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

This paper examines tracer techniques in neuroscience, which are used to identify neural connections in the brain and nervous system. These connections capture a type of “structural connectivity” that is expected to inform our understanding of the functional nature of these tissues. This is due to the fact that neural connectivity constrains the flow of signal propagation, which is a type of causal process in neurons. This work explores how tracers are used to identify causal information, what standards they are (...) expected to meet, the forms of causal information they provide, and how an analysis of these techniques contributes to the philosophical literature, in particular, the literature on mark transmission and mechanistic accounts of causation. (shrink)

The purpose of this work is to discuss which relation can be established between molecular chemistry, on the one hand, and macrochemistry and nanochemistry, on the other hand. In order to do this, we will consider molecular chemistry as an underlying level, and macrochemistry and nanochemistry as emergent levels. Emergence is characterized in very different ways in the philosophical literature; we will not discuss those differences. We will address a distinction between inter-domain emergence and intra-domain emergence. It is our purpose (...) to argue that, from a basal micro-molecular level, macrochemistry and nanochemistry emerge in parallel. The emergence of macrochemistry is an inter-domain emergence, while the emergence of the nanolevel is an intra-domain one. If this is the case, therefore macrochemistry and nanochemistry are not “successive” levels, but parallel ones. This discussion will be held from an ontological point of view, instead of the classical characterization in terms of scale. (shrink)

The use of multiple means of determination to “triangulate” on the existence and character of a common phenomenon, object, or result has had a long tradition in science but has seldom been a matter of primary focus. As with many traditions, it is traceable to Aristotle, who valued having multiple explanations of a phenomenon, and it may also be involved in his distinction between special objects of sense and common sensibles. It is implicit though not emphasized in the distinction between (...) primary and secondary qualities from Galileo onward. It is arguably one of several conceptions involved in Whewell’s method of the “consilience of inductions” (Laudan 1971) and is to be found in several places in Peirce. (From M. Brewer and B. Collins, eds., (1981); Scientific Inquiry in the Social Sciences (a festschrift for Donald T. Campbell), San Francisco: Jossey-Bass, pp. 123–162.). (shrink)

I develop an interdisciplinary framework for understanding the nature of agents and agency that is compatible with recent developments in the metaphysics of science and that also does justice to the mechanistic and normative characteristics of agents and agency as they are understood in moral philosophy, social psychology, neuroscience, robotics, and economics. The framework I develop is internal perspectivalist. That is to say, it counts agents as real in a perspective-dependent way, but not in a way that depends on an (...) external perspective. Whether or not something counts as an agent depends on whether it is able to have a certain kind of perspective. My approach differs from many others by treating possession of a perspective as more basic than the possession of agency, representational content/vehicles, cognition, intentions, goals, concepts, or mental or psychological states; these latter capabilities require the former, not the other way around. I explain what it means for a system to be able to have a perspective at all, beginning with simple cases in biology, and show how self-contained normative perspectives about proper function and control can emerge from mechanisms with relatively simple dynamics. I then describe how increasingly complex control architectures can become organized that allow for more complex perspectives that approach agency. Next, I provide my own account of the kind of perspective that is necessary for agency itself, the goal being to provide a reference against which other accounts can be compared. Finally, I introduce a crucial distinction that is necessary for understanding human agency: that between inclinational and committal agency, and venture a hypothesis about how the normative perspective underlying committal agency might be mechanistically realized. (shrink)

It is the aim of this paper to develop and defend an interpretation of level of scientific discipline within the truth-maker framework. In particular, I exploit the mereological relation of proper parthood, which is integral to truth-maker semantics, in order to provide an account of scientific level.

