Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to (...) handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

Scientific communities as social groupings and the role that such communities play in scientific change and the production of scientific knowledge is currently under debate. I examine theory change as a complex social interaction among individual scientists and the scientific community, and argue that individuals will be motivated to adopt a more radical or innovative attitude when confronted with striking similarities between model systems and a more robust understanding of specialised vocabulary. Two case studies from the biological sciences, Barbara McClintock (...) and Stanley Prusiner, help motivate the idea that sharing of models and specialised vocabulary fill the gap between discovery and scientific change by promoting the dispersal of important information throughout the scientific community. (shrink)

Philosophers of science increasingly believe that much of science is concerned with understanding the mechanisms responsible for the production of natural phenomena. An adequate understanding of scientific research requires an account of how scientists develop and test models of mechanisms. This paper offers a general account of the nature of mechanical models, discussing the representational relationship that holds between mechanisms and their models as well as the techniques that can be used to test and refine such models. The analysis is (...) supported by study of two competing models of a mechanism of speech perception. (shrink)

It is undeniable that much scientific work is model-based. Despite this, the justification for this reliance on models is still controversial. A particular difficulty here is the fact that many scientific models are based on assumptions that do not describe the exact details of many or even any empirical situations very well. This raises the question of why it is that, despite their frequent lack of descriptive accuracy, employing models is scientifically useful.One..

This essay discusses Elliott Sober’s Evidence and Evolution: The Logic Behind the Science. Valuable to both philosophers and biologists, Sober analyzes the testing of different kinds of evolutionary hypotheses about natural selection or phylogenetic history, including a thorough critique of intelligent design. Not at least because of a discussion of different schools of hypothesis testing (Bayesianism, likelihoodism, and frequentism), with Sober favoring a pluralism where different inference methods are appropriate in different empirical contexts, the book has lessons for philosophy of (...) science beyond its evolutionary focus. I criticize Sober for not including epistemic values and social aspects of scientific practice in his epistemological framework. (shrink)

Naturalistic epistemologists frequently assume that their aim is to identify generalities (i.e. general laws) about the effectiveness of particular reasoning processes and methods. This paper argues that the search for this kind of generality fails. Work that has been done thus far to identify generalities (e.g. by Goldman, Kitcher and Thagard) overlooks both the complexity of reasoning and the relativity of assessments to particular contexts (domain, stage and goal of inquiry). Examples of human reasoning which show both complexity and contextuality (...) are given. The paper concludes with a discussion of the kind of multivariate model of reasoning that naturalistic epistemologists can use to evaluate processes and methods for specific domains. (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.

Former discussions of biological generalizations have focused on the question of whether there are universal laws of biology. These discussions typically analyzed generalizations out of their investigative and explanatory contexts and concluded that whatever biological generalizations are, they are not universal laws. The aim of this paper is to explain what biological generalizations are by shifting attention towards the contexts in which they are drawn. I argue that within the context of any particular biological explanation or investigation, biologists employ two (...) types of generations. One type identifies causal regularities exhibited by particular kinds of biological entities. The other type identifies how these entities are distributed in the biological world. (shrink)

This paper considers recent heated debates led by Jerry A. Coyne andMichael J. Wade on issues stemming from the 1929–1962 R.A. Fisher-Sewall Wrightcontroversy in population genetics. William B. Provine once remarked that theFisher-Wright controversy is central, fundamental, and very influential.Indeed,it is also persistent. The argumentative structure of therecent (1997–2000) debates is analyzed with the aim of eliminating a logicalconflict in them, viz., that the two sides in the debates havedifferent aims and that, as such, they are talking past each other. (...) Given aphilosophical analysis of the argumentative structure of the debates,suggestions supportive of Wade's work on the debate are made that areaimed, modestly, at putting the persistent Fisher-Wright controversy on thecourse to resolution. (shrink)

Review essay of The Philosophy of Experimental Biology by Marcel Weber (Cambridge University Press, 2005).

