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)

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)

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)

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)

Long-Term Potentiation (LTP) is a kind of synaptic plasticity that many contemporary neuroscientists believe is a component in mechanisms of memory. This essay describes the discovery of LTP and the development of the LTP research program. The story begins in the 1950's with the discovery of synaptic plasticity in the hippocampus (a medial temporal lobe structure now associated with memory), and it ends in 1973 with the publication of three papers sketching the future course of the LTP research program. The (...) making of LTP was a protracted affair. Hippocampal synaptic plasticity was initially encountered as an experimental tool, then reported as a curiosity, and finally included in the ontic store of the neurosciences. Early researchers were not investigating the hippocampus in search of a memory mechanism; rather, they saw the hippocampus as a useful experimental model or as a structure implicated in the etiology of epilepsy. The link between hippocampal synaptic plasticity and learning or memory was a separate conceptual achievement. That link was formulated in at least three different ways at different times: reductively (claiming that plasticity is identical to learning), analogically (claiming that plasticity is an example or model of learning), and mechanistically (claiming that plasticity is a component in learning or memory mechanisms). The hypothesized link with learning or memory, coupled with developments in experimental techniques and preparations, shaped how researchers understood LTP itself. By 1973, the mechanistic formulation of the link between LTP and memory provided an abstract framework around which findings from multiple perspectives could be integrated into a multifield research program. (shrink)

We argue that intelligible appeals to interlevel causes (top-down and bottom-up) can be understood, without remainder, as appeals to mechanistically mediated effects. Mechanistically mediated effects are hybrids of causal and constitutive relations, where the causal relations are exclusively intralevel. The idea of causation would have to stretch to the breaking point to accommodate interlevel causes. The notion of a mechanistically mediated effect is preferable because it can do all of the required work without appealing to mysterious interlevel causes. When interlevel (...) causes can be translated into mechanistically mediated effects, the posited relationship is intelligible and should raise no special philosophical objections. When they cannot, they are suspect. (shrink)

What are the relative epistemic merits of building prosthetic models versus building nonprosthetic models and simulations? I argue that prosthetic models provide a sufficient test of affordance validity, that is, of whether the target system affords mechanisms that can be commandeered by a prosthesis. In other respects, prosthetic models are epistemically on par with nonprosthetic models. I focus on prosthetics in neuroscience, but the results are general. The goal of understanding how brain mechanisms work under ecologically and physiologically relevant conditions (...) is narrow compared to the search for maker's knowledge about how the brain can be made to work for us. (shrink)

The dominant neuroscientific theory of spatial memory is, like many theories in neuroscience, a multilevel description of a mechanism. The theory links the activities of molecules, cells, brain regions, and whole organisms into an integrated sketch of an explanation for the ability of organisms to navigate novel environments. Here I develop a taxonomy of interlevel experimental strategies for integrating the levels in such multilevel mechanisms. These experimental strategies include activation strategies, interference strategies, and additive strategies. These strategies are mutually reinforcing, (...) providing a kind of interlevel and intratheoretic robustness that has not previously been recognized. (shrink)

The dominant neuroscientific theory of spatial memory is, like many theories in neuroscience, a multilevel description of a mechanism. The theory links the activities of molecules, cells, brain regions, and whole organisms into an integrated sketch of an explanation for the ability of organisms to navigate novel environments. Here I develop a taxonomy of interlevel experimental strategies for integrating the levels in such multilevel mechanisms. These experimental strategies include activation strategies, interference strategies, and additive strategies. These strategies are mutually reinforcing, (...) providing a kind of interlevel and intratheoretic robustness that has not previously been recognized. (shrink)

It is a common assumption in contemporary cognitive neuroscience that discovering a putative realized kind to be dissociably realized (i.e., to be realized in each instance by two or more distinct realizers) mandates splitting that kind. Here I explore some limits on this inference using two deceptively similar examples: the dissociation of declarative and procedural memory and Ramachandran's argument that the self is an illusion.

