•  248
    (Un)Easily Possible Synthetic Biology
    Philosophy of Science (5): 1-14. 2022.
    Synthetic biology has a strong modal dimension that is part and parcel of its engineering agenda. In turning hypothetical biological designs into actual synthetic constructs, synthetic biologists reach towards potential biology instead of concentrating on naturally evolved organisms. We analyze synthetic biology’s goal of making biology easier to engineer through the combinatorial theory of possibility, which reduces possibility to combinations of individuals and their attributes in the actual w…Read more
  •  23
    Mechanism and the problem of abstract models
    European Journal for the Philosophy of Modeling 13 (27). 2023.
    New mechanical philosophy posits that explanations in the life sciences involve the decomposition of a system into its entities and their respective activities and organization that are responsible for the explanandum phenomenon. This mechanistic account of explanation has proven problematic in its application to mathematical models, leading the mechanists to suggest different ways of aligning abstract models with the mechanist program. Initially, the discussion centered on whether the Hodgkin-H…Read more
  •  19
    Natalia Carrillo and Tarja Knuuttila claim that there are two traditions of thinking about idealization offering almost opposite views on their functioning and epistemic status. While one tradition views idealizations as epistemic deficiencies, the other one highlights the epistemic benefits of idealization. Both of them treat idealizations as deliberate misrepresentations, however. They then argue for an artifactual account of idealization, comparing it to the traditional accounts of idealizati…Read more
  •  33
    Holistic Idealization: An Artifactual Standpoint
    with Tarja Knuuttila and Natalia Carrillo
    Studies in History and Philosophy of Science Part A 91 (C): 49-59. 2022.
    Idealization is commonly understood as distortion: representing things differently than how they actually are. In this paper, we outline an alternative artifactual approach that does not make misrepresentation central for the analysis of idealization. We examine the contrast between the Hodgkin-Huxley (1952a, b, c) and the Heimburg-Jackson (2005, 2006) models of the nerve impulse from the artifactual perspective, and argue that, since the two models draw upon different epistemic resources and re…Read more
  •  238
    One of the most conspicuous features of contemporary modeling practices is the dissemination of mathematical and computational methods across disciplinary boundaries. We study this process through two applications of the Ising model: the Sherrington-Kirkpatrick model of spin glasses and the Hopfield model of associative memory. The Hopfield model successfully transferred some basic ideas and mathematical methods originally developed within the study of magnetic systems to the field of neuroscien…Read more
  •  277
    Contrasting Cases: The Lotka-Volterra Model Times Three
    with Tarja Knuuttila and Andrea Loettgers
    Boston Studies in the Philosophy of Science 319 151-178. 2016.
    How do philosophers of science make use of historical case studies? Are their accounts of historical cases purpose-built and lacking in evidential strength as a result of putting forth and discussing philosophical positions? We will study these questions through the examination of three different philosophical case studies. All of them focus on modeling and on Vito Volterra, contrasting his work to that of other theoreticians. We argue that the worries concerning the evidential role of historica…Read more
  •  9
    Modelling gene regulation: (De)compositional and template-based strategies
    with Tarja Knuuttila and Vivette García Deister
    Studies in History and Philosophy of Science Part A 77 101-111. 2019.
    Although the interdisciplinary nature of contemporary biological sciences has been addressed by philosophers, historians, and sociologists of science, the different ways in which engineering concepts and methods have been applied in biology have been somewhat neglected. We examine - using the mechanistic philosophy of science as an analytic springboard - the transfer of network methods from engineering to biology through the cases of two biology laboratories operating at the California Institute…Read more
  •  243
    An Artifactual Perspective on Idealization: Constant Capacitance and the Hodgkin and Huxley Model
    In Alejandro Cassini & Juan Redmond (eds.), Models and Idealizations in Science: Fictional and Artefactual Approaches, Cham: Springer. 2021.
