Keith Farnsworth

• Reader at Queen's University Belfast

Small-scale fisheries, especially in developing countries, are usually data limited and run on a small budget, necessitating rational choice and use of data limited methods (DLMs) for stock assessment. DLMs differ in accuracy, depending on species lifespan as well as data and parameter estimate quality, so the optimal choice of DLM is not simple. W...

To bring clarity, the term ‘information’ is resolved into three distinct meanings: physical pattern, statistical relations and knowledge about things. In parallel, three kinds of ’causation’ are resolved: the action of physical force constrained by physical pattern (efficient cause), cybernetic (formal cause) and statistical inference. Cybernetic c...

Confusion over the terms ‘information’ and ‘causation’ in theoretical biology is a problem. Most of it results from misinterpreting cybernetic systems, or even worse, statistical metrics, for physical information phenomena. Over the past several years, our understanding of causation has developed to recognise it as the constraint on the action of p...

The Egyptian Red Sea (ERS) supports artisanal, commercial and recreational fisheries, managed using a summertime closure, not applied to recreational fishing. Stock status is little known and management options are severely limited. To inform future management, we report the results of a questionnaire survey of artisan fishers from four Red Sea por...

Autonomy, meaning freedom from exogenous control, requires independence of both constitution and cybernetic regulation. Here, the necessity of biological codes to achieve both is explained, assuming that Aristotelean efficient cause is 'formal cause empowered by physical force'. Constitutive independence requires closure to efficient causation (in...

We introduce the group-based approach, use it to develop a multi-group biodiversity theory, and apply it find solutions to the multi-species maximum sustainable yield problem for a mixed species fishery. The group-based approach to community ecology is intermediate between classical species-centric and more recent trait-based (species-less) approac...

This is an un-reviewed, unpublished pre-print of a paper written for a special issue of BioSystems on Code Biology. To see the final published (Open Access) version go to https://doi.org/10.1016/j.biosystems.2023.105013 The paper explains why biological codes are essential for life to be autonomous. The first reason is that autonomy requires fr...

We argue that pain is not needed to protect the body from damage unless the organism is able to make free choices in action selection. Then pain (including its affective and evaluative aspects) provides a necessary prioritising motivation to select actions expected to avoid it, whilst leaving the possibility of alternative actions to serve potentia...

Highlights 1. We introduce a group-based approach to modelling of ecological communities and develop a multi-group biodiversity theory. 2. A classification of intergroup interactions is established , based on the type of contest (which is determined by the relative role of qualitative vs. quantitative factors) and the accounting of resource redi...

Abstract Stock assessment is essential for sustainable fisheries management and has developed into a sophisticated, but data-hungry and expensive procedure in highly developed fisheries. Datalimited methods (DLMs) have proliferated over the past twenty years, but most are oriented towards developed, mechanised fisheries. We reviewed all available D...

Recent research on harvest-induced evolution of behaviour in (especially aquatic) animals has focused on the shy-bold axis, but foraging and dispersal behaviour have received little attention. Here, we consider the selective effect of systematically localised trawl harvesting from a wild population of mobile animals that vary phenotypically in thei...

Here we propose a classification of age-structured populations according to two features: (1) sensitivity to changes in the intensity of environmental fluctuations and (2) sensitivity to changes in the spectrum of environmental fluctuations.

Numerical demonstration of the phenomenon of stock resonance in an age-structured population

Fluctuations in wild fish populations result from interaction between population dynamics and environmental forcing. Age‐structured populations can magnify or dampen particular frequencies of these fluctuations, depending on life cycle and species traits. The transfer function (TF) gives a detailed analytical description of these phenomena. In this...

Living systems have long been a puzzle to physics, leading some to claim that new laws of physics are needed to explain them. Separating physical reality into the general (laws) and the particular (location of particles in space and time), it is possible to see that the combination of these amounts to efficient causation, whereby forces are constra...

Swidden agriculture is a widespread subsistence farming method in the tropics, which is being intensified as human populations grow. This study is the first to investigate the impacts of land degradation from swidden upon ant species (both native and introduced) across the full degradation gradient, from forest, to tree fallows, to shrub fallows, t...

The standard model of a single population fragmented into two patches connected by migration, was first introduced in the 1970s by Freedman and Waltman, since generating long-term research interest, though its full analysis for arbitrary values of migration rate has only been completed relatively recently. Here, we present a model of two competing...

