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)

Surprisingly, modified versions of the confirmation theory (Carnap and Hempel) and truth approximation theory (Popper) turn out to be smoothly sythesizable. The glue between the two appears to be the instrumentalist methodology, rather than that of the falsificationalist. The instrumentalist methodology, used in the separate, comparative evaluation of theories in terms of their successes and problems (hence, even if already falsified), provides in theory and practice the straight road to short-term empirical progress in science ( à la Laudan). It is (...) also argued that such progress is also functional for all kinds of truth approximation: observational, referential, and theoretical. This sheds new light on the long-term dynamics of science and hence on the relation between the main epistemological positions, viz., instrumentalism (Toulmin, Laudan), constructive empiricism (Van Fraassen), referential realism (Hacking, Cartwright), and theory realism of a non-essentialist nature (constructive realism à la Popper). Readership: Open minded philosophers and scientists. The book explains and justifies the scientist's intuition that the debate among philosophers about instrumentalism and realism has almost no practical consequences. (shrink)

This paper examines causal theories of reference with respect to how plausible an account they give of non-physical natural kind terms such as ‘gene’ as well as of the truth of the associated theoretical claims. I first show that reference fixism for ‘gene’ fails. By this, I mean the claim that the reference of ‘gene’ was stable over longer historical periods, for example, since the classical period of transmission genetics. Second, I show that the theory of partial reference does not (...) do justice to some widely held realist intuitions about classical genetics. This result is at loggerheads with the explicit goals usually associated with partial theories of reference, which is to defend a realist semantics for scientific terms. Thirdly, I show that, contrary to received wisdom and perhaps contrary to physics and chemistry, neither reference fixism nor partial reference are necessary in order to hold on to scientific realism about biology. I pinpoint the reasons for this in the nature of biological kinds, which do not even remotely resemble natural kinds (i.e., Lockean real essences) as traditionally conceived. (shrink)

In the early eighties, philosophers of science came to the conviction that discovery and creativity form an integral part of scientific rationality. Ever since, the?positivists? have been criticised for their neglect of these topics. It is the aim of this paper to show that the positivists' approach to scientific discovery is not only much richer than is commonly recognized, but that they even defended an important thesis which some of the `friends of discovery' seem to have forgotten. Contrary to what (...) is generally accepted, I shall also show that there is no reason at all why the positivists should have ignored discovery. (shrink)

The status of population genetics has become hotly debated among biologists and philosophers of biology. Many seem to view population genetics as relatively unchanged since the Modern Synthesis and have argued that subjects such as development were left out of the Synthesis. Some have called for an extended evolutionary synthesis or for recognizing the insignificance of population genetics. Yet others such as Michael Lynch have defended population genetics, declaring "nothing in evolution makes sense except in the light of population genetics" (...) (a twist on Dobzhansky's famous slogan that "nothing in biology makes sense except in the light of evolution"). Missing from this discussion is the use of population genetics to shed light on ecology and vice versa, beginning in the 1940s and continuing until the present day. I highlight some of that history through an overview of traditions such as ecological genetics and population biology, followed by a slightly more in-depth look at a contemporary study of the endangered California Tiger Salamander. I argue that population genetics is a powerful and useful tool that continues to be used and modified, even if it isn't required for all evolutionary explanations or doesn't incorporate all the causal factors of evolution. (shrink)

Linkage (or genetic) maps are graphs, which are intended to represent the linear ordering of genes on the chromosomes. They are constructed on the basis of statistical data concerning the transmission of genes. The invention of this technique in 1913 was driven by Morgan's group's adoption of a set of hypotheses concerning the physical mechanism of heredity. These hypotheses were themselves grounded in Morgan's defense of the chromosome theory of heredity, according to which chromosomes are the physical basis of genes. (...) In this paper, I analyze the 1919 debate between William Castle and Morgan's group, about the construction of genetic maps. The official issue of the debate concerns the arrangement of genes on chromosomes. However, the disputants tend to carry out the discussions about how one should model the data in order to draw predictions concerning the transmission of genes; the debate does not bear on the data themselves, nor does it focus on the hypotheses explaining these data. The main criteria that are appealed to by the protagonists are simplicity and predictive efficacy. However, I show that both parties' assessments of the simplicity and predictive efficacy of different ways of modeling the data themselves depend on background theoretical positions. I aim at clarifying how preference for a given model and theoretical commitments articulate. (shrink)

