Showing papers on "Philosophy of biology published in 2015"

Temporalities of reproduction: practices and concepts from the eighteenth to the early twenty-first century

Abstract: Reproduction is of central interest to the history of the life sciences. Yet our knowledge of the epistemological, scientific and political changes in the history of reproduction over the last two hundered years remains fragmented and limited. Existing studies usually focus on specific epochs—such as the eighteenth century, when the concept of reproduction started to circulate in the context of the emerging sciences of ‘‘the living’’, or the reproductive sciences and medicine of the twentieth and early twentyfirst centuries. Attempts to investigate scientific concepts and practices of reproduction and their social, political and cultural contexts from an interdisciplinary and longue durée perspective are still rare. Our special issue contributes to filling this

Neither logical empiricism nor vitalism, but organicism: what the philosophy of biology was.

Abstract: 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.

Adaptationism and the Logic of Research Questions: How to Think Clearly About Evolutionary Causes

Abstract: This article discusses various dangers that accompany the supposedly benign methods in behavioral evolutionary biology and evolutionary psychology that fall under the framework of “methodological adaptationism.” A “Logic of Research Questions” is proposed that aids in clarifying the reasoning problems that arise due to the framework under critique. The live, and widely practiced, “evolutionary factors” framework is offered as the key comparison and alternative. The article goes beyond the traditional critique of Stephen Jay Gould and Richard C. Lewontin, to present problems such as the disappearance of evidence, the mishandling of the null hypothesis, and failures in scientific reasoning, exemplified by a case from human behavioral ecology. In conclusion the paper shows that “methodological adaptationism” does not deserve its benign reputation.

Philosophy of science viewed through the lense of Referenced Publication Years Spectroscopy (RPYS)

Abstract: We examine the sub-field of philosophy of science using a new method developed in information science, Referenced Publication Years Spectroscopy (RPYS). RPYS allows us to identify peak years in citations in a field, which promises to help scholars identify the key contributions to a field, and revolutionary discoveries in a field. We discovered that philosophy of science, a sub-field in the humanities, differs significantly from other fields examined with this method. Books play a more important role in philosophy of science than in the sciences. Further, Einstein's famous 1905 papers created a citation peak in the philosophy of science literature. But rather than being a contribution to the philosophy of science, their importance lies in the fact that they are revolutionary contributions to physics with important implications for philosophy of science.

Revisiting generality in biology: systems biology and the quest for design principles

Abstract: Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on (the lack of) generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes a different approach in emphasizing a theory-constituting role of general principles. Design principles signify general dependency-relations between structures and functions, given a set of formally defined constraints. I contend that design principles increase our understanding of living systems by relating specific models to general types. The categorization of types is based on a delineation of the scope of biological possibilities, which serves to identify and define the generic features of classes of systems. To characterize the basis for general principles through generic abstraction and reasoning about possibility spaces, I coin the term constraint-based generality. I show that constraint-based generality is distinct from other types of generality in biology, and argue that general principles play a unifying role that does not entail theory reduction.

Explanatory Integration Challenges in Evolutionary Systems Biology

Abstract: Evolutionary systems biology (ESB) aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations of specific traits. Next, these tensions are further clarified by considering a recent case from another field focused on developmental dynamics: stem cell biology. In the stem cell case, incompatible explanatory aims block integration. Experimental approaches aim at mechanistic explanation while dynamical system models offer explanation in terms of general principles. We then discuss an ESB case in which integration succeeds: search for general attractors using a dynamical systems framework synergizes with the experimental search for detailed mechanisms. Contrasts between the positive and negative cases suggest general lessons for achieving an integrated understanding of developmental and evolutionary dynamics. The key integrative move is to acknowledge two complementary aims, both relevant to explanation: identifying the space of possible dynamic states and trajectories, and mechanistic understanding of causal interactions underlying a specific phenomenon of interest. These two aims can support one another in a joint project characterizing dynamic aspects of evolving lineages. This more inclusive project can lead to insights that cannot be reached by either approach in isolation.

