The goal of this paper is to develop a counterfactual theory of explanation. The CTE provides a monist framework for causal and non-causal explanations, according to which both causal and non-causal explanations are explanatory by virtue of revealing counterfactual dependencies between the explanandum and the explanans. I argue that the CTE is applicable to two paradigmatic examples of non-causal explanations: Euler’s explanation and renormalization group explanations of universality.

Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and compare these two (...) accounts of organization and argue that understanding biological organisms as cohesively integrated systems benefits from insights from both. To bring together the two accounts, we focus on the notions of control and regulation as bridge concepts. We start from a characterization of biological mechanisms in terms of constraints and focus on a specific type of mechanism, control mechanisms, that operate on other mechanisms on the basis of measurements of variables in the system and its environment. Control mechanisms are characterized by their own set of constraints that enable them to sense conditions, convey signals, and effect changes on constraints in the controlled mechanism. They thereby allow living organisms to adapt to internal and external variations and to coordinate their parts in such a manner as to maintain viability. Because living organisms contain a vast number of control mechanisms, a central challenge is to understand how they are themselves organized. With the support of examples from both unicellular and multicellular systems we argue that control mechanisms are organized heterarchically, and we discuss how this type of control architecture can, without invoking top-down and centralized forms of organizations, succeed in coordinating internal activities of organisms. (shrink)

An account of distinctively mathematical explanation (DME) should satisfy three desiderata: it should account for the modal import of some DMEs; it should distinguish uses of mathematics in explanation that are distinctively mathematical from those that are not (Baron [2016]); and it should also account for the directionality of DMEs (Craver and Povich [2017]). Baron’s (forthcoming) deductive-mathematical account, because it is modelled on the deductive-nomological account, is unlikely to satisfy these desiderata. I provide a counterfactual account of DME, the Narrow (...) Ontic Counterfactual Account (NOCA), that can satisfy all three desiderata. NOCA appeals to ontic considerations to account for explanatory asymmetry and ground the relevant counterfactuals. NOCA provides a unification of the causal and the non-causal, the ontic and the modal, by identifying a common core that all explanations share and in virtue of which they are explanatory. (shrink)

In this article, network science is discussed from a methodological perspective, and two central theses are defended. The first is that network science exploits the very properties that make a system complex. Rather than using idealization techniques to strip those properties away, as is standard practice in other areas of science, network science brings them to the fore, and uses them to furnish new forms of explanation. The second thesis is that network representations are particularly helpful in explaining the properties (...) of non-decomposable systems. Where part-whole decomposition is not possible, network science provides a much-needed alternative method of compressing information about the behavior of complex systems, and does so without succumbing to problems associated with combinatorial explosion. The article concludes with a comparison between the uses of network representation analyzed in the main discussion, and an entirely distinct use of network representation that has recently been discussed in connection with mechanistic modeling. (shrink)

In “What Makes a Scientific Explanation Distinctively Mathematical?” (2013b), Lange uses several compelling examples to argue that certain explanations for natural phenomena appeal primarily to mathematical, rather than natural, facts. In such explanations, the core explanatory facts are modally stronger than facts about causation, regularity, and other natural relations. We show that Lange's account of distinctively mathematical explanation is flawed in that it fails to account for the implicit directionality in each of his examples. This inadequacy is remediable in each (...) case by appeal to ontic facts that account for why the explanation is acceptable in one direction and unacceptable in the other direction. The mathematics involved in these examples cannot play this crucial normative role. While Lange's examples fail to demonstrate the existence of distinctively mathematical explanations, they help to emphasize that many superficially natural scientific explanations rely for their explanatory force on relations of stronger-than-natural necessity. These are not opposing kinds of scientific explanations; they are different aspects of scientific explanation. (shrink)

A prominent approach to scientific explanation and modeling claims that for a model to provide an explanation it must accurately represent at least some of the actual causes in the event's causal history. In this paper, I argue that many optimality explanations present a serious challenge to this causal approach. I contend that many optimality models provide highly idealized equilibrium explanations that do not accurately represent the causes of their target system. Furthermore, in many contexts, it is in virtue of (...) their independence of causes that optimality models are able to provide a better explanation than competing causal models. Consequently, our account of explanation and modeling must expand beyond the causal approach. (shrink)