Paul Boyer shared a Nobel Prize in 1997 for his work on the mechanism of ATP synthase. His earlier work, though (which contributed indirectly to his triumph), included major errors, both experimental and theoretical. Two benchmark cases offer insight into how scientists err and how they deal with error. Boyer's work also parallels and illustrates the emergence of bioenergetics in the second half of the twentieth century, rivaling achievements in evolution and molecular biology.

Kenneth Waters and Marcel Weber argue that the joint use of distinct gene concepts and the transfer of knowledge between classical and molecular analyses in contemporary scientific practice is possible because classical and molecular concepts of the gene refer to overlapping chromosomal segments and the DNA sequences associated with these segments. However, while pointing in the direction of coreference, both authors also agree that there is a considerable divergence between the actual sequences that count as genes in classical genetics and (...) molecular biology. The thesis advanced in this paper is that the referents of classical and molecular gene concepts are coextensive to a higher degree than admitted by Waters and Weber, and therefore coreference can provide a satisfactory account of the high level of integration between classical genetics and molecular biology. In particular, I argue that the functional units/cistrons identified by classical techniques overlap with functional elements entering the composition of molecular transcription units, and that the precision of this overlap can be improved by conducting further experimentation. (shrink)

Here are some of the most important discoveries in the history of medicine: blood circulation (1620s), vaccination, (1790s), anesthesia (1840s), germ theory (1860s), X- rays (1895), vitamins (early 1900s), antibiotics (1920s-1930s), insulin (1920s), and oncogenes (1970s). This list is highly varied, as it includes basic medical knowledge such has Harvey’s account of how the heart pumps blood, hypotheses about the causes of disease such as the germ theory, ideas about the treatments of diseases such as antibiotics, and medical instruments such (...) as X-ray machines. The philosophy of medicine should be able to contribute to understanding of the nature of discoveries such as these. The great originators of the field of philosophy of science were all concerned with the nature of scientific discovery, including Francis Bacon (1960), William Whewell (1967), John Stuart Mill (1974), and Charles Peirce (1931-1958). The rise of logical positivism in the 1930s pushed discovery off the philosophical agenda, but the topic was revived through the work of philosophers such as Norwood Russell Hanson (1958), Thomas Nickles (1980), Lindley Darden (1991, 2006), and Nancy Nersessian (1984). Scientific discovery has also become an object of investigations for researchers in the fields of cognitive psychology and artificial intelligence, as seen in the work of Herbert Simon, Pat Langley, and others (Langley et al., 1987; Klahr, 2000). Today, scientific September 14, 2009 discovery is an interdisciplinary topic at the intersection of the philosophy, history, and psychology of science. The aim of this chapter is to identify patterns of discovery that illuminate some of the most important developments in the history of medicine. I have used a variety of sources to identify forty great medical discoveries (Adler, 2004; Friedman and Friedland, 1998; Science Channel, 2006; Strauss and Strauss, 2006).. (shrink)

This chapter offers a review of standard views about the requirements for natural selection to shape evolution and for the sorts of ‘units’ on which selection might operate. It then summarizes traditional arguments for genic selectionism, i.e., the view that selection operates primarily on genes (e.g., those of G. C. Williams, Richard Dawkins, and David Hull) and traditional counterarguments (e.g., those of William Wimsatt, Richard Lewontin, and Elliott Sober, and a diffuse group based on life history strategies). It then offers (...) a series of responses to the arguments, based on more contemporary considerations from molecular genetics, offered by Carmen Sapienza. A key issue raised by Sapienza concerns the degree to which a small number of genes might be able to control much of the variation relevant to selection operating on such selectively critical organs as hearts. The response to these arguments suggests that selection acts on many levels at once and that sporadic selection, acting with strong effects, can act successively on different key traits (and genes) while maintaining a balance among many potentially conflicting demands faced by organisms within an evolving lineage. (shrink)