Biological pathology from an organizational perspective

Abstract: In contrast to the “normativist” view, “naturalist” theorists claim that the concept of health refers to natural or normal states and propose different characterizations of healthy and diseased conditions that are meant to be objectivist and biologically grounded. In this article, we examine the core concept of these naturalist accounts of disease, i.e., the concept of biological malfunction, and develop a new formulation of the notion of malfunction following the recent organizational approach to functions in the philosophy of biology. We focus on the notions of adaptive regulation and functional presupposition to develop a new conceptual framework that justifies the ascription of malfunctional behaviors to biological systems according to the embodied normativity of biological organizations.

The proximate–ultimate distinction and evolutionary developmental biology: causal irrelevance versus explanatory abstraction

Abstract: Mayr’s proximate–ultimate distinction has received renewed interest in recent years. Here we discuss its role in arguments about the relevance of developmental to evolutionary biology. We show that two recent critiques of the proximate–ultimate distinction fail to explain why developmental processes in particular should be of interest to evolutionary biologists. We trace these failures to a common problem: both critiques take the proximate–ultimate distinction to neglect specific causal interactions in nature. We argue that this is implausible, and that the distinction should instead be understood in the context of explanatory abstractions in complete causal models of evolutionary change. Once the debate is reframed in this way, the proximate–ultimate distinction’s role in arguments against the theoretical significance of evo-devo is seen to rely on a generally implicit premise: that the variation produced by development is abundant, small and undirected. We show that a “lean version” of the proximate–ultimate distinction can be maintained even when this isotropy assumption does not hold. Finally, we connect these considerations to biological practice. We show that the investigation of developmental constraints in evolutionary transitions has long relied on a methodology which foregrounds the explanatory role of developmental processes. It is, however, entirely compatible with the lean version of the proximate–ultimate distinction.

The Comet Cometh: Evolving Developmental Systems

Abstract: In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule’s prediction is based on a one-sided understanding of systems biology as a science that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach—which is based on reverse engineering, simulation, and mathematical analysis—the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis.

Using causal models to integrate proximate and ultimate causation

Abstract: Ernst Mayr’s classical work on the nature of causation in biology has had a huge influence on biologists as well as philosophers. Although his distinction between proximate and ultimate causation recently came under criticism from those who emphasize the role of development in evolutionary processes, the formal relationship between these two notions remains elusive. Using causal graph theory, this paper offers a unified framework to systematically translate a given “proximate” causal structure into an “ultimate” evolutionary response, and illustrates evolutionary implications of various kinds of causal mechanisms including epigenetic inheritance, maternal effects, and niche construction. These results not only reveal the essential interplay between proximate and ultimate causation in the study of evolution, but also provide a formal method to evaluate or discover non-standard or yet unknown evolutionary phenomena.

The End of Development

Abstract: Recently, there has been a growing interest, both within theoretical biology and the philosophy of biology, in the possibility and desirability of a theory of development. Among the many issues raised within this debate, the questions of the spatial and temporal boundaries of development have received particular attention. In this article, noting that so far the discussion has mostly centered on the processes of morphogenesis and organogenesis, we argue that an important missing element in the equation, namely the development of language and cognition in general, may play an important role in settling the issue of temporal boundaries. After examining the idea that the development of language, cognition, and action are bona fide biological processes, we explore the consequences for a general theory of development of taking them into consideration.

Towards Improving the Ethics of Ecological Research

Abstract: We argue that the ecological research community should develop a plan for improving the ethical consistency and moral robustness of the field. We propose a particular ethics strategy—specifically, an ongoing process of collective ethical reflection that the community of ecological researchers, with the cooperation of applied ethicists and philosophers of biology, can use to address the needs we identify. We suggest a particular set of conceptual (in the form of six core values—freedom, fairness, well being, replacement, reduction, and refinement) and analytic (in the forms of decision theoretic software, 1000Minds) tools that, we argue, collectively have the resources to provide an empirically grounded and conceptually complete foundation for an ethics strategy for ecological research. We illustrate our argument with information gathered from a survey of ecologists conducted at the 2013 meeting of the Canadian Society of Ecology and Evolution.

Causal Mechanisms: Lessons from the Life Sciences

Abstract: This paper reviews recent scholarship on causal mechanisms in both the social and biological sciences. It does so with a particular focus on North America and from the perspective of critical realism. It identifies four conceptions of causal mechanisms within the social sciences: mainstream, analytical, counterfactual and neo-pragmatist. It argues that none are fully realist or sufficiently critical because all are influenced by a physicalist ontology characterized by ‘smallism’ and actualism. It then turns to recent work in the philosophy of biology, focusing in particular on the Chicago School around William Wimsatt. I argue that biological explanation cannot be adequately accounted for in physicalist terms. I conclude with critical reflections on the continuing influence of physicalism, even within critical realism, and on the disanalogies between the biological and social sciences.

