Re-evaluating the omnivory–stability relationship in food webs

Under equilibrium conditions, previous theory has shown that the presence of omnivory destabilizes food webs. Correspondingly, omnivory ought to be rare in real food webs. Although, early food web data appeared to verify this, recently many ecologists have found omnivory to be ubiquitous in food web data gathered at a high taxonomic resolution. In this paper, we re-investigate the role of omnivory in food webs using a non-equilibrium perspective. We find that the addition of omnivory to a simple food chain model (thus a simple food web) locally stabilizes the food web in a very complete way. First, non-equilibrium dynamics (e.g. chaos) tend to be eliminated or bounded further away from zero via period-doubling reversals invoked by the omnivorous trophic link. Second, food chains without interior attractors tend to gain a stable interior attractor with moderate amounts of omnivory.     

Using computer-based tutorials to encourage reflection

There is some evidence to suggest that undergraduate biology students need to be given more opportunities for reflection in their education. Some argue that computer-based learning packages may be able to offer such opportunities. This paper presents four different approaches to defining what reflection is and how it can be promoted. These approaches are then used to discuss and review the different ways in which computer-based tutorials can be used to promote lateral thinking. An example of a web-based biology tutorial called ‘How Now Mad Cow’ is described and preliminary evaluation results are presented, in order to illustrate how students may be encouraged to reflect and what factors may influence that. Finally, the role of the tutor in enspiring students to reflect while using computer-based tutorials is discussed. This distinguishes between the role of the tutor in designing a computer-based tutorial, and the role of the tutor in determining and facilitating how a student uses a tutorial once it has been designed.     

Cereal genome analysis using rice as a model

Researchers are eagerly waiting for the physical map of rice to become completed and available for use as a model for all cereals. The most significant advances of the past year have been the progress toward positional cloning of genes and the identification of quantitative trait loci (QTL) from detailed restriction fragment length polymorphism maps. Future focus will be: first, the enhanced dissemination and integration of the available data in World Wide Web accessible databases for easy comparison of genetic and physical mapping data across various species; second, the expanded distribution of a wide variety of DNA materials (cDNA clones, yeast artificial chromosomes, bacterial artificial chromosomes and other probes) for use in other cereals on the basis of the rice model map; and third, the applied breeding by locating and isolating sequences corresponding to important agronomic traits, often correlating with QTL.     

Role of Utility and Inference in the Evolution of Functional Information

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale.     

Boca: an open-source RDF store for building Semantic Web applications

This article presents the design goals and features of the open-source Boca RDF server in the context of a community of cancer-tumor modeling investigators. Boca supplements the desirable data features of the Semantic Web with important enterprise and application features to power a new generation of Semantic-Web-based applications. The data features enable the integration and retrieval of tremendous quantities of diverse data. The enterprise features promote data integrity, fidelity, provenance and robustness. The application features provide for collaborative applications and dynamic user interfaces.     

The aggregating behaviour of <Emphasis Type="Italic">Argiope radon</Emphasis>, with special reference to web decorations

The existence of aggregations in taxa that are normally solitary poses questions regarding the costs and benefits of group living. Most orb-web spiders are solitary and are aggressive to conspecifics, but a few species aggregate in large numbers. These spiders benefit by enhancing the prey interception potential, but also suffer costs of increased predation and parasitism. In this study, we report on the natural history characteristics of the orb-web spider, Argiope radon, which not only lives in aggregations but also builds silk decorations. Our results show that A. radon aggregates facultatively and that the main benefit of aggregation that we could identify is enhanced mating potential. We also show that decorations built by A. radon are highly visible to both model prey and predator, and suggest that solitary individuals with longer and more frequent decorations may offset the foraging advantage of being in aggregations.     

Blogging Evolution

A weblog (“blog”) is an publication on the WorldWideWeb in which brief entries are displayed in date order, much like a diary or journal. I describe the general characteristics of blogs, contrasting blogs with other of WWW formats for self-publishing. I describe four categories for blogs about evolutionary biology: “professional,” “amateur,” “apostolic,” and “imaginative.” I also discuss blog networks. I identify paradigms of each category. Throughout, I aim to illuminate blogs about evolutionary biology from the point of view of a user looking for information about the topic. I conclude that blogs are not the best type of source for systematic and authoritative information about evolution, and that they are best used by the information-seeker as a way of identifying what issues are of interest in the community of evolutionists and for generating research leads or fresh insights on one’s own work.

Remote engineering for a cheese whey biorefinery: an Internet-based application for process design,economic analysis,monitoring, and control of multiple plant sites

The proteolysis of cheese whey with the aid of immobilized enzymes is an attractive alternative for this by-product of the dairy industry. Among some possible applications for whey protein hydrolysates, one may cite their use as protein source for individuals with reduced capacity of digestion, or with genetic metabolic disorders (phenylketonuria patients, for instance). The multipurpose plant that processes whey is named here as a cheese whey biorefinery. This work presents the remote control and monitoring of the whey biorefineries using the Internet. In an integrated environment, the web application also enables simulation and economic analyses of the process. This technology might allow small companies to access a remote “engineering centre”, with know-how on plant design and advanced control techniques. The idea can also be extended to large dairy companies, providing the remote control of geographically spread sites of production.     

基于Web of Science的生物信息学文献分析

利用文献计量学方法,统计分析了1995—2007年11月Web of Science收录的生物信息学（bioinformatics）研究文献,探讨了生物信息学文献研究的年代分布、语种、期刊分布、作者、文献类型、主题分布以及发文量前10名的国家和机构,以期了解世界各国在这一研究领域的进展情况。     

The design of a novel context-aware policy model to support machine-based learning and reasoning

The purpose of autonomic networking is to manage the business and technical complexity of networked components and systems. However, the lack of a common lingua franca makes it impossible to use vendor-specific network management data to ascertain the state of the network at any given time. Furthermore, the tools used to analyze management data are all different, and hence require different data in different formats. This complicates the construction of context from diverse information sources. This paper describes a new version of the DEN-ng context-aware policy model, which is part of the FOCALE autonomic network architecture. This model has been built using three guiding principles: (1) both the context model and the policy model are rooted in information models, so that they can govern managed entities, (2) each model is expressly constructed to facilitate the generation of ontologies, so that reasoning about policies constructed from the model may be done, and (3) the model is expressly constructed so that a policy language that supports machine-based reasoning and learning can be developed from it.