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)

Currently, there are almost as many conceptions of emergence as authors who address the issue. Most literature on the matter focuses either on discussing, evaluating and comparing particular contributions or accounts of emergence, or on assessing a particular case study. Our aim in this paper is rather different. We here set out to introduce a distinction that has not been sufficiently taken into account in previous discussions on this topic: the distinction between inter-domain emergence—a relation between items belonging to different (...) ontic domains—and intra-domain emergence—a relation between items belonging to a same ontic domain. Our final purpose is not to assume and defend a definite stance on emergence, but to stress the relevance of such distinction when attempting to argue for or against emergence, in the first place. We will also address the connections between emergence so distinguished and more general philosophical perspectives, suggesting where would reductionists and pluralists stand with respect to intra- and inter-domain emergence. (shrink)

Currently, there are almost as many conceptions of emergence as authors who address the issue. Most literature on the matter focuses either on discussing, evaluating and comparing particular contributions or accounts of emergence, or on assessing a particular case study. Our aim in this paper is rather different. We here set out to introduce a distinction that has not been sufficiently taken into account in previous discussions on this topic: the distinction between inter-domain emergence—a relation between items belonging to different (...) ontic domains—and intra-domain emergence—a relation between items belonging to a same ontic domain. Our final purpose is not to assume and defend a definite stance on emergence, but to stress the relevance of such distinction when attempting to argue for or against emergence, in the first place. We will also address the connections between emergence so distinguished and more general philosophical perspectives, suggesting where would reductionists and pluralists stand with respect to intra- and inter-domain emergence. (shrink)

In the last two decades few topics in philosophy of science have received as much attention as mechanistic explanation. A significant motivation for these accounts is that scientists frequently use the term “mechanism” in their explanations of biological phenomena. While scientists appeal to a variety of causal concepts in their explanations, many philosophers argue or assume that all of these concepts are well understood with the single notion of mechanism. This reveals a significant problem with mainstream mechanistic accounts– although philosophers (...) use the term “mechanism” interchangeably with other causal concepts, this is not something that scientists always do. This paper analyses two causal concepts in biology–the notions of “mechanism” and “pathway”–and how they figure in biological explanation. I argue that these concepts have unique features, that they are associated with distinct strategies of causal investigation, and that they figure in importantly different types of explanation. (shrink)

Any successful account of the metaphysics of mechanistic causation must satisfy at least five key desiderata. In this article, I lay out these five desiderata and explain why existing accounts of the metaphysics of mechanistic causation fail to satisfy them. I then present an alternative account that does satisfy the five desiderata. According to this alternative account, we must resort to a type of ontological entity that is new to metaphysics, but not to science: constraints. In this article, I explain (...) how a constraints-based metaphysics fits best with the emerging consensus on the nature of mechanistic explanation. 1Introduction2Renormalizability2.1The first two desiderata: Intrinsicness and productivity2.2The third desideratum: Scientific validity or non-mysteriousness2.3The fourth desideratum: Directionality2.4The fifth desideratum: Perspectival nature of mechanisms3Constraints and Causation3.1Multi-perspectival realism and causal structure3.2Causal structure as laws3.3Causal structures in analytical mechanics: Constraints3.4A metaphysics inspired by analytical mechanics: Constraints as ontologically primitive modal structures4Constraints and Mechanistic Causal Powers 4.1Inter- versus intra-perspectival categories4.2Mechanistic causal powers are grounded by constraints4.3Intrinsicness and constraints4.4Constraints and productiveness4.5Constraints and directionality5Conclusion. (shrink)

This Ph.D. thesis provides a pilosophical account of the structure of the evolutionary synthesis of the 1930s and 40s. The first, more historical part analyses how classical genetics came to be integrated into evolutionary thinking, highlighting in particular the importance of chromosomal mapping of Drosophila strains collected in the wild by Dobzansky, but also the work of Goldschmidt, Sumners, Timofeeff-Ressovsky and others. The second, more philosophical part attempts to answer the question wherein the unity of the synthesis consisted. I argue (...) that it exemplifies a weak of form of explanatory unification. (shrink)

