That genes are the basic units of inheritance is obvious today, as is the fact that the diversity of living forms results from evolution by natural selection. But do we really understand how genes give rise to complex phenotypes?

The problem — how a message encrypted in the DNA sequence gives rise to a complex organism — is encapsulated in figure 1 of the Review by Kenneth Weiss (page 36). The article discusses the phenogenetic logic of life — a principle that provides a way of connecting phenotypes with their underlying genetic basis. A subdiscipline of evo-devo, phenogenetics explains life through form and function and sees it as the product of a somatic history of an organism.

Among the general principles of phenogenetic logic are changes in gene expression and functional divergence, both of which are further discussed in our Research Highlights. On page 7, we highlight a new approach to looking at regulatory sequences, designed to study the evolution of gene expression and ultimately, the mechanisms that shape organismal diversity.

To understand how genes give rise to phenotypic diversity, it is just as important to understand the function of individual genes as their global interactions. Accurate and complete gene annotation can be seen as the first step towards the former. A recent paper by Boffelli et al. (see Research Highlight on page 8) presents a new way to augment genome annotation — by intraspecies genome comparisons. On the global interaction end of the scale, Segré et al. (see Research Highlight on page 6) look at the pattern of genetic epistasis that underlies phenotypic diversity. In the age of high-tech network biology, we might be in danger of forgetting that epistatic interactions, sometimes thought of as the domain of 'hard-core' geneticists, also belong to the realm of systems biology.