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

The most expressive account of explanations in neuroscience is currently the causal-mechanistic model formulated by Carl Craver. According to him, explanations in neuroscience describe mechanisms, in other words, it points out how parts organize themselves and interact to engender the phenomenon. Furthermore, neuroscience is unified as scientists from different areas that compose it work together to develop mechanisms. This model was extensively discussed in the last years and several criticisms were raised towards it. Still, it remains as the soundest model (...) for explanations in neuroscience nowadays. This paper is presented as a review of this model, as well as the critiques worked out against it and finishes with a brief consideration of the problem of explanation in neuroscience. (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)

The central aim of this paper is to shed light on the nature of explanation in computational neuroscience. I argue that computational models in this domain possess explanatory force to the extent that they describe the mechanisms responsible for producing a given phenomenon—paralleling how other mechanistic models explain. Conceiving computational explanation as a species of mechanistic explanation affords an important distinction between computational models that play genuine explanatory roles and those that merely provide accurate descriptions or predictions of phenomena. It (...) also serves to clarify the pattern of model refinement and elaboration undertaken by computational neuroscientists. (shrink)

There are two competing views regarding the role of mechanistic knowledge in inferences about the effectiveness of interventions. One view holds that inferences about the effectiveness of interventions should be based only on data from population-level studies (often statistical evidence from randomised trials). The other view holds that such inferences must be based in part on mechanistic evidence. The competing views are local principles of inference, the plausibility of which can be assessed by a more general normative principle of inference. (...) Bayesianism tells us to base inferences on both the ‘likelihood’ and the ‘prior’. The likelihood represents statistical evidence. One influence on the prior probability of a hypothesis like ‘d causes x’ is mechanistic knowledge of how d causes x. Thus, reasoning about such inferences by appealing to both statistical and mechanistic evidence is vindicated by our best general theory of inference. The primary contribution of this paper is to assess the merits and weaknesses of the arguments on both sides of the debate, using the Bayesian framework. This analysis lends support to those who argue that we should base our causal inferences about interventions in part on mechanistic evidence. (shrink)

Ever since the hard problem of consciousness (Chalmers, 1996, 1995) first entered the scene in the debate over consciousness many have taken it to show the limitations of a scientific or naturalist explanation of consciousness. The hard problem is the problem of explaining why there is any experience associated with certain physical processes, that is, why there is anything it is like associated with such physical processes? The character of one’s experience doesn’t seem to be entailed by physical processes and (...) so an explanation which can overcome such a worry must (1) explain how physical processes give rise to experience (explain the entailment), (2) give an explanation which doesn’t rely on such physical processes, or (3) show why the hard problem is misguided in some sense. Recently, a rather ambitious and novel theory of consciousness has entered the scene – Integrated Information Theory (IIT) of Consciousness (Oizumi et al., 2014; Tononi, 2008; Tononi et al., 2016) – and proposes that consciousness is the result of a specific type of information processing, what those developing the theory call integrated information. The central aim of this dissertation is to philosophically investigate IIT and see whether it has the ability to overcome the hard problem and related worries. I then aim to use this philosophical investigation to answer a set of related questions which guide this dissertation, which are the following: Is it possible to give an information-theoretic explanation of consciousness? What would the nature of such an explanation be and would it result in a novel metaphysics of consciousness? In this dissertation, I begin in chapter one by first setting up the hard problem and related arguments against the backdrop of IIT (Mindt, 2017). I show that given a certain understanding of structural and dynamical properties IIT fails to overcome the hard problem of consciousness. I go on in chapter two to argue that a deflationary account of causation is the best view for IIT to overcome the causal exclusion problem (Baxendale and Mindt, 2018). In chapter three, I explain IIT’s account of how the qualitative character of our experience arises (qualia) and what view of intentionality (the directedness of our mental states) IIT advocates. I then move on in chapter four to show why the hard problem mischaracterizes structural and dynamical properties and misses important nuances that may shed light on giving a naturalized explanation of consciousness. In the last and fifth chapter, I outline a sketch of a novel metaphysics of consciousness that takes the conjunction of Neutral Monism and Information-Theoretic Structural Realism to give what I call Information-Theoretic Neutral-Structuralism. (shrink)

