Fully funded PhD in Computer Science/Computational Biology: Evolution in complex adaptive systems

   School of Biology

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  Prof Kevin Lala  No more applications being accepted  Funded PhD Project (European/UK Students Only)

About the Project

Summary: Applications are invited for a fully-funded PhD studentship exploring the evolution of complex forms of adaptive plasticity including learning, culture and adaptive immunity using a novel computational approach. The student will work with Prof Kevin Laland (Biology, St Andrews), Prof Richard Watson (Computer Science, Southampton) and Prof Thomas Pradeu (Immunology, CNRS & Bordeaux) to devise theoretical models of evolution in complex systems. The student must be of UK or French Nationality with a good degree in Computer Science, Computational Biology or related field, and experience of programming. Start date: January 2021, or soon as possible thereafter.

Background: Living organisms must produce suitable responses to highly diverse, complex and constantly changing inputs (e.g. immunological responses to rapidly evolving bacteria and viruses, or learned adjustments to quickly changing situations). Often organisms respond to such challenges through ‘exploratory mechanisms’, which are complex developmental systems that operate by generating variation (i.e. ‘exploring’ possibilities), largely at random, testing variants’ functionality, and selecting the best solutions for regeneration, in an iterative developmental process. The process of adaptation during development arising from exploratory mechanisms resembles adaptation by natural selection (a.k.a. ‘somatic selection’), except that it allows for ontogenetic information gain rather than the acquisition of genetic information. What the genome encodes is the means to explore, not the outcome of the exploration.

Diverse biological processes function in this way, Including the adaptive immune system, much collective animal behaviour (e.g. central-place foraging), animal learning, the central nervous system, and the vascular system. All operate by exploiting exploratory and selective mechanisms to generate novel functional responses in development.

Exploratory mechanisms are highly complex adaptive systems for which standard conceptions of developmental plasticity (e.g. reaction norms), and established mathematical approaches (e.g. quantitative genetics models), appear over-simplistic. A new general means of modeling how exploratory mechanisms evolve and, reflexively, how evolution is directed by such processes, is required.

The student will join an interdisciplinary team comprising a biologist (Laland), a computer scientist (Watson) and a philosopher/immunologist (Pradeu) to help pioneer a new approach to modeling evolution in complex adaptive systems. Computational models will test a range of hypotheses, including that exploratory mechanisms evolve in a qualitatively different manner from other forms of plasticity, that they bias behaviour in predictable ways, and that they shape the course of biological evolution.

While based at the University of St Andrews, the student will make regular trips to Southampton University to work with Watson and to the University of Bordeaux to work with Pradeu. During the second year the student will spend 6-12 months in Thomas Pradeu’s lab in Bordeaux, where he/she will use the opportunity to acquire expertise in adaptive immunity, refining and testing the model to evaluate its applicability to predicting immune responses. The funding covers a stipend, fees, research and travel expenses.

Further information about the project is available on request.

Keywords: Evolutionary biology, adaptive immunity, animal learning, computational biology

Applications can be made online via our online portal- https://www.st-andrews.ac.uk/study/apply/postgraduate/research/

Funding Notes

The 3.5-year studentship is fully funded by the Defence and Security Technology Laboratory (DSTL) and covers fees, stipend, research costs and travel.

This funding opportunity is only available to British or French Nationals. The candidate will be required to spend a minimum of 6 months in the partner French University.

Suitable applicants will have a good first degree (First or Upper Second Class or equivalent) in Computer Science, Computational Biology or a related field, and experience of computer programming.

For further information, contact Kevin Laland ([Email: [Email Address Removed]]) or Linda Hall ([Email: [Email Address Removed]]).


Relevant references
West-Eberhard MJ 2003. Developmental Plasticity and Evolution. Chapter 3 (Plasticity). Oxford University Press

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