Chronobiology, especially the study of circadian rhythms, provides a model scientific field in which philosophers can study how investigators from a variety of disciplines working at different levels of organization are each contributing to a multi-level account of the responsible mechanism. I focus on how the framework of mechanistic explanation integrates research designed to decompose the mechanism with efforts directed at recomposition that relies especially on computation models. I also examine how recently the integration has extended beyond basic research to (...) the processes through which the disruption of circadian rhythms contributes to disease, including various forms of cancer. Understanding these linkages has been facilitated by discoveries about how circadian mechanisms interact with mechanisms involved in other physiological processes, including the cell cycle and the immune system. (shrink)

Extrapolation from a well-understood base population to a less-understood target population can fail if the base and target populations are not sufficiently similar. Differences between laboratory mice and humans, for example, can hinder extrapolation in medical research. Mice that carry a partial or complete human physiological system, known as humanized mice, are supposed to make extrapolation more reliable by simulating a variety of human diseases. But what justifies our belief that these mice are similar enough to their human counterparts to (...) simulate human disease? I argue that, unless three requirements are met in the process of humanizing mice, very little does. My requirements are not meant to provide necessary and sufficient conditions that guarantee a particular outcome. Instead, they serve as a heuristic for guiding scientific judgments involving extrapolation. In developing each requirement, I engage with philosophical issues concerning the nature of model-based science and the mechanistic approach (and its limits) to making generalizations in the life sciences. (shrink)

Assume that water reduces to H2O. If so water is identical to H2O. At the same time, if water reduces to H2O then H2O does not reduce to water–the reduction relation is asymmetric. This generates a puzzle–if water just is H2O it is hard to see how we can account for the asymmetry of the reduction relation. The paper proposes a solution to this puzzle. It is argued that the reduction predicate generates intensional contexts and that in order to account (...) for the asymmetry, we should develop conditions on the meanings of expressions that flank the reduction predicate in true reduction statements. Finally, it is argued that if we adopt this interpretation, we can illuminate the epistemological difference between reduced and reducing item commonly referred to in the literature. (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)

August Weismann is famous for having argued against the inheritance of acquired characters. However, an analysis of his work indicates that Weismann always held that changes in external conditions, acting during development, were the necessary causes of variation in the hereditary material. For much of his career he held that acquired germ-plasm variation was inherited. An irony, which is in tension with much of the standard twentieth-century history of biology, thus exists – Weismann was not a Weismannian. I distinguish three (...) claims regarding the germ-plasm: (1) its continuity, (2) its morphological sequestration, and (3) its variational sequestration. With respect to changes in Weismann’s views on the cause of variation, I divide his career into four stages. For each stage I analyze his beliefs on the relative importance of changes in external conditions and sexual reproduction as causes of variation in the hereditary material. Weismann believed, and Weismannism denies, that variation, heredity, and development were deeply intertwined processes. This article is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century. (shrink)

Nagel’s official model of theory-reduction and the way it is represented in the literature are shown to be incompatible with the careful remarks on the notion of reduction Nagel gave while developing his model. Based on these remarks, an alternative model is outlined which does not face some of the problems the official model faces. Taking the context in which Nagel developed his model into account, it is shown that the way Nagel shaped his model and, thus, its well-known deficiencies, (...) are best conceived of as a mere by-product of his philosophical background. (shrink)

What drives much of the current philosophical interest in the idea of group cognition is its appeal to the manifestation of psychological properties—understood broadly to include states, processes, and dispositions—that are in some important yet elusive sense emergent with respect to the minds of individual group members. Our goal in this paper is to address a set of related, conditional questions: If human mentality is real yet emergent in a modest metaphysical sense only, then: (i) What would it mean for (...) a group to have emergent cognitive states? (ii) Is this even a metaphysically coherent view? (iii) Relative to which notion of emergence do we have reason to believe that certain groups in fact have emergent cognitive states? We shall argue that evidence from a wide variety of social science domains makes it plausible that there are group cognitive states and processes no less metaphysically emergent than human cognitive (and other special science) states and processes. (shrink)

