Philosophy of biology is often said to have emerged in the last third of the twentieth century. Prior to this time, it has been alleged that the only authors who engaged philosophically with the life sciences were either logical empiricists who sought to impose the explanatory ideals of the physical sciences onto biology, or vitalists who invoked mystical agencies in an attempt to ward off the threat of physicochemical reduction. These schools paid little attention to actual biological science, and as (...) a result philosophy of biology languished in a state of futility for much of the twentieth century. The situation, we are told, only began to change in the late 1960s and early 1970s, when a new generation of researchers began to focus on problems internal to biology, leading to the consolidation of the discipline. In this paper we challenge this widely accepted narrative of the history of philosophy of biology. We do so by arguing that the most important tradition within early twentieth-century philosophy of biology was neither logical empiricism nor vitalism, but the organicist movement that flourished between the First and Second World Wars. We show that the organicist corpus is thematically and methodologically continuous with the contemporary literature in order to discredit the view that early work in the philosophy of biology was unproductive, and we emphasize the desirability of integrating the historical and contemporary conversations into a single, unified discourse. (shrink)

This paper provides a detailed examination of Kit Fine’s sizeable contribution to the development of a neo‐Aristotelian alternative to standard mereology; I focus especially on the theory of ‘rigid’ and ‘variable embodiments’, as defended in Fine 1999. Section 2 briefly describes the system I call ‘standard mereology’. Section 3 lays out some of the main principles and consequences of Aristotle’s own mereology, in order to be able to compare Fine’s system with its historical precursor. Section 4 gives an exposition of (...) Fine’s theory of embodiments and goes on to isolate a number of potential concerns to which this account gives rise. In particular, I argue that Fine’s theory threatens to proliferate primitive sui generis relations of parthood and composition, whose characteristics must be stipulatively imposed on them, relative to particular domains; given its ‘superabundance’ of objects, Fine’s system far outstrips the already inflated ontological commitments of standard mereology; and there is a legitimate question as to why we should consider Fine’s primitive and sui generis relations of parthood and composition to be genuinely mereological at all, given their formal profile. These three objections lead me to conclude that we ought to explore other avenues that preserve the highly desirable, hylomorphic, features of Fine’s mereology, while avoiding its methodological and ontological excesses. (shrink)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his work was (...) disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

Peter Ludlow presents the first book on the philosophy of generative linguistics, including both Chomsky's government and binding theory and his minimalist ...

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Scientific discourse leaves implicit a vast amount of knowledge, assumes that this background knowledge is taken into account – even taken for granted – and treated as undisputed. In particular, the terminology in the empirical sciences is treated as antecedently understood. The background knowledge surrounding a theory is usually assumed to be true or approximately true. This is in sharp contrast with logic, which explicitly ignores underlying presuppositions and assumes uninterpreted languages. We discuss the problems that background knowledge may cause (...) for the formalization of scientific theories. In particular, we will show how some of these problems can be addressed in the context of the computational representation of scientific theories. (shrink)

Many bioethical arguments rely implicitly on the assumption that the concept of “human part” is one on which everyone must agree, because it is unambiguous. But various parties interpret this “unambiguous” term in incompatible ways, leading to contention. This article is an informal presentation of a topomereological system on whose preferred interpretation several distinct but related meanings of “human part” can be isolated: part of a human body, part of the completion of a human body, and part of a human (...) being. A case is analyzed (the first total artificial heart (TAH) implantation), demonstrating in the process much of the apparatus of the system. By means of a casuistic methodology, the analysis is translated into recommendations for the ethical conduct of future TAH research. The more general conclusion, however, is that formal methods may provide useful tools for clarifying thought processes and organizing arguments in debates over bioethical issues. (shrink)

Philosophical analysis of ecological theories has lagged behind the study of evolutionary theory. The semantic conception of scientific theories, which has been employed successfully in the analysis of evolutionary theory, is adopted here to analyse ecological theory. Two general problems in ecology are discussed. One arises from the continued use of covering law models in ecology, and the other concerns the applicability of ecological theory in conservation biology. The semantic conception of ecological theories is used to resolve these problems.

There is a strong philosophical intuition that direct study of the brain can and will constrain the development of psychological theory. When this intuition is tested against case studies on the neurophysiology and psychology of perception and memory, it turns out that psychology has led the way toward knowledge of neurophysiology. An abstract argument is developed to show that psychology can and must lead the way in neuroscientific study of mental function. The opposing intuition is based on mainly weak arguments (...) about the fundamentality or objectivity of physics or physiology in relation to psychology. -/- Philosophy of Science, Vol. 67, Supplement. Proceedings of the 1998 Biennial Meetings of the Philosophy of Science Association. Part II: Symposia Papers (Sep., 2000). (shrink)

Philosophy can shed light on mathematical modeling and the juxtaposition of modeling and empirical data. This paper explores three philosophical traditions of the structure of scientific theory—Syntactic, Semantic, and Pragmatic—to show that each illuminates mathematical modeling. The Pragmatic View identifies four critical functions of mathematical modeling: (1) unification of both models and data, (2) model fitting to data, (3) mechanism identification accounting for observation, and (4) prediction of future observations. Such facets are explored using a recent exchange between two groups (...) of mathematical modelers in plant biology. Scientific debate can arise from different modeling philosophies. (shrink)

In Unifying Biology, Smocovitis offers a series of claimsregarding the relationship between key actors in the synthesisperiod of evolutionary studies and positivism, especially claimsentailing Joseph Henry Woodger and the Unity of Science Movement.This commentary examines Woodger''s possible relevance to key synthesis actors and challenges Smocovitis'' arguments for theexplanatory relevance of logical positivism, and positivism moregenerally, to synthesis history. Under scrutiny, these arguments areshort on evidence and subject to substantial conceptual confusion.Though plausible, Smocovitis'' minimal interpretation – that somegeneralised form of Comtean (...) positivism had a role in synthesishistory – requires more of an evidential basis and must engageexisting scholarship on epistemic reforms in the biological sciencesprior to the synthesis period. Smocovitis is right to investigateepistemology in the synthesis period of evolutionary studies and tolook for links to wider changes in science and philosophy. However,in its present form, Unifying Biology fails to support herbasic interpretation. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

The increasing complexity of biological problems and the increase of mathematical means to handle them on the one hand, and the possibility of automatized computation at the other, necessitate a revaluation of the present interactions between biology and mathematics; in this connection interrelations occur which can be divided into three kinds: mathematical biology, biological mathematics, and general biomathematics or methodology of the biomathematical sciences, by which are meant those scientific branches which arise from the said interactions.

A critical analysis of Woodger's work on formal logic in biology, especially genetics, reveals that the claim for the value of such methods in genetics is misplaced.

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

During the past hundred years or so, those scholars studying science have isolated themselves as much as possible from scientists as well as from workers in other disciplines who study science. The result of this effort is history of science, philosophy of science and sociology of science as separate disciplines. I argue in this paper that now is the time for these disciplinary boundaries to be lowered or at least made more permeable so that a unified discipline of Science Studies (...) might emerge. I discuss representative problems that stand in the way of such an integration. These problems may seem so formidable in the abstract that no one in their right mind would waste their time trying to bring about a unified field of Science Studies. However, those of us who limit ourselves to the study of the biological sciences have already formed a society in which workers from all disciplines can share their expertise -- the International Society for the History, Philosophy and Social Studies of Science. (shrink)