Promoter variation

Why aren't promoters precise like the stop codons etc.? A possible answer is that nature uses the variation in promoters to control expression levels of various genes. That is, the rate of the gene expression process depends on the conservation of the promoter region. This hypothesis is supported by results from chemistry. Experiments show that when a RNA polymerase molecule gets bounded to the promoter region in order to initial transcription, there is an 80% correlation between the weight matrix score of the region and the binding energy. This means that if the promoter region is very conserved, i.e., very similar to the consensus sequence, then the binding energy barrier is low and thus the protein production rate is higher (because the RNA polymerase can easily bind to the protein coding region). When the difference from the consensus sequence is bigger, the energy barrier is higher, and the protein production is slower. One consequence of this insight is that finding regulatory sequences is an inherently stochastic problem.