The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary skills. Quantitative scientists (...) are joining biological departments and collaborations between physicists and biologists are particularly vigorous. This state of affairs raises a number of questions, such as: What are the circumstances under which physicists approach biological problems in systems biology? What kind of interdisciplinary challenges must be tackled? The paper suggests that, concerning physicists’ move to work on biological systems, there are common reasons to move, the transition must be understood in terms of degrees, physicists have a rationale for simplifying systems, and distinct conceptions of model and modeling strategies are recurrent. We identified problems regarding linguistic clarity and integration of epistemological aims. We conclude that cultural unconformities within the systems biology community have important consequences to the flow of scientific knowledge. (shrink)

Philosophy of science is showing an increasing interest in the social aspects and the social organisation of science—the ways social values and social interactions and structures play a role in the creation of knowledge and the ways this role should be taken into account in the organisation of science and science policy. My thesis explores a number of issues related to this theme. I argue that a prominent approach to the social organisation of science—Philip Kitcher’s well-ordered science—runs into a number (...) of problems. They undermine its philosophical plausibility and practical usefulness. I agree with Kitcher that arguments about the social organisation of science should recognise profound societal consequences of science. Kitcher argues that the appropriate organisation of science should therefore take into account laypersons’ values and needs when making decisions concerning research planning, evaluation and application. My criticisms show that this is not enough. Drawing on Helen Longino ideas, I argue that laypersons’ perspectives and knowledge may also be relevant when doing research. In order to show how more inclusive research practices may be possible, I discuss connections between philosophy of science and some developments in science policy, which has also recently shown considerable interest in democratic participation. I demonstrate how public participation experiments in science policy may sometimes be close enough to what the philosopher would recommend. Their analysis can thus be helpful for understanding how societal developments may provide opportunities for the involvement of laypersons in science and what factors may endanger its success. I conclude that a way to pursue a more socially relevant philosophy of science is to focus on the points of contact and possibilities of cooperation between philosophical proposals and these public participation initiatives. (shrink)

According to a doctrine that has been popularized by Kripke and Putnam, a natural kind term like 'bird' rigidly designates the kind with the microstructure of sample birds. This microstructure is the essence of birdhood, so our learning what the relevant microstructure is our discovery of the kind's essence. We have discovered that some statement like 'The bird is the taxon with such and such DNA structure' is true. Further, it is commonly added, the discovered microstructure is essential to each (...) particular bird. ;I argue that this general picture is mistaken. I do accept and defend the view that terms like 'bird' are rigid designators. However, the picture at issue has other difficulties. Individual birds are not essentially birds. And the view that biologists have discovered or will discover that the bird kind is identical to some DNA structure or other type of structure seems wrong. We don't discover just what particular characteristic a kind is to be identified with. Rather, the meaning of natural kind terms changes; as science advances, more sophisticated concepts attending kind terms replace older ones. So the Kripke-Putnam account of our discovering the truth of theoretical identity statements seems wrong. ;Fortunately, the account retains some interest despite its falsity, because of its association with the claim that statements like 'The bird is the taxon with such and such DNA structure' are necessary but a posteriori. The above sentence does not express a truth, much less a necessary truth, but the idea that it could have expressed the sort of necessary a posteriori truth it is supposed to express is epistemologically interesting. The very possibility of such necessary a posteriori knowledge deserves some account. I offer an account, arguing that this sort of knowledge is no more impressive from an epistemological standpoint than is knowledge of analytic necessity: indeed, I argue, it is best understood as knowledge of a species of analytic necessity. Independently of this claim, I argue in a concluding discussion that analyticity ought to be accepted by proponents of the necessary theoretical identity statements in question. (shrink)

Apparently factual disagreement on the level at which selection operates often results from different interpretations of the term “selection”. Attempts to resolve terminological problems must come to grips with a dilemma: a narrow interpretation of “selection” may lead to a restricted view on evolution; a broader, less precise, definition may wrongly suggest that “selection” is the centre of a unified, integrated theory of evolution. Different concepts of selection, therefore, should carefully be kept apart.

