This paper tells the story of G-protein coupled receptors, one of the most important scientific objects in contemporary biochemistry and molecular biology. By looking at how cell membrane receptors turned from a speculative concept into a central element in modern biochemistry over the past 40 years, we revisit the role of manipulability as a criterion for entity realism in wet-lab research. The central argument is that manipulability as a condition for reality becomes meaningful only once scientists have decided how to (...) conceptually coordinate measurable effects distinctly to a specific object. We show that a scientific entity, such as GPCRs, is assigned varying degrees of reality throughout different stages of its discovery. The criteria of its reality, we further claim, cannot be made independently of the question about how this object becomes a standard by which the reality of neighbouring elements of enquiry is evaluated. (shrink)

Empirical success is a central criterion for scientific decision-making. Yet its understanding in philosophical studies of science deserves renewed attention: Should philosophers think differently about the advancement of science when they deal with the uncertainty of outcome in ongoing research in comparison with historical episodes? This paper argues that normative appeals to empirical success in the evaluation of competing scientific explanations can result in unreliable conclusions, especially when we are looking at the changeability of direction in ongoing investigations. The challenges (...) we encounter arise from the inherent dynamics of disciplinary and experimental objectives in research practice. In this paper we discuss how these dynamics inform the evaluation of empirical success by analyzing three of its requirements: data accommodation, instrumental reliability, and predictive power. We conclude that the assessment of empirical success in developing inquiry is set against the background of a model’s interactive success and prospective value in an experimental context. Our argument is exemplified by the analysis of an apparent controversy surrounding the model of a quantum nose in research on olfaction. Notably the public narrative of this controversy rests on a distorted perspective on measures of empirical success. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

An important epistemic issue in climate modelling concerns structural uncertainty: uncertainty about whether the mathematical structure of a model accurately represents its target. How does structural uncertainty affect our knowledge and predictions about the climate? How can we identify sources of structural uncertainty? Can we manage the effect of structural uncertainty on our knowledge claims? These are some of the questions that an epistemology of structural uncertainty faces, and these questions are also important for climate scientists and policymakers. I develop (...) three desiderata for an epistemological account of structural uncertainty. In my view, an account of structural uncertainty should identify sources of structural uncertainty, explain how these sources limit the applicability of a model, and show how the severity of structural uncertainty depends on the questions that can be asked of a model. I argue that analyzing structural uncertainty by paying attention to the details of model building can satisfy these desiderata. I focus on parametrizations, which are representations of important processes occurring at scales that are not resolved by climate models. Parametrizations are often thought to be ad-hoc, but I show that some important parametrizations are theoretically justified by explicit or implicit scale separation assumptions. These assumptions can also be supported empirically. Analyzing these theoretical and empirical justificatory roles of the scale separation assumptions can provide insights into how parametrizations contribute to structural uncertainty. I conclude by sketching how my approach can satisfy the desiderata I set out at the beginning, highlighting its importance for policy-relevant scientific statements about the climate. (shrink)

This essay argues against Richard Joyce, using him as an exemplar of a number of writers who purport to show that the best a naturalized ethics can provide are demands that we can hold only as moral agnostics; that is, that no moral claims can be shown to be epistemically warranted, hence no moral claims have the property of “inescapable authority” necessary for real moral discourse or deliberation. The prudent course of action is therefore to act as if moral claims (...) had categorical standing, knowing full well that we cannot, in principle, know this. The essay proposes instead that a fully naturalized account of moral reasoning and sentiments, compatible with the commitment to understanding human beings as products of evolutionary processes, can provide “existence imperatives” necessarily implicated in our being social animals. It argues that, on the one hand, we're mistaken in believing that real moral discourse must include imperatives that hold with inescapable authority as a foundation and, on the other, that a naturalistic perspective can offer demands that are authoritative enough to make moral judgment sound. (shrink)