Experimental Philosophy of Aesthetics

Abstract: In the past decade, experimental philosophy – the attempt at making progress on philosophical problems using empirical methods – has thrived in a wide range of domains. However, only in recent years has aesthetics succeeded in drawing the attention of experimental philosophers. The present paper constitutes thefirstsurveyoftheseworksandofthenascentfieldof‘experimentalphilosophyofaesthetics’.Wepresent both recentexperimental works byphilosophers on topicssuch as the ontology of aesthetics, aesthetic epistemology, aesthetic concepts, and imagination, as well as research from other disciplines that not only are relevant to philosophy of aesthetics but also open new avenues of research for experimental philosophy of aesthetics. Overall, we conclude that the birth of an experimental philosophy of aesthetics is good news not only for aesthetics but also for experimental philosophy itself, as it contributes to broaden the scope of experimental philosophy.

From the Characterization of ‘European Philosophy of Science’ to the Case of Philosophy of the Social Sciences

Abstract: How distinct is European philosophy of science? The first step is to characterize what is or might be considered as ‘European philosophy of science’. The second is to analyse philosophy of the social sciences as a relevant case in the European contribution to philosophy of science. (1) ‘European perspective’ requires some clarification, which can be done from two main angles: the historical approach and the thematic view. Thus, there are several structural and dynamic things to be considered in European philosophy of science and compare with other conceptions: (i) the topics discussed; (ii) the contents proposed; and (iii) the style of thought used. (2) The case of philosophy of the social sciences is relevant for the historical approach and for the thematic view. Historically, the Erklaren–Verstehen methodological controversy arose in this continent, where the main authors and most of the influential approaches are located. Thematically, we can consider the contributions made by these European approaches...

Biology and Philosophy symposium on Simulation and Similarity: Using Models to Understand the World

Abstract: Contents Preface 1 Introduction 1.1 Two Aquatic Puzzles 1.2 Models of Modeling 2 Three Kinds of Models 2.1 Concrete Model: The San Francisco Bay-Delta Model 2.2 Mathematical Model: Lotka-Volterra Model 2.3 Computational Model: Schelling's Segregation Model 2.4 Common Features of these Models 2.5 Only Three Types of Models? 2.6 Fewer Than Three Types of Model? 3 The Anatomy of Models: Structure & Construal 3.1 Structure 3.1.1 Concrete Structures 3.1.2 Mathematical 3.1.3 Computational 3.2 Model Descriptions 3.3 Construal 3.4 Representational Capacity of Structures 4 Fictions and Folk Ontology 4.1 Against Maths: Individuation, Causes, and Face Value Practice 4.2 A Simple Fictions Account 4.3 Enriching the Simple Account 4.3.1 Waltonian Fictionalism 4.3.2 Fictions without Models 4.4 Why I am not a Fictionalist 4.4.1 Variation 4.4.2 Representational Capacity of Different Models 4.4.3 Making Sense of Modeling 4.4.4 Variation in Practice 4.5 Folk ontology 4.6 Maths, Interpretation, and Folk Ontology 5 Target Directed Modeling 5.1 Model Development 5.2 Analysis of the Model 5.2.1 Complete Analysis 5.2.2 Goal-directed Analysis 5.3 Model/Target Comparison 5.3.1 Phenomena and Target Systems 5.3.2 Establishing the fit between Model and Target 5.3.3 Representations of Targets 6 Idealization 6.1 Three Kinds of Idealization 6.1.1 Galilean idealization 6.1.2 Minimalist idealization 6.1.3 Multiple Models Idealization 6.2 Representational Ideals and Fidelity Criteria 6.2.1 Completeness 6.2.2 Simplicity 6.2.3 1-Causal 6.2.4 Maxout 6.2.5 P-General 6.3 Idealization and Representational Ideals 6.4 Idealization and Target Directed Modeling 7 Modeling Without a Specific Target 7.1 Generalized Modeling 7.1.1 How Possibly Explanations 7.1.2 Minimal Models and First Order Causal Structures 7.2 Hypothetical Modeling 7.2.1 Contingent Non-existence: xDNA 7.2.2 Impossible Targets: Infinite Population Growth and Perpetual Motion 7.3 Targetless Modeling 7.4 A Moving Target: The Case of Three-sex Biology 8 An Account of Similarity 8.1 Desiderata for Model/World Relations 8.2 Model Theoretic Accounts 8.3 Similarity 8.4 Tversky's Contrast Account 8.5 Attributes and Mechanisms 8.6 Feature Sets, Construals, and Target Systems 8.7 Modeling Goals and Weighting Parameters 8.8 Weighting Function and Background Theory 8.9 Satisfying the Desiderata 9 Robustness Analysis and Idealization 9.1 Levins and Wimsatt on Robustness 9.2 Finding Robust Theorems 9.3 Three Kinds of Robustness 9.3.1 Parameter Robustness 9.3.2 Structural Robustness 9.3.3 Representational Robustness 9.4 Robustness and Confirmation 10 Conclusion: The Practice of Modeling References

