After a decade of intense debate about mechanisms, there is still no consensus characterization. In this paper we argue for a characterization that applies widely to mechanisms across the sciences. We examine and defend our disagreements with the major current contenders for characterizations of mechanisms. Ultimately, we indicate that the major contenders can all sign up to our characterization.

Not all models are explanatory. Some models are data summaries. Some models sketch explanations but leave crucial details unspecified or hidden behind filler terms. Some models are used to conjecture a how-possibly explanation without regard to whether it is a how-actually explanation. I use the Hodgkin and Huxley model of the action potential to illustrate these ways that models can be useful without explaining. I then use the subsequent development of the explanation of the action potential to show what is (...) required of an adequate mechanistic model. Mechanistic models are explanatory. (shrink)

According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects of scientific (...) explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (shrink)

Characterization of a form of explanation involving grounding on the model of mechanistic causal explanation.

The concept of mechanism in biology has three distinct meanings. It may refer to a philosophical thesis about the nature of life and biology (‘mechanicism’), to the internal workings of a machine-like structure (‘machine mechanism’), or to the causal explanation of a particular phenomenon (‘causal mechanism’). In this paper I trace the conceptual evolution of ‘mechanism’ in the history of biology, and I examine how the three meanings of this term have come to be featured in the philosophy of biology, (...) situating the new ‘mechanismic program’ in this context. I argue that the leading advocates of the mechanismic program (i.e., Craver, Darden, Bechtel, etc.) inadvertently conflate the different senses of ‘mechanism’. Specifically, they all inappropriately endow causal mechanisms with the ontic status of machine mechanisms, and this invariably results in problematic accounts of the role played by mechanism-talk in scientific practice. I suggest that for effective analyses of the concept of mechanism, causal mechanisms need to be distinguished from machine mechanisms, and the new mechanismic program in the philosophy of biology needs to be demarcated from the traditional concerns of mechanistic biology. (shrink)

The central aim of this article is to specify the ontological nature of constitutive mechanistic phenomena. After identifying three criteria of adequacy that any plausible approach to constitutive mechanistic phenomena must satisfy, we present four different suggestions, found in the mechanistic literature, of what mechanistic phenomena might be. We argue that none of these suggestions meets the criteria of adequacy. According to our analysis, constitutive mechanistic phenomena are best understood as what we will call ‘object-involving occurrents’. Furthermore, on the basis (...) of this notion, we will clarify what distinguishes constitutive mechanistic explanations from etiological ones. 1 Introduction 2 Criteria of Adequacy 2.1 Descriptive adequacy 2.2 Constitutive–etiological distinction 2.3 Constitution 3 The Ontological Nature of Constitutive Mechanistic Phenomena 3.1 Phenomena as input–output relations 3.2 Phenomena as end states 3.3 Phenomena as dispositions 3.4 Phenomena as behaviours 4 Phenomena as Object-Involving Occurrents 4.1 What object-involving occurrents are and why we need them 4.2 The object in the phenomenon 4.3 The adequacy of option 5 Conclusion. (shrink)

The interventionist account of causal explanation, in the version presented by Jim Woodward, has been recently claimed capable of buttressing the widely felt—though poorly understood—hunch that high-level, relatively abstract explanations, of the sort provided by sciences like biology, psychology and economics, are in some cases explanatorily optimal. It is the aim of this paper to show that this is mistaken. Due to a lack of effective constraints on the causal variables at the heart of the interventionist causal-explanatory scheme, as presently (...) formulated it is either unable to prefer high-level explanations to low, or systematically overshoots, recommending explanations at so high of a level as to be virtually vacuous. (shrink)

Mechanistic explanation has an impressive track record of advancing our understanding of complex, hierarchically organized physical systems, particularly biological and neural systems. But not every complex system can be understood mechanistically. Psychological capacities are often understood by providing cognitive models of the systems that underlie them. I argue that these models, while superficially similar to mechanistic models, in fact have a substantially more complex relation to the real underlying system. They are typically constructed using a range of techniques for abstracting (...) the functional properties of the system, which may not coincide with its mechanistic organization. I describe these techniques and show that despite being non-mechanistic, these cognitive models can satisfy the normative constraints on good explanations. (shrink)

