Suggestions(1)
Exact(4)
The model is deliberately oversimplified to allow straightforward conclusions on the relationships between the standard code and various random codes, and we emphasize this in the revised Discussion.
Nevertheless, we believe that the idealized scheme examined here allows for meaningful comparison between the standard code and various classes of random codes.
Authors' response: Again, this work is not an attempt to reconstruct a truly realistic scenario for the evolution of the code but rather to determine the status of the standard code in the code space, compared to various sets of random codes, and delineate possible evolutionary links between the standard code and different random codes.
When the distances between the standard code and the codes from the sets o and R are compared, it is difficult to differentiate between these two sets; however, the code that was obtained as a result of the minimization of the standard code clearly belongs to o (the distances from this code to other sets are much greater).
Similar(55)
The difference between the cost of the standard code (Fig. 1) and the means of the distributions measured in standard deviations is 2.2, 2.65, 2.91, and 2.5 for the cases (a), (b), (c), (d) in Fig. 3, respectively.
The stereochemical theory alone cannot account for the high level of error minimization in the standard code; moreover, the affinity between cognate triplets and amino acids appears to be largely independent of the highly optimized amino acid assignments code [ 57].
Another feature of the standard code is the strong, positive correlation between the number of synonymous codons and amino acid frequencies in proteins.
Again, this result emphasizes the "mediocrity" of the standard code.
The standard code has Phe in this position.
Taken together, the reversal of a non-canonical code to the standard code appears highly unlikely.
Most of the alternative genetic codes display mutation loads larger than for the standard code.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com