Despite the importance of network analysis in biological practice, dominant models of scientific explanation do not account satisfactorily for how this family of explanations gain their explanatory power in every specific application. This insufficiency is particularly salient in the study of the ecology of the microbiome. Drawing on Coyte et al. (2015) study of the ecology of the microbiome, Deulofeu et al. (2021) argue that these explanations are neither mechanistic, nor purely mathematical, yet they are substantially empirical. Building on their (...) criticisms, in the present work we make a step further elucidating this kind of explanations with a general analytical framework according to which scientific explanations are ampliative, specialized embeddings (ASE), which has recently been successfully applied to other biological subfields. We use ASE to reconstruct in detail the Coyte et al.’s case study and on its basis, we claim that network explanations of the ecology of the microbiome, and other similar explanations in ecology, gain their epistemological force in virtue of their capacity to embed biological phenomena in non-accidental generalizations that are simultaneously ampliative and specialized. (shrink)

The epistemic status of Natural Selection has seemed intriguing to biologists and philosophers since the very beginning of the theory to our present times. One prominent contemporary example is Elliott Sober, who claims that NS, and some other theories in biology, and maybe in economics, are peculiar in including explanatory models/conditionals that are a priori in a sense in which explanatory models/conditionals in Classical Mechanics and most other standard theories are not. Sober’s argument focuses on some “would promote” sentences that (...) according to him, play a central role in NS explanations and are both causal and a priori. Lange and Rosenberg criticize Sober arguing that, though there may be some unspecific a priori causal claims, there are not a priori causal claims that specify particular causal factors. Although we basically agree with Lange and Rosenberg’s criticism, we think it remains silent about a second important element in Sober’s dialectics, namely his claim that, contrary to what happens in mechanics, in NS explanatory conditionals are a priori, and that this is so in quite specific explanatory models. In this paper we criticize this second element of Sober’s argument by analyzing what we take to be the four possible interpretations of Sober’s claim, and argue that, terminological preferences aside, the possible senses in which explanatory models in NS can qualify, or include elements that can qualify, as a priori, also apply to CM and other standard, highly unified theories. We conclude that this second claim is unsound, or at least that more needs to be said in order to sustain that NS explanatory models are a priori in a sense in which CM models are not. (shrink)

In this short discussion note, I discuss whether any of the generalizations made in biology should be construed as laws. Specifically, I examine a strategy offered by Elliot Sober ( 1997 ) and supported by Mehmet Elgin ( 2006 ) to reformulate certain biological generalizations so as to eliminate their contingency, thereby allowing them to count as laws. I argue that this strategy entails a conception of laws that is unacceptable on two counts: (1) Sober and Elgin’s approach allows the (...) possibility of formulating laws describing any biological phenomenon whatsoever; and (2) on Sober and Elgin’s view, any interesting contrast between so-called laws and obviously accidental generalizations collapses. I conclude by offering suggestions to refine their view in order to avoid these theoretical problems. (shrink)

This article addresses the question of whether we should conceive of mechanisms as productive of change in a regular way. I argue that, if mechanisms are characterized as fully regular, on the one hand, then not enough processes will count as mechanisms for them to be interesting or useful. If no appeal to regularity is made at all in their characterization, on the other hand, then mechanisms can no longer be useful for grounding prediction and supporting intervention strategies. I conclude (...) that, if the New Mechanistic Philosophy is to be successful, a stochastic characterization of mechanisms must be adopted. (shrink)

Convincing disputes about explanatory reductionism in the philosophy of biology require a clear and precise understanding of what a reductive explanation in biology is. The central aim of this book is to provide such an account by revealing the features that determine the reductive character of a biological explanation. Chapters I-IV provide the ground, on which I can then, in Chapter V, develop my own account of explanatory reduction in biology: Chapter I reveals the meta-philosophical assumptions that underlie my analysis (...) of reduction, Chapter II introduces the previous debate about reduction in the philosophy of biology by pointing out the most crucial lessons one should learn from this debate, Chapter III critically discusses the two perspectives on explanatory reduction that have been proposed in the philosophy of biology so far, and Chapter IV clarifies in what ways the issue of reduction is entangled with the issue of explanation. In Chapter V I present my own account of explanatory reduction. My main claim is that reductive explanations in the biological sciences possess three main characteristics: they explain the behavior of a biological system S, first, exclusively in terms of factors that are located on a lower level of organization than S, second, by focusing on factors that are internal to S , and third, by describing the genuine parts of S only as “parts in isolation”. This account is ontic because it traces the reductivity of an explanation back to certain relations that exist in the world. (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)

