Friday, 18 January
Dr Peter Hines, York
Title: Information flow and assumptions in linguistic models of natural language - Abstract, Peter Hines (PDF , 91kb)
Host: Susan Stepney
(Informal presentation from an YCCSA member: Dr Martin Trafzer: tbc)
Friday, 01 February - in association with IGDC, International Global Development Centre
Dr Roger Cremades, GERICS, Climiate Service Centre, Hamburg
Title: Transforming Human Network Systems to a Sustainable Nexus Multiplex -
Host: Professor Susan Stepney and Professor Piran White
Please note this seminar is taking place at the Berrick Saul building, BS/104
Friday, 2 February
Professor Ann Blandford, UCL Institute of Digital Health
Title: Seven lessons for interdisciplinary research: the case of interactive digital health interventions - Abstract Ann Blandford (PDF , 92kb)
Host: Professor Susan Stepney
Friday, 16 February
Dr Chris Saunter, Department of Physics, Durham University
Title: Exploring the potential for computation within sub-cellular Calcium signalling - Abstract Chris Saunter (PDF , 90kb)
Host: Professor Susan Stepney
Friday, 16 March
Dr Elizabeth Hunter, Queen Mary University of London
Title:Lettuce, poppy seeds and woman’s milk: sleep remedies in seventeenth-century English receipt books - Abstract Elizabeth Hunter (PDF , 93kb)
Host: Dr Pierre-Philippe Dechant
Friday, 25 May
Mr Matthew Dale, YCCSA
Title: Reservoir Computing in materio - Abstract Matthew Dale (PDF , 99kb)
Host: Professor Susan Stepney
Friday, 8 June
Dr Aneurin Kennerley, York
Title: Shedding Light on Brain Activity -
Host: Dr Angelika Sebald
Friday, 13 July
Dr Nikolai Bodie, University of Bristol
Title: Smart swarms or mindless mobs: modelling competition and cooperation in pedestrian crowds - Abstract Nikolai Bode (PDF , 91kb)
Host: Dr Dan Franks
Friday, 5 October
Professor Ivana Gudelj, University of Exeter
Title: The Impact of Micobial Community Interactions on the Evolution of Virulence and Antibiotic Resistance - Abstract Ivana Gudelj (PDF , 723kb)
Host: Professor Reidun Twarock
(Informal presentation from an YCCSA member: Dr Richard Bingham: I will present a model of a viral infection that includes insights into the molecular mechanism of viral assembly, and demonstrate that therapies directed against this mechanism outperform existing antiviral strategies and also reduce the likelihood of therapy resistance through mutants.)
Friday, 19 October
Professor Neil Hunt, Physical Chemistry Department of Chemistry, York
Title: Ultrafast 2D-IR Spectroscopy - Challenges for Real World Biomolecular Applications - Abstract Neil Hunt (PDF , 624kb)
Host: Dr Angelika Sebald
(Informal presentation from an YCCSA member: Dr Angelika Sebald - The maxfacts initiative - where we stand in autumn 2018: Iwill give a brief overview about the current state of the website development and plans for next steps. In addition, I will give a very short outlook about a new project involving real-time MRI on swallowing and speech (collaboration with Aneurin Kennerley).
Friday, 16 November
Professor Vincent Moulton, University of East Anglia - Abstract Vincent Moulton (PDF , 91kb)
Title: Assembling the Network of Life
Host: Dr Eric Dykeman
(Information presentation from an YCCSA member: Dr Eric Dykeman)
Friday, 30 November
Professor Christina van der Feltz-Cornelis, York
Title: Addressing complexity in treatment of mental disorders -Abstract Christins van der Feltz-Cornelis (PDF , 97kb)
Host Professor Reidun Twarock
(Information presentation from an YCCSA member: Professor Susan Stepney)
Friday, 14 December
Dr Halim Kusumaatmaja, Durham Univeristy
Title: Surveying Energy Landscapes: From Protein Folding to Bistable Liquid Crystal Device and Cylindrical Buckling - Abstract Halim Kusumaatmaja (PDF , 616kb)
Host: Professor Reidun Twarock
(Informal presentation from an YCCSA member: Dr Giuliana Indelicato: A mathematical model for the structural transition in Human Rhinovirus 2 - Human Rhinoviruses are causative agents of the common cold. In order to release their RNA genome into the host during a viral infection, these small viruses must undergo conformational changes in their capsids, whose detailed mechanism is strictly related to the process of RNA extrusion, which has been only partially elucidated. We develop here a mathematical model for the structural transition between the native particle of Human Rhinovirus type 2 and its expanded form, viewing the process as an energy cascade, i.e., a sequence of metastable states with decreasing energy connected by Minimum Energy Paths.)
Marta Vallejo, Heriot-Watt University, Edinburgh
Title: Versatility of the use of Evolutionary Strategies in search and classification: from healthcare to green areas - Abstract Marta Vallejo (PDF , 138kb)
Host: Steve Smith
Dr Paul Tiffin, Health Sciences, York
Title: Modelling selection into medical education and training; some mathematical challenges - Abstract Paul Tiffin (PDF , 139kb)
Host: Reidun Twarock
Dr Mike Plank, School of Mathematics & Staticstics, University of Canterbury, NZ
Title: Social network analytics for identifying vulnerable children - Abstract Mike Plank (PDF , 137kb)
Host: Richard Law
These seminars will be held in RCH/204 at 13:30 - 15:30. Refreshments and cake provided.
