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  1. Strategies of Explanatory Abstraction in Molecular Systems Biology.Nicholaos Jones - 2018 - Philosophy of Science 85 (5):955-968.
    I consider three explanatory strategies from recent systems biology that are driven by mathematics as much as mechanistic detail. Analysis of differential equations drives the first strategy; topological analysis of network motifs drives the second; mathematical theorems from control engineering drive the third. I also distinguish three abstraction types: aggregations, which simplify by condensing information; generalizations, which simplify by generalizing information; and structurations, which simplify by contextualizing information. Using a common explanandum as reference point—namely, the robust perfect adaptation of chemotaxis (...)
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  • From physics to biology: physicists in the search for systemic biological explanations.Leyla Mariane Joaquim, Olival Freire Jr & Charbel N. El-Hani - 2019 - European Journal for Philosophy of Science 9 (2):30.
    This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary skills. Quantitative scientists (...)
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  • From physics to biology: physicists in the search for systemic biological explanations.Leyla Mariane Joaquim, Olival Freire Jr & Charbel N. El-Hani - 2019 - European Journal for Philosophy of Science 9 (2):1-32.
    This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary skills. Quantitative scientists (...)
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  • ‘Extreme’ organisms and the problem of generalization: interpreting the Krogh principle.Sara Green, Michael R. Dietrich, Sabina Leonelli & Rachel A. Ankeny - 2018 - History and Philosophy of the Life Sciences 40 (4):65.
    Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that “for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied”. Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has (...)
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  • From physics to biology: physicists in the search for systemic biological explanations.Charbel N. El-Hani, Olival Freire Jr & Leyla Mariane Joaquim - 2019 - European Journal for Philosophy of Science 9 (2):1-32.
    This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary skills. Quantitative scientists (...)
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  • Functional explanation and the problem of functional equivalence.James DiFrisco - 2017 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 65:1-8.
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  • How do networks explain? A neo-hempelian approach to network explanations of the ecology of the microbiome.José Díez & Javier Suárez - 2023 - European Journal for Philosophy of Science 13 (3):1-26.
    Despite the importance of network analysis in biological practice, dominant models of scientific explanation do not account satisfactorily for how this family of explanations gain their explanatory power in every specific application. This insufficiency is particularly salient in the study of the ecology of the microbiome. Drawing on Coyte et al. (2015) study of the ecology of the microbiome, Deulofeu et al. (2021) argue that these explanations are neither mechanistic, nor purely mathematical, yet they are substantially empirical. Building on their (...)
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  • Revisiting generality in the life sciences: Systems biology and the quest for general principles.Sara Green - unknown
    Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes a different (...)
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  • Equilibrium explanation as structural non-mechanistic explanation: The case long-term bacterial persistence in human hosts.Javier Suárez & Roger Deulofeu - 2019 - Teorema: International Journal of Philosophy 3 (38):95-120.
    Philippe Huneman has recently questioned the widespread application of mechanistic models of scientific explanation based on the existence of structural explanations, i.e. explanations that account for the phenomenon to be explained in virtue of the mathematical properties of the system where the phenomenon obtains, rather than in terms of the mechanisms that causally produce the phenomenon. Structural explanations are very diverse, including cases like explanations in terms of bowtie structures, in terms of the topological properties of the system, or in (...)
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