A rule-based approach to the modelling of bacterial ecosystems.

This paper presents an approach to ecological/evolutionary modelling that is inspired by natural bacterial ecosystems and bacterial evolution. An individual-based artificial ecosystem model is proposed, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by rule-based learning classifier systems. The proposed ecosystem model consists of a n-dimensional environmental grid, which can contain different types of artificial resources in arbitrary arrangements. The resources provide the energy that is necessary for the organisms to sustain life, and can trigger different types of behaviour in the organisms, such as movement towards nutrients and away from toxic substances, growth, and the controlled release of signalling resources. The balance between energy and material is modelled carefully to ensure that the ecosystem is dissipative. Those organisms that are able to efficiently exploit the available resources gradually accumulate enough energy to reproduce (by binary fission) and generate copies of themselves in the environment. Organisms are also able to produce their own resources, which can potentially be used as markers to send signals to other organisms (a behaviour known as quorum sensing). The complex relationships between stimuli and actions in the organisms are stochastically altered by means of mutations, thus enabling the organisms to adapt to their environment and maximise their lifespan and reproductive success. In this paper, the proposed bacterial ecosystem model is defined formally and its structure is discussed in detail. This is followed by results from simulation experiments that illustrate the model's operation and how it can be used in evolutionary modelling/computing scenarios.

A particle swarm optimizer with passive congregation.

This paper presents a particle swarm optimizer (PSO) with passive congregation to improve the performance of standard PSO (SPSO). Passive congregation is an important biological force preserving swarm integrity. By introducing passive congregation to PSO, information can be transferred among individuals of the swarm. A particle swarm optimizer with passive congregation (PSOPC) is tested with a set of 10 benchmark functions with 30 dimensions and compared to a global version of SPSO (GSPSO), a local version of SPSO (LSPSO), and PSO with a constriction factor (CPSO), respectively. Experimental results indicate that the PSO with passive congregation improves the search performance on the benchmark functions significantly.

Computational aspects of protein functionality.

The purpose of this short article is to examine certain aspects of protein functionality with relation to some key organizing ideas. This is important from a computational viewpoint in order to take account of modelling both biological systems and knowledge of these systems. We look at some of the lexical dimensions of the function and how certain constructs can be related to underlying ideas. The pervasive computational metaphor is then discussed in relation to protein multifunctionality, and the specific case of von Willebrand factor as a 'smart' multifunctional protein is briefly considered. Some diagrammatic techniques are then introduced to better articulate protein function.

Individual-based modelling of bacterial ecologies and evolution.

This paper presents two approaches to the individual-based modelling of bacterial ecologies and evolution using computational tools. The first approach is a fine-grained model that is based on networks of interactivity between computational objects representing genes and proteins. The second approach is a coarser-grained, agent-based model, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of these computational models is discussed, and some results from simulation experiments are presented. Finally, the potential applications of the proposed models to the solution of real-world computational problems, and their use in improving our understanding of the mechanisms of evolution, are briefly outlined.

Diagrammatic representations for modelling biological knowledge.

The contemporary research and development context in multidisciplinary biology has a serious requirement for integrating knowledge from disparate sources, and facilitating much-needed inter- and intra-disciplinary dialogue. A multiplicity of models arises when pluralistic approaches to modelling are followed, and also when there is not only a requirement to model systems and data, but also knowledge of systems and data. The challenges of addressing this multiplicity do not only include articulating the structure of complex systems, but also placing modelling within the framework of a process as well as a product. The graph representations presented here facilitate dialogue, modelling, clarification and specification of concepts, and the sharing of terms. This paper explores relationships between collections of graph representations. It is hoped that in future, when readers look at a node or a process in a graph, they will have a much deeper appreciation of relationships and context.

Is there a biology of quantum information?

This paper briefly considers the notion of a biology of quantum information from a number of complementary points of view. We begin with a very brief look at some of the biomolecular systems that are thought to exploit quantum mechanical effects and then turn to the issue of measurement in these systems and the concomitant generation of information. This leads us to look at the internalist stance and the exchange interaction of quantum particles. We suggest that exchange interaction can also be viewed using ecological ideas related to apparatus-object. This can also help develop the important notion of complementarity in biosystems in relation to the nature and generation of information at the microphysical scale.

