological issues are found to play a crucial role in both the ecological and evolutionary dynamics. The advantages of a multi!model approach are discussed

Spatial Pattern Formation During Aggregation of the Slime Mould Dictyostelium discoideum

Stream formation and spiral wave behaviour during the aggregation of Dictyostelium discoideum (Dd) are studied in a model based on the Martiel-Goldbeter equations for cAMP relay, combined with chemotactic motion of Dd cells. The results show that stream formation occurs if the turnover rate of intracellular cAMP is increased. This increase in the turnover rate of cAMP[in] leads to a dependence of the speed of the cAMP wave on the cell density. We propose that this dependence of wave speed on cell density is the underlying mechanism for stream formation. Besides stream formation, increasing the turnover rate of cAMP[in] also results in a spiral wave period that decreases during aggregation, a phenomenon that is commonly observed in situ. Furthermore, the dependence of wave speed on cell density is measured empirically[ The speed of the cAMP wave is found to decrease as the wave travels from high to low cell density. This indicates that in situ, wave speed does depend on cell density

Cyanotoxin profiling in the subalpine district lakes

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