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

Of all the demands that mathematics imposes on its practitioners, one of the most fundamental is that proofs ought to be correct. It has been common since the turn of the twentieth century to take correctness to be underwritten by the existence of formal derivations in a suitable axiomatic foundation, but then it is hard to see how this normative standard can be met, given the differences between informal proofs and formal derivations, and given the inherent fragility and complexity of (...) the latter. This essay describes some of the ways that mathematical practice makes it possible to reliably and robustly meet the formal standard, preserving the standard normative account while doing justice to epistemically important features of informal mathematical justification. (shrink)

The Galilean explanatory style is characterized by the search for the underlying structure of phenomena, the positing of "deep" explanatory principles, and a view of the relation between theory and data, on which the search for "crucial data" is of primary importance. In this paper, I trace the dynamics of adopting the Galilean style, focusing on the science of episodic memory. I argue that memory systems, such as episodic and semantic memory, were posited as underlying competences producing the observable phenomena (...) of memory. Considered in idealized isolation from other systems, episodic memory was taken to underlay the ability of individuals to remember events from their personal past. Yet, in reality, memory systems regularly interact, standing in many-to-many relations to actual memory tasks and experiences. Upon this backdrop, I explore a puzzle about the increasing prominence of the notion of autonoetic consciousness in Tulving's theory of episodic memory. I argue that, contrary to widespread belief, the prominence is not best explained by the purported essential link between autonoetic consciousness and episodic memory. Rather, it is explained by the fact that autonoetic consciousness, hypothesized to uniquely accompany episodic retrieval, was considered a source of crucial data, predictable only from theories positing a functionally distinct episodic memory system. However, with the emergence of a new generation of theories, positing wider memory systems for remembering and imagination, the question of the relation between episodic memory and autonoetic consciousness has been reopened. This creates a pressing need for de-idealization, triggering a new search for crucial data. (shrink)

One way that scientifically recognized properties are multiply realized is by “compensatory differences” among realizing properties. If a property G is jointly realized by two properties F1 and F2, then G can be multiply realized by having changes in the property F1 offset changes in the property F2. In some cases, there are scientific laws that articulate how distinct combinations of physical quantities can determine one and the same value of some other physical quantity. One moral to draw is that (...) in such cases we have the multiple realization of a single determinate, “fine grained” property instance that is exactly similar to another instance. As simple as this moral is, it has ramifications for a number of recent discussions of multiple realization in science. Taken collectively, these ramifications indicate that multiple realization by compensatory adjustments merits greater attention in the philosophy of science literature than it has hitherto received. (shrink)

Organisms' environments are thought to play a fundamental role in determining their fitness and hence in natural selection. Existing intuitive conceptions of environment are sufficient for biological practice. I argue, however, that attempts to produce a general characterization of fitness and natural selection are incomplete without the help of general conceptions of what conditions are included in the environment. Thus there is a "problem of the reference environment"—more particularly, problems of specifying principles which pick out those environmental conditions which determine (...) fitness. I distinguish various reference environment problems and propose solutions to some of them. While there has been a limited amount of work on problems concerning what I call "subenvironments", there appears to be no earlier work on problems of what I call the "whole environment". The first solution I propose for a whole environment problem specifies the overall environment for natural selection on a set of biological types present in a population over a specified period of time. The second specifies an environment relevant to extinction of types in a population; this kind of environment is especially relevant to certain kinds of long-term evolution. (shrink)

I describe a realist, ontologically objective interpretation of probability, "far-flung frequency (FFF) mechanistic probability". FFF mechanistic probability is defined in terms of facts about the causal structure of devices and certain sets of frequencies in the actual world. Though defined partly in terms of frequencies, FFF mechanistic probability avoids many drawbacks of well-known frequency theories and helps causally explain stable frequencies, which will usually be close to the values of mechanistic probabilities. I also argue that it's a virtue rather than (...) a failing of FFF mechanistic probability that it does not define single-case chances, and compare some aspects of my interpretation to a recent interpretation proposed by Strevens. (shrink)

