title: Redundancy of the genetic code enables translational pausing.
abstract: The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PIo) purposely slows or speeds up the translation-decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.
authors.affiliation: Control Systems Modeling and Simulation, General Dynamics Sterling Heights, MI, USA ; Department of Humanities and Science, Math Department, College of Humanities and Science, University of Phoenix Detroit, MI, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: D'Onofrio
authors.affiliation: Department of ProtoBioCybernetics/ProtoBioSemiotics, The Gene Emergence Project of The Origin of Life Science Foundation, Inc. Greenbelt, MD, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Abel
keywords: Shine Dalgarno sequences; algorithm; co-translational folding; degeneracy; multi-dimensional code; regulation; ribosome; translational pausing