Philosophers have proposed various kinds of relations between Mendelian genetics and molecular biology: reduction, replacement, explanatory extension. This paper argues that the two fields are best characterized as investigating different, serially integrated, hereditary mechanisms. The mechanisms operate at different times and contain different working entities. The working entities of the mechanisms of Mendelian heredity are chromosomes, whose movements serve to segregate alleles and independently assort genes in different linkage groups. The working entities of numerous mechanisms of molecular biology are larger (...) and smaller segments of DNA plus related molecules. Discovery of molecular DNA mechanisms filled black boxes that were noted, but unilluminated, by Mendelian genetics. (shrink)

This paper analyzes the generation and function of hitherto ignored or misrepresented interfield theories , theories which bridge two fields of science. Interfield theories are likely to be generated when two fields share an interest in explaining different aspects of the same phenomenon and when background knowledge already exists relating the two fields. The interfield theory functions to provide a solution to a characteristic type of theoretical problem: how are the relations between fields to be explained? In solving this problem (...) the interfield theory may provide answers to questions which arise in one field but cannot be answered within it alone, may focus attention on domain items not previously considered important, and may predict new domain items for one or both fields. Implications of this analysis for the problems of reduction and the unity and progress of science are mentioned. (shrink)

Philosophers of neuroscience have traditionally described interfield integration using reduction models. Such models describe formal inferential relations between theories at different levels. I argue against reduction and for a mechanistic model of interfield integration. According to the mechanistic model, different fields integrate their research by adding constraints on a multilevel description of a mechanism. Mechanistic integration may occur at a given level or in the effort to build a theory that oscillates among several levels. I develop this alternative model using (...) a putative exemplar of reduction in contemporary neuroscience: the relationship between the psychological phenomena of learning and memory and the electrophysiological phenomenon known as Long-Term Potentiation. A new look at this historical episode reveals the relative virtues of the mechanistic model over reduction as an account of interfield integration. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with the problem pursued. (...) Solving a complex problem need not require theoretical unification or the stable synthesis of different biological fields, as items of knowledge from traditional disciplines can be related solely for the purposes of a specific problem. Apart from the development of genuine interfield theories, successful integration can be effected by smaller epistemic units (concepts, methods, explanations) being linked. Unification or integration is not an aim in itself, but needed for the aim of solving a particular scientific problem, where the problem's nature determines the kind of intellectual integration required. (shrink)

In the context of mechanistic explanation, reductionistic research pursues a decomposition of complex systems into their component parts and operations. Using research on the mechanisms responsible for circadian rhythms, I consider both the gains that have been made by discovering genes and proteins that figure in these intracellular oscillators and also highlight the increasingly recognized need to understand higher-level integration, both between cells in the central oscillator and between the central and peripheral oscillators. This history illustrates a common need to (...) complement reductionistic inquiry with investigations at higher-levels. Unlike most other accounts of reduction, the mechanistic framework accommodates this complementary relationship between reductionistic and systems approaches. (shrink)

Many studies of the unification of science focus on the theories of different disciplines. The model for integration is the theory reduction model. This paper argues that the embodiment of theories in scientists, and the institutions in which scientists work and the instruments they employ, are critical to the sort of integration that actually occurs in science. This paper examines the integration of scientific endeavors that emerged in cell biology in the period after World War II when the development of (...) cell fractionation and electron microscopy made serious investigations of cell organelles possible. One surprising feature of such integration is that it generated further disintegration as the new institutions of cell biology separated the practitioners of the new discipline from other, closely related biological disciplines. (shrink)

Chronobiology, especially the study of circadian rhythms, provides a model scientific field in which philosophers can study how investigators from a variety of disciplines working at different levels of organization are each contributing to a multi-level account of the responsible mechanism. I focus on how the framework of mechanistic explanation integrates research designed to decompose the mechanism with efforts directed at recomposition that relies especially on computation models. I also examine how recently the integration has extended beyond basic research to (...) the processes through which the disruption of circadian rhythms contributes to disease, including various forms of cancer. Understanding these linkages has been facilitated by discoveries about how circadian mechanisms interact with mechanisms involved in other physiological processes, including the cell cycle and the immune system. (shrink)

