The biological sciences have become increasingly reliant on so-called ‘model organisms’. I argue that in this domain, the concept of a descriptive model is essential for understanding scientific practice. Using a case study, I show how such a model was formulated in a preexplanatory context for subsequent use as a prototype from which explanations ultimately may be generated both within the immediate domain of the original model and in additional, related domains. To develop this concept of a descriptive model, I focus on use of the nematode worm Caenorhabditis elegans and the wiring diagrams that were developed as models of its neural structure. In addition, implications of the concept of a descriptive model, particularly its relevance for the data-phenomena distinction as well as its relation to long-standing debates on realism, are briefly examined.

Caenorhabditis elegans (C. elegans) is a tiny worm that has become the focus of a large number of worldwide research projects examining its genetics, development, neuroscience, and behavior. Recently several groups of investigators have begun to tie together the behavior of the organism and the underlying genes, neural circuits, and molecular processes implemented in those circuits. Behavior is quintessentially organismal—it is the organism as a whole that moves and mates—but the explanations are devised at the molecular and neurocircuit levels, and tested in populations using protocols that span many levels of aggregation. Following a brief review of the main relevant features of C. elegans, I describe some of these circuits, and then discuss two contrasting approaches in behavioral genetics and neural network analysis of the worm. Finally, I outline the rudiments of a “field and focus” explanation model using the two contrasting approaches.

In this paper we argue that an operational organism concept can help to overcome the structural deficiency of mathematical models in biology. In our opinion, the structural deficiency of mathematical models lies mainly in our inability to identify functionally relevant biological characters in biological systems, and not so much in a lack of adequate mathematical representations of biological processes. We argue that the problem of character identification in biological systems is linked to the question of a properly formulated organism concept. Lastly, we demonstrate how a decomposition of an organism into independent characters in the context of a specific biological process—such as adaptation by means of natural selection—depends on the dynamical properties and invariance conditions of the equations that describe this process.

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization—the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established—do not require what would have to be a stipulative sharpening of an organism concept.

Developmental biology has resurfaced in recent years, often without a clearly central role for the organism. The organism is pulled in divergent directions: on the one hand, there is an important body of work that emphasizes the role of the gene in development, as executing and controlling embryological change; on the other hand, there are more theoretical approaches under which the organism disappears as little more than an instance for testing biological generalizations. I press here for the ineliminability of the organism in developmental biology on explanatory grounds. I examine classical work concerned with growth and development, particularly in Drosophila and C. elegans. Some of this work is suggestive of modular development, and accordingly suggests a level below that of the organism as being explanatory. These are not the only type of case. There are other equally well-established results, which indicate greater integration in the developing organism. Though with a modular organization the organism can be thought of as made up of its constituent traits, and though the explanations of these traits may lie in terms of cells or genes, even with modular development the explanations of “genetic” differences require an appeal to the organism. With non-modular organization the organism has an even more central role. This does not mean that these genetic or cellular contributions are unreal in any way, or that development requires some sort of vitalistic contribution; but the genetic contributions make sense only as constituents of the organism, embedded in a larger organic context.

Some central ideas associated with developmental systems theory (DST) are outlined for non-specialists. These ideas concern the nature of biological development, the alleged distinction between “genetic” and “environmental” traits, the relations between organism and environment, and evolutionary processes. I also discuss some criticisms of the DST approach.

In reworking a variety of biological concepts, Developmental Systems Theory (DST) has made frequent use of parity of reasoning. We have done this to show, for instance, that factors that have similar sorts of impact on a developing organism tend nevertheless to be invested with quite different causal importance. We have made similar arguments about evolutionary processes. Together, these analyses have allowed DST not only to cut through some age-old muddles about the nature of development, but also to effect a long-delayed reintegration of development into evolutionary theory.

Our penchant for causal symmetry, however (or ‘causal democracy’, as it has recently been termed), has sometimes been misunderstood. This paper shows that causal symmetry is neither a platitude about multiple influences nor a denial of useful distinctions, but a powerful way of exposing hidden assumptions and opening up traditional formulations to fruitful change.

Developmental systems theory (DST) expands the unit of replication from genes to whole systems of developmental resources, which DST interprets in terms of cycling developmental processes. Expansion seems required by DST's argument against privileging genes in evolutionary and developmental explanations of organic traits. DST and the expanded replicator brook no distinction between biological and cultural evolution. However, by endorsing a single expanded unit of inheritance and leaving the classical molecular notion of gene intact, DST achieves only a nominal reunification of heredity and development. I argue that an alternative conceptualization of inheritance denies the classical opposition of genetics and development while avoiding the singularity inherent in the replicator concept. It also yields a new unit—the reproducer—which genuinely integrates genetic and developmental perspectives. The reproducer concept articulates the non-separability of “genetic” and “developmental” roles in units of heredity, development, and evolution. DST reformulated in terms of reproducers rather than replicators preserves an empirically interesting distinction between cultural and biological evolution.

In this paper I develop three conceptions of the relationship between evolutionary and developmental biology. I further argue that: (a) the choice between them largely turns on as yet unresolved empirical considerations; (b) none of these conceptions demand a fundamental conceptual reevaluation of evolutionary biology; and (c) while developmental systems theorists have constructed an important and innovative alternative to the standard view of the genotype/phenotype relations, in considering the general issue of the relationship between evolutionary and developmental biology, we can remain neutral on this debate.

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.

