Language: The language of biomolecular communication

Molecules communicate when they interact in the crowded cellular environment. This communication requires an evolving molecular language capable of adapting to the varying environments that are internal and external to the cells. Here I explore the existence of a growing vocabulary in the molecules and molecular functions of the cellular world. A genomic census of structural domains and ontological terms of molecular functions provides an opportunity to find meaningful patterns and processes driving biological language change. The census provides evidence supporting the existence of grammar dependencies and statistical laws of language in protein domain structure and organization. Language laws arise from principles of decreasing returns that are responsible for a number of scaling patterns. I illustrate these principles with the Menzerath-Altmann law of language and other language-related universals. Patterns of origin and diversification of repertoires of proteins (proteomes) and functions (functionomes) in organisms reveal that their make up depends on trade-off solutions between economy, flexibility and robustness when optimizing for organismal and molecular persistence. Collectively, organisms of the three superkingdoms of life use different trade-off strategies. Archaea and Bacteria maximize economy, while Eukarya expand flexibility and robustness. Comparative genomic and phylogenomic data suggests that organisms engage in extreme semantic and pragmatic compression of their genetic messages. These tendencies are especially notable when organisms adapt to microbial lifestyles and harsh environments.