By reference to Maxwell's kinetic theory, one feature of hypothetico-deductivism is defended. A scientist need make no inference to a hypothesis when he first proposes it. He may have no reason at all for thinking it is true. Yet it may be worth considering. In developing his kinetic theory there were central assumptions Maxwell made (for example, that molecules are spherical, that they exert contact forces, and that their motion is linear) that he had no reason to believe true. In (...) this paper I develop a position that explains why they were worth considering, and that rejects the retroductive position that a hypothesis is worth considering when, if true, it would explain the observed data. (shrink)

The official model of explanation proposed by the logical empiricists, the covering law model, is subject to familiar objections. The goal of the present paper is to explore an unofficial view of explanation which logical empiricists have sometimes suggested, the view of explanation as unification. I try to show that this view can be developed so as to provide insight into major episodes in the history of science, and that it can overcome some of the most serious difficulties besetting the (...) covering law model. (shrink)

Reductionism encompasses a set of ontological, epistemological, and methodological claims about the relation of different scientific domains. The basic question of reduction is whether the properties, concepts, explanations, or methods from one scientific domain (typically at higher levels of organization) can be deduced from or explained by the properties, concepts, explanations, or methods from another domain of science (typically one about lower levels of organization). Reduction is germane to a variety of issues in philosophy of science, including the structure of (...) scientific theories, the relations between different scientific disciplines, the nature of explanation, the diversity of methodology, and the very idea of theoretical progress, as well as to numerous topics in metaphysics and philosophy of mind, such as emergence, mereology, and supervenience. (shrink)

This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected both to (...) David Lewis’ notion of “influence” and also with the extent to which a causal relation approximates to the ideal of one cause–one effect. Interrelations among these notions and their possible biological significance are also discussed. (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)

This chapter focuses on the view that diseases comprise natural kinds and how this view is in conflict with the essentialist picture of natural kinds as championed by Kripke and Putnam. This essentialist depiction of natural kinds contends that in order for a class of entities to be a natural kind, it is required that all and only members of the class instantiate very specific properties that explain the presence of any other properties typically associated with being a member of (...) the kind; these privileged properties constitute the “essence” of the kind. The problem is that the essentialist picture provides only two options, none of which is desirable: satisfy the essentialist desiderata by locating some etiological feature both necessary and sufficient for kind membership, or reject the thought that similarity between disease instances can be understood in terms of natural kinds. (shrink)

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is (...) concerned, at its core, with justifying the use of multiple, idealized models in population biology. (shrink)

The two major modern accounts of explanation are the causal and unification accounts. My aim in this paper is to provide a kind of unification of the causal and the unification accounts, by using the central technical apparatus of the unification account to solve a central problem faced by the causal account, namely, the problem of determining which parts of a causal network are explanatorily relevant to the occurrence of an explanandum. The end product of my investigation is a causal (...) account of explanation that has many of the advantages of the unification account. (shrink)

The recent literature in philosophy of biology has drawn attention to the different sorts of explanations proffered in the biological sciences—we have molecular, biomedical, and evolutionary explanations. Do these explanations all have a common structure or relation that they seek to capture? This paper will answer in the negative. I defend a pluralistic and pragmatic approach to explanation. Using examples from classical population genetics, I argue that formal demonstrations, and even strictly “mathematical truths,” may serve as explanatory in different historical (...) contexts. (shrink)

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)

In recent cancer research, strong and apparently conflicting epistemological stances have been advocated by different research teams in a mist of an ever-growing body of knowledge ignited by ever-more perplexing and non-conclusive experimental facts: in the past few years, an 'organicist' approach investigating cancer development at the tissue level has challenged the established and so-called 'reductionist' approach focusing on disentangling the genetic and molecular circuitry of carcinogenesis. This article reviews the ways in which 'organicism' and 'reductionism' are used and opposed (...) in this context, with an aim at clarifying the debate. Methodological, epistemological and ontological implications of both approaches are discussed. We argue that the 'organicist/reductionist' opposition in the present case of carcinogenesis is more a matter of diverging heuristics than a claim about theoretical or ontological (ir)reducibility. As a matter of fact, except for the downward causation claim, which we question, we argue that the organicist arguments are compatible with the reductionist approach. Moreover, we speculate that both approaches, which currently focus on specific entities i.e., genes versus tissues, will need to shift their conceptual frameworks to studying complex arrays of relationships potentially ranging over several levels of entities, as is the case with 'systems biology'. (shrink)

