A survey of primary homology assessment: different botanists perceive and define characters in different ways

Cladistic analyses begin with an assessment of variation for a group of organisms and the subsequent representation of that variation as a data matrix. The step of converting observed organismal variation into a data matrix has been considered subjective, contentious, under-investigated, imprecise, unquantifiable, intuitive, as a black-box, and at the same time as ultimately the most influential phase of any cladistic analysis (Pimentel and Riggins, 1987; Bryant, 1989; Pogue and Mickevich, 1990; de Pinna, 1991; Stevens, 1991; Bateman et al., 1992; Smith, 1994; Pleijel, 1995; Wilkinson, 1995; Patterson and Johnson, 1997). Despite the concerns of these authors, primary homology assessment is often perceived as reproducible. In a recent paper, Hawkins et al. (1997) reiterated two points made by a number of these authors: that different interpretations of characters and coding are possible and that different workers will perceive and define characters in different ways. One reviewer challenged us: did we really think that two people working on the same group would come up with different data sets? The conflicting views regarding the reproducibility of the cladistic character matrix provoke a number of questions. Do the majority of workers consistently follow the same guidelines? Has the theoretical framework informing primary homology assessment been adequately explored? The objective of this study is to classify approaches to primary homology assessment, and to quantify the extent to which different approaches are found in the literature by examining variation in the way characters are defined and coded in a data matrix.

First steps in experimental cancer evolution

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research.

How will organic carbon stocks in mineral soils evolve under future climate? Global projections using RothC for a range of climate change scenarios

We use a soil carbon (C) model (RothC), driven by a range of climate models for a range of climate scenarios to examine the impacts of future climate on global soil organic carbon (SOC) stocks. The results suggest an overall global increase in SOC stocks by 2100 under all scenarios, but with a different extent of increase among the climate model and emissions scenarios. The impacts of projected land use changes are also simulated, but have relatively minor impacts at the global scale. Whether soils gain or lose SOC depends upon the balance between C inputs and decomposition. Changes in net primary production (NPP) change C inputs to the soil, whilst decomposition usually increases under warmer temperatures, but can also be slowed by decreased soil moisture. Underlying the global trend of increasing SOC under future climate is a complex pattern of regional SOC change. SOC losses are projected to occur in northern latitudes where higher SOC decomposition rates due to higher temperatures are not balanced by increased NPP, whereas in tropical regions, NPP increases override losses due to higher SOC decomposition. The spatial heterogeneity in the response of SOC to changing climate shows how delicately balanced the competing gain and loss processes are, with subtle changes in temperature, moisture, soil type and land use, interacting to determine whether SOC increases or decreases in the future. Our results suggest that we should stop looking for a single answer regarding whether SOC stocks will increase or decrease under future climate, since there is no single answer. Instead, we should focus on improving our prediction of the factors that determine the size and direction of change, and the land management practices that can be implemented to protect and enhance SOC stocks.

Aerosol forcing in the Climate Model Intercomparison Project (CMIP5) simulations by HadGEM2-ES and the role of ammonium nitrate

The latest Hadley Centre climate model, HadGEM2-ES, includes Earth system components such as interactive chemistry and eight species of tropospheric aerosols. It has been run for the period 1860–2100 in support of the fifth phase of the Climate Model Intercomparison Project (CMIP5). Anthropogenic aerosol emissions peak between 1980 and 2020, resulting in a present-day all-sky top of the atmosphere aerosol forcing of −1.6 and −1.4 W m−2 with and without ammonium nitrate aerosols, respectively, for the sum of direct and first indirect aerosol forcings. Aerosol forcing becomes significantly weaker in the 21st century, being weaker than −0.5 W m−2 in 2100 without nitrate. However, nitrate aerosols become the dominant species in Europe and Asia and decelerate the decrease in global mean aerosol forcing. Considering nitrate aerosols makes aerosol radiative forcing 2–4 times stronger by 2100 depending on the representative concentration pathway, although this impact is lessened when changes in the oxidation properties of the atmosphere are accounted for. Anthropogenic aerosol residence times increase in the future in spite of increased precipitation, as cloud cover and aerosol-cloud interactions decrease in tropical and midlatitude regions. Deposition of fossil fuel black carbon onto snow and ice surfaces peaks during the 20th century in the Arctic and Europe but keeps increasing in the Himalayas until the middle of the 21st century. Results presented here confirm the importance of aerosols in influencing the Earth's climate, albeit with a reduced impact in the future, and suggest that nitrate aerosols will partially replace sulphate aerosols to become an important anthropogenic species in the remainder of the 21st century.

Cosmic effects on the intimate screen: J. B. Priestley, Ralph Richardson and 'Johnson over Jordan' (1965)

This article considers ideas about the suitability of experimental, non-naturalist, narrative forms in theatre and television, through the example of a 1965 BBC2 adaptation of J. B. Priestley's 1939 play Johnson over Jordan. Using both textual analysis of the programme and research into the BBC production documentation, this essay explains how the circumstances and conditions of 1960s television adaptation and the star casting of Sir Ralph Richardson transformed Priestley's stage play. The TV adaptation achieved cosmic effects on an intimate scale, through inference and the imaginative integration of the studio space with dubbed sound.