Spatio-logical processes in intracellular signalling.

Classical models of intracellular signalling describe how small changes in a cell's external environment can bring about major changes in cellular activity. Recent findings from experimental biology indicate that many intracellular signalling systems show a high level of spatial organisation. This permits the modification, by protein kinase or protein phosphatase action, of specific subsets of intracellular proteins - an attribute that is not addressed in classical signalling models. Here we use ideas and concepts from computer science to describe the information processing nature of intracellular signalling pathways and the impact of spatial heterogeneity of their components (e.g. protein kinases and protein phosphatases) on signalling activity. We argue that it is useful to view the signalling ecology as a vast parallel distributed processing network of agents operating in heterogeneous microenvironments, and we conclude with an overview of the mathematical and semantic methodologies that might help clarify this analogy between biological and computational systems.

Intracellular signalling proteins as smart' agents in parallel distributed processes.

In eucaryotic organisms, responses to external signals are mediated by a repertoire of intracellular signalling pathways that ultimately bring about the activation/inactivation of protein kinases and/or protein phosphatases. Until relatively recently, little thought had been given to the intracellular distribution of the components of these signalling pathways. However, experimental evidence from a diverse range of organisms indicates that rather than being freely distributed, many of the protein components of signalling cascades show a significant degree of spatial organisation. Here, we briefly review the roles of 'anchor' 'scaffold' and 'adaptor' proteins in the organisation and functioning of intracellular signalling pathways. We then consider some of the parallel distributed processing capacities of these adaptive systems. We focus on signalling proteins-both as individual 'devices' (agents) and as 'networks' (ecologies) of parallel processes. Signalling proteins are described as 'smart thermodynamic machines' which satisfy 'gluing' (functorial) roles in the information economy of the cell. This combines two information-processing views of signalling proteins. Individually, they show 'cognitive' capacities and collectively they integrate (cohere) cellular processes. We exploit these views by drawing comparisons between signalling proteins and verbs. This text/dialogical metaphor also helps refine our view of signalling proteins as context-sensitive information processing agents.

Quantum mechanics in the present progressive mode and its significance in biological information processing.

Quantum mechanics practiced in the present progressive mode can incorporate into itself the propagation of a signal of a local character. It is possible to view that any movement in the present progressive mode is mutli-agential in the sense of internal interactions due to the absence of an external agency coordinating the global situation simultaneously. The idea of living memory is discussed as carrying the leftover from those actions completed and registered in the present perfect mode and surviving at any present moment. The occurrence of both the signal propagation of a local character and living memory is upheld upon exchange interaction of a quantum mechanical origin. Empirical evidence suggesting the likelihood of such an exchange interaction is found in the neurotransmitter-gated ion channels located on the plasma membrane of the muscle cell in the vicinity of secretory vesicles containing acetylcholine near the nerve terminal. Another case from the empirical evidence is seen in the actomyosin system demonstrating the unidirectional propagation of variations in the acceleration of the displacement of an actin filament sliding on myosin molecules in the presence of ATP molecules.

von Willebrand factor in diabetic retinopathy.

OBJECTIVE: To elucidate the qualitative nature of elevated levels of von Willebrand factor (vWF) in diabetic microagiopathy. DESIGN: A randomized controlled study. SETTING: Oxford Health Authority, Oxfordshire, United Kingdom. SUBJECTS: Insulin dependent diabetic patients with established retinopathy, and an age, sex matched control group. MAIN OUTCOME MEASURES: Diabetic retinopathy, a modified enzyme-linked immunosorbent assay (ELISA), used to distinguish between endothelial and plasma type vWF. RESULTS: vWF is higher in patients with diabetic retinopathy mean (217u/dl) compared with normal subjects mean (8/u/dl). vWF in both patient and control are of the plasma type. CONCLUSION: vWF in diabetic retinopathy is raised and of the plasma type, suggesting it is not due to acute vascular endothelial injury.

Some computational models at the cellular level.

