Many areas of science develop by discovering mechanisms and role functions. Cummins' (1975) analysis of role functions-according to which an item's role function is a capacity of that item that appears in an analytic explanation of the capacity of some containing system-captures one important sense of "function" in the biological sciences and elsewhere. Here I synthesize Cummins' account with recent work on mechanisms and causal/mechanical explanation. The synthesis produces an analysis of specifically mechanistic role functions, one that uses the characteristic (...) active, spatial, temporal, and hierarchical organization of mechanisms to add precision and content to Cummins' original suggestion. This synthesis also shows why the discovery of role functions is a scientific achievement. Discovering a role function (i) contributes to the interlevel integration of multilevel mechanisms, and (ii) provides a unique, contextual variety of causal/mechanical explanation. (shrink)

Biologists are nearing the creation of the first fully synthetic eukaryotic genome. Does this mean that we still soon be able to create genomes that are parts of an existing genetic lineage? If so, it might be possible to bring back extinct species. But do genomes that are synthetically assembled, no matter how similar they are to native genomes, really belong to the genetic lineage on which they were modelled? This article will argue that they are situated within the same (...) genetic lineage. To see why requires closely examining whether material overlap between parents and offspring is a necessary feature of biological reproduction. The processes used to create synthetic genomes shows that these processes are a form of scaffolded reproduction because they use external machinery and take ownership of the material parts used to create synthetic genomes. Closely examining these processes also reveals, surprisingly, that ‘synthetic reproduction’ can take place between entities that don’t participate in the same biological lineages. 1Introduction2The Argument for Lineage-less Genomes3Synthetic Eukaryotic Chromosomes and Material Overlap4Biological Reproduction, Material, and Information5Synthetic Reproductive Processes and Their Implications. (shrink)

David Hume's Treatise of Human Nature, composed before the author was twenty-eight years old, was published in 1739 and 1740. In revising the late L.A. Selby-Bigge's edition of Hume's Treatise Professor Nidditch corrected verbal errors and took account of Hume's manuscript amendments. He also supplied the text of theof the Treatise following the original 1740 edition and provided an apparatus of variant readings.

This is a short overview of the biological functions debate in philosophy. While it was fairly comprehensive when it was written, my short book ​A Critical Overview of Biological Functions has largely supplanted it as a definitive and up-to-date overview of the debate, both because the book takes into account new developments since then, and because the length of the book allowed me to go into substantially more detail about existing views.

Teleological terms such as "function" and "design" appear frequently in the biological sciences. Examples of teleological claims include: A (biological) function of stotting by antelopes is to communicate to predators that they have been detected. Eagles' wings are (naturally) designed for soaring. Teleological notions were commonly associated with the pre-Darwinian view that the biological realm provides evidence of conscious design by a supernatural creator. Even after creationist viewpoints were rejected by most biologists there remained various grounds for concern about the (...) role of teleology in biology, including whether such terms are: 1. vitalistic (positing some special "life-force"); 2. requiring backwards causation (because future outcomes explain present traits); 3. incompatible with mechanistic explanation (because of 1 and 2); 4. mentalistic (attributing the action of mind where there is none); 5. empirically untestable (for all the above reasons). Opinions divide over whether Darwin's theory of evolution provides a means of eliminating teleology from biology, or whether it provides a naturalistic account of the role of teleological notions in the science. Many contemporary biologists and philosophers of biology believe that teleological notions are a distinctive and ineliminable feature of biological explanations but that it is possible to provide a naturalistic account of their role that avoids the concerns above. Terminological issues sometimes serve to obscure some widely-accepted distinctions. (shrink)

In this paper I defend an etiological theory of biological functions (according to which the proper function of a trait is the effect for which it was selected by natural selection) against three objections which have been influential. I argue, contrary to Millikan, that it is wrong to base our defense of the theory on a rejection of conceptual analysis, for conceptual analysis does have an important role in philosophy of science. I also argue that biology requires a normative notion (...) of a "proper function", and that a normative notion is not ahistorical. (shrink)