It’s recently been argued that biological fitness can’t change over the course of an organism’s life as a result of organisms’ behaviors. However, some characterizations of biological function and biological altruism tacitly or explicitly assume that an effect of a trait can change an organism’s fitness. In the first part of the paper, I explain that the core idea of changing fitness can be understood in terms of conditional probabilities defined over sequences of events in an organism’s life. The result (...) is a notion of “conditional fitness” which is static but which captures intuitions about apparent behavioral effects on fitness. The second part of the paper investigates the possibility of providing a systematic foundation for conditional fitness in terms of spaces of sequences of states of an organism and its environment. I argue that the resulting “organism–environment history conception” helps unify diverse biological perspectives, and may provide part of a metaphysics of natural selection. (shrink)

I investigate the structure of an argument that culture cannot be maintained in a population if each individual learns only from a single person. This appears to conflict with many models of cultural transmission and real-world cases. I resolve the first problem by showing that one of the models central to the argument is conceptually analogous and mathematically equivalent to one used to investigate the evolution of sexual reproduction. I resolve the second by arguing that probabilistic models of epistemological coherence (...) can be reinterpreted as models of support between cultural variants—illustrating the idea with a new model. (shrink)

I argue that a common philosophical approach to the interpretation of physical theories—particularly quantum field theories—has led philosophers astray. It has driven many to declare the quantum field theories employed by practicing physicists, so-called ‘effective field theories’, to be unfit for philosophical interpretation. In particular, such theories have been deemed unable to support a realist interpretation. I argue that these claims are mistaken: attending to the manner in which these theories are employed in physical practice, I show that interpreting effective (...) field theories yields a robust foundation for a more refined approach to scientific realism in the context of quantum field theory. The paper concludes by briefly sketching some general morals for interpretive practice in the philosophy of physics. (shrink)

I argue that normative formal epistemology (NFE) is best understood as modelling, in the sense that this is the reconstruction of its methodology on which NFE is doing best. I focus on Bayesianism and show that it has the characteristics of modelling. But modelling is a scientific enterprise, while NFE is normative. I thus develop an account of normative models on which they are idealised representations put to normative purposes. Normative assumptions, such as the transitivity of comparative credence, are characterised (...) as modelling idealisations motivated normatively. I then survey the landscape of methodological options: what might formal epistemologists be up to? I argue the choice is essentially binary: modelling or theorising. If NFE is theorising it is doing very poorly: generating false claims with no clear methodology for separating out what is to be taken seriously. Modelling, by contrast, is a successful methodology precisely suited to the management of useful falsehoods. Regarding NFE as modelling is not costless, however. First, our normative inferences are less direct and are muddied by the presence of descriptive idealisations. Second, our models are purpose-specific and limited in their scope. I close with suggestions for how to adapt our practice. (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)

Policymakers who seek to make scientifically informed decisions are constantly confronted by scientific uncertainty and expert disagreement. This thesis asks: how can policymakers rationally respond to expert disagreement and scientific uncertainty? This is a work of non-ideal theory, which applies formal philosophical tools developed by ideal theorists to more realistic cases of policymaking under scientific uncertainty. I start with Bayesian approaches to expert testimony and the problem of expert disagreement, arguing that two popular approaches— supra-Bayesianism and the standard model of (...) expert deference—are insufficient. I develop a novel model of expert deference and show how it can deal with many of these problems raised for them. I then turn to opinion pooling, a popular method for dealing with disagreement. I show that various theoretical motivations for pooling functions are irrelevant to realistic policymaking cases. This leads to a cautious recommendation of linear pooling. However, I then show that any pooling method relies on value judgements, that are hidden in the selection of the scoring rule. My focus then narrows to a more specific case of scientific uncertainty: multiple models of the same system. I introduce a particular case study involving hurricane models developed to support insurance decision-making. I recapitulate my analysis of opinion pooling in the context of model ensembles, confirming that my hesitations apply. This motivates a shift of perspective, to viewing the problem as a decision theoretic one. I rework a recently developed ambiguity theory, called the confidence approach, to take input from model ensembles. I show how it facilitates the resolution of the policymaker’s problem in a way that avoids the issues encountered in previous chapters. This concludes my main study of the problem of expert disagreement. In the final chapter, I turn to methodological reflection. I argue that philosophers who employ the mathematical methods of the prior chapters are modelling. Employing results from the philosophy of scientific models, I develop the theory of normative modelling. I argue that it has important methodological conclusions for the practice of formal epistemology, ruling out popular moves such as searching for counterexamples. (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 crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

