Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion (...) of “effective” population size, the work of Thomas Park on /Tribolium/ populations, and model-based clustering algorithms such as /Structure/. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality. (shrink)

This inaugural handbook documents the distinctive research field that utilizes history and philosophy in investigation of theoretical, curricular and pedagogical issues in the teaching of science and mathematics. It is contributed to by 130 researchers from 30 countries; it provides a logically structured, fully referenced guide to the ways in which science and mathematics education is, informed by the history and philosophy of these disciplines, as well as by the philosophy of education more generally. The first handbook to cover the (...) field, it lays down a much-needed marker of progress to date and provides a platform for informed and coherent future analysis and research of the subject. -/- The publication comes at a time of heightened worldwide concern over the standard of science and mathematics education, attended by fierce debate over how best to reform curricula and enliven student engagement in the subjects There is a growing recognition among educators and policy makers that the learning of science must dovetail with learning about science; this handbook is uniquely positioned as a locus for the discussion. -/- The handbook features sections on pedagogical, theoretical, national, and biographical research, setting the literature of each tradition in its historical context. Each chapter engages in an assessment of the strengths and weakness of the research addressed, and suggests potentially fruitful avenues of future research. A key element of the handbook’s broader analytical framework is its identification and examination of unnoticed philosophical assumptions in science and mathematics research. It reminds readers at a crucial juncture that there has been a long and rich tradition of historical and philosophical engagements with science and mathematics teaching, and that lessons can be learnt from these engagements for the resolution of current theoretical, curricular and pedagogical questions that face teachers and administrators. (shrink)

In recent years, the philosophical focus of the modeling literature has shifted from descriptions of general properties of models to an interest in different model functions. It has been argued that the diversity of models and their correspondingly different epistemic goals are important for developing intelligible scientific theories. However, more knowledge is needed on how a combination of different epistemic means can generate and stabilize new entities in science. This paper will draw on Rheinberger’s practice-oriented account of knowledge production. The (...) conceptual repertoire of Rheinberger’s historical epistemology offers important insights for an analysis of the modelling practice. I illustrate this with a case study on network modeling in systems biology where engineering approaches are applied to the study of biological systems. I shall argue that the use of multiple means of representations is an essential part of the dynamic of knowledge generation. It is because of – rather than in spite of – the diversity of constraints of different models that the interlocking use of different epistemic means creates a potential for knowledge production. (shrink)

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

In this paper, I shall provide a novel response to the argument from context-sensitivity against truth-conditional semantics. It is often argued that the contextual influences on truth-conditions outstrip the resources of standard truth-conditional accounts, and so truth-conditional semantics rests on a mistake. The argument assumes that truth-conditional semantics is legitimate if and only if natural language sentences have truth-conditions. I shall argue that this assumption is mistaken. Truth-conditional analyses should be viewed as idealised approximations of the complexities of natural language (...) meaning. From this perspective, disparity between the scientific model and its real-world target is to be expected. I elaborate on what such an approach to semantics would look like. (shrink)

Levins and Lewontin have contributed significantly to our philosophical understanding of the structures, processes, and purposes of biological mathematical theorizing and modeling. Here I explore their separate and joint pleas to avoid making abstract and ideal scientific models ontologically independent by confusing or conflating our scientific models and the world. I differentiate two views of theorizing and modeling, orthodox and dialectical, in order to examine Levins and Lewontin’s, among others, advocacy of the latter view. I compare the positions of these (...) two views with respect to four points regarding ontological assumptions: (1) the origin of ontological assumptions, (2) the relation of such assumptions to the formal models of the same theory, (3) their use in integrating and negotiating different formal models of distinct theories, and (4) their employment in explanatory activity. Dialectical is here used in both its Hegelian–Marxist sense of opposition and tension between alternative positions and in its Platonic sense of dialogue between advocates of distinct theories. I investigate three case studies, from Levins and Lewontin as well as from a recent paper of mine, that show the relevance and power of the dialectical understanding of theorizing and modeling. (shrink)

The aim of this paper is to develop ideas about robustness analyses. I introduce a form of robustness analysis that I call sufficient parameter robustness, which has been neglected in the literature. I claim that sufficient parameter robustness is different from derivational robustness, the focus of previous research. My purpose is not only to suggest a new taxonomy of robustness, but also to argue that previous authors have concentrated on a narrow sense of robustness analysis, which they have inadequately distinguished (...) from other investigations of models such as sensitivity analysis. (shrink)

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

ion is one of the important processes in scientific modeling. It has always been implied that abstraction is an agent-centric activity that involves the cognitive processes of scientists in model building. I contend that there is an autonomous aspect of abstraction in many modeling activities. I argue that the autonomous process of abstraction is continuous with the agent-centric abstraction but capable of evolving independently from the modeler’s abstraction activity.

Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli, and the origin of eukaryotic cells through endosymbiosis.