: This paper explores the calibration of laboratory models in population genetics as an experimental strategy for justifying experimental results and claims based upon them following Franklin (1986, 1990) and Rudge (1996, 1998). The analysis provided undermines Coyne et al.'s (1997) critique of Wade and Goodnight's (1991) experimental study of Wright's (1931, 1932) Shifting Balance Theory. The essay concludes by further demonstrating how this analysis bears on Diamond's (1986) claims regarding the weakness of laboratory experiments as evidence, and further how (...) the calibration strategy fits within Lloyd's (1987, 1988) account of the confirmation of ecological and evolutionary models. (shrink)

: Errors in science range along a spectrum from those relatively local to the phenomenon (usually easily remedied in the laboratory) to those more conceptually derived (involving theory or cultural factors, sometimes quite long-term). One may classify error types broadly as material, observational, conceptual or discoursive. This framework bridges philosophical and sociological perspectives, offering a basis for interfield discourse. A repertoire of error types also supports error analytics, a program for deepening reliability through strategies for regulating and probing error.

Long-Term Potentiation (LTP) is a kind of synaptic plasticity that many contemporary neuroscientists believe is a component in mechanisms of memory. This essay describes the discovery of LTP and the development of the LTP research program. The story begins in the 1950's with the discovery of synaptic plasticity in the hippocampus (a medial temporal lobe structure now associated with memory), and it ends in 1973 with the publication of three papers sketching the future course of the LTP research program. The (...) making of LTP was a protracted affair. Hippocampal synaptic plasticity was initially encountered as an experimental tool, then reported as a curiosity, and finally included in the ontic store of the neurosciences. Early researchers were not investigating the hippocampus in search of a memory mechanism; rather, they saw the hippocampus as a useful experimental model or as a structure implicated in the etiology of epilepsy. The link between hippocampal synaptic plasticity and learning or memory was a separate conceptual achievement. That link was formulated in at least three different ways at different times: reductively (claiming that plasticity is identical to learning), analogically (claiming that plasticity is an example or model of learning), and mechanistically (claiming that plasticity is a component in learning or memory mechanisms). The hypothesized link with learning or memory, coupled with developments in experimental techniques and preparations, shaped how researchers understood LTP itself. By 1973, the mechanistic formulation of the link between LTP and memory provided an abstract framework around which findings from multiple perspectives could be integrated into a multifield research program. (shrink)

“What is a gene?” is an important philosophical question that has been asked over and over. This paper approaches this question by understanding it as the individuation problem of genes, because it implies the problem of identifying genes and identifying a gene presupposes individuating the gene. I argue that there are at least two levels of the individuation of genes. The transgenic technique can individuate “a gene” as an individual while the technique of gene mapping in classical genetics can only (...) individuate “a gene” as a type or a kind. The two levels of individuation involve different techniques, different objects that are individuated, and different references of the term “gene”. Based on the two levels of individuation, I discuss important philosophical implications including the relationship between individuality and individuation and that between individuals and kinds in experimental contexts. I also suggest a new gene conception, calling it “the transgenic conception of the gene.”. (shrink)

A striking characteristic of the highly successful techniques in molecular biology is that they are derived from natural systems. RNA interference, for example, utilises a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other examples include restriction enzymes, the polymerase chain reaction, green fluorescent protein and CRISPR-Cas. I propose that biologists exploit natural molecular mechanisms for their effectors’ activity and biological specificity. I also show that the developmental trajectory of novel techniques in molecular biology, such as RNAi, is (...) four characteristic phases. The first phase is discovery of a biological phenomenon, typically as curiosity driven research. The second is identification of the mechanism’s trigger, the effector and biological specificity. The third is the application of the technique. The final phase is the maturation and refinement of the molecular biology technique. The development of new molecular biology techniques from nature is crucial for biological research. These techniques transform scientific knowledge and generate new knowledge. (shrink)

This thesis aims to propose and defend a new way of analysing and understanding the origin of genetics (from Mendel to Bateson). Traditionally philosophers used to analyse the history of genetics in terms of theories. However, I will argue that this theory-based approach is highly problematic. In Chapter 1, I shall critically review the theory-driven approach to analysisng the history of genetics and diagnose its problems. In Chapter 2, inspired by Kuhn’s concept “exemplar”, I shall make a new interpretation of (...) exemplar and introduce an exemplar-based approach. Before introducing my exemplar-based analysis, I find it necessary to scrutinise the origin of genetics from Mendel to Bateson. In Chapter 3, I shall reinterpret Mendel’s work on Pisum by re-examining Mendel’s paper (1865) and its historical research context. In Chapter 4, by carefully examining the conceptual changes, I argue that the rediscovery event in 1900 should be better characterised as attempts of incorporating Mendel’s work with the work of “rediscoverers” (i.e. de Vries, Correns, Tschermak, and Bateson) rather than a mere reintroduction to Mendel’s work. In Chapter 5, I shall use the exemplar-based approach to analysing and interpreting the origin of genetics from Mendel to Bateson. In Chapter 6, I shall defend my exemplar-based characterisation of the origin of genetics by dismissing the potential responses from the theory-driven one, critically examining a potential mechanism-based analysis, and making the further notes on the implication of taking the exemplar-based approach to investigate scientific practice. (shrink)

