Biology and Environment
Strand leader: Prof Adrian Currie and Prof Angela Cassidy
Our species has always intervened, constructed, and adapted the environmental and biological worlds we find ourselves in to our needs: we have domesticated animals, transformed the botanical to the agricultural, and managed forests, plains and rivers. Today, our technological, social, and political capacities to make such interventions have become increasingly complex and opaque, while also becoming increasingly powerful and global, as exemplified by climatic shifts and the modification of organisms through large-scale genetic alteration. Never has it been more important to understand the relationship between the contents and methods of scientific research and the future of human societies, and life on this planet.
To these issues Egenis’ Biology & Environment Stream brings a much-needed perspective informed by the anthropology, history, sociology and philosophy of science. Ranging from reflection on the relationships between humans and non-humans (including animals, plants and microbes), to investigating how systems of intervention interact with social goals and scientific knowledge, to critiquing how human-environment relationships are structured, to examining the conceptual and metaphysical foundations of ideas within the biological and environmental sciences, our work denies that these global problems can be tackled using purely technological or technocratic machinery. Instead, the stream brings a pluralistic, multi-disciplinary and mixed-methods approach to these issues, with a focus on integrating the best of the biological and ecological science with humanistic and social-scientific perspectives.
HUGERA – HUMAN GENOMICS WITHOUT RACISM
PI: Dr Celso Neto
Postdoctoral Fellows: tbd
Lead Institution: University of Exeter
Funding awarded: €1,499,979.00
Sponsor(s): European Union's Horizon ERC Starting Grant 2024
About the research
HUGERA (2025-2029) helps scientists conduct ethically sound research in the field of Human Genomics.
On average, humans are 99.9% identical in their DNA. While the genetic difference among humans is vanishingly small, it is not inconsequential. This difference might help scientists to better understand human evolution and health, which could lead to unprecedented advancements in medicine and care. To unlock these benefits, the field of Human Genomics has received significant public and private funding in recent decades.
However, science does not happen in a silo and scientists worry about the repercussions of studying human differences. During the 19th and early 20th centuries, these studies were driven by empirically flawed methodologies, racism, and unethical conduct. Today, scientists recognize the need for diligent work to ensure that history is not repeated. Geneticists frequently work alongside ethicists, social scientists, and marginalized populations to ensure their research is ethically and empirically sound.
HUGERA project will develop a framework that maps out the ethically sensitive aspects of contemporary genomics research. It will identify the potential risks that could hamper science and lead to harm. Hence, the framework will offer key information for designing ethical recommendations, best practices, and policy decisions. The framework will also motivate new scientific tools, such as new ways to visualize human genetic variation.
HUGERA is innovative. The project uses conceptual resources from the philosophy of science and race to develop a framework that is conceptually robust but also practice oriented. HUGERA combines those philosophical resources with empirical, qualitative methods from the social sciences.
The project has three main phases.
First, we will develop an epistemological account of human genomics research, characterizing how data, models, theories, and experiments interrelate to generate knowledge about human genetic variation.
Second, we will understand the ethical risks that scientists and other stakeholders worry about in that knowledge generation process.
Third, we will create a systematic classification of risks that arise at different stages of human genetic variation research. This work will enable us to identify the most ethically sensitive aspects of that research and what can be done to safeguard them. These safeguards and recommendations will be available to scientists and contribute to the goal of ethically sound human genomics.
Throughout its phases, HUGERA will contribute to important philosophical themes. For instance, we will examine how knowledge is produced and justified in value-laden contexts. While philosophers have discussed different aspects of knowledge production and values in science, a systematic theory concerning the ethics and epistemology of human genomics is lacking. This theory integrates philosophical discussions in data-centric biology, values in science, and race theory. We enrich these discussions with a long and insightful literature on human genetic variation from anthropology, sociology, and STS.
For more information, please check the website of the project to be available in the summer of 2025. In the meantime, you can drop me an e-mail via C.Alves-Neto@exeter.ac.uk
Using Pollinator Pathmaker and citizen science to strengthen pollinator conservation
Sponsor(s): UKRI Cross Council Pilot
Total award: 1,095,526, the net value is 876,821.
PI: Chris Kaiser-Bunbury (University of Exeter, Cornwall).
CoI: Professor John Dupre (University of Exeter), Jane Calvert (University of Edinburgh).