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

Philosophers of science typically associate the causal-mechanical view of scientific explanation with the work of Railton and Salmon. In this paper I shall argue that the defects of this view arise from an inadequate analysis of the concept of mechanism. I contrast Salmon's account of mechanisms in terms of the causal nexus with my own account of mechanisms, in which mechanisms are viewed as complex systems. After describing these two concepts of mechanism, I show how the complex-systems approach avoids certain (...) objections to Salmon's account of causal-mechanical explanation. I conclude by discussing how mechanistic explanations can provide understanding by unification. (shrink)

The reductionist/holist debate seems an impoverished one, with many participants appearing to adopt a position first and constructing rationalisations second. Here I propose an intermediate position of pragmatic holism, that irrespective of whether all natural systems are theoretically reducible, for many systems it is completely impractical to attempt such a reduction, also that regardless if whether irreducible `wholes' exist, it is vain to try and prove this in absolute terms. This position thus illuminates the debate along new pragmatic lines, and (...) refocusses attention on the underlying heuristics of learning about the natural world. (shrink)

The functional complexity, or the number of functions, of organisms hasfigured prominently in certain theoretical and empirical work inevolutionary biology. Large-scale trends in functional complexity andcorrelations between functional complexity and other variables, such assize, have been proposed. However, the notion of number of functions hasalso been operationally intractable, in that no method has been developedfor counting functions in an organism in a systematic and reliable way.Thus, studies have had to rely on the largely unsupported assumption thatnumber of functions can be (...) measured indirectly, by using number ofmorphological, physiological, and behavioral parts as a proxy. Here, amodel is developed that supports this assumption. Specifically, the modelpredicts that few parts will have many functions overlapping in them, andtherefore the variance in number of functions per part will be low. If so,then number of parts is expected to be well correlated with number offunctions, and we can use part counts as proxies for function counts incomparative studies of organisms, even when part counts are low. Alsodiscussed briefly is a strategy for identifying certain kinds of parts inorganisms in a systematic way. (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the (...) use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

Most philosophical accounts of emergence are incompatible with reduction. Most scientists regard a system property as emergent relative to properties of its parts if it depends upon their mode of organization-a view consistent with reduction. Emergence is a failure of aggregativity, in which ``the whole is nothing more than the sum of its parts''. Aggregativity requires four conditions, giving powerful tools for analyzing modes of organization. Differently met for different decompositions of the system, and in different degrees, the structural conditions (...) can provide evaluation criteria for choosing decompositions, ``natural kinds'', and detecting functional localization fallacies, approximations, and various biases of vulgar reductionisms. This analysis of emergence and use of these conditions as heuristics is consistent with a broader reductionistic methodology. (shrink)

The reductionist/holist debate is highly polarised. I propose an intermediate position of pragmatic holism. It derives from two claims: firstly, that irrespective of whether all natural systems are theoretically reducible, for many systems it is utterly impractical to attempt such a reduction, and secondly, that regardless of whether irreducible 'wholes exist, it is vain to try and prove this. This position illuminates the debate along new pragmatic lines by refocussing attention on the underlying heuristics of learning about the natural world.

This paper is about a general methodology for pattern transformation. Patterns are network representations of the relations among structures and functions within an organism. Transformation refers to any realistic or abstract transformation relevant to biology, e.g. ontogeny, evolution and phenotypic clines. The main aim of the paper is a methodology for analyzing the range of effects on a pattern due to perturbing one or more of its structures and/or functions (transformation morphology). Concepts relevant to such an analysis of pattern transformation (...) are reviewed and several new ones introduced: pattern unit; direct and indirect functional demands; compatibility and trade-off; integrating, adding and decoupling; functional effectiveness; spatial, profile and other architectonic constraints; domains of structure-function relations; goal and process adaptability; multiple pathways. The paper is written from the the perspective of architectonic morphology, viz. functional morphology focusing on the relation between anatomical coherence and the compatibility of functions. The advantages and disadvantages of inductive and deductive approaches are discussed. (shrink)