Many accounts of scientific modelling assume that models can be decomposed into the contributions made by their accurate and inaccurate parts. These accounts then argue that the inaccurate parts of the model can be justified by distorting only what is irrelevant. In this paper, I argue that this decompositional strategy requires three assumptions that are not typically met by our best scientific models. In response, I propose an alternative view in which idealized models are characterized as holistically distorted representations that (...) are justified by allowing for the application of various modelling techniques. (shrink)

This article presents a distinct sense of ‘mechanism’, which I call the functional sense of mechanism. According to this sense, mechanisms serve functions, and this fact places substantive restrictions on the kinds of system activities ‘for which’ there can be a mechanism. On this view, there are no mechanisms for pathology; pathologies result from disrupting mechanisms for functions. Second, on this sense, natural selection is probably not a mechanism for evolution because it does not serve a function. After distinguishing this (...) sense fromsimilar explications of ‘mechanism’, I argue that it is ubiquitous in biology and has valuable epistemic benefits. (shrink)

I distinguish three theses associated with the new mechanistic philosophy – concerning causation, explanation and scientific methodology. Advocates of each thesis are identified and relationships among them are outlined. I then look at some recent work on natural selection and mechanisms. There, attention to different kinds of New Mechanism significantly affects of what is at stake.

The Hodgkin–Huxley (HH) model of the action potential is a theoretical pillar of modern neurobiology. In a number of recent publications, Carl Craver ([2006], [2007], [2008]) has argued that the model is explanatorily deficient because it does not reveal enough about underlying molecular mechanisms. I offer an alternative picture of the HH model, according to which it deliberately abstracts from molecular specifics. By doing so, the model explains whole-cell behaviour as the product of a mass of underlying low-level events. The (...) issue goes beyond cellular neurobiology, for the strategy of abstraction exhibited in the HH case is found in a range of biological contexts. I discuss why it has been largely neglected by advocates of the mechanist approach to explanation. 1 Introduction2 A Primer on the HH Model2.1 The basic qualitative picture2.2 The quantitative model3 Interlude: What Did Hodgkin and Huxley Think?4 Craver’s View4.1 Mechanistic explanation4.2 Sketches4.3 Craver's view: The HH model as a mechanism sketch5 An Alternative View of the HH Model5.1 Another look at the equations5.2 The discrete-gating picture5.3 The road paved by Hodgkin and Huxley5.4 Summary and comparison to Craver6 Conclusion: The HH Model and Mechanistic Explanation6.1 Sketches and abstractions6.2 Why has aggregative abstraction been overlooked? (shrink)

Even though the evidence‐based medicine movement (EBM) labels mechanisms a low quality form of evidence, consideration of the mechanisms on which medicine relies, and the distinct roles that mechanisms might play in clinical practice, offers a number of insights into EBM itself. In this paper, I examine the connections between EBM and mechanisms from several angles. I diagnose what went wrong in two examples where mechanistic reasoning failed to generate accurate predictions for how a dysfunctional mechanism would respond to intervention. (...) I then use these examples to explain why we should expect this kind of mechanistic reasoning to fail in systematic ways, by situating these failures in terms of evolved complexity of the causal system(s) in question. I argue that there is still a different role in which mechanisms continue to figure as evidence in EBM: namely, in guiding the application of population‐level recommendations to individual patients. Thus, even though the evidence‐based movement rejects one role in which mechanistic reasoning serves as evidence, there are other evidentiary roles for mechanistic reasoning. This renders plausible the claims of some critics of evidencebased medicine who point to the ineliminable role of clinical experience. Clearly specifying the ways in which mechanisms and mechanistic reasoning can be involved in clinical practice frames the discussion about EBM and clinical experience in more fruitful terms. (shrink)

