Fifty years ago, David Marr and James Albus proposed a computational model of cerebellar cortical function based on the pioneering circuit models described by John Eccles, Masao Ito and Janos Szentagothai. The Marr-Albus model remains one of the most enduring and influential models in computational neuroscience, despite apparent falsification of some of the original predictions. We re-examine the Marr-Albus model in the context of the modern theory of computational neural networks and in the context of expanded interpretations of the connectivity and function of cerebellar cortex within the full motor system. By doing so, we show that the original elements of the codon theory continue to make important predictions for cerebellar mechanism, and we show that evidence appearing to contradict the original model is based on an artificially narrow interpretation of cerebellar structure and motor function.
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http://dx.doi.org/10.1113/JP278745 | DOI Listing |
bioRxiv
December 2024
Duke University, Department of Cell Biology, Durham, NC.
Most amino acids are encoded by multiple codons, making the genetic code degenerate. Synonymous mutations affect protein translation and folding, but their impact on RNA itself is often neglected. We developed a genetic algorithm that introduces synonymous mutations to control the diversity of structures sampled by an mRNA.
View Article and Find Full Text PDFBiosystems
January 2025
The Ionian School, Early Evolution of Life Department, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena, L'Aquila, Italy. Electronic address:
Recently, a new genetic code with 62 sense codons, coding for 21 amino acids, and only 2 termination codons has been identified in archaea. The authors argue that the appearance of this variant of the genetic code is due to the relatively recent and complete recoding of all UAG stop codons to codons encoding for pyrrolysine. I re-evaluate this discovery by presenting arguments that favour the early, i.
View Article and Find Full Text PDFTheory Biosci
December 2024
Institute for Mathematical Biology Faculty of Computer Sciences, Mannheim University of Applied Sciences, 68163, Mannheim, Germany.
Circular codes, which are considered as putative remnants of primaeval comma-free codes, have recently become a focal point of research. These codes constitute a secondary type of genetic code, primarily tasked with detecting and preserving the normal reading frame within protein-coding sequences. The identification of a universal code present across various species has sparked numerous theoretical and experimental inquiries.
View Article and Find Full Text PDFBull Math Biol
November 2024
Theoretical Bioinformatics, ICube, C.N.R.S., University of Strasbourg, 300 Boulevard Sébastien Brant, 67400, Illkirch, France.
Elife
September 2024
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an 'effective population size' is often estimated from the amount of putatively neutral genetic diversity and is assumed to also capture a species' effectiveness of selection.
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