Polger and Shapiro argue that their official recipe, a criterion for judging when the phenomenon of multiple realization exists, renders MR less widespread than its proponents have assumed. I argue that, although Polger and Shapiro’s criterion is a useful contribution, they arrive at their conclusion too hastily. Contrary to Polger and Shapiro, I claim that the phenomenon of multiple realization in the biological world, judged by their criterion, is not as scarce as they suggest. To show this, an updated official (...) recipe, namely a multiple mechanistic realization thesis, integrating Polger and Shapiro’s criterion with a compositional conception of realization, is developed. Then, three examples of varied kinds are examined, showing that cases of MR are not so hard to find in the biological world. (shrink)

This thesis aims to propose and defend a new way of analysing and understanding the origin of genetics (from Mendel to Bateson). Traditionally philosophers used to analyse the history of genetics in terms of theories. However, I will argue that this theory-based approach is highly problematic. In Chapter 1, I shall critically review the theory-driven approach to analysisng the history of genetics and diagnose its problems. In Chapter 2, inspired by Kuhn’s concept “exemplar”, I shall make a new interpretation of (...) exemplar and introduce an exemplar-based approach. Before introducing my exemplar-based analysis, I find it necessary to scrutinise the origin of genetics from Mendel to Bateson. In Chapter 3, I shall reinterpret Mendel’s work on Pisum by re-examining Mendel’s paper (1865) and its historical research context. In Chapter 4, by carefully examining the conceptual changes, I argue that the rediscovery event in 1900 should be better characterised as attempts of incorporating Mendel’s work with the work of “rediscoverers” (i.e. de Vries, Correns, Tschermak, and Bateson) rather than a mere reintroduction to Mendel’s work. In Chapter 5, I shall use the exemplar-based approach to analysing and interpreting the origin of genetics from Mendel to Bateson. In Chapter 6, I shall defend my exemplar-based characterisation of the origin of genetics by dismissing the potential responses from the theory-driven one, critically examining a potential mechanism-based analysis, and making the further notes on the implication of taking the exemplar-based approach to investigate scientific practice. (shrink)

This paper employs a case study from the history of neuroscience—brain reward function—to scrutinize the inductive argument for the so-called ‘Heuristic Identity Theory’ (HIT). The case fails to support HIT, illustrating why other case studies previously thought to provide empirical support for HIT also fold under scrutiny. After distinguishing two different ways of understanding the types of identity claims presupposed by HIT and considering other conceptual problems, we conclude that HIT is not an alternative to the traditional identity theory so (...) much as a relabeling of previously discussed strategies for mechanistic discovery. (shrink)

Despite the ubiquity of “levels of organization” in the scientific literature, a nascent “levels skepticism” now claims that the concept of levels is an inherently flawed, misleading, or otherwise inadequate notion for understanding how life scientists produce knowledge about the natural world. However, levels skeptics rely on the maligned “layer-cake” account of levels stemming from Oppenheim and Putnam’s defense of the unity of science for their critical commentary. Recourse to layer-cake levels is understandable, as it is arguably the default conception (...) of levels in philosophy. However, relying on this conception of levels undermines the initial plausibility of general dismissals of the concept, because the problems skeptics identify within the “basic idea” of the concept “levels” are merely ones already widely acknowledged in this conception. I illustrate this “guilt by association” by looking at the embedded role of “levels” in articulating intertheoretical reductionism during the latter part of the 20th century. I conclude by suggesting a methodological framework focusing on local usage patterns as a promising means for future analysis of the levels concept. (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)

Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the National Academy of (...) Science of the USA, focusing on the recent period 2003–2015. This comparison reveals a significant mismatch between the distributions of these topics. I examine plausible explanations for that mismatch. Finally, I argue that many biological topics underrepresented in philosophy of biology raise important philosophical issues and should therefore play a more central role in future philosophy of biology. (shrink)

