In recent years two groups of taxonomists have attempted to influence the general goals and methods of biological classification. The first group, which emerged in the late 1950’s, has been called variously neo-Adansonian, numerical, computer and phenetic taxonomy. The founders of this school, Robert R. Sokal and P.H.A. Sneath, termed their unified approach to systematics “neo-Adansonian” because of the affinities which they saw between their views and those of the 18th century botanist, Michel Adanson (1727-1806). Today little mention is made (...) of Adanson. His ideas turned out not to be as prescient as Sokal and Sneath had at first thought. Besides, he had served his purpose as a patron saint ([79], p. 23). Sokal and Sneath also termed their approach “numerical” because they believed that taxonomists should make greater use of available mathematical techniques. Not only should taxonomic characters be coded quantitatively but also estimates of affinity should be made on the basis of explicitly stated clustering procedures. (shrink)

Francis Collins, the director of the NEH and well-known Christian, has said that agnosticism is a bit of a cop-out. Either be a Christian or be an atheism, but have the guts to make up your mind. I shall argue in a positive way for agnosticism, showing that it can be as vibrant a position as belief or non-belief. It gives you a renewed appreciation of life and the world in which we live.

The extensive philosophical discussions and analyses in recent decades of function-talk in biology have done much to clarify what biologists mean when they ascribe functions to traits, but the basic metaphysical question—is there genuine teleology and design in the natural world, or only the appearance of this?—has persisted, as recent work both defending, and attacking, teleology from a Darwinian perspective, attest. I argue that in the context of standard contemporary evolutionary theory, this is for the most part a verbal, rather (...) than a substantive dispute: the disputants are talking past one another. To justify this claim I develop a general framework within which reductionist views, such as the standard ‘etiological’ account of biofunctions, occupy an intermediate position between what I call full-blooded realism and full-blooded anti-realism, and suggest that whether such views count as ‘realist’ views has no objective, theory-neutral answer. (shrink)

Though only established as a discipline since the 1970s, philosophy of biology has already triggered investigations about its own history The Oxford handbook of philosophy of biology, Oxford University Press, New York, pp 11–33, 2008). When it comes to assessing the road since travelled—the research questions that have been pursued—manuals and ontologies also offer specific viewpoints, highlighting dedicated domains of inquiry and select work. In this article, we propose to approach the history of the philosophy of biology with a complementary (...) data-driven perspective that makes use of statistical algorithms applied to the complete full-text corpus of one major journal of the field—Biology and Philosophy—from its launch in 1986 up until 2017. By running text-mining and topic-modeling algorithms, we identified 67 key research topics that span across these 32 years. We also investigated the evolution of these topics over time and their fluctuating significance in the journal articles. Our results concur with known episodes or traits of the discipline—for instance, the significance of evolution-related topics or the decrease of articles with a marked historical dimension—but also highlight a diversity of topics that is much richer than what is usually acknowledged. (shrink)

I present and defend the generalized selected effects theory (GSE) of function. According to GSE, the function of a trait consists in the activity that contributed to its bearer’s differential reproduction, or differential retention, within a population. Unlike the traditional selected effects (SE) theory, it does not require that the functional trait helped its bearer reproduce; differential retention is enough. Although the core theory has been presented previously, I go significantly beyond those presentations by providing a new argument for GSE (...) and defending it from a recent objection. I also sketch its implications for teleosemantics and philosophy of medicine. (shrink)

Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory (...) will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metabolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science. (shrink)

According to the received view of scientific theories, a scientific theory is an axiomatic-deductive linguistic structure which must include some set of guidelines (“correspondence rules”) for interpreting its theoretical terms with reference to the world of observable phenomena. According to the semantic view, a scientific theory need not be formulated as an axiomatic-deductive structure with correspondence rules, but need only specify models which are said to be “isomorphic” with actual phenomenal systems. In this paper, I consider both the received and (...) semantic views as they bear on the issue of how a theory relates to the world (Section 1). Then I offer a critique of some arguments frequently put forth in support of the semantic view (Section 2). Finally, I suggest a more convincing “meta-methodological” argument (based on the thought of Bernard Lonergan) in favor of the semantic view (Section 3). (shrink)