As much as assumptions about mechanisms and mechanistic explanation have deeply affected psychology, they have received disproportionately little analysis in philosophy. After a historical survey of the influences of mechanistic approaches to explanation of psychological phenomena, we specify the nature of mechanisms and mechanistic explanation. Contrary to some treatments of mechanistic explanation, we maintain that explanation is an epistemic activity that involves representing and reasoning about mechanisms. We discuss the manner in which mechanistic approaches serve to bridge levels rather than (...) reduce them, as well as the different ways in which mechanisms are discovered. Finally, we offer a more detailed example of an important psychological phenomenon for which mechanistic explanation has provided the main source of scientific understanding. (shrink)

According to the dominant computational approach in cognitive science, cognitive agents are digital computers; according to the alternative approach, they are dynamical systems. This target article attempts to articulate and support the dynamical hypothesis. The dynamical hypothesis has two major components: the nature hypothesis (cognitive agents are dynamical systems) and the knowledge hypothesis (cognitive agents can be understood dynamically). A wide range of objections to this hypothesis can be rebutted. The conclusion is that cognitive systems may well be dynamical systems, (...) and only sustained empirical research in cognitive science will determine the extent to which that is true. (shrink)

A cognitive ethnography of how bioengineering scientists create innovative modeling methods. In this first full-scale, long-term cognitive ethnography by a philosopher of science, Nancy J. Nersessian offers an account of how scientists at the interdisciplinary frontiers of bioengineering create novel problem-solving methods. Bioengineering scientists model complex dynamical biological systems using concepts, methods, materials, and other resources drawn primarily from engineering. They aim to understand these systems sufficiently to control or intervene in them. What Nersessian examines here is how cutting-edge bioengineering (...) scientists integrate the cognitive, social, material, and cultural dimensions of practice. Her findings and conclusions have broad implications for researchers in philosophy, science studies, cognitive science, and interdisciplinary studies, as well as scientists, educators, policy makers, and funding agencies. In studying the epistemic practices of scientists, Nersessian pushes the boundaries of the philosophy of science and cognitive science into areas not ventured before. She recounts a decades-long, wide-ranging, and richly detailed investigation of the innovative interdisciplinary modeling practices of bioengineering researchers in four university laboratories. She argues and demonstrates that the methods of cognitive ethnography and qualitative data analysis, placed in the framework of distributed cognition, provide the tools for a philosophical analysis of how scientific discoveries arise from complex systems in which the cognitive, social, material, and cultural dimensions of problem-solving are integrated into the epistemic practices of scientists. Specifically, she looks at how interdisciplinary environments shape problem-solving. Although Nersessian’s case material is drawn from the bioengineering sciences, her analytic framework and methodological approach are directly applicable to scientific research in a broader, more general sense, as well. (shrink)

A long-standing problem in understanding goal-directed systems has been the insufficiency of mechanistic explanations to make sense of them. This paper offers a solution to this problem. It begins by observing the limitations of mechanistic decompositions when it comes to understanding physical fields. We argue that introducing the field concept, as it has been developed in field theory, alongside mechanisms is able to provide an account of goal directedness in the sciences.

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

Si bien en la filosofía de las ciencias ya se han explorado algunos ejemplos provenientes de la bioquímica como casos de estudio, la filosofía de la bioquímica es una subdisciplina naciente. En este artículo estudiaremos dos problemas filosóficos de relevancia contemporánea en esta ciencia. Por un lado, examinaremos las bases epistemológicas del problema del plegamiento de proteínas. En particular lo relacionado con la predicción de la estructura tridimensional de las proteínas a partir de su secuencia, asunto que ha dado mucho (...) que hablar debido a los nuevos avances utilizando deep learning. Por otro lado, exploraremos el problema in-vitro/in-vivo y, más generalmente, el problema de la extrapolación en las ciencias biológicas. Finalmente, a partir de las consecuencias de ambos temas consideraremos algunas reflexiones filosóficas generales acerca del reduccionismo, el pluralismo y el lugar de la bioquímica en las ciencias biológicas. Palabras clave: Bioquímica, Plegamiento de proteínas, In-vitro/in-vivo, Pluralismo, Reduccionismo. (shrink)