Neuroethology is a branch of biology that studies the neural basis of naturally occurring animal behavior. This science, particularly a recent program called computational neuroethology, has a similar structure to the interdisciplinary endeavor of cognitive science. I argue that it would be fruitful to conceive of cognitive science as the computational neuroethology of humans. However, there are important differences between the two sciences, including the fact that neuroethology is much more comparative in its perspective. Neuroethology is a biological science and as such, evolution is a central notion. Its target organisms are studied in the context of their evolutionary history. The central goal of this paper is to argue that cognitive science can and ought to be more comparative in its approach to cognitive phenomena in humans. I show how the domain of cognitive phenomena can be divided up into four different classes, individuated by the relative phylogenetic uniqueness of the behavior. I then describe how comparative evidence can enrich our understanding in each of these different arenas.

Cases in which people are self-deceived seem to require that the person hold two contradictory beliefs, something which appears to be impossible or implausible. A phenomenon seen in some brain-damaged patients known as confabulation (roughly, an ongoing tendency to make false utterances without intent to deceive) can shed light on the problem of self-deception. The conflict is not actually between two beliefs, but between two representations, a ‘conceptual’ one and an ‘analog’ one. In addition, confabulation yields valuable clues about the structure of normal human knowledge-gathering processes.

The ubiquity of chaos in classical mechanics (CM), as opposed to the situation in standard quantum mechanics (QM), might be taken as speaking against QM being the fundamental theory of physical phenomena. Bohmian mechanics (BM), as a formulation of quantum theory, may clarify both the existence of chaos in the quantum domain and the nature of the classical limit. Two interesting possibilities are (i) that CM and classical chaos are included in and underwritten by quantum mechanics (BM) or (ii) that BM and CM simply possess a common region of (noninclusive) overlap. In the latter case, neither CM nor QM alone would be sufficient, even in principle, to account for all of the physical phenomena we encounter. In this talk I shall summarize and discuss the implications of some recent work on chaos and on the classical limit within the framework of BM.

In a previous essay I argued that quantum chaos cannot be exhibited in models of quantum systems within von Neumann's mathematical framework for quantum mechanics, and that it can be exhibited in models within Dirac's formal framework. In this essay, the negative thesis concerning von Neumann's framework is elaborated further by extending it to the case of Hamiltonian operators having a continuous spectrum. The positive thesis concerning Dirac's formal framework is also elaborated further by constructing a chaotic model of an open quantum system in which an entropy measure is shown to approach its maximum value as time goes to infinity. Having such an entropy measure is a characteristic that is closely connected to chaotic behavior in phase space models of classical systems.

It is natural to wonder what our multitude of successful physical theories tell us about the world—singly, and as a body. What are we to think when one theory tells us about a flat Newtonian spacetime, the next about a curved Lorentzian geometry, and we have hints of others, portraying discrete or higher-dimensional structures which look something like more familiar spacetimes in appropriate limits?

This paper examines the so-called “gauge argument” sometimes used by physicists to motivate the introduction of gauge fields, here facilitated by an informal exposition of the fiber bundle formalism. The discussion suggests some preliminary ways of understanding the connection between gauge fields and interactions.

This paper presents two interpretations of the fiber bundle fonnalism that is applicable to all gauge field theories. The constructionist interpretation yields a substantival spacetime. The analytic interpretation yields a structural spacetime, a third option besides the familiar substantivalism and relationalism. That the same mathematical fonnalism can be derived in two different ways leading to two different ontological interpretations reveals the inadequacy of pure fonnal arguments.

The Reeh-Schlieder theorem asserts the vacuum and certain other states to be spacelike superentangled relative to local quantum fields. This motivates an inquiry into the physical status of various concepts of localization. It is argued that a covariant generalization of Newton-Wigner localization is a physically illuminating concept. When analyzed in terms of nonlocally covariant quantum fields, creating and annihilating quanta in Newton-Wigner localized states, the vacuum is seen to not possess the spacelike superentanglement that the Reeh-Schlieder theorem displays relative to local fields, and to be locally empty as well as globally empty. Newton-Wigner localization is then shown to be physically interpretable in terms of a covariant generalization of the center of energy, the two localizations being identical if the system has no internal angular momentum. Finally, some of the counterintuitive features of Newton-Wigner localization are shown to have close analogues in classical special relativity.

This discussion provides a brief commentary on each of the papers presented in the symposium on the conceptual foundations of field theories in physics. In Section 2 I suggest an alternative to Paul Teller's (1999) reading of the gauge argument that may help to solve, or dissolve, its puzzling aspects. In Section 3 I contend that Sunny Auyang's (1999) arguments against substantivalism and for “objectivism” in the context of gauge field theories face serious worries. Finally, in Section 4 I claim that Gordon Fleming's (1999) proposal for hyperplane-dependent Newton-Wigner fields differs importantly from his previous arguments about hyperplane-dependent properties in quantum mechanics.

The conceptual relation between objective becoming and the direction of time is explored by discussing an ontologically asymmetric notion of causation. It is claimed that such a notion, in terms of which Stein defined objective becoming in Minkowski spacetime, has either a purely metaphysical status or is reducible to physical concepts. In the former case, it is adequate for Stein's purpose but irrelevant to physical theories. In the latter, the causal asymmetry can be related to irreversible physical processes only in an extrinsic way. This dilemma creates additional difficulties both to a unified theory of the direction of time and to the project of making room for becoming in the physical world.