Over the last two decades, network-focused approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While the network approach continues to grow very rapidly, some of its conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. Consequently, the central focus of this theme issue will be on (...) the definition, motivation and application of key concepts in biological network science, such as levels, hierarchies, and explanatory directionality. A unification will be achieved by formulating norms for delimiting the distinctively network-topological class of explanations that connect general as well as very specific biological research questions. The impact of this theme issue is broad and encompassing, as it is highly interdisciplinary and opens a uniquely normative perspective on the foundational aspects of network-based explanations and modelling. This theme issue is intended to become a landmark publication for practical research as well as funding policy decisions, by unifying network approaches in biological sciences in terms of fundamental concepts and informing the public understanding of the network science. (shrink)

Models developed using machine learning are increasingly prevalent in scientific research. At the same time, these models are notoriously opaque. Explainable AI aims to mitigate the impact of opacity by rendering opaque models transparent. More than being just the solution to a problem, however, Explainable AI can also play an invaluable role in scientific exploration. This paper describes how post-hoc analytic techniques from Explainable AI can be used to refine target phenomena in medical science, to identify starting points for future (...) investigations of causal relationships, and to generate possible explanations of target phenomena in cognitive science. In this way, this paper describes how Explainable AI—over and above machine learning itself—contributes to the efficiency and scope of data-driven scientific research. (shrink)

Sometimes, scientific models are either intended to or plausibly interpreted as representing nonactual but possible targets. Call this “hypothetical modeling”. This paper raises two epistemological challenges concerning hypothetical modeling. To begin with, I observe that given common philosophical assumptions about the scope of objective possibility, hypothetical models are fallible with respect to what is objectively possible. There is thus a need to distinguish between accurate and inaccurate hypothetical modeling. The first epistemological challenge is that no account of the epistemology of (...) hypothetical models seems to cohere with the most characteristic function of scientific modeling in general, i.e., surrogative representation. The second epistemological challenge is a version of “reliability challenges” familiar from other areas. There is a challenge to explain how hypothetical models could be a reliable guide to what is possible, given that they are not and cannot be compared against their nonactual targets and updated accordingly. I close with some brief remarks on possible solutions to these challenges. (shrink)

Scientific models typically contain idealizations, or assumptions that are known not to be true. Philosophers have long questioned the nature of idealizations: Are they heuristic tools that will be abandoned? Or rather fictional representations of reality? And how can we reconcile them with realism about knowledge of nature? Immanuel Kant developed an account of scientific investigation that can inspire a new approach to the contemporary debate. Kant argued that scientific investigation is possible only if guided by ideal assumptions—what he calls (...) “regulative ideas”. These ideas are not true of objects of nature, and yet they are not heuristic tools or fictional represen- tations. They are necessary rules governing the construction and assessment of scientific explanations. In this paper, I suggest that some idealizations can be interpreted as having necessary regulative value and as being compatible with scientific realism. I first analyze the puzzle of the nature of idealization and present the main approaches to this topic in the literature. Second, I reconsider the puzzle vis-a-vis a restricted, Kantian definition of idealization and a novel characterization of the relation between idealization and truth. Finally, I discuss in detail an example of idealization (the Hardy-Weinberg equilibrium) along the suggested Kantian lines. (shrink)

Philosophers of science have recently taken care to highlight different modeling practices where scientific models primarily contribute modal information, in the form of for example possibility claims, how-possibly explanations, or counterfactual conditionals. While examples abound, comparatively little attention is being paid to the question of under what conditions, and in virtue of what, models can perform this epistemic function. In this paper, we firstly delineate modal modeling from other modeling practices, and secondly reviewattempts to spell out and explain the epistemic (...) success conditions of modal modeling. The aim is to more clearly expose the respective justificatory strategies of these accounts, and secondly, to identify lacunae where further work is needed. (shrink)

