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.

Recently, in attempting to account for explanatory reasoning in probabilistic terms, Bayesians have proposed several measures of the strength of a potential explanation. These candidate measures of “explanatory power” arguably have interesting normative interpretations and consequences. What has not yet been investigated, however, is whether any of these measures are also descriptive of people's actual explanatory judgments. Here I present my own experimental work investigating this question. I argue that one measure in particular is an accurate descriptor of explanatory judgments. Then I briefly point to some implications of this result for the epistemology and the psychology of explanatory reasoning.

Publications in contemporary science journals often include figures like graphs, diagrams, photographs, and MRIs, which are presented as support for the hypothesis the author is defending. As a first step to explaining how figures contribute to confirmation, I present an account of visual representation and use examples to show how the visual format is involved in the support those figures provide the authors’ conclusions. I then show that attempts to explain what figures contribute to scientific arguments without analyzing them as visual representations (for example by translating them into linguistic representations) will not succeed.

I consider two usages of the expression “gauge theory.” On one, a gauge theory is a theory with excess structure; on the other, a gauge theory is any theory appropriately related to classical electromagnetism. I make precise one sense in which one formulation of electromagnetism, the paradigmatic gauge theory on both usages, may be understood to have excess structure and then argue that gauge theories on the second usage, including Yang-Mills theory and general relativity, do not generally have excess structure in this sense.

Human skin is the one authentic criterion of the universe which philosophers recognize when they appraise knowledge under their professional rubric, epistemology. By and large—except for a few of the great Critics and Sceptics—they view knowledge as a capacity, attribute, possession, or other mysterious inner quality of a “knower”; they view this knower as residing in or at a “body”; they view the body as cut off from the rest of the universe by a “skin”; all of which holds for philosophizing physicists and physiologists even as for the professionals of the arcanum itself. If this assertion seems crude, one may recall that there are times when a bit of crudity is a fair physic for an inflamed subtlety. In the case before us the factual crudity lies in the use of “skin” for a criterion, not in our calling attention to the fact. The “skin” that is so used is, indeed, that of ancient anatomical schematism, unaffected by the transformation of understanding which modern physiological research has brought about. Yet if philosophers cease thus crudely to employ it, all their issues of epistemology will vanish, and the very type of attack they make on cognition will be discredited; whereupon the task of determining the status of knowledge itself will pass from their hands to those of the scientists who have taken over so many regions of philosophical arrogation in the past. This is what I propose here to show.

Hempel and Oppenheim, in their paper ‘The Logic of Explanation’, have offered an analysis of the notion of scientific explanation. The present paper advances considerations in the light of which their analysis seems inadequate. In particular, several theorems are proved with roughly the following content: between almost any theory and almost any singular sentence, certain relations of explainability hold.

I argue for accepting a pluralist approach to species, while rejecting the realism about species espoused by P. Kitcher and a number of other philosophers of biology. I develop an alternative view of species concepts as divisions of organisms into groups for study which are relative to the systematic explanatory interests of biologists at a particular time. I also show how this conception resolves a number of difficult puzzles which plague the application of particular species concepts.

Taking reduction in the traditional deductive sense, the programmatic claim that most of genetics can be reduced by molecular genetics is defended as feasible and significant. Arguments by Ruse and Hull that either the relationship is replacement or at best a weaker form of reduction are shown to rest on a mixture of historical and logical confusions about the nature of the theories involved.

David Buller's recent book, Adapting Minds, is a philosophical critique of the field of evolutionary psychology. Buller argues that evolutionary psychology is utterly bankrupt from both a theoretical and an empirical point of view. Although Adapting Minds has been well received in both the academic press and the popular media, we argue that Buller's critique of evolutionary psychology fails.

Prompted by the “Panel Discussion of Grünbaum's Philosophy of Science” (Philosophy of Science 36, December, 1969) and other recent literature, this essay ranges over major issues in the philosophy of space, time and space-time as well as over problems in the logic of ascertaining the falsity of a scientific hypothesis.

