Quantum Topology Change in (2 + 1)d

The topology of orientable (2 + 1)d spacetimes can be captured by certain lumps of non-trivial topology called topological geons. They are the topological analogues of conventional solitons. We give a description of topological geons where the degrees of freedom related to topology are separated from the complete theory that contains metric (dynamical) degrees of freedom. The formalism also allows us to investigate processes of quantum topology change. They correspond to creation and annihilation of quantum geons. Selection rules for such processes are derived.Comment: LaTeX file, 33 pages, 10 postscript figures, some typos corrected, references updated, and other minor change

Discrete Time Evolution and Energy Nonconservation in Noncommutative Physics

Time-space noncommutativity leads to quantisation of time and energy nonconservation when time is conjugate to a compact spatial direction like a circle. In this context energy is conserved only modulo some fixed unit. Such a possibility arises for example in theories with a compact extra dimension with which time does not commute. The above results suggest striking phenomenological consequences in extra dimensional theories and elsewhere. In this paper we develop scattering theory for discrete time translations. It enables the calculation of transition probabilities for energy nonconserving processes and has a central role both in formal theory and phenomenology. We can also consider space-space noncommutativity where one of the spatial directions is a circle. That leads to the quantisation of the remaining spatial direction and conservation of momentum in that direction only modulo some fixed unit, as a simple adaptation of the results in this paper shows.Comment: 17 pages, LaTex; minor correction

Noncommutative field gas driven inflation

We investigate early time inflationary scenarios in an Universe filled with a dilute noncommutative bosonic gas at high temperature. A noncommutative bosonic gas is a gas composed of bosonic scalar field with noncommutative field space on a commutative spacetime. Such noncommutative field theories was recently introduced as a generalization of quantum mechanics on a noncommutative spacetime. As key features of these theories are Lorentz invariance violation and CPT violation. In the present study we use a noncommutative bosonic field theory that besides the noncommutative parameter $\theta$ shows up a further parameter $\sigma$. This parameter $\sigma$ controls the range of the noncommutativity and acts as a regulator for the theory. Both parameters play a key role in the modified dispersion relations of the noncommutative bosonic field, leading to possible striking consequences for phenomenology. In this work we obtain an equation of state $p=\omega(\sigma,\theta;\beta)\rho$ for the noncommutative bosonic gas relating pressure $p$ and energy density $\rho$, in the limit of high temperature. We analyse possible behaviours for this gas parameters $\sigma$, $\theta$ and $\beta$, so that $-1\leq\omega<-1/3$, which is the region where the Universe enters an accelerated phase.Comment: Reference added. Version to appear in Journal of Cosmology and Astroparticle Physics - JCA

Framing access to medicines in developing countries: an analysis of media coverage of Canada's Access to Medicines Regime

<p>Abstract</p> <p>Background</p> <p>In September 2003, the Canadian government committed to developing legislation that would facilitate greater access to affordable medicines for developing countries. Over the course of eight months, the legislation, now known as Canada's Access to Medicines Regime (CAMR), went through a controversial policy development process and the newspaper media was one of the major venues in which the policy debates took place. The purpose of this study was to examine how the media framed CAMR to determine how policy goals were conceptualized, which stakeholder interests controlled the public debate and how these variables related to the public policy process.</p> <p>Methods</p> <p>We conducted a qualitative content analysis of newspaper coverage of the CAMR policy and implementation process from 2003-2008. The primary theoretical framework for this study was framing theory. A total of 90 articles from 11 Canadian newspapers were selected for inclusion in our analysis. A team of four researchers coded the articles for themes relating to access to medicines and which stakeholders' voice figured more prominently on each issue. Stakeholders examined included: the research-based industry, the generic industry, civil society, the Canadian government, and developing country representatives.</p> <p>Results</p> <p>The most frequently mentioned themes across all documents were the issues of drug affordability, intellectual property, trade agreements and obligations, and development. Issues such as human rights, pharmaceutical innovation, and economic competitiveness got little media representation. Civil society dominated the media contents, followed far behind by the Canadian government, the research-based and generic pharmaceutical industries. Developing country representatives were hardly represented in the media.</p> <p>Conclusions</p> <p>Media framing obscured the discussion of some of the underlying policy goals in this case and failed to highlight issues which are now significant barriers to the use of the legislation. Using the media to engage the public in more in-depth exploration of the policy issues at stake may contribute to a more informed policy development process. The media can be an effective channel for those stakeholders with a weaker voice in policy deliberations to raise public attention to particular issues; however, the political and institutional context must be taken into account as it may outweigh media framing effects.</p

The Ascent of the Abundant: How Mutational Networks Constrain Evolution

Evolution by natural selection is fundamentally shaped by the fitness landscapes in which it occurs. Yet fitness landscapes are vast and complex, and thus we know relatively little about the long-range constraints they impose on evolutionary dynamics. Here, we exhaustively survey the structural landscapes of RNA molecules of lengths 12 to 18 nucleotides, and develop a network model to describe the relationship between sequence and structure. We find that phenotype abundance—the number of genotypes producing a particular phenotype—varies in a predictable manner and critically influences evolutionary dynamics. A study of naturally occurring functional RNA molecules using a new structural statistic suggests that these molecules are biased toward abundant phenotypes. This supports an “ascent of the abundant” hypothesis, in which evolution yields abundant phenotypes even when they are not the most fit

