The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?

The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950-1,259 million years ago (Mya), animals diverged from choanoflagellates 761-957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642-761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be approximate to100 million years more ancient than the Cambrian boundary.

Characterisation of an amphioxus Fringe gene and the evolution of the vertebrate segmentation clock

In mouse and chick embryos, cyclic expression of lunatic fringe has an important role in the regulation of mesoderm segmentation. We have isolated a Fringe gene from the protochordate amphioxus. Amphioxus is the closest living relative of the vertebrates, and has mesoderm that is definitively segmented in a manner that is similar to, and probably homologous with, that of vertebrates. AmphiFringe is placed basal to vertebrate Fringe genes in molecular phylogenetic analyses, indicating that the duplications that formed radical-, manic- and lunatic fringe are specific to the vertebrate lineage. AmphiFringe expression was detected in the anterior neural plate of early neurulae, where it resolved into a series of segmental patches by the mid-neurulae stage. No AmphiFringe transcripts were detected in the mesoderm. Based on these observations, we propose a model depicting a successive recruitment of Fringe in the maintenance then regulation of segmentation during vertebrate evolution.

(Re)enchanting geography? The nature of being critical and the character of critique in human geography

Enchantment is a term frequently used by human geographers to express delight, wonder or that which cannot be simply explained. However, it is a concept that has yet to be subject to sustained critique, specifically how it can be used to progress geographic thought and praxis. This paper makes sense of, and space for, the unintelligibility of enchantment in order to encourage a less repressed, more cheerful way of engaging with the geographies of the world. We track back through our disciplinary heritage to explore how geographers have employed enchantment as a force through which the world inspires affective attachment. We review the terrain of the debate surrounding recent geographical engagements with enchantment, focusing on the nature of being critical and the character of critique in human geography, offering a new ‘enchanted’ stance to our geographical endeavours. We argue that the moment of enchantment has not passed with the current challenging climate; if anything, it is more pressing.

The effect of doubled CO2 and model basic state biases on the monsoon-ENSO system. I: Mean response and interannual variability

The impact of doubled CO2 concentration on the Asian summer monsoon is studied using a coupled ocean-atmosphere model. Both the mean seasonal precipitation and interannual monsoon variability are found to increase in the future climate scenario presented. Systematic biases in current climate simulations of the coupled system prevent accurate representation of the monsoon-ENSO teleconnection, of prime importance for seasonal prediction and for determining monsoon interannual variability. By applying seasonally varying heat flux adjustments to the tropical Pacific and Indian Ocean surface in the future climate simulation, some assessment can be made of the impact of systematic model biases on future climate predictions. In simulations where the flux adjustments are implemented, the response to climate change is magnified, with the suggestion that systematic biases may be masking the true impact of increased greenhouse gas forcing. The teleconnection between ENSO and the Asian summer monsoon remains robust in the future climate, although the Indo-Pacific takes on more of a biennial character for long periods of the flux-adjusted simulation. Assessing the teleconnection across interdecadal timescales shows wide variations in its amplitude, despite the absence of external forcing. This suggests that recent changes in the observed record cannot be distinguished from internal variations and as such are not necessarily related to climate change.

The impact of the stratosphere on the troposphere during the southern hemisphere stratospheric sudden warming, September 2002

Recent research has established that a small but statistically significant link exists between the stratosphere and the troposphere in the northern hemisphere extratropics. In this paper it is shown that a similar link exists between the stratosphere and troposphere during the unprecedented September 2002 sudden warming in the southern hemisphere. Two ensemble forecasts of the stratospheric sudden warming are run which have different stratospheric initial conditions and identical tropospheric initial conditions. Stratospheric initial conditions have an impact on the tropospheric flow at the peak of the major warming (5 days into the run) and on longer time-scales (18 days into the run). The character of this influence is a localized, equatorward shift of the tropospheric storm track. The averaged impact of the change in the position of the storm-track maps strongly onto the Southern Annular Mode structure, but does not have an annular character.

The role of nonhydrostatic dynamics in controlling development of a surface ocean front

Numerical studies of surface ocean fronts forced by inhomogeneous buoyancy loss show nonhydrostatic convective plumes coexisting with baroclinic eddies. The character of the vertical overturning depends sensitively on the treatment of the vertical momentum equation in the model. It is less well known how the frontal evolution over scales of O(10 km) is affected by these dynamics. Here, we compare highly resolved numerical experiments using nonhydrostatic and hydrostatic models and the convective-adjustment parametrization. The impact of nonhydrostatic processes on average cross-frontal transfer is weak compared to the effect of the O(1 km) scale baroclinic motions. For water-mass distribution and formation rate nonhydrostatic dynamics have similar influence to the baroclinic eddies although adequate resolution of the gradients in forcing fluxes is more important. The overall implication is that including nonhydrostatic surface frontal dynamics in ocean general circulation models will have only a minor effect on scales of O(1 km) and greater.