Pollinator Pathmaker is an artwork by Dr Alexandra Daisy Ginsberg that uses an algorithm to generate unique planting designs that prioritise pollinators’ needs over human aesthetic tastes.
Originally commissioned by the Eden Project in Cornwall in 2021, the general public can access the artist’s online tool (www.pollinator.art) to design and plant their own living artwork for local pollinators.
Plant Phenome
1 December 2019 - 30 November 2021
PI/s in Exeter: Professor John Dupré
Research partners: Dr. Özlem Yılmaz
Funding awarded: 212933 Euro
Sponsor(s): European Commission
Project webpage: Plant Phenome
About the research
Plant Phenomics has been growing and advancing rapidly in the last decades. Two important facts drive this growth:
1) the need for growing more food with better nutrition quality for the world population which has been rising enormously along with increasing social inequalities;
2) the need for better understanding of plant-environment interaction so improving the ability to produce crops better adapted to coping with uncertainties in future climate.
This project aims to provide a detailed philosophical analysis of the main concepts and methodologies in phenome research, specifically in plant science. Main methodology will be traditional philosophical analysis both in philosophy and scientific literature. Genotype, phenotype and environment are concepts traditionally at the core of theoretical biology and philosophy of biology. Philosophy of biology has paid far more attention to genotypes than phenotypes, and this project will make an important contribution to redressing this balance.
The ReAlChem - Responsible Innovation Project
1 August 2017 - 31 July 2019
PI/s in Exeter: Professor Susan Molyneux-Hodgson
Research partners: Green Biologics Ltd (project lead, Dr Liz Johnson); BioExtractions (Wales) Ltd; Dynamic Extractions Ltd
Sponsor: Innovate UK
About the research
Understanding responsible innovation in practice: an analysis of the manufacture of renewable alternative chemicals
Researchers: Dr Sally Atkinson and Dr Achim Rosemann
The ‘Manufacture of renewable alternative chemicals’ (ReAlChem) project began in August 2017, is funded by InnovateUK, and is a unique collaboration between social scientists and a biotechnology company and its associates. As part of the project, a team of social scientists will conduct research on responsible innovation in tandem with the company's technical research.
ReAlChem-RI aims to investigate responsible innovation ideas in the wider context of UK industrial biotech. The project aims are:
- to assess different perspectives on notions of responsibility among diverse stakeholders
- to understand key challenges experienced by the industrial biotechnology sector, especially in relation to the social dimensions of the bioeconomy
- to understand how responsible innovation ideas are translated into actual practices
- to contribute to the further development of responsible innovation practices
To achieve these aims, we are conducting interviews with industry practitioners, policy actors and other key stakeholders, as well as documentary analysis and ethnographic research in biotech companies and research labs. Our project partners in the ReAlChem Project are four mid-size biotech companies: Green Biologics, DynamicExtration, BioExtraction, and Keit. However, we also interact with corporate staff and managers, scientists, regulators, industry bodies, funding bodies as well as civil societal organizations and NGOs from all over the UK. Findings from our project will be shared with participants and disseminated to relevant parties such as the UKRI (BBSRC, EPSRC, iUK), the Parliamentary Office for Science and Technology, the UK Industrial Biotech Leadership Forum and others.
You can find out more about the ReAlChem project here.
Representing Biology as Process
1 January 2017 - 1 January 2020
PI/s in Exeter: Professor John Dupré
CI/s in Exeter: Dr Gemma Anderson
Research partners: Dr James Wakefield, Biosciences, University of Exeter
Sponsor(s): AHRC
Project webpage: Representing Biology as Process
About the research
The question – whether we should think of the world as consisting of entities statically defined by essential properties (i.e. in philosophical jargon, “substances”), or as processes, that undergo and persist precisely because of change – is a fundamental metaphysical dichotomy, debated since the pre-Socratics. Since the rise of atomism in the seventeenth century the substance view has dominated scientifically grounded philosophy. John Dupré’s ERC-funded project, A Process Ontology for Contemporary Biology, develops the thesis that for biology, at least, this has been a profound mistake (Dupré 2012: Nicholson and Dupré, in press). Dupré argues that living systems are always dynamic at multiple spatial and temporal scales and their persistence, far from being merely the continued possession of essential properties, is the result of the finely articulated interplay of multiple processes.