John Cook Wilson (1849–1915) was Wykeham Professor of Logic at New College, Oxford and the founder of ‘Oxford Realism’, a philosophical movement that flourished at Oxford during the first decades of the 20th century. Although trained as a classicist and a mathematician, his most important contribution was to the theory of knowledge, where he argued that knowledge is factive and not definable in terms of belief, and he criticized ‘hybrid’ and ‘externalist’ accounts. He also argued for direct realism in perception, (...) criticizing both empiricism and idealism, and argued for a moderate nominalist view of universals as being in rebus and only ‘apprehended’ by their particulars. His influence helped swaying Oxford away from idealism and, through figures such as H. A. Prichard, Gilbert Ryle, or J. L. Austin, his ideas were also to some extent at the origin of ‘moral intuitionism’ and ‘ordinary language philosophy’ which defined much of Oxford philosophy until the second half of the twentieth-century. Nevertheless, his name and legacy were all but forgotten for generations after World War II. Still, his views on knowledge are with us today, being in part at work in the writings of philosophers as diverse as John McDowell, Charles Travis, and Timothy Williamson. (shrink)

Whereas an inference (deductive as well as inductive) is usually viewed as being valid in virtue of its argument form, the present paper argues that scientific reasoning is material inference, i.e., justified in virtue of its content. A material inference is licensed by the empirical content embodied in the concepts contained in the premises and conclusion. Understanding scientific reasoning as material inference has the advantage of combining different aspects of scientific reasoning, such as confirmation, discovery, and explanation. This approach explains (...) why these different aspects (including discovery) can be rational without conforming to formal schemes, and why scientific reasoning is local, i.e., justified only in certain domains and contingent on particular empirical facts. The notion of material inference also fruitfully interacts with accounts of conceptual change and psychological theories of concepts. (shrink)

Scientific anomalies are observations and facts that contradict current scientific theories and they are instrumental in scientific theory change. Philosophers of science have approached scientific theory change from different perspectives as Darden (Theory change in science: Strategies from Mendelian genetics, 1991) observes: Lakatos (In: Lakatos, Musgrave (eds) Criticism and the growth of knowledge, 1970) approaches it as a progressive “research programmes” consisting of incremental improvements (“monster barring” in Lakatos, Proofs and refutations: The logic of mathematical discovery, 1976), Kuhn (The structure (...) of scientific revolutions, 1996) observes that changes in “paradigms” are instigated by a crisis from some anomaly, and Hanson (In: Feigl, Maxwell (eds) Current issues in the philosophy of science, 1961) proposes that discovery does not begin with hypothesis but with some “problematic phenomena requiring explanation”. Even though anomalies are important in all of these approaches to scientific theory change, there have been only few investigations into the specific role anomalies play in scientific theory change. Furthermore, much of these approaches focus on the theories themselves and not on how the scientists and their experiments bring about scientific change (Gooding, Experiment and the making of meaning: Human agency in scientific observation and experiment, 1990). To address these issues, this paper approaches scientific anomaly resolution from a meaning construction point of view. Conceptual integration theory (Fauconnier and Turner, Cogn Sci 22:133–187, 1996; The way we think: Conceptual blending and mind’s hidden complexities, 2002) from cognitive linguistics describes how one constructs meaning from various stimuli, such as text and diagrams, through conceptual integration or blending. The conceptual integration networks that describe the conceptual integration process characterize cognition that occurs unconsciously during meaning construction. These same networks are used to describe some of the cognition while resolving an anomaly in molecular genetics called RNA interference (RNAi) in a case study. The RNAi case study is a cognitive-historical reconstruction (Nersessian, In: Giere (ed) Cognitive models of science, 1992) that reconstructs how the RNAi anomaly was resolved. This reconstruction traces four relevant molecular genetics publications in describing the cognition necessary in accounting for how RNAi was resolved through strategies (Darden 1991), abductive reasoning (Peirce, In: Hartshorne, Weiss (eds) Collected papers, 1958), and experimental reasoning (Gooding 1990). The results of the case study show that experiments play a crucial role in formulating an explanation of the RNAi anomaly and the integration networks describe the experiments’ role. Furthermore, these results suggest that RNAi anomaly resolution is embodied. It is embodied in a sense that cognition described in the cognitive-historical reconstruction is experientially based. (shrink)