Will greenhouse gas-induced warming over the next 50 years lead to higher frequency and greater intensity of hurricanes?

The use of a high resolution atmospheric model at T106 resolution, for studying the influence of greenhouse warming on tropical storm climatology, is investigated. The same method for identifying the storms has been used as in a previous study by Bengtsson et al. The sea surface temperature anomalies have been taken from a previous transient climate change experiment, obtained with a low resolution ocean-atmosphere coupled model. The global distribution of the storms, at the time when the CO2 concentration in the atmosphere had doubled, agrees in geographical position and seasonal variability with that of the present climate, but the number of storms is significantly reduced, particularly at the Southern Hemisphere. The main reason to this, appear to be connected to changes in the large scale circulation, such as a weaker Hadley circulation and stronger upper air westerlies. The low level vorticity in the hurricane genesis regions is generally reduced compared to the present climate, while the vertical tropospheric wind shear is somewhat increased. Most tropical storm regions indicate reduced surface windspeeds and a slightly weaker hydrological cycle.

Implications of climate change for diseases, crop yields and food security

Accelerated climate change affects components of complex biological interactions differentially, often causing changes that are difficult to predict. Crop yield and quality are affected by climate change directly, and indirectly, through diseases that themselves will change but remain important. These effects are difficult to dissect and model as their mechanistic bases are generally poorly understood. Nevertheless, a combination of integrated modelling from different disciplines and multi-factorial experimentation will advance our understanding and prioritisation of the challenges. Food security brings in additional socio-economic, geographical and political factors. Enhancing resilience to the effects of climate change is important for all these systems and functional diversity is one of the most effective targets for improved sustainability.

Economic transformation in Ghana: where will the path lead?

In the context of the Ghanaian government’s objective of structural transformation with an emphasis on manufacturing, this paper provides a case study of economic transformation in Ghana, exploring patterns of growth, sectoral transformation, and agglomeration. We document and examine why, despite impressive growth and poverty reduction figures, Ghana’s economy has exhibited less transformation than might be expected for a country that has recently achieved middle-income status. Ghana’s reduced share of agriculture in the economy, unlike many successfully transformed countries in Asia and Latin America, has been filled by services, while manufacturing has stagnated and even declined. Likely causes include weak transformation of the agricultural sector and therefore little development of agroprocessing, the emergence of consumption cities and consumption-driven growth, upward pressure on the exchange rate, weak production linkages, and a poor environment for private-sector-led manufacturing.

Transcriptional dysregulation of coding and non-coding genes in cellular models of Huntington's disease

HD (Huntington's disease) is a late onset heritable neurodegenerative disorder that is characterized by neuronal dysfunction and death, particularly in the cerebral cortex and medium spiny neurons of the striatum. This is followed by progressive chorea, dementia and emotional dysfunction, eventually resulting in death. HD is caused by an expanded CAG repeat in the first exon of the HD gene that results in an abnormally elongated polyQ (polyglutamine) tract in its protein product, Htt (Huntingtin). Wild-type Htt is largely cytoplasmic; however, in HD, proteolytic N-terminal fragments of Htt form insoluble deposits in both the cytoplasm and nucleus, provoking the idea that mutHtt (mutant Htt) causes transcriptional dysfunction. While a number of specific transcription factors and co-factors have been proposed as mediators of mutHtt toxicity, the causal relationship between these Htt/transcription factor interactions and HD pathology remains unknown. Previous work has highlighted REST [RE1 (repressor element 1)-silencing transcription factor] as one such transcription factor. REST is a master regulator of neuronal genes, repressing their expression. Many of its direct target genes are known or suspected to have a role in HD pathogenesis, including BDNF (brain-derived neurotrophic factor). Recent evidence has also shown that REST regulates transcription of regulatory miRNAs (microRNAs), many of which are known to regulate neuronal gene expression and are dysregulated in HD. Thus repression of miRNAs constitutes a second, indirect mechanism by which REST can alter the neuronal transcriptome in HD. We will describe the evidence that disruption to the REST regulon brought about by a loss of interaction between REST and mutHtt may be a key contributory factor in the widespread dysregulation of gene expression in HD.

Further clarifying the competition–performance relation: reply to D. W. Johnson et al. (2012)

In their commentary, D. W. Johnson, Johnson, and Roseth (2012) provided some laudatory statements about our article, but they also expressed a number of concerns. The concerns focus on the following issues: types and definitions of competition, our choice of control group, the nature of performance-approach and performance-avoidance goals, the comprehensiveness of the opposing processes model, and performance-approach goals and constructive competition. We respond to each of these issues in turn and conclude with a statement regarding working to build an integrative model of the competition–performance relation (and beyond).

What will be the risk-free rate and benchmark yield curve following European monetary union?

Using a linear factor model, we study the behaviour of French, Germany, Italian and British sovereign yield curves in the run up to EMU. This allows us to determine which of these yield curves might best approximate a benchmark yield curve post EMU. We find that the best approximation for the risk free yield is the UK three month T-bill yield, followed by the German three month T-bill yield. As no one sovereign yield curve dominates all others, we find that a composite yield curve, consisting of French, Italian and UK bonds at different maturity points along the yield curve should be the benchmark post EMU.