The author's philosophy of geometry has recently been challenged along three main distinct lines as follows : (i) The Panel article by G. J. Massey calls for a more precise and more coherent account of the Riemannian conception of an intrinsic as opposed to an extrinsic metric, which the author has invoked as his basis for the distinction between non-conventional and convention-laden ascriptions of metrical equality and inequality; (ii) the latter distinction has been claimed to suffer from the liabilities of the so-called “standard conception” of scientific theories [36]; and (iii) pursuant to H. Putnam's “An Examination of Grünbaum's Philosophy of Geometry” [56], J. Earman [16, 17] and R. Swinburne [65] have contended that the difference between intrinsic and extrinsic metrics is scientifically unilluminating, and that the associated distinction between non-conventional and convention-laden metrical comparisons does not have the kind of relevance to extant scientific theories that the author has claimed for it.

The essay consists of two installments. The present installment, comprising the Introduction and Part A, is devoted to the clarification, correction and further development of the author's prior writings on the philosophy of geometry. Its main objective is constructive elaboration rather than offering polemics. But rebuttals to Earman, [16, 17], Swinburne [65] and Demopoulos [13] are included, because their inclusion conduced to clarity in giving the new exposition. Part B is to appear in a subsequent issue and will be devoted to replies to critiques contained in the Panel Discussion and in other recent literature. It will range over issues in the philosophy of geometry and in the logic of ascertaining the falsity of a scientific hypothesis.

By way of merely elliptical anticipation of much more precise statements given in Part A, section 3(ii), the Introduction dissociates the notion of convention-ladenness developed in Part A from the quite different notion integral to the so-called “standard conception” of scientific theories. Thereby, the Introduction prepares the ground for seeing, as a corollary to Part A, section 3(ii), that the notion advocated in the present essay has nothing to fear from the following fact, noted by C. G. Hempel ([36]; cf. also his 1970 Carus Lectures): “even though a sentence may originally be introduced as true by stipulation, it soon joins the club of all other member-statements of the theory and becomes subject to revision in response to further empirical findings and theoretical developments.”

Part A, which begins with a fairly detailed table of contents, endeavors to meet the aforementioned three-fold challenge to the author's philosophy of geometry. Massey's call for the provision of clear and detailed characterizations of intrinsic and extrinsic metrics is answered with the invaluable aid rendered personally by Massey himself. These characterizations are shown to permit a precise explication of the portions of Riemann's Inaugural Dissertation relevant to (1) Riemann's brilliant anticipation of Einstein's dynamical conception of physical geometry, and (2) the author's philosophical characterization of the metrics and geometries of space, time, and space-time {section 2(c)}.

A byproduct of the analysis is to raise two major philosophical doubts concerning Clifford's sketch of a so-called “space-theory of matter” as elaborated in J. A. Wheeler's relativistic geometrodynamics. That theory's vision of understanding matter as a manifestation of empty curved space is questioned in regard to (1) the existence of an intra-geometrodynamic basis for individuating the metrically homogeneous world points of its space-time manifold {section 1(a)}, and (2) the compatibility of the theory with the Riemannian metrical philosophy apparently espoused by its proponents {section 2(c) (i)}.

This paper considers objections to Popper's views on scientific method. It is argued that criticism of Popper's views, developed by Kuhn, Feyerabend, and Lakatos, are not too damaging, although they do require that Popper's views be modified somewhat. It is argued that a much more serious criticism is that Popper has failed to provide us with any reason for holding that the methodological rules he advocates give us a better hope of realizing the aims of science than any other set of rules. Consequently, Popper cannot adequately explain why we should value scientific theories more than other sorts of theories; which in turn means that Popper fails to solve adequately his fundamental problem, namely the problem of demarcation. It is suggested that in order to get around this difficulty we need to take the search for explanations as a fundamental aim of science.