Whether or not viruses are alive remains unsettled. Discoveries of giant viruses with translational genes and large genomes have kept the debate active. Here, a fresh approach is introduced, based on the organisational definition of life from within systems biology. It views living as a circular process of self-organisation and self-construction wh...

Measures of microbial growth, used as indicators of cellular stress, are sometimes quantified at a single time-point. In reality, these measurements are compound representations of length of lag, exponential growth-rate, and other factors. Here, we investigate whether length of lag phase can act as a proxy for stress, using a number of model system...

Invasive alien species continue to arrive in new locations with no abatement in rate, and thus greater predictive powers surrounding their ecological impacts are required. In particular, we need improved means of quantifying the ecological impacts of new invasive species under different contexts. Here, we develop a suite of metrics based upon the n...

Keywords: Predator-prey interaction Size-based population model Fisheries management Model uncertainty Pike and trout Management action evaluation A B S T R A C T When one wild species is food for another and both have their hunting enthusiasts, then conflict can arise. This is particularly true and complicated in fishing, where trophic links are s...

Two broad features are jointly necessary for autonomous agency: organisational closure and the embodiment of an objective-function providing a ‘goal’: so far only organisms demonstrate both. Organisational closure has been studied (mostly in abstract), especially as cell autopoiesis and the cybernetic principles of autonomy, but the role of an inte...

Using insights from cybernetics and an information-based understanding of biological systems, a precise, scientifically inspired, definition of free-will is offered and the essential requirements for an agent to possess it in principle are set out. These are: (a) there must be a self to self-determine; (b) there must be a non-zero probability of mo...

The concept of function arises at all levels of biological study and is often loosely and variously defined, especially within ecology. This has led to ambiguity, obscuring the common structure that unites levels of biological organisation, from molecules to ecosystems. Here we build on already successful ideas from molecular biology and complexity...

Using insights from cybernetics and an information-based understanding of biological systems, a precise, scientifically inspired, definition of free-will is offered and the essential requirements for an agent to possess it in principle are set out. These are: a) there must be a self to self-determine; b) there must be a non-zero probability of more...

Recent advances suggest that the concept of information might hold the key to unravelling the mystery of life's nature and origin. Fresh insights from a broad and authoritative range of articulate and respected experts focus on the transition from matter to life, and hence reconcile the deep conceptual schism between the way we describe physical an...

The concept of function arises at all levels of biological study and is often loosely and variously defined, especially within ecology. This has led to ambiguity, obscuring the common structure that unites levels of biological organisation, from molecules to ecosystems. Here we build on already successful ideas from molecular biology and complexity...

Size spectrum models have emerged from 40 years of basic research on how body size determines individual physiology and structures marine communities. They are based on commonly accepted assumptions and have a low parameter set, making them easy to deploy for strategic ecosystem-oriented impact assessment of fisheries. We describe the fundamental c...

1. We constructed a size- and trait-based dynamic marine community model of the Celtic Sea / Biologically Sensitive Area, including grey seals Halichoerus grypus (Fabricius 1791) and harbour seals Phoca vitulina vitulina (Linnaeus 1758) to examine potential resource conflict between seals and commercial trawl fisheries. The model incorporates seal...

To value something, you first have to know what it is. Bartkowski et al. (2015) reveal a critical weakness: that biodiversity has rarely, if ever, been defined in economic valuations of putative biodiversity. Here we argue that a precise definition is available and could help focus valuation studies, but that in using this scientific definition (a...

We consider the problem of regulating the rate of harvesting a natural resource, taking account of the wider system represented by a set of ecological and economic indicators, given differing stakeholder priorities. This requires objective and transparent decision making to show how indicators impinge on the resulting regulation decision. We offer...

Fishing is well known to curtail the size distribution of fish populations. This paper reports the discovery of small-scale spatial patterns in length appearing in several exploited species of Celtic Sea demersal ‘groundfish’. These patterns match well with spatial distributions of fishing activity, estimated from vessel monitoring records taken ov...

International policy frameworks such as the Common Fisheries Policy and the European Marine Strategy Framework Directive define high-level strategic goals for marine ecosystems. Strategic goals are addressed via general and operational management objectives. To add credibility and legitimacy to the development of objectives, for this study stakehol...

