Kenneth Schaffner

This paper examines the nature of theory structure in biology and considers the implications of those theoretical structures for theory reduction. An account of biological theories as interlevel prototypes embodying causal sequences, and related to each other by strong analogies, is presented, and examples from the neurosciences are provided to illustrate these middle-range theories. I then go on to discuss several modifications of Nagel''s classical model of theory reduction, and indicate at what stages in the development of reductions these models might best apply. Finally I consider several implications of these analyses of theory structure and reduction for disciplinary integration in biology.

This two-part article examines the competition between the clonal selection theory and the instructive theory of the immune response from 1957–1967. In Part I the concept of a temporally extended theory is introduced, which requires attention to the hitherto largely ignored issue of theory individuation. Factors which influence the acceptability of such an extended theory at different temporal points are also embedded in a Bayesian framework, which is shown to provide a rational account of belief change in science. In Part II these factors, as elaborated in the Bayesian framework, are applied to the case of the success of the clonal selection theory and the failure of the instructive theory.

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

Assessing the normative status of concepts of health and disease involves one in questions regarding the relationship between fact and value. Some have argued that Christopher Boorse's conception of health and disease lacks such a valuational element because it cannot account for types of harms which, while disvalued, do not have evolutionarily dysfunctional consequences. I take Boorse's account and incorporate some Humean-like sociobiological assumptions in order to respond to this challenge. The possession of moral sentiments, I argue, offers an evolutionary advantage (thus falling within Boorse's definition of normal functional abilities). However, this does not amount to emotivism: on the contrary, these sentiments can be the basis of a value system. This value structure introduces the concept of sympathizing with a fellow being's suffering as the basis of a normative dimension to disease. For example, it holds the disvalue of disease to lie in the fact that disease involves suffering and functional limitations.The naturalistic Humean type of account presented here thus jumps the normative-descriptive divide. When Boorse's account is extended to include social sentiments and behaviors, a conception of health emerges which is broader than Boorse's or Kass's, but narrower than the WHO's.

the structure of medical science with a special focus on the role of generalizations and universals in medicine, and (2) philosophy of medicine's relation with the philosophy of science. I argue that a usually overlooked aspect of Kuhnian paradigms, namely, their characteristic of being "exemplars", is of considerable significance in the biomedical sciences. This significance rests on certain important differences from the physical sciences in the nature of theories in the basic and the clinical medical sciences. I describe those differences and maintain that they are these differentiating features that require the use of more comparative and analogical reasoning in medicine. I suggest that Kitcher's recent introduction of the notion of a ‘practice’ may have similar implications if it is construed to contain more analogical elements than he appears to recognize in his initial formulation. Finally I argue that though Gorovitz and MacIntyre's characterization of medicine as a "science of particulars" bears some similarities with my thesis, I maintain that such a position without careful qualification can lead to ignoring both the nature of generalizations in these sciences and their role as positive analogies tying together a family of overlapping models. Keywords: medical reasoning, biomedical theories/paradigms, science of particulars, philosophy of medicine CiteULike Connotea Del.icio.us What's this?

Kenneth F. Schaffner compares the practice of biological and medical research and shows how traditional topics in philosophy of science—such as the nature of theories and of explanation—can illuminate the life sciences. While Schaffner pays some attention to the conceptual questions of evolutionary biology, his chief focus is on the examples that immunology, human genetics, neuroscience, and internal medicine provide for examinations of the way scientists develop, examine, test, and apply theories. Although traditional philosophy of science has regarded scientific discovery—the questions of creativity in science—as a subject for psychological rather than philosophical study, Schaffner argues that recent work in cognitive science and artificial intelligence enables researchers to rationally analyze the nature of discovery. As a philosopher of science who holds an M.D., he has examined biomedical work from the inside and uses detailed examples from the entire range of the life sciences to support the semantic approach to scientific theories, addressing whether there are "laws" in the life sciences as there are in the physical sciences. Schaffner's novel use of philosophical tools to deal with scientific research in all of its complexity provides a distinctive angle on basic questions of scientific evaluation and explanation.