In this field guide, I distinguish five separate senses with which the term ‘mechanism’ is used in contemporary philosophy of science. Many of these senses have overlapping areas of application but involve distinct philosophical claims and characterize the target mechanisms in relevantly different ways. This field guide will clarify the key features of each sense and introduce some main debates, distinguishing those that transpire within a given sense from those that are best understood as concerning distinct senses. The ‘new mechanisms’ (...) sense is at the center of most of these contemporary debates and will be treated at greater length; subsequent senses of mechanism will be primarily distinguished from this one. In part I of this paper, I distinguish two senses of the term ‘mechanism’, both of which are explicitly hierarchical and nested in character, such that any given mechanism is comprised of smaller sub-mechanisms, in turn comprised of yet smaller sub-sub-mechanisms and so on. While both of the senses discussed here are anti-reductive, they differ in their focus on scientific practice versus metaphysics, in the degree of regularity they attribute to mechanisms, and in terms of their relationships to the discussions of mechanisms in the history of philosophy and science. (shrink)

The ontic conception of scientific explanation has been constructed and motivated on the basis of a putative lexical ambiguity in the term explanation. I raise a puzzle for this ambiguity claim, and then give a deflationary solution under which all ontically-rendered talk of explanation is merely elliptical; what it is elliptical for is a view of scientific explanation that altogether avoids the ontic conception. This result has revisionary consequences for New Mechanists and other philosophers of science, many of whom have (...) assimilated their conception of explanation to the ontic conception. (shrink)

Craver claims that mechanistic explanation is ontic, while Bechtel claims that it is epistemic. While this distinction between ontic and epistemic explanation originates with Salmon, the ideas have changed in the modern debate on mechanistic explanation, where the frame of the debate is changing. I will explore what Bechtel and Craver’s claims mean, and argue that good mechanistic explanations must satisfy both ontic and epistemic normative constraints on what is a good explanation. I will argue for ontic constraints by drawing (...) on Craver’s work in Sect. 2.1, and argue for epistemic constraints by drawing on Bechtel’s work in Sect. 2.2. Along the way, I will argue that Bechtel and Craver actually agree with this claim. I argue that we should not take either kind of constraints to be fundamental, in Sect. 3, and close in Sect. 4 by considering what remains at stake in making a distinction between ontic and epistemic constraints on mechanistic explanation. I suggest that we should not concentrate on either kind of constraint, to the neglect of the other, arguing for the importance of seeing the relationship as one of integration. (shrink)

Many critics of medicalization express concern that the process privileges individualised, biologically grounded interpretations of medicalized phenomena, inhibiting understanding and communication of aspects of those phenomena that are less relevant to their biomedical modelling. I suggest that this line of critique views medicalization as a hermeneutical injustice—a form of epistemic injustice that prevents people having the hermeneutical resources available to interpret and communicate significant areas of their experience. Interpreting the critiques in this fashion shows they frequently fail because they: neglect (...) the ways in which medicalization may not obscure, but rather illuminate, individuals’ experiences; and neglect the testimony of those experiencing first-hand medicalized problems, thus may be guilty of perpetrating testimonial injustice. However, I suggest that such arguments are valuable insofar as they highlight the unwarranted epistemic privilege frequently afforded to medical institutions and medicalized models of phenomena, and a consequent need for greater epistemic humility on the part of health workers and researchers. (shrink)

