Is The amphibian tree of life really fatally flawed?

Wiens (2007, Q. Rev. Biol. 82, 55-56) recently published a severe critique of Frost et al.'s (2006, Bull. Am. Mus. Nat. Hist. 297, 1-370) monographic study of amphibian systematics, concluding that it is a disaster and recommending that readers simply ignore this study. Beyond the hyperbole, Wiens raised four general objections that he regarded as fatal flaws: (1) the sampling design was insufficient for the generic changes made and taxonomic changes were made without including all type species; (2) the nuclear gene most commonly used in amphibian phylogenetics, RAG-1, was not included, nor were the morphological characters that had justified the older taxonomy; (3) the analytical method employed is questionable because equally weighted parsimony assumes that all characters are evolving at equal rates; and (4) the results were at times clearly erroneous, as evidenced by the inferred non-monophyly of marsupial frogs. In this paper we respond to these criticisms. In brief: (1) the study of Frost et al. did not exist in a vacuum and we discussed our evidence and evidence previously obtained by others that documented the non-monophyletic taxa that we corrected. Beyond that, we agree that all type species should ideally be included, but inclusion of all potentially relevant type species is not feasible in a study of the magnitude of Frost et al. and we contend that this should not prevent progress in the formulation of phylogenetic hypotheses or their application outside of systematics. (2) Rhodopsin, a gene included by Frost et al. is the nuclear gene that is most commonly used in amphibian systematics, not RAG-1. Regardless, ignoring a study because of the absence of a single locus strikes us as unsound practice. With respect to previously hypothesized morphological synapomorphies, Frost et al. provided a lengthy review of the published evidence for all groups, and this was used to inform taxonomic decisions. We noted that confirming and reconciling all morphological transformation series published among previous studies needed to be done, and we included evidence from the only published data set at that time to explicitly code morphological characters (including a number of traditionally applied synapomorphies from adult morphology) across the bulk of the diversity of amphibians (Haas, 2003, Cladistics 19, 23-90). Moreover, the phylogenetic results of the Frost et al. study were largely consistent with previous morphological and molecular studies and where they differed, this was discussed with reference to the weight of evidence. (3) The claim that equally weighted parsimony assumes that all characters are evolving at equal rates has been shown to be false in both analytical and simulation studies. (4) The claimed strong support for marsupial frog monophyly is questionable. Several studies have also found marsupial frogs to be non-monophyletic. Wiens et al. (2005, Syst. Biol. 54, 719-748) recovered marsupial frogs as monophyletic, but that result was strongly supported only by Bayesian clade confidence values (which are known to overestimate support) and bootstrap support in his parsimony analysis was < 50%. Further, in a more recent parsimony analysis of an expanded data set that included RAG-1 and the three traditional morphological synapomorphies of marsupial frogs, Wiens et al. (2006, Am. Nat. 168, 579-596) also found them to be non-monophyletic.Although we attempted to apply the rule of monophyly to the naming of taxonomic groups, our phylogenetic results are largely consistent with conventional views even if not wth the taxonomy current at the time of our writing. Most of our taxonomic changes addressed examples of non-monophyly that had previously been known or suspected (e.g., the non-monophyly of traditional Hyperoliidae, Microhylidae, Hemiphractinae, Leptodactylidae, Phrynobatrachus, Ranidae, Rana, Bufo; and the placement of Brachycephalus within Eleutherodactylus, and Lineatriton within Pseudoeurycea), and it is troubling that Wiens and others, as evidenced by recent publications, continue to perpetuate recognition of non-monophyletic taxonomic groups that so profoundly misrepresent what is known about amphibian phylogeny. (C) The Willi Hennig Society 2007.

CMS physics technical design report, volume II: Physics performance

CMS is a general purpose experiment, designed to study the physics of pp collisions at 14 TeV at the Large Hadron Collider ( LHC). It currently involves more than 2000 physicists from more than 150 institutes and 37 countries. The LHC will provide extraordinary opportunities for particle physics based on its unprecedented collision energy and luminosity when it begins operation in 2007. The principal aim of this report is to present the strategy of CMS to explore the rich physics programme offered by the LHC. This volume demonstrates the physics capability of the CMS experiment. The prime goals of CMS are to explore physics at the TeV scale and to study the mechanism of electroweak symmetry breaking - through the discovery of the Higgs particle or otherwise. To carry out this task, CMS must be prepared to search for new particles, such as the Higgs boson or supersymmetric partners of the Standard Model particles, from the start- up of the LHC since new physics at the TeV scale may manifest itself with modest data samples of the order of a few fb(-1) or less. The analysis tools that have been developed are applied to study in great detail and with all the methodology of performing an analysis on CMS data specific benchmark processes upon which to gauge the performance of CMS. These processes cover several Higgs boson decay channels, the production and decay of new particles such as Z' and supersymmetric particles, B-s production and processes in heavy ion collisions. The simulation of these benchmark processes includes subtle effects such as possible detector miscalibration and misalignment. Besides these benchmark processes, the physics reach of CMS is studied for a large number of signatures arising in the Standard Model and also in theories beyond the Standard Model for integrated luminosities ranging from 1 fb(-1) to 30 fb(-1). The Standard Model processes include QCD, B-physics, diffraction, detailed studies of the top quark properties, and electroweak physics topics such as the W and Z(0) boson properties. The production and decay of the Higgs particle is studied for many observable decays, and the precision with which the Higgs boson properties can be derived is determined. About ten different supersymmetry benchmark points are analysed using full simulation. The CMS discovery reach is evaluated in the SUSY parameter space covering a large variety of decay signatures. Furthermore, the discovery reach for a plethora of alternative models for new physics is explored, notably extra dimensions, new vector boson high mass states, little Higgs models, technicolour and others. Methods to discriminate between models have been investigated. This report is organized as follows. Chapter 1, the Introduction, describes the context of this document. Chapters 2-6 describe examples of full analyses, with photons, electrons, muons, jets, missing E-T, B-mesons and tau's, and for quarkonia in heavy ion collisions. Chapters 7-15 describe the physics reach for Standard Model processes, Higgs discovery and searches for new physics beyond the Standard Model.