Any theory of reduction that goes only so far as carried in Parts I and II does only half the job. Prima facie at least, there are cases of would-be reduction which seem torn between two conflicting intuitions. On the one side there is a strong intuition that reduction is involved, and a strongly retentive reduction at that. On the other side it seems that the concepts at one level cross-classify those at the other level, so that there is no (...) way to identify properties at one level with those at the other. There is evidence to suggest that there will be no unique mental state/neural state association that can be set up, because, e.g., many different parts of the nervous system are all capable of taking over ‘control’ of the one mental function. And it is alleged that infinitely many, worse: indefinitely many, different bio-chemo-physical states could correspond to the economic property ‘has a monetary system of economic exchange’; and similarly for the property ‘has just won a game of tennis’. Yet one doesn't want an economic system or a game of tennis to be some ghostly addition to the actual bio-chemo-physical processes and events involved. Similarly one hopes that neurophysiology allied with the rest of natural science will render human experience and behaviour explicable. (shrink)

Former discussions of biological generalizations have focused on the question of whether there are universal laws of biology. These discussions typically analyzed generalizations out of their investigative and explanatory contexts and concluded that whatever biological generalizations are, they are not universal laws. The aim of this paper is to explain what biological generalizations are by shifting attention towards the contexts in which they are drawn. I argue that within the context of any particular biological explanation or investigation, biologists employ two (...) types of generations. One type identifies causal regularities exhibited by particular kinds of biological entities. The other type identifies how these entities are distributed in the biological world. (shrink)

Doren Recker has criticized the prevailing accounts of Darwin's argument for the theory of natural selection in the Origin of Species. In this note I argue that Recker fails to distinguish between a deductive short argument for the principle of natural selection, and a non-deductive, long argument which aims at establishing that the principle has explanatory power in the various domains of application. I shall try to show that the semantic view of theories, especially in its structuralist form, makes it (...) easy to distinguish between the two arguments and to explain how Darwin's long argument counts as one argument. I also raise a question about Recker's views on Darwin's mid-Victorian background, arguing that Newton's First Rule of Reasoning was not just a constraint on hypotheses involving unobservables, but a general request to keep conjecture and certainty apart. (shrink)

In recent years Sir Karl Popper has been turning his attention more and more towards philosophical problems arising from biology, particularly evolutionary biology. Popper suggests that perhaps neo-Darwinian evolutionary theory is better categorized as a metaphysical research program than as a scientific theory. In this paper it is argued that Popper can draw his conclusions only because he is abysmally ignorant of the current status of biological thought and that Popper's criticisms of biology are without force and his suggestions for (...) its improvement are without need. Also it is suggested that Popper's desire to see scientific theory growth as being in some sense evolutionary may have led him astray about biology. And conversely it is suggested that since his claims about biology are not well taken his analysis of theory growth may well bear reexamination. (shrink)

Functional explanation in the social sciences is the focal point for conflict between individualistic and social modes of explanation. While the agent thought she was acting for reasons, the functional explanation seems to reveal the hidden strings of the puppet master. This essay argues that the conflict is merely apparent. The erotetic model of explanation is used to analyze the forms of intentional action and functional explanations. Two explanations conflict if either the presuppositions of their respective why-questions conflict or the (...) typical answers identified by their relevance criteria conflict. While a functional explanation may have the same topic and foil as an intentional action explanation, both the why-questions and their typical answers are compatible. (shrink)

There are several interpretations of the argument structure of Darwin's Origin of Species, representing Covering-Law, Inference-to-the-Best-Explanation, and (more recently) Semantic models. I argue that while all three types of interpretation enjoy some textual support, none succeeds in capturing the overall strategy of the Origin, consistent with Darwin's claim that it is 'one long argument'. I provide detailed criticisms of all three current models, and then offer an alternative interpretation based on the view that there are three main argument strategies in (...) the Origin, all supporting the 'causal efficacy' of Darwin's theory. This interpretation provides both a more unified treatment of the text, and some important implications concerning the relation between general philosophical models of scientific theory support and specific historical cases. (shrink)

My thesis is that biology is most plausibly regarded as a universal, as distinct from a provincial, science. First, I develop the general notion of a provincial science, formulate three criteria for applying the concept, and present brief examples illustrating their use. Second, I argue that a consideration of population genetics as a characteristic example of a basic biological theory strengthens the prior presumption that biology is not a provincial science. Finally, I examine two arguments to the effect that biology (...) is a provincial science. The first concerns biology's exclusively terrestrial evidence base, the second the logical character of its laws. I introduce considerations that weaken the persuasiveness of the first argument and then show that the second one rests upon a false premise and so should be rejected. (shrink)

Biological species have been treated traditionally as spatiotemporally unrestricted classes. If they are to perform the function which they do in the evolutionary process, they must be spatiotemporally localized individuals, historical entities. Reinterpreting biological species as historical entities solves several important anomalies in biology, in philosophy of biology, and within philosophy itself. It also has important implications for any attempt to present an "evolutionary" analysis of science and for sciences such as anthropology which are devoted to the study of single (...) species. (shrink)