This book is a critical survey of and guidebook to the literature on biological functions. It ties in with current debates and developments, and at the same time, it looks back on the state of discourse in naturalized teleology prior to the 1970s. It also presents three significant new proposals. First, it describes the generalized selected effects theory, which is one version of the selected effects theory, maintaining that the function of a trait consists in the activity that led to (...) its differential persistence or reproduction in a population, and not merely its differential reproduction. Secondly, it advances “within-discipline pluralism” (as opposed to between-discipline pluralism) a new form of function pluralism, which emphasizes the coexistence of function concepts within diverse biological sub-disciplines. Lastly, it provides a critical assessment of recent alternatives to the selected effects theory of function, namely, the weak etiological theory and the systems-theoretic theory. The book argues that, to the extent that functions purport to offer causal explanations for the existence of a trait, there are no viable alternatives to the selected effects view. -/- The debate about biological functions is still as relevant and important to biology and philosophy as it ever was. Recent controversies surrounding the ENCODE Project Consortium in genetics, the nature of psychiatric classification, and the value of ecological restoration, all point to the continuing relevance to biology of philosophical discussion about the nature of functions. In philosophy, ongoing debates about the nature of biological information, intentionality, health and disease, mechanism, and even biological trait classification, are closely related to debates about biological functions. (shrink)

Aristotle’s theory of spontaneous generation offers many puzzles to those who wish to understand his theory both within the context of his biology and within the context of his more general philosophy of nature. In this paper, I approach the difficult and vague elements of Aristotle’s account of spontaneous generation not as weaknesses, but as opportunities for an interesting glimpse into the thought of an early scientist struggling to reconcile evidence and theory. The paper has two goals: to give as (...) charitable and full an account as possible of what Aristotle’s theory of spontaneous generation was, and to examine some of its consequences; and to reflect on Aristotle as a scientist, and what his comments reveal about how he approached a difficult problem. In particular, I propose that the well-recognized problem of the incompatibility between Aristotle’s concept of spontaneity and his theory of spontaneous generation presents an opportunity for insight into his scientific methodology when approaching ill-understood phenomena. (shrink)

Willard van Orman Quine once said that he had a preference for a desert ontology. This was in an earlier day when concerns with logical structure and ontological simplicity reigned supreme. Ontological genocide was practiced upon whole classes of upper-level or ‘derivative’ entities in the name of elegance, and we were secure in the belief that one strayed irremediably into the realm of conceptual confusion and possible error the further one got from ontic fundamentalism. In those days, one paid more (...) attention to generic worries about possible errors than to actual errors derived from distancing oneself too far from the nitty-gritty details of actual theory, actual inferences from actual data, the actual conditions under which we posited and detected entities, calibrated and ‘burned in’ instruments, identified and rejected artifacts, debugged programs and procedures, explained the mechanisms behind regularities, judged correlations to be spurious, and in general, to the real complexities and richness of actual scientific practice. (shrink)

Biologists studying complex causal systems typically identify some factors as causes and treat other factors as background conditions. For example, when geneticists explain biological phenomena, they often foreground genes and relegate the cellular milieu to the background. But factors in the milieu are as causally necessary as genes for the production of phenotypic traits, even traits at the molecular level such as amino acid sequences. Gene-centered biology has been criticized on the grounds that because there is parity among causes, the (...) “privileging” of genes reflects a reductionist bias, not an ontological difference. The idea that there is an ontological parity among causes is related to a philosophical puzzle identified by John Stuart Mill: what, other than our interests or biases, could possibly justify identifying some causes as the actual or operative ones, and other causes as mere background? The aim of this paper is to solve this conceptual puzzle and to explain why there is not an ontological parity among genes and the other factors. It turns out that solving this puzzle helps answer a seemingly unrelated philosophical question: what kind of causal generality matters in biology? (shrink)

Two separate research programs have revealed two different factors that feature in our judgments of whether some entity persists. One program—inspired by Knobe—has found that normative considerations affect persistence judgments. For instance, people are more inclined to view a thing as persisting when the changes it undergoes lead to improvements. The other program—inspired by Kelemen—has found that teleological considerations affect persistence judgments. For instance, people are more inclined to view a thing as persisting when it preserves its purpose. Our goal (...) in this paper is to determine what causes persistence judgments. Across four studies, we pit normative considerations against teleological considerations. And using causal modeling procedures, we find a consistent, robust pattern with teleological and not normative considerations directly causing persistence judgments. Our findings put teleology in the driver’s seat, while at the same time shedding further light on our folk notion of an object. (shrink)

In describing the flawless regularity of developmental processes and the correlation between changes at certain genetic loci and changes in morphology, biologists frequently employ two metaphors: that genes ‘control’ development, and that genomes embody ‘programs’ for development. Although these metaphors have an admirable sharpness and punch, they lead, when taken literally, to highly distorted pictures of developmental processes. A more balanced, and useful, view of the role of genes in development is that they act as suppliers of the material needs (...) of development and, in some instances, as context‐dependent catalysts of cellular changes, rather than as ‘controllers’ of developmental progress and direction. The consequences of adopting this alternative view of development are discussed. (shrink)

Ernest Nagel, one of the world's leading philosophers of science, is an unreconstructed empirical rationalist who continues to believe that the logical methods of the modern natural sciences are the most successful instruments men have devised to acquire reliable knowledge. This book presents "Teleology Revisited"-the John Dewey lectures delivered at Columbia University- and eleven of Nagel's articles on the philosophy of science.

