The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not RandomReport as inadecuate




The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random - Download this document for free, or read online. Document in PDF available to download.

Evolution: Education and Outreach

, Volume 4, Issue 3, pp 502–514

First Online: 24 March 2011

Abstract

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke -design creationism- to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic-philic nature; a selective -pore- for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain 2TM potassium channel, from Streptomyces lividans, with an under-selection scenario, the -jackprot,- which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulationhttp:-faculty.rwu.edu-cbai-JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the -jackprot,- or highest-fitness complete-peptide sequence, required cumulative smaller -wins- rewarded by selection at the first, second, and third positions in each of the 161 KcsA codons -jackdons- that led to -jackacids- that led to the -jackprot-. The -jackprot- is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane 6TM domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide -edition- and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.

KeywordsDesign creationism Ion channels Jackacid Jackdon Molecular evolution Electronic supplementary materialThe online version of this article doi:10.1007-s12052-011-0329-2 contains supplementary material, which is available to authorized users.

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Author: Guillermo Paz-y-Miño C. - Avelina Espinosa - Chunyan Y. Bai

Source: https://link.springer.com/







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