The regeneration of elements of water is the basic goal of the control of the cell. These elements are molecules and complex of molecules of different kinds, but at the end they are molecules of water. The control systems try to allow to these elements to optimize their state depending on circumstances, perhaps in advance. The first of these systems is the cytoplasmic membrane together with the apparatus of input mechanisms. It controls the materialistic and non-materialistic input for the regeneration and at the same time it is the source of the primary information about its state and development at time, too. The other member of the control is the control of the distribution of the energy. This is the control of the ATP economy in connection with the proton economy. The control of the flow of energy is a mean for the regulation of the process of the regeneration on the overall level. It stems out from the overall satisfaction of molecules of water, what is a function of the dynamics of the hydrogen part of molecule. The localizations are mitochondria and occasionally plastids. The system named EM0 controls the procedure of the regeneration on the basis of information concerning the successfulness of elements involved in it. The system EM1 controls the dynamics of the boundary of the cell on the basis of information about the tension on it. Both systems converge into the area of the nucleus. The optimization of the existence of the cell itself as whole, besides the regeneration, is the second goal of the control of the cell. New global criteria arise for this sake and are used during the control.