The Case for an Error Minimizing Standard Genetic Code

  title={The Case for an Error Minimizing Standard Genetic Code},
  author={Stephen J. Freeland and Tao Wu and Nick Keulmann},
  journal={Origins of life and evolution of the biosphere},
Since discovering the pattern by which amino acids are assigned to codons within the standard genetic code, investigators have explored the idea that natural selection placed biochemically similar amino acids near to one another in coding space so as to minimize the impact of mutations and/or mistranslations. The analytical evidence to support this theory has grown in sophistication and strength over the years, and counterclaims questioning its plausibility and quantitative support have yet to… 

Title : Refactoring the Genetic Code for Increased Evolvability

This theoretical study suggests a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements and explores several possible genetic codes that allow a greater degree of accessibility to the mutational landscape.

How to ‘find’ an error minimized genetic code: neutral emergence as an alternative to direct Darwinian selection for evolutionary optimization

How evolutionary optimization in biological systems is not restricted to direct selection, and that additional processes may lead to the production of beneficial traits, via ‘non-Darwinian optimization’ is clarified.

Refactoring the Genetic Code for Increased Evolvability

This theoretical study suggests a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements and explores several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments.

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape

The standard code appears to be the result of partial optimization of a random code for robustness to errors of translation, and is a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak.

Optimization of the standard genetic code according to three codon positions using an evolutionary algorithm

This work investigated the robustness of this code regarding the cost of amino acid replacements resulting from substitutions in these positions separately and the sum of these costs and suggested that the optimality of SGC could be a by-product of other processes.

Origin and evolution of the genetic code: The universal enigma

Much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out.

The Importance of Changes Observed in the Alternative Genetic Codes

The level of error minimization in amino acid replacements generated by the standard genetic code and its alternatives is examined and indicates that the codon reassignments observed in the existing alternative genetic codes could play an adaptive role in their evolution to minimize translational and mutational errors.

An Ode to the Code: Evidence for Fine-Tuning in the Standard Codon Table

The hypothesis that the finely tuned optimization of the SCT originates in external intelligence is compared to the hypothesis that its fine tuning is due to the adaptive selection of earlier codes and it is concluded that external intelligence better explains the origin of theSCT.



Early fixation of an optimal genetic code.

It is shown that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space.

The Impact of Message Mutation on the Fitness of a Genetic Code

It is established that selection for mutational load minimization acts at the level of an individual in a single generation, and the number of mutant codons in each individual at equilibrium reflects a long-term evolutionary balance between mutations in messages and selection on proteins.

The Genetic Code Is One in a Million

It is concluded that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.

Optimality of the genetic code with respect to protein stability and amino-acid frequencies

Taking the amino-acid frequency into account decreases the fraction of random codes that beat the natural code, and leads to an attempt to propose a tentative picture of primitive life.

On the Evolution of Redundancy in Genetic Codes

The results suggest that various omnipresent phenomena that distribute codons over sites with different selective requirementspredispose the evolution of redundancy and of reduced amino acid diversity in genetic codes.

The Darwinian Genetic Code: An Adaptation for Adapting?

  • S. Freeland
  • Biology
    Genetic Programming and Evolvable Machines
  • 2004
This work has suggested that the assignments of amino acids to codons appear to be organized so as to minimize the change in amino acid hydrophobicity that results from random mutations, and may in fact represent an adaptation to maximize the efficiency of adaptive evolution.

Testing a biosynthetic theory of the genetic code: fact or artifact?

It is shown that coevolution theory cannot adequately explain the structure of the genetic code because the theory's definition of "precursor-product" amino acid pairs is unjustified biochemically because it requires the energetically unfavorable reversal of steps in extant metabolic pathways to achieve desired relationships.

The origin and evolution of the genetic code.

We argue that a primitive genetic code with only 20 separate words explains that there are 20 coded amino acids in modern life. The existence of 64 words on the modern genetic code requires modern

The Level and Landscape of Optimization in the Origin of the Genetic Code

The results seem to favor the coevolution theory because the fact that only a few amino acid exchanges would have been sufficient to transform the genetic code into a much better optimized code, and that such exchanges did not actually take place, seems to suggest that, for instance, the reduction of translation errors was not the main adaptive theme structuring the Genetic code.

Physicochemical Optimization in the Genetic Code Origin as the Number of Codified Amino Acids Increases

The results are in agreement with the coevolution theory, which attributes a role to the physicochemical properties of amino acids that, while important, is nevertheless subordinate to the mechanism which concedes codons from the precursor amino acids to the product amino acids as the primary factor determining the evolutionary structuring of the genetic code.