"The purpose of this thread is to discuss recent findings on the optimality of the genetic code . Selected articles in the OP include the following : Early Fixation of an Optimal Genetic Code Evolution of the genetic code : partial optimization of a random code for robustness to translation error in a rugged fitness landscape The genetic code is nearly optimal for allowing additional information within protein-coding sequences An extension of the coevolution theory of the origin of the genetic code Can the genetic code be mathematically described ? On the Hypercube Structure of the Genetic Code Topological structure of the triplet genetic code A Neutral Origin for Error Minimization in the Genetic Code . Does codon bias have an evolutionary origin ? A chemical toolkit for proteins & # 8212 ; an expanded genetic code Evolution and multilevel optimization of the genetic code Feel free to add more interesting articles as the discussion continues . Article 1 Thus , to begin , in the first article it was determined by the researchers that : No better codes out of a million biosynthetically restricted codes . This conclusion might be misleading though ( addressed here ) , as the paper states that the tested codes were from a biosynthetically restricted set based on the current hypothesis of the evolution of the genetic code from pre-biotic scenarios . When not viewed from this point of view , other , more optimized codes are possible . The next article ( nr 2 ) shows that : Thus showing in that analysis which include all possible codes ( not only biosynthetically restricted codes ) that the genetic code is partially optimal with regards to error minimization . It should be noted though that analysis only included a subset of the possible optimality feature of the code . From article 3 The analysis above did not include other nearly optimal features of the genetic code including : A ) The actual code is far better than other possible codes in minimizing the number of amino acids incorporated until translation is interrupted after a frameshift error occurred . B ) The code is highly optimal for encoding arbitrary additional information , i.e. , information other than the amino acid sequence in protein-coding sequences . Thus , two more features for which the code is close to being optimal . What is interesting about these two optimal features is that they may facilitate evolution i.e . the code is primed for the future by being optimal in allowing future incorporation of additional information . In article nr.4 The coevolution theory of the origin of the genetic code is discussed . The theory suggests that the genetic code is an imprint of the biosynthetic ( biosynthetically restricted ) relationships between amino acids . A few interesting observations can be made : Firstly , from the article : It should be noted that other exotic amino acids are also used by a few other codes ( derived form the original ) . E.g . Selenocysteine and pyrrolysine are encoded for in many archaea and vertebrates . Archaea , however seem to be the most primitive organisms , thus these encoded amino acids must have been fixated early on . Thus an interesting question can be applied to an `` evolving `` code as posited in the above quote : Are these `` still evolving `` mRNAs , still evolving ? Or did it hit an inevitable global optimum ? Secondly , from the article : Is it correct to assume that in the presence of the precursors of the standard genetic code ( e.g . intermediates of glucose degradation and the citric acid cycle ) , the intimate relationship between these molecules resulted in the inevitable organization of the genetic code ( global optimum of the system ) ? Articles 5-7 These articles discuss fascinating mathematical representation of the genetic code . For example , in article 6 a representation of the genetic code as a six & # 8211 ; dimensional Boolean hypercube is proposed . Abstract : Article 8 : In this article it once again discusses the optimality of the code and a few fascinating conclusions were made . For example : Also form the article : Thus , an important point is raised : The article cautions on blithely using natural selection as an explanation for the features of the genetic code . Article 9 : In this article , the functional integrity and how the architecture of the code relates to it is discussed . From the article : Thus , the properties of the code allow it to maintain its own functional integrity . Also form the article : The maintenance of the integrity of the code is not dependent on selection , but dependent on internal variables ( feedback system ) for maintaining functional integrity . Again , showing another form of optimality . In article 10 : Fascinating research was conducted whereby a sundry of different unnatural amino acids with novel three and four base codons have been selectively incorporated ( engineered ) into proteins yielding viable organisms . An intriguing question arises from this research . It is easy to imagine these to arise through chance and selection ( e.g . amino acids with photoaffinity ) and then be incorporated into the standard code . Yet the code seems to remain stagnant . For billions of year after fixation , little evolution happened in the code . Why ? Did it arrive at a global optimum in a pre-existing fitness landscape , with a pre-existing fitness function ? Finally , Article 11 : The article cites many of the optimal properties above and concludes : Indeed . The genetic code sure is interesting . Whatever the explanation for the origins of the code , whether intentional agency , only RV+NS , self-organization or a combination of these , the fact that these processes converged on a single , reasonably optimal code that is able to facilitate evolution makes it look like it was an inevitable result from the system . The system seems to be rigged and biased towards certain outcomes similar to the evolution of life ."
"Again , as an ignorant layman , I can only get the gist of this material , but how anyone could possibly argue against the genetic code as a product of intelligent design is beyond me ."
"maintenance of the integrity of the code is not dependent on selection"
"how anyone could possibly argue against the genetic code as a product of intelligent design is beyond me"