Jonathan Y. Tsou examines and defends positions on central issues in philosophy of psychiatry. The positions defended assume a naturalistic and realist perspective and are framed against skeptical perspectives on biological psychiatry. Issues addressed include the reality of mental disorders; mechanistic and disease explanations of abnormal behavior; definitions of mental disorder; natural and artificial kinds in psychiatry; biological essentialism and the projectability of psychiatric categories; looping effects and the stability of mental disorders; psychiatric classification; and the validity of the DSM's (...) diagnostic categories. The main argument defended by Tsou is that genuine mental disorders are biological kinds with harmful effects. This argument opposes the dogma that mental disorders are necessarily diseases that result from biological dysfunction. Tsou contends that the broader ideal of biological kinds offers a more promising and empirically ascertainable naturalistic standard for assessing the reality of mental disorders and the validity of psychiatric categories. (shrink)

A large part of the controversy surrounding the publication of DSM-5 stems from the possibility of replacing the purely descriptive approach to classification favored by the DSM since 1980. This paper examines the question of how mental disorders should be classified, focusing on the issue of whether the DSM should adopt a purely descriptive or theoretical approach. I argue that the DSM should replace its purely descriptive approach with a theoretical approach that integrates causal information into the DSM’s descriptive diagnostic (...) categories. The paper proceeds in three sections. In the first section, I examine the goals (viz., guiding treatment, facilitating research, and improving communication) associated with the DSM’s purely descriptive approach. In the second section, I suggest that the DSM’s purely descriptive approach is best suited for improving communication among mental health professionals; however, theoretical approaches would be superior for purposes of treatment and research. In the third section, I outline steps required to move the DSM towards a hybrid system of classification that can accommodate the benefits of descriptive and theoretical approaches, and I discuss how the DSM’s descriptive categories could be revised to incorporate theoretical information regarding the causes of disorders. I argue that the DSM should reconceive of its goals more narrowly such that it functions primarily as an epistemic hub that mediates among various contexts of use in which definitions of mental disorders appear. My analysis emphasizes the importance of pluralism as a methodological means for avoiding theoretical dogmatism and ensuring that the DSM is a reflexive and self-correcting manual. (shrink)

This paper argues against the view that the standard explanation of phase transitions in statistical mechanics may be considered a causal explanation, a distortion that can nevertheless successfully represent causal relations.

Some recent accounts of constitutive relevance have identified mechanism components with entities that are causal intermediaries between the input and output of a mechanism. I argue that on such accounts there is no distinctive inter-level form of mechanistic explanation and that this highlights an absence in the literature of a compelling argument that there are such explanations. Nevertheless, the entities that these accounts call ‘components’ do play an explanatory role. Studying causal intermediaries linking variables Xand Y provides knowledge of the (...) counterfactual conditions under which X will continue to bring about Y. This explanatory role does not depend on whether intermediate variables count as components. The question of whether there are distinctively mechanistic explanations remains open. (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)

Reduction and reductionism have been central philosophical topics in analytic philosophy of science for more than six decades. Together they encompass a diversity of issues from metaphysics and epistemology. This article provides an introduction to the topic that illuminates how contemporary epistemological discussions took their shape historically and limns the contours of concrete cases of reduction in specific natural sciences. The unity of science and the impulse to accomplish compositional reduction in accord with a layer-cake vision of the sciences, the (...) seminal contributions of Ernest Nagel on theory reduction and how they strongly conditioned subsequent philosophical discussions, and the detailed issues pertaining to different accounts of reduction that arise in both physical and biological science (e.g., limit-case and part-whole reduction in physics, the difference-making principle in genetics, and mechanisms in molecular biology) are explored. The conclusion argues that the epistemological heterogeneity and patchwork organization of the natural sciences encourages a pluralist stance about reduction. (shrink)

