Genetic codes optimized as a traveling salesman problem

Attie, Oliver; Sulkow, Brian; Di, Chong; Qiu, Wang

doi:10.1371/journal.pone.0224552

Cited by 8 publications

(12 citation statements)

References 65 publications

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“…Since error minimization has adaptive value, a prevalent and intuitive view is that this property arose through natural selection 5,6,62 . However, an alternative view is that this trait emerged as a by-product during the initial expansion of the genetic code 36,37,39 . For example, it has been suggested that duplication of aminoacyl-tRNA synthetases would lead to emergence of a conservative pairing, as the tRNA and amino acid would be similar to the ancestral versions 63 .…”

Section: Discussionmentioning

confidence: 99%

“…This 'error minimization' confers a clear selective advantage as it reduces the deleterious impact of mutations on the resultant protein 32,33 . However, the standard genetic code does not appear to be particularly optimal with respect to error minimization [34][35][36][37] . This raises a fundamental open question about the origin of error minimization, namely, whether error minimization of the standard genetic code is the product of natural selection, or a serendipitous by-product of the evolution of protein translation 3 .…”

Section: Introductionmentioning

confidence: 99%

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Error minimization and specificity could emerge in a genetic code as by-products of prebiotic evolution

Janzen

Shen

Liu

et al. 2021

Preprint

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The emergence of the genetic code was a major transition in the evolution from a prebiotic RNA world to the earliest modern cells. A prominent feature of the standard genetic code is error minimization, or the tendency of mutations to be unusually conservative in preserving biophysical features of the amino acid. While error minimization is often assumed to result from natural selection, it has also been speculated that error minimization may be a by-product of emergence of the genetic code. During establishment of the genetic code in an RNA world, self-aminoacylating ribozymes would enforce the mapping of amino acids to anticodons. Here we show that expansion of the genetic code, through co-option of ribozymes for new substrates, could result in error minimization as an emergent property. Using self-aminoacylating ribozymes previously identified during an exhaustive search of sequence space, we measured the activity of thousands of candidate ribozymes on alternative substrates (activated analogs for tryptophan, phenylalanine, leucine, isoleucine, valine, and methionine). Related ribozymes exhibited preferences for biophysically similar substrates, indicating that co-option of existing ribozymes to adopt additional amino acids into the genetic code would itself lead to error minimization. Furthermore, ribozyme activity was positively correlated with specificity, indicating that selection for increased activity would also lead to increased specificity. These results demonstrate that by-products of the evolution and functional expansion of a ribozyme system could lead to adaptive properties of a genetic code. Such 'spandrels' could thus underlie significant prebiotic developments.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Error minimization and specificity could emerge in a genetic code as by-products of prebiotic evolution

Janzen

Shen

Liu

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…The objective is to analyze all travel points with the lowest distance. These data will affect the travel e ciency in terms of duration and fuel consumption and route management system (Pintea et al 2017;Attie et al 2019) TSP is a model of the travel to N Cities or N Places which this travel will travel from any one of N Cities by that route. Through all cities in N and return to the starting city to walk like a walking loop (Hougardy & Wilde 2015).…”

Section: Discussionmentioning

confidence: 99%

Vehicles Routing Arrangement for Prevention and Suppression Patrol: Process Model of Police Stations in Thailand

Muangpan

Muangpan²

2021

Preprint

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Coronavirus disease has affected to economic economics and society results in the, resulting in increasing crime problems increasing. Under circumstances with limited patrol officers, the prevention and suppression operations must be analyzed for vehicle routing for prevention and suppression patrols to reduce the patrol distance, time and fuel. This research aims to analyze the vehicle routing arrangement of the prevention and suppression patrol officers and to develop a routing process model of the prevention and suppression patrol management. Quantitative research is applied with Traveling Salesman Problem (TSP) the traveling salesman problem (TSP), which is utilized to established the establish prevention and suppression patrol routes. The qualitative Qualitative research is applied with content analysis, which is utilized to develop to the routing process model. The vehicle routes of the prevention and suppression patrol are arranged in the route set. These results are shown show the average of the route, distance and shortest patrol time of the patrol officers, which are cover all risk point patrol. Also, patrols. Additionally, a patrol routing model is presented to arrange the process of prevention and suppression patrol operation. This key process is applied to well manage the prevention and suppression patrol well, and these benefits are to reduce the patrol distance, patrol time and fuel cost. Additionally, this practice has increased the patrol rounds at risk points, resulting in the reduction in crimes and upgrading the good practices in patrol operations.

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“…The randomness of the standard genetic code [26] as related to the power law (or Zipf's law) was investigated recently [27]. It should be pointed out that the origin of the triplet code is being investigated from several different perspectives of optimization [28] [29]. The previous study, therefore, may be seen as belonging to this larger class of studies.…”

Section: The Genetic Codementioning

confidence: 99%

Data Amplification Using the Iterated Newcomb-Benford Distribution

Kak¹

2021

Preprint

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<p>The Newcomb-Benford (NB) distribution of first digits has been applied widely in many areas ranging from engineering to natural and biological sciences for the investigation of self-similarity and randomness. In this article, we consider systems for which the data is not enough to obtain proper first digit statistics, and we propose the use of an iterated version of the distribution where the statistics are aggregated over different scales on grounds that the first digit distribution is approximately scale invariant across a wide range of phenomena and also because scaling and recomputing first digits is not a linear process and so this process generates new data. We provide examples of the use of the iterated test for data in two different biological applications, viz. that of the secretome and the genetic code in both of which the raw data does not include all the nine different first digits. The paper includes proposals for further research on the idea of data amplification using scaling transformations.</p>

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Genetic codes optimized as a traveling salesman problem

Cited by 8 publications

References 65 publications

Error minimization and specificity could emerge in a genetic code as by-products of prebiotic evolution

Error minimization and specificity could emerge in a genetic code as by-products of prebiotic evolution

Vehicles Routing Arrangement for Prevention and Suppression Patrol: Process Model of Police Stations in Thailand

Data Amplification Using the Iterated Newcomb-Benford Distribution

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