Relationships of counterfactual dependence have played a major role in recent debates of explanation and understanding in the philosophy of science. Usually, counterfactual dependencies have been viewed as the explanantia of explanation, i.e., the things providing explanation and understanding. Sometimes, however, counterfactual dependencies are themselves the targets of explanations in science. These kinds of explanations are the focus of this paper. I argue that “micro-level model explanations” explain the particular form of the empirical regularity underlying a counterfactual dependency by representing (...) it as a physical necessity on the basis of postulated microscopic entities. By doing so, micro-level models rule out possible forms the regularity could have taken. Micro-model explanations, in other words, constrain empirical regularities and their associated counterfactual dependencies. I introduce and illustrate micro-level model explanations in detail, contrast them to other accounts of explanation, and consider potential problems. (shrink)

Computer simulations are widely used for surrogative reasoning in scientific research. They also play a crucial role in engineering, more specifically in the design of new robotic systems, yet the nature of this role has been little discussed so far in the philosophy of technology literature. The main claim made in this article is that the notion of surrogative reasoning is central to understanding how computer simulations can serve the purpose of designing new robots. More specifically, it is argued that (...) computer simulations can support two forms of surrogative reasoning, which are called model-oriented and prediction-oriented, whose inferential structure is reconstructed to some extent. And it is argued that, when computer simulations are used to design new robots, they are distinctively used in the model-oriented way. By unravelling the structure of the computer simulation-supported methods adopted in robotic design, this article may contribute to a finer-grained understanding of the epistemic processes involved in technological research. (shrink)

Along three measurements at the Large Hadron Collider (LHC), a high energy particle accelerator, we analyze procedures and consequences of exploratory experimentation (EE). While all of these measurements fulfill the requirements of EE: probing new parameter spaces, being void of a target theory and applying a broad range of experimental methods, we identify epistemic differences and suggest a classification of EE. We distinguish classes of EE according to their respective goals: the exploration where an established global theory cannot provide the (...) details of a local phenomenon, exploration of an astonishing discovery and exploration to find a new entity. We find that these classes also differ with respect to the existence of an identifiable target and their impact on the background theory. The characteristics distinguish EE from other kinds of experimentation, even though these different kinds have not yet been systematically studied. The formal rigor and precision of LHC physics facilitates to analyze concept formation in its early state. In particular we emphasize the importance for nil–results for conceptualization and argue that conceptualization can also be achieved from nil–results only. (shrink)

In this paper I give an overview of a perspectival realist ontology. I discuss the role of situated knowledge and multiculturalism in perspectival ontology and offer a working definition of ‘phenomena’ as the minimal unit of such ontological commitment. I clarify how the view differs from Kuhn’s view, and highlight some of its implications for how to think of scientific knowledge as a multicultural and cosmopolitan inquiry.

The goal of this article is to address the problem of inconsistent models and the challenge it poses for perspectivism. I analyze the argument, draw attention to some hidden premises behind it, and deflate them. Then I introduce the notion of perspectival models as a distinctive class of modeling practices whose primary function is exploratory. I illustrate perspectival modeling with two examples taken from contemporary high-energy physics at the Large Hadron Collider at the European Organization for Nuclear Research, which are (...) designed to show how a plurality of seemingly incompatible models is methodologically crucial to advance the realist quest in cutting-edge areas of scientific inquiry. (shrink)

Several recent accounts of modeling have focused on the modal dimension of scientific inquiry. More precisely, it has been suggested that there are specific models and modeling practices that are best understood as being geared towards possibilities, a view recently dubbed modal modeling. But modalities encompass much more than mere possibility claims. Besides possibilities, modal modeling can also be used to investigate contingencies, necessities or impossibilities. Although these modal concepts are logically connected to the notion of possibility, not all models (...) are equal in their affordances for these richer modal inferences. This paper investigates the modal extent of selected models and argues that analyzing singular model-target pairings by themselves is typically not enough to explain their modal aptness or to identify the kinds of modalities they can be used to reason about. Furthermore, it is argued that some important concepts that are not explicitly modal - like biological robustness - can be understood modally through their relational nature to a background space of possibilities. In conclusion, it is suggested that the strategy of modal modeling is contrastive, situating particular possibilities in larger modal spaces and studying the structural relations within them. (shrink)