An adequate understanding of the ubiquitous practice of mechanistic explanation requires an account of what Craver termed “constitutive relevance.” Entities or activities are constitutively relevant to a phenomenon when they are parts of the mechanism responsible for that phenomenon. Craver’s mutual manipulability account extended Woodward’s account of manipulationist counterfactuals to analyze how interlevel experiments establish constitutive relevance. Critics of MM argue that applying Woodward’s account to this philosophical problem conflates causation and constitution, thus rendering the account incoherent. These criticisms, we (...) argue, arise from failing to distinguish the semantic, epistemic, and metaphysical aspects of the problem of constitutive relevance. In distinguishing these aspects of the problem and responding to these critics accordingly, we amend MM into a refined epistemic criterion, the “matched interlevel experiments” account. Further, we explain how this epistemological thesis is grounded in the plausible metaphysical thesis that constitutive relevance is causal betweenness. (shrink)

This paper will examine the nature of mechanisms and the distinction between the relevant and irrelevant parts involved in a mechanism’s operation. I first consider Craver’s account of this distinction in his book on the nature of mechanisms, and explain some problems. I then offer a novel account of the distinction that appeals to some resources from Mackie’s theory of causation. I end by explaining how this account enables us to better understand what mechanisms are and their various features.

In this paper I return to Hegel's dispute with Kant over the conceptual ordering of external and internal purposiveness to distinguish between two conceptions of teleology at play in the contemporary function debate. I begin by outlining the three main views in the debate (the etiological, causal role and organizational views). I argue that only the organizational view can maintain the capacity of function ascriptions both to explain the presence of a trait and to identify its contribution to a current (...) system, for it is the only view that considers teleology as a natural cause. To establish how teleology can be considered as a natural cause, advocates of the organizational view return to Kant's analysis of internal purposiveness. However, while Kant identifies the requirements that an object must meet to satisfy the demands of teleological judgment, I suggest that he denies that we can know whether they are truly met. I argue that Hegel's philosophy of nature is better equipped to determine how internal purposiveness can be considered as a natural cause, for it grounds organization in a form of purposiveness that is more fundamental than a designer's intention. (shrink)

I analyze a tension at the core of the mechanistic view of computation generated by its joint commitment to the medium independence of computational vehicles and to computational systems possessing teleological functions to compute. While computation is individuated in medium-independent terms, teleology is sensitive to the constitutive physical properties of vehicles. This tension spells trouble for the mechanistic view, suggesting that there can be no teleological functions to compute. I argue that, once considerations about the relevant function-bestowing factors for computational (...) systems are brought to bear, the tension dissolves: physical systems can have the teleological function to compute. (shrink)

Ever since Wesley Salmon’s theory, the mechanical approach to causality has found an increasing number of supporters who have developed it in different directions. Mechanical views such as those advanced by Stuart Glennan, Jim Bogen and Peter Machamer, Lindley Darden and Carl Craver have met with broad consensus in recent years. This paper analyses the main features of these mechanical positions and some of the major problems they still face, referring to the latest debate on mechanisms, causal explanation and the (...) relationship between mechanisms and counterfactuals. I shall claim that the mechanical approach can be recognised as having a fundamental explanatory power, whereas the counterfactual approach, recently developed mainly by Jim Woodward and essentially linked to the notion of intervention, has an important heuristic role. Claiming that mechanisms are by no means to be seen as parasitic on counterfactuals or less fundamental than them – as it has been recently suggested –, and that yet counterfactuals can play a part in a conceptual analysis of causation, I shall look for hints in support of the peaceful coexistence of the two. (shrink)

The terms “perspectivism” and “perspectivalism” have been the focus of an intense philosophical discussion with important repercussions for the debate about the role of mechanisms in scientific explanations. However, leading exponents of the new mechanistic philosophy have conceded more than was necessary to the radically subjectivistic perspectivalism, and fell into the opposite error, by retaining not negligible residues of objectivistic views about mechanisms. In order to remove this vacillation between the subjective-cultural and the objective-natural sides of mechanisms, we shall raise (...) the question about theory-ladenness over again and interpret it in its connection with the technical–experimental nature of scientific knowledge, as affirming the perspectival character of scientific knowledge: It is because of the character at once theory-laden and practice-laden, i.e. technique-laden, of our putting questions to nature that empirical reality must be investigated from particular perspectives: nature can be known scientifically only from a potentially infinite number of perspectives or theoretical points of view, concretely exemplified by mechanisms or experimental ‘machines’ that allow specific access to specific aspects of sensible reality. (shrink)

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

Nowadays, philosophers and scientists tend to agree that, even though human and artificial intelligence work quite differently, they can still illuminate aspects of each other, and knowledge in one domain can inspire progress in the other. For instance, the notion of “artificial” or “synthetic” phenomenology has been gaining some traction in recent AI research. In this paper, we ask the question: what (if anything) is the use of thinking about phenomenology in the context of AI, and in particular machine learning? (...) We will isolate one sense of “phenomenology”, namely the sense in which it is commonly understood within analytic philosophy of perception. Then, we will give examples of projects within sensory substitution and restoration science that rely heavily on machine learning and to which, according to us, phenomenology in the sense specified makes a relevant contribution. Finally, we will shed some light on what this contribution looks like and why it is important. (shrink)