Critical mutation rate has an exponential dependence on population size for eukaryotic-length genomes with crossover

The critical mutation rate (CMR) determines the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness (“flattest”). We identify an inverse relationship between CMR and sequence length in an in silico system with a two-peak fitness landscape; CMR decreases to no more than five orders of magnitude above estimates of eukaryotic per base mutation rate. We confirm the CMR reduces exponentially at low population sizes, irrespective of peak radius and distance, and increases with the number of genetic crossovers. We also identify an inverse relationship between CMR and the number of genes, confirming that, for a similar number of genes to that for the plant Arabidopsis thaliana (25,000), the CMR is close to its known wild-type mutation rate; mutation rates for additional organisms were also found to be within one order of magnitude of the CMR. This is the first time such a simulation model has been assigned input and produced output within range for a given biological organism. The decrease in CMR with population size previously observed is maintained; there is potential for the model to influence understanding of populations undergoing bottleneck, stress, and conservation strategy for populations near extinction

Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation

Evolve and resequence (E&R) is a new approach to investigate the genomic responses to selection during experimental evolution. By using whole genome sequencing of pools of individuals (Pool-Seq), this method can identify selected variants in controlled and replicable experimental settings. Reviewing the current state of the field, we show that E&R can be powerful enough to identify causative genes and possibly even single-nucleotide polymorphisms. We also discuss how the experimental design and the complexity of the trait could result in a large number of false positive candidates. We suggest experimental and analytical strategies to maximize the power of E&R to uncover the genotype–phenotype link and serve as an important research tool for a broad range of evolutionary questions.C Schlötterer, R Kofler, E Versace, R Tobler and SU Fransse

Heritable determinants of male fertilization success in the nematode Caenorhabditis elegans

<p>Abstract</p> <p>Background</p> <p>Sperm competition is a driving force in the evolution of male sperm characteristics in many species. In the nematode <it>Caenorhabditis elegans</it>, larger male sperm evolve under experimentally increased sperm competition and larger male sperm outcompete smaller hermaphrodite sperm for fertilization within the hermaphrodite reproductive tract. To further elucidate the relative importance of sperm-related traits that contribute to differential reproductive success among males, we quantified within- and among-strain variation in sperm traits (size, rate of production, number transferred, competitive ability) for seven male genetic backgrounds known previously to differ with respect to some sperm traits. We also quantified male mating ability in assays for rates of courtship and successful copulation, and then assessed the roles of these pre- and post-mating traits in first- and second-male fertilization success.</p> <p>Results</p> <p>We document significant variation in courtship ability, mating ability, sperm size and sperm production rate. Sperm size and production rate were strong indicators of early fertilization success for males that mated second, but male genetic backgrounds conferring faster sperm production make smaller sperm, despite virgin males of all genetic backgrounds transferring indistinguishable numbers of sperm to mating partners.</p> <p>Conclusions</p> <p>We have demonstrated that sperm size and the rate of sperm production represent dominant factors in determining male fertilization success and that <it>C. elegans </it>harbors substantial heritable variation for traits contributing to male reproductive success. <it>C. elegans </it>provides a powerful, tractable system for studying sexual selection and for dissecting the genetic basis and evolution of reproduction-related traits.</p

Recombinational Landscape and Population Genomics of Caenorhabditis elegans

Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in Caenorhabditis elegans are poorly understood. We performed high-density SNP genotyping on a large panel of recombinant inbred advanced intercross lines (RIAILs) of C. elegans to characterize the landscape of recombination and, on a panel of wild strains, to characterize population genomic patterns. We confirmed that C. elegans autosomes exhibit discrete domains of nearly constant recombination rate, and we show, for the first time, that the pattern holds for the X chromosome as well. The terminal domains of each chromosome, spanning about 7% of the genome, exhibit effectively no recombination. The RIAILs exhibit a 5.3-fold expansion of the genetic map. With median marker spacing of 61 kb, they are a powerful resource for mapping quantitative trait loci in C. elegans. Among 125 wild isolates, we identified only 41 distinct haplotypes. The patterns of genotypic similarity suggest that some presumed wild strains are laboratory contaminants. The Hawaiian strain, CB4856, exhibits genetic isolation from the remainder of the global population, whose members exhibit ample evidence of intercrossing and recombining. The population effective recombination rate, estimated from the pattern of linkage disequilibrium, is correlated with the estimated meiotic recombination rate, but its magnitude implies that the effective rate of outcrossing is extremely low, corroborating reports of selection against recombinant genotypes. Despite the low population, effective recombination rate and extensive linkage disequilibrium among chromosomes, which are techniques that account for background levels of genomic similarity, permit association mapping in wild C. elegans strains