Today there are two major theoretical frameworks in biology. One is the ‘chemical paradigm’, the idea that life is an extremely complex form of chemistry. The other is the ‘information paradigm’, the view that life is not just ‘chemistry’ but ‘chemistry-plus-information’. This implies the existence of a fundamental difference between information and chemistry, a conclusion that is strongly supported by the fact that information and information-based-processes like heredity and natural selection simply do not exist in the world of chemistry. Against (...) this conclusion, the supporters of the chemical paradigm have pointed out that information processes are no different from chemical processes because they are both described by the same physical quantities. They may appear different, but this is only because they take place in extremely complex systems. According to the chemical paradigm, in other words, biological information is but a shortcut term that we use to avoid long descriptions of countless chemical reactions. It is intuitively appealing, but it does not represent a new ontological entity. It is merely a derived construct, a linguistic metaphor. The supporters of the information paradigm insist that information is a real and fundamental entity of Nature, but have not been able to prove this point. The result is that the chemical view has not been abandoned and the two paradigms are both coexisting today. Here it is shown that an alternative does exist and is a third theoretical framework that is referred to as the ‘code paradigm’. The key point is that we need to introduce in biology not only the concept of information but also that of meaning because any code is based on meaning and a genetic code does exist in every cell. The third paradigm is the view that organic information and organic meaning exist in every living system because they are the inevitable results of the processes of copying and coding that produce genes and proteins. Their true nature has eluded us for a long time because they are nominable entities, i.e., objective and reproducible observables that can be described only by naming their components in their natural order. They have also eluded us because nominable entities exist only in artifacts and biologists have not yet come to terms with the idea that life is artifact making. This is the idea that life arose from matter and yet it is fundamentally different from it because inanimate matter is made of spontaneous structures whereas life is made of manufactured objects. It will be shown, furthermore, that the existence of information and meaning in living systems is documented by the standard procedures of science. We do not have to abandon the scientific method in order to introduce meaning in biology. All we need is a science that becomes fully aware of the existence of organic codes in Nature. (shrink)

Through an examination of the actual research strategies and assumptions underlying the Human Genome Project, it is argued that the epistemic basis of the initial model organism programs is not best understood as reasoning via causal analog models. In order to answer a series of questions about what is being modeled and what claims about the models are warranted, a descriptive epistemological method is employed that uses historical techniques to develop detailed accounts which, in turn, help to reveal forms of (...) reasoning that are explicit, or more often implicit, in the practice of a particular field of scientific study. It is suggested that a more valid characterization of the reasoning structure at work here is a form of case-based reasoning. This conceptualization of the role of model organisms can guide our understanding and assessment of these research programs, their knowledge claims and progress, and their limitations, as well as how we educate the public about this type of biomedical research. (shrink)

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.

Leading philosophical accounts presume that Thomas H. Morgan’s transmission theory can be understood independently of experimental practices. Experimentation is taken to be relevant to confirming, rather than interpreting, the transmission theory. But the construction of Morgan’s theory went hand in hand with the reconstruction of the chief experimental object, the model organism Drosophila melanogaster . This raises an important question: when a theory is constructed to account for phenomena in carefully controlled laboratory settings, what knowledge, if any, indicates the theory’s (...) relevance to phenomena outside highly controlled settings? The answer, I argue, is found within the procedural knowledge embedded within laboratory practice. †To contact the author, please write to: Minnesota Center for Philosophy of Science, University of Minnesota, Department of Philosophy, 831 Heller Hall, 271 19th Ave., University of Minnesota, Minneapolis, MN 55455‐0310; e‐mail: [email protected]. (shrink)