A number of viewpoints on how a cell can be modelled are discussed in this paper in light of the ability it has to process information. The paper begins with a very brief summary of four general types of computation: sequential, parallel, distributed, and emergent. These form the general framework from which a number of comparisons are made. Several metaphors are introduced to enable reflections to be made about cellular computational properties. The most important metaphor, namely the cell as a machine, is discussed, and then a number of other ideas are introduced that complement much current thinking in this area. The idea of networks or circuits in the cell is then developed, as this provides a means of describing the mechanisms within a machine. Following on from this, three further metaphors are applied in order to overcome certain limitations in current machine thinking, cell-as-society, cell-as-text, and cell-as-field.

Platelets and diabetic vascular disease.

Tests of platelet behaviour in vitro, particularly aggregation and retention and in vivo tests such as measurement of platelet survival and plasma levels of beta-thromboglobulin are frequently abnormal in diabetic patients, particularly in those with vascular disease. The concept has therefore arisen that platelet hyper-reactivity is one factor responsible for diabetic microangiopathy. Whereas there is experimental and histological evidence for the mediation of platelets in the pathogenesis of atherosclerosis, direct evidence of platelet involvement in microangiopathy is scanty. Similar alterations in platelet behaviour have been observed in a variety of other conditions with vessel wall damage in common and evidence is presented which suggests that these platelet abnormalities may be secondary to vessel wall injury. In diabetic subjects, some changes in platelet behaviour are reversed by improved glycaemic control. Evidence that platelets are involved in the pathogenesis of diabetic microangiopathy therefore remains circumstantial, though current trials of anti-platelet agents may enable a more precise evaluation of their role.

Fibrinogen, a modulator of erythrocyte adhesion to vascular endothelium.

The high incidence of thrombosis in inflammatory states and previous reports of increased adhesion of erythrocytes to endothelial cells in diabetes mellitus and sickle cell anemia prompted us to study the effect of fibrinogen and fibronectin on erythrocyte-endothelial interactions. Purified human fibrinogen enhanced erythrocyte adhesion in a concentration-dependent fashion. Erythrocytes from normal subjects, diabetics, and patients with sickle cell anemia were studied. The ratio between the adhesion of normal red cells in a 4 gm/L fibrinogen to adhesion in buffer without fibrinogen was 3.6 (p less than 0.001). Fibronectin also increased red cell adhesion but the effect was less than that of fibrinogen. The addition of fibronectin to fibrinogen limited the enhancing effect of fibrinogen, although the effect of the mixture was greater than that of fibronectin alone (p less than 0.05). Anti-von Willebrand factor and antifibronectin, which react with endothelial cells, also produced an increase in erythrocyte adhesion. The potentiation of adhesion by fibrinogen was also seen in experiments using red cells from patients with sickle cell anemia or diabetes mellitus. These observations provide possible mechanisms for the involvement of plasma proteins in vascular occlusive diseases.

Aspirin, dipyridamole and platelet survival in patients with diabetes mellitus.

1. Platelet survival in 27 insulin-dependent diabetic patients with severe retinopathy was studied in a double-blind cross-over trial using placebo, aspirin (990 mg/day) and a combination of dipyridamole (225 mg/day) with aspirin at two dosage levels (330 mg and 990 mg/day). 2. Twenty patients (group I) had 51Cr-labelled-platelet survival after treatment with placebo and the high-dose-aspirin/dipyridamole combination. The remaining seven patients (group II) had platelet-regeneration times measured after each of the four treatment periods. 3. Treatment of group I patients with the high-dose-aspirin/dipyridamole combination resulted in significant (P less than 0.001) prolongation of platelet survival from 7.3 +/- 0.2 (mean +/- SEM days to 8.4 +/- 0.1 days. 4. In group II patients, when compared with the mean placebo result of 7.2 +/- 0.2 days, the mean aspirin-labelled-platelet-regeneration time was significantly (P less than 0.01) longer only after high-dose-aspirin/dipyridamole (9.8 +/- 0.5 days) but not after low-dose-aspirin/dipyridamole (8.3 +/- 0.5 days) or aspirin alone (7.3 +/- 0.3 days). 5. These results suggest that it may be premature to consider reducing the dose of aspirin in aspirin/dipyridamole combinations below 1 g/day when used as antithrombotic therapy.