It is a common complaint that antireductionist arguments are primarily negative. Here I describe an alternative nonreductionist epistemology based on considerations taken from multidisciplinary research in biology. The core of this framework consists in seeing investigation as coordinated around sets of problems (problem agendas) that have associated criteria of explanatory adequacy. These ideas are developed in a case study, the explanation of evolutionary innovations and novelties, which demonstrates the applicability and fruitfulness of this nonreductionist epistemological perspective. This account also bears (...) on questions of conceptual change and theory structure in philosophy of science. †To contact the author, please write to: Department of Philosophy, University of Minnesota, 831 Heller Hall, 271 19th Ave. S., Minneapolis, MN 55455; e‐mail: [email protected]. (shrink)

A precise formulation of the structure of modern evolutionary theory has proved elusive. In this paper, I introduce and develop a formal approach to the structure of population genetics, evolutionary theory's most developed sub-theory. Under the semantic approach, used as a framework in this paper, presenting a theory consists in presenting a related family of models. I offer general guidelines and examples for the classification of population genetics models; the defining features of the models are taken to be their state (...) spaces, parameters, and laws. The suggestions regarding the various aspects of the characterization of population genetics models provide an outline for further detailed research. (shrink)

This paper argues that conceptualizing unity as "interconnection" (rather than reduction) provides a more fruitful and versatile framework for the philosophical study of scientific unification. Building on the work of Darden and Maull, Kitcher, and Kincaid, I treat unity as a relationship between fields: two fields become more integrated as the number and/or significance of interfield connections grow. Even when reduction fails, two theories or fields can be unified (integrated) in significant ways. I highlight two largely independent dimensions of unification. (...) Fields are theoretically unified to the extent that we understand how the ontologies, concepts, and generalizations of these fields are connected. (Reductionism is one form of theoretical unity, but not the only form). Fields are practically unified through heuristic connections (e.g., using the heuristics of one field to generate hypotheses in another field) and by the development of methods for integrating the qualitatively distinct bodies of data generated by the two fields. I discuss the relationship between paleontological and neontological systematics to illustrate the utility of conceptualizing unity as interconnection. (shrink)

By what mechanisms of organizational and institutional change do different specialties succeed in accommodating and working with one another? How do these mechanisms function over time to support and retard the emergence and stability of new knowledge? This paper considers two such mechanisms, metawork and common knowledge. These mechanisms integrate specialties by making the activities of multiple specialties dependent upon one another, and by segmenting the common effort from the parent specialties. Integration of specialties can lead to the development of (...) new specialties.Integration is facilitated and impeded by the anchoring of specialties in the system of institutions that participate in research. Host organizations, degree programs, sponsors, associations, regulators, and other organizations provide resources and impose demands that shape research. Some of these impacts are obvious and direct; others are indirect and more subtle.The research specialties form a network in which connections constantly form and reform, and in which the influence of different anchoring institutions are constantly waxing and waning. The complexity of connections and their pattern of change are especially obvious in the life sciences, which are an especially good place to study problems of integration. (shrink)

Somatic mutation plays a key role in transforming normal cells into cancerous cells. The analysis of cancer progression therefore requires the study of how point mutations and chromosomal mutations accumulate in cellular lineages. The spread of somatic mutations depends on the mutation rate, the number of cell divisions in the history of a cellular lineage, and the nature of competition between different cellular lineages. We consider how various aspects of tissue architecture and cellular competition affect the pace of mutation accumulation. (...) We also discuss the rise and fall of somatic mutation rates during cancer progression. BioEssays 26:291–299, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Between 1940 and 1970 pioneers in the new field of cell biology discovered the operative parts of cells and their contributions to cell life. They offered mechanistic accounts that explained cellular phenomena by identifying the relevant parts of cells, the biochemical operations they performed, and the way in which these parts and operations were organised to accomplish important functions. Cell biology was a revolutionary science but in this book it also provides fuel for yet another revolution, one that focuses on (...) the very conception of science itself. Laws have traditionally been regarded as the primary vehicle of explanation, but in the emerging philosophy of science it is mechanisms that do the explanatory work. Bechtel emphasises how mechanisms were discovered, focusing especially on the way in which new instruments made these inquiries possible. He also describes how new journals and societies provided institutional structure to this new enterprise. (shrink)

