Thursday, 6 May 2010

Systematicity of RNA

I've been looking at evolutionary precursors to bilingualism. What does this mean? At the moment, I'm thinking about it in the sense of having two or more signals which correspond to the same action or meaning. Not much before language, you say? How about going all the way back to RNA codes?

RNA converts genetic information stored in DNA into proteins which regulate processes within cells. The ‘code’ for translating DNA into proteins is redundant but not ambiguous. There are varieties of code. Different organisms use different proportions of codons. ‘Error’ is defined as sum of protein changes when changing from each codon to each other codon, weighted by the frequency of the codon’s use (Marquez, Smit & Knight, 2005). In this sense, the error rate is comparable with the RegMap index of redundancy.

RegMap was developed to calculate the degree of regularity in the mappings between signals and meanings (Tamariz & Smith, 2008). Essentially, it's the relative entropy modified by the frequency of use.

RegMap was applied to RNA coding frequencies of various organisms. Info was taken from the codon usage database for about 16,500 organisms. As a baseline, the same coding transcriptions were used, but with randomised frequencies. The RegMap index of genetic code and actual usage frequencies is significantly higher than randomised frequencies (Mean RegMap for actual = 0.711, random = 0.708, t = 4.8, df = 7196, p less than 0.0001).

The graph is not much use, but here it is:

Marquez R, Smit S, & Knight R (2005). Do universal codon-usage patterns minimize the effects of mutation and translation error? Genome biology, 6 (11) PMID: 16277746

Monica Tamariz, Andrew D. M. Smith (2008). Quantifying the regularity of the mappings between signals and meanings Proceedings of the 7th Conference on the Evolution of Language. pdf

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