Upshot: In our response we focus on five questions that point to important common themes in the commentaries: why start in wicked problems, what kind of system is a scientific perspective, what is the nature of second-order research processes, what does this mean for understanding interdisciplinary work, and how may polyocular research help make real-world decisions.

Animal welfare has a long history of disregard. While in recent decades the study of animal welfare has become a scientific discipline of its own, the difficulty of measuring animal welfare can still be vastly underestimated. There are three primary theories, or perspectives, on animal welfare - biological functioning, natural living and affective state. These come with their own diverse methods of measurement, each providing a limited perspective on an aspect of welfare. This paper describes a perspectival pluralist account of (...) animal welfare, in which all three theoretical perspectives and their multiple measures are necessary to understand this complex phenomenon and provide a full picture of animal welfare. This in turn will offer us a better understanding of perspectivism and pluralism itself. (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)

Scientific realists argue that a good track record of multi-agent, and multiple method, validation of empirical claims is itself evidence that those claims, at least partially and approximately, reflect ways nature actually is independent of the ways we conceptualize it. Constructivists contend that successes in validating empirical claims only suffice to establish that our ways of modelling the world, our “constructions,” are useful and adequate for beings like us. This essay presents a thought experiment in which beings like us intersubjectively (...) validate claims about properties of particular things in nature under conditions in which those beings have profoundly different personal phenomenological experiences of those properties. I submit that the thought experiment scenario parallels our actual situation, and argue that this shows that successes in intersubjectively validating empirical claims are indeed enough to claim victory for the realist. More specifically, I champion a variation of realism that marries Ronald Giere’s brand of ‘perspectival realism’ with Philip Kitcher’s ‘real realism,’ and posits that causal relations between ourselves and properties instantiated in nature ground our references to the relevant properties even though our conceptions of them are perspective relative. (shrink)

Despite the burgeoning interest in new and more complex accounts of the organism-environment dyad by biologists and philosophers, little attention has been paid in the resulting discussions to the history of these ideas and to their deployment in disciplines outside biology—especially in the social sciences. Even in biology and philosophy, there is a lack of detailed conceptual models of the organism-environment relationship. This volume is designed to fill these lacunae by providing the first multidisciplinary discussion of the topic of organism-environment (...) interaction. It brings together scholars from history, philosophy, psychology, anthropology, medicine, and biology to discuss the common focus of their work: entangled life, or the complex interaction of organisms and environments. (shrink)

This paper offers a critique of an account of explanatory integration that claims that explanations of cognitive capacities by functional analyses and mechanistic explanations can be seamlessly integrated. It is shown that achieving such explanatory integration requires that the terms designating cognitive capacities in the two forms of explanation are stable but that experimental practice in the mind-brain sciences currently is not directed at achieving such stability. A positive proposal for changing experimental practice so as to promote such stability is (...) put forward and its implications for explanatory integration are briefly considered. (shrink)

In this chapter I investigate the kinds of changes that psychiatric kinds undergo when they become explanatory targets of areas of sciences that are not “mature” and are in the early stages of discovering mechanisms. The two areas of science that are the targets of my analysis are cognitive neuroscience and cognitive neurobiology.