Public concern over biodiversity loss is often rationalized as a threat to ecosystem functioning, but biodiversity-ecosystem functioning (BEF) relations are hard to empirically quantify at large scales. We use a realistic marine food-web model, resolving species over five trophic levels, to study how total fish production changes with species richn...

Pelagic fish are key elements in marine foodwebs and thus comprise an important part of overall ecosystem health. We develop a suite of ecological indicators that track pelagic fish community state and evaluate state of specific objectives against Good Environmental Status (GES) criteria. Indicator time-series are calculated for the EU Marine Strat...

Invasion ecology urgently requires predictive methodologies that can forecast the ecological impacts of existing, emerging and potential invasive species. We argue that many ecologically damaging invaders are characterised by their more efficient use of resources. Consequently, comparison of the classical ‘functional response’ (relationship between...

Demersal fisheries targeting a few high-value species often catch and discard other “non-target” species. It is difficult to quantify the impact of this incidental mortality when population biomass of a non-target species is unknown. We calculate biomass for 14 demersal fish species in ICES Area VIIg (Celtic Sea) by applying species- and length-bas...

A size and trait-based marine community model was used to investigate interactions, with potential implications for yields, when a fishery targeting forage fish species (whose main adult diet is zooplankton) co-occurs with a fishery targeting larger-sized predator species. Predicted effects on the size structure of the fish community, growth and re...

Forecasting the ecological impacts of invasive species is a major challenge that has seen little progress, yet the development of robust predic-tive approaches is essential as new invasion threats continue to emerge. A common feature of ecologically damaging invaders is their ability to rapidly exploit and deplete resources. We thus hypothesized th...

A dynamic food-web model of more than 1000 species was used to quantify the recovery trajectory of marine community size-structure under different hypothetical fishing regimes, using the Northeast Atlantic as an example. Size-structure was summarised by 4 indicators: the Large Fish Indicator (LFI), the Large Species Indicator (LSI), the biomass-wei...

We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; (b) this informa...

The Large Fish Indicator (LFI) is a size-based indicator of fish community state. The indicator describes the proportion by biomass of a fish community represented by fish larger than some size threshold. From an observed peak value of 0.49 in 1990, the Celtic Sea LFI declined until about 2000 and then fluctuated around 0.10 throughout the 2000s. T...

The influence of predation in structuring ecological communities can be informed by examining the shape and magnitude of the functional response of predators towards prey. We derived functional responses of the ubiquitous intertidal amphipod Echinogammarus marinus towards one of its preferred prey species, the isopod Jaera nordmanni. First, we exam...

Biodiversity may be seen as a scientific measure of the complexity of a biological sys tem, implying an information basis. Complexity cannot be directly valued, so economist have tried to define the services it provides, though often just valuing the services of ‘key species. Here we provide a new definition of biodiversity as a measure of function...

Biodiversity is a measure of the total difference within a biological system. It is understood to arise at genetic, species and multiple levels of community organisation, hence is multidimensional in nature. Biodiversity indices have proliferated in attempts to capture this complexity but may now have confounded it. Here we attempt a reduction to t...

We assessed ten trophodynamic indicators of ecosystem status for their sensitivity and specificity to fishing management using a size-resolved multispecies fish community model. The responses of indicators to fishing depended on effort and the size selectivity (sigmoid or Gaussian) of fishing mortality. The highest specificity against sigmoid (traw...

Shephard, S., Fung, T., Houle, J. E., Farnsworth, K. D., Reid, D. G., and Rossberg, A. G. 2012. Size-selective fishing drives species composition in the Celtic Sea. – ICES Journal of Marine Science, 69: 223–234. Fishing alters community size structure by selectively removing larger individual fish and by changing the relative abundance of different...

Fung, T., Farnsworth, K. D., Reid, D. G., Rossberg, A. G. 2012. Recent data suggest no further recovery in North Sea Large Fish Indicator. – ICES Journal of Marine Science, 69: 235–239. We detail the calculations of North Sea Large Fish Indicator values for 2009–2011, demonstrating an apparent stall in recovery. Therefore, recovery to the Marine St...

The increased involvement of stakeholders in the ecosystem approach to fisheries management presents a challenge in (i) priority‐setting among competing interests and (ii) the communication of complex ecological information among diverse stakeholders. This study reports the first stage in the creation of an interface between stakeholders and ecolog...