This paper attempts to address the general questionwhether information technologies, as applied in thearea of medicine and health care, have or are likelyto change fundamental concepts regarding disease andhealth. After a short excursion into the domain ofmedical informatics I provide a brief overview of someof the current theories of what a disease is from amore philosophical perspective, i.e. the ``valuefree'' and ``value laden'' view of disease. Next, Iconsider at some length, whether health careinformatics is currently modifying fundamentalconcepts of disease. To this question I will answerlargely in the negative, and I will provide the sketchof some arguments from current research programs inmedical informatics why I think this is the case. Thisargumentation is supported by a detailed account ofhow the disease profile for beriberi heart disease,used in one of the major medical informaticsdiagnostic programs, QMR (and its ancestorINTERNIST-1), was developed, and why at least thisprogram essentially follows received views oftraditional medicine.The one main exception to theconformity of this program to ``received'' views of adisease occurs when the program's designers need tofine-tune a disease definition. This fine-tuning is tocomport with the expert's perspective on the disease,including his or her epistemic values, as well as theprogram's other resources for diagnosing components ofa disease.

We are gratified at the largely positive comments on our essay on the dopamine hypothesis of schizophrenia (DHS) by these two distinguished commentators from the fields of biological psychiatry (Dr. Tamminga) and the philosophy of psychiatry (Dr. Murphy). There is little that they have said with which we disagree. Rather, we want to expand briefly on their commentaries.We found Dr. Tamminga's reactions to be particularly fascinating because she has been an "insider" to the story of the DHS as it has unfolded. She provides substantial insight into the "extra-scientific" reasons for the persistence of the DHS despite its poor empirical record.She validates our impression that the DHS was in its first years of ..

I have not attempted to provide here an analysis of the methodology of molecular biology or molecular genetics which would demonstrate at what specific points a more reductionist aim would make sense as a research strategy. This, I believe, would require a much deeper analysis of scientific growth than philosophy of science has been able to provide thus far. What I have tried to show is that a straightforward reductionist strategy cannot be said to be follwed in important cases of theory development in molecular biology, and that in at least one important case, the Jacob-Monod operon theory, the methodology followed was more biological than chemical. It should be noted in closing, however, that since biological systems are thought by molecular biologists to be nothing but chemical systems, in the long run detailed investigations of such systems will be in full accord with the dictates suggested by the general reduction model

It seems that the above account of explanation-strategy in the area of temperature adaptation underscores many of the points made earlier. First, it discloses the fruitful interaction of classical, evolutionary, and molecular approaches. Secondly, it indicates that biological characterizations are not rival accounts to chemical ones. Thirdly, it stresses the importance of the DNA sequence order in chemical explanations of biological organisms.One feature which this area does not seem to reveal, which genetics does, is the development of a biological (that is, non-chemical) theory which would explain temperature adaptation in nonchemical terms. What this shows is that one should not always expect systematization at the biological level, in the sense of being able to refer many phenomena to a small number of basic principles. The future development of laws and theories in biological terms in this area is, of course, not precluded by the fact that none have yet been discovered. The case does indicate that physical and chemical language and theories are extremely useful in biological investigations, and the physicochemical approach may well be the best approach in this area. In any event, ultimate reduction of the biological to the chemical seems to be a foregone non-controversial conclusion here as elsewhere

In this paper I discuss the nature of a broad class of biomedical theories which I have termed "middle-range theories." I define them and relate the nature of biomedical theorizing to other investigations, such as a recent inquiry by the National Academy of Sciences. I also suggest that some of the knowledge representation tools from artificial intelligence may give us a purchase on this type of biological theorizing, and try to show in a rather preliminary and exploratory manner by using the lac operon model of genetic control, what some of those AI applications, such as frames and semantic nets, might look like in this context. Finally, I suggest some difficulties, such as the non-monotonicity of reasoning, which such tools may generate.