There has been relatively little effort to provide a systematic overview of different forms of exploratory experimentation (EE). The present paper examines the growing subdiscipline of nanotoxicology and suggests that it illustrates at least four ways that researchers can engage in EE: searching for regularities; developing new techniques, simulation models, and instrumentation; collecting and analyzing large swaths of data using new experimental strategies (e.g., computer-based simulation and "high-throughput" instrumentation); and structuring an entire disciplinary field around exploratory research agendas. In order (...) to distinguish these and other activities more effectively, the paper proposes a taxonomy that includes three dimensions along which types of EE vary: (1) the aim of the experimental activity, (2) the role of theory in the activity, and (3) the methods or strategies employed for varying experimental parameters. (shrink)

In this paper I respond to Wim van der Steen''s arguments against the supposed current overemphasis on norms ofcoherence andinterdisciplinary integration in biology. On the normative level, I argue that these aremiddle-range norms which, although they may be misapplied in short-term attempts to solve (temporarily?) intractable problems, play a guiding role in the longer-term treatment of biological problems. This stance is supported by a case study of apartial success story, the development of the one gene — one enzyme hypothesis. As (...) that case shows, thegoal of coherent interdisciplinary integration not only provides guidance for research, but also provides the standard for recognizingfailed integrations of the sort that van der Steen criticizes. (shrink)

In his influential paper, 'Why Was the Logic of Discovery Abandoned?', Laudan contends that there has been no philosophical rationale for a logic of discovery since the emergence of consequentialism in the 19th century. It is the purpose of this paper to show that consequentialism does not involve the rejection of all types of logic of discovery. Laudan goes too far in his interpretation of the historical shift from generativism to consequentialism, and his claim that the context of pursuit belongs (...) to neither discovery nor justification is based on narrow interpretations of the contexts of discovery and justification. As a result, Laudan draws unwarranted conclusions concerning both the early and contemporary defenders of a logic of discovery. A methodological logic of discovery - which involves self-corrective methods of hypothesis generation that promote the long-term goals of science and which require consequential support for justification - is a type of logic of discovery that survives the shift to consequentialism. (shrink)

The biological effects of low doses of toxic and carcinogenic chemicals are currently a matter of significant scientific controversy. This paper argues that philosophers of science can contribute to alleviating this controversy by examining it with the aid of a novel account of scientific anomaly. Specifically, analysis of contemporary research on chemical hormesis (i.e., alleged beneficial biological effects produced by low doses of substances that are harmful at higher doses) suggests that scientists may initially describe anomalous phenomena in terms of (...) multiple distinct "characterizations," each of which is compatible with current empirical evidence. By focusing attention on this feature of scientific anomalies, philosophers of science can alleviate the controversy over low-dose chemical effects in at least two ways: (1) they can pinpoint the significant ways in which particular characterizations frame the controversy, and (2) they can identify the methodological value judgments at stake in researchers' choice of characterizations. (shrink)

The discovery of RNA interference in 1998 has made a lasting impact on biological research. Identifying the regulatory role of small RNAs changed the modes of molecular biological inquiry as well as biologists' understanding of genetic regulation. This article examines the early years of small RNA biology's success story. I query which factors had to come together so that small RNA research came into life in the blink of an eye. I primarily look at scientific repertoires as facilitators of rapid (...) scientific change. I show that for a short period of time, between the years 1998 and 2002, different model organism communities, investigative strategies, technological innovations, and research interests could be successfully aligned to take small RNA research off the ground. I discuss how the keystone discoveries were situated in specific experimental traditions and what strategies were employed to establish these discoveries as more general phenomena. Providing thus a practice-based approach of rapid scientific change, I ask how to relate the change in propositional bits of scientific knowledge with changes in scientific practice. (shrink)

