Statistical mechanics of ontology based annotations

We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.Comment: 27 pages, 5 figure

Can possible evolutionary outcomes be determined directly from the population dynamics?

Traditionally, to determine the possible evolutionary behaviour of an ecological system using adaptive dynamics, it is necessary to calculate the fitness and its derivatives at a singular point. We investigate the claim that the possible evolutionary behaviour can be predicted directly from the population dynamics, without the need for calculation, by applying three criteria - one based on the form of the density dependent rates and two on the role played by the evolving parameters. Taking a general continuous time model, with broad ecological range, we show that the claim is true. Initially, we assume that individuals enter in class 1 and move through population classes sequentially; later we relax these assumptions and find that the criteria still apply. However, when we consider models where the evolving parameters appear non-linearly in the dynamics, we find some aspects of the criteria fail; useful but weaker results on possible evolutionary behaviour now apply

Pathogen exclusion from eco-epidemiological systems

Increasing concerns about the changing environment and the emergence of pathogens that cross species boundaries have added to the urgency of understanding the dynamics of complex ecological systems infected by pathogens. Of particular interest is the often counterintuitive way in which infection and predation interact and the consequent difficulties in designing control strategies to manage the system. To understand the mechanisms involved, we focus on the pathogen exclusion problem, using control maps (on which the network of exclusion thresholds are plotted) in order to readily identify which exclusion strategies will work and why others will not. We apply this approach to the analysis of parasite exclusion in two game bird ecologies. For higher dimensions, we propose a computational scheme that will generate the optimal exclusion strategy, taking into account all operational constraints on the pathogen invasion matrix, populations, and controls. The situation is further complicated when external forcing distorts pathogen thresholds. This distortion is highly sensitive to the lags between forcing components, a sensitivity that can be exploited by management using correctly lagged cyclically varying controls to reduce the effort involved in pathogen exclusion

The evolution of costly acquired immune memory

A key feature of the vertebrate adaptive immune system is acquired immune memory, whereby hosts launch a faster and heightened response when challenged by previously encountered pathogens, preventing full infection. Here, we use a mathematical model to explore the role of ecological and epidemiological processes in shaping selection for costly acquired immune memory. Applying the framework of adaptive dynamics to the classic SIR (Susceptible-Infected-Recovered) epidemiological model, we focus on the conditions that may lead hosts to evolve high levels of immunity. Linking our work to previous theory, we show how investment in immune memory may be greatest at long or intermediate host lifespans depending on whether immunity is long lasting. High initial costs to gain immunity are also found to be essential for a highly effective immune memory. We also find that high disease infectivity and sterility, but intermediate virulence and immune period, increase selection for immunity. Diversity in host populations through evolutionary branching is found to be possible but only for a limited range of parameter space. Our model suggests that specific ecological and epidemiological conditions have to be met for acquired immune memory to evolve

Exclusion of generalist pathogens in multihost communities

Knowing how to control a pathogen that infects more than one host species is of increasing importance because the incidence of such infections grows with continuing environmental change. Of concern are infections transmitted from wildlife to humans or livestock. To determine which options are available to control a pathogen in these circumstances, we analyze the pathogen invasion matrix for the multihost susceptible-infected-susceptible model. We highlight the importance of both community structure and the column sum or row sum index, an indicator of both force of infection and community stability. We derive a set of guidelines for constructing culling strategies and suggest a hybrid strategy that has the advantages of both the bottom-up and the top-down approaches, which we study in some detail. The analysis holds for an arbitrary number of host species, enabling the analysis of large-scale ecological systems and systems with spatial dimensions. We test the robustness of our methods by making two changes in the structure of the underlying dynamic model, adding direct competition and introducing frequency-dependent infection transmission. In particular, we show that the introduction of an additional host can eliminate the pathogen rather than eliminate the resident host. The discussion is illustrated with a reference to bovine tuberculosis

When is evolutionary branching in predator-prey systems possible with an explicit carrying capacity?

In this study we use the theory of adaptive dynamics firstly to explore the differences in evolutionary behaviour of a generalist predator (or more specifically an omnivorous or intraguild predator) in a predator-prey model, with a Holling Type II functional response, when two distinct forms for the carrying capacity are used. The first of these involves the carrying capacity as an emergent property, whilst in the second it appears explicitly in the dynamics. The resultant effect this has on the intraspecific competition in each case is compared. Taking an identical trade-off in each case, we find that only with an emergent carrying capacity is evolutionary branching possible. Our study then concentrates solely on the case where the carrying capacity appears explicitly. Using the same model as above, but choosing alternate trade-offs, we find branching can occur with an explicit carrying capacity. Our investigation finishes by taking a more general functional response in an attempt to derive a condition for when branching can or cannot occur. For a predator-prey model, branching cannot occur if the functional response can be separated into two components, one a function of the population densities, X and Z, and the other a function of the evolving parameter z (traded off against the intrinsic growth rate), i.e. if F(z, X, Z) = F1(z)F2(X, Z). This search for evolutionary branching is motivated by its possible role in speciation

