Systems biology for the virtual plant.

Systems thinking is used in a variety of scientific and technological fields. Indeed, this paradigm has proved indispensable in disciplines as disparate as commerce, production, and the aviation industry. Aleksander Bogdanov (1873–1928) was probably the first exponent of systems thinking. In his ‘‘Tektology: Universal Organization Science’’ (1913–1922), Bogdanov ambitiously proposed that all physical, biological, and human sciences could be unified by treating them as sets of relationships and by seeking the organizational principles that underlie all systems (Poustilnik, 1998). The foundation of general systems theory was later developed extensively by the biologist Ludwig von Bertalanffy (for review, see von Bertalanffy, 1968). Bertalanffy’s statements on the topic appeared as early as the mid-1920s. Why then is it only now in the genomic era that it is so ‘‘hip’’ to talk about systems biology? Analogous to past developments in other scientific disciplines, biologists in the post-genomic era are challenged with huge volumes of data (e.g. genome sequences, expression data), originating from heterogeneous technologies (e.g. microarray, yeast two-hybrid, ChIP-chip) and representing innumerable states of the system (experimental conditions). This massive influx of information and the desire to make it biologically coherent has forced us to think not in terms of single molecules but in terms of ‘‘systems.’’ Although ecologists and physiologists have been using a systems approach to study plants for many years, a systems biology approach that reaches to and includes molecular details is only feasible now with the advent of genomic technologies. Thus, the exciting prospect of the post-genomic era is for the first time to be able to integrate knowledge across different levels of biological organization and to anchor this at the molecular level. Systems biology is sometimes loosely associated with the use of genomic technologies to understand specific biological processes. We believe systems biology has a larger and more ambitious scope, and we advocate a definition anchored in the general systems theory put forth by Bogdanov and Bertalanffy: The exercise of integrating the existing knowledge about biological components, building a model of the system as a whole and extracting the unifying organizational principles that explain the form and function of living organisms. The practical implementation of this definition is addressed in the next section. It should be emphasized that the intention of this article is not to be a literature review or update on plant systems biology, which is indeed in a nascent state, but rather to provide our ‘‘vision’’ for systems biology in plant research—and the path that will take us there.