This is the second paper in a two-part series describing the patterns of inquiry used in ecology. Three classes of research parts are identified from the literature: individual organisms or species, pairs of organisms or species, and groups of organisms or species. Research emphasizing these parts rather than the community as a whole is analyzed in terms of the principles of biological inquiry discussed in the first paper. A second section of the paper shows how accounts of the community as a whole can be built from the results of research on parts, and discusses different conceptions of the relationship between parts and whole. The third section analyzes research beginning with an emphasis on the whole. A summary of the patterns of inquiry found in ecology relates the four principles of inquiry to the five problem areas defined in the first paper, giving eighteen different patterns of inquiry. (EB)