It is often argued that biological generalizations have a distinctive and special status by comparison with the generalizations of other natural sciences, such as that biological generalizations are riddled with exceptions defying systematic and simple treatment. This special status of biology is used as a premise in arguments that posit a deprived explanatory, nomological, or methodological status in the biological sciences. I will discuss the traditional and still almost universally held idea that the biological sciences cannot deal with exceptions and (...) application conditions of their generalizations with their own distinctive and proprietary explanantia, but need the help of lower-level sciences to carry out this task. The idea of lower-level explanations of exceptions is connected to the idea that the biological sciences need lower-level sciences to better themselves and to the idea that biological sciences cannot provide reliable and extrapolatable results or explanations by themselves. I present counterexamples to the idea of lower-level explanations of exceptions in biology. I also discuss and refute more general arguments why the idea of lower-level explanations of exceptions has been held to hold in the special sciences, such as the screening-off and openness arguments. This suggest that there might be nothing special about the biological sciences vis-à-vis the more fundamental natural sciences, such as physics insofar as explanations of exceptions are concerned, and that the biological sciences can provide reliable and extrapolatable results or explanations by themselves. (shrink)

Cancer is not one, but many diseases, and each is a product of a variety of causes acting at distinct temporal and spatial scales, or ‘‘levels’’ in the biological hierarchy. In part because of this diversity of cancer types and causes, there has been a diversity of models, hypotheses, and explanations of carcinogenesis. However, there is one model of carcinogenesis that seems to have survived the diversification of cancer types: the multi-stage model of carcinogenesis. This paper examines the history of (...) the multistage theory, and uses the theory as a case study in the limits and goals of unification as a theoretical virtue, comparing and contrasting it with ‘‘integrative’’ research. (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)

In this paper, I propose two theses, and then examine what the consequences of those theses are for discussions of reduction and emergence. The first thesis is that what have traditionally been seen as robust, reductions of one theory or one branch of science by another more fundamental one are a largely a myth. Although there are such reductions in the physical sciences, they are quite rare, and depend on special requirements. In the biological sciences, these prima facie sweeping reductions (...) fade away, like the body of the famous Cheshire cat, leaving only a smile.... The second thesis is that the "smiles" are fragmentary patchy explanations, and though patchy and fragmentary, they are very important, potentially Nobel-prize winning advances. To get the best grasp of these "smiles," I want to argue that, we need to return to the roots of discussions and analyses of scientific explanation more generally, and not focus mainly on reduction models, though three conditions based on earlier reduction models are retained in the present analysis. I briefly review the scientific explanation literature as it relates to reduction, and then offer my account of explanation. The account of scientific explanation I present is one I have discussed before, but in this paper I try to simplify it, and characterize it as involving field elements and a preferred causal model system abbreviated as FE and PCMS. In an important sense, this FE and PCMS analysis locates an "explanation" in a typical scientific research article. This FE and PCMS account is illustrated using a recent set of neurogenetic papers on two kinds of worm foraging behaviors: solitary and social feeding. One of the preferred model systems from a 2002 Nature article in this set is used to exemplify the FE and PCMS analysis, which is shown to have both reductive and nonreductive aspects. The paper closes with a brief discussion of how this FE and PCMS approach differs from and is congruent with Bickle's "ruthless reductionism" and the recently revived mechanistic philosophy of science of Machamer, Darden, and Craver. (shrink)

An important strategy in the discovery of biological mechanisms involves the piecing together of experimental results from interventions. However, if mechanisms are investigated by means of ideal interventions, as defined by James Woodward and others, then the kind of information revealed is insufficient to discriminate between modular and non-modular causal contributions. Ideal interventions suffice for constructing webs of causal dependencies that can be used to make some predictions about experimental outcomes, but tell us little about how causally relevant factors are (...) organized together and how they interact with each other in order to produce a phenomenon. I argue that lab research relies on more elaborated types of interventions targeting in a controlled fashion multiple variables at the same time in order to probe the temporal organization of causally-relevant factors along distinct causal pathways and to test for non-modular interaction effects, thus providing crucial spatial-temporal constraints guiding the formulation of more detailed mechanistic explanations. (shrink)

