Reply to "Unrealistic nonphysiological amounts of reagents and a disregard for published literature"

Peer reviewedPublisher PD

The Middle Way versus Extremism

Extremism is a perennial problem in our civilisation. It has constantly impeded our progress by leading to unnecessary wars, conflicts, enmity and hatred. Understanding the middle way between these two extremes helps us to clarify what extremism is and how it arises. Such an understanding can be made part of the education system so that children are taught from an early age to detect extremist tendencies in their own thinking and to control them for their own good and the good of society. This paper extends the views expressed in my book, The Promise of Dualism (Almostic Publications) and other papers on the subject of extremism. It is focused on the following table which shows how the middle way stands between the extremes of too much power and too much belief. After the introduction, the rest of this paper explicates this table’s contents in considerable detail – line by line and word by word – in explanatory notes

Using abundance data to assess the relative role of sampling biases and evolutionary radiations in Upper Muschelkalk ammonoids

The Middle Triassic ammonoid genus Ceratites diversified spectacularly within the Germanic Muschelkalk Basin during the Anisian/Ladian (244–232 Mya). Previous studies have interpreted this diversification as a sequence of rapid, endemic radiations from a few immigrant taxa. Here we investigate the possibility that geological and sampling biases, rather than ecological and evolutionary processes, are responsible for this pattern. A new specimen based dataset of Ceratites species-richness and abundance was assembled. This dataset was combined with 1:200000 geological maps in a geodatabase to facilitate geospatial analyses. One set of analyses compared species richness per geological map with the number of occurrences and localities per map. Per-map change in the amount of rock available to sample for fossils was also included as a variable. Of these three variables, number of occurrences is the most strongly correlated with richness. Variation in the amount of rock is not a strong determinant of species-richness. However, rarefaction of basin-wide species/abundance data demonstrates that differences in species-richness through time are not attributable to sample size differences. The average percent similarity among sites remained close to 50% throughout the Upper Muschelkalk. The rank abundance distribution (RAD) of species from the first interval of the Upper Muschelkalk is consistent with colonization of a disturbed environment, while the other two intervals have RADs consistent with more stable ecosystems. These results indicate that genuine ecological and evolutionary events are partly responsible for the observed differences in richness and abundance. Although changes in the RADs through time support changes in the ammonoid assemblage structure, the processes underlying increasing richness and change in RADS cannot be explained by increasing geographic distinctiveness or isolation among the ammonoid assemblages present at different localities

SELF-ENFORCING INTERNATIONAL ENVIRONMENTAL AGREEMENTS REVISITED

In Barrett's (1994) paper on transboundary pollution abatement is shown that if the signatories of an international environmental agreement act in a Stackelberg fashion, then, depending on parameter values, a self-enforcing IEA can have any number of signatories between two and the grand coalition. Barrett obtains this result using numerical simulations and also ignoring the fact that emissions must be non-negative. Recent attempts to use analytical approaches and to explicitly recognize the non-negativity constraints have suggested that the number of signatories of a stable IEA may be very small. The way such papers have dealt with non-negativity constraints is to restrict parameter values to ensure interior solutions for emissions. We argue that a more appropriate approach is to use Kuhn-Tucker conditions to derive the equilibrium of the emissions game. When this is done we show, analytically, that the key results from Barrett's paper go through. Finally, we explain why his main conclusion is correct although his analysis can implicitly imply negative emissions.international externalities, self-enforcing environmental agreements, Stackelberg equilibrium, non-negative emissions constraints

Posttranslational modifications of proteins in the pathobiology of medically relevant fungi

Peer reviewedPublisher PD

Institutionalising Performance Management in R&D Organisations: Key Concepts and Aspects

In an era in which accountability, cost effectiveness and impact orientation are at premium, Research and Technological Organisations are under pressure not only to improve their performance but also to be able to demonstrate this improvement. This pressure is particularly hard-felt by agricultural research organisations, where funders’ perceptions of a lack of evidence for the uptake and impact of products and services are raising questions about their efficacy and existence. Such pressures can be traced back to several factors, including changes in management trends and the growing scarcity of donor funding in the face of proliferation of Non-Governmental Organisations. These pressures have focussed R&D Organisations attention on the need to develop monitoring and evaluation systems that are capable of ensuring and demonstrating improved performance. In recognising that the developmental impact of research is notoriously difficult to assess, the paper is predicated on the belief that indicators of organisational uptake can provide reliable proxies, or ‘leading’ indicators of development impact. The background to this paper is a DFID-funded pilot action research project that ran between September 2001 and December 2002. The project aimed to adapt and test a novel approach to performance management within three agricultural research and development agencies. The key concepts and aspects of this novel approach and similar work done are discussed.Performance Management; Impact; Evaluation; DFID

Large-scale instabilities in a STOVL upwash fountain

The fountain flow created by two underexpanded axisymmetric, turbulent jets impinging on a ground plane was studied through the use of laser-based experimental techniques. Velocity and turbulence data were acquired in the jet and fountain flow regions using laser doppler velocimetry and particle image velocimetry. Profiles of mean and rms velocities along the jet centreline are presented for nozzle pressure ratios of two, three and four. The unsteady nature of the fountain flow was examined and the presence of large-scale coherent structures identified. A spectral analysis of the fountain flow data was performed using the Welch method. The results have relevance to ongoing studies of the fountain flow using large eddy simulation techniques

Indirect observation of phase conjugate magnons from non-degenerate four-wave mixing

A phase conjugate mirror utilising four-wave mixing in a magnetic system is experimentally realised for the first time. Indirect evidence of continuous-wave phase conjugation has been observed experimentally and is supported by simulations. The experiment utilizes a pump-probe method to excite a four-wave mixing process. Two antennae are used to pump a region of a thin-film yttrium iron garnet waveguide with magnons of frequency $f_{1}$ to create a spatio-temporally periodic potential. As the probe magnons of $f_{\mathrm{p}}$ impinge on the pumped region, a signal with frequency $f_{\mathrm{c}} = 2f_{1}-f_{\mathrm{p}}$ is observed. The amplitude of the nonlinear signal was highly dependent on the applied magnetic field $H$. Width modes of the probe magnons and standing wave modes of the pump magnons were shown to affect the amplitude of the signal at $f_{\mathrm{c}}$. Experimental data is compared with simulations and theory to suggest that $f_{\mathrm{c}}$ is a phase conjugate of $f_{\mathrm{p}}$.Comment: 6 pages, 6 figure

Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterising cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialised compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterised. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and heme, is incomplete. We discuss tools that may aid characterisation of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterisation of individual proteins