Despite their success in describing and predicting cognitive behavior, the plausibility of so-called ‘rational explanations’ is often contested on the grounds of computational intractability. Several cognitive scientists have argued that such intractability is an orthogonal pseudoproblem, however, since rational explanations account for the ‘why’ of cognition but are agnostic about the ‘how’. Their central premise is that humans do not actually perform the rational calculations posited by their models, but only act as if they do. Whether or not the problem (...) of intractability is solved by recourse to ‘as if’ explanations critically depends, inter alia, on the semantics of the ‘as if’ connective. We examine the five most sensible explications in the literature, and conclude that none of them circumvents the problem. As a result, rational ‘as if’ explanations must obey the minimal computational constraint of tractability. (shrink)

This essay offers a motivational conception of solidarity that can be employed across the entire range of sciences and humanities, while also filling a gap in the motivational spectrum conceived by decision theorists and economists—and expanding the two-part division between altruistic and selfish motivations into a tripartite analysis that suggests a spectrum instead. According to the present proposal, solidarity is a condition of action-readiness on behalf of a group or its interests. The proposal will admit of measuring the extent to (...) which Prisoner’s Dilemmas are overcome in real life via acts of solidarity. (shrink)

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

This paper addresses whether the often-bemoaned loss of unity of knowledge about humans, which results from the disciplinary fragmentation of science, is something to be overcome. The fragmentation of being human rests on a couple of distinctions, such as the nature-culture divide. Since antiquity the distinction between nature (roughly, what we inherit biologically) and culture (roughly, what is acquired by social interaction) has been a commonplace in science and society. Recently, the nature/culture divide has come under attack in various ways, (...) in philosophy as well as in cultural anthropology. Regarding the latter, for instance, the divide was quintessential in its beginnings as an academic dis-cipline, when Alfred L. Kroeber, one of the first professional anthropologists in the US, rallied for (what I call) the right to ignore—in his case, human nature—by adopting a separationist epistemic stance. A separationist stance will be understood as an epistemic research heuristic that defends the right to ignore a specif-ic phenomenon (e.g., human nature) or a specific causal factor in an explanation typical for a disciplinary field. I will use Kroeber’s case as an example for making a general point against a bias towards integration (synthesis bias, as I call it) that is exemplified, for instance, by defenders of evolutionary psychology. I will claim that, in principle, a separationist stance is as good as an integrationist stance since both can be equally fruitful. With this argument from fruitful sepa-ration in place, not just the separationist stance but also the nature/culture di-vide can be defended against its critics. (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical taxonomists sought (...) to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

A classic analytic approach to biological phenomena seeks to refine definitions until classes are sufficiently homogenous to support prediction and explanation, but this approach founders on cases where a single process produces objects with similar forms but heterogeneous behaviors. I introduce object spaces as a tool to tackle this challenging diversity of biological objects in terms of causal processes with well-defined formal properties. Object spaces have three primary components: (1) a combinatorial biological process such as protein synthesis that generates objects (...) with parts that are modular, independent, and organized according to an invariant syntax; (2) a notion of “distance” that relates the objects according to rules of change over time as found in nature or useful for algorithms; (3) mapping functions defined on the space that map its objects to other spaces or apply an evaluative criterion to measure an important quality, such as parsimony or biochemical function. Once defined, an object space can be used to represent and simulate the dynamics of phenomena on multiple scales; it can also be used as a tool for predicting higher-order properties of the objects, including stitching together series of causal processes. Object spaces are the basis for a strategy of theorizing, discovery, and analysis in biology: as heuristic idealizations of biology, they help us transform inchoate, intractable problems into articulated, well-structured ones. Developing an object space is a research strategy with a long, successful history under many other names, and it offers a unifying but not overreaching approach to biological theory. (shrink)