According to conventional wisdom, local gauge symmetry is not a symmetry of nature, but an artifact of how our theories represent nature. But a study of the so-called theta-vacuum appears to refute this view. The ground state of a quantized non-Abelian Yang-Mills gauge theory is characterized by a real-valued, dimensionless parameter theta—a fundamental new constant of nature. The structure of this vacuum state is often said to arise from a degeneracy of the vacuum of the corresponding classical theory, which degeneracy (...) allegedly arises from the fact that “large” (but not “small”) local gauge transformations connect physically distinct states of zero field energy. If that is right, then some local gauge transformations do generate empirical symmetries. In defending conventional wisdom against this challenge I hope to clarify the meaning of empirical symmetry while deepening our understanding of gauge transformations. I distinguish empirical from theoretical symmetries. Using Galileo’s ship and Faraday’s cube as illustrations, I say when an empirical symmetry is implied by a theoretical symmetry. I explain how the theta-vacuum arises, and how “large” gauge transformations differ from “small” ones. I then present two analogies from elementary quantum mechanics. By applying my analysis of the relation between empirical and theoretical symmetries, I show which analogy faithfully portrays the character of the vacuum state of a classical non-Abelian Yang-Mills gauge theory. The upshot is that “large” as well as “small” gauge transformations are purely formal symmetries of non-Abelian Yang-Mills gauge theories, whether classical or quantized. It is still worth distinguishing between these kinds of symmetries. An analysis of gauge within the constrained-Hamiltonian formalism yields the result that “large” gauge transformations should not be classified as gauge transformations; indeed, nor should “global” gauge transformations. In a theory in which boundary conditions are modeled dynamically, “global” gauge transformations may be associated with physical symmetries, corresponding to translations of these extra dynamical variables. Such translations are symmetries if and only if charge is conserved. But it is hard to argue that these symmetries are empirical, and in any case they do not correspond to any constant phase change in a quantum state. (shrink)

Philosophical analyses of causation have been centred on the question of what causation is. More precisely speaking, philosophers tend to address four different issues: metaphysical (what is causation out there?), epistemological (how can a causal claim be established and assessed?), conceptual (what does the word ‘cause’ mean?), and methodological (what methods ought one to use in order to establish and assess causal claims?). This chapter argues that the practical issue of causation (what is a causal claim for in practice?) is (...) highly relevant to the metaphysical, epistemological, conceptual, and methodological issues of causation. Any philosophical enquiry into causation without an examination of this practical issue is incomplete. In other words, a promising approach to causation ought to take all of the metaphysical, epistemological, conceptual, methodological, and practical issues into account. (shrink)

What is it to base a belief on reasons? Existing attempts to give an account of the basing relation encounter a dilemma: either one appeals to some kind of neutral process that does not adequately reflect the way basing is a content‐sensitive first‐personal activity, or one appeals to linking or bridge principles that over‐intellectualize and threaten regress. We explain why this dilemma arises, and diagnose the commitments that are key obstacles to providing a satisfactory account. We explain why they should (...) be rejected anyway, and then offer a new, knowledge‐first virtue epistemological theory of the basing relation that shows how we can substantially theorize about mental processes without these commitments. The resulting view plausibly captures the way in which basing is an inherently mental and content‐sensitive process. (shrink)

The paper presents, and discusses, four candidate explanations of the structure, and construction, of the bees’ honeycomb. So far, philosophers have used one of these four explanations, based on the mathematical Honeycomb Conjecture, while the other three candidate explanations have been ignored. I use the four cases to resolve a dispute between Pincock and Baker about the Honeycomb Conjecture explanation. Finally, I find that the two explanations focusing on the construction mechanism are more promising than those focusing exclusively on the (...) resulting, optimal structure. The main reason for this is that optimal structures do not uniquely determine the relevant optimization leading to the optimal structure. (shrink)

After Wesley Salmon’s causal-mechanical stance on explanation in the 1980s, the ontic-epistemic debate of scientific explanations appeared to be resolved in the philosophy of science. However, since the twenty-first century, this debate has been rekindled among philosophers who focus on mechanistic explanations. Nevertheless, its issues have evolved, necessitating scrutiny of the new trends in this debate and a comparison with the original controversy between Carl Hempel and Salmon. The primary objective of this paper is to elucidate three categorical dimensions in (...) the ontic-epistemic debates, spanning from the original to the recent controversies. Subsequently, it will explore why the conception of explanation is linked to representations, what conditions are necessary for linguistic expressions to be explanatory, and what roles norms play in explanation. Consequently, contrary to the common stereotype, it will be argued that mechanistic explanations are more likely to be epistemic rather than ontic. (shrink)

