Accurate age estimation in small-scale societies

Precise estimation of age is essential in evolutionary anthropology, especially to infer population age structures and understand the evolution of human life history diversity. However, in small-scale societies, such as hunter-gatherer populations, time is often not referred to in calendar years, and accurate age estimation remains a challenge. We address this issue by proposing a Bayesian approach that accounts for age uncertainty inherent to fieldwork data. We developed a Gibbs sampling Markov chain Monte Carlo algorithm that produces posterior distributions of ages for each individual, based on a ranking order of individuals from youngest to oldest and age ranges for each individual. We first validate our method on 65 Agta foragers from the Philippines with known ages, and show that our method generates age estimations that are superior to previously published regression-based approaches. We then use data on 587 Agta collected during recent fieldwork to demonstrate how multiple partial age ranks coming from multiple camps of hunter-gatherers can be integrated. Finally, we exemplify how the distributions generated by our method can be used to estimate important demographic parameters in small-scale societies: here, age-specific fertility patterns. Our flexible Bayesian approach will be especially useful to improve cross-cultural life history datasets for small-scale societies for which reliable age records are difficult to acquire

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods

Positivity of Entropy in the Semi-Classical Theory of Black Holes and Radiation

Quantum stress-energy tensors of fields renormalized on a Schwarzschild background violate the classical energy conditions near the black hole. Nevertheless, the associated equilibrium thermodynamical entropy $\Delta S$ by which such fields augment the usual black hole entropy is found to be positive. More precisely, the derivative of $\Delta S$ with respect to radius, at fixed black hole mass, is found to vanish at the horizon for {\it all} regular renormalized stress-energy quantum tensors. For the cases of conformal scalar fields and U(1) gauge fields, the corresponding second derivative is positive, indicating that $\Delta S$ has a local minimum there. Explicit calculation shows that indeed $\Delta S$ increases monotonically for increasing radius and is positive. (The same conclusions hold for a massless spin 1/2 field, but the accuracy of the stress-energy tensor we employ has not been confirmed, in contrast to the scalar and vector cases). None of these results would hold if the back-reaction of the radiation on the spacetime geometry were ignored; consequently, one must regard $\Delta S$ as arising from both the radiation fields and their effects on the gravitational field. The back-reaction, no matter how "small",Comment: 19 pages, RevTe

Gauge Field Back-reaction on a Black Hole

The order $\hbar$ fluctuations of gauge fields in the vicinity of a blackhole can create a repulsive antigravity region extending out beyond the renormalized Schwarzschild horizon. If the strength of this repulsive force increases as higher orders in the back-reaction are included, the formation of a wormhole-like object could occur.Comment: 17 pages, three figures available on request, in RevTe

The optical spectrum of a large isolated polycyclic aromatic hydrocarbon: hexa-peri-hexabenzocoronene, C42H18

The first optical spectrum of an isolated polycyclic aromatic hydrocarbon large enough to survive the photophysical conditions of the interstellar medium is reported. Vibronic bands of the first electronic transition of the all benzenoid polycyclic aromatic hydrocarbon hexa-peri-hexabenzocoronene were observed in the 4080-4530 Angstrom range by resonant 2-color 2-photon ionization spectroscopy. The strongest feature at 4264 Angstrom is estimated to have an oscillator strength of f=1.4x10^-3, placing an upper limit on the interstellar abundance of this polycyclic aromatic hydrocarbon at 4x10^12 cm^-2, accounting for a maximum of ~0.02% of interstellar carbon. This study opens up the possibility to rigorously test neutral polycyclic aromatic hydrocarbons as carriers of the diffuse interstellar bands in the near future.Comment: 9 pages, 1 figure. Fixed a typo on the frequency of the 'b' ban

Effective Potential of a Black Hole in Thermal Equilibrium with Quantum Fields

Expectation values of one-loop renormalized thermal equilibrium stress-energy tensors of free conformal scalars, spin-${1 \over 2}$ fermions and U(1) gauge fields on a Schwarzschild black hole background are used as sources in the semi-classical Einstein equation. The back-reaction and new equilibrium metric are solved for at $O({\hbar})$ for each spin field. The nature of the modified black hole spacetime is revealed through calculations of the effective potential for null and timelike orbits. Significant novel features affecting the motions of both massive and massless test particles show up at lowest order in $\epsilon= (M_{Pl}/M)^2 < 1$, where $M$ is the renormalized black hole mass, and $M_{Pl}$ is the Planck mass. Specifically, we find the tendency for \underline{stable} circular photon orbits, an increase in the black hole capture cross sections, and the existence of a gravitationally repulsive region associated with the black hole which is generated from the U(1) back-reaction. We also consider the back-reaction arising from multiple fields, which will be useful for treating a black hole in thermal equilibrium with field ensembles belonging to gauge theories.Comment: 25 pages (not including seven figures), VAND-TH-93-6. Typed in Latex, uses RevTex macro

High Energy Colliders as Black Hole Factories: The End of Short Distance Physics

If the fundamental Planck scale is of order a TeV, as the case in some extra-dimensions scenarios, future hadron colliders such as the Large Hadron Collider will be black hole factories. The non-perturbative process of black hole formation and decay by Hawking evaporation gives rise to spectacular events with up to many dozens of relatively hard jets and leptons, with a characteristic ratio of hadronic to leptonic activity of roughly 5:1. The total transverse energy of such events is typically a sizeable fraction of the beam energy. Perturbative hard scattering processes at energies well above the Planck scale are cloaked behind a horizon, thus limiting the ability to probe short distances. The high energy black hole cross section grows with energy at a rate determined by the dimensionality and geometry of the extra dimensions. This dependence therefore probes the extra dimensions at distances larger than the Planck scale.Comment: Latex, 28 pages. v4: minor changes, largely to agree with published version; appendix added comparing convention