This volume provides a guide to the discussion among biologists and philosophersabout the role of concepts such as function and design in an evolutionary understanding oflife.

In the biological realm, a complete explanation of a trait seems to include an explanation in terms of function. It is natural to ask of some trait, "What is its function?" or "What purpose in the organism does the particular trait serve?" or "What is the goal of its activity?" There are several views concerning the appropriate definition of function for biological matters. Two popular views of function with respect to living things are Cummins' organizational account and the Griffiths/Godfrey-Smith modern (...) history account. Whereas Cummins argues that a trait functions so as to contribute to the general organization of some organism's present structure, Griffiths, and Godfrey-Smith argue that a trait functions because of its fitness with respect to the organism's recent evolutionary history. In this paper, I show how these accounts can be made compatible and compliment one another. Given that structure, organization, operational flexibility, function, and evolutionary history are all factors to be considered in an organism's makeup, we should expect that the traits of an organism function the way they do because such traits presently contribute to the overall organization of the organism (Cummins) as well as were selected for in the organism's species' recent ancestry (Griffiths/Godfrey-Smith). (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

Many objects in the world have functions. Typewriters are for typing. Can-openers are for opening cans. Lawnmowers are for cutting grass. That is what these things are for. Every day around the world people attribute functions to objects. Some of the objects with functions are organs or parts of living organisms. Hearts are for pumping blood. Eyes are for seeing. Countless works in biology explain the “Form, Function, and Evolution of... ” everything from bee dances to elephant tusks to pandas’ (...) ‘thumbs’. Many scientific explanations, in areas as diverse as psychology, sociology, economics, medical research, and neuroscience, rest on appeals to the function and/or malfunction of things or systems. They talk of how humans and other organisms or their parts work, what their functions are, why they are present, and how different situations will affect them and how they will react. Philosophers, going back to Aristotle, used to make generous use of functions in describing objects, organisms, their interactions, and even as the basis of ethics and metaphysics. And yet, since the Enlightenment, talk of the function of natural objects, teleological function, began to be viewed with suspicion, as the mechanical model of the world replaced the old Aristotelian model. From a religious standpoint, it used to be easy to see how objects in the natural world could have natural functions, for God was said to instill functions by design throughout Creation. But philosophers became increasingly reluctant to invoke God to solve every difficult philosophical problem, and became unwilling to indulge in such religious explanations of teleology. (shrink)

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

In order to develop the ontology of tendencies for use in the representation of medical knowledge, tendencies are compared with other kinds of entities possessing the realizable-realization structure, specifically: dispositions, propensities, abilities and virtues. The peculiarities of tendencies are discussed and a standard schema of tendency ascription is developed in order to represent the relations between the ascriptions of tendency tokens to particulars and the ascriptions of tendency types to universals. Two nonstandard cases and their epistemic variants are discussed.

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

This is the first philosophical study of artifacts that is book length. In it Randall Dipert develops a theory of what artifacts are and applies it extensively to one of the most complex and intriguing kind of artifacts, art works. He presents his own account of what agents, intentions, and actions are, then uses these notions to clarify what it is for an agent to "make" something. From this starting point, he develops a full theory of artifacts and other artificial (...) things - and, especially, a theory of art works and performances of art works as artifacts. He proposes a theory of nature and of the value of nature as what is essentially nonartificial. Two chapters are devoted to value considerations: merit in artifacts generally, and the evaluation of art works and performance art as artifacts or intentional gestures. Believing that a developed theory of action and philosophy of mind is necessary for a developed aesthetics and philosophy of art, Dipert relies on classical and contemporary research on agency, actions, and intentions, and on the intentionalist theory of mental objects of Brentano and Meinong. Dipert considers artifacts to be physical entities, but he also includes in the definition thoughts, utterances, and performances. This vast category encompasses everyday household objects and tools, streets and edifices, as well as communicative and artistic artifacts. Especially with regard to artistic artifacts, Dipert proposes a theory of expression and communication as actions and extensively discusses the problems of interpreting and recognizing actions, artifacts, and art works. (shrink)

Preface by Daniel C. Dennett Beginning with a general theory of function applied to body organs, behaviors, customs, and both inner and outer representations, ...

This 2001 book offers an examination of functional explanation as it is used in biology and the social sciences, and focuses on the kinds of philosophical presuppositions that such explanations carry with them. It tackles such questions as: why are some things explained functionally while others are not? What do the functional explanations tell us about how these objects are conceptualized? What do we commit ourselves to when we give and take functional explanations in the life sciences and the social (...) sciences? McLaughlin gives a critical review of the debate on functional explanation in the philosophy of science. He discusses the history of the philosophical question of teleology, and provides a comprehensive review of the post-war literature on functional explanation. What Functions Explain provides a sophisticated and detailed Aristotelian analysis of our concept of natural functions, and offers a positive contribution to the ongoing debate on the topic. (shrink)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)