one takes to be the most salient, any pair could be judged more similar to each other than to the third. Goodman uses this second problem to showthat there can be no context-free similarity metric, either in the trivial case or in a scientifically ...

This fine collection of essays by a leading philosopher of science presents a defence of integrative pluralism as the best description for the complexity of scientific inquiry today. The tendency of some scientists to unify science by reducing all theories to a few fundamental laws of the most basic particles that populate our universe is ill-suited to the biological sciences, which study multi-component, multi-level, evolved complex systems. This integrative pluralism is the most efficient way to understand the different and complex (...) processes - historical and interactive - that generate biological phenomena. This book will be of interest to students and professionals in the philosophy of science. (shrink)

Approaches to explanation -- Causal and explanatory relevance -- The kairetic account of /D making -- The kairetic account of explanation -- Extending the kairetic account -- Event explanation and causal claims -- Regularity explanation -- Abstraction in regularity explanation -- Approaches to probabilistic explanation -- Kairetic explanation of frequencies -- Kairetic explanation of single outcomes -- Looking outward -- Looking inward.

Carl Craver investigates what we are doing when we sue neuroscience to explain what's going on in the brain.

As Aristotle stated, scientific explanation is based on deductive argument--yet, Wesley C. Salmon points out, not all deductive arguments are qualified explanations. The validity of the explanation must itself be examined. _Four Decades of Scientific Explanation_ provides a comprehensive account of the developments in scientific explanation that transpired in the last four decades of the twentieth century. It continues to stand as the most comprehensive treatment of the writings on the subject during these years. Building on the historic 1948 essay (...) by Carl G. Hempel and Paul Oppenheim, "Studies in the Logic of Explanation,” which introduced the deductive-nomological model on which most work on scientific explanation was based for the following four decades, Salmon goes beyond this model's inherent basis of describing empirical knowledge to tells us “not only _what,_ but also _why_.” Salmon examines the predominant models in chronological order and describes their development, refinement, and criticism or rejection. _Four Decades of Scientific Explanation_ underscores the need for a consensus of approach and ongoing evaluations of methodology in scientific explanation, with the goal of providing a better understanding of natural phenomena. (shrink)

This chapter explores the idea that causal inference is warranted if and only if the mechanism underlying the inferred causal association is identified. This mechanistic stance is discernible in the epidemiological literature, and in the strategies adopted by epidemiologists seeking to establish causal hypotheses. But the exact opposite methodology is also discernible, the black box stance, which asserts that epidemiologists can and should make causal inferences on the basis of their evidence, without worrying about the mechanisms that might underlie their (...) hypotheses. I argue that the mechanistic stance is indeed a bad methodology for causal inference. However, I detach and defend a mechanistic interpretation of causal generalisations in epidemiology as existence claims about underlying mechanisms. (shrink)

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because (...) they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations. (shrink)

1. A Historical Look at Unity 2. Field Guide to Modern Concepts of Reduction and Unity 3. Kitcher's Revisionist Account of Unification 4. Critics of Unity 5. Integration Instead of Unity 6. Reduction via Mechanisms 7. Case Studies in Reduction and Unification across the Disciplines.

The standard view of explanation in science---the covering law model---assumes that knowledge of laws lies at the basis of our ability to explain phenomena. But in fact most of the high-level claims in science are ceteris paribus generalizations, which are false unless certain precise conditions obtain. Given the explanatory force of ceteris paribus generalizations but the paucity of true laws, the covering law model of explanation must be false. There is, it is argued, a trade-off between truth and explanatory power.