Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins’ amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism’s biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the GþC content of the first codon position. An unexpected bias (...) is driven, in many proteomes, by the AANbox of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction. (shrink)

Two decades ago, Rolf Landauer (1991) argued that “information is physical” and ought to have a role in the scientific analysis of reality comparable to that of matter, energy, space and time. This would also help to bridge the gap between biology and mathematics and physics. Although it can be argued that we are living in the ‘golden age’ of biology, both because of the great challenges posed by medicine and the environment and the significant advances that have been made—especially (...) in genetics and molecular and cell biology—we feel that information as an essential aspect of life has been neglected, or at least misunderstood. We therefore summon Maxwell’s Demon and its distant relative the ratchet, and apply these to biology. (shrink)