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.

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.

Early last year, the GenEthics Consortium (GEC) of the Washington Metropolitan Area convened at George Washington University to consider a complex case about genetic testing for Alzheimer disease (AD). The GEC consists of scientists, bioethicists, lawyers, genetic counselors, and consumers from a variety of institutions and affiliations. Four of the 8 co-authors of this paper delivered presentations on the case. Supplemented by additional ethical and legal observations, these presentations form the basis for the following discussion.

In this rejoinder to the three preceding comments, I provide some additional philosophical warrant for the biomedical sciences' focus on model organisms. I then relate the inquiries on model systems to the concept of ‘deep homology’, and indicate that the issues that appear to divide my commentators and myself are in part empirical ones. I cite recent work on model organisms, and especially C. elegans that supports my views. Finally, I briefly readdress some of the issues raised by Developmental Systems Theory.

The question of the influence of genes on behavior raises difficult philosophical and social issues. In this paper I delineate what I call the Developmentalist Challenge (DC) to assertions of genetic influence on behavior, and then examine the DC through an indepth analysis of the behavioral genetics of the nematode, C. elegans, with some briefer references to work on Drosophila. I argue that eight “rules” relating genes and behavior through environmentally-influenced and tangled neural nets capture the results of developmental and behavioral studies on the nematode. Some elements of the DC are found to be sound and others are criticized. The essay concludes by examining the relations of this study to Kitcher's antireductionist arguments and Bechtel and Richardson's decomposition and localization heuristics. Some implications for human behavioral genetics are also briefly considered.

In this paper, I revisit a problem in immunology and molecular genetics that I had first tried to understand some philosophical implications of over twenty years ago. At that time, some immunologists such as Mel Cohn at the Salk Institute, referred to it as the GOD problem, which was the acronym for Generator Of Diversity (also see Cohn's more recent discussion in his 1994, 41-48). In the early 1970s there were three or four different theories that had been proposed to account for the way in which antibody diversity is generated and considerable argument among the proponents of the different approaches to the problem (see Cohn, 1994). In 1971-72 I attempted to assess the strengths and weaknesses of the competing theories of antibody diversity from the perspective of a “logic of comparative theory evaluation” that had seemed to work reasonably well in physics (Schaffner, 1970), and I drafted an essay that ultimately sided with one of those theories (somatic mutation).

At a recent conference I attended involving physicists, biologists, historians, and sociologists, a question about the development of theory in biology in comparison with theory in physics arose, with special interest in the nature of the theorists in the two domains and where they ranked in prestige. The biologists, primarily biochemists, maintained that “theory had a bad name in contemporary biology.” As they saw it from the perspective of biochemists and bench scientists, experimental work was much more highly regarded than theoretical work in biology, in interesting contrast to physics.

Certainly not all biologists are theory averse. In the preface to the first of three volumes edited by C.H. Waddington, the late distinguished geneticist wrote in 1968 that he felt” …that the time is ripe to formulate some skeleton of concepts and methods around which Theoretical Biology can grow….

Explications of what it means for one science to be reduced to another have been the focus of considerable interest in recent years, and when the reducing science is physics (and chemistry) and the reduced science is biology, additional concerns seem to arise. In this paper I wish to represent a model for theory reduction which has occupied my attention for some years now, and consider its applicability in the area of the biological sciences.

I should state in advance that the model to be discussed represents an ideal standard for accomplished reductions, and does not characterize the research programmes of molecular biologists. Recently I have argued, in point of fact, that a research programme which might be generated from the tenets of the reduction model to be outlined in this paper would not represent some of the most significant advances in molecular biology, such as the development of the Watson-Crick model of DNA or the genesis of the Jacob-Monod operon theory.

The traditional role which correspondence rules, coordinating definitions, or semantical rules, have in a logical analysis of a scientific theory is questioned by providing an alternative analysis. The alternative account suggests that scientific theories are “meaningful” prior to the establishment of correspondence rules, and that correspondence rules are introduced to permit explanation and testing in the “observational” sector. The role of models is briefly assessed in connection with this prior or “antecedent theoretical meaning,” and a causal sequence analysis of a class of correspondence rules is presented which makes explicit the interdependence of scientific theories.

Four current accounts of theory reduction are presented, first informally and then formally: (1) an account of direct theory reduction that is based on the contributions of Nagel, Woodger, and Quine, (2) an indirect reduction paradigm due to Kemeny and Oppenheim, (3) an “isomorphic model” schema traceable to Suppes, and (4) a theory of reduction that is based on the work of Popper, Feyerabend, and Kuhn. Reference is made, in an attempt to choose between these schemas, to the explanation of physical optics by Maxwell's electromagnetic theory, and to the revisions of genetics necessitated by partial biochemical reductions of genetics. A more general reduction schema is proposed which: (1) yields as special cases the four reduction paradigms considered above, (2) seems to be in better accord with both the canons of logic and actual scientific practice, and (3) clarifies the problems of meaning variance and ontological reduction.