A common misunderstanding of the selected effects theory of function is that natural selection operating over an evolutionary time scale is the only functionbestowing process in the natural world. This construal of the selected effects theory conflicts with the existence and ubiquity of neurobiological functions that are evolutionary novel, such as structures underlying reading ability. This conflict has suggested to some that, while the selected effects theory may be relevant to some areas of evolutionary biology, its relevance to neuroscience is (...) marginal. This line of reasoning, however, neglects the fact that synapses, entire neurons, and potentially groups of neurons can undergo a type of selection analogous to natural selection operating over an evolutionary time scale. In the following, I argue that neural selection should be construed, by the selected effect theorist, as a distinct type of function-bestowing process in addition to natural selection. After explicating a generalized selected effects theory of function and distinguishing it from similar attempts to extend the selected effects theory, I do four things. First, I show how it allows one to identify neural selection as a distinct function-bestowing process, in contrast to other forms of neural structure formation such as neural construction. Second, I defend the view from one major criticism, and in so doing I clarify the content of the view. Third, I examine drug addiction to show the potential relevance of neural selection to neuroscientific and psychological research. Finally, I endorse a modest pluralism of function concepts within biology. (shrink)

This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely accepted (...) that there is an ‘incremental constraint’ on evolutionary change, in an important class of cases it is difficult to see how to satisfy this constraint. I show that lineage explanations answer important questions about evolutionary change, but do so by demonstrating differences between individuals rather than invoking population processes, such as natural selection.1. Introduction2. Turning a ‘Scale’ into a ‘Plume’3. Lineage Explanations in Biology3.1. The evolution of eyes3.2. The evolution of feathers4. The Two Dimensions of a Lineage Explanation4.1. The production dimension4.2. The continuity dimension4.3. The dual role of the parts5. Constraining the Explanations6. Operational and Generative Lineages7. Explaining Change Without Populations8. Conclusion. (shrink)

Defending or attacking either functionalism or computationalism requires clarity on what they amount to and what evidence counts for or against them. My goal here is not to evaluate their plausibility. My goal is to formulate them and their relationship clearly enough that we can determine which type of evidence is relevant to them. I aim to dispel some sources of confusion that surround functionalism and computationalism, recruit recent philosophical work on mechanisms and computation to shed light on them, and (...) clarify how functionalism and computationalism may or may not legitimately come together. (shrink)

In light of recent criticisms by Woodward (2017) and Rescorla (2018), we examine the relationship between mechanistic explanation and phenomenological laws. We disambiguate several uses of the phrase “phenomenological law” and show how a mechanistic theory of explanation sorts them into those that are and are not explanatory. We also distinguish the problem of phenomenological laws from arguments about the explanatory power of purely phenomenal models, showing that Woodward and Rescorla conflate these problems. Finally, we argue that the temptation to (...) pit mechanistic and interventionist theories of explanation against one another occludes important and scientifically relevant research questions. (shrink)

How regular do mechanisms need to be, in order to count as mechanisms? This paper addresses two arguments for dropping the requirement of regularity from the definition of a mechanism, one motivated by examples from the sciences and the other motivated by metaphysical considerations regarding causation. I defend a broadened regularity requirement on mechanisms that takes the form of a taxonomy of kinds of regularity that mechanisms may exhibit. This taxonomy allows precise explication of the degree and location of regular (...) operation within a mechanism, and highlights the role that various kinds of regularity play in scientific explanation. I defend this regularity requirement in terms of regularity’s role in individuating mechanisms against a background of other causal processes, and by prioritizing mechanisms’ ability to serve as a model of scientific explanation, rather than as a metaphysical account of causation. It is because mechanisms are regular, in the expanded sense described here, that they are capable of supporting the kinds of generalizations that figure prominently in scientific explanations. (shrink)

Francesco Guala once wrote that ‘The problem of extrapolation is a minor scandal in the philosophy of science’. This paper agrees with the statement, but for reasons different from Guala’s. The scandal is not, or not any longer, that the problem has been ignored in the philosophy of science. The scandal is that framing the problem as one of external validity encourages poor evidential reasoning. The aim of this paper is to propose an alternative—an alternative which constitutes much better evidential (...) reasoning about target systems of interest, and which makes do without consideration of external validity. (shrink)

