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

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 Simulation http://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.

Educators of Prospective Teachers Hesitate to Embrace Evolution Due to Deficient Understanding of Science/Evolution and High Religiosity

“…In conceptually mistaken, type-I-error-based arguments to discredit evolution, ID has attributed randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time or population size for molecular improvements to occur, and invoked “design intervention” to account for complexity in molecular structures and biological processes (Paz-y-Miño-C and Espinosa 2010; Paz-y-Miño-C et al 2011). In 2005, ID was exposed in court (Dover, Pennsylvania, Kitzmiller et al versus Dover School District et al 2005; Padian and Matzke 2009; Wexler 2010) for violating the rules of science by “invoking and permitting supernatural causation” in matters of evolution, and for “failing to gain acceptance in the scientific community.” Today, “design creationism” (as we refer to ID due to its designer/creator-based foundations; Pennock 2001; Paz-y-Miño-C and Espinosa 2010, 2011b; Paz-y-Miño-C et al 2011) although defeated by science and in the courts, grows influential in the U.S., Europe, Australia and South America (Cornish-Bowden and Cárdenas 2007; Padian 2009; Branch et al 2010; Forrest 2010; Matzke 2010; Wexler 2010). …”