The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the unbinding of a repressor (negative control). What determines the choice of mode of control for each gene? This study proposes rules for gene regulation based on the assumption that free regulatory sites are exposed to nonspecific binding errors, whereas sites bound to their cognate regulators are protected from errors. Hence, the selected mechanisms keep the sites bound to their designated regulators for most of the time, thus minimizing fitness-reducing errors. This offers an explanation of the empirically demonstrated Savageau demand rule: Genes that are needed often in the natural environment tend to be regulated by activators, and rarely needed genes tend to be regulated by repressors; in both cases, sites are bound for most of the time, and errors are minimized. The fitness advantage of error minimization appears to be readily selectable. The present approach can also generate rules for multi-regulator systems. The error-minimization framework raises several experimentally testable hypotheses. It may also apply to other biological regulation systems, such as those involving protein-protein interactions.biological physics ͉ complex networks ͉ systems biology ͉ transcriptional regulation B iological regulation systems convert input signals into specified outputs. The same input-output relationship can generally be carried out by several different mechanisms. For example, transcription regulation is carried out by regulatory proteins that bind specific sites in the promoter region of the regulated genes. A gene that is fully expressed only in the presence of a signal ( Fig. 1) can be regulated by two different mechanisms (1). In the first mechanism, called positive control, an activator binds the promoter to turn on expression. In the second mechanism, called negative control, a repressor binds the promoter to turn expression off. These two mechanisms realize the same input-output relationship: Expression is turned on by the binding of an activator in the positive mode of control and by the unbinding of a repressor in the negative mode of control. More generally, a gene controlled by N regulators, each of which can be either an activator or a repressor, has 2 N possible mechanisms for a given input-output mapping.Among these equivalent mechanisms, evolutionary selection chooses one for each system. Are there rules that govern the selection of mechanisms in biological systems? One possibility is that evolution chooses randomly between equivalent designs. Hence, the selected mechanism is determined by historical precedent. Another possibility is that general principles exist that govern the choice of mechanism in each system.The question of rules for gene regulation was raised by M. A. Savageau (2-6) in his pioneering study of transcriptional control. Savageau found that the mode of control is correlated with the demand...