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Biological Knowledge Through Modeling and Engineering

English title Biological Knowledge Through Modeling and Engineering
Applicant Weber Marcel
Number 146772
Funding scheme Project funding
Research institution Département de Philosophie Faculté des Lettres Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Philosophy
Start/End 01.07.2013 - 30.06.2017
Approved amount 324'803.00
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Keywords (5)

Synthetic biology; Engineering; Philosophy of science; Representation; Modeling

Lay Summary (German)

Lead
Dieses Projekt untersucht die Praxis des Konstruierens, Manipulierens und Anwendens von Modellen anhand von aktuellen Beispielen aus der synthetischen Biologie. Im Mittelpunkt stehen dabei die synthetischen Modellsysteme selbst, die in diesem Forschungszweig hergestellt werden (z.B. Bakterien mit neuen Eigenschaften). Diese haben nicht bloss eine technologische Funktion, sondern führen darüber hinaus auch zu neuen Erkenntnissen. Wir möchten herausfinden, wie das möglich ist.
Lay summary

Synthetische Modelle sind komplexe epistemische Objekte. Unter  Verwendung von biologischen Komponenten und Konzepten, Techniken und Methoden aus der Biologie, Physik sowie Computer- und Ingenieurswissenschaften werden Modelle konstruiert, die sich durch ihren hohen Grad an Interdisziplinarität auszeichnen.  Neben dieser Interdisziplinarität  zeichnen sich synthetische Modelle durch zwei sich überlappende Anwendungsbereiche aus. In einem eher basisorientierten Ansatz werden synthetische Modelle zur Exploration von möglichen design principles in biologischen Systemen verwendet. Dieser Ansatz ist über Konzepte, Techniken, Methoden und Praktiken mit einem eher anwendungsorientiertem Ansatz verknüpft, in dem synthetische Modelle  als  mögliche Produktionseinheiten von Medikamenten, Impfstoffen und Biotreibstoffen konstruiert werden.  Im vorliegenden Projekt steht die Frage nach der Beziehung zwischen den beiden Anwendungsbereichen synthetischer Modelle und deren epistemischer Status im Mittelpunkt. Die Einbeziehung der bislang in den Diskussionen um die Modellierungspraxis in der Wissenschaftsphilosophie vernachlässigten ingenieurswissenschaftlichen Seite wird  zu einem vollständigeren Bild der Modellierungspraxis führen. Darüberhinaus werden mehr spezifisch Beiträge zu der zum Teil sehr kontrovers verlaufenden Diskussionen in Politik und Gesellschaft über mögliche Potentiale und Gefahren des neuen Wissenschaftszweiges geleistet.

Direct link to Lay Summary Last update: 17.04.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Mathematization in Synthetic Biology: Analogies, Templates and Fictions
Knuuttila Tarja, Loettgers Andrea (2017), Mathematization in Synthetic Biology: Analogies, Templates and Fictions, in Carrier Martin, Lenhart Johannes (ed.), Springer, Cham, 37-56.
Model templates within and between disciplines: from magnets to gases - and socio-economic systems
Knuuttila Tarja, Loettgers Andrea (2016), Model templates within and between disciplines: from magnets to gases - and socio-economic systems, in EUROPEAN JOURNAL FOR PHILOSOPHY OF SCIENCE, 6(3), 377-400.
Contrasting Cases: The Lotka-Volterra Model Times Three
Knuuttila Tarja, Loettgers Andrea (2016), Contrasting Cases: The Lotka-Volterra Model Times Three, in Sauer Tilman, Scholl Raphael (ed.), Springer, Cham, 151-179.
Modelling as Indirect Representation? The Lotka-Volterra Model Revisited
Knuuttila Tarja, Loettgers Andrea (2015), Modelling as Indirect Representation? The Lotka-Volterra Model Revisited, in British Journal for the Philosophy of Science, 1-30.
Nicolas Rashevsky and Alfred Lotka: Different modelling strategies in the beginning of mathematical biology in the early 20th century
Hoff Kjeldsen Tinne, Loettgers Andrea (2015), Nicolas Rashevsky and Alfred Lotka: Different modelling strategies in the beginning of mathematical biology in the early 20th century, in Oberwolfach Report , 47, 2779-2783.
Experimental Modeling in Biology: In Vivo Representation and Stand-Ins as Modeling Strategies
Weber Marcel (2014), Experimental Modeling in Biology: In Vivo Representation and Stand-Ins as Modeling Strategies, in PHILOSOPHY OF SCIENCE, 81(5), 756-769.
Varieties of noise: Analogical reasoning in synthetic biology
Knuuttila Tarja, Loettgers Andrea (2014), Varieties of noise: Analogical reasoning in synthetic biology, in STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE, 48, 76-88.
MAGNETS, SPINS, AND NEURONS: THE DISSEMINATION OF MODEL TEMPLATES ACROSS DISCIPLINES
Knuuttila Tarja, Loettgers Andrea (2014), MAGNETS, SPINS, AND NEURONS: THE DISSEMINATION OF MODEL TEMPLATES ACROSS DISCIPLINES, in MONIST, 97(3), 280-300.
Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond
Knuuttila Tarja, Loettgers Andrea (2013), Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond, in PHILOSOPHY OF SCIENCE, 80(5), 874-885.
’Basic Science Through Engineering: Synthetic Modeling and the Idea of Biology-inspired Engineering
Knuuttila Tarja, Loettgers Andrea (2013), ’Basic Science Through Engineering: Synthetic Modeling and the Idea of Biology-inspired Engineering, in Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 158-169.
Models as Experimental Objects: Mathematical and Synthetic Modeling in the Study of Genetic Circuits
Knuuttila Tarja, Loettgers Andrea, Models as Experimental Objects: Mathematical and Synthetic Modeling in the Study of Genetic Circuits, in Peschard Isabelle, Van Fraassen Bas (ed.).