This paper argues that the account of teleology previously proposed by the authors is consistent with the physical determinism that is implicit across many of the sciences. We suggest that much of the current aversion to teleological thinking found in the sciences is rooted in debates that can be traced back to ancient natural science, which pitted mechanistic and deterministic theories against teleological ones. These debates saw a deterministic world as one where freedom and agency is impossible. And, because teleological (...) entities seem to be free to either reach their ends or not, it was assumed that they could not be deterministic. Mayr’s modern account of teleonomy adheres to this basic assumption. Yet, the seeming tension between teleology and determinism is illusory because freedom and agency do not, in fact, conflict with a deterministic world. To show this, we present a taxonomy of different types of freedom that we see as inherent in teleological systems. Then we show that our taxonomy of freedom, which is crucial to understanding teleology, shares many of the features of a philosophical position regarding free will that is known in the contemporary literature as ‘compatibilism’. This position maintains that an agent is free when the sources of its actions are internal, when the agent itself is the deterministic cause of those actions. Our view shows that freedom is not only indispensable to teleology, but also that, contrary to common intuitions, there is no conflict between teleology and causal determinism. (shrink)

Even though complexity is a concept that is ubiquitously used by biologists and philosophers of biology, it is rarely made precise. I argue that a clarification of the concept is neither trivial nor unachievable, and I propose a unifying framework based on the technical notion of “effective complexity” that allows me to do justice to conflicting intuitions about biological complexity, while taking into account several distinctions in the usage of the concept that are often overlooked. In particular, I propose a (...) distinction between two kinds of complexity, “mechanical” and “emergent”, which can be understood as different ways of relating the effective complexity of mechanisms and of behaviors in biological explanations. I illustrate the adequacy of this framework by discussing different attempts to understand intracellular organization in terms of pathways and networks. My framework provides a different way of thinking about recent philosophical debates, for example, on the difference between mechanistic and topological explanations and about the concept of emergence. Moreover, it can contribute to a proper assessment of metascientific arguments that invoke biological complexity. (shrink)

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

Functional robustness refers to a system’s ability to maintain a function in the face of perturbations to the causal structures that support performance of that function. Modularity, a crucial element of standard methods of causal inference and difference-making accounts of causation, refers to the independent manipulability of causal relationships within a system. Functional robustness appears to be at odds with modularity. If a function is maintained despite manipulation of some causal structure that supports that function, then the relationship between that (...) structure and function fails to be manipulable independent of other causal relationships within the system. Contrary to this line of reasoning, I argue that functional robustness often attends feedback control, rather than failures of modularity. Feedback control poses its own challenges to causal explanation and inference, but those challenges do not undermine modularity—and indeed, modularity is crucial to grappling with them. (shrink)

Evolutionary Transitions in Individuality have been responsible for the major transitions in levels of selection and individuality in natural history, such as the origins of prokaryotic and eukaryotic cells, multicellular organisms, and eusocial insects. The integrated hierarchical organization of life thereby emerged as groups of individuals repeatedly evolved into new and more complex kinds of individuals. The Social Protocell Hypothesis proposes that the integrated hierarchical organization of human culture can also be understood as the outcome of an ETI—one that produced (...) a “cultural organism” from a substrate of socially learned traditions that were contained in growing and dividing social communities. The SPH predicts that a threshold degree of evolutionary individuality would have been achieved by 2.0–2.5 Mya, followed by an increasing degree of evolutionary individuality as the ETI unfolded. We here assess the SPH by applying a battery of criteria—developed to assess evolutionary individuality in biological units—to cultural units across the evolutionary history of Homo. We find an increasing agreement with these criteria, which buttresses the claim that an ETI occurred in the cultural realm. (shrink)

Cancer is typically spoken of as a “complex” disease. But, in what sense are cancers “complex”? Is there one sense, or several? What implications does this complexity have – both for how we study, and how we intervene upon cancers? The aim of this paper is first, to clarify the variety of senses in which cancer is spoken of as "complex" in the scientific literature, and second, to discover what explanatory and predictive roles such features play.