This paper explores multiple experimental interventions in molecular biology. By “multiple,” we mean that molecular biologists often use different modes of experimental interventions in a series of experiments for one and the same subject. In performing such a series of experiment, scientists may use different modes of interventions to realize plural goals such as testing given hypotheses and exploring novel phenomena. In order to illustrate this claim, we develop a framework of multiple modes of experimental interventions to analyze a series (...) of experiments for a single subject. Our argument begins with a brief characterization of Craver and Darden’s taxonomy of experiments, because the taxonomy they have made implies various modes of interventions. We propose to extract two interventional directions and two interventional effects from their taxonomy as the basis of classification. The vertical or inter-level direction means that an intervention is performed between different levels of organization and the horizontal or inter-stage direction means that an intervention is performed between different stages of a mechanism. Interventions may produce an excitatory or an inhibitory effect. As a consequence, we can classify modes of interventions according to different directions and effects. We illustrate our claims by doing a case study of the PaJaMo experiment, which is a series of experiments for a single subject. The final goal in this paper is to provide a taxonomy of characteristics of experimentation in which the PaJaMo experiment is adequately located. (shrink)

The aim of the present paper is to contribute to the discussion on the constitutive a priori in science by linking it with the discussion on scientific laws and theories, in such a way to show how the different senses of the notion of constitutive a priori are not incompatible to each other and that they can be precised in a unified, though differentiated, manner.

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 discuss the problem of scientific laws in general and laws of biology in particular. After reviewing the debate around the existence of laws in biology, I examine the subject in the light of the structuralist notion of a fundamental law and argue for the law of matching as the fundamental law of genetics.

William Bateson (1861-1926) has long occupied a controversial role in the history of biology at the turn of the twentieth century. For the most part, Bateson has been situated as the British translator of Mendel or as the outspoken antagonist of W. F. R. Weldon and Karl Pearson's biometrics program. Less has been made of Bateson's transition from embryologist to advocate for discontinuous variation, and the precise role of British and American influences in that transition, in the years leading up (...) to the publication of his massive Materials for the Study of Variation (1894). In this paper, I first attempt to trace Bateson's development in his early career before turning to search for the development of the moniker "anti-Darwinist" that has been attached to Bateson in well-known histories of the neo-Darwinian Synthesis. (shrink)

In 1958, Francis Crick distinguished the flow of information from the flow of matter and the flow of energy in the mechanism of protein synthesis. Crick’s claims about information flow and coding in molecular biology are viewed from the perspective of a new characterization of mechanisms and from the perspective of information as holding a key to distinguishing work in molecular biology from that of biochemistry in the 1950s–1970s . Flow of matter from beginning to end does not occur in (...) the protein synthesis mechanism; flow of information does. The flow of information and coding in molecular biological mechanisms are distinguished, on the one hand, from formal information theory, and, on the other, from information as used in cognitive neuroscience, where information and representation are often coupled. (shrink)

Please follow the link below for the most recent version of this paper: http://philsci-archive.pitt.edu/archive/00004005/.

Metaphor influences the construction of biological models and theories and the analysis of its use can reveal important tools of thought. Some aspects of biological organisation are investigated through the analysis of metaphors associated with treating biosystems as a kind of text. In particular, the use of glue and verbs is considered. Some of the reasons why glue is important in the construction of hierarchies are pursued in the light of specific examples, and some of the conceptual links between glue (...) in biology and other domains is discussed. Verbs are shown to be important in the construction of networks. Some of the relations between glue, verb and text are considered and the text metaphor is placed within a much broader context of ideas associated with form, relation and system. The paper concludes with comments on the nature of biological information and the need for extending or better understanding the verbal vocabulary. (shrink)

We respond to Morris and Richardson 's claim that Pickering and Chater's arguments about the lack of a relation between cognitive science and folk psychology are flawed. We note that possible controversies about the appropriate uses for the two terms do not affect our arguments. We then address their claim that computational explanation of knowledge-rich processes has proved possible in the domains of problem solving, scientific discovery, and reasoning. We argue that, in all cases, computational explanation is only possible for (...) aspects of those processes that do not make reference to general knowledge. We conclude that consideration of the issues raised by Morris and Richardson reinforces our original claim that there are two fundamentally distinct projects for understanding the mind, one based on justification, and the other on computational explanation, and that these apply to non-overlapping aspects of mental life. (shrink)