Both clinical research and basic science rely on the epistemic practice of extrapolation from surrogate models, to the point that explanatory accounts presented in review papers and biology textbooks are in fact composite pictures reconstituted from data gathered in a variety of distinct experimental setups. This raises two new challenges to previously proposed mechanistic-similarity solutions to the problem of extrapolation: one pertaining to the absence of mechanistic knowledge in the early stages of research and the second to the large number (...) of extrapolations underpinning explanatory accounts. An analysis of the strategies deployed in experimental research supports the conclusion that while results from validated surrogate models are treated as a legitimate line of evidence supporting claims about target systems, the overall structure of research projects also demonstrates that extrapolative inferences are not considered definitive or sufficient evidence, but only partially justified hypotheses subjected to further testing. 1 Introduction2 Surrogate Models2.1 What exactly is a surrogate model?2.2 Why use surrogate models?3 Prior Validation of Surrogate Models3.1 The validation and ranking of surrogate models in the early stages of basic research3.2 The validation of surrogate models in later stages of basic research and in clinical research4 ‘Big Picture’ Accounts and the Extrapolations Underpinning Them4.1 The mosaic nature of mechanistic descriptions in basic science4.2 Challenges for mechanistic-similarity-based validation protocols5 Retrospective Testing of Extrapolated Knowledge5.1 Holistic confirmation5.2 Fallback strategies6 Conclusions. (shrink)

In this contribution, I comment on Raffaella Campaner’s defense of explanatory pluralism in psychiatry (in this volume). In her paper, Campaner focuses primarily on explanatory pluralism in contrast to explanatory reductionism. Furthermore, she distinguishes between pluralists who consider pluralism to be a temporary state on the one hand and pluralists who consider it to be a persisting state on the other hand. I suggest that it would be helpful to distinguish more than those two versions of pluralism – different understandings (...) of explanatory pluralism both within philosophy of science and psychiatry – namely moderate/temporary pluralism, anything goes pluralism, isolationist pluralism, integrative pluralism and interactive pluralism. Next, I discuss the pros and cons of these different understandings of explanatory pluralism. Finally, I raise the question of how to implement or operationalize explanatory pluralism in scientific practice; how to structure the “genuine dialogue” or shape “the pluralistic attitude” Campaner is referring to. As tentative answers, I explore a question-based framework for explanatory pluralism as well as social-epistemological procedures for interaction among competing approaches and explanations. (shrink)

Russell’s claim that only structural knowledge of the world is possible was influentially criticized by Newman as rendering scientific discoveries trivial. I show that a version of this criticism also applies to the “structural realism” more recently advocated by Worrall, which requires continuity of formal structure between predecessor and successor scientific theories. The problem is that structure, in its common set-theoretical construal, is radically underdetermined by the entities and relations over which it is defined, rendering intertheoretic continuity intolerably cheap. I (...) show that this problem may be overcome by supplementing the purely formal relation of intertheoretic isomorphism with the semiformal “Ontological Reductive Links” developed by Moulines and others of the German “structuralist” approach to the philosophy of science. (shrink)

A systematic theory of naturalism, bridging metaphysics and the science of complexity and emergence.

Science depends on judgments of the bearing of evidence on theory. Scientists must judge whether an observation or the result of an experiment supports, disconfirms, or is simply irrelevant to a given hypothesis. Similarly, scientists may judge that, given all the available evidence, a hypothesis ought to be accepted as correct or nearly so, rejected as false, or neither. Occasionally, these evidential judgments can be made on deductive grounds. If an experimental result strictly contradicts a hypothesis, then the truth of (...) the data deductively entails the falsity of the hypothesis. In the great majority of cases, however, the connection between evidence and hypothesis is non-demonstrative, or inductive. In particular, this is so whenever a general hypothesis is inferred to be correct on the basis of the available data, since the truth of the data will not deductively entail the truth of the hypothesis. It always remains possible that the hypothesis is false even though the data are correct. (shrink)

This chapter contains sections titled: Highlights of Past Literature Current Work Future Work.

