Despite the voluminous literature on biological functions produced over the last 40 years, few philosophers have studied the concept of function as it is used in neuroscience. Recently, Craver (forthcoming; also see Craver 2001) defended the causal role theory against the selected effects theory as the most appropriate theory of function for neuroscience. The following argues that though neuroscientists do study causal role functions, the scope of that theory is not as universal as claimed. Despite the strong prima facie superiority (...) of the causal role theory, the selected effects theory (when properly developed) can handle many cases from neuroscience with equal facility. It argues this by presenting a new theory of function that generalizes the notion of a ‘selection process’ to include processes such as neural selection, antibody selection, and some forms of learning—that is, to include structures that have been differentially retained as well as those that have been differentially reproduced. This view, called the generalized selected effects theory of function, will be defended from criticism and distinguished from similar views in the literature. (shrink)

It is often thought that non-junk or coding DNA is more significant than other cellular elements, including so-called junk DNA. This is for two main reasons: because coding DNA is often targeted by historical or current selection, it is considered functionally special and because its mode of action is uniquely specific amongst the other actual difference makers in the cell, it is considered causally special. Here, we challenge both these presumptions. With respect to function, we argue that there is previously (...) unappreciated reason to think that junk DNA is significant, since it can alter the cellular environment, and those alterations can influence how organism-level selection operates. With respect to causality, we argue that there is again reason to think that junk DNA is significant, since it too is remarkably causally specific. As a result, something is missing from the received view of significance in molecular biology—a view which emphasizes specificity and neglects something we term ‘reach’. With the special case of junk DNA in mind, we explore how to model and understand the causal specificity, reach, and corresponding efficacy of difference makers in biology. The account contains implications for how evolution shapes the genome, as well as advances our understanding of multi-level selection. (shrink)

This paper is concerned with reasonings that purport to explain why certain organisms have certain traits by showing that their actual design is better than contrasting designs. Biologists call such reasonings 'functional explanations'. To avoid confusion with other uses of that phrase, I call them 'design explanations'. This paper discusses the structure of design explanations and how they contribute to scientific understanding. Design explanations are contrastive and often compare real organisms to hypothetical organisms that cannot possibly exist. They are not (...) causal but appeal to functional dependencies between an organism's different traits. These explanations point out that because an organism has certain traits, it cannot be alive if the trait to be explained were replaced by a specified alternative. They can be understood from a mechanistic point of view as revealing the constraints on what mechanisms can be alive. (shrink)

Biological boundaries are important because of what they reveal about the evolution of a lineage, the relationship between organisms of different lineages, the structure and function of particular subsystems of the organism, the interconnection between an organism and its environment, and a myriad of other important issues related to individuality, development, and evolution. Since there is no single unifying theory for all biological sciences, there are various possible theoretical characterizations of what counts as a biological boundary. Theoretical specificity is crucial (...) for the full characterization of a boundary; to this end, it is useful to begin with general properties and then to compare these to those properties specific to a particular biological boundary. This dual heuristic approach—top-down and bottom-up—can then be repeated to increase the robustness of the boundary characterization. In what follows, I explore both the general structural and functional aspects of biological boundaries and those specific to a biological subsystem, which itself is critical to boundary formation, maintenance, and evolution—the vertebrate immune system. It is a remarkable and sobering regularity of nature that organisms remain whole because their parts are constantly being built up and broken down, and this is no less true of their boundaries. The vertebrate immune system is at the center of this process of biological boundary maintenance and breakdown. (shrink)

This book is a synthesis of more than three decades of research into the concept of time and its semiotic nature. If traditional philosophy – and philosophy of time should be no exception – in the shadow of advancing biology can be said to have reached an impasse, one important reason for this, in harmony with Wittgenstein’s vision, appears to have been its lack of appropriate tools for explicating language. The present theory of time proceeds, accordingly, from the exploration of (...) temporal expressions in language as an evolutionary fact. It derives in a hypothetical, coherent feedback process of hierarchically ordered distinctions the semantics of time from its biologically dictated perceptual and cognitive-pragmatic origins. The corresponding abductive-regulative model is anchored in the assumption of biological rhythmization as the very foundation of perception and mental/physical action. Understood to originate in space and spatial perspective, time reveals itself as an instrument for temporal perspective on motion (events and situations) in a process of analysis, i.e., discontinuation of chaos made divisible and continuous by the rhythmical screen. Whereas traditional philosophy of time paid attention almost exclusively to the temporal category of tense, the biopragmatic model sees strong evidence in the perspectival nature of time for ascribing the decisive, and probably universal, role in temporal analysis to the linguistic category of aspect. Aspect may, according to the present findings, be assumed to partake already of change-of-state and cause-effect analysis without which man’s adaptation to new situations – and precondition for survival – would be inconceivable. The proposed model of space/time cognition, inspired by Hegelian dialectics, Heidegger-Gadamer’s hermeneutic circle and Peircean logic, makes Kantian a priori superfluous and liberates time from its enigmatic appearance. For the first time in temporal studies it thus appears possible to derive hypothetically linguistic expressions of time all the way from pretemporal, homogeneous continuity effected by biological rhythmization, via pretemporal metonymic (Gestalt), chunk-wise partitioning – as a general precondition for the perception and, based on primary metaphorization, the cognition of things, space and motion – to temporal analysis/discontinuation proper, primarily by aspectual perspective, and the subsequent synthesized, heterogeneous continuity of temporally ordered events. The conception of time, so disastrous for modern temporal logic, i.e., as moving object assigned extension, divisible continuity (‛linearity’) and direction, can be shown to have emerged as a result of secondary metaphorization. (shrink)