Biodiversity is thought to be a major determinant of ecological resilience. While previous studies have found signs of increased resilience with higher species richness, they did not consider large marine communities, important in fisheries management. Thus, we study how resilience in large marine communities changes with biodiversity loss. First,...

We use a minimal model of metabolism-based chemotaxis to show how a coupling between metabolism and behavior can affect evolutionary dynamics in a process we refer to as behavioral metabolution. This mutual influence can function as an in-the-moment, ...

Spalinger and Hobbs proposed a mechanistic model of forage intake based on the mutually exclusive actions of biting and chewing. A necessary consequence of this model is that an animal postpones the intake of more food by biting when it is processing food by chewing. In previous work, the Spalinger-Hobbs model successfully predicted short-term inta...

Density-dependence in population-dynamics denotes the phenomenon that the growth rate of a population depends on its own abundance (or population density) and on the densities of the pop- ulations of other species. Mathematically, density-dependencies introduce non-linearities into the equations describing population-dynamics. Any interactions betw...

How quickly and to what level do commercial fish stocks recover, following release from fishing? Addressing these questions is imperative for long-term management of overexploited stocks. We use an innovative multi-trophic model to predict how fish community structure recovers from different fishing scenarios, when fishing is reduced. This model re...

Many ecological indicators have been proposed as being suitable to measure marine ecosystem health in response to shing pressure, and it is often di cult to tell from empirical data how well these indicators will perform. This work takes an engineering system identication approach which is designed to isolate and understand the dynamic response of...

The European Union’s Marine Strategy Framework Directive (MSFD) “establishes a framework within which Member States shall take the necessary measures to achieve or maintain good environmental status [GES] in the marine environment by the year 2020 at the latest.” In 2010, the EU Commission adopted criteria for GES and a corresponding set of indicat...

The aim of this study is to maximise the applicability of ecological community models in fisheries management through the use of efficient communication indicators. Indicators that are hard to understand will be translated into “Common Language Indicators” which stakeholders can easily relate to. To facilitate the communication a Decision Support S...

A central question in community ecology is how the number of trophic links relates to community species richness. For simple dynamical food-web models, link density (the ratio of links to species) is bounded from above as the number of species increases; but empirical data suggest that it increases without bounds. We found a new empirical upper bou...

Goldstone’s idea of slow dynamics resulting from spontaneously broken symmetries is applied to Hubbell’s neutral hypothesis of community dynamics, to efficiently simplify stage-structured multi-species models—introducing the quasi-neutral approximation (QNA). Rather than assuming population-dynamical neutrality in the QNA, deviations from ideal neu...

Invasive species can have profound impacts on communities and it is increasingly recognized that such effects may be mediated by parasitism. The 'enemy release' hypothesis posits that invaders may be successful and have high impacts owing to escape from parasitism. Alternatively, we hypothesize that parasites may increase host feeding rates and hen...

Life-history theory predicts an optimal offspring size, irrespective of reproductive effort; however, in some species offspring size correlates positively with maternal size. We examine hypotheses for why this latter situation should occur in the whelk Buccinum undatum. The trade-offs between aspects of reproduction in whelks are complicated due to...

Economic valuation is the only quantitative justification for public decisions on conservation, but its poor foundations are starkly exposed when we try to value marine biodiversity. Substitutability and individual preference ranking, fundamental assumptions of welfare economics, are invalid for marine biodiversity. We cannot substitute for lost bi...

Building on work by Andersen and Beyer (2006), Hartvig et al. recently developed a numer- ical model for community size-spectra that resolves both species, characterized by maturation body size, and the individual size distributions within species. Empirical values for all model parameters are known. Here, an analytic characterization of static and...

Andersen, K. H., Farnsworth, K. D., Pedersen, M., Gislason, H., and Beyer, J. E. 2009. How community ecology links natural mortality, growth, and production of fish populations. – ICES Journal of Marine Science, 66: 1978–1984. Size-spectrum theory is used to show that (i) predation mortality is a decreasing function of individual size and proportio...

We present a model of the ideal free distribution (IFD) where differences between phenotypes other than those involved in direct competition for resources are considered. We show that these post‐acquisitional differences can have a dramatic impact on the predicted distributions of individuals. Specifically, we predict that, when the relative abilit...