This inaugural handbook documents the distinctive research field that utilizes history and philosophy in investigation of theoretical, curricular and pedagogical issues in the teaching of science and mathematics. It is contributed to by 130 researchers from 30 countries; it provides a logically structured, fully referenced guide to the ways in which science and mathematics education is, informed by the history and philosophy of these disciplines, as well as by the philosophy of education more generally. The first handbook to cover the (...) field, it lays down a much-needed marker of progress to date and provides a platform for informed and coherent future analysis and research of the subject. -/- The publication comes at a time of heightened worldwide concern over the standard of science and mathematics education, attended by fierce debate over how best to reform curricula and enliven student engagement in the subjects There is a growing recognition among educators and policy makers that the learning of science must dovetail with learning about science; this handbook is uniquely positioned as a locus for the discussion. -/- The handbook features sections on pedagogical, theoretical, national, and biographical research, setting the literature of each tradition in its historical context. Each chapter engages in an assessment of the strengths and weakness of the research addressed, and suggests potentially fruitful avenues of future research. A key element of the handbook’s broader analytical framework is its identification and examination of unnoticed philosophical assumptions in science and mathematics research. It reminds readers at a crucial juncture that there has been a long and rich tradition of historical and philosophical engagements with science and mathematics teaching, and that lessons can be learnt from these engagements for the resolution of current theoretical, curricular and pedagogical questions that face teachers and administrators. (shrink)

Methodological individualism is a thesis generally associated with the social sciences, the thesis that ultimately all social explanations should be given in terms of properties only of individuals, never of social groups, societies, etc. It is a methodological thesis grounded on a metaphysical view: it is impossible for a social group to have any property not entailed by properties of its constituent individuals. This latter thesis, finally, is a straightforward consequence of a standard reductionist assumption, that the behavior of wholes (...) can be fully accounted for in terms of the behavior of their parts. (shrink)

David Chalmers and Frank Jackson have promoted a strong program of conceptual analysis, which accords a significant philosophical role to the a priori analysis of concepts. They found this methodological program on an account of concepts using two-dimensional semantics. This paper argues that Chalmers and Jackson’s account of concepts, and the related approach by David Braddon-Mitchell, is inadequate for natural kind concepts as found in biology. Two-dimensional semantics is metaphysically faulty as an account of the nature of concepts and concept (...) possession. It is also methodologically flawed as a guideline for how to study scientific concepts. Proponents of two-dimensional semantics are criticized for not taking seriously semantic variation between persons and for failing to adequately account for the rationality of semantic change. I suggest a more pragmatic approach to natural kind term meaning, arguing that the epistemic goal pursued by a term’s use is an additional semantic property. (shrink)

En este trabajo argumento a favor de la idea de que una explicación científica es una respuesta a una pregunta, aunque no necesariamente a una pregunta-por-qué. Esto no quiere decir que las preguntas-por-qué no sean elementos fundamentales de toda investigación científica: su importancia radica en que son capaces de organizar y sistematizar un conjunto dado de creencias. Para justificar esta afirmación, comienzo por identificar tres estadios básicos en los cuales pueden surgir preguntas-por-qué, y luego procedo a caracterizar su estructura. Muestro (...) finalmente cómo usar este análisis para elucidar la noción de poder de unificación de hipótesis rivales. Entiendo que esta última noción, a su vez, constituye uno de los criterios que debemos considerar a la hora de evaluar cuál de dichas hipótesis rivales es la mejor explicación disponible, comparativamente hablando. In this paper I take scientific explanations to be answers to questions, though not necessarily to why-questions. This, however, is not meant to imply that why-questions are not fundamental in their own peculiar way. As I understand it, why-questions are crucial elements in any research process because they are able to organize and systematize an agent's belief set. In order to justify my claim I start by identifying three basic stages in which whyquestions can arise, and then I proceed to characterize their structure. I also show how to use this analysis to elucidate the notion of comparative unification power of rival hypotheses. The notion of comparative unification power, in turn, can be thought of as one of the criteria that we should take into account at the time of assessing which of such rival hypotheses is the best explanation available, comparatively speaking. (shrink)

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

In this article, against the background of a notion of ‘assembled’ truth, the evolutionary progressiveness of a theory is suggested as novel and promising explanation for the success of science. A new version of realism in science, referred to as ‘naturalised realism’ is outlined. Naturalised realism is ‘fallibilist’ in the unique sense that it captures and mimics the self-corrective core of scientific knowledge and its progress. It is argued that naturalised realism disarms Kyle Stanford’s anti-realist ‘new induction’ threats by showing (...) that ‘explanationism’ and his ‘epistemic instrumentalism’ are just two positions among many on a constantly evolving continuum of options between instrumentalism and full-blown realism. In particular it is demonstrated that not only can naturalised realism redefine the terms of realist debate in such a way that no talk of miracles need enter the debate, but it also promises interesting defenses against inductive- and under-determination-based anti-realist arguments. (shrink)