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)

A common strategy for simplifying complex systems involves partitioning them into subsystems whose behaviors are roughly independent of one another at shorter timescales. Dynamic causal models clarify how doing so reveals a system’s nonequilibrium causal relationships. Here I use these models to elucidate the idealizations and abstractions involved in representing a system at a timescale. The models reveal that key features of causal representations—such as which variables are exogenous—may vary with the timescale at which a system is considered. This has (...) implications for debates regarding which systems can be represented causally. (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)

There have been repeated attempts in the history of comparative biology to provide a mechanistic account of morphological homology. However, it is well-established that homologues can develop from diverse sets of developmental causes, appearing not to share any core causal architecture that underwrites character identity. We address this challenge with a new conceptual model of Character Identity Mechanisms. ChIMs are cohesive mechanisms with a recognizable causal profile that allows them to be traced through evolution as homologues despite having a diverse (...) etiological organization. Our model hypothesizes that anatomical units at different levels of organization—cell types, tissues, and organs—have level-specific ChIMs with different conserved parts, activities, and organization. Relying on a methodology of conceptual engineering, we show how the ChIM concept advances our understanding of the developmental basis of morphological characters, while forging an important link between comparative and mechanistic biology. (shrink)

This is a thesis about interdisciplinarity, scientific integration, and problem solving in sustainability science. Sustainability science is an emerging and highly interdisciplinary field that seeks to integrate vastly differentiated bodies of knowledge in addressing the challenge of transitioning contemporary societies towards sustainability. Interdisciplinarity is paramount. Interdisciplinarity in general, and in the context of sustainability science in particular, has often been associated with solving particular problems and problem solving is one important theme in this thesis. A central idea that is developed (...) is that of problem-feeding. Sometimes problems arise within one discipline that can only be solved with the help of another. This concept, that has predecessors in e.g. the work of Lindley Darden and Nancy Maull, is explored considerably. It is argued that in interdisciplinary contexts—such as sustainability science—where collaboration is sought it is important to maintain cross-boundary problem stability. That is to say, as the problem is transferred from one discipline to another transformations will often be necessary. These transformations then, need to be acceptable to all involved parties to maintain an active interdisciplinary connection. Another topic that is discussed both in the introductory essay and some of the papers included is that of scientific imperialism. Scientific imperialism—the infringement of one discipline upon the domain of another—is here suggested to be primarily a threat to in-terdisciplinary collaborations. A distinction is introduced between imperialist failures of expansionism and failures of replacement. These are labelled type-I and type-II imperialism respectively. Particular attention is devoted to the latter form. Type-II imperialism concerns cases where imperialist infringements fail as the imperial- izing framework replaces viable, or compatible alternatives. Such an error of replacement does, importantly, not imply that the framework or theory should be disregarded completely. This type of imperialist error can both be quite subtle, and damaging. For one, if one directs the attention to specific contexts knowledge is actually lost in the process. This is particularly serious in fields such as sustainability science that are, to such an large extent, aimed at influencing concrete policy. Finally, interdisciplinarity is difficult to achieve and in many cases represents a grand challenge in itself. There are however many different ways in which interdisciplinarity may be accomplished and different forms are suitable in different contexts. In a field such as sustainability science where complexity is such a prevalent feature, an inclusive, pluralist, approach is likely to be appropriate. (shrink)

