Philosophy of Experimental Biology explores some central philosophical issues concerning scientific research in experimental biology, including genetics, biochemistry, molecular biology, developmental biology, neurobiology, and microbiology. It seeks to make sense of the explanatory strategies, concepts, ways of reasoning, approaches to discovery and problem solving, tools, models and experimental systems deployed by scientific life science researchers and also integrates developments in historical scholarship, in particular the New Experimentalism. It concludes that historical explanations of scientific change that are based on local laboratory (...) practice need to be supplemented with an account of the epistemic norms and standards that are operative in science. This book should be of interest to philosophers and historians of science as well as to scientists. (shrink)

_Insensitive Semantics_ is an overview of and contribution to the debates about how to accommodate context sensitivity within a theory of human communication, investigating the effects of context on communicative interaction and, as a corollary, what a context of utterance is and what it is to be in one. Provides detailed and wide-ranging overviews of the central positions and arguments surrounding contextualism Addresses broad and varied aspects of the distinction between the semantic and non-semantic content of language Defends a distinctive (...) and explanatorily powerful combination of semantic minimalism and speech act pluralism Confronts core problems which not only run to the heart of philosophy of language and linguistics, but which arise in epistemology, metaphysics, and moral philosophy as well. (shrink)

A historical and critical analysis of the concept of the gene that attempts to provide new perspectives and metaphors for the transformation of biology and its philosophy.

The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher eukaryotes (...) and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoletic development and phenotypic variation. BioEssays 25:930-939,2003. (C) 2003 Wiley Periodicals, Inc. (shrink)

The paper argues against the central dogma and its interpretation by C. Kenneth Waters and Alex Rosenberg. I argue that certain phenomena in the regulation of gene expression provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. My thesis of 'molecular epigenesis' with its three classes of phenomena, sequence 'activation', 'selection', and 'creation', is exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA editing. It argues (...) that other molecular resources share the causal role of genes; the sequence specificity for the linear sequence of any gene product is distributed between the coding sequence, cis-acting sequences, trans-acting factors, environmental signals, and the contingent history of the cell (thesis of distributed causal specificity). I conclude that the central dogma has unnecessarily restricted genetic research to the sequencing of protein-coding genes, unilinear pathway analyses, and the focus on exclusive specificity. (shrink)

According to Conceptual Role Semantics, the meaning of a representation is the role of that representation in the cognitive life of the agent, e.g. in perception, thought and decision-making. It is an extension of the well known "use" theory of meaning, according to which the meaning of a word is its use in communication and more generally, in social interaction. CRS supplements external use by including the role of a symbol inside a computer or a brain. The uses appealed to (...) are not just actual, but also counterfactual: not only what effects a thought does have, but what effects it would have had if stimuli or other states had differed. The view has arisen separately in philosophy and in cognitive science. The source of the view is Wittgenstein and Sellars, but the source in contemporary philosophy is a series of papers by Harman and Field. Other proponents in philosophy have included Block, Horwich, Loar, McGinn and Peacocke. In cognitive science, they include Woods and Miller and Johnson-Laird. (shrink)

What should philosophers of science accomplish when they analyze scientific concepts and interpret scientific knowledge? What is concept analysis if it is not a description of the way scientists actually think? I investigate these questions by using Hans Reichenbach's account of the descriptive, critical, and advisory tasks of philosophy of science to examine Karola Stotz and Paul Griffiths' idea that poll-based methodologies can test philosophical analyses of scientific concepts. Using Reichenbach's account as a point of departure, I argue that philosophy (...) of science should identify and clarify epistemic virtues and describe scientific knowledge in relation to these virtues. The role of concept analysis is to articulate scientific concepts in ways that help reveal epistemic virtues and limitations of particular sciences. This means an analysis of the gene concept should help clarify the explanatory power and limitations of gene-based explanations, and should help account for the investigative utility and biases of gene-centered sciences. I argue that a philosophical analysis of gene concept that helps achieve these critical aims should not be rejected on the basis of poll-based studies even if such studies could show that professional biologists don't actually use gene terminology in precise ways corresponding to the philosophical analysis. (shrink)

This paper describes one complete and one ongoing empirical study in which philosophical analyses of the concept of the gene were operationalized and tested against questionnaire data obtained from working biologists to determine whether and when biologists conceive genes in the ways suggested. These studies throw light on how different gene concepts contribute to biological research. Their aim is not to arrive at one or more correct 'definitions' of the gene, but rather to map out the variation in the gene (...) concept and to explore its causes and its effects. (shrink)