In his later years, Wesley Salmon believed that the two dominant models of scientific explanation (his own causal-mechanical model and the unificationist model) were reconcilable. Salmon envisaged a 'new consensus' about explanation: he suggested that the two models represent two 'complementary' types of explanation, which may 'peacefully coexist' because they illuminate different aspects of scientific understanding. This paper traces the development of Salmon's ideas and presents a critical analysis of his complementarity thesis. Salmon's thesis is rejected on the basis of (...) two objections, and an alternative view of the relation between different types of explanation is proposed. (shrink)

The act of understanding is at the heart of all scientific activity; without it any ostensibly scientific activity is as sterile as that of a high school student substituting numbers into a formula. Ordinary language often uses visual metaphors in connection with understanding. When we finally understand what someone is trying to point out to us, we exclaim: “I see!” When someone really understands a subject matter, we say that she has “insight”. There appears to be a link between visualization (...) and understanding, and between visualizability and intelligibility. This applies in science no less than in daily life: visualization is regarded as a useful means of achieving scientific understanding, even in the .. (shrink)

It is often claimed—especially by scientific realists—that science provides understanding of the world only if its theories are (at least approximately) true descriptions of reality, in its observable as well as unobservable aspects. This paper critically examines this ‘realist thesis’ concerning understanding. A crucial problem for the realist thesis is that (as study of the history and practice of science reveals) understanding is frequently obtained via theories and models that appear to be highly unrealistic or even completely fictional. So we (...) face the dilemma of either giving up the realist thesis that understanding requires truth, or allowing for the possibility that in many if not all practical cases we do not have scientific understanding. I will argue that the first horn is preferable: the link between understanding and truth can be severed. This becomes a live option if we abandon the traditional view that scientific understanding is a special type of knowledge. While this view implies that understanding must be factive, I avoid this implication by identifying understanding with a skill rather than with knowledge. I will develop the idea that understanding phenomena consists in the ability to use a theory to generate predictions of the target system’s behavior. This implies that the crucial condition for understanding is not truth but intelligibility of the theory, where intelligibility is defined as the value that scientists attribute to the theoretical virtues that facilitate the construction of models of the phenomena. I will show, first, that my account accords with the way practicing scientists conceive of understanding, and second, that it allows for the use of idealized or fictional models and theories in achieving understanding. (shrink)

One thing about technical artefacts that needs to be explained is how their physical make-up, or structure, enables them to fulfil the behaviour associated with their function, or, more colloquially, how they work. In this paper I develop an account of such explanations based on the familiar notion of mechanistic explanation. To accomplish this, I outline two explanatory strategies that provide two different types of insight into an artefact’s functioning, and show how human action inevitably plays a role in artefact (...) explanation. I then use my own account to criticize other recent work on mechanistic explanation and conclude with some general implications for the philosophy of explanation.Keywords: Artefact; Technical function; Explanation; Levels of explanation; Mechanisms. (shrink)

I argue that Darwinian evolutionary theory has a rhetorical dimension and that rhetorical criticism plays a role in how evolutionary science acquires knowledge. I define what I mean by rhetoric by considering Darwin’s Origin. I use the Modern Evolutionary Synthesis to show how rhetoric conceived as situated and addressed argumentation enters into evolutionary theorizing. Finally, I argue that rhetorical criticism helps judge the success, limits, and failures of these theories.

This paper gives a philosophical outline of the importance of plausible ontologies in the social sciences and argues how mechanisms and processes should be placed as the foundation in the social world. The argumentation is mainly based on a critical appraisal of the use of mechanisms and processes in the works of Norbert Elias, Charles Tilly, and Jon Elster. I start by elaborating on how inquiries of scientific interest evolve to shed light on cases, facts and the things that constitute (...) such facts, whilst the actual explanation demands the description of mechanisms and processes. Basically, focusing on variation and difference making is not sufficient to sustain claims of ontological plausibility and reasonableness. It is thus pointed out how the practices and proceedings of the social sciences can be ontologically enhanced by embracing the complementary roles of mechanisms plus processes together with difference making, as is performed in a special science such as biology, as well as is informally but promisingly pursued in the works of the discussed social scientists. While discussing their work, it is also argued that we should differentiate between processes and mechanisms in order to formalize this approach, which highlights the role of technologies and institutions as prime building blocks for social explanation. I conclude by presenting a claim that in taking seriously that the purported relations between beings and entities need to make discursive sense and historical sense, the social sciences will increase our cognitive success about the things of the world. (shrink)