Evolution of host resistance towards pathogen exclusion: the role of predators

Question: Can increased host resistance drive a pathogen to extinction? Do more complex ecosystems lead to significantly different evolutionary behaviour and new potential extinctions? Mathematical method: Merging host-parasite models with predator-prey models. Analytically studying evolution using adaptive dynamics and trade-off and invasion plots, and carrying out numerical simulations. Key assumptions: Mass action (general mixing). All individuals of a given phenotype are identical. Only prey vulnerable to infection. Mutations are small and rare (however, the assumption on the size of mutation is relaxed later). In simulations, very small (negligible) populations are at risk of extinction. Conclusions: The presence of the predator can significantly change evolutionary outcomes for host resistance to a pathogen and can create branching points where none occurred previously. The pathogen (and sometimes the predator) is protected from exclusion if we take mutations to be arbitrarily small; however, relaxing the assumption on mutation size can lead to its exclusion. Increased resistance can drive the predator and/or pathogen to extinction depending on inter-species dynamics, such as the predator's preference for infected prey. Predator co-evolution can move exclusion boundaries and prevent the predator's own extinction if its rate of mutation is high enough (with respect to that of the prey)

Maternal effects on offspring consumption can stabilize fluctuating predator–prey systems

Maternal effects, where the conditions experienced by mothers affect thephenotype of their offspring, are widespread in nature and have the potentialto influence population dynamics. However, they are very rarelyincluded in models of population dynamics. Here, we investigate a recentlydiscovered maternal effect, where maternal food availability affects the feedingrate of offspring so that well-fed mothers produce fast-feeding offspring.To understand how this maternal effect influences population dynamics, weexplore novel predator–prey models where the consumption rate of predatorsis modified by changes in maternal prey availability. We address the‘paradox of enrichment’, a theoretical prediction that nutrient enrichmentdestabilizes populations, leading to cycling behaviour and an increasedrisk of extinction, which has proved difficult to confirm in the wild. Ourmodels show that enriched populations can be stabilized by maternal effectson feeding rate, thus presenting an intriguing potential explanation for thegeneral absence of ‘paradox of enrichment’ behaviour in natural populations.This stabilizing influence should also reduce a population’s risk ofextinction and vulnerability to harvesting

Child Social-Care Recording and the Information Rights of Care-Experienced People : A Recordkeeping Perspective

Recent reports by the Independent Inquiry into Child Sexual Abuse (IICSA) emphasised the critical importance of records throughout the lives of care-experienced people. Records not only contain information about what happened to a person in their past, but also have long-term effects on memory and identity. Research emerging in the context of analogous national inquiries into the systemic abuse and neglect of children in care—particularly the Royal Commission in Australia and the Shaw Report in Scotland—have highlighted the significance of records to campaigns for reparative justice. This article introduces MIRRA: Memory—Identity—Rights in Records—Access, which is a participatory action research project co-produced with care-leavers and researchers based at University College London (UCL). This ongoing study seeks to deepen our understanding of the creation, use and management of care records and protocols to access them. In this article, we consider the practice of social work recording with children and families in England since the 1970s from a ‘recordkeeping perspective’, importing theory from the information studies field to provide a new perspective on the information rights of care-leavers

Towards a Human-Centred Participatory Approach to Child Social Care Recordkeeping

In 2019 there were over 75,000 children and young people in out-of-home care in England and Wales. Recent estimates suggest that up to half a million British people were in state or voluntary care as children, around 1% of the adult population. While individual experiences vary enormously by time and place, care-experienced people share in common the intensive documentation of their lives by social workers, educators, health professionals and associated practitioners. A complex, fragmented legislative and regulatory framework governs the creation and use of these records at the national level. Under UK law a ‘care file’ must be retained for at least seventy-five years, so that a substantial legacy of care data is held across the public, voluntary and private sectors. MIRRA: Memory – Identity – Rights in Records – Access, a participatory research project co-produced with care leavers, investigated recordkeeping practices in child social care from multiple perspectives. Interviews, focus groups and workshops with stakeholders identified critical failings in the creation, use, management and access of care records, which do not account for the needs and capabilities of multiple stakeholders. These failings have direct impact on the wellbeing and health of care-experienced people throughout their lives. MIRRA researchers developed a human-centred participatory recordkeeping approach to child social care, which this article describes. The approach combines the participatory continuum model (Rolan, 2017) and the capabilities approach to social work, rooting child social care recordkeeping in information rights principles