On the Fundamental Nature and Evolution of the Genetic Code

No accident: genetic codes freeze in error–correcting patterns of the standard genetic code

“…However, even with the relatively simple model we have described and studied here, we may have obtained insights to open questions regarding the origin of the genetic code. For instance, figure 7 may shed insight to a puzzle raised by Woese and others (Woese 1965a;Woese et al 1966;Alff-Steinberger 1969;Swanson 1984;Haig & Hurst 1991;Goldman 1993), who argued that if the code had evolved to correct for mutational biases, because mutation is identical along different codon positions, one would expect the three codon positions to be equally conservative. Order-of-magnitude differences in rates of misreading in the first and second codon positions could have left the first and second codon positions in entirely different dynamic regimes, a possibility suggested by the sharpness of the transition between mutation-and misreadingdominated dynamics seen in figure 7.…”

“…The two main alternatives are stereochemical predetermination of the genetic code through intrinsic affinities of the various amino acids with distinct components of the translation apparatus (e.g. Woese 1965bWoese , 1967Woese , 1973Pelc & Welton 1966;Woese et al 1966;Juncgk 1978;Shimizu 1982;Lacey & Mullins 1983;Yarus 2000, and references therein) and coevolution with amino acid biosynthesis wherein the code vocabulary of amino acids is thought to have expanded through the reassignment of codons from amino acids to their biosynthetic products (e.g. Wong 1975Wong , 1980Taylor & Coates 1989;Di Giulio 1995;Di Giulio & Medugno 1999, and references therein).…”

The Origin of the Genetic Code: Matter of Metabolism or Physicochemical Determinism?

“…Indeed, the physicochemical theory of the origin of the genetic code suggests that these properties have been the main selective pressure that determined the organisation of the genetic code (Sonneborn 1965;Woese et al 1966;Fitch and Upper 1987;Di Giulio 1997). A prediction in part equivalent is also made by the stereochemical theory of the origin of the genetic code that maintains that interactions between codons or anticodons and amino acids have been the main forces that organised the genetic code (Woese 1967;Shimizu 1982;Szathmáry 1993;Yarus 1998;Yarus et al 2009). Therefore, also for the stereochemical hypothesis the physicochemical properties of amino acids were essential in organising the code.…”

“…The first puts at the core of the origin of the genetic code the physicochemical properties of amino acids (1967;Woese et al 1966;Jungck 1978;Weber and Lacey 1978;Lacey and Mullins 1983;Di Giulio 1989a, b;Taylor and Coates 1989;Di Giulio 1996;Freeland and Hurst 1998;Lacey et al 1992). Indeed, the physicochemical theory of the origin of the genetic code suggests that these properties have been the main selective pressure that determined the organisation of the genetic code (Sonneborn 1965;Woese et al 1966;Fitch and Upper 1987;Di Giulio 1997).…”

“…The first puts at the core of the origin of the genetic code the physicochemical properties of amino acids (1967;Woese et al 1966;Jungck 1978;Weber and Lacey 1978;Lacey and Mullins 1983;Di Giulio 1989a, b;Taylor and Coates 1989;Di Giulio 1996;Freeland and Hurst 1998;Lacey et al 1992). Indeed, the physicochemical theory of the origin of the genetic code suggests that these properties have been the main selective pressure that determined the organisation of the genetic code (Sonneborn 1965;Woese et al 1966;Fitch and Upper 1987;Di Giulio 1997). A prediction in part equivalent is also made by the stereochemical theory of the origin of the genetic code that maintains that interactions between codons or anticodons and amino acids have been the main forces that organised the genetic code (Woese 1967;Shimizu 1982;Szathmáry 1993;Yarus 1998;Yarus et al 2009).…”