Over the summer vacation YCCSA is hosting a series of interdisciplinary seminars focused on the University of York's research themes. The seven Research Champions will deliver a series of talks about their specific interdisciplinary themes. Each session will have two speakers followed by an extended discussion period. All are welcome to come to the seminars, join in the discussions and enjoy the cake.
Please book your free place on Eventbrite
Friday, 21 July
Introduction to Interdisciplinary - Professor Susan Stepney, YCCSA Director
Professor John McDermid - Risk, evidence and decision making
Risk for the real world: in an increasingly complex world, our research is penetrating deep into how decisions on risk are made and how they are shaped by technological, social and cultural factors. By drawing on our understanding of these factors, we can provide government and industry with better risk models and help influence policies resulting in better-informed decision making. Explore this theme
Host: Dr Simon O'Keefe - Computer Science
Friday, 11 August
Dr Damian Murphy - Creativity
Creativity is a key driver of modern, dynamic societies and is at the centre of our research excellence. Our work considers the nature of creativity and the creative process across linguistic, cultural, aesthetic and cognitive dimensions. Research at the convergence of technology, digital games and interactive media, together with leading partners in the creative economy, enables us to deliver new experiences to provoke, inform and entertain for the wider benefit of society. Explore this theme
Dr Mark Jenner - Culture and Communication
Working on all periods from prehistory to the present and on places across the globe, York researchers explore every kind of cultural activity, product and practice from poetry to pollution, alongside every aspect of communications from syntax to cyberspace. They are advancing and challenging how we understand the world, and developing new intellectual tools to make sense of human thought, human behaviour and our relation to the natural world. Explore this theme
Host: Professor Reidun Twarock - Biology/Maths
Friday, 25 August
Professor Thomas Krauss - Technologies for the future
Our researchers are developing novel technologies, processes and materials with the potential to transform the economic, environmental, and social landscape. From precision plasma manufacturing, to plants that can devour toxins, fundamental research is being rapidly translated into real world solutions. Explore this theme
Professor Kate Pickett - Justice and equality
Fairness, inclusivity, equality, and welfare, are policy fields where our research sets the political agenda. These themes also define our values and approach to meeting the grand social challenges of our time at national and international level. Explore this theme
Host: Dr Leo Caves - Biology
Friday, 1 September
Professor Karen Bloor - Health and wellbeing
Our global reputation in biomedicine, health science, economics and the medical humanities is built on research excellence that begins with the fundamental understanding of health and disease in the past and the present, and progresses to evidence-based decision-making about future healthcare policies and therapies. Explore this theme
Professor Sue Hartley - Environmental sustainability and resilience
Whether it is food scarcity and energy security, or climate change and pollution, our interdisciplinary research is providing the evidence base for policy makers to address the key global challenges facing ourselves and our planet, and so shape a more sustainable future for us all. Explore this theme
Host: Professor Susan Stepney - Computer Science
Friday, 24 November
Jesús Jorge Brezmes Llecha, Universitat Rovira i Virgili, Tarragona
Title: Not to be sniffed at: from electronic noses to AI and metabolomics - Abstract Jesús Jorge Brezmes Llecha (PDF , 93kb)
Host: Dr Julie Wilson
Professor Veronica Strang, Institute of Advanced Study, Durham University
Title: Complex relations: interdisciplinary collaboration and bioethics in river catchment research Abstract Veronica Strang (PDF , 88kb)
Host: Professor Susan Stepney
David A Mitchell, FDS FRCS FRCS (Maxfac), Consulting Oral/Maxillofacial and Head & Neck Surgeon
Title: Why we cut - a surgeons view of the "wicked" - Abstract David A Mitchell (PDF , 169kb)
Host: Angelika Sebald
Dr Sarah Harris, The Astbury Centre for Structural Molecular Biology, University of Leeds
Title: DNA Minicircles for Synthetic Biocomputing - Abstract Sarah Harris (PDF , 136kb)
Host: Susan Stepney
Professor Bruce Edmonds, Centre for Policy Modelling Manchester Metropolitan University
Title: The Modelling of Context-Dependent Causal Processes – A Recasting of Robert Rosen’s Thought - Abstract Bruce Edmonds (PDF , 149kb)
Host: Leo Caves
Dr Jessie Barker, Aarhus University
Title: Cooperation within and among groups in humans - Abstract Jessica Barker (PDF , 137kb)
Dr Caitlin Stern, Santa Fe Institute
Title: Social and ecological factors favouring the evolution of group living - Abstract Caitlin Stern (PDF , 137kb)
Host: Elva Robinson
Dr Hermes Gadêlha, Department of Mathematics, York
Title: Mathematical tales of a sperm tail -
Host: Richard Law
Dr Pen Holland, Department of Biology, York, Landcare Research New Zealand
Title: Playing possum: modelling brushtail possum imacts in New Zealand - Abstract Pen Holland (PDF , 89kb)
Host: Richard Law
Professor Maia Angelova, University of Northumbria
Title: Complexity Analysis of Physiological Signals Based on Non-Invasive Techniques - Abstract Maia Angelova (PDF , 84kb)
Host: Reidun Twarock
Dr Keith De'Bell, St. Francis Xavier University, Nova Scotia
Title: Connectivity, dynamics and evaluation in models of health equity interventions - Abstract Keith De'Bell (PDF , 94kb)
Dr Mark Coles, Centre for Immunology and Infection, York
