Synthetic biology; Engineering; Philosophy of science; Representation; Modeling
Knuuttila Tarja, Loettgers Andrea (2017), Mathematization in Synthetic Biology: Analogies, Templates and Fictions, in Lenhart Johannes, Carrier Martin (ed.), Springer, Cham, 37-56.
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.
Knuuttila Tarja, Loettgers Andrea (2016), Contrasting Cases: The Lotka-Volterra Model Times Three, in Scholl Raphael, Sauer Tilman (ed.), Springer, Cham, 151-179.
Knuuttila Tarja, Loettgers Andrea (2015), Modelling as Indirect Representation? The Lotka-Volterra Model Revisited, in British Journal for the Philosophy of Science
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.
Weber Marcel (2014), Experimental Modeling in Biology: In Vivo Representation and Stand-Ins as Modeling Strategies, in PHILOSOPHY OF SCIENCE
, 81(5), 756-769.
Knuuttila Tarja, Loettgers Andrea (2014), Varieties of noise: Analogical reasoning in synthetic biology, in STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE
, 48, 76-88.
Knuuttila Tarja, Loettgers Andrea (2014), MAGNETS, SPINS, AND NEURONS: THE DISSEMINATION OF MODEL TEMPLATES ACROSS DISCIPLINES, in MONIST
, 97(3), 280-300.
Knuuttila Tarja, Loettgers Andrea (2013), Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond, in PHILOSOPHY OF SCIENCE
, 80(5), 874-885.
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.
Knuuttila Tarja, Loettgers Andrea, Models as Experimental Objects: Mathematical and Synthetic Modeling in the Study of Genetic Circuits, in Van Fraassen Bas, Peschard Isabelle (ed.), Chicago University Press, Chicago.
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.