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that the (...) most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (shrink)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his work was (...) disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

One important aspect of biological explanation is detailed causal modeling of particular phenomena in limited experimental background conditions. Recognising this allows one to appreciate that a sufficient condition for a reduction in biology is a molecular model of (1) only the demonstrated causal parameters of a biological model and (2) only within a replicable experimental background. These identities—which are ubiquitous in biology and form the basis of ruthless reductions (Bickle, Philosophy and neuroscience: a ruthlessly reductive account, 2003)—are criticised as merely (...) “local” (Sullivan, Synthese 167:511–539, 2009) or “fragmentary” (Schaffner, Synthese, 151(3):377–402, 2006). However, in an instructive case, a biological model is preserved in molecular terms, demonstrating a complex phenomenon that has been successfully reduced. (shrink)

Recently, some mechanists have embraced reductionism and some reductionists have endorsed mechanism. However, the two camps disagree sharply about the extent to which mechanistic explanation is a reductionistic enterprise. Reductionists maintain that cellular and molecular mechanisms can explain mental phenomena without necessary appeal to higher-level mechanisms. Mechanists deny this claim. I argue that this dispute turns on whether reduction is a transitive relation. I show that it is. Therefore, mechanistic explanations at the cellular and molecular level explain mental phenomena. I (...) make my case in part by noting that mechanisms at higher levels are composed of mechanisms at lower levels. Compositional relations are transitive. In addition, they are explanatory. I conclude that there are explanatory linkages from cellular and molecular mechanisms to mental phenomena within a hierarchy of nested mechanisms. (shrink)

This paper first queries what type of concept of emergence, if any, could be connected with the different chemical activities subsumed under the label ‘quantum chemistry’. In line with Roald Hoffmann, we propose a ‘rotation to research laboratory’ in order to point out how practitioners hold a molecular whole, its parts, and the surroundings together within their various methods when exploring chemical transformation. We then identify some requisite contents that a concept of emergence must incorporate in order to be coherent (...) from the standpoint of the scientific practices involved. In this respect, we finally propose a relational form of emergence which pays attention to the constitutive role of the modes of intervention and to the co-definition of the levels of organization. No metaphysical distinction between the higher and basic levels of organization is supposed, but only a plurality of modes of access. Moreover, these modes of access are not construed as mere ways of revealing intrinsic patterns of organization but, on the contrary, are considered to be active elements on which the constitution of those patterns depends. What is at stake in this paper is therefore not an ontological form of emergence but an agnostic one which fits what chemists do in their daily work. (shrink)

In this paper I argue that it is finally time to move beyond the Nagelian framework and to break new ground in thinking about epistemic reduction in biology. I will do so, not by simply repeating all the old objections that have been raised against Ernest Nagel’s classical model of theory reduction. Rather, I grant that a proponent of Nagel’s approach can handle several of these problems but that, nevertheless, Nagel’s general way of thinking about epistemic reduction in terms of (...) theories and their logical relations is entirely inadequate with respect to what is going on in actual biological research practice. (shrink)

Abstract Although noting the importance of organization in mechanisms, the new mechanistic philosophers of science have followed most biologists in focusing primarily on only the simplest mode of organization in which operations are envisaged as occurring sequentially. Increasingly, though, biologists are recognizing that the mechanisms they confront are non-sequential and the operations nonlinear. To understand how such mechanisms function through time, they are turning to computational models and tools of dynamical systems theory. Recent research on circadian rhythms addressing both intracellular (...) mechanisms and the intercellular networks in which these mechanisms are synchronized illuminates this point. This and other recent research in biology shows that the new mechanistic philosophers of science must expand their account of mechanistic explanation to incorporate computational modeling, yielding dynamical mechanistic explanations. Developing such explanations, however, is a challenge for both the scientists and the philosophers as there are serious tensions between mechanistic and dynamical approaches to science, and there are important opportunities for philosophers of science to contribute to surmounting these tensions. Content Type Journal Article Category Original paper in Philosophy of Science Pages 1-16 DOI 10.1007/s13194-012-0046-x Authors William Bechtel, Department of Philosophy, Center for Chronobiology, and Science Studies Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0119, USA Journal European Journal for Philosophy of Science Online ISSN 1879-4920 Print ISSN 1879-4912. (shrink)