This paper takes a critical look at the idea that evolutionary theory is a statistical theory. It argues that despite the strong instrumental motivation for statistical theories, they are not necessary to explain deterministic systems. Biological evolution is fundamentally a result of deterministic processes. Hence, a statistical theory is not necessary for describing the evolutionary forces of genetic drift and natural selection, nor is it needed for describing the fitness of organisms. There is a computational advantage to the statistical theory (...) of population genetics, but population genetics succeeds only by eliminating causes from its account of evolutionary change. (shrink)

An examination of difficulties in three standard accounts of functions leads to the suggestion that sentences of the form "the function of x is to do y" are used to make a variety of different claims, all of which involve a means-end relationship and the idea of design, or use, or benefit. The analysis proposed enables us to see what is right and also wrong with accounts that analyze the meaning of function statements in terms of good consequences, goals, and (...) etiological explanation. It also enables us to show that function sentences can be used in providing various types of explanations, including, in certain cases, noncausal explanations of the presence of the item with the function. (shrink)

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)

Although life and questions connected with its definition among traditional philosophical topics, at the beginning of the twenty-first century and after roughly two and a half thousand years of philosophical tradition no satisfactory definition of life is at one’s disposal. Though difficulties bond up with life definition don´t accompany philosophy alone, but also almost all fields touched by this topic. Causes of this state of affairs can be viewed as a combination of several complementary connected facts. Those facts are in (...) the text stated as reasons against the possibility of creating universal definition of life and apply here one by one to the origin of life a postulated boarder line between life and nonlife, evolution of life and its variedness, multiplicity of definitions of life and still going discoveries of new organisms, philosophical tradition and lack of clarity of concepts, evolution of life as a historical process, critique of definitions of life from the point of view of „sample one“ and reflection of the concept life by conceptual analysis. Particular sources are about to be analyzed from the point of philosophy of biology with care for philosophical tradition, to questions linked with life and its selected definitions, to actual findings and explorations focused on life and possible contribution of philosophy to the endeavor of finding definition of life as such. Ground of proposed text is naturalism, physicalism and reductionism. (shrink)

Classifying is a fundamental operation in the acquisition of knowledge. Taxonomic theory can help students of cognition, evolutionary psychology, ethology, anatomy, and sociobiology to avoid serious mistakes, both practical and theoretical. More positively, it helps in generating hypotheses useful to a wide range of disciplines. Composite wholes, such as species and societies, are “individuals” in the logical sense, and should not be treated as if they were classes. A group of analogous features is a natural kind, but a group of (...) homologous features is not. Imposing hypotheses justified only on the basis of nominalist, realist, phenomenalist, or conceptualist metaphysics upon the neurophysiology of organisms or upon the causes of behavior exemplifies the “psychologist's fallacy” of William James. Levels should be distinguished from their members and from classes of levels, and the ontological status of entities ranked at levels should be made clear. It is important not to confuse such categories as substance and process with one another. Several genetical terms, such as “gene” and chromosome,” are even more equivocal than has been realized. Discussions about units of selection, behavior, and thinking suffer from the ambiguity of a “unit of” an entity. An important source of misunderstanding about natural selection is the habit of treating it as an “agent”: in an important sense, natural selection does not “act” at all. (shrink)

The dissertation criticizes two analogical applications of Darwinism to the spheres of mind and culture: the Darwinian approach to creativity and memetics. These theories rely on three basic analogies: the ontological analogy states that the basic ontological units of culture are so-called memes, which are replicators like genes; the origination analogy states that novelty in human creativity emerges in a "blind" Darwinian manner; and the explanatory units of selection analogy states that memes are "egoistic" and that they can spread independently (...) of our mind. The detailed philosophical analysis offered in the dissertation shows that these three analogies rely on either wrong or trivial statements: they provide either wrong or no new descriptions or explanations of the phenomena at hand. In Chapter One, I introduce the diverse ways, in which contemporary Darwinism is used today outside of evolutionary biology. Chapter Two explains what it means to claim that something evolves in a Darwinian manner. Chapter Three to Five address each of the three analogies separately. Darwinism applied to culture and mind, at least in the way discussed in this study, is not a dangerous idea. It leads either to wrong claims or to a re-telling in Darwinian terms of what we have already known. (shrink)

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.