This paper explores the question of whether all or most explanations in biology are, or ideally should be, ‘mechanistic’. I begin by providing an account of mechanistic explanation, making use of the interventionist ideas about causation I have developed elsewhere. This account emphasizes the way in which mechanistic explanations, at least in the biological sciences, integrate difference‐making and spatio‐temporal information, and exhibit what I call fine‐tunedness of organization. I also emphasize the role played by modularity conditions in mechanistic explanation. I (...) will then argue, in agreement with John Dupré, that, given this account, it is plausible that many biological systems require explanations that are relatively non‐mechanical or depart from expectations one associates with the behaviour of machines. (shrink)

This article examines three candidate cases of non-causal explanation in computational neuroscience. I argue that there are instances of efficient coding explanation that are strongly analogous to examples of non-causal explanation in physics and biology, as presented by Batterman, Woodward, and Lange. By integrating Lange’s and Woodward’s accounts, I offer a new way to elucidate the distinction between causal and non-causal explanation, and to address concerns about the explanatory sufficiency of non-mechanistic models in neuroscience. I also use this framework to (...) shed light on the dispute over the interpretation of dynamical models of the brain. _1_ Introduction _1.1_ Efficient coding explanation in computational neuroscience _1.2_ Defining non-causal explanation _2_ Case I: Hybrid Computation _3_ Case II: The Gabor Model Revisited _4_ Case III: A Dynamical Model of Prefrontal Cortex _4.1_ A new explanation of context-dependent computation _4.2_ Causal or non-causal? _5_ Causal and Non-causal: Does the Difference Matter? (shrink)

In this paper, I aim to provide access to the current debate on non-causal explanations in philosophy of science. I will first present examples of non-causal explanations in the sciences. Then, I will outline three alternative approaches to non-causal explanations – that is, causal reductionism, pluralism, and monism – and, corresponding to these three approaches, different strategies for distinguishing between causal and non-causal explanation. Finally, I will raise questions for future research on non-causal explanations.

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)

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)

Batterman and Rice ([2014]) argue that minimal models possess explanatory power that cannot be captured by what they call ‘common features’ approaches to explanation. Minimal models are explanatory, according to Batterman and Rice, not in virtue of accurately representing relevant features, but in virtue of answering three questions that provide a ‘story about why large classes of features are irrelevant to the explanandum phenomenon’ ([2014], p. 356). In this article, I argue, first, that a method (the renormalization group) they propose (...) to answer the three questions cannot answer them, at least not by itself. Second, I argue that answers to the three questions are unnecessary to account for the explanatoriness of their minimal models. Finally, I argue that a common features account, what I call the ‘generalized ontic conception of explanation’, can capture the explanatoriness of minimal models. (shrink)

In this paper, I first argue against various attempts to justify idealizations in scientific models that explain by showing that they are harmless and isolable distortions of irrelevant features. In response, I propose a view in which idealized models are characterized as providing holistically distorted representations of their target system. I then suggest an alternative way that idealized modeling can be justified by appealing to universality.

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)

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.

The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from (...) the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity. (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)

While mechanistic explanation and, to a lesser extent, nomological explanation are well-explored topics in the philosophy of biology, topological explanation is not. Nor is the role of diagrams in topological explanations. These explanations do not appeal to the operation of mechanisms or laws, and extant accounts of the role of diagrams in biological science explain neither why scientists might prefer diagrammatic representations of topological information to sentential equivalents nor how such representations might facilitate important processes of explanatory reasoning unavailable to (...) scientists who restrict themselves to sentential representations. Accordingly, relying upon a case study about immune system vulnerability to attacks on CD4+ T-cells, I argue that diagrams group together information in a way that avoids repetition in representing topological structure, facilitate identification of specific topological properties of those structures, and make available to controlled processing explanatorily salient counterfactual information about topological structures, all in ways that sentential counterparts of diagrams do not. (shrink)