Title: Solving immunological challenges using computational and mathematical approaches - Abstract Mark Coles (PDF , 85kb)
Host: Fiona Polack
Professor Kevin Gurney, University of Sheffield
Title: Deciding what to do next: Models of action selection in the basal ganglia at multiple levels of description - Abstract Kevin Gurney (PDF , 80kb)
Host: Simon O'Keefe
Professor Russ Abbott, California State Univerity, Los Angeles
Title: Abstractions and implementations: a computer science perspective on emergence, causality, and multi-level autonomy - Abstract Russ Abbott (PDF , 91kb)
Host: Susan Stepney
Dr Omer Markovitch, Newcastle University
Title: Compositional Lipid Assemblies as Evolving Protocells -
Host: Susan Stepney
|5 December||Dr Alejandro Pena, Politics, York||
Back in the Loop: Complexity in International Relations
There is substantial agreement in the International Relations (IR) community that its object of study is ‘complex’. Notwithstanding, IR inquiry continues to operate under theoretical and methodological premises that minimize complexity effects, system dynamics, and non-linearity. This article considers that this inconsistency has hampered systemic thinking within IR arguments and models, independently of theoretical orientation. The article argues that System Dynamics modelling (SD) provides a sophisticated and flexible meta-theoretical framework capable of tackling this problem. Drawing from this body of knowledge, the article presents a heuristic platform – a set of conceptual notions and graphic notation – to schematize and model causal mechanisms, feedback structures, and nonlinear behaviours in world politics. This platform, it is claimed, has potential to complement existing IR arguments, theories and methods and enhance the manner in which complexity effects are analyzed and communicated, while narrowing the distance between the complexity of global affairs and the conceptual and methodological tools available to deal with it.
|28 November||Professor Frank P Ryan, University of Sheffield||
The Holobiontic Human Genome
Our human genome defines us. It lies at the very core of our being. To understand it is to
|14 November||Dr Lydia Pedoth, EURAC||
Understanding community resilience to multiple hazards in mountain areas
In the Alps, natural hazards are part of everyday life. Communities live with continuous risk and cope frequently impact events. Every year, different kinds of natural hazard events cause damages, losses and deaths. Over centuries, communities have developed means to cope. These became part of local society and culture, including aspects such as risk perception and the role of social networks, and shape the resilience of communities towards natural hazards. But how to assess, describe and measure these abilities and their influence on community resilience?
|24 October||Professor Rachel Armstrong, Newcastle||
A design-led approach to Natural Computing
This talk explores new possibilities for making 21st century design practices as a response to a range of novel computing practices that aim to reach escape velocity from conventional digital computing paradigms and identify ways of counting, sorting and ordering that are more like Nature. A range of subjects will be discussed including a philosophical and ontological engagement with these systems, which may help us imagine and innovate differently. Additionally, design-led experiments and projects will also be presented that start to explore and suggest initial guidelines for what it means to design and engineer with living systems.
|10 October||Adrienne Tecza, University of Oxford||
Status, deference, and information sharing among fishermen: How re-conceptualizing altruistic behaviour can change the way we understand natural resource use
The tragedy of the commons is ubiquitous in discussions of natural resource use and has led many to conclude that the only way to combat the depletion of ecological commodities such as fish, forests and farmland is through government intervention and privatization. However, in recent years scholars have
|19 September||Dr Keith De'Bell, St Francis Xavier University, Canada||
Complexity analysis in social development and the social determinants of health
Since the late 1980s, complexity theory has enjoyed a rapid adoption across many disciplines. The generality of complexity theory has led to different formulations in different areas of application. In this talk, I will focus on how complexity theory has been used in social development work and public health promotion. A brief overview of evaluation strategies used in these applications will also be given. The talk will close with a discussion of the potential benefits of mathematical and computer modeling approaches to complexity in these applications.
|12 September||YCCSA||Summer School Presentations|
Summer School Presentations
|15 August||Professor Roya Zandi, University of California, Physics and Astronomy||
The robust assembly of small symmetric nano-shells
Highly symmetric nano-shells are found in many biological systems, such as clathrin cages and viral shells. Many studies have shown that highly symmetric shells appear in nature as a result of free energy minimization of a generic interaction between their constituent subunits. In this talk, I show that the symmetric structures observed both in equilibrium simulations and in self-assembly experiments can readily grow from identical subunits under non equilibrium conditions. Our minimal model of nano-shell assembly shows that the spontaneous curvature regulates the size of the shell while the mechanical properties of the subunit determines the type of symmetry of the assembled structure. Understanding the minimum requirements for the formation of closed nano-shells is a necessary step toward engineered nano-containers, which will have far reaching impact in both material science and medicine.