Predictivism asserts that novel confirmations carry special probative weight. Epistemic pluralism asserts that the judgments of agents (about, e.g., the probabilities of theories) carry epistemic import. In this paper, I propose a new theory of predictivism that is tailored to pluralistic evaluators of theories. I replace the orthodox notion of use-novelty with a notion of endorsement-novelty, and argue that the intuition that predictivism is true has two roots. I provide a detailed Bayesian rendering of this theory and argue that pluralistic (...) theory evaluation pervades scientific practice. I compare my account of predictivism with those of Maher and Worrall. Introduction Why construction is a red herring for pluralist evaluators The unvirtuous accommodator Virtuous endorsers and the two roots of predictivism The two roots in Bayesian terms: the priors and background beliefs of endorsers Who are the pluralist evaluators? Two contemporary theories of predictivism 7.1 Maher: Reliable methods of theory construction 7.2 Worrall: The confirmation of core ideas Conclusion. (shrink)

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

The concept of dominance poses several dilemmas. First, while entrenched in genetics education, the metaphor of dominance promotes several misconceptions and misleading cultural perspectives. Second, the metaphors of power, prevalence and competition extend into science, shaping assumptions and default concepts. Third, because genetic causality is complex, the simplified concepts of dominance found in practice are highly contingent or inconsistent. The conceptual problems are illustrated in the history of studies on the evolution of dominance. Conceptual clarity may be fostered, I claim, (...) by viewing diploid organisms as diphenic and by framing genetic causality modestly through individual alleles and their corresponding haplophenotypes. (shrink)

As a working hypothesis for philosophy of science, the unity of science thesis has been decisively challenged in all its standard formulations; it cannot be assumed that the sciences presuppose an orderly world, that they are united by the goal of systematically describing and explaining this order, or that they rely on distinctively scientific methodologies which, properly applied, produce domain-specific results that converge on a single coherent and comprehensive system of knowledge. I first delineate the scope of arguments against global (...) unity theses. However implausible old-style global unity theses may now seem, I argue that unifying strategies of a more local and contingent nature do play an important role in scientific inquiry. This is particularly clear in archaeology where, to establish evidential claims of any kind, practitioners must exploit a range of inter-field and inter-theory connections. At the same time, the robustness of these evidential claims depends on significant disunity between the sciences from which archaeologists draw background assumptions and auxiliary hypotheses. This juxtaposition of unity with disunity poses a challenge to standard positions in the debate about scientific unity. (shrink)

: Where there are cases of underdetermination in scientific controversies, such as the case of the molecular clock, scientists may direct the course and terms of dispute by playing off the multidimensional framework of theory evaluation. This is because assessment strategies themselves are underdetermined. Within the framework of assessment, there are a variety of trade-offs between different strategies as well as shifting emphases as specific strategies are given more or less weight in assessment situations. When a strategy is underdetermined, scientists (...) can change the dynamics of a controversy by making assessments using different combinations of evaluation strategies and/or weighting whatever strategies are in play in different ways. Following an underdetermination strategy does not end or resolve a scientific dispute. Consequently, manipulating underdetermination is a feature of controversy dynamics and not controversy closure. (shrink)

The dominant neuroscientific theory of spatial memory is, like many theories in neuroscience, a multilevel description of a mechanism. The theory links the activities of molecules, cells, brain regions, and whole organisms into an integrated sketch of an explanation for the ability of organisms to navigate novel environments. Here I develop a taxonomy of interlevel experimental strategies for integrating the levels in such multilevel mechanisms. These experimental strategies include activation strategies, interference strategies, and additive strategies. These strategies are mutually reinforcing, (...) providing a kind of interlevel and intratheoretic robustness that has not previously been recognized. (shrink)

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

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. (shrink)

Scientific revolution has been one of the most controversial topics in the history and philosophy of science. Yet it has been no consensus on what is the best unit of analysis in the historiography of scientific revolutions. Nor is there a consensus on what best explains the nature of scientific revolutions. This chapter provides a critical examination of the historiography of scientific revolutions. It begins with a brief introduction to the historical development of the concept of scientific revolution, followed by (...) an overview of the five main philosophical accounts of scientific revolutions. It then challenges two historiographical assumptions of the philosophical analyses of scientific revolutions. (shrink)

Argues that the path to the good life does not consist in working toward some abstract concept of the good, but rather by ameliorating the problems of the practices and institutions that make up our practical life.