Three accounts of effective realism (ER) have been advanced to solve three problems for scientific realism: Fraser and Vickers (forthcoming) develop a version of ER about non-relativistic quantum mechanics that they argue is compatible with all the main realist versions (‘interpretations’) of quantum mechanics avoiding the problem of underdetermination among them; Williams (2019) and Fraser (2020b) propose ER about quantum field theory as a response to the problems facing realist interpretations; Robertson and Wilson (forthcoming) propose ER to deal with the (...) dubious ontological status of the entities belonging to superseded theories. This paper argues for the unification of these proposals based on realism about modal structure and the idea of scale relativity of ontology developed by ontic structural realists. This solves problems some or all the accounts of ER face, especially that of making explicit in what way they are realist. Furthermore, we respond to a recent critique that has been raised against the ontic structural realist account of quantum mechanics that we employ. (shrink)

This chapter examines the influence of the empirical sciences (e.g., physics, biology, psychology) in contemporary analytic philosophy, with focus on philosophical theories that are guided by findings from the empirical sciences. Scientific approaches to philosophy follow a tradition of philosophical naturalism associated with Quine, which strives to ally philosophical methods and theories more closely with the empirical sciences and away from a priori theorizing and conceptual analysis.

Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what (...) the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems. (shrink)

Scientific models share one central characteristic with fiction: their relation to the physical world is ambiguous. It is often unclear whether an element in a model represents something in the world or presents an artifact of model building. Fiction, too, can resemble our world to varying degrees. However, we assign a different epistemic function to scientific representations. As artifacts of human activity, how are scientific representations allowing us to make inferences about real phenomena? In reply to this concern, philosophers of (...) science have started analyzing scientific representations in terms of fictionalization strategies. Many arguments center on a dyadic relation between the model and its target system, focusing on structural resemblances and “as if” scenarios. This chapter provides a different approach. It looks more closely at model building to analyze the interpretative strategies dealing with the representational limits of models. How do we interpret ambiguous elements in models? Moreover, how do we determine the validity of model-based inferences to information that is not an explicit part of a representational structure? I argue that the problem of ambiguous inference emerges from two features of representations, namely their hybridity and incompleteness. To distinguish between fictional and non-fictional elements in scientific models my suggestion is to look at the integrative strategies that link a particular model to other methods in an ongoing research context. To exemplify this idea, I examine protein modeling through X-ray crystallography as a pivotal method in biochemistry. (shrink)

This is a contribution to the encyclopedia of systems biology on complexity.

There is an active research program currently underway, which treats cancer progression as an evolutionary process. This contribution investigates the ways that cancer progression is like and unlike evolution in other contexts. The aim is to take a multi-level perspective on cancer, investigating the levels at which selection may be acting, the unit or target of selection, the relative roles of selection and drift, and the idea that cancer progression may be a by-product of selection at other levels of organization.

Does epistemology collapse for lack of resources other than logic, conceptual analysis and descriptions of one’s own apparent experiences, thoughts and beliefs? No, but understanding how and why not requires, Kant noted, a ‘changed method of thinking’. Some of these methodological changes are summarised in §2 in order to identify a philosophical role for thought experiments to help identify logically contingent, though cognitively fundamental capacities and circumstances necessary to human thought, experience and knowledge. As Kant also noted, experiments are only (...) informative in response to posing the right question, indeed: the right kind of question. Accordingly, preparations for these epistemological thought experiments fill half of this chapter. The second half, examines three such thought experiments, variously developed by Kant, Hegel, C. I. Lewis, Austin, Wittgenstein and F. L. Will. (shrink)

