Hierarchy of the Codes

The commonly considered information flow from DNA to RNA and to protein is accompanied by massive loss of the sequences involved. Indeed, neither all DNA is transcribed, nor is the whole mass of RNA transcripts translated. This is especially obvious in eukaryotic genomes that contain large intergenic regions, and large intervening sequences that are passed from DNA to pre-mRNA. Is that loss of sequences also a loss of information? The multiplicity of the codes and their superposition suggest that some information is lost, indeed, together with those sequences that are not transcribed and not translated. In other words, DNA carries the sequence codes, serving at the DNA level, of which some are transferred to pre-mRNA. The sequences of the transcripts carry codes serving at RNA level, of which some are passed to the protein sequences, via mRNA. One, thus, has to consider the codes characteristic for the three sequence levels, hierarchically.

One could think of yet higher-level codes, beyond the purely molecular level. Among them would be organ/tissue-specific codes, i.e. genomic sequence features characteristic for one or another physiological function. These could be specifically placed tandem repeats, dispersed repeats, amplified genes, or whole groups of genes. One could also imagine "personal code(s)" - various sequence details responsible for individual traits, such as distinct facial features (Fondon and Garner, 2004) and mimic (Peleg et al., 2006) body set, favorite postures and gestures, and, perhaps, personal behavioral traits. Well-documented existence of population-specific genetic diseases and disorders indicates that there are also sequence features responsible for ethnicity traits. These may include specific sequence polymorphisms and, perhaps, some "guest" sequences present in one ethnical group and absent in others. The higher-level codes are likely to become a major focus of molecular medicine in coming decades. In the mean time the sequence codes of molecular levels are still struggling to make it from singular to plural.

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