The CMS experiment at the CERN LHC

The Compact Muon Solenoid (CMS) detector is described. The detector operates at the Large Hadron Collider (LHC) at CERN. It was conceived to study proton-proton (and lead-lead) collisions at a centre-of-mass energy of 14 TeV (5.5 TeV nucleon-nucleon) and at luminosities up to 10(34)cm(-2)s(-1) (10(27)cm(-2)s(-1)). At the core of the CMS detector sits a high-magnetic-field and large-bore superconducting solenoid surrounding an all-silicon pixel and strip tracker, a lead-tungstate scintillating-crystals electromagnetic calorimeter, and a brass-scintillator sampling hadron calorimeter. The iron yoke of the flux-return is instrumented with four stations of muon detectors covering most of the 4 pi solid angle. Forward sampling calorimeters extend the pseudo-rapidity coverage to high values (vertical bar eta vertical bar <= 5) assuring very good hermeticity. The overall dimensions of the CMS detector are a length of 21.6 m, a diameter of 14.6 m and a total weight of 12500 t.

The amphibian tree of life

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit HI (12S and 16S ribosomal RNA and tRNA(Valine) genes, 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (approximate to 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x ($) over bar = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons.

RESULTS FROM THE SLD BARREL CRID DETECTOR

We report on operational experience with an experimental performance of the SLD barrel Cherenkov Ring Imaging Detector from the 1992 and 1993 physics runs. The liquid (C6F14) and gas (C5F12) radiator recirculation systems have performed well, and the drift gas supply system has operated successfully with TMAE for three years. Cherenkov rings have been observed from both the liquid and gas radiators. The number and angular resolution of Cherenkov photons have been measured, and found to be close to design specifications.

PERFORMANCE OF THE SLD BARREL CRID DURING THE 1992 PHYSICS DATA RUN

The SLD Barrel Cherenkov Ring Imaging Detector was fully operational in the 1992 physics data run. The electron drift velocity and magnetic field deflection of electron trajectories have been measured. Cherenkov rings have been observed from both the liquid and gas radiators. The number and the resolution of the angle of Cherenkov photons have been measured to be approximately equal to design specifications.

THE FLUID SYSTEMS FOR THE SLD CHERENKOV RING IMAGING DETECTOR

We describe the design and operation of the fluid delivery, monitor and control systems for the SLD barrel Cherenkov Ring Imaging Detector (CRID). The systems deliver drift gas (C2H6+TMAE), radiator gas (C5F12+N2) and radiator liquid (C6F14). MeasUred critical quantities such as electron lifetime in the drift gas and ultra-violet (UV) transparencies of the radiator fluids, together with the operational experience, are also reported.

Practising Arithmetic Using Educational Video Games with an Interpersonal Computer

Studies show the positive effects that video games can have on student performance and attitude towards learning. In the past few years, strategies have been generated to optimize the use of technological resources with the aim of facilitating widespread adoption of technology in the classroom. Given its low acquisition and maintenance costs, the interpersonal computer allows individual interaction and simultaneous learning with large groups of students. The purpose of this work was to compare arithmetical knowledge acquired by third-grade students through the use of game-based activities and non-game-based activities using an interpersonal computer, with knowledge acquired through the use of traditional paper-and-pencil activities, and to analyze their impact in various socio-cultural contexts. To do this, a quasi-experimental study was conducted with 271 students in three different countries (Brazil, Chile, and Costa Rica), in both rural and urban schools. A set of educational games for practising arithmetic was developed and tested in six schools within these three countries. Results show that there were no significant differences (ANCOVA) in the learning acquired from game-based vs. non-game-based activities. However, both showed a significant difference when compared with the traditional method. Additionally, both groups using the interpersonal computer showed higher levels of student interest than the traditional method group, and these technological methods were seen to be especially effective in increasing learning among weaker students.