Engineering and Biology: Counsel for a Continued Relationship.

Abstract: Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology.

Explanation in Systems Biology: Is It All About Mechanisms?

Abstract: As the mechanistic understanding of how biological systems function continues to become more refined, the power of scientists to manipulate and control them for the sake of achieving concrete practical goals increases. Proponents of the recent movement for a new mechanistic philosophy of biology have taken up the task of defining the theoretical conditions that would promote such understanding. In this paper, the case of systems biology serves to highlight some of the limitations of the explanatory models that are grounded on their philosophical accounts of mechanism. In light of the prominent role played by mechanisms in top-down and bottom-up systems biology, I argue that a purely mechanism-based framework that complies with the constraints stipulated by the new mechanists is adequate for producing useful explanations of biological phenomena in the context of the systems approach. Nevertheless, this framework remains limited in its capacity to carry out the comprehensive explanatory integration demanded for the holistic understanding of complex biological systems whose attainment constitutes systems biology’s most ambitious objective. In addition, in their current formulation the models endorsed by the new mechanists are not sufficient for capturing the rich explanatory pluralism that characterizes the practice of systems biology. The fact that a pragmatic view of the practice of systems biology reveals its pluralistic character suggests that moving beyond theoretical considerations provides useful insights into the nature of explanation. I propose, however, that philosophers do not need to make a choice between adopting either a theoretical or a pragmatic attitude: both perspectives contribute in a mutually complementary way to constructive thinking about explanation in biology.

What’s so great about Feyerabend? Against Method, forty years on: Paul Feyerabend: Against Method, 4th edition. London: Verso, 2010, 336 pp, $24.95

Abstract: It is forty years since Paul Feyerabend published Against Method, the book that marked both the high point of his career as a philosopher of science, and, perhaps also, the beginning of its end (Feyerabend 1975a). The book was, as its author liked to put it, both a ‘collage’ of earlier works, including a long 1970 essay of the same name, and also a ‘personal letter’ to Feyerabend’s friend and sparring partner, Imre Lakatos (Feyerabend 1970). Indeed, the published book was originally intended to be a collaboration between Feyerabend and Lakatos, to be titled For and Against Method—a title now borne by a volume published in 2000 that collects together Lakatos’s lectures on scientific method, his correspondence with Feyerabend concerning their never-to-be-completed work-in-progress, and several other contemporaneous pieces on science, philosophy, and education (Lakatos and Feyerabend 1999). In 2010, a fourth edition was published, with an introduction by Ian Hacking, a testament to the enduring interest in Against Method by a diverse audience that has always included, but never been limited to, philosophers of science (Feyerabend 2010). For many philosophers of science, Feyerabend is typically associated with Against Method, but the book actually marked the halfway point of his career. Another 20 years of writing and work followed, much of it still largely ignored by philosophers of science, partly because it deals with themes that were and still are not in the mainstream of analytic philosophy of science—such as the complicity of science in cultural and environmental destruction—and partly because Feyerabend made little effort to engage with philosophers of science after the mid-1970s. But he did continue to write, and the last 20 or so years has seen a steady stream of new ‘Feyerabendiana’, including two books, Conquest of Abundance (1999a) and Naturphilosophie (2009), the third volume of his collected writings (1999b)—with a