Reductionism is a central issue in the philosophy of biology. One common objection to reduction is that molecular explanation requires reference to higher-level properties, which I refer to as the context objection. I respond to this objection by arguing that a well-articulated notion of a mechanism and what I term mechanism extension enables one to accommodate the context-dependence of biological processes within a reductive explanation. The existence of emergent features in the context could be raised as an objection to the (...) possibility of reduction via this strategy. I argue that this objection can be overcome by showing that there is no tenable argument for the existence of emergent properties that are not susceptible to a reductive explanation. (shrink)

It is argued that John Bickle’s Ruthless Reductionism is flawed as an account of the practice of neuroscience. Examples from genetics and linguistics suggest, first, that not every mind-brain link or gene-phenotype link qualifies as a reduction or as a complete explanation, and, second, that the higher (psychological) level of analysis is not likely to disappear as neuroscience progresses. The most plausible picture of the evolving sciences of the mind-brain seems a patchwork of multiple connections and partial explanations, linking anatomy, (...) mechanisms and functions across different domains, levels, and grain sizes. Bickle’s claim that only the molecular level provides genuine explanations, and higher level concepts are just heuristics that will soon be redundant, is thus rejected. In addition, it is argued that Bickle’s recasting of philosophy of science as metascience explicating empirical practices, ignores an essential role for philosophy in reflecting upon criteria for reduction and explanation. Many interesting and complex issues remain to be investigated for the philosophy of science, and in particular the nature of interlevel links found in empirical research requires sophisticated philosophical analysis. (shrink)

This article, the first of a two-part essay, presents an account of Aristotelian hylomorphic animalism that engages with recent work on neuroscience and philosophy of mind. I show that Aristotelian hylomorphic animalism is compatible with the new mechanist approach to neuroscience and psychology, but that it is incompatible with strong emergentism in the philosophy of mind. I begin with the basic claims of Aristotelian hylomorphic animalism and focus on its understanding of psychological powers embodied in the nervous system. Next, I (...) introduce the new mechanist approach to neuroscience and psychology and illustrate how it can enrich the more abstract ontological framework of Aristotelian hylomorphic animalism. In the third section of this article I establish in detail the many ways Aristotelian hylomorphic animalism is incompatible with strong emergentism in the philosophy of mind. Based on these fundamental differences I show why a criticism leveled against emergentism by the new mechanist philosophy does not hamper my proposed rapprochement between hylomorphism and the new mechanist philosophy. This conclusion, however, leaves untouched the problem I address in the second article, namely, is the new mechanist philosophy compatible with Aristotelian philosophical anthropology’s contention that intellectual operations are immaterial and interact with the psychosomatic operations of the rational animal? (shrink)

In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different "degrees of contingency". We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For illustrative (...) purposes, we provide an example from population genetics, the Wright-Fisher Model. (shrink)

In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different “degrees of contingency”. We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For illustrative (...) purposes, we provide an example from population genetics, the Wright-Fisher Model. (shrink)

During the first half of the twentieth century, many philosophers of memory opposed the postulation of memory traces based on the claim that a satisfactory account of remembering need not include references to causal processes involved in recollection. However, in 1966, an influential paper by Martin and Deutscher showed that causal claims are indeed necessary for a proper account of remembering. This, however, did not settle the issue, as in 1977 Malcolm argued that even if one were to buy Martin (...) and Deutscher’s argument for causal claims, we still don’t need to postulate the existence of memory traces. This paper reconstructs the dialectic between realists and anti-realists about memory traces, suggesting that ultimately realists’ arguments amount to inferences to the best explanation. I then argue that Malcolm’s anti-realist strategy consists in the suggestion that causal explanations that do not invoke memory traces are at least as good as those that do. But then, Malcolm, I argue that there are a large number of memory phenomena for which explanations that do not postulate the existence of memory traces are definitively worse than explanations that do postulate them. Next, I offer a causal model based on an interventionist framework to illustrate when memory traces can help to explain memory phenomena and proceed to substantiate the model with details coming from extant findings in the neuroscience of memory. (shrink)

