A common strategy for simplifying complex systems involves partitioning them into subsystems whose behaviors are roughly independent of one another at shorter timescales. Dynamic causal models clarify how doing so reveals a system’s nonequilibrium causal relationships. Here I use these models to elucidate the idealizations and abstractions involved in representing a system at a timescale. The models reveal that key features of causal representations—such as which variables are exogenous—may vary with the timescale at which a system is considered. This has (...) implications for debates regarding which systems can be represented causally. (shrink)

The neural reuse framework developed primarily by Michael Anderson proposes that brain regions are involved in multiple and diverse cognitive tasks and that brain regions flexibly and dynamically interact in different combinations to carry out cognitive functioning. We argue that the evidence cited by Anderson and others falls short of supporting the fundamental principles of neural reuse. We map out this problem and provide solutions by drawing on recent advances in network neuroscience, and we argue that methods employed in network (...) neuroscience provide the means to fully engage in a research program operating under the principles of neural reuse. (shrink)

Complexity sciences have become famous worldwide thanks to several popular books that served as echo chambers of their promises. These consisted in departing from “classical science” defined as deterministic, reductionist, analytic and mono-disciplinary. Their founders and supporters declared that complexity sciences were going to give rise (or that they have given rise) to a post-Laplacian, antireductionist, holistic and interdisciplinary approach. By taking a closer look at their content and practices, I argue in this article that, because of their physics-oriented, computationalist, (...) and mathematical assumptions, complexity sciences have paradoxically produced knowledge at odds with these four tenets. (shrink)

Accounts of mental disorders focusing either on the brain as neurophysiological substrate or on systematic connections between symptoms are insufficient to account for the multifactorial nature of mental illnesses. Recently, multiplexes have been suggested to provide a holistic view of psychopathology that integrates data from different factors, at different scales, or across time. Intuitively, these multi-layered network structures present quite appealing models of mental disorders that can be constructed by powerful computational machinery based on increasing amounts of real-world data. In (...) this paper, I systematically examine what challenges psychopathology models face and to what extent different species of psychopathology models can address them. My analysis highlights that while multiplexes, as they are usually conceived, appear promising, they suffer from the same problems as other approaches. To remedy this, I suggest, we must go a step further and combine different kinds of multiplexes into 4D models. Once we embrace 4D multiplexes and identify appropriate ways to constrain them, we might unlock the true potential of multiplexes for making headway in psychopathology research. (shrink)

The relationship between topological explanation and mechanistic explanation is unclear. Most philosophers agree that at least some topological explanations are mechanistic explanations. The crucial question is how to make sense of this claim. Zednik (Philos Psychol 32(1):23–51, 2019) argues that topological explanations are mechanistic if they (i) describe mechanism sketches that (ii) pick out organizational properties of mechanisms. While we agree with Zednik’s conclusion, we critically discuss Zednik’s account and show that it fails as a general account of how and (...) when topological explanations are mechanistic. First, if topological explanations were just mechanism sketches, this implies that they could be enriched by replacing topological terms with mechanistic detail. This, however, conflicts how topological explanations are used in scientific practice. Second, Zednik’s account fails to show how topological properties can be organizational properties of mechanisms that have a place in mechanistic explanation. The core issue is that Zednik’s account ignores that topological properties often are _global_ properties while mechanistic explanantia refer to _local_ properties. We demonstrate how these problems can be solved by a recent account of mechanistic completeness (Craver and Kaplan in Br J Philos Sci 71(1):287–319, 2020; Kohár and Krickel in Calzavarini and Viola (eds) Neural mechanisms—new challenges in the philosophy of neuroscience, Springer, New York, 2021) and use a multilayer network model of Alzheimer’s Disease to illustrate this. (shrink)

In the last couple of years a few seemingly independent debates on scientific explanation have emerged, with several key questions that take different forms in different areas. For example, the questions what makes an explanation distinctly mathematical and are there any non-causal explanations in sciences sometimes take a form of the question what makes mathematical models explanatory, especially whether highly idealized models in science can be explanatory and in virtue of what they are explanatory. These questions raise further issues about (...) counterfactuals, modality, and explanatory asymmetries: i.e., do mathematical and non-causal explanations support... (shrink)