|18 July||Dr Matthew Patrick, Department of Plant Sciences, Cambridge||
Accurate Host Landscapes for Modelling the Spread of Plant Diseases
Host landscapes are used to describe the spatial patterns and locations of infectious or susceptible plants in a heterogeneous environment. Inaccuracies may exist in host landscapes because the data they are constructed from are incomplete, noisy or inconsistent. Inaccuracies typically occur due to errors in attributes, spatial positioning or temporal validity. It is unclear how much of an effect these errors have on models for the spread of plant diseases or whether some errors are more detrimental to modelling predictions than others. Errors and inaccuracies are inherent to a certain degree in all spatial data. Therefore, unless we understand how inaccuracies in the host landscape affect our models, it is difficult to have confidence in their recommendations for control. This presentation considers potential errors that may be introduced into the landscape, describes ways to detect these errors and methods to check whether the predictions of our models are correct. Although these issues are discussed from an epidemiological perspective, the techniques described in this presentation are relevant to a wide range of spatial modelling applications, including ecology, demographics and urban planning.
|7 July||Dr Mike Perkins, British University Vietnam||
Public Confidence Modelling: a locally based approach to police performance management
In the UK, the ability of the police to function effectively depends on the authority that they can command, rather than the force that they can deploy. It is therefore essential that police retain their legitimacy in their role of defenders of the British Public. This can only be achieved through maintaining and improving levels of public confidence in policing.
|4 July||Professor David Zeitlyn, University of Oxford||
Getting answers to unasked questions using modelling to unpack ideas and assumptions about peasant farming and fishing in Africa
|27 June||Dr Steven Tipper, Psychology, York||
In this talk I will review the evidence that when we simply look at objects, such as a coffee cup, the actions we would typically produce, such as grasping it, are automatically activated in the brain. Similarly, when we observe another person’s actions we covertly simulate their actions. For example, when we observe a person kick a soccer ball, motor areas in our brain that control our own feet become activated and actions with the same body part (foot) are made more quickly. It has been proposed that such action simulation processes aid our understanding of objects and people. For example, preparing to produce an action can facilitate perception of certain objects, pain in a body part can impair the perception of another person’s action, and motor simulation of another person’s actions can aid empathy and prediction. Hence states of our motor system aid understanding of our visual world.
|20 June||Agostino Nobile, York||
A composite Bayesian hierarchical model of compositional data with zeros
We present an approach to modelling compositional data with large concentrations of zeros and several levels of variation, applied to a database of elemental compositions of forensic glass of various use types. The procedure consists of (i) partitioning the dataset in subsets characterized by the same pattern of presence/absence ofb chemical elements and (ii) fitting a Bayesian hierarchical model to the transformed compositions in each data subset, using MCMC methods.
|16 May||Dr Roger Schurch, University of Sussex||
Dancing bees improve colony foraging success as long-term benefits outweigh short-term costs
Waggle dancing bees provide nestmates with spatial information about high quality resources. Surprisingly, attempts to quantify the benefits of this encoded spatial information have failed to find positive effects on colony foraging success under many ecological circumstances. Experimental designs have often involved measuring the foraging success of colonies that were repeatedly switched between oriented dances versus disoriented dances (i.e. communicating vectors versus not communicating vectors). However, if recruited bees continue to visit profitable food sources for more than one day, this procedure would lead to confounded results because of the long-term effects of successful recruitment events. Using agent-based simulations, we found that spatial information was beneficial in almost all ecological situations. Contrary to common belief, the benefits of recruitment increased with environmental stability because benefits can accumulate over time to outweigh the short-term costs of recruitment. Furthermore, we found that in simulations mimicking previous experiments, the benefits of communication were considerably underestimated (low food density) or not detected at all (medium and high densities). Our results suggest that the benefits of waggle dance communication are currently underestimated and that different experimental designs, which account for potential long-term benefits, are needed to measure empirically how spatial information affects colony foraging success.
|9 May||Dr Mariam Kiran, University of Sheffield||
Social and Economic Models and Equilibrium
In 1776, Adam Smith envisioned the presence of an invisible hand playing an active role in economic markets. These ideologies have supported the concept that all economic models eventually reach an equilibrium, supporting the traditional research of using differential equations encouraging the birth of rational people making rational decisions at the correct time. However, the 2008 credit crunch has highlighted the flaws in these theories.
|2 May||Professor Giuseppe Longobardi, Department of Language and Linguistics, University of York||
Darwin’s last challenge
Beyond its theoretical success, the development of molecular biology has brought about the possibility of extraordinary progress in the historical study of classification and distribution of different species and different human populations, introducing a new level of evidence (molecular genetic markers) apt, among other things, to quantitative and computational treatment. Even in the cognitive sciences, purely theoretical progress in a certain discipline, such as linguistics, may have analogous historical impact, equally contributing to Renfrew’s so-called ‘New Synthesis’. Thus, I will argue that the parallelism between the study of linguistic history and genetic evolution goes beyond methodological similarities, and may begin to encompass substantive results. Darwin (1859) had hypothesised that the ultimate genealogical tree of languages should correspond to the biological one of human populations: however, testing this challenging hypothesis has so far been practically impossible. Over the past 30 years, geneticists developed ever more sophisticated techniques to compare the biological layout of even distant populations, but this is not enough; so far linguists have relied on comparing words from different languages, to reconstruct their ancestry: this method, though sometimes extraordinarily successful, goes back in time for few millennia, too little to relate distant languages on a continental or global basis. However, fortunately, languages are not mere word lists, but also sets of abstract syntactic rules to combine words into correct sentences. Exploiting dramatic progress in the theory of universal grammar, I have developed for the past 10 years a radically new method to compare languages and quantify their distances in order to reconstruct their histories from syntactic differences/similarities. We are currently applying it successfully to areas as vast as Europe and parts of Asia. On these grounds , I am now cooperating with geneticists, as the PI of an ERC grant, to finally compare genetically and linguistically distant populations, and we discovered that some results of the two disciplines may for the first time be correlated and complement each other for reconstructing ever deeper histories of human culture and biology.