The main purpose of this dissertation is to examine critically and discuss the role of imagination in science and religion, with particular emphasis on its possible epistemic, creative, and meaning-making functions. In order to answer my research questions, I apply theories and concepts from contemporary philosophy of mind on scientific and religious practices. This framework allows me to explore the mental state of imagination, not as an isolated phenomenon but, rather, as one of many mental states that co-exist and interplay (...) in our cogntive architecture. Based on the philosophical discourse of philosophy of mind, four types of imagination are indentified and conceptualized: sensory, propositional, experiential, and creative imagination. These categories are then employed on five phenomena that can be found in scientific and religious environments: metaphors, models, thought experiments, aspect perception, and - in the religious case - rituals. In relation to the concept of religious "seeing" I consider how imaginings may influence visionary experiences and visualization, and compare these phenomena with cases of scientific visualization and eureka experiences. In regard to scientific and religious models, a distinction is made between, on the one hand, two notions of truth and, on the other hand, truth-independent meaning-making. In light of these categories, I differentiate between, and critically discuss, the use of imagination in doxastic, non-doxastic and fictionalist accounts. In light of this investigation, I formulate and defend the position of interactivism, which acknowledges a constant interplay between different attitudes and mental states. In my examination of rituals and scientific and religious thought experiments, special attention is given to the mental capacity to recreate the experiences that are entailed in an imagined scenario. At the end of the investigation, I consider the possible impact that my study might have on how we view science and religion as well as the dialogue bewteen these two fields. (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)

Two metascientific concepts that have been ― and still are ― object of philosophical analysis are the concepts of model and theory. But while the concept of scientific theory was one of the concepts to which philosophers of science devoted most attention during the 20th century, it is only in recent decades that the concept of scientific model has come to occupy a central position in philosophical reflection. However, it has done so in such a way that, at present, as (...) Jim Bogen states in the back cover of the book Scientific Models in the Philosophy of Science, by Daniela Bailer-Jones, “[t]he standard philosophical literature on the role of models in scientific reasoning is voluminous, disorganized, and confusing”. In spite of this, one of the axes that would allow us to organize at least part of this literature, and with which Bailer-Jones’ book closes, is that which is identified as one of the “contemporary philosophical issues: how theories and models relate to each other” (Bailer-Jones 2009, p. 208).That is why, in this introduction to the special issues of Metatheoria devoted to the topic of “Models and Theories in Biology”, we will present the main advances that have been made in the philosophical analysis of the concepts of model and theory in general and in biology in particular, and we will also do the same with the answers that have been given to the problem of "how theories and models relate to each other”. (shrink)

Imagination is necessary for scientific practice, yet there are no in vivo sociological studies on the ways that imagination is taught, thought of, or evaluated by scientists. This article begins to remedy this by presenting the results of a qualitative study performed on two systems biology laboratories. I found that the more advanced a participant was in their scientific career, the more they valued imagination. Further, positive attitudes toward imagination were primarily due to the perceived role of imagination in problem-solving. (...) But not all problem-solving episodes involved clear appeals to imagination, only maximally specific problems did. This pattern is explained by the presence of an implicit norm governing imagination use in the two labs: only use imagination on maximally specific problems, and only when all other available methods have failed. This norm was confirmed by the participants, and I argue that it has epistemological reasons in its favour. I also found that its strength varies inversely with career stage, such that more advanced scientists do (and should) occasionally bring their imaginations to bear on more general problems. A story about scientific pedagogy explains the trend away from (and back to) imagination over the course of a scientific career. Finally, some positive recommendations are given for a more imagination-friendly scientific pedagogy. (shrink)