The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of (...) ‘levels’ is best seen in the heuristic contributions the concept makes to treating and structuring scientific problems. We illustrate this with two examples from biological research. (shrink)

Recent work on epistemic integration in the life sciences has emphasized the importance of integration in thinking about explanatory practice in science, particularly for articulating a robust alternative to reductionism and anti-reductionism. This paper analyzes the role of models in balancing the relative contributions of lower- and higher-level epistemic resources involved in this process. Integration between multiple disciplines proceeds by constructing a problem agenda (Love 2008), a set of interrelated problems that structures the problem space of a complex phenomenon that (...) is investigated by many disciplines. The usage of models, it is argued, mark changes in a phenomenon’s problem agenda depending on the task that is expected of it. Particularly, it emphasizes the sensitivity of a problem agenda to changing attitudes in the solutions to the conceptual and empirical items constituting that agenda. The analysis will proceed by means of a case study, the Reichardt motion detector, a model that has been vital to the methodological and conceptual development of research on motion detection, especially in invertebrates. As will be seen, the history of the Reichardt model will exemplify the dynamic changes that occur in the interdisciplinary negotiations that comprise the active efforts of various sciences working to integrate their resources. (shrink)

Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, to (...) provide structure to scientific problems, delegates tasks whose execution generates the term’s expressed content in a given instance. This treatment of levels does not diminish the concept’s general importance to science, but rather allows for its use in, and usefulness for, scientific practice to be better contextualized to particular tasks encompassing varying breadths of activity. (shrink)

We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad's classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system's parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

Not only has the philosophical debate on causation been gaining ground in the last few decades, but it has also increasingly addressed the sciences. The biomedical sciences are among the most prominent fields that have been considered, with a number of works tackling the understanding of the notion of cause, the assessment of genuinely causal relations and the use of causal knowledge in applied contexts. Far from denying the merits of the debate on causation and the major theories it comprises, (...) this paper is meant as a stimulus for theorists of causation in the philosophy of biomedicine, with a focus on clinical matters. Without aiming at putting forward an original theory of causation and starting from the narration of two actual but paradigmatic cases at the joints between biomedical research and clinical practice, we want to point out that some pathological situations addressed by molecular medicine actually prove resistant to some of our major epistemological accounts of causal explanation. Given this scenario, which is very frequent in our hospitals, our analysis aims to provide a stimulus for the debate among theorists of causation in biomedicine interested in real cases in science in practice. We believe that this might in turn encourage some more general rethinking of the complex intertwinement of science, philosophy of science and ethics, as well as of the role of philosophy of science for clinical medicine itself. (shrink)

The property of being the implementation of a computational structure has been argued to be vacuously instantiated. This claim provides the basis for most antirealist arguments in the field of the philosophy of computation. Standard manoeuvres for combating these antirealist arguments treat the problem as endogenous to computational theories. The contrastive analysis of computational and other mathematical representations put forward here reveals that the problem should instead be treated within the more general framework of the Newman problem in structuralist accounts (...) of mathematical representation. It is argued that purely structuralist and purely functionalist accounts of implementation are inadequate to tackle the problem. An extensive evaluation of semantic accounts is provided, arguing that semantic properties are, unlike structural and functional ones, suitable to restrict the intended domain of implementation of computational properties in such a way as to block the Newman problem. The semantic hypothesis is defended from a number of recent objections. (shrink)

Function talk is a constant across different life sciences. From macro-evolution to genetics, functions are mentioned everywhere. For example, a limb’s function is to allow movement and RNA polymerases’ function is to transcribe DNA. Biochemistry is not immune from such a characterization; the biochemical world seems to be a chemical world embedded within biological processes. Specifically, biochemists commonly ascribe functions to biomolecules and classify them accordingly. This has been noticed in the recent philosophical literature on biochemical kinds. But while a (...) lot has been written on biological and psychological functions, little has been said explicitly about biochemical fuctions. Here, I explore functional attribution to biochemical molecules. I argue that if we accept this attribution, then biochemical functions are constituted by chemical dispositional properties that causally contribute to selected biological processes. In section 2, I discuss the controversy concerning the characterization of biochemical functions. In section 3, I consider whether a biological or a chemical under- standing of function can be applied to biochemical functions, illustrating the account with the example of vitamin B12. The result is that none of the theories on their own provides an adequate characterization. In section 4, I present an account of biochemical functions. In section 5, I assess this account taking into consideration common requirements for a theory of functions and an objection. (shrink)