Besides mechanistic explanations of phenomena, which have been seriously investigated in the last decade, biology and ecology also include explanations that pinpoint specific mathematical properties as explanatory of the explanandum under focus. Among these structural explanations, one finds topological explanations, and recent science pervasively relies on them. This reliance is especially due to the necessity to model large sets of data with no practical possibility to track the proper activities of all the numerous entities. The paper first defines topological explanations (...) and then explains why topological explanations and mechanisms are different in principle. Then it shows that they are pervasive both in the study of networks—whose importance has been increasingly acknowledged at each level of the biological hierarchy—and in contexts where the notion of selective neutrality is crucial; this allows me to capture the difference between mechanisms and topological explanations in terms of practical modelling practices. The rest of the paper investigates how in practice mechanisms and topologies are combined. They may be articulated in theoretical structures and explanatory strategies, first through a relation of constraint, second in interlevel theories, or they may condition each other. Finally, I explore how a particular model can integrate mechanistic informations, by focusing on the recent practice of merging networks in ecology and its consequences upon multiscale modelling. (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)

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)

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...) broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation. (shrink)

In the last 20 years or so, since the publication of a seminal paper by Watts and Strogatz :440–442, 1998), an interest in topological explanations has spread like a wild fire over many areas of science, e.g. ecology, evolutionary biology, medicine, and cognitive neuroscience. The topological approach is still very young by all standards, and even within special sciences it still doesn’t have a single methodological programme that is applicable across all areas of science. That is why this special issue (...) is important as a first systematic philosophical study of topological explanations and their relation to a well understood and widespread explanatory strategy, such as mechanistic one. (shrink)

Biologists explain organisms’ behavior not only as having been programmed by genes and shaped by natural selection, but also as the result of an organism’s agency: the capacity to react to environmental changes in goal-driven ways. The use of such ‘agential explanations’ reopens old questions about how justified it is to ascribe agency to entities like bacteria or plants that obviously lack rationality and even a nervous system. Is organismic agency genuinely ‘real’ or is it just a useful fiction? In (...) this paper we focus on two questions: whether agential explanations are to be interpreted ontically, and whether they can be reduced to non-agential explanations (thereby dispensing with agency). The Kantian approach we identify interprets agential explanations non-ontically, yet holds agency to be indispensable. Attributing agency to organisms is not to be taken literally in the way we attribute physical properties such as mass or acceleration, but nor is it a mere heuristic or predictive tool. Rather, it is an inevitable consequence of our own rational capacity: as long as we are rational agents ourselves, we cannot avoid seeing agency in organisms. (shrink)

There have been recent disagreements in the philosophy of neuroscience regarding which sorts of scientific models provide mechanistic explanations, and which do not. These disagreements often hinge on two commonly adopted, but conflicting, ways of understanding mechanistic explanations: what I call the “representation-as” account, and the “representation-of” account. In this paper, I argue that neither account does justice to neuroscientific practice. In their place, I offer a new alternative that can defuse some of these disagreements. I argue that individual models (...) do not provide mechanistic explanations by themselves. Instead, individual models are always used to complement a huge body of background information and pre-existing models about the target system. With this in mind, I argue that mechanistic explanations are distributed across sets of different, and sometimes contradictory, scientific models. Each of these models contributes limited, but essential, information to the same mechanistic explanation, but none can be considered a mechanistic explanation in isolation of the others. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

Medical explanations have often been thought on the model of biological ones and are frequently defined as mechanistic explanations of a biological dysfunction. In this paper, I argue that topological explanations, which have been described in ecology or in cognitive sciences, can also be found in medicine and I discuss the relationships between mechanistic and topological explanations in medicine, through the example of network medicine and medical genetics. Network medicine is a recent discipline that relies on the analysis of various (...) disease networks in order to find organizing principles in disease explanation. My aim is to show how topological explanations in network medicine can help solving the conceptual issues that pure mechanistic explanations of the genetics of disease are currently facing, namely the crisis of the concept of genetic disease, the progressive geneticization of diseases and the dissolution of the distinction between monogenic and polygenic diseases. However, I will also argue that topological explanations should not be considered as independent and radically different from mechanistic explanations for at least two reasons. First, in network medicine, topological explanations depend on and use mechanistic information. Second, they leave out some missing gaps in disease explanation that require, in turn, the development of new mechanistic explanations. Finally, I will insist on the specific contribution of topological explanations in medicine: they push us to develop an explanation of disease in general, instead of focusing on single explanations of individual diseases. This last point may have major consequences for biomedical research. (shrink)

If ontic dependence is the basis of explanation, there cannot be mathematical explanations. Accounting for the explanatory dependency between mathematical properties and empirical phenomena poses i...