My purpose in this paper is to show how a re-examination of Snow’s famous South London water study, widely taken to have established that cholera is water-borne, highlights some problems with current, scientific realist accounts of theory-change. When examining scientific controversies, such accounts focus disproportionately on the ‘winning’ theories and their properties, or on those of the reasoning of the scientists who proposed them. I argue that this focus is misguided and leads us to neglect much of what is epistemically (...) valuable in episodes of theory-change, thereby leading to inaccurate views about both the dynamics of theory-change and the notion of scientific progress that accompanies it. I end by sketching some implications for the philosophy of epidemiology. (shrink)

In this paper, I offer an analysis of the radical disagreement over the adequacy of string theory. The prominence of string theory despite its notorious lack of empirical support is sometimes explained as a troubling case of science gone awry, driven largely by sociological mechanisms such as groupthink (e.g. Smolin 2006). Others, such as Dawid (2013), explain the controversy by positing a methodological revolution of sorts, according to which string theorists have quietly turned to nonempirical methods of theory assessment given (...) the technological inability to directly test the theory. The appropriate response, according to Dawid, is to acknowledge this development and widen the canons of acceptable scientific methods. As I’ll argue, however, the current situation in fundamental physics does not require either of these responses. Rather, as I’ll suggest, much of the controversy stems from a failure to properly distinguish the “context of justification” from the “context of pursuit”. Both those who accuse string theorists of betraying the scientific method and those who advocate an enlarged conception of scientific methodology objectionably conflate epistemic justification with judgements of pursuit-worthiness. Once we get clear about this distinction and about the different norms governing the two contexts, the current situation in fundamental physics becomes much less puzzling. After defending this diagnosis of the controversy, I’ll show how the argument patterns that have been posited by Dawid as constituting an emergent methodological revolution in science are better off if reworked as arguments belonging to the context of pursuit. (shrink)

Stein has raised a fundamental problem for any attempt to characterize instrumentalism and realism as substantive alternatives. This is the distinguishability problem, which consists in the problem of developing a form of instrumentalism that is substantially different from a plausible realist alternative and the problem of showing that this form of instrumentalism does justice to actual scientific practice. Using Stein’s own discussion of Maxwell, I formulate instrumentalism and realism as a scientist’s attitudes toward models, where an attitude is understood to (...) be a complex of the scientist’s belief and intention regarding models. Developing a case study of Benzer’s modeling practice, I show that each attitude can structure inquiry differently and argue that to understand certain aspects of scientific practice, such as the practice of genetic mapping in Benzer’s work, we sometimes need to appeal to the coexistence of these attitudes. (shrink)

La filosofía de la ciencia se desarrolló durante la primera mitad del siglo xx bajo el supuesto de que la ciencia podía caracterizarse por la estructura lógica tanto del conocimiento articulado en las teorías más exitosas como de sus explicaciones. En la segunda mitad del siglo xx se cuestiona fuertemente esa idea, pero se sigue asumiendo que la filosofía de la ciencia debe hacerse siguiendo los cánones de una epistemología fundamentalista que considera que el avance de la ciencia pasa por (...) una ontología cada vez mas austera guiada por la idea de "mientras menos mejor". Desde esta perspectiva fundamentalista, el que las diferentes ciencias hablen de diferentes tipos de cosas es un obstáculo al entendimiento, producto de la imperfección del conocimiento actual. Este ideal nos invita a pensar que la epistemología debe hacerse reflexionando sobre el conocimiento articulado en nuestras teorías más austeras y nos compromete con propuestas reduccionistas problemáticas que no permiten explicar la diversidad de recursos epistémicos que de hecho utilizan los científicos. En este libro promovemos una epistemología que no sigue el lema de "mientras menos mejor", sino el de "organizar nuestros recursos epistémicos de manera que se genere entendimiento". Así, la misma estructura de las explicaciones y las prácticas (que incluye métodos y normas respecto de lo que se considera plausible y valioso) es lo que nos da la pauta para responder a la pregunta de qué es lo que hay. Esta estrategia epistémica nos obliga a hacer una filosofía de la ciencia muy cercana a la ciencia, reconociendo la pluralidad de sus métodos, objetivos y prácticas, sin reducir la filosofía de la ciencia a la sociología o a cualquier otra ciencia en particular. (shrink)