“Realization” is a technical term that is used by metaphysicians, philosophers of mind, and philosophers of science to denote some dependence relation that is thought to obtain between higher-level properties and lower-level properties. It is said that mental properties are realized by physical properties; functional and computational properties are realized by first-order properties that occupy certain causal/functional roles; dispositional properties are realized by categorical properties; so on and so forth. Given this wide usage of the term “realization”, it would be (...) right to think that there might be different dependence relations that this term denotes in different cases. Any relation that is aptly picked out by this term can be taken to be a realization relation. The aim of this state-of-the-field article is to introduce the central questions about the concept of realization, and provide formulations of a number of realization relations. In doing so, I identify some theoretical roles realization relations should play, and discuss some theories of realization in relation to these theoretical roles. (shrink)

Dynamical systems play a central role in explanations in cognitive neuroscience. The grounds for these explanations are hotly debated and generally fall under two approaches: non-mechanistic and mechanistic. In this paper, I first outline a neurodynamical explanatory schema that highlights the role of dynamical systems in cognitive phenomena. I next explore the mechanistic status of such neurodynamical explanations. I argue that these explanations satisfy only some of the constraints on mechanistic explanation and should be considered pseudomechanistic explanations. I defend this (...) argument against three alternative interpretations of the neurodynamical explanatory schema. The independent interpretation holds that neurodynamical explanations and mechanisms are independent. The constitutive interpretation holds that neurodynamical explanations are constitutive but otherwise non-mechanistic. Both the independent and constitutive interpretations fail to account for all the features of neurodynamical explanations. The partial interpretation assumes that the targets of dynamical systems models are mechanisms and so holds that neurodynamical explanations are incomplete because they lack mechanistic details. I contend instead that the targets of those models are dynamical systems distinct from mechanisms and defend this claim against several objections. I conclude with a defense of the pseudomechanistic interpretation and a discussion of the source of their explanatory power in relation to a causal-mechanical description of the world. (shrink)

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the Ônew mechanical philosophyÕ to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence— namely, whether divergence in the absence of geographic isolation is possible (or (...) significant). Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate—namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. Ó 2005 Elsevier Ltd. All rights reserved. (shrink)

David Chalmers advocates the view that the phenomenon of consciousness is fundamentally different from all other phenomena studied in the life sciences, positing a uniquely hard problem that precludes the possibility of a mechanistic explanation. In this paper, I evaluate three demarcation criteria for dividing phenomena into hard and easy problems: functional definability, the puzzle of the accompanying phenomenon, and the first-person data of subjective experience. I argue that none of the proposed criteria can accurately discriminate between the phenomenon of (...) consciousness and mechanistically explainable phenomena. (shrink)

The paper discusses methodological guidelines for evaluating mechanistic explanations. According to current accounts, a satisfactory mechanistic explanation should include all of the relevant features of the mechanism, its component entities and activities, and their properties and organization, as well as exhibit productive continuity. It is not specified, however, how this kind of mechanistic completeness can be demonstrated. I argue that parameter sufficiency inferences based on mathematical model simulations provide a way of determining whether a mechanism capable of producing the phenomenon (...) of interest can be constructed from mechanistic components organized, acting, and having the properties described in the mechanistic explanation. (shrink)

A survey of models in immunology is conducted and distinct kinds of models are characterized based on whether models are material or conceptual, the distinctiveness of their epistemic purpose, and the criteria for evaluating the goodness of a model relative to its intended purpose. I argue that the diversity of models in interdisciplinary fields such as immunology reflects the fact that information about the phenomena of interest is gathered from different sources using multiple methods of investigation. To each model is (...) attached a description specifying how information about a phenomenon of interest has been acquired, highlighting points of commonality and difference between the methodological and epistemic histories of the information encapsulated in different models. These points of commonality and difference allow investigators to integrate findings from different models into more comprehensive explanatory accounts, as well as to troubleshoot anomalies and faulty accounts by going back to the original building blocks. (shrink)

Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). I (...) argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims. (shrink)