The epistemic value of models has traditionally been approached from a representational perspective. This paper argues that the artifactual approach evades the problem of accounting for representation and better accommodates the modal dimension of modeling. From an artifactual perspective, models are viewed as erotetic vehicles constrained by their construction and available representational tools. The modal dimension of modeling is approached through two case studies. The first portrays mathematical modeling in economics, while the other discusses the modeling practice of synthetic biology, (...) which exploits and combines models in various modes and media. Neither model intends to represent any actual target system. Rather, they are constructed to study possible mechanisms through the construction of a model system with built-in dependencies. (shrink)

The aim of this article is to use a model from the origin of life studies to provide some depth and detail to our understanding of exploratory models by suggesting that some of these models should be understood as indeterminate. Models that are indeterminate are a type of exploratory model and therefore have extensive potential and can prompt new lines of research. They are distinctive in that, given the current state of scientific understanding, we cannot specify how and where the (...) model will be useful in understanding the natural world: in this case, the origin of life on Earth. The purpose of introducing indeterminacy is to emphasize the epistemic uncertainty associated with modeling, a feature of this practice that has been under emphasized in the literature in favor of attempts to understand the more specific epistemic successes afforded by models. (shrink)

Recent epistemology of modality has seen a growing trend towards metaphysics-first approaches. Contrastingly, this paper offers a more philosophically modest account of justifying modal claims, focusing on the practices of scientific modal inferences. Two ways of making such inferences are identified and analyzed: actualist-manipulationist modality and relative modality. In AM, what is observed to be or not to be the case in actuality or under manipulations, allows us to make modal inferences. AM-based inferences are fallible, but the same holds for (...) practically all empirical inquiry. In RM, modal inferences are evaluated relative to what is kept fixed in a system, like a theory or a model. RM-based inferences are more certain but framework-dependent. While elements from both AM and RM can be found in some existing accounts of modality, it is worth highlighting them in their own right and isolating their features for closer scrutiny. This helps to establish their relevant epistemologies that are free from some strong philosophical assumptions often attached to them in the literature. We close by showing how combining these two routes amounts to a view that accounts for a rich variety of modal inferences in science. (shrink)

That science is more than the unilinear application of general theories to specific empirical circumstances is, one hopes, no longer something that is controversial or requires detailed argument. To be sure, there were times when devising universally applicable theories was seen as the most worthy task of science, with less lofty activities such as experimentation and scientific modeling being relegated to the underbelly of “proper science.” Arguing for a pluralistic recognition of the diversity of scientific practices, methods, and goals, might—at (...) least on the pages of this journal—amount to preaching to the converted. Yet, once the diversity and heterogeneity of science is acknowledged, the real work only starts:... (shrink)

La critique de la métaphysique dans la Dialectique transcendantale de la Critique de la raison pure débouche sur la doctrine de l’usage régulateur des idées transcendantales de la raison pure. La théorie de l’usage régulateur de ces idées est relativement abstraite et demande à être clarifiée. Kant affirme que ces idées ont un usage dans les sciences empiriques. Cependant il ne spécifie pas quel usage les sciences peuvent faire de ces idées. Dans cet article je compare les caractéristiques des idées (...) transcendantales aux caractéristiques des modèles scientifiques. Ainsi la thèse principale de mon article est que la théorie kantienne de l’usage régulateur des idées est comparable à la modélisation en science. C’est ce que je nomme « l’approche modélisatrice des idées transcendantales chez Kant ». D’après cette interprétation, on trouve chez ce dernier une conception relativement élaborée de la modélisation que l’on peut comprendre comme signifiant que la métaphysique fournit aux sciences les formes les plus universelles de modèles qui peuvent être spécifiés pour des objectifs particuliers par les sciences. (shrink)