The current view of the relationship between areas of the mind-brain sciences is one where cross-disciplinary collaboration is required to advance claims about the mind-brain that stand on firm epistemic footing. My goal in this dissertation is to analyze what it means for information from different areas of science to fit together to produce strong epistemic claims by addressing how and to what extent claims about the mind-brain are corroborated in scientific practice. Philosophers of science have advanced various concepts of (...) the notion of fitting together information from different areas of science and its relation to scientific progress (e.g., Bickle, 1998, 2003, 2006; Darden and Maull, 1977; Mitchell, 2002, 2003; Mitchell and Dietrich, 2006; Nagel 1949, 1970, 1979; Piccinini and Craver, 2011; and Roskies, 2010). However, each concept of fitting together is vague and subject to multiple clarificatory questions. To get a handle on the notion of fitting together, I introduce the term ‘interdisciplinary corroboration’ as a placeholder for the various accounts of fitting together to facilitate my investigation of how claims about the mind-brain are corroborated in scientific practice. I argue review papers are a good place to begin analyzing interdisciplinary corroboration; accordingly, I conduct a two-part analysis of a review paper by Eichenbaum (2013) entitled ‘Memory on Time’. I use the lessons from my analysis to develop and advance a methodology for philosophers of science interested in knowledge production for evaluating review papers for corroboration in the mind-brain sciences. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Levels of organization and their use in science have received increased philosophical attention of late, including challenges to the well-foundedness or widespread usefulness of levels concepts. One kind of response to these challenges has been to advocate a more precise and specific levels concept that is coherent and useful. Another kind of response has been to argue that the levels concept should be taken as a heuristic, to embrace its ambiguity and the possibility of exceptions as acceptable consequences of its (...) usefulness. In this chapter, I suggest that each of these strategies faces its own attendant downsides, and that pursuit of both strategies (by different thinkers) compounds the difficulties. That both kinds of approaches are advocated is, I think, illustrative of the problems plaguing the concept of levels of organization. I end by suggesting that the invocation of levels may mislead scientific and philosophical investigations more than it informs them, so our use of the levels concept should be updated accordingly. (shrink)

We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call “epistemic competition” that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe—contrary to many other accounts of scientific change—that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape. (shrink)

Ecological communities are seldom, if ever, biological individuals. They lack causal boundaries as the populations that constitute communities are not congruent and rarely have persistent functional roles regulating the communities’ higher-level properties. Instead we should represent ecological communities indexically, by identifying ecological communities via the network of weak causal interactions between populations that unfurl from a starting set of populations. This precisification of ecological communities helps identify how community properties remain invariant, and why they have robust characteristics. This respects the (...) diversity and aggregational nature of these complex systems while still vindicating them as units worthy of investigation. (shrink)

Token physicalism is often viewed as a modest and unproblematic physicalist commitment, as contrasted with type physicalism. This paper argues that the prevalence of functional individuation in biology creates serious problems for token physicalism, because the latter requires that biological entities can be individuated physically and without reference to biological functioning. After characterizing the main philosophical roles for token physicalism, I describe the distinctive uses of functional individuation in models of biological processes. I then introduce some requirements on token identity (...) claims that arise from a position on individuation and identity known as sortalism. An examination of biological examples shows that these sortalist requirements cannot be plausibly met due to differences between individuation by functional biological criteria and by physical criteria. Even without assuming sortalism, token physicalism faces the more basic problem of excluding functionally irrelevant detail from the individuation of biological tokens. I close by suggesting that the philosophical roles for token identity are better fulfilled by a notion of token composition, which promotes a hierarchical picture of individuality. (shrink)

Philosophy of biology is often said to have emerged in the last third of the twentieth century. Prior to this time, it has been alleged that the only authors who engaged philosophically with the life sciences were either logical empiricists who sought to impose the explanatory ideals of the physical sciences onto biology, or vitalists who invoked mystical agencies in an attempt to ward off the threat of physicochemical reduction. These schools paid little attention to actual biological science, and as (...) a result philosophy of biology languished in a state of futility for much of the twentieth century. The situation, we are told, only began to change in the late 1960s and early 1970s, when a new generation of researchers began to focus on problems internal to biology, leading to the consolidation of the discipline. In this paper we challenge this widely accepted narrative of the history of philosophy of biology. We do so by arguing that the most important tradition within early twentieth-century philosophy of biology was neither logical empiricism nor vitalism, but the organicist movement that flourished between the First and Second World Wars. We show that the organicist corpus is thematically and methodologically continuous with the contemporary literature in order to discredit the view that early work in the philosophy of biology was unproductive, and we emphasize the desirability of integrating the historical and contemporary conversations into a single, unified discourse. (shrink)