Part I Introduction The specific problem adressed in this thesis is: what is the rational use of theory and experiment in the process of scientific discovery, in theory and in the practice of drug research for Parkinson’s disease? The thesis aims to answer the following specific questions: what is: 1) the structure of a theory?; 2) the process of scientific reasoning?; 3) the route between theory and experiment? In the first part I further discuss issues about rationality in science as (...) introduction to part II, and I present an overview of my case-study of neuropharmacology, for which I interviewed researchers from the Groningen Pharmacy Department, as an introduction to part III. Part II Discovery In this part I discuss three theoretical models of scientific discovery according to studies in the fields of Logic, Cognition, and Computation. In those fields the structure of a theory is respectively explicated as: a set of sentences; a set of associated memory chunks; and as a computer program that can generate the observed data. Rationality in discovery is characterized by: finding axioms that imply observation sentences; heuristic search for a hypothesis, as part of problem solving, by applying memory chunks and production rules that represent skill; and finding the shortest program that generates the data, respectively. I further argue that reasoning in discovery includes logical fallacies, which are neccesary to introduce new hypotheses. I also argue that, while human subjects often make errors in hypothesis evaluation tasks from a logical perspective, these evaluations are rational given a probabilistic interpretation. Part III Neuropharmacology In this last part I discusses my case-study and a model of discovery in a practice of drug research for Parkinson’s disease. I discuss the dopamine theory of Parkinson’s disease and model its structure as a qualitative differential equation. Then I discuss the use and reasons for particular experiments to both test a drug and explore the function of the brain. I describe different kinds of problems in drug research leading to a discovery. Based on that description I distinguish three kinds of reasoning tasks in discovery, inference to: the best explanation, the best prediction and the best intervention. I further demonstrate how a part of reasoning in neuropharmacology can be computationally modeled as qualitative reasoning, and aided by a computer supported discovery system. (shrink)

Philosophers of science have in recent years become increasingly interested in the notion of interdisciplinarity. One important form interdisciplinarity can take is that of a dynamic exchange of problems and solutions between disciplines—what has recently been called problem-feeding. On this model problems arising within specific disciplines are sometimes solved more effectively by, or in collaboration with, other disciplines. In this paper we explore this model as a framework for thinking about, and actively structuring, interdisciplinary research. We point to the applicability (...) of the problem-feeding model, and to some of the prerequisites of problem-feeding interdisciplinarity, highlighting in particular the harmonisation of goals and the establishment of mutual trust between disciplines. (shrink)

Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, to (...) provide structure to scientific problems, delegates tasks whose execution generates the term’s expressed content in a given instance. This treatment of levels does not diminish the concept’s general importance to science, but rather allows for its use in, and usefulness for, scientific practice to be better contextualized to particular tasks encompassing varying breadths of activity. (shrink)

In this paper, I critique two conceptions of mechanisms, namely those put forth by Stuart Glennan (Erkenntnis 44:49–71, 1996; Philosophy of Science 69:S342–S353, 2002) and Machamer et al. (Philosophy of Science 67:1–25, 2000). Glennan’s conception, I argue, cannot account for mechanisms involving negative causation because of its interactionist posture. MDC’s view encounters the same problem due to its reificatory conception of activities—this conception, I argue, entails an onerous commitment to ontological dualism. In the place of Glennan and MDC, I propose (...) a “modified conception” of mechanisms, which (a) obviates the problem of negative causation by reinterpreting MDC’s activities according to a “descriptivist” account, and (b) avoids MDC’s problem by postulating a monistic ontology of entities. Thus, by solving these problems, my modified conception offers a cogent, more adequate alternative to Glennan’s and MDC’s conceptions of mechanisms. (shrink)

This article presents a reconstruction of the so-called classical, formal or Mendelian genetics, which is intended to be more complete and adequate than existing reconstructions. This reconstruction has been carried out with the instruments, duly modified and extended with respect to the case under consideration, of the structuralist conception of theories. The so-called Mendel’s Laws, as well as linkage genetics and gene mapping are formulated in a precise manner while the global structure of genetics is represented as a theory-net. These (...) results are of methodological, philosophical and didactical relevance. (shrink)