The purpose of this article is to develop an epistemology of scientific models in scientific research practices, and to show that disciplinary perspectives have crucial role in such an epistemology. A transcendental approach is taken, aimed at explanations of the kinds of questions relevant to the intended epistemology, such as “How is it possible that models provide knowledge about aspects of reality?” The approach is also pragmatic in the sense that the questions and explanations must be adequate and relevant to (...) concrete scientific practice. First it is explained why the idea of models as representations in terms of similarity or isomorphism between a model and its target is too limited as a basis for this epistemology. An important finding is that the target-phenomenon is usually not something that can be observed in a straightforward manner, but requires both characterization in terms of measurable variables and subsumption under concepts. The loss of this basis leads to a number of issues, such as: how can models be interpreted as representations if models also include conceptually meaningful linguistic content; how can researchers identify non-observable real-world target-phenomena that are then represented in the model; how do models enable inferential reasoning in performing epistemic tasks by researchers; and, how to justify scientific models. My proposal is to deal with these issues by analyzing how models are constructed, rather than by looking at ready-made models. Based on this analysis, I claim that the identification of phenomena and the construction of scientific models is guided and also confined by the disciplinary perspective within which researchers in a scientific discipline have learned to work. I propose a Kuhnian framework by which the disciplinary perspective can be systematically articulated. Finally, I argue that harmful forms of subjectivism, due to the loss of the belief that models objectively represent aspects of reality, can be overcome by making the disciplinary perspective in a research project explicit, thereby enabling its critical assessment, for which the proposed Kuhnian framework provides a tool. (shrink)

While the predominant focus of the philosophical literature on scientific modeling has been on single-scale models, most systems in nature exhibit complex multiscale behavior, requiring new modeling methods. This challenge of modeling phenomena across a vast range of spatial and temporal scales has been called the tyranny of scales problem. Drawing on research in the geosciences, I synthesize and analyze a number of strategies for taming this tyranny in the context of conceptual, physical, and mathematical modeling. This includes several strategies (...) that can be deployed in physical modeling, even when strict dynamical scaling fails. In all cases, I argue that having an adequate conceptual model—given both the nature of the system and the particular purpose of the model—is essential. I draw a distinction between depiction and representation, and use this research in the geosciences to advance a number of debates in the philosophy of modeling. (shrink)

In this review article, I situate Michela Massimi’s 2022 Perspectival Realism book in the broader state of the art of the contemporary philosophy of science by examining critically its contribution to the perspectival realism debate. Setting up a new agenda of philosophical problems for the perspectival realist, Massimi’s book is the most comprehensive assessment of perspectival realism since the publication of Giere’s 2006 Giere, Ronald. Ed. 2006. Scientific Perspectivism. Chicago: The University of Chicago Press.[Crossref], [Google Scholar] Scientific Perspectivism (the starting (...) point of the debate). The author carries out a scrupulous analysis of the historical, epistemological, and metaphysical foundations of perspectival realism—while she engages critically with the existing literature, she does so by giving a generous homage to the previous contributions to the state of the art (the works of Giere, Morrison, van Fraassen and others). However, I raise a batterie of questions about Massimi’s (perspectival) commitments, to bring into question the reach and the ambitions of her global project, specifically the rising tension between her modest epistemological beliefs in a plurality of culturally and historically situated perspectives and her ambitious metaphysical commitments towards a primitivist view about laws of nature. (shrink)

In this paper, we explore the conceptual problems arising when using network analysis in person- centered care (PCC) in psychiatry. Personalized network models are potentially helpful tools for PCC, but we argue that using them in psychiatric practice raises boundary problems, i.e., problems in demarcating what should and should not be included in the model, which may limit their ability to provide clinically-relevant knowledge. Models can have explanatory and representational boundaries, among others. We argue that we can make more explicit (...) what kind of questions personalized network models can address in PCC, given their representational and explanatory boundaries, using perspectival reasoning. (shrink)