While we can usually understand the impacts of invasive species on recipient communities, invasion biology lacks methodologies that are potentially more predictive. Such tools should ideally be straightforward and widely applicable. Here, we explore an approach that compares the functional responses (FRs) of invader and native amphipod crustaceans....

Baited cameras are often used for abundance estimation wherever alternative tech- niques are precluded, e.g. in abyssal systems and areas such as reefs. This method has thus far used models of the arrival process that are deterministic and, therefore, permit no estimate of precision. Furthermore, errors due to multiple counting of fish and missin...

Recent observations suggest fishing pressure is driving the evolution of smaller female maturation size in some fish stocks. We construct a general size-based theoretical framework to derive the rate and ultimate destination of this evolution based on life-history, community ecology and evolutionary theory. For Baltic cod (Gadus morhua), we find a...

There have been numerous recent observations of changes in the behavior and dynamics of migratory bird populations, but the plasticity of the migratory trait and our inability to track small animals over large distances have hindered investigation of the mechanisms behind migratory change. We used habitat-specific stable isotope signatures to show...

This paper derives optimal life histories for fishes or other animals in relation to the size spectrum of the ecological community in which they are both predators and prey. Assuming log-linear size-spectra and well known scaling laws for feeding and mortality, we first construct the energetics of the individual. From these we find, using dynamic p...

Previous "explanations" of sexual segregation in ungulates establish no more than a prerequisite for habitat segregation because they do not include a model of competitive habitat selection. Here we provide one based on the ideal free distributions of mutually competing, optimally foraging, individual deer. We parameterised our model using field da...

Firstly, I wish to record a permanent apology to John Pastor of Minnesota who certainly should have been in the author list of this one. John Introduced me to this interesting problem, in which vegetation distributions show persistent patterns that reflect the subtle dynamics (reaction-diffusion processes) generated by herbivorous foraging decision...

We develop a new approach to modeling grazing systems that links foraging characteristics (intake and digestive constraints) with resource dynamics via the probability of encounter with different grass heights. Three complementary models are presented: the generation of a grass height structure through selective grazing; investigating the condition...

We develop a new approach to modeling grazing systems that links foraging characteristics (intake and digestive constraints) with resource dynamics via the probability of encounter with different grass heights. Three complementary models are presented: the generation of a grass height structure through selective grazing; investigating the condition...

A new model to explain animal spacing, based on a trade-off between foraging efficiency and predation risk, is derived from biological principles. The model is able to explain not only the general tendency for animal groups to form, but some of the attributes of real groups. These include the independence of mean animal spacing from group populatio...

A conceptual model is described for generating distributions of grazing animals, according to their searching behavior, to investigate the mechanisms animals may use to achieve their distributions. The model simulates behaviors ranging from random diffusion, through taxis and cognitively aided navigation (i.e., using memory), to the optimization ex...

A conceptual model is described for generating distributions of grazing animals, according to their searching behavior, to investigate the mechanisms animals may use to achieve their distributions. The model simulates behaviors ranging from random diffusion, through taxis and cognitively aided navigation (i.e., using memory), to the optimization ex...

A model system, HOOFS (Hierarchical Object Orientated Foraging Simulator), has been developed to study foraging by animals in a complex environment. The model is implemented using an individual-based object-orientated structure. Different species of animals inherit their general properties from a generic animal object which inherits from the basic...

1. A more general contingency model of optimal diet choice is developed, allowing for simultaneous searching and handling, which extends the theory to include grazing and browsing by large herbivores. 2. Foraging resolves into three modes: purely encounter-limited, purely handling-limited and mixed-process, in which either a handling-limited prey t...

The ideal free distribution model which relates the spatial distribution of mobile consumers to that of their resource is shown to be a limiting case of a more general model which we develop using simple concepts of diffusion. We show how the ideal free distribution model can be derived from a more general model and extended by incorporating simple...

The geometry of tree branches can have considerable effect on their efficiency in terms of carbon export per unit carbon investment in structure. The purpose of this study was to evaluate different design criteria using data describing the form of Picea sitchensis branches. Allometric analysis of the data suggests that resources are distributed to...

There was no published abstract for this. I collaborated with the celebrated expert in plant form Prof Karl Niklas (Cornel), having myself been inspired by anatomical trees such as the pulmonary tree (in our lungs) and its arterial structures. Using a functional analysis and a generic model of rules for branching, we explained how the space of poss...