This Ph.D. thesis provides a pilosophical account of the structure of the evolutionary synthesis of the 1930s and 40s. The first, more historical part analyses how classical genetics came to be integrated into evolutionary thinking, highlighting in particular the importance of chromosomal mapping of Drosophila strains collected in the wild by Dobzansky, but also the work of Goldschmidt, Sumners, Timofeeff-Ressovsky and others. The second, more philosophical part attempts to answer the question wherein the unity of the synthesis consisted. I argue (...) that it exemplifies a weak of form of explanatory unification. (shrink)

Alexander Bird indicates that the significance of Thomas Kuhn in the history of philosophy of science is somehow paradoxical. On the one hand, Kuhn was one of the most influential and important philosophers of science in the second half of the twentieth century. On the other hand, nowadays there is little distinctively Kuhn’s legacy in the sense that most of Kuhn’s work has no longer any philosophical significance. Bird argues that the explanation of the paradox of Kuhn’s legacy is that (...) Kuhn took a direction opposite to that of the mainstream of the philosophy of science in his later academic career. This paper aims to provide a new way to understand and develop Kuhn’s legacy by revisiting the development of Kuhn’s philosophy of science in 1970s and proposing a new account of exemplar. Firstly, I propose my diagnosis of Kuhn’s “wrong turning” by identifying Kuhn’s two novel contributions: the introduction of paradigm and the proposal of the incommensurability thesis. Secondly, I argue that Kuhn made a conceptual/terminological turn from paradigm to theory, which undermined Kuhn’s novel contributions. Thirdly, I propose a new articulation of exemplar and propose an exemplar-based approach to analysing the history of science. Finally, I show how the exemplar-based approach can be applied to analyse the history of science by my case study of the early development of genetics. (shrink)

Methodological reductionists practice ‘wannabe reductionism’. They claim that one should pursue reductionism, but never propose how. I integrate two strains in prior work to do so. Three kinds of activities are pursued as “reductionist”. “Successional reduction” and inter-level mechanistic explanation are legitimate and powerful strategies. Eliminativism is generally ill-conceived. Specific problem-solving heuristics for constructing inter-level mechanistic explanations show why and when they can provide powerful and fruitful tools and insights, but sometimes lead to erroneous results. I show how traditional metaphysical (...) approaches fail to engage how science is done. The methods used do so, and support a pragmatic and non-eliminativist realism. (shrink)

1. Overview and organizing themes 2. Historical Review: Aristotle to Mill 3. Logic of method and critical responses 3.1 Logical constructionism and Operationalism 3.2. H-D as a logic of confirmation 3.3. Popper and falsificationism 3.4 Meta-methodology and the end of method 4. Statistical methods for hypothesis testing 5. Method in Practice 5.1 Creative and exploratory practices 5.2 Computer methods and the ‘third way’ of doing science 6. Discourse on scientific method 6.1 “The scientific method” in science education and as seen (...) by scientists 6.2 Privileged methods and ‘gold standards’ 6.3 Scientific method in the court room 6.4 Deviating practices 7. Conclusion Bibliography Academic Tools Other Internet Resources Related Entries . (shrink)

Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.

This chapter contains sections titled: Highlights of Past Literature Current Work Future Work.

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

Today, mechanisms and mechanistic explanation are very popular in philosophy of science and are deemed a welcome alternative to laws of nature and deductive‐nomological explanation. Starting from Mitchell's pragmatic notion of laws, I cast doubt on their status as a genuine alternative. I argue that (1) all complex‐systems mechanisms ontologically must rely on stable regularities, while (2) the reverse need not hold. Analogously, (3) models of mechanisms must incorporate pragmatic laws, while (4) such laws themselves need not always refer to (...) underlying mechanisms. Finally, I show that Mitchell's account is more encompassing than the mechanistic account *Received August 2008; revised January 2010. †To contact the author, please write to: Centre for Logic and Philosophy of Science, Ghent University, Blandijnberg 2, B‐9000 Belgium; e‐mail: [email protected]. (shrink)