This article demonstrates that non-mechanistic, dynamical explanations are a viable approach to explanation in the special sciences. The claim that dynamical models can be explanatory without reference to mechanisms has previously been met with three lines of criticism from mechanists: the causal relevance concern, the genuine laws concern, and the charge of predictivism. I argue, however, that these mechanist criticisms fail to defeat non-mechanistic, dynamical explanation. Using the examples of Haken et al.’s model of bimanual coordination, and Thelen et al.’s (...) dynamical field model of infant perseverative reaching, I show how each mechanist criticism fails once the standards of Woodward’s interventionist framework are applied to dynamical models. An even-handed application of Woodwardian interventionism reveals that dynamical models are capable of producing genuine explanations without appealing to underlying mechanistic details. 1Introduction2Interventionism and Mechanistic Explanation 2.1Causal relevance and ideal interventions2.2Invariance2.3Explanation3Covering-Laws and Dynamical Explanation 3.1Dynamical models3.2Covering-law explanation3.3Prediction4Causal Relevance 4.1The causal relevance concern4.2Intervening on dynamical models4.3Test case I: The Haken–Kelso–Bunz model4.4Test case II: Dynamical field model5Genuine Laws 5.1The genuine laws concern5.2Using invariance in place of laws5.3Test case I: The Haken–Kelso–Bunz model5.4Test case II: Dynamical field model6Prediction 6.1Predictivism6.2Crude and invariant prediction7Interventionist Criticism of the Haken–Kelso–Bunz Model8Dynamical Explanation8Conclusion. (shrink)

In the recent philosophy of explanation, a growing attention to and discussion of non-causal explanations has emerged, as there seem to be compelling examples of non-causal explanations in the sciences, in pure mathematics, and in metaphysics. I defend the claim that the counterfactual theory of explanation (CTE) captures the explanatory character of both non-causal scientific and metaphysical explanations. According to the CTE, scientific and metaphysical explanations are explanatory by virtue of revealing counterfactual dependencies between the explanandum and the explanans. I (...) support this claim by illustrating that CTE is applicable to Euler’s explanation (an example of a non-causal scientific explanation) and Loewer’s explanation (an example of a non-causal metaphysical explanation). (shrink)

Explanation is asymmetric: if A explains B, then B does not explain A. Tradition- ally, the asymmetry of explanation was thought to favor causal accounts of explanation over their rivals, such as those that take explanations to be inferences. In this paper, we develop a new inferential approach to explanation that outperforms causal approaches in accounting for the asymmetry of explanation.

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 (...) approach in emphasizing a theory-constituting role of general principles. Design principles signify general dependency-relations between structures and functions, given a set of formally defined constraints. I contend that design principles increase our understanding of living systems by relating specific models to general types. The categorization of types is based on a delineation of the scope of biological possibilities, which serves to identify and define the generic features of classes of systems. To characterize the basis for general principles through generic abstraction and reasoning about possibility spaces, I coin the term constraint-based generality. I show that constraint-based generality is distinct from other types of generality in biology, and argue that general principles play a unifying role that does not entail theory reduction. (shrink)

In the recent philosophy of explanation, a growing attention to and discussion of non-causal explanations has emerged, as there seem to be compelling examples of non-causal explanations in the sciences, in pure mathematics, and in metaphysics. I defend the claim that the counterfactual theory of explanation captures the explanatory character of both non-causal scientific and metaphysical explanations. According to the CTE, scientific and metaphysical explanations are explanatory by virtue of revealing counterfactual dependencies between the explanandum and the explanans. I support (...) this claim by illustrating that CTE is applicable to Euler’s explanation and Loewer’s explanation. (shrink)

Although they are continually compositionally reconstituted and reconfigured, organisms nonetheless persist as ontologically unified beings over time – but in virtue of what? A common answer is: in virtue of their continued possession of the capacity for morphological invariance which persists through, and in spite of, their mereological alteration. While we acknowledge that organisms‟ capacity for the “stability of form” – homeostasis - is an important aspect of their diachronic unity, we argue that this capacity is derived from, and grounded (...) in a more primitive one – namely, the homeodynamic capacity for the “specified variation of form”. In introducing a novel type of causal power – a „structural power‟ – we claim that it is the persistence of their dynamic potential to produce a specified series of structurally adaptive morphologies which grounds organisms‟ privileged status as metaphysically “one over many” over time. (shrink)