Misremembering is a systematic and ordinary occurrence in our daily lives. Since it is commonly assumed that the function of memory is to remember the past, misremembering is typically thought to happen because our memory system malfunctions. In this paper I argue that not all cases of misremembering are due to failures in our memory system. In particular, I argue that many ordinary cases of misremembering should not be seen as instances of memory’s malfunction, but rather as the normal result (...) of a larger cognitive system that performs a different function, and for which remembering is just one operation. Building upon extant psychological and neuroscientific evidence, I offer a picture of memory as an integral part of a larger system that supports not only thinking of what was the case and what potentially could be the case, but also what could have been the case. More precisely, I claim that remembering is a particular operation of a cognitive system that permits the flexible recombination of different components of encoded traces into representations of possible past events that might or might not have occurred, in the service of constructing mental simulations of possible future events. So that imagination and memory are but one thing, which for diverse considerations hath diverse names.Thomas Hobbes, Leviathan 1.2. (shrink)

Bionic technologies connecting biological nervous systems to computer or robotic devices for therapeutic purposes have been recently claimed to provide novel experimental tools for the investigation of biological mechanisms. This claim is examined here by means of a methodological analysis of bionics-supported experimental inquiries on adaptive sensory-motor behaviours. Two broad classes of bionic systems (regarded here as hybrid simulations of the target biological system) are identified, which differ from each other according to whether a component of the biological target system (...) is replaced by an artificial component, or else a component of an artificial system is replaced by a biological component. The role of these hybrid systems in the modelling of adaptive sensory-motor biological behaviours is discussed with reference to bionics-supported experiments on the mechanisms of body stabilization in lampreys. Methodological problems emerging from these case studies often arise in computer-based and biorobotic simulations of biological behaviours too. Accordingly, the present analysis contributes to identifying a more general regulative methodological framework for the machine-based modelling of biological systems. (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 the contemporary biomedical literature, every disease is considered genetic. This extension of the concept of genetic disease is usually interpreted either in a trivial or genocentrist sense, but it is never taken seriously as the expression of a genetic theory of disease. However, a group of French researchers defend the idea of a genetic theory of infectious diseases. By identifying four common genetic mechanisms (Mendelian predisposition to multiple infections, Mendelian predisposition to one infection, and major gene and polygenic predispositions), (...) they attempt to unify infectious diseases from a genetic point of view. In this article, I analyze this explicit example of a genetic theory, which relies on mechanisms and is applied only to a specific category of diseases, what we call “a regional genetic theory.” I have three aims: to prove that a genetic theory of disease can be devoid of genocentrism, to consider the possibility of a genetic theory applied to every disease, and to introduce two hypotheses about the form that such a genetic theory could take by distinguishing between a genetic theory of diseases and a genetic theory of Disease. Finally, I suggest that network medicine could be an interesting framework for a genetic theory of Disease. (shrink)

In the 1950s and 1960s, an interfield interaction between molecular biologists and biochemists integrated important discoveries about the mechanism of protein synthesis. This extended discovery episode reveals two general reasoning strategies for eliminating gaps in descriptions of the productive continuity of mechanisms: schema instantiation and forward chaining/backtracking. Schema instantiation involves filling roles in an overall framework for the mechanism. Forward chaining and backtracking eliminate gaps using knowledge about types of entities and their activities. Attention to mechanisms highlights salient features of (...) this historical episode while providing general reasoning strategies for mechanism discovery. (shrink)

Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.

Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.

Philosophers have proposed various kinds of relations between Mendelian genetics and molecular biology: reduction, replacement, explanatory extension. This paper argues that the two fields are best characterized as investigating different, serially integrated, hereditary mechanisms. The mechanisms operate at different times and contain different working entities. The working entities of the mechanisms of Mendelian heredity are chromosomes, whose movements serve to segregate alleles and independently assort genes in different linkage groups. The working entities of numerous mechanisms of molecular biology are larger (...) and smaller segments of DNA plus related molecules. Discovery of molecular DNA mechanisms filled black boxes that were noted, but unilluminated, by Mendelian genetics. (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)