Visual representation is essential both to the practice and the communication of science. However, whereas drawing in the past played a central role in fields such as morphology and embryology, the rise of photographic and digital technologies and the growing emphasis on molecules as opposed to whole organisms have increasingly marginalized drawing practices. Therefore, a serious problem faced in the development of a fully processual biology is that most visual representation strongly suggests a realm of static things. For example, the presentation of an organism will be of a particular developmental ‘stage’, typically the mature adult, which confounds the fact that this is a momentary temporal stage of the developmental process. Even where representation of something as plainly dynamic as metabolism, for example, will include arrows representing time, the natural reading will be of transitions between a fixed array of things (instances of chemical kinds). Moreover, while visual images or ‘visual explanations’ (Tufte 1997) in science depend on a variety of graphic devices ranging from the use of video, and photography to the use of computational graphic software, simulation and hand-drawing, these means of making images largely depend on mechanistic models (for, or of, their objects) which are already intertwined with their methods of production.
The decline of drawing in scientific practice is epitomised by Wakefield’s research field, cell division and mitosis. Whereas 20 years ago, as a PhD student, his learning was centred around direct participation, through microscope-based observation and drawing of cells, his own PhD students are now further removed, watching 2D representations of cells on computer screens and printing out screen-shots. For the last 5 years, his interest in this distinction has grown, leading to an exploratory collaboration with the PI and, through this application, the Co-I. Anderson’s work over a number of years has highlighted the epistemic costs of the decline of graphic skills in the Life Sciences. She has researched the ways in which scientists have used drawing as a way of developing deep insights into their subject matters, and in her own practice, under the rubric of ‘Isomorphology’, she has developed classificatory methods that highlight formal parallels cutting across the traditional boundaries of animal, mineral and vegetable. This work has been carried out in collaboration with a variety of scientists and museum curators and has resulted in residencies, exhibitions, talks and workshops. Building on the Isomorphology project, her more recent work, guided in part by extensive discussions with Dupré, has begun to explore ways of representing biological process, under the new rubric of Isomorphogenesis.
In line with the growing interest in process-centred understandings of biology, the present project will address the need for novel image-making practices to provide more intuitively dynamic representations of living systems through an innovative collaboration between art, biology and philosophy.
Organisms and Us: How Living Things Help Us to Understand Our World
1 January 2016 - 30 December 2020
PI/s in Exeter: Professor Sabina Leonelli
Research partners: Professor Rachel Ankeny (University of Adelaide) (Project Lead); Professor Michael Dietrich (Arizona State University)
Funding awarded: £ 12,500
Sponsor(s): Australian Research Council
About the research
How do researchers learn from and 'think with' non-human organisms? This project seeks to develop a comprehensive historical and philosophical exploration of the changing roles and understandings of research with organisms in 20th and early 21st century science. Advances in the content and technologies in the biological and biomedical sciences have resulted in new understandings of what we can know and learn from organisms, particularly with regard to human functioning, health, and well-being, yet we have no integrated scholarship examining these developments across a range of fields. This project seeks to produce useful scholarship which is relevant for humanities scholars, scientists, clinicians, and policymakers.
The DETOX-Responsible Innovation Project
1 January 2016 - 1 January 2021
PI/s in Exeter: Professor Susan Molyneux-Hodgson
Research partners: Academic research partners: Universities of York (PI: Prof. Gavin H. Thomas); Sheffield, Nottingham and Cambridge Industrial partnerships: Lucite International, Green Biologics, Ingenza, and CPI.
Sponsor(s): BBSRC
About the research
Project DETOX was launched in 2016 through the award of a 5-year Translation Grant through the Industrial Biotechnology Catalyst (Innovate UK, BBSRC, EPSRC). It is led from the Department of Biology at the University of York by Dr. Gavin H. Thomas with collaborators at the Universities of Nottingham, Sheffield, Exeter and Cambridge. Working with industrial partners Lucite, Green Biologics, Ingenza and CPI, the team aim to understand the physiological changes that microbes use to enable survival when exposed to bio-manufacturing chemicals that are toxic to them. DETOX solutions will then provide engineered chassis strains for its key partners for use in bioproduction to yield higher final titres of product – a problem that currently limits the financial viability of some processes.
Co-investigator Professor Susan Molyneux-Hodgson and Research Associate Sally Atkinson from the University of Exeter are in charge of the Responsible Research and Innovation component of the project.