|11 April||Dr Briony Thomas, School of Design, University of Leeds||
Atoms, Patterns and Polyhedra: A Journey through Complexity in Art and Science
The presence of symmetry in nature has fascinated both scientists and artists for centuries. Geometry has been used across the disciplines by artists, engineers, biochemists, physicists and mathematicians, as a tool to understand, explain and order phenomena in the world around us. In the late 19th century biologist and philosopher Ernst Haeckel made detailed studies of microscopic life forms exhibiting unusual symmetric characteristics, illustrating over 4,000 species of Radiolaria. In 1940, inspired by these forms, French structural innovator Robert le Ricolaris proposed a geodesic shell structure based on the triangulated networks of radiolaria. Buckminster Fuller’s independent innovation of the geodesic dome, dating from 1948, also displays a similar structure to many radiolaria. Fuller’s ideas on geodesic structures stimulated significant scientific developments, with the 1985 discovery of a super-stable all-carbon C60 molecule, appropriately named Buckminsterfullerene. Fuller’s ideas also had an impact in the field of virology when scientists again drew ideas from the structure of his geodesic domes in the quest to understand the structure of virion protein shells. Although science and the creative disciplines of art and design are usually considered as polar opposites, both rely on a process of observation, experimentation and synthesis. An elegant example of the connections between science, art and design is shown through the parallels between crystallographic theory and pattern analysis and construction, both of which are underpinned by geometry. This paper discusses the cross-fertilisation of ideas between crystallography and design, from the early-twentieth century perspective on pattern analysis pioneered by the Russian crystallographer Federov to recent work exploring the translation of pattern from two to three dimensions.
|10 January||Professor Paul Kaye,
Biology, University of York
How does the distribution of Leishmania in its mammalian host affect transmission dynamics to the sandfly vector (and is there value in modeling this)?
Leishmania parasites have varied distributions within their mammalian host (skin, different internal organs, bone marrow) and are transmitted between humans by female sandflies that take blood meals. My lab has a long-standing interest in the pathology of leishmaniasis and how immune responses operate in different tissue sites. We have developed a therapeutic vaccine that has just finished Phase I clinical trial, which might have value in reducing transmission efficiency, but we know very little about what governs "efficiency". We have established a sandfly transmission model in York to test the vaccine experimentally and to ask fundamental questions about how different types of immune response (e.g that might sequester parasites together or that result in greater dispersal in tissues) impact on transmission. I will be applying for a WT SIA at the end of February. Is there a fruitful modeling dimension to this work (e.g. as a PhD or RA project)?
|6 December||Professor Karl Claxton, CHE||
CIDCATS Seminar: Expected health benefits of additional evidence: Principles, methods and applications
In this talk we demonstrate how the principles of Bayesian decision theory and value of information analysis can be routinely used in prioritising evaluative research in health care in a way that is sufficiently general to be relevant across a range of different types of health care systems and decision making contexts. In particular, the purpose is to illustrate: i) the principles of what assessments are required when considering the need for additional evidence about the performance of health care interventions and the priority of proposed research; and ii) how these assessments might be informed by quantitative analysis based on standard methods of systematic review and meta-analysis of the results of existing studies. We briefly outline the principles of what type of assessments are needed when considering research prioritization and commissioning. These are then more fully examined through the integration of the principles of value of information analysis with the type of meta-analysis commonly conducted in systematic review and its application to four topics or case studies. The case studies illustrate a number of contexts in which these assessments are likely to be required.
|22 November||Dr. Michael Pocklington, Leicester||
The Imaginary Chemostat, the Natural Interaction Map, and the Causal Plexus
The genetic interaction map is taken as the starting point for an investigation of fundamental biological structure using thought-experiments. In laboratory experiments, genetic interaction maps are constructed using a chemostat to accurately measure the fitness of the organism containing defined single and pairwise combinations of mutations. Complex biochemical, physiological, and behavioural structures are visualised as a map of genetic interactions, entirely constructed from measurements of fitness and environmental perturbations. Here, I employ an “imaginary chemostat”, and I use it to construct a “natural interaction map” depicting all the functional genetic elements, all the relevant environmental features, and all the natural interactions in the functional network that constitutes the organism. I show that the imaginary chemostat must be equivalent to the niche; the organism must be equivalent to a population occupying the niche; and functional genetic elements are self-maintaining feedback structures, of which genes are the most conspicuous, but not the only, type. Underlying the natural interaction map must be a naturally-selected functional network object, here called the “causal plexus”. I will show it also refers to entities other than the organism, and defines a universal niche-structure. It can be used to frame and answer long-standing questions about reality, emergence, complexity and computation.