Teleology has a complicated history in the biological sciences. Some have argued that Darwin’s theory has allowed biology to purge itself of teleological explanations. Others have been content to retain teleology and to treat it as metaphorical, or have sought to replace it with less problematic notions like teleonomy. And still others have tried to naturalize it in a way that distances it from the vitalism of the nineteenth century, focusing on the role that function plays in teleological explanation. No (...) consensus has seemed possible in this debate. This paper takes a different approach. It argues that teleology is a perfectly acceptable scientific notion, but that the debate took an unfortunate misstep some 2300 years ago, one that has confused things ever since. The misstep comes in the beginning of Aristotle’s Physics when a distinction is made between two types of teleological explanation. One type pertains to artifacts while the other pertains to entities in nature. For Aristotle, artifacts are guided by something external to themselves, human intentions, while natural entities are guided by an internal nature. We aim to show that there is, in fact, only one type of legitimate teleological explanation, what Aristotle would have considered a variant of an artifact model, where entities are guided by external fields. We begin with an analysis of the differences between the two types of explanation. We then examine some evidence in Aristotle’s biological works suggesting that on account of his natural-artifactual distinction, he encountered difficulties in trying to provide teleological accounts of spontaneous generation. And we show that it is possible to resolve these difficulties with a more robust version of an artifact model of teleology, in other words, with an externalist teleology. This is McShea’s model, in which goal-directed entities are guided by a nested series of upper-level fields. To explain teleological behavior, this account invokes only external physical forces rather than mysterious internal natures. We then consider how field theory differs from other efforts to naturalize teleology in biology. And finally, we show how the account enables us to grapple with certain difficult cases – genes and intentions – where, even in biology today, the temptation to posit internal natures remains strong. (shrink)

p style="text-indent: 0cm; line-height: normal" class="MsoBodyTextIndent3"span style="font-size: 11pt"In this paper, I argue that starting with the organelles that constitute a cellmdash;and continuing up the hierarchy of components in processes and subsystems of an organismmdash;there exist clear instances of emergent biological phenomena that can be considered ldquo;livingrdquo; entities.spannbsp; /spanThese components and their attending processes are living emergent phenomena because of the way in which the components are organized to maintain homeostasis of the organism at the various levels in the hierarchy.spannbsp; /spanI (...) call this view the emhomeostatic organization view/em of biological phenomena, and, as is shown, it comports well with the standard philosophical accounts of nomological emergence and representational emergence.spannbsp; /spanTo proffer HOV, I describe properties of biological entities that include internal-hierarchical data exchange, data selectivity, informational integration, and environmental-organismic information exchange.spannbsp; /spanFurther, a distinction is drawn between particularized homeostasis and generalized homeostasis, and I argue that because the various processes and subsystems of an organism are functioning properly in their internal environments, the organism is able to exist as a hierarchically-organized entity in some environment external to it.spannbsp; /spanStated simply: that components of biological phenomena are organized to perform some function resulting in homeostasis marks them out to be living emergent entities distinguishable, in description and in reality, from the very physico-chemical processes of which they are composed./span/p p style="text-indent: 0cm; line-height: normal" class="MsoBodyTextIndent3"span style="font-size: 11pt"nbsp;/span/p. (shrink)

The present thesis explores some metaphysical issues concerning biochemical kinds and the relations between chemical and biological properties and phenomena. The main result of this thesis is that there is something sui generis about biochemical kinds. This result is motivated by two theoretical steps. The first is characterising biochemical functions as weakly emergent from the chemical structure [Chapter 3, Chapter 6]. The second is via an account for which biochemical kinds are natural categories [Chapter 4, Chapter 7]. The thesis comprises (...) four parts. Part I [Chapter 1, Chapter 2] aims to offer the methodological and conceptual tools that underpin this research. Chapter 1 presents the debate on the unity of science and the motivation of the research. Chapter 2 presents the account of natural kinds that will be used throughout the thesis. Part II [Chapter 3, Chapter 4] offers a detailed metaphysical analysis of the molecular gene. Chapter 3 argues that molecular genes are weakly emergent from nucleic acids. Chapter 4 argues that the category "molecular gene" can be deemed a natural kind, following the account presented in Chapter 2. Part III [Chapter 5, Chapter 6, Chapter 7] explores some of the themes related to biochemical kinds and generalises some of the results from Part II. Chapter 5 considers biochemical functions and how functional attribution should be interpreted for biochemical molecules. Chapter 6 considers the relation between biochemical functions and structure, spelt in terms of weak emergence and explores unity in biochemistry. Chapter 7 considers the topic of biochemical kinds per se and argues that biochemical kinds are natural categories. Part IV [Chapter 8] elucidates the main outcome and the implications that this research can have for future discussion in the philosophy and metaphysics of biochemistry and the unity of science. (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