The main aim of this paper is to revisit the curve fitting problem using the reliability of inductive inference as a primary criterion for the ‘fittest’ curve. Viewed from this perspective, it is argued that a crucial concern with the current framework for addressing the curve fitting problem is, on the one hand, the undue influence of the mathematical approximation perspective, and on the other, the insufficient attention paid to the statistical modeling aspects of the problem. Using goodness-of-fit as the primary criterion for ‘best’, the mathematical approximation perspective undermines the reliability of inference objective by giving rise to selection rules which pay insufficient attention to ‘accounting for the regularities in the data’. A more appropriate framework is offered by the error-statistical approach, where (i) statistical adequacy provides the criterion for assessing when a curve captures the regularities in the data adequately, and (ii) the relevant error probabilities can be used to assess the reliability of inductive inference. Broadly speaking, the fittest curve (statistically adequate) is not determined by the smallness if its residuals, tempered by simplicity or other pragmatic criteria, but by the nonsystematic (e.g. white noise) nature of its residuals. The advocated error-statistical arguments are illustrated by comparing the Kepler and Ptolemaic models on empirical grounds.

Recent versions of objectivism can reply to the argument from metamers. The deeper rift between subjectivists and objectivists lies in the question of how to explain the structure of qualitative similarities among the colors. Subjectivism grounded in this fashion can answer the circularity objection raised by Dedrick. It endorses skepticism about the claim that there is some one property of objects that it is the function of color vision to detect. Color vision may enable us to detect differences in spectral composition without granting us the capacity to detect identities.

This article supports calls for an increased integration of patients into taxonomic decision making in psychiatry by arguing that their exclusion constitutes a special kind of epistemic injustice: preemptive testimonial injustice, which precludes the opportunity for testimony due to a wrongly presumed irrelevance or lack of expertise. Here, this presumption is misguided for two reasons: (1) the role of values in psychiatric classification and (2) the potential function of first-person knowledge as a corrective means against implicitly value-laden, inaccurate, or incomplete diagnostic criteria sets. This kind of epistemic injustice leads to preventable epistemic losses in psychiatric classification, diagnosis, and treatment.

In this paper I argue for the cognitive impenetrability of perception by undermining the argument from reentrant pathways. To do that I will adduce psychological and neuropsychological evidence showing that (a) early vision processing is not affected by our knowledge about specific objects and events, and (b) that the role of the descending pathways is to enable the early-vision processing modules to participate in higher-level visual or cognitive functions. My thesis is that a part of observation, which I will call perception, is bottom-up and theory neutral. As such, perception could play the role of common ground on which a naturalized epistemology can be built and relativism avoided.

Although the recent emphasis on models in philosophy of science has been an important development, the consequence has been a shift away from more traditional notions of theory. Because the semantic view defines theories as families of models and because much of the literature on “scientific” modeling has emphasized various degrees of independence from theory, little attention has been paid to the role that theory has in articulating scientific knowledge. This paper is the beginning of what I hope will be a redress of the imbalance. I begin with a discussion of some of the difficulties faced by various formulations of the semantic view not only with respect to their account of models but also with their definition of a theory. From there I go on to articulate reasons why a notion of theory is necessary for capturing the structure of scientific knowledge and how one might go about formulating such a notion in terms of different levels of representation and explanation. The context for my discussion is the BCS account of superconductivity, a ‘theory’ that was, and still is, sometimes referred to as a `model'. BCS provides a nice focus for the discussion because it illuminates various features of the theory/model relationship that seem to require a robust notion of theory that is not easily captured by the semantic account.

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.

This essay examines logical empiricism and American pragmatism, arguing that American philosophy's embrace of logical empiricism in the 1930s was not a turning away from Dewey's pragmatism. It places both movements within scientific philosophy and finds two key points on which they agreed: their revolutionary ambitions and their social engineering sensibility. The essay suggests that the disagreement over emotivism in ethics should be placed within the context of a larger issue on which the movements disagreed: demarcationism and imperialism.

We argue that Brandon and Carson's (1996) “The Indeterministic Character of Evolutionary Theory” fails to identify any indeterminism that would require evolutionary theory to be a statistical or probabilistic theory. Specifically, we argue that (1) their demonstration of a mechanism by which quantum indeterminism might “percolate up” to the biological level is irrelevant; (2) their argument that natural selection is indeterministic because it is inextricably connected with drift fails to join the issue with determinism; and (3) their view that experimental methodology in botany assumes indeterminism is both false and incompatible with the commitment to discoverable causal mechanisms underlying biological processes. We remain convinced that the probabilism of the theory of evolution is epistemically, not ontologically, motivated.