The purpose of this paper is to test the contemporary concept of biological species against some of the problems caused by treating species as spatiotemporally extended entities governed by criteria of persistence, identity, etc. After outlining the general problem of symmetric division in natural objects, I set out some useful distinctions (section 1) and confirm that species are not natural kinds (section 2). Section 3 takes up the separate issue of species definition, focusing on the Biological Species Concept (BSC). Sections (...) 4 and 5 examine the matter of species identity over space and time respectively, as determined by the BSC. Both gradualistic and punctuated equilibrium models of speciation are discussed. In section 6 I argue that the BSC fails to determine adequate criteria for dealing with certain kinds of speciation. Section 7 moves speculatively beyond the BSC to a brief examination of alternatives. (shrink)

The term “cladist” has distinct meanings in distinct contexts. Communication between philosophers, historians, and biologists has been hindered by different understandings of the term in various contexts. In this paper I trace historical and conceptual connections between several broadly distinct senses of the term “cladist”. I propose seven specific definitions that capture distinct contemporary uses. This serves to disambiguate some cases where the meaning is unclear, and will help resolve apparent disagreements that in fact result from conflicting understandings of the (...) term. (shrink)

This article considers claims that biology should seek general theories similar to those found in physics but argues for an alternative framework for biological theories as collections of prototypical interlevel models that can be extrapolated by analogy to different organisms. This position is exemplified in the development of the Hodgkin‐Huxley giant squid model for action potentials, which uses equations in specialized ways. This model is viewed as an “emergent unifier.” Such unifiers, which require various simplifications, involve the types of heuristics (...) discussed in Wimsatt’s writings on reduction, but with a twist. Here, the heuristics are used to generate emergent rather than reductive explanations. †To contact the author, please write to: Department of History and Philosophy of Science, University of Pittsburgh, 1017 Cathedral of Learning, Pittsburgh, PA 15260; e‐mail: [email protected]. (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)

The concept of "fitness" is a notion of central importance to evolutionary theory. Yet the interpretation of this concept and its role in explanations of evolutionary phenomena have remained obscure. We provide a propensity interpretation of fitness, which we argue captures the intended reference of this term as it is used by evolutionary theorists. Using the propensity interpretation of fitness, we provide a Hempelian reconstruction of explanations of evolutionary phenomena, and we show why charges of circularity which have been levelled (...) against explanations in evolutionary theory are mistaken. Finally, we provide a definition of natural selection which follows from the propensity interpretation of fitness, and which handles all the types of selection discussed by biologists, thus improving on extant definitions. (shrink)

In a recent paper, William K. Goosens objects to the arguments I set out some time ago attacking the logical empiricist analysis of reduction as applied to genetics. In these works I did not argue against the claim that Mendelian genetics was being reduced to molecular biology. Nor did I conclude, as Goosens asserts, that in the case of genetics, “reduction is insignificant”. To the contrary, I repeatedly stated that, “given our pre-analytic intuitions about reduction,” the reduction of Mendelian to (...) molecular genetics “is a case of reduction, a paradigm case”. And in agreement with Kenneth Schaffner I argued that reduction “in some very important, pre-analytic sense has taken place and is taking place in genetics”. The target of my objections to reduction in genetics was not “reduction” in some pre-analytic sense. Nor was it the various explications which have appeared since. Rather it was the notion of theory reduction set out a generation ago by such logical empiricists as Ernest Nagel, The particular version of this analysis which I chose to attack was that presented by Schaffner ; for Schaffner's later views, see his. I chose Schaffner's explication to attack because I thought it was the best of its kind and because it was the only defense of the logical empiricist analysis at the time which used genetics as one of its chief examples. Contrary to Goosens' assumption, in criticizing Schaffner's explication, I did not thereby “endorse” it. (shrink)

We claim that much of the confusion associated with the "tautology problem" about survival of the fittest is due to the mistake of attributing fitness to individuals instead of to types. We argue further that the problem itself cannot be solved merely by taking fitness as the aggregate cause of reproductive success. We suggest that a satisfying explanation must center not on logical analysis of the concept of general adaptedness but on the empirical analysis of single adapted traits and their (...) causal relationship to changes in allele frequencies. (shrink)

In recent years, philosophers have come to realize that the relationship between science and values raises questions which are both important and not readily answered. It is true that the major figures in that tradition known as ‘logical empiricism’ appreciated that science always exceeds its empirical grasp and that it is necessary for scientists to be guided and constrained by so-called ‘epistemic values,’ these being values (in the words of one supporter) ‘presumed to promote the truth-like character of science, its (...) character as the most secure knowledge available to us of the world we seek to understand.’ However, these values — such things as internal and external consistency, simplicity, predictive accuracy and fertility, unificatory power (consilience) — were considered special. Inasmuch as they could not be reduced to basic principles of logic — and there were attempts to do this — they were still thought of, in some sense, as beyond the vagaries of human emotion. Their importance was not a function of the individual’s personal inclinations, nor of those of the group, whether this group be understood as a closely knit band of researchers or even up to a complete society. (shrink)