Recent work on gene concepts has been influenced by recognition of the extent to which RNA transcripts from a given DNA sequence yield different products in different cellular environments. These transcripts are altered in many ways and yield many products based, somehow, on the sequence of nucleotides in the DNA. I focus on alternative splicing of RNA transcripts (which often yields distinct proteins from the same raw transcript) and on 'gene sharing', in which a single gene produces distinct proteins with (...) the exact same amino acid sequence. These are instances of molecular pleiotropy, in which distinct molecules are derived from a single putative gene. In such cases the cellular and external environments play major roles in determining which protein is produced. Where there is molecular pleiotropy, alternative gene concepts are naturally deployed; molecular epigenesis (revision of sequence-based information by altering molecular conformations or by action of non-informational molecules) plays a major role in orderly development. These results show that gene concepts in molecular biology do, and should, have both structural and functional components. They also show the need for a plurality of gene concepts and reveal fundamental difficulties in stabilizing gene concepts solely by reference to nucleotide sequence. (shrink)

A scientific community cannot practice its trade without some set of received beliefs. These beliefs form the foundation of the "educational initiation that prepares and licenses the student for professional practice". The nature of the "rigorous and rigid" preparation helps ensure that the received beliefs are firmly fixed in the student's mind. Scientists take great pains to defend the assumption that scientists know what the world is like...To this end, "normal science" will often suppress novelties which undermine its foundations. Research (...) is therefore not about discovering the unknown, but rather "a strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education". (shrink)

This book presents a critical analysis of the semantic incommensurability thesis of Thomas Kuhn and Paul Feyerabend. In putting forward the thesis of incommensurability, Kuhn and Feyerabend drew attention to complex issues concerning the phenomenon of conceptual change in science. They raised serious problems about the semantic and logical relations between the content of theories which deploy unlike systems of concepts. Yet few of the more extreme claims associated with incommensurability stand scrutiny. The argument of this book is as follows. (...) The terms of theories with different concepts diverge semantically and the vocabularies of such theories may not be fully intertranslatable. Given the possibility of referential overlap between the terms of conceptually divergent theories, it does not follow that the content of such theories is incomparable. Nor, given the distinction between understanding a language and translation from one language into another, does it follow that the proponents of mutually untranslatable theories are unable to communicate. Neither is it the case that the shift between conceptually divergent theories involves a discontinuous transition between theories which have no common reference or that refer to distinct worlds of their own making. The semantic differences resulting from conceptual variance may be embraced within a thoroughly realist framework on which they are construed as diverse linguistic relations to a fixed and independent reality. -/- The book, which was originally published in 1994, has now been re-issued in the Routledge Revivals series. -/- . (shrink)

Compares classic and contemporary theories of genetics and evolution and explores the role of teleological thought in biology.

PARTI The Philosophical Situation: A Critical Appraisal We must begin with the mistake and find out the truth in it. That is, we must uncover the source of ...

Objectivity Under Attack: a fundamental feature of science is its ideal of objectivity, an ideal that subjects ...

Thomas S. Kuhn's classic book is now available with a new index.

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)

The historian Raphael Falk has described the gene as a ‘concept in tension’ (Falk 2000) – an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology ‘gene’ is no more than a handy term which acquires a specific meaning only in a specific scientific context in which it occurs. Hence the best way to answer the question ‘what is a gene’, and (...) the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences . Finally, we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept looks set to be at as turbulent as the past. (shrink)

(i) Scientific realism is primarily a metaphysical doctrine about the existence and nature of the unobservables of science. (ii) There are good explanationist arguments for realism, most famously that from the success of science, provided abduction is allowed. Abduction seems to be on an equal footing, at least, with other ampliative methods of inference. (iii) We have no reason to believe a doctrine of empirical equivalence that would sustain the underdetermination argument against realism. (iv) The key to defending realism from (...) the pessimistic meta-induction is that we have greatly improved our capacity to understand the unobservable world over recent centuries. (shrink)

This paper investigates what molecular biology has done for our understanding of the gene. I base a new account of the gene concept of classical genetics on the classical dogma that gene differences cause phenotypic differences. Although contemporary biologists often think of genes in terms of this concept, molecular biology provides a second way to understand genes. I clarify this second way by articulating a molecular gene concept. This concept unifies our understanding of the molecular basis of a wide variety (...) of phenomena, including the phenomena that classical genetics explains in terms of gene differences causing phenotypic differences. (shrink)