Interdisciplinary integration has fundamental limitations. This is not sufficiently realized in science and in philosophy. Concerning scientific theories there are many examples of pseudo-integration which should be unmasked by elementary philosophical analysis. For example, allegedly over-arching theories of stress which are meant to unite biology and psychology, upon analysis, turn out to represent terminological rather than substantive unity. They should be replaced by more specific, local theories. Theories of animal orientation, likewise, have been formulated in unduly general terms. A natural (...) history approach is more suitable for the study of animal orientation. The tendency to formulate overgeneral theories is also present in evolutionary biology. Philosophy of biology can only deal with these matters if it takes a normative turn. Undue emphasis on interdisciplinary integration is a modern variant of the old unity of science ideal. The replacement of the ideal by a better one is an important challenge for the philosophy of science. (shrink)

The miracle argument for scientific realism can be cast in two forms: according to the miraculous theory argument, realism is the only position which does not make the empirical successes of particular theories miraculous. According to the miraculous choice argument, realism is the only position which does not render the fact that empirically successful theories have been chosen a miracle. A vast literature discusses the miraculous theory argument, but the miraculous choice argument has been unjustifiably neglected. I raise two objections (...) to Richard Boyd's defense of the latter: (1) we have no miracle free account of the emergence of take-off theories and (2) the anti-realist can account for the non-miraculous choice of empirically successful theories by attributing mere empirical adequacy to background theory. I argue that the availability of extra-empirical criteria that are arguably truth conductive but not theory-laden suffices to answer (1), and the unavailability of extra-empirical criteria that are conductive to empirical adequacy but not necessarily to truth (and are also not theory-laden) constitutes to reply to (2). The prospects for a realist victory are at least somewhat promising, on a controversial assumption about the rate at which empirically successful theories emerge. (shrink)

Richard Levins’ distinction between aggregate, composed and evolved systems acquires new significance as we recognize the importance of mechanistic explanation. Criteria for aggregativity provide limiting cases for absence of organization, so through their failure, can provide rich detectors for organizational properties. I explore the use of failures of aggregativity for the analysis of mechanistic systems in diverse contexts. Aggregativity appears theoretically desireable, but we are easily fooled. It may be exaggerated through approximation, conditions of derivation, and extrapolating from some conditions (...) of decomposition illegtimately to others. Evolved systems particularly may require analyses under alternative complementary decompositions. Exploring these conditions helps us to better understand the strengths and limits of reductionistic methods. (shrink)

There has been little research into the weak kindsof negating hypotheses. Hypotheses may be unfalsifiable. In this case it is impossible tofind a contradiction in some area of the conceptualsystems in which they are incorporated.Notwithstanding this fact, it is sometimes necessaryto construct ways of rejecting the unfalsifiablehypothesis at hand by resorting to some external forms of negation, external because wewant to avoid any arbitrary and subjectiveelimination, which would be rationally orepistemologically unjustified. I will consider akind of ``weak'''' (unfalsifiable) hypotheses that (...) arehard to negate and the ways for making it easy. Inthese cases the subject can ``rationally'''' decide towithdraw his hypotheses even in contexts where it is``impossible'''' to find ``explicit'''' contradictions: theuse of negation as failure (an interestingtechnique for negating hypotheses and accessing newones suggested by artificial intelligence) isilluminating. I plan to explore whether this kind ofnegation can be employed to model hypothesiswithdrawal in Poincaré''s conventionalism of theprinciples of physics and in Freudian analyticreasoning. (shrink)

This paper primarily deals with theconceptual prospects for generalizing the aim ofabduction from the standard one of explainingsurprising or anomalous observations to that ofempirical progress or even truth approximation. Itturns out that the main abduction task then becomesthe instrumentalist task of theory revision aiming atan empirically more successful theory, relative to theavailable data, but not necessarily compatible withthem. The rest, that is, genuine empirical progress aswell as observational, referential and theoreticaltruth approximation, is a matter of evaluation andselection, and possibly new (...) generation tasks forfurther improvement. The paper concludes with a surveyof possible points of departure, in AI and logic, forcomputational treatment of the instrumentalist taskguided by the `comparative evaluation matrix''. (shrink)

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn’s terminology, this (...) discovery of a major biological entity was made during a ‘normal science’ project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese’s project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies. (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)

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