In the last couple of years a few seemingly independent debates on scientific explanation have emerged, with several key questions that take different forms in different areas. For example, the question what makes an explanation distinctly mathematical and are there any non-causal explanations in sciences (i.e. explanations that don’t cite causes in the explanans) sometimes take a form of the question what makes mathematical models explanatory, especially whether highly idealized models in science can be explanatory and in virtue of what (...) they are explanatory. These questions raise further issues about counterfactuals, modality and explanatory asymmetries, i.e. do mathematical and non-causal explanations support counterfactuals, and how to understand explanatory asymmetries in non-causal explanations. Even though these are very common issues in the philosophy of physics and mathematics, they can be found in different guises in the philosophy of biology, where there is the statistical interpretation of the Modern Synthesis theory of evolution, according to which the post-Darwinian theory of natural selection explains evolutionary change by citing statistical properties of populations and not the causes of changes. These questions also arise in philosophy of ecology or neuroscience in regard to the nature of topological explanations. The question here is whether in network models in biology, ecology, neuroscience and computer science the mathematical or more precisely topological properties can be explanatory of physical phenomena, or they are just different ways to represent causal structures. The aim of the special issue is to unify all these debates around several overlapping questions. (shrink)

In this paper, I argue that the newly developed network approach in neuroscience and biology provides a basis for formulating a unique type of realization, which I call topological realization. Some of its features and its relation to one of the dominant paradigms of realization and explanation in sciences, i.e. the mechanistic one, are already being discussed in the literature. But the detailed features of topological realization, its explanatory power and its relation to another prominent view of realization, namely the (...) semantic one, have not yet been discussed. I argue that topological realization is distinct from mechanistic and semantic ones because the realization base in this framework is not based on local realisers, regardless of the scale but on global realizers. In mechanistic approach, the realization base is always at the local level, in both ontic and epistemic accounts. The explanatory power of realization relation in mechanistic approach comes directly from the realization relation-either by showing how a model is mapped onto a mechanism, or by describing some ontic relations that are explanatory in themselves. Similarly, the semantic approach requires that concepts at different scales logically satisfy microphysical descriptions, which are at the local level. In topological framework the realization base can be found at different scales, but whatever the scale the realization base is global, within that scale, and not local. Furthermore, topological realization enables us to answer the “why” questions, which according to Polger 2010 make it explanatory. The explanatoriness of topological realization stems from understanding mathematical consequences of different topologies, not from the mere fact that a system realizes them. (shrink)

In this paper, I outline a heuristic for thinking about the relation between explanation and understanding that can be used to capture various levels of “intimacy”, between them. I argue that the level of complexity in the structure of explanation is inversely proportional to the level of intimacy between explanation and understanding, i.e. the more complexity the less intimacy. I further argue that the level of complexity in the structure of explanation also affects the explanatory depth in a similar way (...) to intimacy between explanation and understanding, i.e. the less complexity the greater explanatory depth and vice versa. (shrink)

The philosophical literature on scientific explanation in neuroscience has been dominated by the idea of mechanisms. The mechanist philosophers often claim that neuroscience is in the business of finding mechanisms. This view has been challenged in numerous ways by showing that there are other successful and widespread explanatory strategies in neuroscience. However, the empirical evidence for all these claims was hitherto lacking. Empirical evidence about the pervasiveness and uses of various explanatory strategies in neuroscience is particularly needed because examples and (...) case studies that are used to illustrate philosophical claims so far tend to be hand-picked. The risk of confirmation bias is therefore considerable: when looking for white swans, all one finds is that swans are white. The more systematic quantitative and qualitative bibliometric study of a large body of relevant literature that we present in this paper can put such claims into perspective. Using bibliometric tools, we identify the typical linguistic patterns used in the alleged mechanistic, dynamical, and topological explanations in the literature, their preponderance and how they change over time. Our findings show abundant use of mechanistic language, but also the presence of a significant neuroscience literature using topological and dynamical explanatory language, which grows over time and increasingly differentiates from each other and from mechanistic explanations. (shrink)