In this paper, I argue that what counts as the proper function of a trait is a matter of the de facto perspective that the biological system, itself, possesses on what counts as proper functioning for that trait. Unlike non-perspectival accounts, internal perspectivalism does not succumb to generality problems. But unlike external perspectivalism, internal perspectivalism can provide a fully naturalistic, mind-independent grounding of proper function and natural norms. The attribution of perspectives to biological systems is intended to be neither metaphorical (...) nor anthropomorphic: I do not mean to imply that such systems thereby must possess agency, cognition, intentions, concepts, or mental or psychological states. Instead, such systems provide the grounding for norms of performance when they internally enforce their own standard of (i.e., their own perspective on) what constitutes proper functioning or malfunctioning. By operating with a fixed, determinate level of generality, such systems provide the basis for an account of proper function that is immune to generality problems. (shrink)

I argue that despite the merits of Jefferson’s account of a brain disorder, which are many, the notion of function she deploys is unsuitable to the overall goals of that account. In particular, Jefferson accepts Cummins’ causal role theory of function and dysfunction. As the causal role view, in its standard elaborations, is wedded to human interests, goals, and values, it cannot serve as a value-neutral anchor for her hybrid “harm-dysfunction” account of disorder. I argue that the selected effects theory, (...) or some comparably value-neutral account, would serve her purposes better. (shrink)

Descriptive accounts of the nature of explanation in neuroscience and the global goals of such explanation have recently proliferated in the philosophy of neuroscience and with them new understandings of the experimental practices of neuroscientists have emerged. In this paper, I consider two models of such practices; one that takes them to be reductive; another that takes them to be integrative. I investigate those areas of the neuroscience of learning and memory from which the examples used to substantiate these models (...) are culled, and argue that the multiplicity of experimental protocols used in these research areas presents specific challenges for both models. In my view, these challenges have been overlooked largely because philosophers have hitherto failed to pay sufficient attention to fundamental features of experimental practice. I demonstrate that when we do pay attention to such features, evidence for reduction and integrative unity in neuroscience is simply not borne out. I end by suggesting some new directions for the philosophy of neuroscience that pertain to taking a closer look at the nature of neuroscientific experiments. (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.

This is a short overview of the biological functions debate in philosophy. While it was fairly comprehensive when it was written, my short book ​A Critical Overview of Biological Functions has largely supplanted it as a definitive and up-to-date overview of the debate, both because the book takes into account new developments since then, and because the length of the book allowed me to go into substantially more detail about existing views.

This article aims to show that fundamentality is construed differently in the two most prominent strategies of analysis we find in physical science and engineering today: (1) atomistic, reductive analysis and (2) Systems analysis. Correspondingly, atomism is the conception according to which the simplest (smallest) indivisible entity of a certain kind is most fundamental; while systemism, as will be articulated here, is the conception according to which the bonds that structure wholes are most fundamental, and scale and/or constituting entities are (...) of no significance whatsoever for fundamentality. Accordingly, atomists maintain that the basic entities—the atoms—are fundamental, and together with the “external” interactions among them, are sufficient for illuminating all the features and behaviors of the wholes they constitute; whereas systemists proclaim that it is instead structural qualities of systems, that flow from internal relations among their constituents and translate directly into behaviors, that are fundamental, and by themselves largely (if not entirely) sufficient for illuminating the features and behaviors of the wholes thereby structured. Systemism, as will be argued, is consistent with the nonexistence of a fundamental “level” of nondecomposable entities, just as it is consistent with the existence of such a level. Still, systemism is a conception of the fundamental in quite different, but still ontological terms. Systemism can serve the special sciences—the social sciences especially—better than the conception of fundamentality in terms of atoms. Systemism is, in fact, a conception of fundamentality that has rather different uses—and importantly, different resonances. This conception of fundamentality makes contact with questions pertaining to natural kinds and their situation in the metaphysics of the special sciences—their situation within an order of autonomous sciences. The controversy over fundamentality is evident in the social sciences too, albeit somewhat imperfectly, in the terms of debate between methodological individualists and functionalists/holists. This article will thus clarify the difference between systemism and holism. (shrink)