Collaboration

Group / person Country
Types of collaboration
Dr. Tarja Knuuttila/University of Helsinki Finland (Europe)
- Publication
Prof. Sven Panke/BSSE-ETHZ Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. David Sprinzak/Tel Aviv University Israel (Asia)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Michael Elowitz/California Institute of Technology United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Jordi Gracia-Ojalvo/BarcelonaTECH Spain (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Nancy Nersessian/Georgia Institute of Technology, Atlanta United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Understanding Life Talk given at a conference Why multiple definitions of life may (for the moment) be unavoidable 26.06.2016 Bern, Switzerland Loettgers Andrea;
(Re)Engineering Biology: The Emerging Engineering Paradigm in Biomedical Engineering, Systems Biology, and Synthetic Biology Talk given at a conference Abstraction and model construction in systems and synthetic biology 15.04.2016 Pittsburgh, United States of America Loettgers Andrea;
4th Biennieal Conference of European Philosophy of Science Association (EPSA2014) Talk given at a conference Concrete Fictions: Synthetic Genetic Circuits in the Study of Biological Organization 28.08.2015 Helsinki, Finland Loettgers Andrea;
Panel Discussion Talk given at a conference Philosophy of Biology 26.06.2015 Bern, Switzerland Loettgers Andrea;
Chance at the Heart of the Cell Talk given at a conference Varieties of Noise 27.04.2015 Paris, France Loettgers Andrea;
Biology Club, University of Geneva Individual talk Models and Experiments in Syntheetic Biology 04.06.2014 Geneva, Switzerland Weber Marcel;
Modeling/Experimenting? The Synthetic Strategy in Circadian Clock Research Talk given at a conference Philosophy of Scientific Experimentation 4 (PSX4) 11.04.2014 Pittsburgh, United States of America Loettgers Andrea;
Philosophy Department Individual talk Varieties of Noise: Analogical Reasoning in Synthetic Biology 27.11.2013 Copenhagen, Denmark Loettgers Andrea;
The Philosophy of Historical Case Studies Talk given at a conference The Lotka-Volterra Model Revisited 21.11.2013 Bern, Switzerland Loettgers Andrea;
8th Conference in the International Conference, Series "Causality in the Sciences" Talk given at a conference Is Causal Inference All You Need in Experimental Biology? 01.07.2013 Paris, France Weber Marcel;


Self-organised

Title Date Place
Toward a More Integrative View on Modeling, Experimenting, and Simulating 27.06.2014 Genève, Switzerland

Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions Synthetische Organismen als wissenschaftliche Modelle International 2015

Abstract

This project investigates the interplay of two kinds of scientific activity, modeling and engineering, in the production of biological knowledge. While modeling in all its guises (mathematical, computational, physical) has been subject to much debate in the philosophy of science, the engineering dimension has been largely neglected, probably because it is thought to be only of technological importance. However, there are clear signs that this dimension is becoming more important in biology, as witnessed for instance (but not only) in the recent move towards systems biology and synthetic biology. Our previous research strongly indicates that, to an increasing extent, biological engineering is not only a means of advancing technology or applied science, but also an important epistemic tool that complements and extends both the traditional experimental approaches as well as the standard modeling techniques in important and fruitful ways. At the same time, the use of engineering to advance biological knowledge raises many profound philosophical questions, not the least of which is how this approach is able to deliver reliable knowledge of some real world systems, given their “borrowed” and highly artificial nature. In this project we want to make a contribution towards an epistemology of biological modeling and engineering by engaging both in philosophical analysis and the close observation of scientific practice.Our first guiding hypothesis is that biological engineering and modeling are closely interconnected and are driven by the often cross-disciplinary transfer of representational tools, computational templates, research materials and modeling methods, which are locally adapted to various tasks, depending on the discipline in question. Our second guiding hypothesis is that the artificial living systems that biologists engineer in increasing numbers are used to represent and simulate certain kinds of natural processes.Our research plan consists of three parts. The first part of the project, Module 1, will consist of a detailed study of the transfer and adoption of concepts, computational templates, research materials and modeling methods in synthetic biology. We are going to examine how the introduction of new technologies and modeling methods functioned as an entry point for concepts originating in engineering, physics and chemistry into synthetic biology. In Module 2, we will examine how scientists choose between different concepts, modeling methods, research materials and computational templates and how these become embedded in and adjusted to their new environment. This will be the subject of a detailed lab study in the synthetic biology lab of Prof. Panke at the ETH-BSSE (Swiss Federal Institute of Technology Department of Biosystems Science and Engineering) in Basel, Switzerland. Module 3 addresses the epistemological question of representation, in other words, how models are related to the world. The combined use of mathematical models, model organisms and synthetic systems that is characteristic for synthetic biology makes it difficult to see what exactly is being represented in this kind of biological knowledge. We plan to approach this question by drawing on the copious philosophical literature on scientific modeling and representation. One approach that we will examine critically is based on the idea that scientific modeling is a form of fiction. Perhaps the synthetic systems engineered by biologists can be viewed as concrete fictions that, much like literary fictions, are intended to represent a typical kind of situation or development except that the players are biological entities instead of people. Furthermore, we want to examine what kind of properties or relations are represented in different kinds of biological models, including synthetic biological systems.
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