The philosophy of science that grew out of logical positivism construed scientific knowledge in terms of set of interconnected beliefs about the world, such as theories and observation statements. Nowadays science is also conceived of as a dynamic process based on the various practices of individual scientists and the institutional settings of science. Two features particularly influence the dynamics of scientific knowledge: epistemic standards and aims (e.g., assumptions about what issues are currently in need of scientific study and explanation). While (...) scientific beliefs are representations of the world, scientific standards and aims are epistemic values. The relevance of epistemic aims and values for belief change has been previously recognized. My paper makes a similar point for scientific concepts, both by studying how an individual concept changes (in its semantic properties) and by viewing epistemic aims and values tied to individual concepts. (shrink)

Holism and reductionism are usually seen as opposite and mutually exclusive approaches to nature. Recently, some have come to see them as complementary rather than mutually exclusive. In this book I have argued that, even stronger, they should be seen as mutually dependent and co-operating research programmes. I have discussed holism and reductionism in biology in general and in ecology in particular. After an introductory chapter I have provided an overview of holistic and reductionistic positions in biology, and of the (...) reduction problems to which they relate. I have argued that it is extremely important to distinguish between ontological, epistemological and methodological aspects of these problems. The overview has shown that there are actually several approaches to reduction problems in biology, which can be characterized as more or less radically or moderately holistic or reductionistic. It has shown also that there are three major ’contradistinctions’ between holism and reductionism in biology, to wit the doctrine of emergence versus the reduction thesis; functional explanations versus causal explanations; and phenomenology versus mechanicism. In later chapters I have shown that these ’contradistinctions’ are not really contradistinctions at all. In the next chapters I have discussed the terms ’reduce’ and ’reduction’ in science. In chapter 3 I have discussed the reduction of laws and theories. I have shown that there are many different types of reduction depending on the auxiliary hypotheses that are being used in addition to the reducing theory: approximation-, aggregation, correlation and/or identification-hypotheses. The distinctions between these types has later, in chapter 5, proved to be of great importance in defining the concept of ’emergence’. The major conclusion of chapter 3 was that reduction is an epistemological issue, pertaining to logical relations between statements or systems of statements. It should not be confused, therefore, with ’ontological reduction’, certainly not in one of its ordinary senses, such as diminishing, devaluating or the like. Scientific reductions are, with the exception of instrumentalistic reductions, kinds of explanation, and, moreover, non-eliminative kinds of explanation. This means that a reduced law or theory is not eliminated by the reducing theory but rather consolidated or even reinforced. The ontology of the reduced law or theory is thereby also being consolidated. In chapter 4 I have argued that the same holds for reductions of concepts. Concept reductions are supposed to be accomplished by means of so-called ontological identity relations, which are in turn supposed to connect terms in the law or theory to be reduced, which do not occur in the reducing theory, with theoretical terms of the reducing theory. Because they are called ontological identity relations, several philosophers have thought that concept reductions imply some form of ontological reduction. And because they often occur in the context of micro-reductions, some have even thought that concept reductions are themselves micro-reductions. As a result, the idea has arisen that ontological identity relations are connections between macro-concepts and micro-concepts. However, concept reductions by means of ontological identity relations cannot be micro-reductions, because micro-reduction is, by definition, reduction with an aggregation step. Moreover, ontological identity relations are relations between different representations of and the same type of thing or attribute. That is, they express different epistemological sides of the same ontological coin. Therefore, concept reductions cannot be considered ontological reductions either, certainly not in the ordinary sense of diminishing, devaluating or the like. Thus, concept reduction is, like law or theory reduction, an epistemological issue: it pertains to relations between, in this case, different concepts or representations of one and the same type of thing or attribute. ’Ontological reduction’, then, may, in the context of scientific reductions, actually be considered a contradiction of terms. In chapter 5 I have linked this conclusion to the emergence thesis and to the alleged contradistinction between this thesis and the reduction thesis. I have shown that the doctrine of emergence actually consists of two separate claims, namely an ontological thesis stating that a whole has emergent properties which the component parts do not possess, neither separately nor in other partial combinations; and an epistemological thesis stating that emergent properties of wholes are ’in principle’ irreducible. I have argued that the first claim may be regarded as a valid, universal thesis about relations between properties of wholes and properties of parts, but that the second claim is untenable. I have discussed many emergent properties of wholes, biological as well as physico-chemical, that have proved to be explainable in terms of micro-theories about the component parts and auxiliary hypotheses. Once again, however, it is important to realize that reduction is an epistemological issue, whereas emergence, in the sense of thesis, is an ontological one. It is not ’wholes’ or ’emergent properties of wholes’ that are being reduced but statements about them. Reduction is a kind of explanation, not of explaining-away. Thus, it leaves the ontology of whatever is reduced fully intact. I have developed a new definition of the term ’emergence’ which expresses emergence in terms of the auxiliary hypotheses that may be used in reductions, in particular aggregation-, correlation- and identification-hypotheses. This has even lead to two very remarkable conclusions. First, emergence may be considered the opposite of ontological identity. And second, if there were no emergence, there wouldn’t be any reductions either. to reduce.) In this respect, therefore, there is absolutely no contradistinction between holism and reductionism. On these grounds I have introduced my thesis that holism and reductionism should rather be seen as mutually dependent, and hence co-operating, research programmes than as conflicting views of nature or of relations between sciences. Holistic programmes play an important role in science as guide programmes for reductionistic programmes by discovering or developing macro-laws or -theories about phenomena at the level of wholes, which they themselves, however, cannot explain. For these explanations they depend on the fruits of reductionistic programmes. If the latter succeed in providing the explanations they act as supply programmes for the holistic guide programmes. Reductionistic programmes depend in turn on holistic programmes for providing the macro-laws or -theories that call for these explanations. In chapter 6 I have discussed an example of this mutual dependency in the form of the reduction of the Bohr-effect in animal physiology. I have shown that this law has been reduced to the theory of allostery, applied to hemoglobin molecules in red blood cells, and that this application of the theory of allostery has been reduced to the theory of chemical bonding. I have also shown that at least six research programmes were involved in these reductions, and that the relations between these programmes can be characterized very well in terms of the model of holistic guide