A Process Ontology for Contemporary Biology (PROBIO)
1 May 2013 - 30 April 2018
About the research
This project aims, first, to rethink central issues in the philosophy of biology by elaborating an ontology for biology that takes full account of the processual nature of living systems. Starting with a careful survey of existing positions, especially Whitehead and the American Pragmatists, the goal will be to develop a concept of process adequate for addressing the multiple levels of interacting processes at different time scales characteristic of living systems. The concept of a stable biological thing will be analysed as a stabilised process relative to an appropriate time scale, and this conception should make possible a better understanding of familiar biological pluralisms (about genes, organisms, species, etc..) in terms of different ways in which distinct scientific practices intersect with biological processes.
Second, the concept of process developed will be used to rethink some further highly topical philosophical issues in contemporary philosophy of biology (and philosophy of science generally). The project will explore the potential of a processual perspective to provide a critique of the widely discussed recent versions of mechanism. The latter have been deployed to offer accounts of explanation and, eventually, causation. Such accounts will be assessed for the possibility of revision in the light of modifications suggested by a processual perspective. The project will explore generally the relevance of this perspective to influential contemporary accounts of causation and explanation.
Finally the project will apply the preceding ideas to several highly active and important areas of contemporary biology: systems biology, synthetic biology, and microbiology. These investigations, in fact, will be carried on in parallel with the more general philosophical enquiries, with the idea that the two will be mutually informative: the philosophical analyses will not only be applied to scientific concepts, but will also themselves be evaluated for their relevance to real cutting edge biology. This evaluation will be guided by interaction with scientific practitioners and an expert Advisory Board, as well as text-based study. The project aims to be of direct relevance to both philosophy and science.
Post Docs on the project
Workshops organised as part of the project:
“Process Philosophy of Biology”
20-21 November 2014, Egenis, Exeter
Organised by John Dupré and Daniel Nicholson
19-20 November 2015, Egenis, Exeter
Organised by John Dupré and Stephan Güttinger
“Organisms: Living Systems and Processes”
9-10 March 2016, Egenis
Organised by John Dupré and Anne Sophie Meincke
Workshop associated with the project:
2-3 June 2016, Institute of Philosophy, London
Organised by Anne Sophie Meincke and John Dupré
Funded by the Institute of Philosophy, London (annual conference grant 2015/16), by the British Society of Philosophy of Science and by the European Research Council through the PROBIO research project
Key Output:
Nicholson, D.J. & Dupré, J. (Eds.): Everything Flows. Towards a Processual Philosophy of Biology, Oxford: Oxford University Press, 1st May 2018. Table of Contents
Introduction by John Dupré and Daniel Nicholson: “A Manifesto for a Processual Philosophy of Biology”
Chapters by project members:
• John Dupré (with Marta Bertolaso): “A Processual Perspective on Cancer”
• Stephan Güttinger: “A Process Ontology for Macromolecular Biology”.
• Anne Sophie Meincke: “Persons as Biological Processes. A Bio-Processual Way Out of the Personal Identity Dilemma”
• Daniel Nicholson: “Reconceptualizing the Organism: From Complex Machine to Flowing Stream”
Other Outputs:
John Dupré:
“Metaphysics of metamorphosis.” Aeon. Published online, November 30, 2017.
“The Metaphysics of Evolution.” Interface Focus. Published online, August 18, 2017.
(With Cordelia Fine and Daphna Joel). “Sex-Linked Behavior: Evolution, Stability, and Variability.” Trends in Cognitive Sciences, 2017, 21 (9): 666–673.
"Postgenomic Perspectives on Sex and Gender." In How Biology Shapes Philosophy: New Foundations for Naturalism, edited by David Livingstone Smith, Cambridge: Cambridge University Press, 2016: 227-246.
“A Process Ontology for Biology.” Physiology News, 2015, 100: 32-34.
“The Role of Behaviour in the Recurrence of Biological Processes.” Biological Journal of the Linnean Society, 2014, 112: 306–314.
"Animalism and the Persistence of Human Organisms", The Southern Journal of Philosophy, (Spindel Supplement), 2014, 52: 6-23.
“Living Causes.” Proceedings of the Aristotelian Society, Supplementary Volume, 2013, 87: 19-38.
Stephan Güttinger:
(With John Dupré). “Viruses as living processes.” Studies in History and Philosophy of Biological and Biomedical Sciences, 2016, 59: 109-116.
“Trust in Science: CRISPR-Cas9 and the Ban on Human Germline Editing”. Science and Engineering Ethics. Published online, June 26, 2017. https://doi.org/10.1007/s11948-017-9931-1
(With John Dupré). “Genomics and Postgenomics.” The Stanford Encyclopedia of Philosophy (Winter 2016 Edition), Edward N. Zalta (ed.).
