Cognitive simulation of analogical processing can be used to answer comparison questions such as: What are the similarities and/or differences between A and B, for concepts A and B in a knowledge base (KB). Previous attempts to use a general-purpose analogical reasoner to answer such questions revealed three major problems: (a) the system presented too much information in the answer, and the salient similarity or difference was not highlighted; (b) analogical inference found some incorrect differences; and (c) some expected similarities were not found. The cause of these problems was primarily a lack of a well-curated KB and, and secondarily, algorithmic deficiencies. In this paper, relying on a well-curated biology KB, we present a specific implementation of comparison questions inspired by a general model of analogical reasoning. We present numerous examples of answers produced by the system and empirical data on answer quality to illustrate that we have addressed many of the problems of the previous system.