Thermodynamics has always been a remarkable science in that it studies macroscopic properties that are only partially determined by the properties of individual molecules. Entropy and free energy only exist in constellations of more than a single molecule (degree of freedom). They are the so-called emergent properties. Tendency towards increased entropy is an essential determinant for the behaviour of ideal gas mixtures, showing that even in the simplest physical/chemical systems, (dys)organisation of components is crucial for the behaviour of systems. This presentation aims at illustrating the thesis that the aforesaid holds a fortiori for the living cell : Much of the essence of the live state depends more on the manner in which the molecules are organised than on the properties of single molecules.This is due to the phenomenon of 'Complexity'. BioComplexity is defined here as the phenomenon that the behaviour of two functionally interacting biological components (molecules, protein domains, pathways, organelles) differs from the behaviour these components would exhibit in isolation from one another, where the difference should be essential for the maintenance and growth of the living state, For a true understanding of this BioComplexity, modem thermodynamic concepts and methods (nonequilibrium thermodynamics, metabolic and hierarchical control analysis) will be needed.We shall propose to redefine nonequilibrium thermodynamics as : The science that aims at understanding the behaviour of nonequilibrium systems by taking into account both the molecular properties and the emergent properties that are due to (dys)organisation. This redefinition will free nonequilibrium thermodynamics from the limitations imposed by earlier near-equilibrium assumptions, resolve the duality with kinetics, and bridge the apparent gap with metabolic control analysis. Subsequently, the complexity of the control of the energy metabolism of E. coli will be analysed in detail. New control theorems will be derived for newly defined control coefficients. It will become transparent that molecular genetic experimentation will allow one to penetrate into the mechanisms of the complex regulation of energy metabolism.