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  1. Tarja Knuuttila & Andrea Loettgers (forthcoming). Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond. Philosophical Explorations 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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  2. 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.
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  3. 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 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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  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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  5. 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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  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. 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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  8. 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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  9. 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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  10. Andrea Loettgers (2007). Getting Abstract Mathematical Models in Touch with Nature. Science in Context 20 (1):97.
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