|8 November||Dr Yuan Ju, Economics & Related Studies||
Coalitional Externalities, Strategic Bargaining, and Effcient Values
This paper provides a °exible strategic framework to analyze bargaining and values in
|25 October||Dr. Karoline Wiesner, Bristol||
Thermodynamics of complexity measures
Physical systems are often simulated using a stochastic computation where different final states result from identical initial states. Here, I derive the minimum energy cost of simulating a data sequence of a general physical system by stochastic computation. Using information theory, I show that the cost is proportional to the difference between two information- theoretic measures of complexity of the data—the statistical complexity and the predictive information. I derive the difference as the amount of information erased during the computation. To this framework I will add a quantum mechanical measure of complexity. The resulting triple opens an interesting view on thermodynamics, quantum mechanics and complexity.
|18 October||Grazziela Figueredo, Nottingham||
The use of Agent-based Simulation to Discover Extreme Cases in Immune-Interactions with Early-Stage Cancer Scenarios
Early-stage cancer and its interactions with the immune system are still not fully understood. In order to better understand these processes, researchers employ different methods. Simulation and in particular, agent-based simulation (ABS) have been found useful tools for understanding it.
|20 September||Professor Mark Leakem York||
Illuminating the machines of life
Many of the challenging, unresolved questions in the life sciences cannot be adequately addressed by conventional bulk ensemble average techniques, but rather demand pioneering techniques of single-molecule biophysics, and an ability to perform such experiments with the native biological context intact is of enormous advantage. Here, I discuss examples of such investigations that have emerged from my group, primarily using well-characterized bacteria as the experimental test system. Using a combination of cutting-edge genetics technology and state-of-the-art bespoke fluorescence imaging and photophysical analysis we can now see into living cells in “real-time” at a single-molecule precision over length scales of a few tens of nanometre accuracy and a time scale as a short as a millisecond1. Previously, this has allowed us to monitor a variety of different molecular machines, including the molecular-level architecture of functional DNA replication factories2, and more recently has given us significant new insight into the mechanism by which key DNA-binding proteins called Single Molecule Condensins (SMCs) act ubiquitously in all domains of life in chromosome processing, to package, condense and segregate DNA3. I will also introduce the concepts of the new Biological Physical Sciences Institute at the University of York4, and the scope for complementing the interfacial activities of YCCSA.
|13 September||YCCSA||Summer School Presentations|
Summer School Presentations
|23 August||Dr Alastair Droop, Leeds||
Copy Number Analysis using Next Generation Sequencing
In this talk I'll introduce the Illumina HiSeq 2000 system, and outline how we can investigate copy number variations (CNVs) in the Leeds Melanoma Cohort. I'll discuss several problems we're having and discuss how we can proceed.
|16 August||Peter Dudley||
Fast and Loose Through Systems Theory
In terms of both the development of models and their application, systems theoretical ideas have a relatively long and somewhat chequered history. These are ideas that, although
What follows is a personal (and probably heretical) account of the development of these ideas and which, no doubt, demonstrates my own dogma and pays homage to my own prophets.
|9 August||Dr Jose Cuesta, University Carlos III, Madrid||Human behavior on networks: What experiments tell us
For the last two decades it was believed that a population structure (induced, e.g., by a network of contact) could promote cooperative behavior. The reason is that constraining interactions only to the closest contacts in the network enhances the formation of clusters of cooperators who can resist the exploitation of external defectors. Since Nowak and May's 1992 pioneering simulations of iterative prisoner's dilemmas on lattices, the evidence extracted from a priori modeling human behavior was inconclusive: results suggest that the details (the kind of network, the update strategies, etc.) of the model may be very relevant to the final outcome. In spite of that, in some cases (scale-free networks are prominent on that) the promotion of cooperation seemed hard to argue. In 2009 we started a research program to test this effect in real experiment involving relatively large networks (comparable to those of the theoretical models). Since then we have conducted three experiments in two type of networks (a lattice and a scale-free network) and in isolated groups, and have reanalyzed existing experimental results. The conclusion we have reached out of them is that the network of contact does not play any role in promoting cooperation; in other words, people behave within a network as in isolated groups. More than that, the collected data point to a model of human behavior in which indivuals act cooperating or defecting according to what their neighbors and themselves recently did, exhibiting not just reciprocity to the received cooperation but also a personal “mood”, shuch that they only reciprocate if they feel in a cooperative mood and ignore their neighbors otherwise. Our results ask for a deep revision of the available theoretical models and demand an answer to the question why we behave the way we do
|26 July||Professor Yvette Hancock, Physics, York||
Graphene - Wonder Material
Graphene, which looks like carbon chicken wire, is a single layer of the more well-known material, graphite, which has modest application as the writing component in pencils. In comparison, graphene has remarkable properties from being a bench-top version of a CERN experiment, with charge-carriers that travel unimpeded and at a fraction of the speed of light, to it being the strongest known material, with record thermal conductivity, high elasticity and tunable optical transmission. Unlike graphite, its potential applications are stellar and beyond ordinary. This presentation will provide an accessible overview of graphene; from the bulk to the nanoscale, highlighting its potential for being engineered, as well as future applications, including bio-medical.
