Around 98% of all transcriptional output in humans is non-coding RNA. RNA-mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference, co-suppression, transgene silencing, imprinting, methylation, and possibly position-effect variegation and transvection, all involve intersecting pathways based on or connected to RNA signaling. I suggest that the central dogma is incomplete, and that intronic and other non-coding RNAs have evolved to comprise a second tier of gene expression in eukaryotes, which enables the integration and networking of complex suites of gene activity. Although proteins are the fundamental effectors of cellular function, the basis of eukaryotic complexity and phenotypic variation may lie primarily in a control architecture composed of a highly parallel system of trans-acting RNAs that relay state information required for the coordination and modulation of gene expression, via chromatin remodeling, RNA–DNA, RNA–RNA and RNA–protein interactions. This system has interesting and perhaps informative analogies with small world networks and dataflow computing.

The genome sequencing projects have revealed an unexpected problem in our understanding of the molecular basis of developmental complexity in the higher organisms: complex organisms have lower numbers of protein coding genes than anticipated. The fruitfly Drosophila melanogaster and the nematode Caenorhabditis elegans appear to have only about twice as many protein coding genes (∼ 12–14 000) as microorganisms such as Saccharomyces cerevisiae (∼ 6200) and Pseudomonas aeruginosa (∼ 5500)(Rubin et al., 2000; Stover et al., 2000). Humans appear to have only twice as many again (∼ l30 000)(International Human Genome Sequencing Consortium, 2001; Venter et al., 2001), although there is some debate about this (Wright et al., 2001; see also below). While the repertoire of protein isoforms expressed in the higher organisms is greatly increased by alternative splicing (Graveley, 2001), the other striking feature of the evolution of the higher organisms, which has been largely overlooked to date, is the huge increase in the amount of non-protein-coding RNA, which in humans accounts for∼ 98% of all genomic output (see below).