programmes and reductionistic supply programmes. The only, but highly significant, qualification appearing from example was that the terms ’holistic’ and ’reductionistic’ are extremely relative and should always be related to a certain given level of organization. In chapter 7 I have resolved the remaining contradistinction between holism and reductionism in biology, viz. the need for functional explanations and the demand that explanations be causal. I have shown that functional explanations are perfectly legitimate explanations which in a sense can be reconstrued as causal explanations. I have argued that functional explanations are indispensable components of more comprehensive, causal-evolutionary explanations, because the latter appeal to the adaptive value, and hence the function, of the property to be explained. In that sense functions can be regarded as adaptations, and functional explanations can be regarded as a sort of ’short-hand’ for evolutionary explanations. Finally, I have shown that in the context of functional explanations, too, co-operation of holistic and reductionistic research programmes occurs. In part 2 I have applied my thesis to ecology. I have shown that in ecology too, holismreductionism disputes notwithstanding, co-operation of holistic and reductionistic research programmes occurs, or, in so far as this appears to be not the case, that it should be strived after. In chapter 8 I have given an overview of reduction problems in ecology and of the various approaches to these problems. I have noticed that in ecology, too, there are several, radical, moderate and anti-reductionistic research strategies, with respect to the levels of both ecosystems, communities and populations. I have also noticed, however, that concrete solutions to reduction problems in ecology are frustrated by what is called the intellectual immaturity or the anomalous status of ecology. This refers to the almost complete lack of general laws and theories in ecology, at least at the higher levels of communities and ecosystems. Of a number of possible causes I have lifted out two, which lend themselves to philosophical analysis and clarification. The first one is the ambiguity of a major part of the ecological vocabulary. This was the subject of chapters 9 and 10. The second is the inhibitory effect which holism-reductionism disputes have on the growth of knowledge. This was the subject of chapter 13. In chapter 9 I have discussed the concept of an community. It appeared that the term ’community’ is used for several different entities at various levels of organization. This ambiguity alone seems to be sufficient for the lack of ’general’ laws and theories about ’communities’. My purpose in chapter 9 was to try and contribute to a solution of this problem. In doing so I have argued, first, that it seems wise to use the term ’community’ only for groups of species belonging to a single taxonomic or phylogenetic group, and to use the term ’biocoenosis’ for the higher level of organization, defined as the biotic component of an ecosystem. Next I have argued that, although species within communities may of course interact with each other, interaction is itself not a necessary or sufficient condition for community membership. Finally, I have hit upon what is known as the most notorious problem in community ecology, to wit the boundary problem, as well as the problem of heterogeneity. I have found that the cause of these problems lies in the fact that communities are almost invariably being seen as groups of populations occurring together in space and time, whereas the empirical fact is rather that populations of different species mostly do not occur together in the same space, and, moreover, that the species composition of communities changes continuously. This has lead to the suggestion that a community had better be defined as the group of individuals of two or more species occurring in the area of intersection of populations of these species. It is only in such intersection areas that one can really talk of the co-occurrence of species. I have shown the empirical adequacy of this definition by discussing various salt marsh plant communities on the Dutch island of Schiermonnikoog. In chapter 10 I have clarified two other important, yet highly controversial, concepts in ecology, to wit habitat and niche. It appeared that there are at least four different habitat concepts in ecology, and as many niche concepts, the additional complication being that two of these habitat concepts correspond to two of these niche concepts, whence the distinction between habitat and niche is blurred. In addition, different habitat concepts appeared to correspond to different environment concepts and also to different biotope concepts. My purpose in chapter 10 was to disentangle all these concepts from one another and to supply each of them with a suitable term. I have done so by keeping a close eye on commonly accepted notions about habitat differentiation and niche differentiation, two ’principles’ allowing one to explain the coexistence or non-coexistence of species in communities. The results can be found in boxes 5 and 7 in chapter 10. In chapter 11 I was finally able to substantiate my claim that in ecology, too, co-operation of holistic and reductionistic research programmes occurs. I have discussed the reduction of the classical competition model of Lotka and Volterra to modern niche theory. The Lotka/Volterra model is a phenomenological model: it describes the possible effects of competition between two species. Modern niche theory, on the other hand, is a mechanistic theory, in which both the objects of competition and a mechanism are being specified. I have shown that the reduction was established with the help of a relatively simple identification hypothesis and two relatively simple aggregation hypotheses, making it yet another example of heterogeneous microreduction in biology. In the reduction, the Lotka/Volterra model acted as a holistic guide programme and modern niche theory acted as a reductionistic supply programme. In chapter 12 I have discussed another example of co-operation in the form of the approximative reduction of MacArthur and Wilson’s equilibrium theory of island biogeography. I have argued that this can be seen as a holistic model, which has been of great unifying and especially heuristic value, but which in time has been found to be a bit too simple and in some respects had to be corrected. Therefore, it can also be seen as an idealization in the sense of the model of idealization and concretization, which subsequent research programmes have concretized. Because these concretizations have a reductive character, we can see in this structure of idealization and concretization yet another example of the co-operation of holistic and reductionistic research programmes in ecology. A philosophically interesting side-conclusion was that the model of idealization and concretization thus appears to apply also to relations between research programmes, and not only to programme-internal developments. In chapter 13 I have discussed an example of the inhibitory effect that holism-reductionism disputes may have on the growth of knowledge. The example concerns a controversy in island biogeography over the role of interspecific competition in structuring communities. This controversy has lasted for about ten years, appeares to have died out rather than to have been resolved, and has produced nothing new in the field of explanations of community structure. I have shown that the major factors underlying the controversy were differing, in casu holistic and reductionistic, views of communities. Though this presented a problem for my thesis, I have argued that, ultimately, the controversy can be resolved, and in a sense has been resolved, in a way that corroborates my thesis. In the epilogue, finally, I have mentioned some remaining problems concerning the adequacy of the present reduction model in dealing with reduction in ecology. These problems pertain to the question of specificty of ecological laws and theories, the likelihood that reductions in ecology generally occur on the basis of several reducing micro-theories, and the possible relationship between the former two points. (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)