The article analyses in detail the Meselson–Stahl experiment, identifying two novel difficulties for the crucial experiment account, namely, the fragility of the experimental results and the fact that the hypotheses under scrutiny were not mutually exclusive. The crucial experiment account is rejected in favour of an experimental-mechanistic account of the historical significance of the experiment, emphasizing that the experiment generated data about the biochemistry of DNA replication that is independent of the testing of the semi-conservative, conservative, and dispersive hypotheses. _1_ (...) Introduction _2_ The Meselson–Stahl Experiment _3_ Some Difficulties for the Crucial Experiment Account _3.1_ Additional experiments were required _3.2_ Simplicity considerations are unconvincing _3.3_ The fragility of the experimental results _3.4_ The problematic interpretation of falsifyng results _3.5_ Not all possible hypotheses considered or tested _3.6_ The tested hypotheses were not mutually exclusive _4_ The Historical and Scientific Significance of the Meselson–Stahl Experiment _4.1_ The challenge for the crucial experiment account _4.2_ A mechanistic perspective on the experiment _4.3_ The experimental design and its independence from theoretical speculations _4.4_ The advantages of a ‘bottom-up’ mechanistic account _5_ Conclusion. (shrink)

This volume argues for a new image of science that understands both natural and social phenomena to be the product of mechanisms, casting the work of science as an effort to understand those mechanisms. Glennan offers an account of the nature of mechanisms and of the models used to represent them in physical, life, and social sciences.

Mechanisms are said to consist of two kinds of components, entities and activities. In the first half of this chapter, I examine what entities and activities are, how they relate to well-known ontological categories, such as processes or dispositions, and how entities and activities relate to each other (e.g., can one be reduced to the other or are they mutually dependent?). The second part of this chapter analyzes different criteria for individuating the components of mechanisms and discusses how real the (...) boundaries of mechanisms are. (shrink)

The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed models of metabolic and cell-signaling (...) pathways by conducting her own wet-lab experimentation while building simulation models. We show how this coupling of experiment and simulation enabled her to build and validate her models and also triangulate and localize errors and uncertainties in them. This method can be contrasted with the unimodal modeling strategy in systems biology which relies more on mathematical or algorithmic methods to reduce complexity. We discuss the relative affordances and limitations of these strategies, which represent distinct opinions in the field about how to handle the investigation of complex biological systems. (shrink)

Wants, preferences, and cares are physical things or events, not ideas or propositions, and therefore no chain of pure logic can conclude with a want, preference, or care. It follows that no pure-logic machine will ever want, prefer, or care. And its behavior will never be driven in the way that deliberate human behavior is driven, in other words, it will not be motivated or goal directed. Therefore, if we want to simulate human-style interactions with the world, we will need (...) to first understand the physical structure of goal-directed systems. I argue that all such systems share a common nested structure, consisting of a smaller entity that moves within and is driven by a larger field that contains it. In such systems, the smaller contained entity is directed by the field, but also moves to some degree independently of it, allowing the entity to deviate and return, to show the plasticity and persistence that is characteristic of goal direction. If all this is right, then human want-driven behavior probably involves a behavior-generating mechanism that is contained within a neural field of some kind. In principle, for goal directedness generally, the containment can be virtual, raising the possibility that want-driven behavior could be simulated in standard computational systems. But there are also reasons to believe that goal-direction works better when containment is also physical, suggesting that a new kind of hardware may be necessary. (shrink)

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