Abstract
Relating the genotype and environment of an organism to its phenotypic repertoire is widely recognized as one of the major challenges in modern biology. Although we now have a generic concept of ‘genotype’ provided by the detailed DNA sequence of an organism, there is no corresponding generic concept of ‘phenotype’. Without this conceptual foundation there can be no context for a deep, predictive understanding of the biological design principles arrived at by natural selection. This chapter aims to provide such a context by focusing on three goals. First, background will be provided for perspective and to clarify the use of terms such as system, module, interface and design. This is particularly important in the case of the term ‘system’ in biology, since this term has come to mean many different things following the recent rise of interest in systems biology. Second, a concept of qualitatively distinct phenotypes is rigorously defined that applies to systems at levels from the molecular to the organismal. Third, examples are presented to demonstrate how this concept is manifested within a system design space in which qualitatively distinct phenotypes can be identified and counted, their relative fitness analyzed and compared, their tolerance to global change measured, and biological design principles identified.
Published Version
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