Hierarchy is considered as a central and essential aspect of systems biology. In a theoretical section on hierarchy considerations include discussion of the simultaneous spatiotemporal operation in both top-down and bottom-up modes. Emergent biological systems are not reducible to their parts or modules. Reactions to signals may be different and even opposite at different integrated hierarchical levels. Therefore, the top-down and bottom-up flow of information through hierarchically organized systems is an essential feature supporting robustness and stability of the hierarchical systems. In a empirical section, examples are collected spanning scalar levels from electrons and whole plant physiology up the ecosystems. Analysis of hierarchy is appropriate for establishing systemic understanding models of the complex interactions between plants and their changing environment. However, the search for unique indicators that can be used to determine or predict a global plant behavior in response to environmental cues may be, actually, a search for a “holy grail”.
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