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Hierarchy theory provides an essential conceptual base for building coherent models of complex systems (Allen and Starr 1982; O'Neill et al. 1986; Salthe 1985; Gibson et al. 2000). Hierarchy is an organizational principle that yields models of nature that are partitioned into nested levels that share similar time and space scales. In a constitutive hierarchy, an entity at any level is part of an entity at a higher level and contains entities at a lower level. In an exclusive hierarchy, there is no containment relation between entities, and levels are distinguished by other criteria, e.g. trophic levels. Entities are to a certain extent insulated from entities at other levels in the sense that, as a rule, they do not directly interact; rather they provide mutual constraints. For example, individual organisms see the ecosystem they inhabit as a slowly changing set of external (environmental) constraints and the complex dynamics of component cells as a set of internal (behavioral) constraints.
From the scaling perspective, hierarchy theory is a tool for partitioning complex systems in order to minimize aggregation error (Thiel 1967; Hirata and Ulanowicz 1985). The most important aspect of hierarchy theory is that ecological systems' behavior is limited by both the potential behavior of its components (biotic potential) and environmental constraints imposed by higher levels (O'Neill et al. 1989). The flock of birds that can fly only as fast as its slowest member, or a forested landscape that cannot fix atmospheric nitrogen if specific bacteria are not present are examples of biotic potential limitation. Animal populations limited by available food supply and plant communities limited by nutrient remineralization are examples of limits imposed by environmental constraints. O'Neill et al. (1989) use hierarchy theory to define a 'constraint envelope' based upon the physical, chemical and biological conditions within which a system must operate. They argue that hierarchy theory and the resulting 'constraint envelope' enhance predictive power. Although they may not be able to predict exactly what place the system occupies within the constraint envelope, they can state with confidence that a system will be operating within its constraint envelope.
Viewing biocomplexity through the lens of hierarchy theory should serve to illuminate the general principles of life systems that occur at each level of the hierarchy. While every level will necessarily have unique characteristics, it is possible to define forms and processes that are isomorphic across levels (as are many laws of nature). Troncale (1985) has explored some of these isomorphisms in the context of general system theory. In the context of scaling theory we can seek isomorphisms which assist in the vertical integration of scales. These questions feed into the larger question of scaling, and how to further develop the four basic methods of scaling mentioned above for application to complex systems.
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