The dominant view today on evolutionary progress is that it has been thoroughly debunked. Even value-neutral progress concepts are seen to lack important theoretical underpinnings: natural selection provides no rationale for progress, and natural selection need not even be invoked to explain large-scale evolutionary trends. In this paper I challenge this view by analysing how natural selection acts in heterogeneous environments. This not only undermines key debunking arguments, but also provides a selectionist rationale for a pattern of “evolutionary unfolding”, where (...) life radiates across an increased range of exploitation of environmental heterogeneity. (shrink)

Recent philosophical work has explored the distinction between causal and non-causal forms of explanation. In this literature, topological explanation is viewed as a clear example of the non-causal variety–it is claimed that topology lacks temporal information, which is necessary for causal structure. This paper explores the distinction between topological and causal forms of explanation and argues that this distinction is not as clear cut as the literature suggests. One reason for this is that some explanations involve both topological and causal (...) information. In these “borderline” cases scientists explain some outcome by appealing to the causal topology of the system of interest. These cases help clarify a type of topological explanation that is genuinely causal, but that differs from standard topological and interventionist accounts of explanation. (shrink)

Biological individuals are usually defined by evolutionists through a reference to natural selection. This article looks for a concept of individuality that would hold at the same time for organisms and for communities or ecosystems, the latter being unaffected by natural selection. In the wake of Simon’s notion of “quasi-independence,” I elaborate a concept of “weak individuality” defined by probabilistic connections between sub-entities, read off our knowledge of their interactions. This formal scheme of connections allows one to infer what are (...) the individuals in the domain addressed by the theory of the interactions. The article argues that if ecosystems do not have strong individuality, they still possess a weak individuality, ecological theories providing the values of the variables in the formula for individuality. (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)

Life scientists increasingly rely upon abstraction-based modeling and reasoning strategies for understanding biological phenomena. We introduce the notion of constraint-based reasoning as a fruitful tool for conceptualizing some of these developments. One important role of mathematical abstractions is to impose formal constraints on a search space for possible hypotheses and thereby guide the search for plausible causal models. Formal constraints are, however, not only tools for biological explanations but can be explanatory by virtue of clarifying general dependency-relations and patterning between (...) functions and structures. We describe such situations as constraint-based explanations and argue that these differ from mechanistic strategies in important respects. While mechanistic explanations emphasize change-relating causal features, constraint-based explanations emphasize formal dependencies and generic organizational features that are relatively independent of lower-level changes in causal details. Our distinction between mechanistic and constraint-based explanations is pragmatically motivated by the wish to understand scientific practice. We contend that delineating the affordances and assumptions of different explanatory questions and strategies helps to clarify tensions between diverging scientific practices and the innovative potentials in their combination. Moreover, we show how constraint-based explanation integrates several features shared by otherwise different philosophical accounts of abstract explanatory strategies in biology. (shrink)

Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)

Traditionally, a scientific model is thought to provide a good scientific explanation to the extent that it satisfies certain scientific goals that are thought to be constitutive of explanation. Problems arise when we realize that individual scientific models cannot simultaneously satisfy all the scientific goals typically associated with explanation. A given model’s ability to satisfy some goals must always come at the expense of satisfying others. This has resulted in philosophical disputes regarding which of these goals are in fact necessary (...) for explanation, and as such which types of models can and cannot provide explanations. Explanatory monists argue that one goal will be explanatory in all contexts, while explanatory pluralists argue that the goal will vary based on pragmatic considerations. In this paper, I argue that such debates are misguided, and that both monists and pluralists are incorrect. Instead of any goal being given explanatory priority over others in a given context, the different goals are all deeply dependent on one another for their explanatory power. Any model that sacrifices some explanatory goals to attain others will always necessarily undermine its own explanatory power in the process. And so when forced to choose between individual scientific models, there can be no explanatory victors. Given that no model can satisfy all the goals typically associated with explanation, no one model in isolation can provide a good scientific explanation. Instead we must appeal to collections of models. Collections of models provide an explanation when they satisfy the web of interconnected goals that justify the explanatory power of one another. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