In Science, Truth, and Democracy (2001a), Kitcher moderates the strongest ontological realist thesis he defended in The Advancement of Science (1993a), with the aim of making compatible the correspondence theory of truth with conceptual relativity. However, it is not clear that both things could be harmonized. If our knowledge of the world is mediated by our categories and concepts; if the selection of these categories and concepts may vary according to our interests, and they are not the consequence of the (...) existence of certain supposed natural kinds or some intrinsic structure of the world, it is very problematic to establish what our true statements correspond to. This paper analyzes the transformation in Kitcher's realism and expounds the main difficulties in this project. Finally, a modality of moderate ontological realism will be proposed that, despite of keeping the sprit of the conceptual relativity, is strong enough to support the correspondence theory of truth. (shrink)

The discussion presents a framework of concepts that is intended to account for the rationality of semantic change and variation, suggesting that each scientific concept consists of three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept’s use. I argue that in the course of history a concept can change in any of these components, and that change in the concept’s inferential role and reference can be accounted for as being rational relative (...) to the third component, the concept’s epistemic goal. This framework is illustrated and defended by application to the history of the gene concept. It is explained how the molecular gene concept grew rationally out of the classical gene concept despite a change in reference, and why the use and reference of the contemporary molecular gene concept may legitimately vary from context to context. (shrink)

