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

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    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

    On the Quantum Chromodynamics of a Massive Vector Field in the Adjoint Representation

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    In this paper, we explore the possibility of constructing the quantum chromodynamics of a massive color-octet vector field without introducing higher structures like extended gauge symmetries, extra dimensions or scalar fields. We show that gauge invariance is not enough to constraint the couplings. Nevertheless the requirement of unitarity fixes the values of the coupling constants, which otherwise would be arbitrary. Additionally, it opens a new discrete symmetry which makes the coloron stable and avoid its resonant production at a collider. On the other hand, a judicious definition of the gauge fixing terms modifies the propagator of the massive field making it well-behaved in the ultra-violet limit. The relation between our model and the more general approach based on extended gauge symmetries is also discussed.Comment: Subsection 2.1 rewritten in order to make it more pedagogical. This version match the text accepted in IJMP

    The Planck Scale from Top Condensation

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    We propose a scenario in which the Planck scale is dynamically linked to the electroweak scale induced by top condensation. The standard model field content, without the Higgs, is promoted to a 5D warped background. There is also an additional 5D fermion with the quantum numbers of the right-handed top. Localization of the zero-modes leads, at low energies, to a Nambu-Jona-Lasinio model that also stabilizes the radion field dynamically thus explaining the hierarchy between the Planck scale and v_EW = 174 GeV. The top mass arises dynamically from the electroweak breaking condensate. The other standard model fermion masses arise naturally from higher-dimension operators, and the fermion mass hierarchies and flavor structure can be explained from the localization of the zero-modes in the extra dimension. If any other contributions to the radion potential except those directly related with electroweak symmetry breaking are engineered to be suppressed, the KK scale is predicted to be about two orders of magnitude above the electroweak scale rendering the model easily consistent with electroweak precision data. The model predicts a heavy (composite) Higgs with a mass of about 500 GeV and standard-model-like properties, and a vector-like quark with non-negligible mixing with the top quark and mass in the 1.6 - 2.9 TeV range. Both can be within the reach of the LHC. It also predicts a radion with a mass of a few GeV that is very weakly coupled to standard model matter.Comment: 41 pages, 7 figures; added references, minor changes in the electroweak precision constraints section; final version in PR
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