Unified, all-purpose, philosophical models of reduction in science lack resources for capturing varieties of cross-scientific relations that have proven critical to understanding some scientific achievements. Not only do those models obscure the distinction between successional and cross-scientific relations, their preoccupations with the structures of both theories and things provide no means for accommodating the contributions to various sciences of theories and research about long-term diachronic processes involving large-scale, distributed systems. Darwin's theory of evolution by natural selection is the parade case. (...) Explanatory pluralism accommodates a wider range of connections between theories and inquiries in science than all-purpose models of reduction do. Consequently, it provides analytical tools for understanding the roles of the theoretical proposals about the evolution of the human mind/brain that have proliferated over the last two decades. Those proposals have testable implications pertaining to both structure and processing in the modern human mind/brain. An example of such research illustrates how those proposals and investigative tools and experiments cut across both explanatory levels and modes of analysis within the cognitive sciences and how those studies can yield evidence that bears on the assessment of competing theories and models. (shrink)

The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...) molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

This book analyses the impact computerization has had on contemporary science and explains the origins, technical nature and epistemological consequences of the current decisive interplay between technology and science: an intertwining of formalism, computation, data acquisition, data and visualization and how these factors have led to the spread of simulation models since the 1950s. -/- Using historical, comparative and interpretative case studies from a range of disciplines, with a particular emphasis on the case of plant studies, the author shows how (...) and why computers, data treatment devices and programming languages have occasioned a gradual but irresistible and massive shift from mathematical models to computer simulations. -/- . (shrink)

Philosophical analyses of scientific methodology have long understood intuition to be incompatible with a rule based reasoning that is often considered necessary for a rational scientific method. This paper seeks to challenge this contention by highlighting the indispensable role that intuition plays in the application of methodologies for scientific discovery. In particular, it seeks to outline a positive role for intuition and personal judgment in scientific discovery by exploring a comparison between the use of heuristic reasoning in scientific practice and (...) engineering design. While these discussions share many features, it will also be shown that the successful use of heuristics in engineering design is often considered to depend on a crucial factor that is markedly absent from accounts of the use of heuristics in scientific discovery; experienced judgment. In the final sections of this paper, I will compare attitudes to the role of computer analysis in scientific and engineering practices, with the aim of showing how the limitations of scientific discovery machines reveal the need for including intuition in philosophical accounts of heuristic reasoning in scientific discovery. (shrink)

This comment discusses Kaidesoja and raises the issue whether his analysis justifies stronger conclusions than he presents in the book. My comments focus on four issues. First, I argue that his naturalistic reconstruction of critical realist transcendental arguments shows that transcendental arguments should be treated as a rare curiosity rather than a general argumentative strategy. Second, I suggest that Kaidesoja’s analysis does not really justify his optimism about the usefulness of causal powers ontology in the social sciences. Third, I raise (...) some doubts about the heuristic value of Mario Bunge’s social ontology that Kaidesoja presents as a replacement for critical realist ontology. Finally, I propose an alternative way to analyze failures of aggregativity that might better serve Kaidesoja’s purposes than the Wimsattian scheme he employs in the book. (shrink)

Reliability and external validity are two fundamental values that pose incompatible constraints on neurobiological experiments. The more reliability an experimental result achieves, the less external validity it earns, and vice versa. In this article, I propose an externalist interpretation of external validity: the external validity of an experimental result depends not only on how much complexity is built into an experimental design, but also on the relationship between the experimental result and other related experiments. This externalist interpretation, which explains how (...) a neurobiological experiment can be reliable and externally valid simultaneously, suggests a new way to understand the epistemology of neurobiological experimentation. (shrink)

The practice of model-building is very common in analytic philosophical theology. Yet many other theologians worry that any attempt to model God must be hubristic and idolatrous. A better understanding of scientific modeling can set the stage for a more fruitful engagement between analytic theologians and their critics. I first present an account of scientific modeling that draws on recent work in the philosophy of science. I then apply that account to a prominent analytic model of the trinity, Michael Rea (...) and Jeffrey Brower’s “material constitution model.” I argue that modeling – whether scientific or theological – need not be understood as a hubristic enterprise. A model does not always try to grasp its target at all, let alone grasp it fully and completely. Even theologians who are committed to a strong doctrine of divine mystery can therefore find value in analytic modeling. (shrink)