The view that special science properties are multiply realizable has been attacked in recent years by Shapiro, Bechtel and Mundale, Polger, and others. Focusing on psychological and neuroscientific properties, I argue that these attacks are unsuccessful. By drawing on interspecies physiological comparisons I show that diverse physical mechanisms can converge on common functional properties at multiple levels. This is illustrated with examples from the psychophysics and neuroscience of early vision. This convergence is compatible with the existence of general constraints on (...) the evolution of cognitive systems, and does not involve any ad hoc typing of coarse-grained higher level properties. The mechanisms that realize these common higher level properties are really distinct by the criteria laid down by critics of multiple readability. Finally, I present an account of how such functional properties might constitute special science kinds by playing a central explanatory role in a range of cognitive models. Behavioral science kinds in particular are the functionally defined constituents picked out by our most successful models of the multilevel systems and mechanisms that explain cognitive capacities. (shrink)

This paper critiques the new mechanistic explanatory program on grounds that, even when applied to the kinds of examples that it was originally designed to treat, it does not distinguish correct explanations from those that blunder. First, I offer a systematization of the explanatory account, one according to which explanations are mechanistic models that satisfy three desiderata: they must 1) represent causal relations, 2) describe the proper parts, and 3) depict the system at the right ‘level.’ Second, I argue that (...) even the most developed attempts to fulfill these desiderata fall short by failing to appropriately constrain explanatorily apt mechanistic models. -/- *This paper used to be called "The Emperor's New Mechanisms". (shrink)

Life-science phenomena are often explained by specifying the mechanisms that bring them about. The new mechanistic philosophers have done much to substantiate this claim and to provide us with a better understanding of what mechanisms are and how they explain. Although there is disagreement among current mechanists on various issues, they share a common core position and a seeming commitment to some form of scientific realism. But is such a commitment necessary? Is it the best way to go about mechanistic (...) explanation? In this article, we propose an alternative antirealist account that also fits explanatory practice in the life sciences. We pay special attention to mechanistic models, i.e. scientific models that involve a mechanism, and to the role of coherence considerations in building such models. To illustrate our points, we consider the mechanism for the action potential. 1 Introduction2 Some Core Features of Mechanistic Explanation3 Scientific Realism and Mechanistic Explanation4 Antirealist Mechanistic Explanation: The Case of the Action Potential5 Some Outstanding Issues for the Antirealist Mechanist6 Two Problems for the Realist Mechanist7 Conclusions. (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)

According to the new mechanistic approach, an acting entity is at a lower mechanistic level than another acting entity if and only if the former is a component in the mechanism for the latter. Craver and Bechtel :547–563, 2007. doi:10.1007/s10539-006-9028-8) argue that a consequence of this view is that there cannot be causal interactions between acting entities at different mechanistic levels. Their main reason seems to be what I will call the Metaphysical Argument: things at different levels of a mechanism (...) are related as part and whole; wholes and their parts cannot be related as cause and effect; hence, interlevel causation in mechanisms is impossible. I will analyze this argument in more detail and show under which conditions it is valid. This analysis will reveal that interlevel causation in mechanisms is indeed possible, if we take seriously the idea that the relata of the mechanistic level relation are acting entities and accept a slightly modified notion of a mechanistic level that is highly plausible in the light of the first clarification. (shrink)

Mechanistic philosophy of science views a large part of scientific activity as engaged in modelling mechanisms. While science textbooks tend to offer qualitative models of mechanisms, there is increasing demand for models from which one can draw quantitative predictions and explanations. Casini et al. (Theoria 26(1):5–33, 2011) put forward the Recursive Bayesian Networks (RBN) formalism as well suited to this end. The RBN formalism is an extension of the standard Bayesian net formalism, an extension that allows for modelling the hierarchical (...) nature of mechanisms. Like the standard Bayesian net formalism, it models causal relationships using directed acyclic graphs. Given this appeal to acyclicity, causal cycles pose a prima facie problem for the RBN approach. This paper argues that the problem is a significant one given the ubiquity of causal cycles in mechanisms, but that the problem can be solved by combining two sorts of solution strategy in a judicious way. (shrink)