It is argued that the major interpretations of tobacco mosaic virus which were suggested in the first half of the 20th century can be ordered into two conflicting approaches. It is shown that explaining the existence of these different approaches as views from different perspectives, is a mistaken metaphor. The different approaches resulted in the "construction" of different research objects as answers to the questions "What is a virus"? Although these different conceptions did exclude each other, they co-existed because of (...) the consensus concerning the existence of tobacco mosaic "disease". (shrink)

This paper shows that two questions productively overlap: first, in virtue of what does an agent infer one hypothesis rather than another? Second, in virtue of what does an agent refer to one natural kind rather than another? Peter Lipton answers the first question by articulating the model of inference to the best explanation. Lipton’s answer to the first question is appropriated as an answer to the second.Keywords: Reference; Explanation; Natural kind; Qua problem; Peter Lipton.

Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically ‘the carriers of hereditary information.’ Nevertheless, a number of researchers consider such talk as inadequate and ‘just metaphorical,’ thus expressing a skepticism about the use of the term ‘information’ and its derivatives in biology as a natural science. First, because the meaning of that term in biology is not as precise as it is, for instance, in (...) the mathematical theory of communication. Second, because it seems to refer to a purported semantic property of genes without theoretically clarifying if any genuinely intrinsic semantics is involved. Biosemiotics, a field that attempts to analyze biological systems as semiotic systems, makes it possible to advance in the understanding of the concept of information in biology. From the perspective of Peircean biosemiotics, we develop here an account of genes as signs, including a detailed analysis of two fundamental processes in the genetic information system (transcription and protein synthesis) that have not been made so far in this field of research. Furthermore, we propose here an account of information based on Peircean semiotics and apply it to our analysis of transcription and protein synthesis. (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)

Mendelian genes have become molecular genes, with increasing puzzlement about locating them, due to increasing complexity in genomic webworks. Genome science finds modular and conserved units of inheritance, identified as homologous genes. Such genes are cybernetic, transmitting information over generations; this too requires multi-leveled analysis, from DNA transcription to development and reproduction of the whole organism. Genes are conserved; genes are also dynamic and creative in evolutionary speciation—most remarkably producing humans capable of wondering about what genes are.

There are a number of reasons for doubting the standard view that scientific theories (understood as sets of connected statements) are the best units for investigating scientific continuity and change (that is, research programs continue as long as groups of scientists accept the central tenets of such theories). Here it is argued that one weakness of this approach is that it cannot be used to demarcate adequately scientific communities or conceptual systems (that is, it fails as a classificatory scheme). Recent (...) alternative proposals by Philip Kitcher and David Hull are assessed in terms of their usefulness in demarcating "Darwinism" and the "Darwinians" in the first decade or so after the publication of The Origin of Species, focusing on the case of Charles Lyell. (shrink)

While purely causal theories of reference have provided a plausible account of the meanings of names and natural kind terms, they cannot handle vacuous theoretical terms. The causal homeostasis theory can but incurs other difficulties. Theories of reference that are intensional and not purely causal tend to be molecularist or holist. Holist theories threaten transtheoretic reference, whereas molecularist theories must supply a principled basis for selecting privileged meaning-determining relations between terms. The causal homeostasis theory is a two-factor molecularist theory, but (...) it fails to provide such a principled basis and collapses into holism. A naturalistic, non-foundationalist holism that deploys strategies of intertheoretic reduction and co-evolutionary pluralism can, however, yield a credible version of transtheoretic reference. (shrink)

I defend a view of the species category, pluralistic realism, which is designed to do justice to the insights of many different groups of systematists. After arguing that species are sets and not individuals, I proceed to outline briefly some defects of the biological species concept. I draw the general moral that similar shortcomings arise for other popular views of the nature of species. These shortcomings arise because the legitimate interests of biology are diverse, and these diverse interests are reflected (...) in different legitimate approaches to the classification of organisms. In the final section, I show briefly how the pluralistic approach can help to illuminate some areas of biological and philosophical dispute. (shrink)