|20 June||Professor Priyanga Amarasekare, Dept of Ecology & Evoluationary Biology||
A trait-based perspective of ecological and evolutionary dynamics
Populations and communities are complex systems whose properties result from the interplay between non-linear feedbacks that are intrinsic to the system (e.g., biotic interactions that lead to density- and frequency-dependence) and external inputs (e.g., abiotic factors) that are outside the feedback structure of the system. Understanding this interplay requires that we understand the mechanisms by which the effects of external inputs on lower levels of the system (e.g., traits of organisms) influence properties at higher levels (e.g., population viability, species diversity). Using temperature as the axis of abiotic variation, I develop a mechanistic theoretical framework for elucidating how abiotic effects on traits translate into population dynamics and species interactions, and how these ecological dynamics in turn feedback into the trait response, causing trait evolution. I test model predictions with data on insects. The integration of theory and data paves the way for making testable predictions about the effects of climate warming on population viability, biodiversity and the control of invasive species.
|14 June||Dr. Carla Pinheiro, Instituto de Tecnologia Química e Biológica||
Understanding drought stress response in plants through analysis of multiple data sources
With increasing concerns about the impact of drought on plant growth and survival, the molecular responses to progressive soil water deficit of two model plants with contrasting stress tolerance have been investigated. The well-characterised model plant system, Arabidopsis thaliana, is not stress tolerant, whereas the closely related Thellungiella salsuginea is a so-called extremophile, exhibiting high stress tolerance and the ability to grow under harsh conditions. Plants perceive and respond to alterations in soil water content via a series of physiological, cellular, and molecular events that develop in parallel and our working hypothesis is that the combined alterations in hormone and carbohydrate levels play an important role in the stress response mechanism. After withholding water, the rate of soil water depletion was similar for both plants for the first 2 days, but after 3-5 days Arabidopsis plants took up more water from the soil (5-10%). For similar soil water contents, the performances of Arabidopsis and Thellungiella were quite different, and were accompanied by distinct effects on the carbohydrate metabolism. Plant responses have been characterised using multivariate analyses for both targeted and untargeted metabolomics alongside physiological studies. Arabidopsis and Thellungiella show distinct growth and metabolomic profiles both under control conditions and in response to progressive soil water deficit and the direct comparison of these two contrasting plant systems offers the possibility to improve understanding of physiological and biochemical drought-related mechanisms
|7 June||Dr Mauro Mobilia, University of Leeds||
Large fluctuations and metastability in evolutionary games
Evolutionary game theory (EGT), where the succes of one species depends on what the others are doing, provides a promising
|31 May||Dr Anje-Margriet Neutel, British antarctic Survey||
Beyond symmetry and asymmetry: Complexity and the stability of ecological networks
In ecology, interactions are important. That is why ecologists use network models to study communities and ecosystems. It is only a small step to recognise that some interactions will be more important than others. Yet, until recently, in ecological theory the strengths of the interactions in ecological networks have been largely neglected. In this talk I will show how observations of the energy flow in ecosystems reveal characteristic patterns in interaction strength underlying system stability. Through the quantification of feedbacks, closed chains of interactions, these patterns shed light on the much debated relation between complexity and stability in ecosystems.
Neutel AM & Thorne MAS (submitted) Observed interaction strengths, critical feedbacks, and the absence of a relation between ecosystem complexity and stability.Neutel AM et al. (2007) Reconciling complexity with stability in naturally assembling food webs. Nature 449(7162): 599-602.
|17 May||Dr Mike Plank, University of Canterbury, NZ||
So long and thanks for all the fish
Overfishing is a worldwide problem. More than half the world's population is dependent on fish for part of their diet, yet many fish stocks have been depleted to dangerously low levels. Most commercial fisheries have strict regulations on the size and species of fish that can be targeted, usually prohibiting the landing of fish under a minimum legal size. However, this strategy is coming under increasing criticism and it has been suggested that a more balanced approach, in which fishing effort is spread over a wide range of sizes and species, could be beneficial. In this talk, I will present a size-spectrum model that describes how the density of individuals of a given body mass changes over time. I will use this model to compare the traditional minimum catch size approach to fisheries management with the alternative balanced harvesting. The results show that balanced harvesting can give improvements in total sustainable yield with less impact on ecosystem structure and reduced risk of stock collapse. I will discuss how these results compare with available empirical evidence
|3 May||Ken Kahn, University of Oxford||
Modelling for All, participatory ABM project
The Modelling4All Project has built a web-based tool called the Behaviour Composer for constructing, running, visualising, analysing, and sharing agent-based models. These models can be constructed by non-experts by composing pre-built modular components called micro-behaviours. We are attempting to seed and nurture a Web 2.0 community to support modelling. Models, micro-behaviours, lesson plans, tutorials, and other supporting material can be shared, discussed, reviewed, rated, and tagged. The Behaviour Composer has been used extensively in teaching and a few research projects.Ken Kahn and Howard Noble are researchers at the Oxford University IT Services. The focus of Ken's research is making programming and computer modelling accessible to a wide audience. He is the creator of ToonTalk, a programming language used by young children. His earlier research at MIT, Uppsala University, and Xerox PARC was focused on AI and programming language design.