We provide three innovations to recent debates about whether topological or “network” explanations are a species of mechanistic explanation. First, we more precisely characterize the requirement that all topological explanations are mechanistic explanations and show scientific practice to belie such a requirement. Second, we provide an account that unifies mechanistic and non-mechanistic topological explanations, thereby enriching both the mechanist and autonomist programs by highlighting when and where topological explanations are mechanistic. Third, we defend this view against some powerful mechanist objections. (...) We conclude from this that topological explanations are autonomous from their mechanistic counterparts. (shrink)

This paper argues that in some explanations mathematics are playing an explanatory rather than a representational role, and that this feature unifies many types of non-causal or non-mechanistic explanations that some philosophers of science have been recently exploring under various names. After showing how mathematics can play either a representational or an explanatory role by considering two alternative explanations of a same biological pattern—“Bergmann’s rule”—I offer an example of an explanation where the bulk of the explanatory job is done by (...) a mathematical theorem, and where mechanisms involved in the target systems are not explanatorily relevant. Then I account for the way mathematical properties may function in an explanatory way within an explanation by arguing that some mathematical propositions involving variables non directly referring to the target system features constitute constraints to which a whole class of systems should comply, provided they are describable by a mathematical object concerned by those propositions. According to such “constraint account”, those mathematical facts are directly entailing the explanandum, as a consequence of such constraints. I call those explanations “structural”, because here properties of mathematical structures are accounting for the explanandum; various kinds of mathematical structures thereby define various types of structural explanations. (shrink)

This paper proposes an account of neurocognitive activity without leveraging the notion of neural representation. Neural representation is a concept that results from assuming that the properties of the models used in computational cognitive neuroscience must literally exist the system being modelled. Computational models are important tools to test a theory about how the collected data has been generated. While the usefulness of computational models is unquestionable, it does not follow that neurocognitive activity should literally entail the properties construed in (...) the model. While this is an assumption present in computationalist accounts, it is not held across the board in neuroscience. In the last section, the paper offers a dynamical account of neurocognitive activity with Dynamical Causal Modelling that combines dynamical systems theory mathematical formalisms with the theoretical contextualisation provided by Embodied and Enactive Cognitive Science. (shrink)

In the last 20 years network science has become an independent scientific field. We argue that by building network models network scientists are able to tame the vagueness of propositions about complex systems and networks, that is, to make these propositions precise. This makes it possible to study important vague properties such as modularity, near-decomposability, scale-freeness or being a small world. Using an epistemic model of network science, we systematically analyse the specific nature of network models and the logic behind (...) the taming mechanism. (shrink)

It is generally accepted that, in the cognitive and neural sciences, there are both computational and mechanistic explanations. We ask how computational explanations can integrate into the mechanistic hierarchy. The problem stems from the fact that implementation and mechanistic relations have different forms. The implementation relation, from the states of an abstract computational system to the physical, implementing states is a homomorphism mapping relation. The mechanistic relation, however, is that of part/whole; the explaining features in a mechanistic explanation are the (...) components of the explanandum phenomenon and their causal organization. Moreover, each component in one level of mechanism is constituted and explained by components of an underlying level of mechanism. Hence, it seems, computational variables and functions cannot be mechanistically explained by the medium-dependent states and properties that implement them. How then, do the computational and the implementational integrate to create the mechanistic hierarchy? After explicating the general problem, we further demonstrate it through a concrete example, of reinforcement learning, in the cognitive and neural sciences. We then examine two possible solutions. On one solution, the mechanistic hierarchy embeds at the same levels computational and implementational properties. This picture fits with the view that computational explanations are mechanistic sketches. On the other solution, there are two separate hierarchies, one computational and another implementational, which are related by the implementation relation. This picture fits with the view that computational explanations are functional and autonomous explanations. It is less clear how these solutions fit with the view that computational explanations are full-fledged mechanistic explanations. Finally, we argue that both pictures are consistent with the reinforcement learning example, but that scientific practice does not align with the view that computational models are merely mechanistic sketches. (shrink)