Advances in molecular biology have generally been taken to support the claim that biology is reducible to chemistry. I argue against that claim by looking in detail at a number of central results from molecular biology and showing that none of them supports reduction because (1) their basic predicates have multiple realizations, (2) their chemical realization is context-sensitive and (3) their explanations often presuppose biological facts rather than eliminate them. I then consider the heuristic and confirmational implications of irreducibility and (...) argue that purely biochemical approaches are likely to be unsound and to be unable to confirm an important range of statements. I conclude by sketching criteria for scientific unity that do not entail reducibility and yet leave an important place for identifying underlying mechanisms. Molecular biology, properly understood, provides an excellent paradigm of non-reductive unity between different explanatory levels. (shrink)

This paper discusses a philosophical issue in taxonomy. At least one philosopher has suggested thc taxonomic principle that scientific kinds are disjoint. An opposing position is dcfcndcd here by marshalling examples of nondisjoint categories which belong to different, cocxisting classification schcmcs. This dcnial of thc disjoinmcss principle can bc recast as thc claim that scientific classification is "int<-:rcst—rclativc". But why would anyone have held that scientific categories arc disjoint in the first place'? It is argued that this assumption is nccdcd (...) in one attempt t0 dcrivc csscntialism. This shows why the csscntialist and intc-:rcst—r<-zlativc approaches to classification arc in conflict. (shrink)

A classification of models of reduction into three categories — theory reductionism, explanatory reductionism, and constitutive reductionism — is presented. It is shown that this classification helps clarify the relations between various explications of reduction that have been offered in the past, especially if a distinction is maintained between the various epistemological and ontological issues that arise. A relatively new model of explanatory reduction, one that emphasizes that reduction is the explanation of a whole in terms of its parts is (...) also presented in detail. Finally, the classification is used to clarify the debate over reductionism in molecular biology. It is argued there that while no model from the category of theory reduction might be applicable in that case, models of explanatory reduction might yet capture the structure of the relevant explanations. (shrink)

The purpose of the paper is twofold. I first outline a philosophical theory of concepts based on conceptual role semantics. This approach is explicitly intended as a framework for the study and explanation of conceptual change in science. Then I point to the close similarities between this philosophical framework and the theory theory of concepts, suggesting that a convergence between psychological and philosophical approaches to concepts is possible. An underlying theme is to stress that using a non-atomist account of concepts (...) is crucial for the successful study of conceptual development and change. (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

Thomas Kuhn’s relativistic position is usually expounded in terms of its subjectivist and irrationalist consequences and, accordingly, as a contribution to anti-scientificism. This paper explains his pluralism in semantics and ontology and shows in it a kind of relativism from which those consequences do not follow. It is also argued that, despite that, this version does not converge to empiricism or scientific realism.

Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different (...) fields of biological research. (shrink)

Two recently popular metaphilosophical movements, formal philosophy and experimental philosophy, promote what seem to be conflicting methodologies. Nonetheless, I argue that the two can be mutually supportive. I propose an experimentally-informed variation on explication, a powerful formal philosophical tool introduced by Carnap. The resulting method, which I call “experimental explication,” provides the formalist with a means of responding to explication's gravest criticism. Moreover, this method introduces a philosophically salient, positive role for survey-style experiments while steering clear of several objections that (...) critics of “positive experimental philosophy” raise. Thus, it provides the experimentalist with a more defensible example of how empirical work can have positive philosophical import. For these reasons, experimental explication should appeal to experimental philosophers and formal philosophers alike. (shrink)

I investigate a new understanding of realism in science, referred to as ‘interactive realism’, and I suggest the ‘evolutionary progressiveness’ of a theory as novel criterion for this kind of realism. My basic claim is that we cannot be realists about anything except the progress affected by myriad science-reality interactions that are constantly moving on a continuum of increased ‘fitness’ determined according to empirical constraints. Moreover to reflect this movement accurately, there is a corresponding continuum of verdicts about the status (...) of the knowledge conveyed by theories – ranging from stark instrumentalism to full-blown realism. This view may sound like a pessimistic inductivist's dream, but actually this is so only if one evaluates it from within a traditional context where the ‘truth’ of a single theory is the exclusive criterion for realism. I, on the other hand, want to redefine the terms of realist debate in such a way that the units of assessment of realism are sequences of theories evaluated according to their ‘evolutionary progressiveness’. I unpack ‘interactive realism’ by defining my notion of ‘evolutionary progressiveness’, the notion of ‘truth-as-historied reference’ underpinning it, and the continuum of interaction between theories and aspects of reality it affects. I conclude that, although interactive realism is a radically non-standard kind of realism, it is at least more realistic about science as a fractured complex multi-faceted enterprise than most other kinds of realism on the block, because it shows coherence amidst fragmentation. (shrink)