This paper investigates the relationship between structural explanation and the New Mechanistic account of explanation. The aim of this paper is twofold: firstly, to argue that some phenomena in the domain of fundamental physics, although mechanically brute, are structurally explained; and secondly, by elaborating on the contrast between SE and mechanistic explanation to better clarify some features of SE. Finally, this paper will argue that, notwithstanding their apparently antithetical character, SE and ME can be reconciled within a unified account of (...) general scientific explanation. (shrink)

In this paper we identify six theses that constitute core results of philosophical investigation into the nature of mechanisms, and of the role that the search for and identification of mechanisms play in the sciences. These theses represent the fruits of the body of research that is now often called New Mechanism. We concisely present the main arguments for these theses. In the literature, these arguments are scattered and often implicit. Our analysis can guide future research in many ways: it (...) provides critics of New Mechanism with clear targets, it can reduce misunderstandings, it can clarify differences of opinion among New Mechanists and it helps to define a research agenda for New Mechanists. (shrink)

Mechanisms, in the prominent biological sense of the term, are historical entities. That is, whether or not something is a mechanism for something depends on its history. Put differently, while your spontaneously-generated molecule-for-molecule double has a heart, and its heart pumps blood around its body, its heart does not have a mechanism for pumping, since it does not have the right history. My argument for this claim is that mechanisms have proper functions; proper functions are historical entities; so, mechanisms are (...) historical entities, too. This thesis runs against the mainstream new mechanist way of thinking about mechanisms, where mechanisms are generally thought of in an ahistorical way. After arguing for this thesis, I draw out some consequences for philosophy of science and metaphysics. (shrink)

Wesley Salmon’s version of the ontic conception of explanation is a main historical root of contemporary work on mechanistic explanation. This paper examines and critiques the philosophical merits of Salmon’s version, and argues that his conception’s most fundamental construct is either fundamentally obscure, or else reduces to a non-ontic conception of explanation. Either way, the ontic conception is a misconception.

ABSTRACT Proponents of mechanistic explanation have recently suggested that all explanation in the cognitive sciences is mechanistic, even functional explanation. This last claim is surprising, for functional explanation has traditionally been conceived as autonomous from the structural details that mechanistic explanations emphasize. I argue that functional explanation remains autonomous from mechanistic explanation, but not for reasons commonly associated with the phenomenon of multiple realizability. 1Introduction 2Mechanistic Explanation: A Quick Primer 3Functional Explanation: An Example 4Autonomy as Lack of Constraint 5The Price (...) of Autonomy 6Another Argument against Autonomy 7Conclusion: Autonomy and Multiple Realization. (shrink)

Modeling mechanisms is central to the biological sciences – for purposes of explanation, prediction, extrapolation, and manipulation. A closer look at the philosophical literature reveals that mechanisms are predominantly modeled in a purely qualitative way. That is, mechanistic models are conceived of as representing how certain entities and activities are spatially and temporally organized so that they bring about the behavior of the mechanism in question. Although this adequately characterizes how mechanisms are represented in biology textbooks, contemporary biological research practice (...) shows the need for quantitative, probabilistic models of mechanisms, too. In this paper we argue that the formal framework of causal graph theory is well-suited to provide us with models of biological mechanisms that incorporate quantitative and probabilistic information. On the ba-sis of an example from contemporary biological practice, namely feedback regulation of fatty acid biosynthesis in Brassica napus, we show that causal graph theoretical models can account for feedback as well as for the multi-level character of mechanisms. However, we do not claim that causal graph theoretical representations of mechanisms are advantageous in all respects and should replace common qualitative models. Rather, we endorse the more balanced view that causal graph theoretical models of mechanisms are useful for some purposes, while being insufficient for others. (shrink)

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic modeling as (...) a kind of material recomposition strategy also points beyond the mechanistic paradigm. (shrink)