Newsome ((2003). The debate between current versions of covariation and mechanism approaches to causal inference. Philosophical Psychology, 16, 87-107.) recently published a critical review of psychological theories of human causal inference. In that review, he characterized covariation and mechanism theories, the two dominant theory types, as competing, and offered possible ways to integrate them. I argue that Newsome has misunderstood the theoretical landscape, and that covariation and mechanism theories do not directly conflict. Rather, they rely on distinct sets of reliable (...) indicators of causation, and focus on different types of causation (type vs. token). There are certainly debates in the research field, but the theoretical landscape is not as fractured as Newsome suggests, and a potential unifying framework has already emerged using causal Bayes nets. Philosophical work on causal epistemology matters for psychologists, but not in the way Newsome suggests. (shrink)

This is a teaching and learning guide to accompany "Explanation in Mathematics: Proofs and Practice".

Mathematicians distinguish between proofs that explain their results and those that merely prove. This paper explores the nature of explanatory proofs, their role in mathematical practice, and some of the reasons why philosophers should care about them. Among the questions addressed are the following: what kinds of proofs are generally explanatory (or not)? What makes a proof explanatory? Do all mathematical explanations involve proof in an essential way? Are there really such things as explanatory proofs, and if so, how do (...) they relate to the sorts of explanation encountered in philosophy of science and metaphysics? (shrink)

Geologists, Paleontologists and other historical scientists are frequently concerned with narrative explanations targeting single cases. I show that two distinct explanatory strategies are employed in narratives, simple and complex. A simple narrative has minimal causal detail and is embedded in a regularity, whereas a complex narrative is more detailed and not embedded. The distinction is illustrated through two case studies: the ‘snowball earth’ explanation of Neoproterozoic glaciation and recent attempts to explain gigantism in Sauropods. This distinction is revelatory of historical (...) science. I argue that at least sometimes which strategy is appropriate is not a pragmatic issue, but turns on the nature of the target. Moreover, the distinction reveals a counterintuitive pattern of progress in some historical explanation: shifting from simple to complex. Sometimes, historical scientists rightly abandon simple, unified explanations in favour of disunified, complex narratives. Finally I compare narrative and mechanistic explanation, arguing that mechanistic approaches are inappropriate for complex narrative explanations. (shrink)

. Philosophers and scientists often cite ontic factors when explaining the methods and success of scientific inquiry. That is, the adoption of a method or approach is explained in reference to the kind of system in which the scientist is interested: these are explanations of why scientists do what they do, that appeal to properties of their target systems. We present a framework for understanding such “Opticks to his Principia. Newton’s optical work is largely experiment-driven, while the Principia is primarily (...) mathematical, so usually, each work is taken to exemplify a different kind of science. However, Newton himself often presented them in terms of a largely consistent method. We use our framework to articulate an original and plausible position: that the differences between the Opticks and the Principia are due to the kinds of systems targeted. That is, we provide an ontic-driven explanation of methodological differences. We suspect that ontic factors should have a more prominent role in historical explanations of scientific method and development. (shrink)

Abstract‘Behavioural modernity’ isn’t what it used to be. Once conceived as an integrated package of traits demarcated by a clear archaeological signal in a specific time and place, it is now disparate, archaeologically equivocal, and temporally and spatially spread. In this paper we trace behavioural modernity’s empirical and theoretical developments over the last three decades, as surprising discoveries in the material record, as well the reappraisal of old evidence, drove increasingly sophisticated demographic, social and cultural models of behavioural modernity. We (...) argue, however, that some approaches to identifying and categorizing modernity have not kept up with this new picture. This is due to what we term ‘Rubicon expectations’: classificatory and interpretive practices which look for or assume clear demarcations in behavioural and cultural processes. We develop a philosophical account of ‘investigative disintegration’ to capture how our understanding of behavioural modernity has changed, and how Rubicon-based practices have become inadequate. Disintegration, in the form we analyse, occurs when scientists’ conception of a phenomenon shifts sufficiently to reshape an investigation’s epistemic structure. For behavioural modernity, the explanatory weight which once lay on identifying ‘switch-points’ in the innate suite of hominin cognitive capacities, lies now in understanding the social and demographic environments that were capable of sustaining and nourishing more complex material cultures. Finally, we argue that the phenomenon itself has not disintegrated to the point that we are left with no interesting explanandum: for all its mosaic, disparate nature, there are still good reasons for behavioural modernity to retain its central place in investigation of our species' origins. (shrink)