This paper provides an account of the experimental conditions required for establishing whether correlating or causally relevant factors are constitutive components of a mechanism connecting input (start) and output (finish) conditions. I argue that two-variable experiments, where both the initial conditions and a component postulated by the mechanism are simultaneously manipulated on an independent basis, are usually required in order to differentiate between correlating or causally relevant factors and constitutively relevant ones. Based on a typical research project molecular biology, a (...) flowchart model detailing typical stages in the formulation and testing of hypotheses about mechanistic components is also developed. (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)

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

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two facets distinct (...) facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics. (shrink)

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...) forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context. (shrink)

How are scientific explanations possible in ecology, given that there do not appear to be many—if any—ecological laws? To answer this question, I present and defend an account of scientific causal explanation in which ecological generalizations are explanatory if they are invariant rather than lawlike. An invariant generalization continues to hold or be valid under a special change—called an intervention—that changes the value of its variables. According to this account, causes are difference-makers that can be intervened upon to manipulate or (...) control their effects. I apply the account to ecological generalizations to show that invariance under interventions as a criterion of explanatory relevance provides interesting interpretations for the explanatory status of many ecological generalizations. Thus, I argue that there could be causal explanations in ecology by generalizations that are not, in a strict sense, laws. I also address the issue of mechanistic explanations in ecology by arguing that invariance and modularity constitute such explanations. (shrink)

For several decades, economists have been preoccupied with an attempt to place their entire subject on the ‘sound microfoundations’ of general equilibrium theory, with its individualistic premises. However, this project has run into seemingly intractable problems. This essay examines underlying questions such as the appropriate building block of analysis and the structure of explanation in economics. The examination of biology is found to be instructive, due to debates concerning the limitations of reductionism within that discipline. The final part of the (...) paper argues for the autonomy of a non‐reductionist macroeconomics, based on the institution as the unit of analysis. (shrink)

Schaffner’s model of theory reduction has played an important role in philosophy of science and philosophy of biology. Here, the model is found to be problematic because of an internal tension. Indeed, standard antireductionist external criticisms concerning reduction functions and laws in biology do not provide a full picture of the limits of Schaffner’s model. However, despite the internal tension, his model usefully highlights the importance of regulative ideals associated with the search for derivational, and embedding, deductive relations among mathematical (...) structures in theoretical biology. A reconstructed Schaffnerian model could therefore shed light on mathematical theory development in the biological sciences and on the epistemology of mathematical practices more generally. *Received November 2006; revised March 2009. †To contact the author, please write to: Philosophy Department, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064; e‐mail: [email protected]. (shrink)

In Molecular Models: Philosophical Papers on Molecular Biology, Sahotra Sarkar presents a historical and philosophical analysis of four important themes in philosophy of science that have been influenced by discoveries in molecular biology. These are: reduction, function, information and directed mutation. I argue that there is an important difference between the cases of function and information and the more complex case of scientific reduction. In the former cases it makes sense to taxonomise important variations in scientific and philosophical usage of (...) the terms function and information . However, the variety of usage of reduction across scientific disciplines (and across philosophy of science) makes such taxonomy inappropriate. Sarkar presents reduction as a set of facts about the world that science has discovered, but the facts in question are remarkably disparate; variously semantic, epistemic and ontological. I argue that the more natural conclusion of Sarkar’s analysis is eliminativism about reduction as a scientific concept. (shrink)

The importance of the exclusion argument for contemporary physicalism is emphasized. The recent attempts to vindicate reductive physicalism by invoking certain needed revisions to the Nagelian model of reduction are then discussed. It is argued that such revised views of reduction offer in fact much less help to reductive physicalism than is sometimes supposed, and that many of these views lead to trouble when combined with the exclusion argument.