Comparative process tracing is the best analysis of extrapolation inferences in the philosophical and scientific literature so far. In this essay I examine some similarities and differences between comparative process tracing and former attempts to capture the logic of extrapolation, such as the analogical approach. I show that these accounts are not different in spirit, although comparative process tracing supersedes previous proposals in terms of analytical detail. I also examine some qualms about the possibility of drawing extrapolation inferences in the (...) social sciences and conclude by suggesting that there may be cases of extrapolation without process tracing. (shrink)

In this paper, we examine what is to be said in defence of Machamer, Darden and Craver’s (MDC) controversial dualism about activities and entities (Machamer, Darden and Craver’s in Philos Sci 67:1–25, 2000). We explain why we believe the notion of an activity to be a novel, valuable one, and set about clearing away some initial objections that can lead to its being brushed aside unexamined. We argue that substantive debate about ontology can only be effective when desiderata for an (...) ontology are explicitly articulated. We distinguish three such desiderata. The first is a more permissive descriptive ontology of science, the second a more reductive ontology prioritising understanding, and the third a more reductive ontology prioritising minimalism. We compare MDC’s entities-activities ontology to its closest rival, the entities-capacities ontology, and argue that the entities-activities ontology does better on all three desiderata. (shrink)

Some New Mechanists have proposed that claims of compositional relations are justified by combining the results of top-down and bottom-up interlevel interventions. But what do scientists do when they can perform, say, a cellular intervention, but not a subcellular detection? In such cases, paired interlevel interventions are unavailable. We propose that scientists use abduction and we illustrate its use through a case study of the ionic theory of resting and action potentials.

Although there has been much recent discussion on mechanisms in philosophy of science and social theory, no shared understanding of the crucial concept itself has emerged. In this paper, a distinction between two core concepts of mechanism is made on the basis that the concepts correspond to two different research strategies: the concept of mechanism as a componential causal system is associated with the heuristic of functional decomposition and spatial localization and the concept of mechanism as an abstract form of (...) interaction is associated with the strategy of abstraction and simple models. The causal facts assumed and the theoretical consequences entailed by an explanation with a given mechanism differ according to which concept of mechanism is in use. Research strategies associated with mechanism concepts also involve characteristic biases that should be taken into account when using them, especially in new areas of application. (shrink)

In this paper I address the current debate on ontic versus epistemic conceptualizations of mechanistic explanation in the mechanisms literature. Illari recently argued that good explanations are subject to both ontic and epistemic constraints: they must describe mechanisms in the world (ontic aim) in such fashion that they provide understanding of their workings (epistemic aim). Elaborating upon Illari’s ‘integration’ account, I argue that causal role function discovery of mechanisms and their components is an epistemic prerequisite for achieving these two aims. (...) This analysis extends Illari’s account in important ways, putting more pressure on ontic readings of mechanistic explanation and providing an answer to the question how ontic and epistemic constraints on mechanistic explanation are related. I argue these point in terms of cases on memory research drawn from neuroscience and research on extinct neurogenetic mechanisms from early nervous systems biology. (shrink)

In this thesis, I give a metascientific account of causality in medicine. I begin with two historical cases of causal discovery. These are the discovery of the causation of Burkitt’s lymphoma by the Epstein-Barr virus, and of the various viral causes suggested for cervical cancer. These historical cases then support a philosophical discussion of causality in medicine. This begins with an introduction to the Russo- Williamson thesis (RWT), and discussion of a range of counter-arguments against it. Despite these, I argue (...) that the RWT is historically workable, given a small number of modifications. I then expand Russo and Williamson’s account. I first develop their suggestion that causal relationships in medicine require some kind of evidence of mechanism. I begin with a number of accounts of mechanisms and produce a range of consensus features of them. I then develop this consensus position by reference to the two historical case studies with an eye to their operational competence. In particular, I suggest that it is mechanistic models and their representations which we are concerned with in medicine, rather than the mechanism as it exists in the world. -/- I then employ these mechanistic models to give an account of the sorts of evidence used in formulating and evaluating causal claims. Again, I use the two human viral oncogenesis cases to give this account. I characterise and distinguish evidence of mechanism from evidence of difference-making, and relate this to mechanistic models. I then suggest the relationship between types of evidence presents us with a means of tackling the reference-class problem. This sets the scene for the final chapter. Here, I suggest the manner in which these two different classes of evidence become integrated is also reflected in the way that developing research programmes change as their associated causal claims develop. (shrink)