This paper examines the "causal theory of reference", according to which science aims at the discovery of "essences" which are the objects of reference of natural kind terms (among others). This theory has been advanced as an alternative to traditional views of "meaning", on which a number of philosophical accounts of science have relied, and which have been criticized earlier by the present author. However, this newer theory of reference is shown to be equally subject to fatal internal difficulties, and (...) to be incompatible with actual science as well. Indeed, it rests on assumptions which it shares with the purportedly opposing theory of meaning. Behind those common assumptions is the supposition that the nature of science can be illuminated by an examination of alleged necessities of language which are independent of the results and methods of scientific inquiry. An alternative view of science is proposed, according to which the goals and language of science develop as integral parts of the process of demarcating science from non-science, a process in which the notion of a "reason" gradually assumes a decisive role. On this view, the comparability, competition, and development of scientific ideas are understood without reliance on either common "meanings" or common "references" as fundamental tools of analysis. (shrink)

The linear sequence specification of a gene product is not provided by the target DNA sequence alone but by the mechanisms of gene expressions. The main actors of these mechanisms, proteins and functional RNAs, relay environmental information to the genome with important consequences to sequence selection and processing. This `postgenomic' reality has implications for our understandings of development not as predetermined by genes but as an epigenetic process. Critics of genetic determinism have long argued that the activity of `genes' and (...) hence their contribution to the phenotype depends on intra- and extraorganismal `environmental' elements. As will be shown here, even the mere physical existence of a `gene' is dependent on its phenotypic context. (shrink)

CRS says that the meanings of expressions of a language or other symbol system or the contents of mental states are determined and explained by the way symbols are used in thinking. According to CRS one.

CRS says that the meanings of expressions of a language or other symbol system or the contents of mental states are determined and explained by the way symbols are used in thinking. According to CRS one.

Advances in molecular biological research in the latter half of the twentieth century have made the story of the gene vastly complicated: the more we learn about genes, the less sure we are of what a gene really is. Knowledge about the structure and functioning of genes abounds, but the gene has also become curiously intangible. This collection of essays renews the question: what are genes? Philosophers, historians and working scientists re-evaluate the question in this volume, treating the gene as (...) a focal point of interdisciplinary and international research. It will be of interest to professionals and students in the philosophy and history of science, genetics and molecular biology. (shrink)

Developments in the sequencing of whole genomes and in simultaneously surveying many thousands of transcription and translation products of specific cells have ushered in a conceptual revolution in genetics that rationally introduces top-down, holistic analyses. This emphasized the futility of attempts to reduce genes to structurally discrete entities along the genome, and the need to return to Johannsen's definition of a gene as 'something' that refers to an invariant entity of inheritance and development. We may view genes either as generic (...) terms for units of inheritance whose referents are pragmatic ad hoc and context-dependent, or as (epistemologically) representing entities of cell functions. It is cellular functions that determine the structural referents along the DNA. Structures that happened to secure specific functions that were essential for or conducive to the survival of cells were selected for. With natural selection being the etiological background of genes as functions, genes obtain again their theoretical role as intervening variables, abstractive variables that purely 'summarize' characters. The importance of DNA sequences is that of all possible phenotypes these are the most basic ones from which we can read off the genotype directly. (shrink)

According to Conceptual Role Semantics ("CRS"), the meaning of a representation is the role of that representation in the cognitive life of the agent, e.g. in perception, thought and decision-making. It is an extension of the well known "use" theory of meaning, according to which the meaning of a word is its use in communication and more generally, in social interaction. CRS supplements external use by including the role of a symbol inside a computer or a brain. The uses appealed (...) to are not just actual, but also counterfactual: not only what effects a thought does have, but what effects it would have had if stimuli or other states had differed. The view has arisen separately in philosophy (where it is sometimes called "inferential," or "functional" role semantics) and in cognitive science (where it is sometimes called "procedural semantics"). The source of the view is Wittgenstein (1953) and Sellars, but the source in contemporary philosophy is a series of papers by Harman (see his 1987) and Field (1977). Other proponents in philosophy have included Block, Horwich, Loar, McGinn and Peacocke (1992). In cognitive science, they include Woods (1981) and Miller and Johnson-Laird (1976). (See references in Block, 1987.). (shrink)

In this paper I provide a novel argument against the claim that classical genetics is being reduced to molecular genetics. Specifically, I demonstrate that reductionists must subscribe to the unargued and problematic thesis that molecular genetics is 'independent' of classical genetics. I also argue that several standard antireductionist positions can be faulted for unnecessarily conceding the Independence Thesis to the reductionists. In place of a 'tale of two sciences', I offer a 'heroic' stance that denies classical genetics is being reduced, (...) yet sees classical and molecular genetics as fundamentally unified. (shrink)