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 (...) criticisms, in the present work we make a step further elucidating this kind of explanations with a general analytical framework according to which scientific explanations are ampliative, specialized embeddings (ASE), which has recently been successfully applied to other biological subfields. We use ASE to reconstruct in detail the Coyte et al.’s case study and on its basis, we claim that network explanations of the ecology of the microbiome, and other similar explanations in ecology, gain their epistemological force in virtue of their capacity to embed biological phenomena in non-accidental generalizations that are simultaneously ampliative and specialized. (shrink)

Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems (...) is usually provided in terms of their mathematical properties, and not in mechanistic terms. They have intensively studied the explanation of the properties of ecosystems that behave following the rules of a non-random network. However, no attention has been devoted to the study of the nature of the explanation in those that form a random network. In this paper, we cover that gap by analysing the explanation of the stability behaviour of the microbiome recently elaborated by Coyte and colleagues, to determine whether it fits with the model of explanation suggested by the new-mechanist or by the defenders of mathematical explanation. Our analysis of this case study supports three theses: (1) that the explanation is not given solely in terms of mechanisms, as the new-mechanists understand the concept; (2) that the mathematical properties that describe the system play an essential explanatory role, but they do not exhaust the explanation; (3) that a non-previously identified appeal to the type of interactions that the entities in the network can exhibit, as well as their abundance, is also necessary for Coyte and colleagues’ account to be fully explanatory. From the combination of these three theses we argue for the necessity of an integrative pluralist view of the nature of behaviour explanation when this is given by appealing to the existence of a random network. (shrink)

Borsboom and colleagues have recently proposed a “network theory” of psychiatric disorders that conceptualizes psychiatric disorders as relatively stable networks of causally interacting symptoms. They have also claimed that the network theory should include non-symptom variables such as environmental factors. How are environmental factors incorporated in the network theory, and what kind of explanations of psychiatric disorders can such an “extended” network theory provide? The aim of this article is to critically examine what explanatory strategies the network theory that includes (...) both symptoms and environmental factors can accommodate. We first analyze how proponents of the network theory conceptualize the relations between symptoms and between symptoms and environmental factors. Their claims suggest that the network theory could provide insight into the causal mechanisms underlying psychiatric disorders. We assess these claims in light of network analysis, Woodward’s interventionist theory, and mechanistic explanation, and show that they can only be satisfied with additional assumptions and requirements. Then, we examine their claim that network characteristics may explain the dynamics of psychiatric disorders by means of a topological explanatory strategy. We argue that the network theory could accommodate topological explanations of symptom networks, but we also point out that this poses some difficulties. Finally, we suggest that a multilayer network account of psychiatric disorders might allow for the integration of symptoms and non-symptom factors related to psychiatric disorders and could accommodate both causal/mechanistic and topological explanations. (shrink)

Network analysis is increasingly used to discover and represent the organization of complex systems. Focusing on examples from neuroscience in particular, I argue that whether network models explain, how they explain, and how much they explain cannot be answered for network models generally but must be answered by specifying an explanandum, by addressing how the model is applied to the system, and by specifying which kinds of relations count as explanatory.

Mechanist philosophers have examined several strategies scientists use for discovering causal mechanisms in neuroscience. Findings about the anatomical organization of the brain play a central role in several such strategies. Little attention has been paid, however, to the use of network analysis and causal modeling techniques for mechanism discovery. In particular, mechanist philosophers have not explored whether and how these strategies incorporate information about the anatomical organization of the brain. This paper clarifies these issues in the light of the distinction (...) between structural, functional and effective connectivity. Specifically, we examine two quantitative strategies currently used for causal discovery from functional neuroimaging data: dynamic causal modeling and probabilistic graphical modeling. We show that dynamic causal modeling uses findings about the brain’s anatomical organization to improve the statistical estimation of parameters in an already specified causal model of the target brain mechanism. Probabilistic graphical modeling, in contrast, makes no appeal to the brain’s anatomical organization, but lays bare the conditions under which correlational data suffice to license reliable inferences about the causal organization of a target brain mechanism. The question of whether findings about the anatomical organization of the brain can and should constrain the inference of causal networks remains open, but we show how the tools supplied by graphical modeling methods help to address it. (shrink)

