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)

Comprehensive evaluation and study of man's theories and knowledge of genetical characteristics and the evolutionary processes.

Danchin argues that if scientists can reach a level of understanding of genomes, they will be able to resolve the major biological puzzle of the 21st century: the enigma of the living machine that creates the living machine.

As to the misconceptions: In the first place, the existence of "undecidable propositions" or "unsolvable problems" has only remote connections with the failure of excluded middle. More precisely, from the fact that a certain problem is unsolvable, one cannot infer that the affirmative and negative answers to that problem are both incorrect. Both Gödel's and Church's theorems were originally proved for systems with the excluded middle, i.e. for systems in which 'p or not p' is provable for every proposition 'p'; (...) though in the light of Gödel's theorem there are propositions 'p' such that neither 'p' nor 'not p' is provable in those systems. Careful distinction should be made between the following locutions. (shrink)