Laws of nature take center stage in philosophy of science. Laws are usually believed to stand in a tight conceptual relation to many important key concepts such as causation, explanation, confirmation, determinism, counterfactuals etc. Traditionally, philosophers of science have focused on physical laws, which were taken to be at least true, universal statements that support counterfactual claims. But, although this claim about laws might be true with respect to physics, laws in the special sciences (such as biology, psychology, economics etc.) (...) appear to have—maybe not surprisingly—different features than the laws of physics. Special science laws—for instance, the economic law “Under the condition of perfect competition, an increase of demand of a commodity leads to an increase of price, given that the quantity of the supplied commodity remains constant” and, in biology, Mendel's Laws—are usually taken to “have exceptions”, to be “non-universal” or “to be ceteris paribus laws”. How and whether the laws of physics and the laws of the special sciences differ is one of the crucial questions motivating the debate on ceteris paribus laws. Another major, controversial question concerns the determination of the precise meaning of “ceteris paribus”. Philosophers have attempted to explicate the meaning of ceteris paribus clauses in different ways. The question of meaning is connected to the problem of empirical content, i.e., the question whether ceteris paribus laws have non-trivial and empirically testable content. Since many philosophers have argued that ceteris paribus laws lack empirically testable content, this problem constitutes a major challenge to a theory of ceteris paribus laws. (shrink)

Mechanisms have become much-discussed, yet there is still no consensus on how to characterise them. In this paper, we start with something everyone is agreed on – that mechanisms explain – and investigate what constraints this imposes on our metaphysics of mechanisms. We examine two widely shared premises about how to understand mechanistic explanation: (1) that mechanistic explanation offers a welcome alternative to traditional laws-based explanation and (2) that there are two senses of mechanistic explanation that we call ‘epistemic explanation’ (...) and ‘physical explanation’. We argue that mechanistic explanation requires that mechanisms are both real and local. We then go on to argue that real, local mechanisms require a broadly active metaphysics for mechanisms, such as a capacities metaphysics. (shrink)

Scientific explanation is an important goal of scientific practise. Philosophers have proposed a striking diversity of seemingly incompatible accounts of explanation, from deductive-nomological to statistical relevance, unification, pragmatic, causal-mechanical, mechanistic, causal intervention, asymptotic, and model-based accounts. In this dissertation I apply two novel methods to reexamine our evidence about scientific explanation in practise and thereby address the fragmentation of philosophical accounts. I start by collecting a data set of 781 articles from one year of the journal Science. Using automated text (...) mining techniques I measure the frequency and distribution of several groups of philosophically interesting words, such as "explain", "cause", "evidence", "theory", "law", "mechanism", and "model". I show that "explain" words are much more common in scientific writing than in other genres, occurring in roughly half of all articles, and that their use is very often qualified or negated. These results about the use of words complement traditional conceptual analysis. Next I use random samples from the data set to develop a large number of small case studies across a wide range of scientific disciplines. I use a sample of "explain" sentences to develop and defend a new general philosophical account of scientific explanation, and then test my account against a larger set of randomly sampled sentences and abstracts. Five coarse categories can classify the explanans and explananda of my cases: data, entities, kinds, models, and theories. The pair of the categories of the explanans and explanandum indicates the "form" of an explanation. The explain-relation supports counterfactual reasoning about the dependence of qualities of the explanandum on qualities of the explanans. But for each form there is a different "core relation" between explanans and explanandum that supports the explain-relation. Causation, modelling, and argument are the core relations for different forms of scientific explanation between different categories of explanans and explananda. This flexibility allows me to resolve some of the fragmentation in the philosophical literature. I provide empirical evidence to show that my general philosophical account successfully describes a wide range of scientific practise across a large number of scientific disciplines. (shrink)

We take the potentialities that are studied in the biological sciences (e.g., totipotency) to be an important subtype of biological dispositions. The goal of this paper is twofold: first, we want to provide a detailed understanding of what biological dispositions are. We claim that two features are essential for dispositions in biology: the importance of the manifestation process and the diversity of conditions that need to be satisfied for the disposition to be manifest. Second, we demonstrate that the concept of (...) a disposition (or potentiality) is a very useful tool for the analysis of the explanatory practice in the biological sciences. On the one hand it allows an in-depth analysis of the nature and diversity of the conditions under which biological systems display specific behaviors. On the other hand the concept of a disposition may serve a unificatory role in the philosophy of the natural sciences since it captures not only the explanatory practice of biology, but of all natural sciences. Towards the end we will briefly come back to the notion of a potentiality in biology. (shrink)

Proponents of mechanistic explanation have argued that dynamical models are mere phenomenal models, in that they describe rather than explain the scientific phenomena produced by complex systems. I argue instead that dynamical models can, in fact, be explanatory. Using an example from neuroscientific research on epilepsy, I show that dynamical models can meet the explanatory demands met by mechanistic models, and as such occupy their own unique place within the space of explanatory scientific models.