Frigg and Reiss (2009) argue that philosophical problems in simulation bear enough resemblance to recognized issues in the philosophy of modeling that they only pose challenges analogous to those found in standard analytic models used to represent natural systems. They suggest that there are no new philosophical problems in computer simulation modeling beyond those found in traditional mathematical modeling. Winsberg (2009) has countered that there appear to be genuinely new epistemological problems in simulation modeling because the knowledge obtained from them (...) is ‘downward, motley, and autonomous.’ Here I draw out some specific ways that these epistemological problems are manifest in complex ecological simulation, especially in agent-based models. These models contain novel features that were impossible to anticipate prior to the computer revolution, and continue to present difficulties and challenges of both a practical and philosophical nature (Humphreys 2002). (shrink)

Computer simulation has become important in ecological modeling, but there have been few assessments on how complex simulation models differ from more traditional analytic models. In Part I of this paper, I review the challenges faced in complex ecological modeling and how models have been used to gain theoretical purchase for understanding natural systems. I compare the use of traditional analytic simulation models and point how that the two methods require different kinds of practical engagement. I examine a case study (...) of three models from the insect resistance literature in transgenic crops to illustrate and explore differences in analytic and computer simulation models. I argue that analyzing simulation models has been often inappropriately managed with expectations derived from handling analytic models. In Part II, I look at simulation as a hermeneutic practice. I argue that simulation models are a practice or techné. I the explore five aspects of philosophical hermeneutics that may be useful in complex ecological simulation: (1) an openness to multiple perspectives allowing multiple levels of scientific pluralism, (2) the hermeneutic circle, a back and forth in active communication among both modelers and ecologists; (3) the recognition of human factors and the nature of human practices as such, including recognizing the role of judgments and choices in the modeling enterprise; (4) the importance of play in modeling; (5) the non-closed nature of hermeneutic engagement, continued dialogue, and recognizing the situatedness, incompleteness, and tentative nature of simulation models. (shrink)

In addition to their core explanatory and predictive assumptions, scientific models include simplifying assumptions, which function as idealizations, approximations, and abstractions. There are methods to investigate whether simplifying assumptions bias the results of models, such as robustness analyses. However, the equally important issue – the focus of this paper – has received less attention, namely, what are the methodological and epistemic strengths and limitations associated with different simplifying assumptions. I concentrate on one type of simplifying assumption, the use of mega (...) parameters as abstractions in ecological models. First, I argue that there are two kinds of mega parameters qua abstractions, sufficient parameters and aggregative parameters, which have gone unnoticed in the literature. The two are associated with different heuristics, holism and reductionism, which many view as incompatible. Second, I will provide a different analysis of abstractions and the associated heuristics than previous authors. Reductionism and holism and the accompanying abstractions have different methodological and epistemic functions, strengths, and limitations, and the heuristics should be viewed as providing complementary research perspectives of cognitively limited beings. This is then, third, used as a premise to argue for epistemic and methodological pluralism in theoretical ecology. Finally, the presented taxonomy of abstractions is used to comment on the current debate whether mechanistic accounts of explanation are compatible with the use of abstractions. This debate has suffered from an abstract discussion of abstractions. With a better taxonomy of abstractions the debate can be resolved. (shrink)

This article attempts to assess Mario Bunge’s important but widely neglected criticisms of dialectics. It begins by providing a contextualized interpretation of Friedrich Engels’s metaphysics of the dialectics of nature before embarking on a detailed discussion of Leon Trotsky’s and contemporary “dialectical” scientists’ views on materialist dialectics. It argues that while some of Bunge’s criticisms are eminently sensible, the principles underlying the works of dialectical scientists are compatible with Bunge’s emergentist and systemic approach and can shed light on such issues (...) as the levels of organization, the diachronic and synchronic aspects of emergence, and the individualism-holism-systemism trilemma. This article also submits that dialectics is best interpreted as a guideline for a philosophy of change instead of a magical wand that liberates the investigator from study of facts. Understood as something that serves heuristic purposes, dialectics can be sensibly utilized by scientists to shore up or refine their methodological principles and thereby to facilitate empirical research. (shrink)

This article attempts to assess Mario Bunge’s important but widely neglected criticisms of dialectics. It begins by providing a contextualized interpretation of Friedrich Engels’s metaphysics of the dialectics of nature before embarking on a detailed discussion of Leon Trotsky’s and contemporary “dialectical” scientists’ views on materialist dialectics. It argues that while some of Bunge’s criticisms are eminently sensible, the principles underlying the works of dialectical scientists are compatible with Bunge’s emergentist and systemic approach and can shed light on such issues (...) as the levels of organization, the diachronic and synchronic aspects of emergence, and the individualism-holism-systemism trilemma. This article also submits that dialectics is best interpreted as a guideline for a philosophy of change instead of a magical wand that liberates the investigator from study of facts. Understood as something that serves heuristic purposes, dialectics can be sensibly utilized by scientists to shore up or refine their methodological principles and thereby to facilitate empirical research. (shrink)

Ecology has gradually gained salience during the last few decades and ecological issues, including land use changes, global warming, biodiversity loss, food shortage, and so forth, seem to be gaining public attention. Though philosophers of science had given little attention to ecology, there is a lot of interesting work being currently pursued in philosophy of ecology and environmental philosophy. As Colyvan and colleagues put it, “ecology is an important and fascinating branch of biology, with distinctive philosophical issues” (Colyvan et al. (...) 2009, p. 21). Given its conceptual and methodological familiarity with the social sciences, ecology occupies a unique position among other disciplines (Cooper 2003). (shrink)