The accuracy of digital elevation models derived from digitised contour data

Although accuracy of digital elevation models (DEMs) can be quantified and measured in different ways, each is influenced by three main factors: terrain character, sampling strategy and interpolation method. These parameters, and their interaction, are discussed. The generation of DEMs from digitised contours is emphasised because this is the major source of DEMs, particularly within member countries of OEEPE. Such DEMs often exhibit unwelcome artifacts, depending on the interpolation method employed. The origin and magnitude of these effects and how they can be reduced to improve the accuracy of the DEMs are also discussed.

The role of the Madden-Julian Oscillation in the El Nino and Indian drought of 2002

In 2002 India experienced a severe drought, one among the five worst droughts since records began in 1871, notable for its countrywide influence. The drought was primarily due to an unprecedented break in the monsoon during July, which persisted for almost the whole month and affected most of the sub-continent. The failure of the monsoon in 2002 was not predicted and India was not prepared for the devastating impacts on, for example, agriculture. This paper documents the evolution of the 2002 Indian summer monsoon and considers the possible factors that contributed to the drought and the failure of the forecasts. The development of the 2002/2003 El Nino and the unusually high levels of Madden-Julian Oscillation (MJO) activity during the monsoon season are identified as the central players. The 2002/2003 El Nino was characterised by very high sea-surface temperatures (SSTs) in the central Pacific that developed rapidly during the monsoon season. It is suggested that the unusual character of the developing El Nino was associated with the MJO and was a consequence of the eastward extension of the West Pacific Warm Pool, brought about primarily by a series of westerly wind events (WWEs) as part of the eastward movement of the active phase of the MJO. During the boreal summer, the MJO is usually characterised by northward movement, but in 2002 the northward component of the MJO was weak and the MJO was dominated by a strong eastward component, probably driven by the abnormally high SSTs in the central Pacific. It is suggested that a positive feedback existed between the developing El Nino and the eastward component of the MJO, which weakened the active phases of the monsoon. In particular, the unprecedented monsoon break in July could be associated with the juxtaposition of strong MJO activity with a developing El Nino, both of which interfered constructively with each other to produce major perturbations to the distribution of tropical heating. Subsequently, the main impact of the developing El Nino was a modulation of the Walker circulation that led to the overall suppression of the Indian monsoon during thess latter part of the season. It is argued that the unique combination of a rapidly developing El Nino and strong MJO activity, which was timed within the seasonal cycle to have maximum impact on the Indian summer monsoon, meant that prediction of the prolonged break in July and the seasonally deficient rainfall was a challenge for both the empirical and dynamical forecasting systems. Copyright (C) 2006 Royal Meteorological Society.

Transient teleconnection event at the onset of a planet-encircling dust storm on Mars

We use proper orthogonal decomposition (POD) to study a transient teleconnection event at the onset of the 2001 planet-encircling dust storm on Mars, in terms of empirical orthogonal functions (EOFs). There are several differences between this and previous studies of atmospheric events using EOFs. First, instead of using a single variable such as surface pressure or geopotential height on a given pressure surface, we use a dataset describing the evolution in time of global and fully three-dimensional atmospheric fields such as horizontal velocity and temperature. These fields are produced by assimilating Thermal Emission Spectrometer observations from NASA's Mars Global Surveyor spacecraft into a Mars general circulation model. We use total atmospheric energy (TE) as a physically meaningful quantity which weights the state variables. Second, instead of adopting the EOFs to define teleconnection patterns as planetary-scale correlations that explain a large portion of long time-scale variability, we use EOFs to understand transient processes due to localised heating perturbations that have implications for the atmospheric circulation over distant regions. The localised perturbation is given by anomalous heating due to the enhanced presence of dust around the northern edge of the Hellas Planitia basin on Mars. We show that the localised disturbance is seemingly restricted to a small number (a few tens) of EOFs. These can be classified as low-order, transitional, or high-order EOFs according to the TE amount they explain throughout the event. Despite the global character of the EOFs, they show the capability of accounting for the localised effects of the perturbation via the presence of specific centres of action. We finally discuss possible applications for the study of terrestrial phenomena with similar characteristics.