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-Huxley model is explanatory. Network models provided another complication, as they apply to (...) a wide number of materially diverse systems. In this article, we examine the various attempts to integrate abstract models within the mechanist program, also presenting a further challenge: the Heimburg-Jackson model, which was introduced as an alternative to the Hodgkin-Huxley model. We argue that although the notion of abstraction as the omission of irrelevant mechanistic details appears to give a mechanistic solution for accommodating abstract models, this notion does not suit models whose epistemic strategy is not decompositional. As a result, the mechanist has to choose whether to dilute the mechanistic approach nearly beyond recognition or to claim that many, if not most, abstract theoretical models do not deliver mechanistic explanations, or qualify as explanatory at all. (shrink)

Functional decomposition is an important goal in the life sciences, and is central to mechanistic explanation and explanatory reduction. A growing literature in philosophy of science, however, has challenged decomposition-based notions of explanation. ‘Holists’ posit that complex systems exhibit context-sensitivity, dynamic interaction, and network dependence, and that these properties undermine decomposition. They then infer from the failure of decomposition to the failure of mechanistic explanation and reduction. I argue that complexity, so construed, is only incompatible with one notion of decomposition, (...) which I call ‘atomism’, and not with decomposition writ large. Atomism posits that function ascriptions must be made to parts with minimal reference to the surrounding system. Complexity does indeed falsify atomism, but I contend that there is a weaker, ‘contextualist’ notion of decomposition that is fully compatible with the properties that holists cite. Contextualism suggests that the function of parts can shift with external context, and that interactions with other parts might help determine their context-appropriate functions. This still admits of functional decomposition within a given context. I will give examples based on the notion of oscillatory multiplexing in systems neuroscience. If contextualism is feasible, then holist inferences are faulty—one cannot infer from the presence of complexity to the failure of decomposition, mechanism, and reductionism. (shrink)

The article investigates what happens when philosophy meets and begins to establish connections with two formal research methods such as game theory and network science. We use citation analysis to identify, among the articles published in Synthese and Philosophy of Science between 1985 and 2021, those that cite the specialistic literature in game theory and network science. Then, we investigate the structure of the two corpora thus identified by bibliographic coupling and divide them into clusters of related papers by automatic (...) community detection. Lastly, we construct by the same bibliometric techniques a reference map of philosophy, on which we overlay our corpora to map the diffusion of game theory and network science in the various sub-areas of recent philosophy. Three main results derive from this study. Philosophers are interested not only in using and investigating game theory as a formal method belonging to applied mathematics and sharing many relevant features with social choice theory, but also in considering its applications in more empirically oriented disciplines such as social psychology, cognitive science, or biology. Philosophers focus on networks in two research contexts and in two different ways: in the debate on causality and scientific explanation, they consider the results of network science; in social epistemology, they employ network science as a formal tool. In the reference map, logic—whose use in philosophy dates back to a much earlier period—is distributed in a more uniform way than recently encountered disciplines such as game theory and network science. We conclude by discussing some methodological limitations of our bibliometric approach, especially with reference to the problem of field delineation. (shrink)

