Structural and functional changes in biological systems under physiological conditions are considered diurnal as well as normal characteristic symptoms. Deviations from the so-called normal modifications may be brought about by unusual stress conditions which often cause irreversible structural changes. Access to measurements of the effects of stress conditions on the structure/function relationship of the biological system before detection by the usual activity measurements is the main objective. It involves the early diagnosis of damages to higher plants prior to the appearance of external symptoms. The theoretical basis is the synergetics of the photosynthetic apparatus, that means the cooperation between energy fluxes in varying structures. The Theory of Energy Fluxes and the Thermodynamics of Open Systems allow for the modelling of the total energetic view. The models can be tested by means of fluorescence measurements in vivo and in situ. These methods are applicable in agricultural research, gene technology and environmental research.