COVID-19 has substantially affected our lives during 2020. Since its beginning, several epidemiological models have been developed to investigate the specific dynamics of the disease. Early COVID-19 epidemiological models were purely statistical, based on a curve-fitting approach, and did not include causal knowledge about the disease. Yet, these models had predictive capacity; thus they were used to ground important political decisions, in virtue of the understanding of the dynamics of the pandemic that they offered. This raises a philosophical question about (...) how purely statistical models can yield understanding, and if so, what the relationship between prediction and understanding in these models is. Drawing on the model that was developed by the Institute of Health Metrics and Evaluation, we argue that early epidemiological models yielded a modality of understanding that we call descriptive understanding, which contrasts with the so-called explanatory understanding which is assumed to be the main form of scientific understanding. We spell out the exact details of how descriptive understanding works, and efficiently yields understanding of the phenomena. Finally, we vindicate the necessity of studying other modalities of understanding that go beyond the conventionally assumed explanatory understanding. (shrink)

We address the question of whether and to what extent explanatory and modelling strategies in systems biology are mechanistic. After showing how dynamic mathematical models are actually required for mechanistic explanations of complex systems, we caution readers against expecting all systems biology to be about mechanistic explanations. Instead, the aim may be to generate topological explanations that are not standardly mechanistic, or to arrive at design principles that explain system organization and behaviour in general, but not specific mechanisms. These abstraction (...) strategies serve various aims, including prediction and control, that are central to understanding the epistemic diversity of systems biology. (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)

In the recent literature on causal and non-causal scientific explanations, there is an intuitive assumption according to which an explanation is non-causal by virtue of being abstract. In this context, to be ‘abstract’ means that the explanans in question leaves out many or almost all causal microphysical details of the target system. After motivating this assumption, we argue that the abstractness assumption, in placing the abstract and the causal character of an explanation in tension, is misguided in ways that are (...) independent of which view of causation or causal explanation one takes to be most accurate. On major accounts of causation, as well as on major accounts of causal explanation, the abstractness of an explanation is not sufficient for it being non-causal. That is, explanations are not non-causal by dint of being abstract. (shrink)

This paper examines various ways in which philosophy of science can be interdisciplinary. It aims to provide a map of relations between philosophy and sciences, some of which are interdisciplinary. Such a map should also inform discussions concerning the question “How much philosophy is there in the philosophy of science?” In Sect. 1, we distinguish between synoptic and collaborative interdisciplinarity. With respect to the latter, we furthermore distinguish between two kinds of reflective forms of collaborative interdisciplinarity. We also briefly explicate (...) how complexity triggers interdisciplinarity. In Sect. 2, we apply the distinctions of Sect. 1 to philosophy of science and analyze in which sense different styles of philosophy of science are interdisciplinary. The styles that we discuss are a synoptic-general, a reflective-general, a reflective-particular, a particular-embedded and a descriptive or normative style. (shrink)

Systems biology has provided new resources for discovering and reasoning about mechanisms. In addition to generating databases of large bodies of data, systems biologists have introduced platforms such as Cytoscape to represent protein–protein interactions, gene interactions, and other data in networks. Networks are inherently flat structures. One can identify clusters of highly connected nodes, but network representations do not represent these clusters as at a higher level than their constituents. Mechanisms, however, are hierarchically organized: they can be decomposed into their (...) parts and their activities can be decomposed into component operations. A potent bridge between flat networks and hierarchical mechanisms is provided by biological ontologies, both those curated by hand such as Gene Ontology and those extracted directly from databases such as Network Extracted Ontology. I examine several examples in which by applying ontologies to networks, systems biologists generate new hypotheses about mechanisms and characterize these novel strategies for developing mechanistic explanations. (shrink)

In the philosophy of science, increasing attention has been given to the methodological novelties associated with the study of complex systems. However, there is little agreement on exactly what complex systems are. Although many characterizations of complex systems are available, they tend to be either impressionistic or overly formal. Formal definitions rely primarily on ideas from the study of computational complexity, but the relation between these formal ideas and the messy world of empirical phenomena is unclear. Here, I give a (...) definition of complex systems that draws on algorithmic complexity theory, but also provides a way of interpreting the formal idea in an empirical setting. I then use the definition to show that two canonical forms of scientific idealization are empirically inadequate when applied to complex systems. The inadequacy of these forms of idealization is shown to be the primary reason that complex systems require novel methods. Moreover, this demand for novel methods helps explain the rise of complex systems science as an autonomous discipline. (shrink)