The effect of Parkinson's disease on time estimation as a function of stimulus duration range and modality

The present research sought to investigate the role of the basal ganglia in timing of sub- and supra-second intervals via an examination of the ability of people with Parkinson's disease (PD) to make temporal judgments in two ranges, 100-500 ms, and 1-5 s. Eighteen nondemented medicated patients with PD were compared with 14 matched controls on a duration-bisection task in which participants were required to discriminate auditory and visual signal durations within each time range. Results showed that patients with PD exhibited more variable duration judgments across both signal modality and duration range than controls, although closer analyses confirmed a timing deficit in the longer duration range only. The findings presented here suggest the bisection procedure may be a useful tool in identifying timing impairments in PD and, more generally, reaffirm the hypothesised role of the basal ganglia in temporal perception at the level of the attentionally mediated internal clock as well as memory retrieval and/or decision-making processes. (c) 2007 Elsevier Inc. All rights reserved.

Spectacle/gender/history: the case of Gone with the Wind

The essay asserts that, since pioneering work in the 1970s and 80s (in Screen in particular), the study of classical Hollywood cinema has failed adequately to acknowledge and understand the role of spectacle therein. This essay outlines theoretical but, even more, practical understandings of particular kinds of spectacle; they are susceptible to the practice of close analysis. Seeking to discuss spectacle in precise terms and in particular contexts, I define two kinds of spectacle associated with the historical film: ‘the decor of history’ and ‘the spectacular vista’. The example of Gone with the Wind illustrates the interrelationship between these two kinds of spectacle and their associations with particular ideas of femininity and masculinity. This gendering of spectacle is related to ‘the historical gaze’, a performative gesture that exemplifies the wider rhetoric of historical films, in their seeking to address the historical knowledge of the film spectator and to uphold a vision of history as being driven by powerful men, aware of their own destiny. Over the course of the three famous hilltop scenes in Gone with the Wind, one can plot Scarlett O'Hara's increased access to this kind of foresight and fortitude coded as ‘masculine’. This character arc can also be traced through Scarlett's shifting place within the film's use of spectacle: she begins the film wholly preoccupied with the domestic world of lavish parties and beautiful gowns; however, after her encounter with cataclysmic history visualized as a vast, terrible spectacle (the fall of Atlanta), Scarlett assumes the role occupied by her broken and emasculated father.

Floral ontogeny in Polygalaceae and its bearing on the homologies of keeled flowers in Fabales

Keeled flowers are characteristic of many species of Polygalaceae (tribe Polygaleae), in which there is often a distinctive crest located at the abaxial petal. This study of floral ontogeny across the entire family highlights potential suites of characters that relate to the evolution of keeled and crested flowers. One character suite encompasses interconnected transformations of the lateral perianth organs acting as an evolutionary module: bracteoles, lateral sepals (with delayed initiation and petaloid appearance), and lateral petals (suppressed or lost). The plastochron between initiation of the lateral sepals and that of the other sepals is relatively long in the tribe Polygaleae, in which the calyx is usually heteromorphic. By contrast, in the petal whorl, the difference between a zygomorphic and an actinomorphic corolla involves organ suppression rather than heterochrony. Four primary androecial patterns are identified in the family, and the gynoecium ranges between syncarpous‐bicarpellate and multicarpellate. Stigma diversity is based on two primary morphological types: one in which the papillate stigmatic surfaces lie close together, the other in which they are physically separated. The floral ontogeny of Polygalaceae is considered alongside comparative data available for other members of the order Fabales, and hypotheses to account for the similarities and differences between keeled flowers are discussed.

The evolution of strategy: thinking war from antiquity to the present

Latin had no word for "strategy", but the East Romans, whom we call the Byzantines, did. This book tracks the evolution of the concept of warfare being subjected to higher political aims from Antiquity to the Present, using Greek, Latin, French, Spanish, Italian, English and German sources. It tracks the rise, fall, and resurrection of the belief in the Roman and later the medieval and early modern world that warfare was only legitimate if it pursued the higher goal of a just peace, which in the 19th century gave way to a blinkered concentration on military victory as only war aim. It explains why one school of thought, from Antiquity to the present, emphasised eternal principles of warfare, while others emphasised, in Clausewitz's term, the "changing character of war". It tracks ideas from land warfare to naval warfare to air power and nuclear thinking, but it also stresses great leaps and discontinuities in thinking about strategy. It covers asymmetric wars both from the point of view of the weaker power seeking to overthrow a stronger power, and from the stronger power dealing with insurgents and other numerically inferior forces. It concludes with a commentary of the long-known problems of bureaucratic politics, non-centralised command and inter-service rivalry, which since the 16th century or earlier has created obstacles to coherent strategy making.