Anne Sophie Meincke:
(With John Dupré). (Ed.): Biological Identity. Perspectives from Metaphysics and the Philosophy of Biology. Milton Park, Abingdon, Oxon: Routledge (History and Philosophy of Biology Series), forthcoming. (with contributions by Ellen Clarke, John Dupré, Arantza, Etxeberria, Adam Ferner, Philippe Huneman, Anne Sophie Meincke, Alvaro Moreno, Matteo Mossio, David Oderberg, Eric T. Olson, Paul F. Snowdon, Denis Walsh, David Wiggins)
“Bio-Agency and the Possibility of Artificial Agents.” In Philosophy of Science - Between the Natural Sciences, the Social Sciences, and the Humanities. Selected Papers from the 2016 conference of the German Society of Philosophy of Science, edited by Alexander Christian et al. Dordrecht: Springer (European Philosophy of Science Association Series), forthcoming (February 19, 2018) (double-blind peer reviewed).
“How to stay the same while changing. Personal Identity as a Test Case for Reconciling ‘Analytic’ and ‘Continental’ Philosophy Through Process Ontology.” In Analytic-Bridge-Continental + (ABC+) Process Philosophy, edited by Robert Booth. Berlin et al.: de Gruyter (Process Thought Series), forthcoming.
“Haben menschliche Embryonen eine Disposition zur Personalität?” (“Do Human Embryos Have a Disposition to Personhood?”) In Der manipulierbare Embryo, edited by Martin Hähnel, Markus Rothhaar and Roland Kipke. Münster: Mentis, forthcoming (December 2017): 147-171. http://www.mentis.de/index.php?id=00000005&article_id=00000028&category=&book_id=00000952&SID=ccd12fb3d0489632ad2e4115d12b5e57
“Personale Identität ohne Persönlichkeit? Anmerkungen zu einem vernachlässigten Zusammenhang.” (“Personal Identity Without Personality? Reflections on a Neglected Relation.”) Philosophisches Jahrbuch, 2016, 123 (1): 114-145.
“Potentialität und Disposition in der Diskussion über den Status des menschlichen Embryos: Zur Ontologie des Potentialitätsarguments.” (“Potentiality and Disposition in the Debate on the Status of the Human Embryo: On the Ontology of the Argument from Potentiality.”) Philosophisches Jahrbuch, 2015, 122 (2): 271-303.
Daniel Nicholson:
(With Richard Gawne). “Neither logical empiricism nor vitalism, but organicism: what the philosophy of biology was”. History and Philosophy of the Life Sciences, 2015, 37(4): 345-381.
“The Machine Conception of the Organism in Development and Evolution: A Critical Analysis”. Studies in History and Philosophy of Biological and Biomedical Sciences, 2014, 48 (B): 162-174.
“The Return of the Organism as a Fundamental Explanatory Concept in Biology”. Philosophy Compass, 2014, 9 (5): 347-359.
(With Richard Gawne). Rethinking Woodger’s Legacy in the Philosophy of Biology. Journal of the History of Biology, 2014, 47 (2): 243-292.
Questioning the Tree of Life
1 October 2008 - 30 September 2010
Project webpage: Questioning the Tree of Life
About the research
The Questioning the Tree of Life (QtoL) network brought together biologists in a range of fields, philosophers and historians to integrate a variety of disciplinary perspectives on the conceptual challenges inherent in the Darwinian conception of the Tree of Life (ToL). The ToL represents the evolutionary relationships amongst organismal lineages as a single ever-bifurcating pattern. The primary objective of the network was to clarify the assumptions of Tree of Life thinking, examine the alternatives, and develop scientifically grounded, philosophical approaches to novel ways of thinking about and representing the evolution of organismal lineages.
New directions in biology: Metagenomics and microbiology
1 March 2006 - 29 May 2008
PI in Exeter: Professor John Dupré
CI in Exeter: Dr Maureen O'Malley
Funding awarded: £ 97,208
Sponsor: AHRC
Project webpage: New directions in biology: Metagenomics and microbiology
About the research
Molecular biology is developing at a dizzying pace and suggests radical reinterpretations of some fundamental issues in our understanding of biology and life. This project aimed to make these developments more accessible to non-specialists and to explore some of their implications.