One of the perhaps most awkward results of the Genome Project was that the number of genes is much lower than had been expected and is, in fact, surprisingly similar for very different organisms. It is therefore clear that the biological complexity of organisms is not reflected merely by the number of genes but by the number of physiologically relevant interactions, spanning across different levels as they are not restricted to cell’s networks. Indeed, there is no linear relationship among genotype and phenotype. Contrary to what has been hold during the last 50 years, along the framework suggested by the seminal experiment performed by Beadle and Tatum in which a simple and univocal correlation was established among gene expression and organism phenotype.
Most genotype-phenotype relationships arise from a much higher underlying complexity. Combinations of identical genotypes and nearly identical environments do not always give rise to identical phenotypes. Identical twins, although strikingly similar, nevertheless often exhibit many differences. Likewise, genotypically undistinguishable bacterial or yeast cells grown side-by-side can express different subsets of transcripts and gene products at any given moment. Even straightforward Mendelian traits are not immune to complex genotype-phenotype relationships.