Rate variation during molecular evolution: creationism and the cytochrome c molecular clock

Molecular clocks based upon amino acid sequences in proteins have played a major role in the clarification of evolutionary phylogenies. Creationist criticisms of these methods sometimes rely upon data that might initially seem to be paradoxical. For example, human cytochrome c differs from that of an alligator by 13 amino acids but differs by 14 amino acids from a much more closely related primate, Otolemur garnettii. The apparent anomaly is resolved by taking into consideration the variable substitution rate of cytochrome c, particularly among primates. This paper traces some of the history of extensive research into the topic of rate heterogeneity in cytochrome c including data from cytochrome c pseudogenes

Computational strategy for the solution of large strain nonlinear problems using the Wilkins explicit finite-difference approach

The STEALTH code system, which solves large strain, nonlinear continuum mechanics problems, was rigorously structured in both overall design and programming standards. The design is based on the theoretical elements of analysis while the programming standards attempt to establish a parallelism between physical theory, programming structure, and documentation. These features have made it easy to maintain, modify, and transport the codes. It has also guaranteed users a high level of quality control and quality assurance

Two-sided Certification: The market for Rating Agencies

Certifiers contribute to the sound functioning of markets by reducing a symmetric information. They, however, have been heavily criticized during the 2008-09 financial crisis. This paper investigates on which side of the market a monopolistic profit-maximizing certifier offers his service. If the seller demands a rating, the certifier announces the product quality publicly, whereas if the buyer requests a rating it remains his private information. The model shows that the certifier offers his service to sellers and buyers to maximize his own profit with a higher share from the sellers. Overall, certifiers increase welfare in specific markets. Revenue shifts due to the financial crisis are also explained

Calculation of the Regularized Vacuum Energy in Cavity Field Theories

A novel technique based on Schwinger's proper time method is applied to the Casimir problem of the M.I.T. bag model. Calculations of the regularized vacuum energies of massless scalar and Dirac spinor fields confined to a static and spherical cavity are presented in a consistent manner. While our results agree partly with previous calculations based on asymptotic methods, the main advantage of our technique is that the numerical errors are under control. Interpreting the bag constant as a vacuum expectation value, we investigate potential cancellations of boundary divergences between the canonical energy and its bag constant counterpart in the fermionic case. It is found that such cancellations do not occur.Comment: 14 pages, 4 figures, accepted for publication in Eur.Phys.J.

Complex joint probabilities as expressions of determinism in quantum mechanics

The density operator of a quantum state can be represented as a complex joint probability of any two observables whose eigenstates have non-zero mutual overlap. Transformations to a new basis set are then expressed in terms of complex conditional probabilities that describe the fundamental relation between precise statements about the three different observables. Since such transformations merely change the representation of the quantum state, these conditional probabilities provide a state-independent definition of the deterministic relation between the outcomes of different quantum measurements. In this paper, it is shown how classical reality emerges as an approximation to the fundamental laws of quantum determinism expressed by complex conditional probabilities. The quantum mechanical origin of phase spaces and trajectories is identified and implications for the interpretation of quantum measurements are considered. It is argued that the transformation laws of quantum determinism provide a fundamental description of the measurement dependence of empirical reality.Comment: 12 pages, including 1 figure, updated introduction includes references to the historical background of complex joint probabilities and to related work by Lars M. Johanse

Note on finite temperature sum rules for vector and axial-vector spectral functions

An updated analysis of vector and axial-vector spectral functions is presented. The resonant contributions to the spectral integrals are shown to be expressible as multiples of 4 pi^2 f_pi^2, encoding the scale of spontaneous chiral symmetry breaking in QCD. Up to order T^2 this behavior carries over to the case of finite temperature.Comment: 10 pages, 2 figure

Vacuum structure of a modified MIT Bag

An alternative to introducing and subsequently renormalizing classical parameters in the expression for the vacuum energy of the MIT bag for quarks is proposed in the massless case by appealing to the QCD trace anomaly and scale separation due to asymptotic freedom. The explicit inclusion of gluons implies an unrealistically low separation scale.Comment: 5 pages, 2 figure