Three features contribute to the complexity of an entity: number of parts, their order, and their iteration. Many functional biological entities are complex when measured by those attributes, and although they are produced in tree-like architectures, the organizational structures that permit them to function are in the form of hierarchies. Natural hierarchies can be thought of as organizing structures that are emergent properties of complex functional entities, and which are transformed from trees by process networks. For example, hierarchies are observed in the architecture of metazoan bodies (the somatic hierarchy) and in the biotic structure of ecogeographic units (the ecological hierarchy). As the metazoan developmental genome is quite complex and has been evolved through tree-like processes, it must harbor at least one hierarchy, which is most clearly indicated in the developmental processes that create the somatic hierarchy. For multicellular organisms, the processes that serve to transform trees of gene expression events into a somatic hierarchy have produced complicated signaling networks whose histories can probably be recovered in general outline.