Network neuroscience represents the brain as a collection of regions and inter-regional connections. Given its ability to formalize systems-level models, network neuroscience has generated unique explanations of neural function and behavior. The mechanistic status of these explanations and how they can contribute to and fit within the field of neuroscience as a whole has received careful treatment from philosophers. However, these philosophical contributions have not yet reached many neuroscientists. Here we complement formal philosophical efforts by providing an applied perspective from (...) and for neuroscientists. We discuss the mechanistic status of the explanations offered by network neuroscience and how they contribute to, enhance, and interdigitate with other types of explanations in neuroscience. In doing so, we rely on philosophical work concerning the role of causality, scale, and mechanisms in scientific explanations. In particular, we make the distinction between an explanation and the evidence supporting that explanation, and we argue for a scale-free nature of mechanistic explanations. In the course of these discussions, we hope to provide a useful applied framework in which network neuroscience explanations can be exercised across scales and combined with other fields of neuroscience to gain deeper insights into the brain and behavior. (shrink)

Marcello Barbieri has presented code biology as an alternative to the Peircean approach to biosemiotics. Some critics questioned the viability of code biology on grounds that Barbieri’s conception of science is limited. It has been argued that code biology’s mechanistic tendency is the cause of the allegedly limited conception of science. In this paper, I evaluate the scientific viability of the code model from the perspective of scientific realism in the philosophy of science. To be more precise, I draw on (...) resources of the mechanistic view in philosophy to argue that far from harbouring a limited conception of science, code biology could indeed improve the scientific prospects of biosemiotics. I show that the mechanistic and model-based tendency of the code model enhances its vigour as a full-blooded scientific approach to the study of meaning in living systems. To consolidate my claim, I draw on some recent debates in the mechanistic philosophy to argue that even relational approaches to understanding the meaning in living systems—such as an approach that is defended by Vega in a recent paper—could be underpinned by mechanistic processes at a foundational level. (shrink)

This chapter provides a systematic overview of topological explanations in the philosophy of science literature. It does so by presenting an account of topological explanation that I (Kostić and Khalifa 2021; Kostić 2020a; 2020b; 2018) have developed in other publications and then comparing this account to other accounts of topological explanation. Finally, this appraisal is opinionated because it highlights some problems in alternative accounts of topological explanations, and also it outlines responses to some of the main criticisms raised by the (...) so-called new mechanists. (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)

We provide two programmatic frameworks for integrating philosophical research on understanding with complementary work in computer science, psychology, and neuroscience. First, philosophical theories of understanding have consequences about how agents should reason if they are to understand that can then be evaluated empirically by their concordance with findings in scientific studies of reasoning. Second, these studies use a multitude of explanations, and a philosophical theory of understanding is well suited to integrating these explanations in illuminating ways.

In this paper, I present a general theory of topological explanations, and illustrate its fruitfulness by showing how it accounts for explanatory asymmetry. My argument is developed in three steps. In the first step, I show what it is for some topological property A to explain some physical or dynamical property B. Based on that, I derive three key criteria of successful topological explanations: a criterion concerning the facticity of topological explanations, i.e. what makes it true of a particular system; (...) a criterion for describing counterfactual dependencies in two explanatory modes, i.e. the vertical and the horizontal; and, finally, a third perspectival one that tells us when to use the vertical and when to use the horizontal mode. In the second step, I show how this general theory of topological explanations accounts for explanatory asymmetry in both the vertical and horizontal explanatory modes. Finally, in the third step, I argue that this theory is universally applicable across biological sciences, which helps to unify essential concepts of biological networks. (shrink)

At the beginning of the 20th century, Gestalt psychologists put forward the concept of psychoneural isomorphism, which was meant to replace Fechner’s obscure notion of psychophysical parallelism and provide a heuristics that may facilitate the search for the neural correlates of the mind. However, the concept has generated much confusion in the debate, and today its role is still unclear. In this contribution, I will attempt a little conceptual spadework in clarifying the concept of psychoneural isomorphism, focusing exclusively on conscious (...) visual perceptual experience and its neural correlates. Firstly, I will outline the history of our concept, and its alleged metaphysical and epistemic roles. Then, I will clarify the nature of isomorphism and rule out its metaphysical role. Finally, I will review some epistemic roles of our concept, zooming in on the work of Jean Petitot, and suggest that it does not play a relevant heuristic role. I conclude suggesting that psychoneural isomorphism might be an indicator of robustness for certain mathematical descriptions of perceptual content. (shrink)