Abstract
The ubiquity of the linguistic metaphor in molecular biology, and particularly in sequence analysis was one of the main topics of the 1991 Open Problems in Computational Biology Workshop. This year I consider the application of a mechanical analogy to sequence analysis and in particular to protein sequences and structures. The mechanistic metaphor is easily recognized as one of the fundamental concepts behind experimental disciplines such as biochemistry, genetics, and cell biology. Its application to analysis of protein sequences is most clearly seen in the application of comparative approaches to associating structure with function.
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