How shall we understand apparently teleological systems? What explains their persistence and their plasticity? Here I argue that all seemingly goal-directed systems—e.g., a food-seeking organism, human-made devices like thermostats and torpedoes, biological development, human goal seeking, and the evolutionary process itself—share a common organization. Specifically, they consist of an entity that moves within a larger containing structure, one that directs its behavior in a general way without precisely determining it. If so, then teleology lies within the domain of the theory (...) of compositional hierarchies. (shrink)

This article presents an analogical account of the meaning of function attributions in biology. To say that something has a function analogizes it with an artifact, but since the analogy rests on a necessary (but possibly insufficient) basis, function statements can still be assessed as true or false in an objective sense.

Damasio, an eminent neuroscientist explores the science of human emotion and what the great Dutch philosopher Baruch Spinoza can teach of how and why we feel. Damasio shows how joy and sorrow, those most defining of human feelings, are in fact the cornerstones of our survival and culture.

Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...) important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

Based upon a study of arguments in the Treatise and the Enquiry, this work proposes a theory of motivation and of the making of moral judgements which defends much of John Hume's sentimentalism. However the author also argues for an equal partnership view of reason and feeling.

In addition to being one of the world's most influential philosophers, Aristotle can also be credited with the creation of both the science of biology and the philosophy of biology. He was the first thinker to treat the investigations of the living world as a distinct inquiry with its own special concepts and principles. This book focuses on a seminal event in the history of biology - Aristotle's delineation of a special branch of theoretical knowledge devoted to the systematic investigation (...) of animals. Aristotle approached the creation of zoology with the tools of subtle and systematic philosophies of nature and of science that were then carefully tailored to the investigation of animals. The papers collected in this volume, written by a pre-eminent figure in the field of Aristotle's philosophy and biology, examine Aristotle's approach to biological inquiry and explanation, his concepts of matter, form and kind, and his teleology. (shrink)

Preface ix 1 Meaning and the Means to an Understanding of Ends 2 Why Is an Eye? 21 3 Adaptationism and Engineering 39 4 On Five "-Isms" 67 5 Function, Selection, and Explanation 87 6 Deflating Function 119 7 Artifacts and Organisms 139 References 167 Index 177.

INTRODUCTION The appeal to teleological principles of explanation within the body of natural science has had an unfortunate history. ...

In Aristotle's teleological view of the world, natural things come to be and are present for the sake of some function or end. Whereas much of recent scholarship has focused on uncovering the physical underpinnings of Aristotle's teleology and its contrasts with his notions of chance and necessity, this book examines Aristotle's use of the theory of natural teleology in producing explanations of natural phenomena. Close analyses of Aristotle's natural treatises and his Posterior Analytics show what methods are used for (...) the discovery of functions or ends that figure in teleological explanations, how these explanations are structured, and how well they work in making sense of phenomena. The book will be valuable for all who are interested in Aristotle's natural science, his philosophy of science, and his biology. (shrink)

This book offers a philosophy for error-prone humans trying to understand messy systems in the real world.

Aristotle is properly recognized as the originator of the scientific study of life. This is true despite the fact that many earlier Greek natural philosophers occasionally speculated on the origins of living things and much of the Hippocratic medical corpus, which was written before or during Aristotle's lifetime, displays a serious interest in human anatomy, physiology and pathology. Even Plato has Timaeus devote a considerable part of his speech to the human body and its functions (and malfunctions). Nevertheless, before Aristotle, (...) only a few of the Hippocratic treatises are both systematic and empirical, and their focus is exclusively on human health and disease. (shrink)

Traditionally, species have been treated as classes. In fact they may be considered individuals. The logical term “individual” has been confused with a biological synonym for “organism.” If species are individuals, then: 1) their names are proper, 2) there cannot be instances of them, 3) they do not have defining properties, 4) their constituent organisms are parts, not members. “ Species " may be defined as the most extensive units in the natural economy such that reproductive competition occurs among their (...) parts. Species are to evolutionary theory as firms are to economic theory: this analogy resolves many issues, such as the problems of “reality” and the ontological status of nomenclatorial types. (shrink)