This chapter utilises scholarship in philosophy of biology and philosophy of chemistry to produce meaningful implications for biology and chemistry education. The primary purpose for studying philosophical literature is to identify different perspectives on the nature of laws and explanations within these disciplines. The goal is not to resolve ongoing debates about the nature of laws and explanations but to consider their multiple forms and purposes in ways that promote deep and practical understanding of biological and chemical knowledge in educational (...) contexts. Most studies on the nature of science in science education tend to focus on general features of scientific knowledge and underemphasise disciplinary nuances. The authors aim to contribute to science education research by focusing on the characterisations of laws and explanations in biology and chemistry in the philosophical literature and illustrating how the typical coverage of biology and chemistry textbooks does not problematise meta-perspectives on the nature of laws and explanations. The chapter concludes with suggestions for making science teaching, learning and curriculum more inclusive of the epistemological dimensions of biology and chemistry. (shrink)

This chapter provides an introduction to the study of the philosophical notions of mechanisms and causality in biology and economics. This chapter sets the stage for this volume, Mechanism and Causality in Biology and Economics, in three ways. First, it gives a broad review of the recent changes and current state of the study of mechanisms and causality in the philosophy of science. Second, consistent with a recent trend in the philosophy of science to focus on scientific practices, it in (...) turn implies the importance of studying the scientific methods employed by researchers. Finally, by way of providing an overview of each chapter in the volume, this chapter demonstrates that biology and economics are two fertile fields for the philosophy of science and shows how biological and economic mechanisms and causality can be synthesized. (shrink)

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

Three metascientific concepts that have been object of philosophical analysis are the concepts oflaw, model and theory. The aim ofthis article is to present the explication of these concepts, and of their relationships, made within the framework of Sneedean or Metatheoretical Structuralism (Balzer et al. 1987), and of their application to a case from the realm of biology: Population Dynamics. The analysis carried out will make it possible to support, contrary to what some philosophers of science in general and of (...) biology in particular hold, the following claims: a) there are "laws" in biological sciences, b) many of the heterogeneous and different "models" of biology can be accommodated under some "theory", and c) this is exactly what confers great unifying power to biological theories. (shrink)

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects of scientific (...) explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (shrink)

Leuridan (2011) questions whether mechanisms can really replace laws at the heart of our thinking about science. In doing so, he enters a long-standing discussion about the relationship between the mech-anistic structures evident in the theories of contemporary biology and the laws of nature privileged especially in traditional empiricist traditions of the philosophy of science (see e.g. Wimsatt 1974; Bechtel and Abrahamsen 2005; Bogen 2005; Darden 2006; Glennan 1996; MDC 2000; Schaffner 1993; Tabery 2003; Weber 2005). In our view, Leuridan (...) misconstrues this discussion. His weak positive claim that mechanistic sciences appeal to generalizations is true but uninteresting. His stronger claim, that all causal claims require laws, is unsupported by his arguments. Though we proceed by criticizing Leuridan’s arguments, our greater purpose is to embellish his arguments in order to show how thinking about mechanisms enriches and transforms old philosophical debates about laws in biology and provides new insights into how generalizations afford prediction, explanation and control. (shrink)

The goal of this article is to show that formal analysis and reconstructions may be useful to discuss and shed light on substantive meta-theoretical issues. We proceed here by exemplification, analysing and reconstructing as a case study a paradigmatic biochemical theory, the Monod-Wyman-Changeux theory of allosterism, and applying the reconstruction to the discussion of some issues raised by prominent representatives of the new mechanist philosophy. We conclude that our study shows that at least in this case mechanicism and more traditional (...) accounts are not rivals but complementary approaches. (shrink)

Las corrientes manipulabilistas tradicionales consideran que una implementación de política efectiva debe estar fundamentada en un conocimiento invariante. Este modo de pensamiento está basado en el supuesto ontológico de que existen factores causales estables tanto en las ciencias naturales como en las sociales. También asumen que un sólo tipo de intervención ex-ante es pertinente para una implementación efectiva. En el presente artículo se realizará una crítica a estos enfoques. En particular, se mostrará que los procesos sociales responden a una lógica (...) de “árboles de posibilidades” o “resultados de final abierto”. Sobre la base de esta variante ontológica se argumentará que más que un conocimiento de factores invariantes, el sustento de una buena política debe buscarse en los condicionamientos explicitados dentro de un anteproyecto y en la factibilidad de que los mismos se satisfagan en el sistema objetivo. Asimismo, se mostrará cómo las típicas intervenciones ex-ante no son adecuadas en el reino de lo social. Contrario a ellos, las intervenciones deberán ser sistemáticas. (shrink)

Mechanism is undoubtedly a causal concept, in the sense that ordinary definitions and philosophical analyses explicate the concept in terms of other causal concepts such as production and interaction. Given this fact, many philosophers have supposed that analyses of the concept of mechanism, while they might appeal to philosophical theories about the nature of causation, could do little to inform such theories. On the other hand, methods of causal inference and explanation appeal to mechanisms. Discovering a mechanism is the gold (...) standard for establishing and explaining causal connections. This fact suggests that it might be possible to provide an analysis of causation that appeals to mechanisms. (shrink)