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  1.  5
    Tarja Knuuttila & Andrea Loettgers (2014). Varieties of Noise: Analogical Reasoning in Synthetic Biology. Studies in History and Philosophy of Science Part A 48:76-88.
    The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by (...)
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  2.  10
    Tarja Knuuttila & Andrea Loettgers (2013). Basic Science Through Engineering? Synthetic Modeling and the Idea of Biology-Inspired Engineering. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):158-169.
    Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is (...)
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  3.  32
    Tarja Knuuttila & Andrea Loettgers (2011). Causal Isolation Robustness Analysis: The Combinatorial Strategy of Circadian Clock Research. Biology and Philosophy 26 (5):773-791.
    This paper distinguishes between causal isolation robustness analysis and independent determination robustness analysis and suggests that the triangulation of the results of different epistemic means or activities serves different functions in them. Circadian clock research is presented as a case of causal isolation robustness analysis: in this field researchers made use of the notion of robustness to isolate the assumed mechanism behind the circadian rhythm. However, in contrast to the earlier philosophical case studies on causal isolation robustness analysis (Weisberg and (...)
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  4.  19
    Tarja Knuuttila & Andrea Loettgers, Modeling and Experimenting: The Combinatorial Strategy in Synthetic Biology.
    In which respects do modeling and experimenting resemble or differ from each other? We explore this question through studying in detail the combinatorial strategy in synthetic biology whereby scientists triangulate experimentation on model organisms, mathematical modeling, and synthetic modeling. We argue that this combinatorial strategy is due to the characteristic constraints of the three epistemic activities. Moreover, our case study shows that in some cases materiality clearly matters, in fact it provides the very rationale of synthetic modeling. We will show (...)
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  5.  19
    Andrea Loettgers (2009). Synthetic Biology and the Emergence of a Dual Meaning of Noise. Biological Theory 4 (4):340-356.
    The question is discussed how noise gained a functional meaning in the context of biology. According to the common view, noise is considered a disturbance or perturbation. I analyze how this understanding changed and what kind of developments during the last 10 years contributed to the emergence of a new understanding of noise. Results gained during a field study in a synthetic biology laboratory show that the emergence of this new research discipline—its highly interdisciplinary character, its new technologies and novel (...)
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  6. Tarja Knuuttila & Andrea Loettgers (2011). The Productive Tension : Mechanisms Vs. Templates in Modeling the Phenomena. In Paul Humphreys & Cyrille Imbert (eds.), Models, Simulations, and Representations. Routledge
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  7.  2
    Andrea Loettgers (2007). Getting Abstract Mathematical Models in Touch with Nature. Science in Context 20 (1):97.
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  8.  5
    Tarja Knuuttila & Andrea Loettgers (forthcoming). Modelling as Indirect Representation? The Lotka–Volterra Model Revisited. British Journal for the Philosophy of Science:axv055.
    Is there something specific about modelling that distinguishes it from many other theoretical endeavours? We consider Michael Weisberg’s thesis that modelling is a form of indirect representation through a close examination of the historical roots of the Lotka–Volterra model. While Weisberg discusses only Volterra’s work, we also study Lotka’s very different design of the Lotka–Volterra model. We will argue that while there are elements of indirect representation in both Volterra’s and Lotka’s modelling approaches, they are largely due to two other (...)
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  9.  15
    Tarja Knuuttila & Andrea Loettgers (2013). Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond. Philosophy of Science 80 (5):874-885.
    Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic modeling as (...)
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  10.  27
    Andrea Loettgers (2007). Model Organisms and Mathematical and Synthetic Models to Explore Gene Regulation Mechanisms. Biological Theory 2 (2):134-142.
    Gene regulatory networks are intensively studied in biology. One of the main aims of these studies is to gain an understanding of how the structure of genetic networks relates to specific functions such as chemotaxis and the circadian clock. Scientists have examined this question by using model organisms such as Drosophila and mathematical models. In the last years, synthetic models—engineered genetic networks—have become more and more important in the exploration of gene regulation. What is the potential of this new approach (...)
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  11.  4
    Jane Maienschein, Manfred Laubichler & Andrea Loettgers (2008). How Can History of Science Matter to Scientists? Isis: A Journal of the History of Science 99:341-349.
    History of science has developed into a methodologically diverse discipline, adding greatly to our understanding of the interplay between science, society, and culture. Along the way, one original impetus for the then newly emerging discipline—what George Sarton called the perspective “from the point of view of the scientist”—dropped out of fashion. This essay shows, by means of several examples, that reclaiming this interaction between science and history of science yields interesting perspectives and new insights for both science and history of (...)
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  12.  1
    Tarja Knuuttila & Andrea Loettgers (forthcoming). Model Templates Within and Between Disciplines: From Magnets to Gases – and Socio-Economic Systems. European Journal for Philosophy of Science:1-24.
    One striking feature of the contemporary modelling practice is its interdisciplinary nature. The same equation forms, and mathematical and computational methods, are used across different disciplines, as well as within the same discipline. Are there, then, differences between intra- and interdisciplinary transfer, and can the comparison between the two provide more insight on the challenges of interdisciplinary theoretical work? We will study the development and various uses of the Ising model within physics, contrasting them to its applications to socio-economic systems. (...)
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  13.  3
    Tarja Knuuttila & Andrea Loettgers, Synthetic Modeling and the Functional Role of Noise.
    In synthetic biology the use of engineering metaphors to describe biological organisms and their behavior has become a common practice. The concept of noise provides one of the most compelling examples of such transfer. But this notion is also confusing: While in engineering noise is a destructive force perturbing artificial systems, in synthetic biology it has acquired an additional functional meaning. It has been found out that noise is an important factor in driving biological processes such as gene regulation, development, (...)
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  14.  4
    Tarja Knuuttila & Andrea Loettgers (2013). Synthetic Biology as an Engineering Science? Analogical Reasoning, Synthetic Modeling, and Integration. In Hanne Andersen, Dennis Dieks, Wenceslao González, Thomas Uebel & Gregory Wheeler (eds.), New Challenges to Philosophy of Science. Springer Verlag 163--177.
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