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Chapter 8. Reconstituting the Phenomena
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CHAPTER 8 Reconstituting the Phenomena 1. INTRODUCTION: BIOCHEMICAL GENETICS In the last two chapters we have illustrated the use of localization and decomposition in developing models of complex systems. In all the cases we have discussed, the development of explanatory models was significantly constrained by lower-level theories as well as systemic behavior. These constraints varied in relative strength. In Chapter 6 the initial models of brain function incorporated simple decomposability. Linguistic functions on the one hand, and memory functions on the other, were assumed to be functionally independent and discretely localized. However, research did not limit itself to simple localization. The initial localizationist models were followed by an attempt to reveal underlying physical mechanisms. Decomposability nonetheless was retained, as providing at least a first-order approximation of systemic function. Both higher-level, behavioral, constraints and lower-level, physical, constraints were significant in the development of the resulting models of system behavior and organization. In these cases the lower-level constraints on the resulting model were largely correlational and empirical. Though important, they were relatively weak. The primary constraints on the structure of the resulting model were imposed by the higher level. Cognitive models of memory function, or of linguistic processing, were projected top-down onto the physical level. In Chapter 7 we turned to research into fermentation. There was once more an initial commitment to localization and decomposition, but it eventually resulted in a model emphasizing integration and organization of physical components rather than decomposition. Here again there was initially a commitment to discrete physical units realizing distinct higherlevel functions. Single enzymes were supposed to mediate complex biochemical activities; however, the organization revealed by research into fermentation eventually showed that the biochemical mechanisms provided an interactive and integrated system, rather than one that was simply or nearly decomposable. Once again there were higher-level constraints on the models. Fermentation, including the formation of lactic acid and alcohol, was the overall process to be explained, and it was important that a model embody biologically realistic processes. Moreover, there were important empirical constraints. We emphasized, particularly, 174 . III. Elaborating Mechanisms the requirement that intermediaries be isolable and that their rate offermentation be commensurate with the rate of the overall process. The lower-level constraints in Chapter 7 are far more restrictive than in the cases discussed in Chapter 6. They imposed strict limitations on the actual structure of the resulting explanatory models, by limiting biochemical processes to simple chemical reactions or sequences of chemical reactions . As a result of the attempt to satisfy the constraints simultaneously, linearity was abandoned, and with it, even near decomposability. The case that will be at the focus of the current chapter, biochemical genetics, has substantial parallels to the cases in both ofthe previous chapters . Two traditions converged in influenCing the development of biochemical genetics; they provide, respectively, the higher- and lower-level constraints on the development ofthe field. The first tradition consisted of classical Mendelian investigations into the structure and organization of the genetic material. With the "rediscovery" of Mendel's experimental results at the beginning of the twentieth century,1 there was a commitment to a particulate model of inheritance, with segregation, dominance, and independent assortment. There was also a commitment to "autonomy " in the expression ofgenes. Jointly, these Mendelian principles were tantamount to simple decomposability. Deviations from these principles were noticed almost immediately, and they provided the basis for a rich characterization of the phenomena and mechanisms of inheritance in the hands of the Morgan school. As the research program developed, it became clear that simple decomposability could not be maintained. As we will see in the following section, with this recognition it also became apparent that some of the central phenomena revealed in the Mendelian program could not be explained in Mendelian terms, but required a lower-level explanation. The second tradition influencing biochemical genetics was research into biochemical pathways and their significance for development. While this research included work in physiological chemistry, it focused on work connecting genetic differences and development. This method incorporated assumptions paralleling those affecting research into fermentation. In particular, it required that the basic processes involved in developmental models be known chemical reactions; that intermediaries in metabolic processes be independently isolable; and, initially at least, that there be linear organization. As a result this method imposed strong physical constraints on the resulting models. The synthesis ofthese two traditions in the development ofbiochemical genetics placed strong independent constraints on the resulting genetic models from both levels; models of...