Robots are being extensively used for the purpose of discovering and testing empirical hypotheses about biological sensorimotor mechanisms. We examine here methodological problems that have to be addressed in order to design and perform “good” experiments with these machine models. These problems notably concern the mapping of biological mechanism descriptions into robotic mechanism descriptions; the distinction between theoretically unconstrained “implementation details” and robotic features that carry a modeling weight; the role of preliminary calibration experiments; the monitoring of experimental environments for (...) disturbing factors that affect both modeling features and theoretically unconstrained implementation details of robots. Various assumptions that are gradually introduced in the process of setting up and performing these robotic experiments become integral parts of the background hypotheses that are needed to bring experimental observations to bear on biological mechanism descriptions. (shrink)

In this paper, I evaluate recently defended mechanistic accounts of the unity of neuroscience from a metaphysical point of view. Considering the mechanistic framework in general , I argue that explanations of this kind are essentially reductive . The reductive character of mechanistic explanations provides a sufficiency criterion, according to which the mechanism underlying a certain phenomenon is sufficient for the latter. Thus, the concept of supervenience can be used in order to describe the relation between mechanisms and phenomena . (...) Against this background, I show that the mechanistic framework is subject to the causal exclusion problem and faces the classical metaphysical options when it comes to the relations obtaining between different levels of mechanisms . Finally, an attempt to improve the metaphysics of mechanisms is made and further difficulties are pointed out. (shrink)

In this paper I apply the mechanistic account of explanation to engineering science. I discuss two ways in which this extension offers further development of the mechanistic view. First, functional individuation of mechanisms in engineering science proceeds by means of two distinct sub types of role function, behavior function and effect function, rather than role function simpliciter. Second, it offers refined assessment of the explanatory power of mechanistic explanations. It is argued that in the context of malfunction explanations of technical (...) systems, two key desiderata for mechanistic explanations, ‘completeness and specificity’ and ‘abstraction’, pull in opposite directions. I elaborate a novel explanatory desideratum to accommodate this explanatory context, dubbed ‘local specificity and global abstraction’, and further argue that it also holds for mechanistic explanations of malfunctions in the biological domain. The overall result is empirically-informed understanding of mechanistic explanation in engineering science, thus contributing to the ongoing project of understanding mechanistic explanation in novel or relatively unexplored domains. I illustrate these claims in terms of reverse engineering and malfunction explanations in engineering science. (shrink)

This paper is about mechanisms and models, and how they interact. In part, it is a response to recent discussion in philosophy of biology regarding whether natural selection is a mechanism. We suggest that this debate is indicative of a more general problem that occurs when scientists produce mechanistic models of populations and their behaviour. We can make sense of claims that there are mechanisms that drive population-level phenomena such as macroeconomics, natural selection, ecology, and epidemiology. But talk of mechanisms (...) and mechanistic explanation evokes objects with well-defined and localisable parts which interact in discrete ways, while models of populations include parts and interactions that are neither local nor discrete in any actual populations. This apparent tension can be resolved by carefully distinguishing between the properties of a model and those of the system it represents. To this end, we provide an analysis that recognises the flexible relationship between a mechanistic model and its target system. In turn, this reveals a surprising feature of mechanistic representation and explanation: it can occur even when there is a mismatch between the mechanism of the model and that of its target. Our analysis reframes the debate, providing an alternative way to interpret scientists’ mechanism-talk , which initially motivated the issue. We suggest that the relevant question is not whether any population-level phenomenon such as natural selection is a mechanism, but whether it can be usefully modelled as though it were a particular type of mechanism. (shrink)