Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system

Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive nature of replicating DNA. Here we further unpack ideas related to computability, algorithmic information theory and software engineering, in the context of the extent to which biology can be (re)programmed, and with how we may go about doing so in a more systematic way with all the tools and concepts offered by theoretical computer science in a translation exercise from computing to molecular biology and back. These concepts provide a means to a hierarchical organization thereby blurring previously clear-cut lines between concepts like matter and life, or between tumour types that are otherwise taken as different and may not have however a different cause. This does not diminish the properties of life or make its components and functions less interesting. On the contrary, this approach makes for a more encompassing and integrated view of nature, one that subsumes observer and observed within the same system, and can generate new perspectives and tools with which to view complex diseases like cancer, approaching them afresh from a software-engineering viewpoint that casts evolution in the role of programmer, cells as computing machines, DNA and genes as instructions and computer programs, viruses as hacking devices, the immune system as a software debugging tool, and diseases as an information-theoretic battlefield where all these forces deploy. We show how information theory and algorithmic programming may explain fundamental mechanisms of life and death.Comment: 30 pages, 8 figures. Invited chapter contribution to Information and Causality: From Matter to Life. Sara I. Walker, Paul C.W. Davies and George Ellis (eds.), Cambridge University Pres

Information processing in biology

To survive, organisms must respond appropriately to a variety of challenges posed by a dynamic and uncertain environment. The mechanisms underlying such responses can in general be framed as input-output devices which map environment states (inputs) to associated responses (output. In this light, it is appealing to attempt to model these systems using information theory, a well developed mathematical framework to describe input-output systems. Under the information theoretical perspective, an organism’s behavior is fully characterized by the repertoire of its outputs under different environmental conditions. Due to natural selection, it is reasonable to assume this input-output mapping has been fine tuned in such a way as to maximize the organism’s fitness. If that is the case, it should be possible to abstract away the mechanistic implementation details and obtain the general principles that lead to fitness under a certain environment. These can then be used inferentially to both generate hypotheses about the underlying implementation as well as predict novel responses under external perturbations. In this work I use information theory to address the question of how biological systems generate complex outputs using relatively simple mechanisms in a robust manner. In particular, I will examine how communication and distributed processing can lead to emergent phenomena which allow collective systems to respond in a much richer way than a single organism could

Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

Spatial Modelling of Within-Field Weed Populations - a Review

Concerns around herbicide resistance, human risk, and the environmental impacts of current weed control strategies have led to an increasing demand for alternative weed management methods. Many new weed management strategies are under development; however, the poor availability of accurate weed maps, and a lack of confidence in the outcomes of alternative weed management strategies, has hindered their adoption. Developments in field sampling and processing, combined with spatial modelling, can support the implementation and assessment of new and more integrated weed management strategies. Our review focuses on the biological and mathematical aspects of assembling within-field weed models. We describe both static and spatio-temporal models of within-field weed distributions (including both cellular automata (CA) and non-CA models), discussing issues surrounding the spatial processes of weed dispersal and competition and the environmental and anthropogenic processes that affect weed spatial and spatio-temporal distributions. We also examine issues surrounding model uncertainty. By reviewing the current state-of-the-art in both static and temporally dynamic weed spatial modelling we highlight some of the strengths and weaknesses of current techniques, together with current and emerging areas of interest for the application of spatial models, including targeted weed treatments, economic analysis, herbicide resistance and integrated weed management, the dispersal of biocontrol agents, and invasive weed species

Combining evolutionary algorithms and agent-based simulation for the development of urbanisation policies

Urban-planning authorities continually face the problem of optimising the allocation of green space over time in developing urban environments. To help in these decision-making processes, this thesis provides an empirical study of using evolutionary approaches to solve sequential decision making problems under uncertainty in stochastic environments. To achieve this goal, this work is underpinned by developing a theoretical framework based on the economic model of Alonso and the associated methodology for modelling spatial and temporal urban growth, in order to better understand the complexity inherent in this kind of system and to generate and improve relevant knowledge for the urban planning community. The model was hybridised with cellular automata and agent-based model and extended to encompass green space planning based on urban cost and satisfaction. Monte Carlo sampling techniques and the use of the urban model as a surrogate tool were the two main elements investigated and applied to overcome the noise and uncertainty derived from dealing with future trends and expectations. Once the evolutionary algorithms were equipped with these mechanisms, the problem under consideration was defined and characterised as a type of adaptive submodular. Afterwards, the performance of a non-adaptive evolutionary approach with a random search and a very smart greedy algorithm was compared and in which way the complexity that is linked with the configuration of the problem modifies the performance of both algorithms was analysed. Later on, the application of very distinct frameworks incorporating evolutionary algorithm approaches for this problem was explored: (i) an ‘offline’ approach, in which a candidate solution encodes a complete set of decisions, which is then evaluated by full simulation, and (ii) an ‘online’ approach which involves a sequential series of optimizations, each making only a single decision, and starting its simulations from the endpoint of the previous run

91st Annual Meeting of the Virginia Academy of Science: Proceedings

Proceedings of the 91st Annual Meeting of the Virginia Academy of Science, held at Virginia Polytechnic Institute and State University, May 22-24, 2013

Reciprocity and resilience: teaching and learning sustainable social enterprise through gaming

Against a backdrop of increased global environmental and economic uncertainty, the resilience and sustainability of urban communities is a paramount concern for decision makers. The work presented here aims to explore how teaching and learning around transition initiatives, based upon social enterprise and reciprocity, might be supported by game theory and strategy simulation environments. Key elements for this are the coevolutionary nature of internal and external organisational contexts. The gaming prototype developed here (Exploring Community Resilience, ExCoRe)is based upon an extension of the Prisoner’s Dilemma as a medium for active learning, but is enacted through a multi-player and dynamic environment. The key learning objectives for the game are to introduce a broad concept of reciprocity and collaboration on a systems level, and the importance of an emergent and responsive ‘learning strategy’ for new start-ups and enterprises. The static nature of the traditional strengths, weaknesses, opportunities, and threats (SWOT) approach is challenged and students are encouraged to appreciate, through establishing game strategy, a much more fluid and dynamic relationship between internal and external environments