Of all contemporary social theorists, Luhmann has best understood the centrality of the concept of meaning to social theory and has most extensively worked out the notion's implications. However, despite the power of his theory, the theory suffers from difficulties impeding its reception. This article attempts to remedy this situation with some critical arguments and proposals for revision. First, the theory Luhmann adopted from biology as the basis of his own theory was a poor choice since that theory has no (...) explanatory power, being purely descriptive; furthermore, that theory is fundamentally flawed since it implies that viruses are impossible. Second, Luhmann's theory of meaning cannot coherently make the social domain autonomous as he desires since Luhmann does not take into account the distinction between syntax and semantics. By introducing this distinction, making clear that social systems consist of rules, not just communications, and raising the rule concept to the same prominence in social theory as those of actor and system, autonomy can be maintained while avoiding the counterintuitive aspects of Luhmann's theory. (shrink)

Definitions of the term gene typically superimpose molecular genetics onto Mendelism. What emerges are persistent attempts to regard the gene as a unit of structure and/or function, language that creates multiple meanings for the term and fails to acknowledge the diversity of gene architecture. I argue that coherence at the molecular level requires abandonment of the classical unit concept and recognition that a gene is constructed from an assemblage of domains. Hence, a domain set (1) conforms more closely to empirical (...) evidence for genetic organization of DNA regions capable of transcription and (2) has ontological properties lacking in the traditional unit definition. (shrink)

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

The so-called ‘type method’ widely employed in biological taxonomy is often seen as conforming to the causal-historical theory of reference. In this paper, I argue for an alternative account of reference for biological nomenclature in which taxon names are understood as descriptive names. A descriptive name, as the concept came to be known from the work of Gareth Evans, is a referring expression introduced by a definite description. There are three main differences between the DN and the causal account. First, (...) according to the DN account, rather than fixing a name to a referent, the assignment of a type specimen to serve as the name-bearer for a taxon should be seen as performatively establishing a synonymy between a name and a definite description of the form “the taxon whose type is t”. Each taxon name is therefore associated with a criterion of application, a semantic rule that establishes the connection between the name and the descriptive content. This is the second major difference from the causal account: taxon names do have some descriptive content associated with them. The final locus of dissent concerns the strength of the modality resulting from the usage of taxon names. In order to address this point, I use the DN account to focus on the debate between Matt Haber and Joeri Witteveen concerning misidentification of type specimens, misapplication of names, and the truth conditions of Joseph LaPorte’s de dicto necessary sentence “Necessarily, any species with a type specimen contains its type specimen”. Using a pragmatic variant of the distinction between attributive and referential uses of descriptions, I argue that a metalinguistic version of the de dicto sentence is in fact falsified, as previously argued by Haber. (shrink)

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

Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the National Academy of (...) Science of the USA, focusing on the recent period 2003–2015. This comparison reveals a significant mismatch between the distributions of these topics. I examine plausible explanations for that mismatch. Finally, I argue that many biological topics underrepresented in philosophy of biology raise important philosophical issues and should therefore play a more central role in future philosophy of biology. (shrink)

Various philosophers and evolutionary biologists have recently defended the thesis that species are individuals rather than sets. A decade of debates, however, did not suffice to settle the matter. Conceptual analysis shows that many of the key terms involved are ambiguous. Current disagreements should dissolve once this is recognized. Explication of the concepts involved leads to new programs for philosophical research. It could also help biology by showing how extant controversies concerning evolution may have conceptual rather than factual roots.

The view that species are individuals, as developed by Ghiselinand Hull, has been touted as explaining the role of type specimens intaxonomy. The kinship of this explanation with the Kripke-Putnam theoryof names has long been recognized. In light of this kinship, however,Hull's account of type specimens can be seen to entail two relatedinscrutability problems – unreasonable limits placed on the natureand extent of biological knowledge. An appreciation for these problemsinvites us to consider the proper relation between metaphysical andepistemological inquires in (...) the philosophy of science. (shrink)

The present paper discusses Kitcher’s framework for studying conceptual change and progress. Kitcher’s core notion of reference potential is hard to apply to concrete cases. In addition, an account of conceptual change as change in reference potential misses some important aspects of conceptual change and conceptual progress. I propose an alternative framework that focuses on the inferences and explanations supported by scientific concepts. The application of my approach to the history of the gene concept offers a better account of the (...) conceptual progress that occurred in the transition from the Mendelian to the molecular gene than Kitcher’s theory. (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)