 The above and other experimental successes underpin Eric Davidson’s theory of “the regulatory genome” (2006), which combines new experimental data (mainly from Drosophila and sea urchin) with systems and network concepts—in effect, updating Jacob and Monod’s notion of the genetic program. On this view, development is controlled by a DNA-encoded program made up of short sequences that specifically bind transcription factor proteins and thereby make a difference to gene expression. The first step of gene expression in higher organisms is typically the binding of one or more protein factors to a regulatory region of DNA located near the sequence to be transcribed (“read” into mRNA and thence to protein). Davidson terms these DNA sequences “cis-regulatory modules”. Each module’s effect is represented as a conditional rule of the form: “If protein X is present, then gene Y is expressed at level Z”. Each gene has a set of such modules associated with it, which collectively specify its expression pattern under various conditions. That expression pattern, in turn, determines a cell’s phenotype and developmental fate. Control of development is therefore attributed entirely to the DNA components of molecular complexes that make a difference to gene expression. Transcription factor proteins and other components are conceived as “inputs” to the information-processing modules, and effects on gene expression as “outputs”.