In this sense hierarchy is a purley descriptive term. The other use is classify levels of organisation in organisms or ecologies - E.O. Wilson uses the term this way to describe pyramids of biomass, population, and energy (1992, p.37). Although in some ways these pyramids are compromises between the mathematical ideas of web relationships and hierarchies - a major problem for energy pyramids is the position of decomposers (Miller 1996). - a compromise that also occurs in the cataloguing of books.
Maynard Smith & Szathmary use hierarchies to describe the semantic relations of words - a use that might not be entirely justified.
Hofstadter specifically uses the term to distinguish levels of action of proteins which act on proteins and proteins which act on proteins which act on proteins... (1979, p. 533). In this way he finds a correspondence between molecular biology and mathematical logic. In this sense hierarchies might have an authoritarian aspect. If each level of organisation controls the next level, then we are finally reduced to a 'biological dictatorship' of that level. Political ideas generally acknowledge that dictorships are bad at predicting and handling change.
Mayr recognises multiple levels of organisation in organism, and orders them into levels, each of which may be higher or lower than another level. But he does not use the term hierarchy (1998, p. 20). He also states that different levels of organisation, although interacting, cannot be reduced to a single level of control.