    There are two traditions of thinking about idealization offering almost opposite views on their functioning and epistemic status. While one tradition views idealizations as epistemic deficiencies, the other one highlights the epistemic benefits of idealization. Both of these, however, identify idealization with misrepresentation. In this article, we instead approach idealization from the artifactual perspective, comparing it to the distortion-to-reality accounts of idealization, and exemplifying…Read more
  •  256
    In his famous article “The Unreasonable Effectiveness of Mathematics in the Natural Sciences” Eugen Wigner argues for a unique tie between mathematics and physics, invoking even religious language: “The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve”. The possible existence of such a unique match between mathematics and physics has been extensively discussed by philosophers and h…Read more
  •  235
    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 …Read more
  •  312
    Varieties of noise: Analogical reasoning in synthetic biology
    Studies in History and Philosophy of Science Part A 48 76-88. 2014.
    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 typic…Read more
  •  36
    Modes, Media, and Formats of Scientific Representation
    with M. Vorms
    Erkenntnis: An International Journal of Analytic Philosophy. forthcoming.
  •  29
    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 …Read more
  •  390
    The attempt to define life has gained new momentum in the wake of novel fields such as synthetic biology, astrobiology, and artificial life. In a series of articles, Cleland, Chyba, and Machery claim that definitions of life seek to provide necessary and sufficient conditions for applying the concept of life—something that such definitions cannot, and should not do. We argue that this criticism is largely unwarranted. Cleland, Chyba, and Machery approach definitions of life as classifying device…Read more
  •  188
    Scientific Models in Philosophy of Science
    International Studies in the Philosophy of Science 24 (4): 437-440. 2010.
    Scientists have used models for hundreds of years as a means of describing phenomena and as a basis for further analogy. In Scientific Models in Philosophy of Science, Daniela Bailer-Jones assembles an original and comprehensive philosophical analysis of how models have been used and interpreted in both historical and contemporary contexts. Bailer-Jones delineates the many forms models can take (ranging from equations to animals; from physical objects to theoretical constructs), and how they are…Read more
  •  99
    Elämä ja mahdollinen elämä - Filosofisia näkökulmia
    In Kari Enqvist, Ilari Hetemäki & Teija Tiilikainen (eds.), Kaikki vapaudesta, . pp. 247-259. 2017.
  •  224
    Models, Representation, and Mediation
    Philosophy of Science 72 (5): 1260-1271. 2005.
    Representation has been one of the main themes in the recent discussion of models. Several authors have argued for a pragmatic approach to representation that takes users and their interpretations into account. It appears to me, however, that this emphasis on representation places excessive limitations on our view of models and their epistemic value. Models should rather be thought of as epistemic artifacts through which we gain knowledge in diverse ways. Approaching models this way stresses the…Read more
  •  336
    The recent discussion of fictional models has focused on imagination, implicitly considering fictions as something nonconcrete. We present two cases from synthetic biology that can be viewed as concrete fictions. Both minimal cells and alternative genetic systems are modal in nature: they, as well as their abstract cousins, can be used to study unactualized possibilia. We approach these synthetic constructs through Vaihinger’s notion of a semi-fiction and Goodman’s notion of semifactuality. Our …Read more
  •  317
    Models, Fictions and Artifacts
    In Wenceslao J. Gonzalez (ed.), Language and Scientific Research, Springer Verlag. pp. 199-22. 2021.
    This paper discusses modeling from the artifactual perspective. The artifactual approach conceives models as erotetic devices. They are purpose-built systems of dependencies that are constrained in view of answering a pending scientific question, motivated by theoretical or empirical considerations. In treating models as artifacts, the artifactual approach is able to address the various languages of sciences that are overlooked by the traditional accounts that concentrate on the relationship of …Read more
  •  6
    Representaatio: tiedon kivijalasta tieteiden työkaluksi (edited book)
    Gaudeamus Helsinki University Press. 2010.
  •  211
    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 w…Read more
  •  38
    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. pp. 163--177. 2013.
  •  39
    Modelling gene regulation: (De)compositional and template-based strategies
    with Vivette García Deister
    Studies in History and Philosophy of Science Part A 77 101-111. 2019.
  •  49
    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 fa…Read more
  •  87
    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 …Read more