The examples and concepts that Shoemaker cites are rather heterogeneous. Some distinctions need to be drawn. An optimality thesis involves not just an ordering of options, but a value judgment about them. So let us begin by distinguishing minimality from optimality. And the concept of minimality can play a variety of roles, among which I distinguish between extremum descriptions, statements hypothesizing an optimizing process, and methodological recommendations. Finally, I consider how the three categories relate to Shoemaker’s question that “Who is (...) optimizing: the scientist or nature?” . (shrink)

Thought experiments de facto play many different roles in biology: economical, ethical, technical and so forth. This paper, however, is interested in whether there are any distinctive features of biological TEs as such. The question may be settled in the affirmative because TEs in biology have a function that is intimately connected with the epistemological and methodological status of biology. Peculiar to TEs in biology is the fact that the reflexive, typically human concept of finality may be profitably employed to (...) discover mechanical-experimental causal relations in all living beings—with the obvious caveat that we do not hypostatise and interpret this concept as an ontological quality, since this would land one in an implicitly animistic, pre-Galilean view of nature. From a methodical point of view, the concept of finality is an essential assumption as well as a powerful heuristic tool in the practice of biology, that is, in the investigation of living beings in an intersubjectively testable and reproducible way. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)

neglected aspect: knowledge of error, or ‘‘negative’’ knowledge. The development of knowledge of what counts as error occurs via a kind of internal variation and selection, or quasi-evolutionary, process. Processes of reflection generate a hierarchy of principles of error.

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...) confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court. (shrink)

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...) confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court. (shrink)

Several decades ago, Christopher Boorse formulated an influential statistical theory of normative biological functions but it has often been claimed that his theory suffers from insuperable problems such as an inability to handle cases of epidemic and universal diseases. This paper develops a new statistical theory of normative functions that is capable of dealing with the notorious problem of epidemic and universal diseases. The theory is also more detailed than its predecessors and offers other important advantages over them. It is (...) argued here that statistical theories of biological functions should not be so quickly dismissed. (shrink)

In these notes, unadorned page numbers under 350 refer to Dennett (1987) - The Intentional Stance, hereafter referred to as Stance - and ones over 495 refer to Dennett (1988) - mostly to material by him but occasionally to remarks of his critics. Since the notes will focus on disagreements, I should say now that I am in Dennett’s camp and am deeply in debt to his work in the philosophy of mind, which I think is wider, deeper, more various (...) and more fruitful than mine or anyone else’s. Still, I have some ideas and emphases that I think he could profit from. In the final chapter of Stance Dennett compares his work with that of several others, including me. He sees me as having a position like his, the main difference being that I think (as he doesn’t) that our attributions of mental content can always be highly determinate (pp. 347f). In fact, there are differences between us but this isn’t one of them. I want to get this straight, so as to clear the decks for the positive points I am going to make. There is some indeterminacy and there could be lots of it; Dennett’s case for that is unanswerable. As for how much there actually is: I don’t know and don’t even suspect; there is simply no declared issue between Dennett and myself on that. Nor do we disagree on a related matter. If there is no evidence that settles whether the animal believes that P or believes that Q, should we say that nevertheless one of these is right, and it’s just that we can’t know which it is? Dennett says No. I perfectly agree. (shrink)

Organisms' environments are thought to play a fundamental role in determining their fitness and hence in natural selection. Existing intuitive conceptions of environment are sufficient for biological practice. I argue, however, that attempts to produce a general characterization of fitness and natural selection are incomplete without the help of general conceptions of what conditions are included in the environment. Thus there is a "problem of the reference environment"—more particularly, problems of specifying principles which pick out those environmental conditions which determine (...) fitness. I distinguish various reference environment problems and propose solutions to some of them. While there has been a limited amount of work on problems concerning what I call "subenvironments", there appears to be no earlier work on problems of what I call the "whole environment". The first solution I propose for a whole environment problem specifies the overall environment for natural selection on a set of biological types present in a population over a specified period of time. The second specifies an environment relevant to extinction of types in a population; this kind of environment is especially relevant to certain kinds of long-term evolution. (shrink)