|26 April||Iain Weaver. University of Southampton||
Tipping points in Complex Coupled Life-Environment Systems
Simple models of complex phenomena provide powerful insights and suggest low-level mechanistic descriptions. The Earth system arises from the interaction of subsystems with multi-scale temporal and spatial variability; from the microbial to continental scales, operating over the course of days to geological time. Often, the challenge is in determining the fundamental mechanisms responsible for the coarse behaviour, omitting details which would otherwise obfuscate the dynamics.The advantage of abstract models is in the prospect of a thorough and transparent analysis. In particular stability, criticality and transitions are of great relevance to understanding the history, and future of the Earth system. We introduce a general model for a coupled life-environment model, concentrating on a minimal set of assumptions, and explore the consequences of interaction between simple life elements and their shared, multidimensional environment. The model is shown to share salient features with other abstract systems such as Ashby's Homeostat and Watson and Lovelock's Daisyworld. Our generic description is free to explore high-dimensional, complex environments, and provide insights into the complex network of states which emerge.
|19 April||Dr Miles Whittington, HYMS, York||
Modelling for All, participatory ABM project
Deep sleep is characterised by large, slow rhythmic changes in the electrical activity of the brain. This rhythmic activity takes many forms but the most common is the delta rhythm - a 1-4 Hz oscillation in cortical potential readily observable in EEG and MEG recordings. Current consensus is that delta is generated by interaction between the cortex and thalamus, with a dominant thalamic rhythm generating circuit being well characterised. However, recent detailed analysis of delta rhythms in humans reveals discrepancies that do not fit with the idea of a purely thalamic generator. This presentation will show evidence for a local neocortical delta-generating neuronal circuit and demonstrate how it controls interactions between different layers facilitating an unsupervised synaptic learning environment. Taking cues from precedented aberrations in cortical dynamics associated with deep sleep and learning disability in humans, evidence for a specific mechanism underlying disruption of this learning environment will be considered
|15 March||Pirmin Nietlisbach||
Causes and consequences of genetic diversity: Investigating natural and sexual selection on heterozygosity
The importance of individual genetic diversity, i.e. heterozygosity, as a factor influencing individual fitness has long been recognized
|22 February||Richard Cotton, Health & Safety Laboratory||
Blood Sweat and Urine
Richie Cotton is a data scientist who spent six years working at the Health and Safety Laboratory. In this talk he recounts his job swap with a chemist, and tells you what he learnt from the experience. The talk includes:
|1 February||Dr Christ Sutton, University of Bradford||
Molecular complexity of collagens – new opportunities for proteomics and chemometrics
As part of a breast cancer proteomics study, a number of collagens were identified, some of which were increased in tumours compared to normal breast tissue. The proteomics data revealed an extensive array of peptides which defined two-dimensional heterogeneity, in degree and location of hydroxyproline modification, within collagen structure. The data provided a census of hydroxyproline levels using novel definitions for the rate of site occupancy (r) for each peptide isomer and the total site occupancy (t) for each proline residue. Potential applications of the approach in the characterisation of collagens will be discussed.
|25 January||Professor Thomas McLeish, University of Durham||
Medieval Science: Uncovering meaning with an interdisciplinary methodology
A novel interdisciplinary project within the Institute of Medieval and Renaissance Studies at Durham University brings medieval scholars together with practising scientists to work together on important documents from the “13th century renaissance”.
This seminar focuses on two important works by Robert Grosseteste, Franciscan Master at Oxford and Bishop of Lincoln, from the period around 1220. De Luce and De Colore (“On Light” and “On Colour”) give us access to a remarkable medieval mind intent on exploring the scientific structure and function of light, already theologically central to his thought.
|11 January||Dr Oliver Craig, Archaeology, York||
Chemical and isotopic analysis of archaeological pottery – dealing with mixtures through Bayesian inference
Analysis of food residues in ceramic cooking pots is a major field in science based archaeology and has led to some high profile discoveries, such as the earliest evidence for dairying, evidence for Stone Age culinary practices and how hunter-gatherer’s used pottery. State-of-the-art involves comparing the stable carbonisotope ratios of major saturated fatty acids (palmitic and stearic acid) extracted from archaeological pots with authentic modern reference fats. Recently wecompleted the analysis of over 200 pots from a site next to Stonehenge to look at how the people who gathered at this monument used pottery. Now in the final stages of the data analysis we have hit the problem of what to do when different products were mixed in pots (either at the same time or sequentially). This issue has been considered less than you may think considering the field is over 40 years old. We had the idea of using a Bayesian mixing model developedfor interpreting stable isotope data of animal tissues in order to resolve mixtures of different dietary sources (Parnell et al. 2010). This model also is able to cope with concentration dependence of the sources which makes it particularly appealing for our application. Whilst partially successful, the distribution of thesource data means that the model itself might need to bere-designed in order to produce realistic probability density distributions. At the limits of my knowledge (of R and Bayesian models), I am looking for a collaborator in order to re-interpret the data in preparation for publication. Other alternative approaches also welcomed.
Parnell, A., Inger, R., Bearhop, S. & Jackson, A.L. (2010) Source partitioning using stable isotopes: coping with too much variation.PlosOne, 5(3):e9672.